title: AC17 at T2 1

description:
AC Patient AC17 Time Point T2 1
A110X.S0037


title: E027 RPMI R1

status: Public on Aug 30 2021

type: SRA

city: Doha

first: Nico

last: Marr

address: Education City

country: Qatar

institute: Hamad Bin Khalifa University

library_source: transcriptomic

data_processing:
Raw RNA-seq reads were aligned with UCSC human genome assembly version hg38, with STAR aligner (Dobin et al., 2013).
HTseq-count (Anders et al., 2015) was used to count the reads mapping to each gene feature. Downstream analysis and heatmap generation were performed with an in-house script in R [R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.], with DESEq2 (Love et al., 2014), and ComplexHeatmap (Gu et al., 2016)
Downstream analysis and heatmap generation were performed with an in-house script in R [R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.], with DESEq2 (Love et al., 2014), and ComplexHeatmap (Gu et al., 2016)
Genome_build: hg38
Supplementary_files_format_and_content: HTSeq-count is used to get the count files, followed by DESeq2 package in R for normalization and log2 transformation.

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

growth_protocol: PBMCs were isolated from buffy coat using Ficoll-Plaque density gradient. PBMCs were cultured in RPMI 1640+Glutamax

extract_protocol:
RNeasy mini kit (Qiagen): cDNA was prepared with the SMART-Seq RNA kit (Takara Bio) for low-input RNA and DNA library preparation and used the Nextera XT DNA Library Preparation Kit (Illumina) and the Nextera XT Index Kit v2 set A (Illumina), respectively
cDNA

treatment_protocol: stimulated for 2 h with IFNa/IFNb, PMA+Ionomycin, cGAMP and MDP. LyoVec were used as reagent control. RPMI is the unstimulated condition.

tag: cell type

value: PBMC

tag: disease state

value: Healthy Control

tag: treatment

value: RPMI

tag: timepoint


title: LMN08-T

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

country: USA

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCm38 reference GENCODE annotation (p6) using STAR (2.6.0c)
Reads counts are obtained using featureCounts from SubRead (v1.6.4)
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

molecule: total RNA

organism: Mus musculus

source_name: Intestinal Tissue

growth_protocol: Villin-Cre mice were bred to Msh2 flox/flox mice to generate VCMsh2 mice. Mice were genotyped to confirm knock-in/knock-out status of Cre transgene and Msh2, respectively.

extract_protocol:
Total RNA for Library Preparation and Sequencing analysis was purified from microdissected VcMsh2 FFPE tumor and normal intestinal tissue using the RNAeasy Plus Kit (QIAGEN) that included a genomic DNA elimination step.
Coding RNA transcripts were enriched using mouse exome panel hybridization (Twist Biosciences).  Size, concentration, and integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were generated using Illumina’s TruSeq RNA sample Prep Kit v3, following the manufacurer’s protocol.
Sequencing of 8–10 pM of each library was done on the NovaSeq sequencer as 75bp paired-end read runs.

treatment_protocol: Aspirin or Naproxen impregnated pelleted NWD1 (400 ppm Aspirin or 166 ppm Naproxen) at the age of weaning were given to mice assigned to those arms. Starting at the age of 6-8 weeks, mice enrolled in FSP vaccine alone and FSP vaccine plus NSAID arms were vaccinated subcutaneously in either left or right hind 4 times bi-weekly followed by 4 times monthly. Per shot, each mouse received 50 μg of each FSP combined with 20 μg of the adjuvant. Mice were monitored over their lifetime by RARC Veterinary Services and the investigator twice a week for the following signs to determine euthanasia; (1) weight loss (2) poor coat quality (3) hunched posture (4) pale limbs (anemia).

tag: tissue

value: Intestinal Tissue

tag: tissue type

value: Tumor

tag: group

value: R

value: Western Diet


title: E025 PMA + Ionomycin R1

value: PMA+Ionomycin


title: LMN07-T


title: AC17 at T1 3

city: Cambridge

first: Jonathan

middle: Morris

last: Urbach

state: Massachusetts

address: 400 Technology Sq Rm 851

institute: Ragon Institute of MGH, MIT and Harvard

description:
AC Patient AC17 Time Point T1 3
A110X.S0030

data_processing:
Illumina sequencing run was deemultiplexed using bcl2fastq veersion 2.19.1.403.
Reads were then mappeed to the hg38 transcriptome using the RSEM pipeline version 1.3.0 with bowtie aligner version 1.2.2. Read counts were calculated as expected counts, and rounded to integer values for analysis with DESeq2, or used without rounding in edgeR.
Differential expression analysis was performed using DESeq2 version 1.26.0 using a model including the following terms: "~ Patient.Category + Batch + UGPS + Pct.Mitochondrial.Transcripts + Align.Rate + CD4.Count"
Prior to differential expression analysis, genes were filtered to have at least 5 expected counts in at least 10% of samples.
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: The expected counts matrix (GEO.EC.gz) includes counts for samples and genes listed by their respective ENSEMBL gene IDs and gene symbols, delimited by an underscore. The GEO.sample_metadata.gz file is complete sample metadata including QC evaluations in tab-separated format. A0173.A110X.T3.REST.PCvSC.dv2.rslt.tsv.gz is the DESeq2 result set as tab-separated values.

source_name: Sorted tetramer positive CD8+ lymphocytes

growth_protocol: Cryopreserved PBMCs were thawed and rested overnight in RPMI + 10% FBS.

extract_protocol:
Replicate populations of viable tetramer+ CD8+ T cells were sorted into RLT Plus lysis buffer supplemented with 1% betamercaptoethanol and frozen at -80°C. RNA was extracted using QIAGEN AllPrep kits.
Smartseq2 bulk protocol using oligo-dT primers to amplify cDNA from mRNA, followed by Illumina Nextera XT tagmentation and NextSeq 550 sequencing.

treatment_protocol: CD8 T cells were enriched by magnetic isolation then stained for peptide-HLA tetramer, anti-CD8 and viability dye and sorted by FACS at 4°C.

tag: patientid

value: AC

tag: replicate

tag: Sex

value: M

tag: batch

tag: ugps


title: spinal motor neurons, WT-3

city: Parkville

first: fatemeh

last: zanganeh

state: Victoria

address: 30 royal pde

country: Australia

institute: Florey

description:
E12_Transcriptomics_DeSeq2.CSV
E12_FeatureCount.txt
E12_W_R5

data_processing:
Align reads to mouse Genome and Output concordant aligned reads as fastq - HiSat2  (v 2.1.0) : hisat2  -x "UCSC_mm10"  --al-conc  "output"  --rna-strandness fr  --no-mixed --no-discordant. Output concordant aligned reads as BAM
Generate  read counts for each gene - Feature-count  (v 1.6.3) : Feature count -t 'exon' -g 'gene_id'
Differential Expression Analysis - DESeq2 (v1.12.4) : DESeq2  (test = "Wald")
Genome_build: Mus_musculus_UCSC_mm10
Supplementary_files_format_and_content: CSV file containing DESeq2 output

source_name: spinal cord

extract_protocol:
The spinal cord  were rapidly dissected from the embryo day 12.5. The isolated tissue was dissociated using Neural Tissue Dissociation Kit (Miltenyi Biotec). Motor neurons were sorted using FACS AriaTM Fusion Flow Cytometer (Becton Dickinson). The cells were directly collected in RLT lysis Buffer (Qiagen). Total RNA extracted using the RNeasy Mini Kit (Qiagen) including DNase treatment.
cDNA libraries were prepared using NeuGen Ovation® SoLo kit.

value: spinal motor neurons

tag: developmental stage

value: Embryonic day 12.5

tag: genotype

value: control


title: spinal motor neurons, WT-4

description:
E12_Transcriptomics_DeSeq2.CSV
E12_FeatureCount.txt
E12_W_R6


title: AC17 at T1 2

description:
AC Patient AC17 Time Point T1 2
A110X.S0029

value: Sorted tetramer positive CD8+ lymphocytes


title: E025 IFNa-IFNb R1

value: IFNa-IFNb


title: AC17 at T1 1

description:
AC Patient AC17 Time Point T1 1
A110X.S0028


title: AC10 at T3 3

description:
AC Patient AC10 Time Point T3 3
A110X.S0021


title: LMN06-T


title: LMN05-T


title: AC17 at T2 3

description:
AC Patient AC17 Time Point T2 3
A110X.S0039


title: E025 RPMI R1


title: spinal motor neurons, WT-2

description:
E12_Transcriptomics_DeSeq2.CSV
E12_FeatureCount.txt
E12_W_R4


title: spinal motor neurons, WT-1

description:
E12_Transcriptomics_DeSeq2.CSV
E12_FeatureCount.txt
E12_W_R1


title: LMN42-T

value: A

value: Aspirin


title: M01 IFNa-IFNb R2

value: PBMC

value: Mother


title: AC10 at T3 2

description:
AC Patient AC10 Time Point T3 2
A110X.S0020


title: AC10 at T3 1

description:
AC Patient AC10 Time Point T3 1
A110X.S0019


title: LMN40-T


title: M01 RPMI R2

value: RPMI


title: SV003_Met+LPS_A

city: Jersey City

first: Thomas

middle: S

last: Postler

state: New Jersey

address: 95 Greene Street 5-018

department: Discovery Science

institute: International AIDS Vaccine Initiative

data_processing:
Raw sequencing results were aligned to the Mus musculus genome GRCm38, annotation release 94, using STAR v2.6.1d
SAM files were converted to BAM files and indexed using Samtools v1.9
Quality control was performed using QoRTs v1.3.6 and IGV v2.4.10
Aligned reads were counted using the featureCounts setting of the Subread v1.6.3 package
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: csv-file with TPM values and ENSEMBL annotation for each sample.

source_name: Bone-marrow-derived macrophages

growth_protocol: Femur and tibia of hindlegs were resected and crushed using a mortar and pestle. Erythrocytes were lysed using Red Cell Lysis Buffer. Cell suspensions were filtered repeatedly through 70-mm nylon cell strainers. Bone marrow cells were seeded on untreated plates to allow selection of macrophages. To differentiate monocytes into macrophages, bone-marrow-derived cells were seeded in DMEM supplemented with 10% FBS, 100 U/ml penicillin, 100 mg/ml streptomycin and 33%  medium previously conditioned for one week with L929 cells. Macrophages were harvested after 6 days of incubation at 37°C in with 5% atmospheric CO2 and seeded at a concentration of 8x10^5 cells/ml approximately 16 h prior to stimulation.

extract_protocol:
Total RNA was isolated using TRIzol.
Poly-A pull-down was used to enrich mRNAs from total RNA samples and libraries were prepared by using the Illumina TruSeq RNA prep kit.

treatment_protocol: Cells were treated with metformin and/or LPS as indicated.

tag: strain

tag: celltype

value: Bone-marrow-derived macrophages

value: 5 mM metformin for 6 h -> 100 ng/ml lipopolysaccharide (LPS) for 2 h


title: SV005_LPS_B

value: 100 ng/ml lipopolysaccharide (LPS), 2 h


title: AC10 at T2 3

description:
AC Patient AC10 Time Point T2 3
A110X.S0012


title: F01 PMA + Ionomycin R2

value: Father


title: LMN04-T

value: Intestinal Tissue

value: Tumor

value: R

value: Western Diet


title: SV002_LPS_A


title: reporter-EtOH3

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
A bowtie2 index was built for the GRCm38 genome assembly using bowtie12 version 2.2.3. The RNA-seq reads of each of the 8 samples were mapped using Tophat13 version 2.0.9 supplied by Ensembl annotation file; GRCm38.78.gtf. Each sample's transcripts were assembled and their expression quantified using Cufflinks version 2.2.1 supplied by GRCm38.78.gtf. Normalization was performed via the median of the geometric means of fragment counts across all libraries.
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized log2FPKM values are provided in a Supplementary Table 1.xlsx file.

source_name: primary motor neuron from CD1 mouse

growth_protocol: The pHSE-FLPo plasmid encoding FLPo (codon optimized Flippase) under the control of HS response element and the pFRT-RFP (reporter) and the pCAGIG (labeling all electroporated cells) constructs (2 µg/µl each) were transfered to into primary motor cortex (M1) by directional in utero electroporation at E (embryonic day) 15.

extract_protocol:
Intracellular contents were obtained from live single neurons in M1 of the mouse cortex at P (postnatal day) 30. The collected single-cell contents were expelled into a thin-walled RNA-free PCR tube (Eppendorf, NY), with 1% (final) IGEPAL CA-630 (Sigma-Aldrich, MO), and immediately frozen on dry ice for storage at −80°C until further processing.
The cDNA libraries were prepared using the SMARTer Ultra Low Input RNA Kit for Sequencing - v3 (TAKARA Bio) and Nextera XT DNA Library Prep Kit (Illumina) as per the manufacturer's instructions. The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies) and Kapa Library Quantification Kit (Kapa Biosystems).
The libraries were pooled and diluted to 2 nM in EB buffer (Qiagen) and then denatured using the Illumina protocol. The denatured libraries were diluted to 10 pM by pre-chilled hybridization buffer and loaded onto TruSeq SR v3 flow cells on an Illumina HiSeq 2500 (Illumina) and run for 51 cycles using a single-read recipe (TruSeq SBS Kit v3, Illumina) according to the manufacturer's instructions. Illumina CASAVA pipeline (released version 1.8, Illumina) was used to obtain de-multiplexed sequencing reads (fastq files) passed the default purify filter. Additional quality filtering used FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit) to keep only reads that have at least 80% of bases with a quality score of 20 or more (conducted by fastq_quality_filter function) and reads left with > 10 bases after being trimmed with reads with a quality score of < 20 (conducted by fastq_quality_trimmer function).

treatment_protocol: Following electroporation, pregnant mice received intraperitoneal (i.p.) injections of 25% EtOH in PBS at 4.0 or 1.0 g/kg weight daily at E16 and E17. PBS alone was used as the control.

tag: reporter gene expression

value: pCAGIG (GFP) positive but RFP negative (didn't respond to heat shock)

tag: exposure in utelus

value: EtOH

tag: time course

value: exposed to EtOH at E16-E17, neurons/RNA extracted at P30


title: LMN39-T

value: NV

tag: treatment

value: Naproxen + FSP vaccine


title: AC10 at T2 2

description:
AC Patient AC10 Time Point T2 2
A110X.S0011

tag: cell type

value: Sorted tetramer positive CD8+ lymphocytes

value: AC

value: M


title: F01 IFNa-IFNb R2

value: PBMC

tag: disease state

value: IFNa-IFNb

tag: timepoint


title: AC10 at T2 1

description:
AC Patient AC10 Time Point T2 1
A110X.S0010


title: M01 PMA + Ionomycin R2

value: Mother

value: PMA+Ionomycin


title: F01 RPMI R2

value: Father

value: RPMI


title: SV006_Met+LPS_B

value: Bone-marrow-derived macrophages

value: 5 mM metformin for 6 h -> 100 ng/ml lipopolysaccharide (LPS) for 2 h


title: P01 PMA + Ionomycin R2

value: STK4 deficient patient


title: AC10 at T1 3

description:
AC Patient AC10 Time Point T1 3
A110X.S0003


title: SV004_Untreated_B

value: untreated


title: LMN37-T

tag: tissue

value: Intestinal Tissue

tag: tissue type

value: Tumor

tag: group

value: RC

value: Regular Chow


title: AC10 at T1 2

description:
AC Patient AC10 Time Point T1 2
A110X.S0002

value: Sorted tetramer positive CD8+ lymphocytes

tag: patientid

tag: replicate

tag: Sex


title: LMN38-T

value: RV

value: FSP vaccine


title: P01 IFNa-IFNb R2

value: PBMC


title: LMN36-T


title: AC10 at T1 1

description:
AC Patient AC10 Time Point T1 1
A110X.S0001

value: AC

value: M

tag: batch

tag: ugps


title: LMN41-T

value: AV

value: Aspirin + FSP vaccine


title: LMN35-T


title: P01 RPMI R2

value: RPMI


title: AC17 at T3 2

description:
AC Patient AC17 Time Point T3 2
A110X.S0047


title: DC15 at T3 3

description:
DC Patient DC15 Time Point T3 3
A0173.S0072

value: DC


title: M01 RPMI R1

value: Mother


title: LMN33-T


title: F01 PMA + Ionomycin R1

value: Father

value: PMA+Ionomycin


title: DC15 at T3 1

description:
DC Patient DC15 Time Point T3 1
A0173.S0070


title: LMN31-T

value: Intestinal Tissue


title: SV001_Untreated_A

tag: strain

value: Bone-marrow-derived macrophages

value: untreated


title: KO-ST2

city: Melbourne

first: David

middle: A

last: Jans

state: Clayton

address: 23 Innovation Walk

department: Biochemistry and Molecular Biology

institute: Monash University

data_processing:
Illumina Real Time Analysis (RTA) software 2.4.1.1 used for basecalling.
Sequenced sample reads were trimmed for adaptor sequence and clusters producing mixed signal and demultiplexed using bcl2fastq then mapped to mm10 whole genome using STAR v2.3.1
htseq-count used to count how many reads overlap the exons of each gene
Limma/Voom calculated CPM and DEG
Genome_build: mm10
Supplementary_files_format_and_content: csv text file including raw read counts for every sample and the CPM values for every sample

source_name: KO_ESC_oxidative stress

growth_protocol: Embryonic stem cells were cultured in feeder-free culture condition in DMEM suplemented with 12.5% FBS, 1X Glutamax, 0.1mM NEAA, 0.1mM β mercaptoethanol and 1000 U/ml LIF on 0.1% gelatin-coated surfaces.

extract_protocol:
RNA was extracted from cells using Isolate II RNA Mini Kit (Bioline)
Illumina TruSeq mRNA Peparation Kit with 1ug input RNA for the construction of sequencing libraries.  Libraries were pooled in equimolar concentrations to a single sequencing lane of an Illumina HiSeq2500, using paired end 100 bp sequencing configurations. TruSeq LT adaptors used for each sample.

treatment_protocol: Oxidative stress was induced with 1 h 125 uM H2O2 followed by 2 h recovery in clean stem cell media.

tag: strain background

tag: age

value: day 5 preimplantation

tag: genotype

value: blastocysts

value: Embryonic Stem Cells

tag: treated with


title: WT-ST2

source_name: WT_ESC_oxidative stress

value: Wild type

value: 1 h 125 uM H2O2 followed by 2 h recovery


title: KO-NS1

value: none (untreated)


title: KO-NS2


title: KO-ST1


title: WT-ST1


title: LMN30-T

value: Tumor

tag: treatment


title: DC15 at T2 2

description:
DC Patient DC15 Time Point T2 2
A0173.S0068

tag: cell type

value: Sorted tetramer positive CD8+ lymphocytes

value: M


title: WT-NS2


title: LMN29-T

value: AV

value: Aspirin + FSP vaccine


title: F01 RPMI R1

value: PBMC

tag: disease state

value: RPMI


title: P01 PMA + Ionomycin R1

value: STK4 deficient patient

value: PMA+Ionomycin

tag: timepoint


title: LMN03-T

tag: tissue

value: Intestinal Tissue

value: R

value: Western Diet


title: DC15 at T2 1

description:
DC Patient DC15 Time Point T2 1
A0173.S0067

value: DC


title: DC15 at T2 3

description:
DC Patient DC15 Time Point T2 3
A0173.S0069


title: P01 RPMI R1


title: WT-NS1

value: day 5 preimplantation

value: blastocysts

value: Embryonic Stem Cells


title: P01 IFNa-IFNb R1

value: IFNa-IFNb


title: LMN26-T

tag: tissue type

value: Tumor

value: RC

value: Regular Chow


title: MSFB_3

city: Shenyang

first: Jianhua

last: Chen

state: Liaoning

address: No.120 Dongling Road, Shenhe District

country: China

institute: Shenyang Agricultural University

data_processing:
The sequencing-obtained raw image data were converted to sequence reads using CASAVA.
The raw data was filtered by R language, and finally the clean reads for subsequent analysis were obtained.
Trinity v2.4.0 program was used to stitch and assemble clean reads of all samples. Redundancy was removed by clustering with Corset hierarchy, The longest transcript of each gene was selected as Unigene for subsequent analysis.
The transcript sequence obtained by splicing with Trinity was used as a reference sequence. RSEM software (version v1.2.15) (bowtie2, mismatch=0) (bowtie2 default parameters, mismatch = 0)was used to compare clean reads of each repeated sample with reference sequences, and the readcount of each gene was counted and compared. FPKM (fragments per kilobase of exon per million mapped fragments) was used to standardize the readcount of genes.
The DEGseq R package (1.12.0) was used for differential expression analyses. The P-value was calculated based on a negative binomial distribution model. P-values was adjusted using the Benjamini-Hochberg mothed (Benjamini and Hochberg, 1995). Genes with an adjusted P-value < 0.05 and log2(Fold change) > 1 were assigned as differentially expressed.
Supplementary_files_format_and_content: FPKM file includes gene ID and expression for each sample.

organism: Prunus sibirica

source_name: Male sterile flower buds

extract_protocol:
Flower buds were grinned under liquid nitrogen to fine powder using cooled mortar and pestle. Samples were placed in Eppendorf tubes. Total RNA was extracted from male sterile flower buds and fertile flower buds by RNA extraction kit of Tiangen Biotech (Beijing) Co..
The six RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Prunus sibirica clone

value: Flower buds

tag: developmental stage

value: microspore developmental stage


title: DC15 at T1 3

description:
DC Patient DC15 Time Point T1 3
A0173.S0066

value: Sorted tetramer positive CD8+ lymphocytes

tag: patientid

tag: replicate

value: M


title: MSFB_2


title: MSFB_1


title: DC15 at T1 1

description:
DC Patient DC15 Time Point T1 1
A0173.S0064

tag: Sex

tag: batch


title: HEK2

city: La Jolla

first: Sheng

last: Zhong

state: California

address: 9500 Gilman Drive, MC 0412

department: Department of Bioengineering

institute: University of California, San Diego

data_processing:
library strategy: PROPER-seq (PROtein Protein intERaction sequencing)
Cutadapt 2.5 for adaptor trimming
fastp0.14.1 for reads quality filtering
bwa0.7.12-r1039 for reads alignment
Python3.6.9 for chimeric read pairs identificatio and deduplication
Genome_build: hg38
Supplementary_files_format_and_content: Comma delimited files with counts of gene pairs

source_name: Human embryonic kidney (HEK) 293T cells

extract_protocol:
Total RNA was isolated from cells with TRIzol™ Reagent (Invitrogen, 15596026) according to the manufacturer’s recommendations. Subsequently, poly-A RNAs were enriched with the Dynabeads™ mRNA Purification Kit (Invitrogen, 61006) and then remaining rRNA was depleted with the Ribo-Zero H/M/R Kit (Illumina, MRZH116) or the RiboMinus Transcriptome Isolation Kit (Invitrogen, K155002).
The DNA product of PROPER-seq was NEBNext® Ultra™ II FS DNA Module (NEB, E7810S). Libraries were then generated with the NxSeq® UltraLow DNA Library Kit (Lucigen, 15012-1) up to the final AMPure XP Bead purification before amplification. Each sample was immobalized on Dynabeads™ MyOne™ Streptavidin T1. Library amplification was then performed with the NxSeq® UltraLow DNA Library Kit as directed with the beads as input.

tag: cell line

value: Human embryonic kidney (HEK) 293T cells

tag: procedure

value: Intact


title: LMN24-T

value: Intestinal Tissue

tag: group

value: RV

value: FSP vaccine


title: DC01 at T3 1

description:
DC Patient DC01 Time Point T3 1
A0173.S0062

value: DC

value: F

tag: ugps


title: LMN25-T


title: MFFB_3

source_name: Male fertile flower buds


title: DC15 at T3 2

description:
DC Patient DC15 Time Point T3 2
A0173.S0071


title: F01 IFNa-IFNb R1

value: PBMC

value: Father


title: HEK1


title: MFFB_2


title: LMN22-T

value: Tumor


title: DC01 at T2 2

description:
DC Patient DC01 Time Point T2 2
A0173.S0061


title: LMN21-T

value: NV

value: Naproxen + FSP vaccine


title: DC01 at T2 1

description:
DC Patient DC01 Time Point T2 1
A0173.S0060


title: LMN20-T


title: AGO3_Sil

city: Zurich

first: Antonin

last: Marchais

address: Universitatstrasse 2

department: Department of Biology

country: Switzerland

institute: ETHZ

description: small RNAs

data_processing:
Basecalls performed using HiSeq Control Soft. v. 2.0.12.0, RTA 1.17.21.3 and CASAVA 1.8 for Hiseq 2500 runs and using HiSeq Control Soft. v. 1.5.15.1, RTA 1.13.48.0 and CASAVA 1.8.2 for Hiseq 2000 runs.
sRNAseq reads were aligned to the TAIR10 genome assembly using ncPRO pipeline.
Genome_build: TAIR10
Supplementary_files_format_and_content: Sequence count for A. thaliana derived small RNAs

organism: Arabidopsis thaliana

source_name: AGO3 IP@FLAG Siliques

growth_protocol: Arabidopsis thaliana plants grown on soil underlong day light conditions for the siliques experiment and on MS plate under continuous light for the syringolin experiment

extract_protocol:
Total RNA was isolated with Trizol
Libraries construction was contracted out to Fasteris SA. At Fasteris SA, barcoded libraries were prepared such that four samples could be run per lane.
Libraries were prepared according to Illumina's instructions accompanying the sequencing Kit TruSeq™ SBS v5.

tag: ecotype

tag: genotype/variation

value: ago3-3 pAGO3-FHA-AGO3

tag: tissues

value: Siliques 1-5DAP

tag: ip reagent

value: EZview Red ANTI-FLAG M2 Affinity Gel from Sigma


title: DC15 at T1 2

description:
DC Patient DC15 Time Point T1 2
A0173.S0065

tag: cell type

value: Sorted tetramer positive CD8+ lymphocytes


title: DC01 at T1 2

description:
DC Patient DC01 Time Point T1 2
A0173.S0059


title: ago3-3_Sil_n2

data_processing:
Basecalls performed using CASAVA 1.8.
RNAseq reads were aligned to the TAIR10 genome assembly using Tophat2.
Genome_build: TAIR10
Supplementary_files_format_and_content: Cufflink output
Supplementary_files_format_and_content: merged.gtf is linked as a supplementary file on the Series record (because extra transcripts annotated by Cufflinks as CUFF are not detailed in the cufflinks files.)

growth_protocol: Arabidopsis thaliana  plants grown on soil under long day light conditions

extract_protocol:
Total RNA was isolated with Quiagen RNAeasy mini kit
Libraries construction was contracted out to Functionnal Genomic Center Zurich , barcoded libraries were prepared such that four samples could be run per lane.
Libraries were prepared according to Illumina's instructions accompanying the stranded sequencing Kit TruSeq™ SBS v3 and RNA enrichment was performed with RNA-Ribosomal Depletion (Ribo Zero).

value: ago3-3 mutant


title: LMN02-T

tag: tissue

value: R

tag: treatment

value: Western Diet


title: DC01 at T1 1

description:
DC Patient DC01 Time Point T1 1
A0173.S0058


title: Total_Sil

description: small RNAs

source_name: Col0 Total Siliques

value: WT


title: LMN23-T

value: Intestinal Tissue

tag: tissue type

value: RV


title: ago3-3_Sil_n1


title: Embryonic anole lung E18

city: Princeton

first: Michael

middle: A.

last: Palmer

address: 25 William Street

department: Chemical and Biological Engineering

institute: Princeton University

data_processing:
Basecalls performed using RTA version 1.18.64.0
Concatenated fastq files from both lanes of flowcell
Demultiplexed reads using barcode_splitter 0.18.2 (https://bitbucket.org/princeton_genomics/barcode_splitter)
Single cell analysis (alignment, cell identification, gene counts, etc.) performed by CellRanger count version 3.0
Single cell analysis by Seurat (v3)
Genome_build: Anolis carolinensis reference genome AnoCar2.0
Supplementary_files_format_and_content: 10x Cell Ranger HDF5 formatted matrix files

organism: Anolis sagrei

source_name: E18 lung

extract_protocol:
Lungs were dissected from embryonic anoles in cold PBS. Isolated lungs were placed in dispase, and mechanically dissociated with tungsten needles. After 10 minutes in dispase at room temperature, DMEM without HEPES and supplemented with 5% fetal bovine serum (FBS, Atlanta Biologicals) was added, and cell suspensions were passed through a filter with 40-µm-diameter pores. The resultant cell suspensions were then processed by the Princeton Genomics Core Facility.  Cells were loaded and processed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 on the Chromium Controller (10X Genomics) following manufacturer protocols. Individual cells were encapsulated in droplets with single gel beads carrying unique barcoded primers and then lysed. Then cDNA fragments were synthesized, barcoded, and amplified by PCR.
Illumina sequencing libraries were prepared from the amplified cDNA from each sample group using the Nextra DNA library prep kit (Illumina). The v3 libraries were sequenced on Illumina HiSeq 2500 Rapid flowcells (Illumina) as paired-end 26 + 50 nucleotide reads following manufacturer protocols.

tag: developmental stage

value: whole lung


title: LMN19-T

value: RC

value: Regular Chow


title: DC03 at T3 3

description:
DC Patient DC03 Time Point T3 3
A0173.S0048

tag: patientid

value: DC

value: M


title: MFFB_1

tag: cultivar

value: Prunus sibirica clone

value: Flower buds

value: microspore developmental stage


title: LMN18-T

value: Tumor

value: AV

value: Aspirin + FSP vaccine


title: WT_Sil

description: small RNAs

source_name: Col0 IP@FLAG Siliques

value: Siliques 1-5DAP

value: EZview Red ANTI-FLAG M2 Affinity Gel from Sigma


title: Intestinal Enteroid 70hr (Hs)

city: Cincinnati

first: Andrew

middle: E

last: Rosselot

state: OH

address: 231, Albert Sabin way

department: Department of Pharmacology and Systems Biology

institute: University of Cincinnati, College of Medicine

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_70

data_processing:
RNA-Seq data were pseudoaligned and quantified (transcript per million estimates) using a call to the software Kallisto within AltAnalyze version 2.1.4 and an Ensembl version 72 reference database.
Genome_build: hg19
Supplementary_files_format_and_content: processed-data-file_TPM.csv
Supplementary_files_format_and_content: Human-enteroids_RAIN-24h_EMBO.xlsx

source_name: Intestinal Enteroid 70hr

growth_protocol: Rhythmic gene expression was determined via time course sample collection. bHIE were collected every 4-hours over a 48-hour period, two full circadian cycles. Enteroids were expanded by suspending pelleted enteroids in Matrigel and plating as three separate 10μL domes/well in a 24-well plate. Intesticult organoid growth medium (StemCell Technologies) was used for enteroid expansion. Human enteroid differentiation was initiated by replacing expansion media with differentiation (Intesticult Component A (StemCell Technologies) mixed at a 1:1 ratio with DMEM/F12 supplemented with 15mM HEPES) media 2-days post-passaging. Human enteroids were maintained in differentiation media at least four days before being used for experiments.

extract_protocol:
At each collection timepoint, cells were pelleted, suspended in 1mL TRI reagent (Molecular Research Center) and snap frozen in liquid N2. After completion of the time course, RNA was isolated via a RNeasy mini-kit column (Qiagen).
The cDNA synthesis and amplification were done as recommended by Clontech. cDNA libraries were prepared using Nextera XT DNA Sample preparation reagents. Fragmented and tagged libraries were quantified using an agilent bio-analyzer, pooled and sequenced on a HiSeq 2500 platform (Illumina) using the pair-end 100-bp sequencing strategy.

treatment_protocol: Samples were collected every two hours for 48-hours starting at 24-hours post circadian synchronization using dexamethasone.

value: Intestinal Enteroid

tag: passage

value: passaged every 4-7 days

tag: circadian clock


title: Intestinal Enteroid 68hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_68

source_name: Intestinal Enteroid 68hr


title: LMN16-T

value: Intestinal Tissue


title: Intestinal Enteroid 64hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_64

source_name: Intestinal Enteroid 64hr


title: DC03 at T2 3

description:
DC Patient DC03 Time Point T2 3
A0173.S0045

value: Sorted tetramer positive CD8+ lymphocytes

tag: replicate

tag: Sex

tag: batch


title: LMN15-T

source_name: Intestinal Tissue

tag: group

value: N

value: Naproxen


title: DC03 at T3 1

description:
DC Patient DC03 Time Point T3 1
A0173.S0046

source_name: Sorted tetramer positive CD8+ lymphocytes

tag: ugps


title: Intestinal Enteroid 62hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_62

source_name: Intestinal Enteroid 62hr


title: LMN17-T


title: LMN13-T

value: A

value: Aspirin


title: DC03 at T2 1

description:
DC Patient DC03 Time Point T2 1
A0173.S0043

value: DC

value: M


title: DC03 at T2 2

description:
DC Patient DC03 Time Point T2 2
A0173.S0044


title: Non_target_4H_3

city: Kansas City

first: Shiyuan

middle: (Cynthia)

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome hg38 with STAR aligner (version 2.7.3a ), using Ensembl 98 gene models. TPM values were generated using RSEM (version v1.3.0 ).
Genome_build: hg38
Supplementary_files_format_and_content: TPM gene expression in csv file

growth_protocol: HCT116 cells were cultured under an atmosphere of 5% CO2 at 37 °C in McCoy’s 5A medium (Lonza) supplemented with 10% (v/v) fetal bovine serum (Invitrogen), 1% Penicillin-Streptomycin (Thermo Fisher Scientific), 1% GlutaMAX (Thermo Fisher Scientific) and 1% non-essential amino acids (Thermo Fisher Scientific).

extract_protocol:
For RNA-seq, total RNA was extracted using Maxwell® RSC simplyRNA Tissue Kit (Promega) and quantified using RNA 6000 Nano Kit (Agilent Technologies) in Bioanalyzer. 1µg of total RNA was subjected to oligo-dT selection (TruSeq Stranded mRNA Preparation Kit ,Illumina).
PolyA-selected RNA-seq libraries were prepared using TruSeq Stranded mRNA kit (Illumina, #20020594) following manufacturer's instructions. Both TruSeq kits add Illumina-compatible adapter and indexes for sequencing.  Libraries were checked for quality (Bioanalyzer) and quantity (Qubit). Equimolar concentrations of libraries were pooled, requantified and sequenced as 50bp single reads on the Illumina HiSeq 2500 instrument.

treatment_protocol: HCT116 cells in six-well tissue culture plates (~1 × 105 cells per well) or 10 cm dishes (~2 × 106 cells per dish) were transfected with 10 nM siRNAs targeting human ELOA (ON-TARGET plus SMARTPool, L-005143-00, siRNA #1, J-005143-07-0002; or siRNA #3, J-005143-09-0002; Dharmacon), or with 10 nM siSTABLE Non-targeting siRNA #1 (D-001700-01; Dharmacon) using Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen). siRNA sequences are listed in Table S1. siRNA containing media was removed after 6 hours. ~42 hours later cells were supplemented with thapsigargin in DMSO (final concentration of 300 nM), and cells were incubated a further 4 hours for RNA-seq.

tag: sirna

value: siSTABLE Non-targeting siRNA #1, Dharmacon D-001700-01

tag: agent

value: 300nM Thapsigargin

tag: time point


title: Intestinal Enteroid 60hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_60

source_name: Intestinal Enteroid 60hr

tag: cell type


title: LMN12-T

tag: tissue

value: Tumor


title: DC03 at T1 3

description:
DC Patient DC03 Time Point T1 3
A0173.S0042


title: LMN11-T

tag: treatment


title: DC03 at T3 2

description:
DC Patient DC03 Time Point T3 2
A0173.S0047


title: Non_target_4H_2


title: Intestinal Enteroid 58hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_58

source_name: Intestinal Enteroid 58hr


title: DC03 at T1 2

description:
DC Patient DC03 Time Point T1 2
A0173.S0041


title: Non_target_4H_1


title: Intestinal Enteroid 56hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_56

source_name: Intestinal Enteroid 56hr


title: Intestinal Enteroid 66hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_66

source_name: Intestinal Enteroid 66hr


title: LMN10-T

tag: tissue type

value: R

value: Western Diet


title: DC03 at T1 1

description:
DC Patient DC03 Time Point T1 1
A0173.S0040


title: Non_target_0H_3


title: Sham_2

type: RNA

city: Hangzhou

first: XIN

last: YE

state: China

address: No.3 Qingchun East Road

department: Department of Neurosurgery

institute: SIR Run Run Shaw Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 12.0 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: SHAM, 3hr, replicate 1,Young adult C57BL/6 mice

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: strain

value: spinal cord

tag: gender

value: female

value: SHAM


title: LMN83-N

value: normal


title: Sham_3

source_name: SHAM, 3hr, replicate 2,Young adult C57BL/6 mice


title: Intestinal Enteroid 54hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_54

source_name: Intestinal Enteroid 54hr

value: Intestinal Enteroid

value: passaged every 4-7 days


title: LMN82-N

value: Intestinal Tissue

value: N


title: Intestinal Enteroid 52hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_52

source_name: Intestinal Enteroid 52hr


title: DC04 at T3 2

description:
DC Patient DC04 Time Point T3 2
A0173.S0039

value: Sorted tetramer positive CD8+ lymphocytes

tag: patientid


title: SCI_48h_3

source_name: SCI, 48hr, replicate 2,Young adult C57BL/6 mice

value: SCI


title: SCI_48h_2

source_name: SCI, 48hr, replicate 1,Young adult C57BL/6 mice


title: Non_target_0H_2


title: DC04 at T3 1

description:
DC Patient DC04 Time Point T3 1
A0173.S0038

value: DC


title: Sham_4

source_name: SHAM, 3hr, replicate 3,Young adult C57BL/6 mice


title: SCI_48h_5

source_name: SCI, 48hr, replicate 3,Young adult C57BL/6 mice


title: Non_target_0H_1


title: DC04 at T2 2

description:
DC Patient DC04 Time Point T2 2
A0173.S0037

value: M


title: EloA_siRNA10nM_4H_3

value: ON-TARGETplus Human ELOA siRNA-SMARTPool, Dharmacon L-005143-00


title: Intestinal Enteroid 48hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_48

source_name: Intestinal Enteroid 48hr

tag: passage


title: LMN81-N

value: Naproxen


title: EloA_siRNA10nM_4H_2

value: 300nM Thapsigargin


title: LMN80-N


title: DC04 at T2 1

description:
DC Patient DC04 Time Point T2 1
A0173.S0036


title: DC04 at T1 2

description:
DC Patient DC04 Time Point T1 2
A0173.S0035


title: LMN79-N

value: A

value: Aspirin


title: Intestinal Enteroid 44hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_44

source_name: Intestinal Enteroid 44hr

tag: circadian clock


title: EloA_siRNA10nM_4H_1


title: DC04 at T1 1

description:
DC Patient DC04 Time Point T1 1
A0173.S0034

tag: replicate


title: LMN78-N

source_name: Intestinal Tissue


title: EloA_siRNA10nM_0H_3


title: Intestinal Enteroid 46hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_46

source_name: Intestinal Enteroid 46hr


title: LMN72-N

value: R

value: Western Diet


title: LMN71-N


title: EloA_siRNA10nM_0H_2


title: LMN73-N


title: DC05 at T3 3

description:
DC Patient DC05 Time Point T3 3
A0173.S0033

source_name: Sorted tetramer positive CD8+ lymphocytes

tag: Sex


title: Intestinal Enteroid 42hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_42

source_name: Intestinal Enteroid 42hr


title: Intestinal Enteroid 36hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_36

source_name: Intestinal Enteroid 36hr


title: EloA_siRNA10nM_0H_1


title: 2.90-D12-2

city: Leiden

first: Antoine

last: de Vries

address: Albinusdreef 2

department: Cardiology

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Image analysis, base calling and quality check were performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq (v2.20)
Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic (v0.30).
Reads were aligned to the Homo sapiens reference genome (GRCh37.75) using Tophat (v2.0.14) and read counts were determined using HTSeq (v0.6.1p1).
Genome_build: GRCh37.75
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample

source_name: hiAM-2.90_Differentiated (D12)

extract_protocol:
Total RNA was extracted from proliferating and differentiated hiAMs seeded at a density of 10^5 cells/cm2 (10^6 cells per sample) using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions.
Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

tag: cell line/monoclone

value: conditionally immortalized human atrial cardiomyocytes (hiAMs)

tag: state

value: Differentiated (D12)


title: DC05 at T2 3

description:
DC Patient DC05 Time Point T2 3
A0173.S0030

tag: batch

tag: ugps


title: 2.90-D12-3


title: LMN70-N

value: normal

tag: group

value: RV

value: FSP vaccine


title: DC05 at T2 2

description:
DC Patient DC05 Time Point T2 2
A0173.S0029


title: Intestinal Enteroid 34hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_34

source_name: Intestinal Enteroid 34hr

value: Intestinal Enteroid

value: passaged every 4-7 days


title: Intestinal Enteroid 38hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_38

source_name: Intestinal Enteroid 38hr


title: 2.90-D12-1


title: LMN69-N

value: Intestinal Tissue


title: Intestinal Enteroid 32hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_32

source_name: Intestinal Enteroid 32hr


title: DC05 at T2 1

description:
DC Patient DC05 Time Point T2 1
A0173.S0028

value: Sorted tetramer positive CD8+ lymphocytes

value: DC


title: 2.52-D12-3

source_name: hiAM-2.52_Differentiated (D12)


title: Intestinal Enteroid 30hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_30

source_name: Intestinal Enteroid 30hr


title: Intestinal Enteroid 40hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_40

source_name: Intestinal Enteroid 40hr


title: LMN67-N

value: NV

value: Naproxen + FSP vaccine


title: DC05 at T1 3

description:
DC Patient DC05 Time Point T1 3
A0173.S0027

value: M


title: 2.52-D12-2


title: LMN68-N


title: DC05 at T3 1

description:
DC Patient DC05 Time Point T3 1
A0173.S0031


title: DC05 at T1 2

description:
DC Patient DC05 Time Point T1 2
A0173.S0026


title: Intestinal Enteroid 28hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_28

source_name: Intestinal Enteroid 28hr


title: Intestinal Enteroid 50hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_50

source_name: Intestinal Enteroid 50hr


title: 2.52-D12-1


title: Intestinal Enteroid 26hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_26

source_name: Intestinal Enteroid 26hr


title: LMN64-N

value: AV

value: Aspirin + FSP vaccine


title: LMN65-N


title: DC05 at T1 1

description:
DC Patient DC05 Time Point T1 1
A0173.S0025


title: AC05 at T3 3

description:
AC Patient AC05 Time Point T3 3
A0173.S0024

value: AC


title: 2.38-D12-2

source_name: hiAM-2.38_Differentiated (D12)


title: AC05 at T3 2

description:
AC Patient AC05 Time Point T3 2
A0173.S0023


title: AC05 at T3 1

description:
AC Patient AC05 Time Point T3 1
A0173.S0022


title: LMN62-N

value: N

value: Naproxen


title: ChIP-seq from in vitro activated B cells (3 million cells) Bhlhe40_ChIP_3M

city: Vienna

first: Maria

last: Fischer

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology

library_source: genomic

data_processing:
Single cell RNA-seq: The sequenced 10X Chromium libraries from two samples were mapped to mm10 mouse genome and assigned to droplets with Cell Ranger software (version 3.0.1) with default parameters (Zheng et al, 2017). Transcriptomes of 7,324 WT cells with the median read coverage of 2,292 (days 2.5), 2,089 WT cells with a median read coverage of 2,507 (day 3.5-4) and 1,677 KO cells with a median read coverage of 3823 (day 3.5-4) were obtained. To obtain the individual embeddings at day 2.5 and day 3.5-4, the resulting read count matrices were analyzed with Seurat (version 3.0.2), (Stuart et al., 2019). We filtered the cells with the number of detected genes higher than 200 and lower than 7.000 and the percentage of reads mapped to mitochondrial genes not higher than 25. Principal component analysis was performed on 2000 genes with the most variable expression was selected by Seurat. First 6 principal components were used to perform UMAP embedding (parameter k=100). Clustering of cells was performed based on PCA embedding (first 6 PCs taken into account). The data was scaled to regress out total number of detected features and total percentage of mitochondrial reads. Joined embedding for days 2.5 and 3.5-4 was performed with scanpy based on spliced transcripts from velocyto (version 0.17.13) (La Manno et al, 2018). First, the data were normalized and filtered with scanpy.pp.recipe_seurat workflow (Satija et al, 2015). Next, UMAP embedding was performed with default parameters. Cells were clustered with louvain algorithm (Blondel et al, 2008) and cell populations were defined as groups of clusters identified by this algorithm. GC B cell signature was used from Mabbott et al (Mabbott and Gray, 2014) with Bcl6 and Gcsam manually added to the signature.
Bulk RNA-seq: Sequence reads that passed the Illumina quality filtering were considered for alignment. Reads corresponding to mouse ribosomal RNAs (BK000964.1 and NR046144.1) were removed. The remaining reads were cut down to a read length of 44 bp and aligned to the mouse transcriptome (genome assembly version of July 2007 NCBI37/mm9) using TopHat version 1.4.1 (Trapnell et al, 2009). The calculation of RNA expression values was all based on the RefSeq database, which was downloaded from UCSC on January 10th, 2014. The annotation of immunoglobulin and T cell receptor genes was incorporated from the Ensembl release 67 (Cunningham et al, 2015). Genes with overlapping exons were flagged and double entries (i.e. exactly the same gene at two different genomic locations) were renamed. Genes with several transcripts were merged to consensus-genes consisting of a union of all underlying exons using the fuge software (I. Tamir, unpublished), which resulted in 25,726 gene models.  For analysis of differential gene expression, the number of reads per gene was counted using HTseq version 0.5.3 (Anders et al, 2014) with the overlap resolution mode set to 'union'. The datasets were analyzed using the R package DESeq2 version 1.2.10 (Love et al, 74). Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings. Transcripts per million (TPM) were calculated from RNA-seq data, as described (Wagner et al, 2012).  GSEA was performed using the GSEA software from the Broad Institute (Subramanian et al, 2005). Genes were ranked on the basis of their change in expression (log2 fold values) as determined by the DESeq2 package and were compared to gene sets from the MSigDB or defined gene sets from literature or our data. GC B cell signature was used from Mabbott et al (Mabbott and Gray, 2014) with Bcl6 and Gcsam manually added to the signature. Early GC B cell signature was generated by pairwise comparison of our WT day 4 GC B and CCR6+ B cell datasets, using top 500 GC B cell-upregulated genes.
ChIP-seq: The Bhlhe40 ChIP-seq experiment with in vitro activated B cells was performed with two technical replicates (3x10^6 and 22x10^6 cells) and reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using the Bowtie2 program (Langmead and Salzberg, 2012) (usegalaxy.eu; galaxy version 2.3.4.2 (Afgan et al, 2018)) and bam files for 3x10^6 and 22x10^6 cell samples were merged. Peaks were called with a P value below 10<-10> by using the MACS program version 1.3.6.1 (Feng et al, 2012) with default parameters. The identified peaks were then assigned to target genes as described (Revilla-i-Domingo et al, 2012). Bhlhe40 peaks overlapping with the transcription start site (TSS) were referred to as promoter peaks. For motif discovery, we used the MEME-ChIP suite (usegalaxy.eu; galaxy version 4.11.2 (Afgan et al, 2018)) (Machanick and Bailey, 2011) to predict the most significant motifs present in the 300 bp centered at the peak summit of the top 500 sequences, as sorted by the fold enrichment score of the MACS program.
Genome_build: MM9 (MM10 for scRNA-seq)
Supplementary_files_format_and_content: bigwig = bigWig Track format of read counts per base (.cov.all.rpm.bw) or bigWig Track format of read density coverage in reads per million; text tab delim = TPM values in ASCII text format tab delimited

molecule: genomic DNA

source_name: Splenic B cells

extract_protocol:
No extraction
ChIP tagmentation protocol (Gustafsson et al, 2018)

tag: genotype

tag: cell preparation

value: CD43-depleted, in vitro-activated, FACS-sorted

tag: cell sorting strategy

value: Live CD19+

tag: chip antibody

value: anti-Bhlhe40, Novus Biologicals, NB100-1800, lot C2


title: LMN61-N

source_name: Intestinal Tissue

tag: tissue

tag: tissue type

value: normal

tag: treatment


title: 2.38-D12-1

tag: cell type

value: conditionally immortalized human atrial cardiomyocytes (hiAMs)

value: Differentiated (D12)


title: 2.90-D0-3

source_name: hiAM-2.90_Proliferating (D0)

value: Proliferating (D0)


title: ChIP-seq from in vitro activated B cells (22 million cells) Bhlhe40_ChIP_22M

tag: strain


title: RNA-seq Bhlhe40-/- tetramer+ T cells CD4T_KO_5

description: RNA-seq Bhlhe40-/- tetramer+ T cells

source_name: Splenic T cells

extract_protocol:
Single cell lysis kit
NEBNext Ultra II

value: Ex vivo, FACS-sorted from spleens

value: CD19- CD11c- CD11b- F4/80- CD8a- Tetramer+ CD4+ TCRb+ CD45.1+


title: AC05 at T2 3

description:
AC Patient AC05 Time Point T2 3
A0173.S0021

source_name: Sorted tetramer positive CD8+ lymphocytes

tag: patientid


title: LMN66-N

extract_protocol:
Total RNA for Library Preparation and Sequencing analysis was purified from microdissected VcMsh2 FFPE tumor and normal intestinal tissue using the RNAeasy Plus Kit (QIAGEN) that included a genomic DNA elimination step.
Coding RNA transcripts were enriched using mouse exome panel hybridization (Twist Biosciences).  Size, concentration, and integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were generated using Illumina’s TruSeq RNA sample Prep Kit v3, following the manufacurer’s protocol.
Sequencing of 8–10 pM of each library was done on the NovaSeq sequencer as 75bp paired-end read runs.

value: Intestinal Tissue

value: NV


title: 2.90-D0-2


title: LMN59-N


title: 2.90-D0-1


title: RNA-seq Bhlhe40+/+ tetramer+ T cells CD4T_WT_5

description: RNA-seq Bhlhe40+/+ tetramer+ T cells

value: CD19- CD11c- CD11b- F4/80- CD8a- Tetramer+ CD4+ TCRb+ CD45.1+ CD45.2+


title: Intestinal Enteroid 24hr (Hs)

description:
HIOs were transplanted into the kidney capsule of immune-deficient NOD-SCID IL-2Rγnull (NSG) (Jackson Laboratories) mice, as previously described5. Crypt domains from transplanted HIOs were isolated and suspended in Matrigel domes to form kidney capsule-matured human intestinal enteroids (kcHIEs)6. Frozen duodenal patient biopsy derived human intestinal enteroids (bHIEs) were provided by the lab of Dr. Noah Shroyer (Baylor College of Medicine).
CH_24

source_name: Intestinal Enteroid 24hr

value: Intestinal Enteroid

tag: passage

value: passaged every 4-7 days

tag: circadian clock


title: 2.38-D12-3

tag: cell line/monoclone


title: RNA-seq Bhlhe40-/- tetramer+ T cells CD4T_KO_4

description: RNA-seq Bhlhe40-/- tetramer+ T cells


title: LMN57-N

value: RV

value: FSP vaccine


title: 2.52-D0-3

source_name: hiAM-2.52_Proliferating (D0)

tag: state


title: AC05 at T2 1

description:
AC Patient AC05 Time Point T2 1
A0173.S0019

extract_protocol:
Replicate populations of viable tetramer+ CD8+ T cells were sorted into RLT Plus lysis buffer supplemented with 1% betamercaptoethanol and frozen at -80°C. RNA was extracted using QIAGEN AllPrep kits.
Smartseq2 bulk protocol using oligo-dT primers to amplify cDNA from mRNA, followed by Illumina Nextera XT tagmentation and NextSeq 550 sequencing.

value: Sorted tetramer positive CD8+ lymphocytes

value: AC

tag: replicate

tag: Sex

value: M

tag: batch


title: 2.52-D0-2


title: LMN56-N

tag: group


title: AC05 at T1 2

description:
AC Patient AC05 Time Point T1 2
A0173.S0017

tag: ugps


title: LMN54-N


title: LMN60-N

value: N

value: Naproxen


title: RNA-seq Bhlhe40+/+ tetramer+ T cells CD4T_WT_4

description: RNA-seq Bhlhe40+/+ tetramer+ T cells

tag: genotype

tag: cell preparation

tag: cell sorting strategy


title: 2.52-D0-1

value: conditionally immortalized human atrial cardiomyocytes (hiAMs)


title: AC04 at T3 2

description:
AC Patient AC04 Time Point T3 2
A0173.S0015

value: F


title: 2.38-D0-3

source_name: hiAM-2.38_Proliferating (D0)

value: Proliferating (D0)


title: AC05 at T1 1

description:
AC Patient AC05 Time Point T1 1
A0173.S0016


title: RNA-seq Bhlhe40-/- tetramer+ T cells CD4T_KO_3

description: RNA-seq Bhlhe40-/- tetramer+ T cells

value: Ex vivo, FACS-sorted from spleens

tag: chip antibody


title: AC05 at T2 2

description:
AC Patient AC05 Time Point T2 2
A0173.S0020


title: LMN53-N

tag: tissue

tag: tissue type

value: normal

value: AV

tag: treatment

value: Aspirin + FSP vaccine


title: 2.38-D0-2

tag: cell type


title: RNA-seq Bhlhe40-/- tetramer+ T cells CD4T_KO_2

description: RNA-seq Bhlhe40-/- tetramer+ T cells

tag: strain

value: CD19- CD11c- CD11b- F4/80- CD8a- Tetramer+ CD4+ TCRb+ CD45.1+


title: RNA-seq Bhlhe40+/+ tetramer+ T cells CD4T_WT_3

description: RNA-seq Bhlhe40+/+ tetramer+ T cells

value: CD19- CD11c- CD11b- F4/80- CD8a- Tetramer+ CD4+ TCRb+ CD45.1+ CD45.2+


title: LMN51-N

value: Intestinal Tissue

value: NV

value: Naproxen + FSP vaccine


title: LMN52-N


title: 2.38-D0-1


title: RNA-seq Bhlhe40+/+ tetramer+ T cells CD4T_WT_2

description: RNA-seq Bhlhe40+/+ tetramer+ T cells


title: AC04 at T3 1

description:
AC Patient AC04 Time Point T3 1
A0173.S0014

value: Sorted tetramer positive CD8+ lymphocytes

tag: patientid


title: AC05 at T1 3

description:
AC Patient AC05 Time Point T1 3
A0173.S0018

value: AC


title: AC04 at T2 2

description:
AC Patient AC04 Time Point T2 2
A0173.S0013


title: AC04 at T2 1

description:
AC Patient AC04 Time Point T2 1
A0173.S0012


title: HUVEC2

source_name: Human Umbilical Vein Endothelial Cells (HUVEC)

tag: cell line

tag: procedure

value: Intact


title: RNA-seq Bhlhe40+/+ tetramer+ T cells CD4T_WT_1

description: RNA-seq Bhlhe40+/+ tetramer+ T cells


title: LMN47-N

value: A

value: Aspirin


title: LMN46-N

value: R

value: Western Diet


title: HUVEC1

value: Human Umbilical Vein Endothelial Cells (HUVEC)


title: JKT2

source_name: Human T-Lymphocyte (Jurkat) cells

value: Human T-Lymphocyte (Jurkat) cells


title: AC04 at T1 1

description:
AC Patient AC04 Time Point T1 1
A0173.S0010

tag: replicate

value: F


title: JKT1


title: LMN48-N

value: normal


title: scRNA-seq Bhlhe40-/- d3.5-4 after immunization 73641

description:
scRNA-seq Bhlhe40-/- d3.5-4 after immunization
d2_d3_wtko.seurat.rds

extract_protocol:
Cells 10X Genomics Chromium 10x RNA
Cells 10X Genomics Chromium 10x RNA

value: Ex vivo, FACS-sorted from spleens


title: RNA-seq Bhlhe40-/- tetramer+ T cells CD4T_KO_1

description: RNA-seq Bhlhe40-/- tetramer+ T cells

value: CD19- CD11c- CD11b- F4/80- CD8a- Tetramer+ CD4+ TCRb+ CD45.1+


title: LMN44-N


title: LMN45-N


title: scRNA-seq WT d2.5 after immunization 97051

description:
scRNA-seq WT d2.5 after immunization
d2_d3_wtko.seurat.rds, d2_d3_wt.seurat.rds, d2.seurat.rds


title: scRNA-seq WT d3.5-4 after immunization 73640

description:
scRNA-seq WT d3.5-4 after immunization
d2_d3_wtko.seurat.rds, d2_d3_wt.seurat.rds, d3_wt.seurat.rds


title: AC04 at T1 2

description:
AC Patient AC04 Time Point T1 2
A0173.S0011

tag: Sex


title: fca_thyroid_input_rep1

status: Public on Aug 29 2021

city: College Station

first: William

middle: J

last: Murphy

state: TX

address: 4458 TAMU

department: Veterinary Integrative Biosciences

institute: Texas A&M University

data_processing:
Data was processed according to the ENCODE3 pipeline v1 specifications (https://docs.google.com/document/d/1lG_Rd7fnYgRpSIqrIfuVlAz2dW1VaSQThzk836Db99c/edit#), following the guidelines for histone modifications. Briefly, reads were mapped to a highly contiguous, single-haplotype domestic cat reference genome assembly (GCA_018350175.1) using Bowtie2 v.2.4.2. Domestic cat Y chromosome sequences (GenBank accession KP081775.1 plus sequences from Y chromosome ampliconic regions) were added during mapping to act as bait for male cat Y reads. Relaxed peaks were generated with MACS2 v.2.2.5 for narrow marks(-g 1.61e9 -p 1e-2 --nomodel --keep-dup all -B --SPMR) and epic2 v.0.0.51 for the broad mark(--effective-genome-fraction 0.66) for each biological replicate, pooled replicates, and pooled pseudoreplicates (pseudoreplicates consist of half the reads of a true replicate sampled without replacement). Peaks from the pooled replicate set were retained in the final replicated peak set if they overlapped by at least half their length in bases with peaks from both biological replicates. Additionally, peaks that overlapped both pooled pseudoreplicates were also included in the final replicated peak set. Final peak files are not filtered for blacklisted regions as a blacklist has not yet been developed for Felis catus.
Genome_build: GCA_018350175.1 (tentatively felCat10)
Supplementary_files_format_and_content: narrowPeak; broadPeak; bigWig; peak files from individual replicates contain relaxed peak calls while the final replicated peak files contain the optimal peak sets for each tissue.

organism: Felis catus

source_name: thyroid

extract_protocol:
Tissue samples were collected from adult male domestic shorthair cats (2 biological replicates). Tissues included: heart, liver, kidney, small intestine, testes, lung, and thyroid. No lesions were identified grossly in the collected tissues. Tissues were flash frozen within 30 minutes of euthanasia and stored at -80 C. All steps leading up to and including chromatin immunoprecipitation (ChIP) and ChIP qPCR were performed using the iDeal ChIP-seq Kit for Histones (Diagenode) per manufacturer guidelines. This included DNA sonication to 100-300 bp using a Bioruptor Pico (Diagenode) at 7 cycles of 30 seconds on and 30 seconds off.
Library preparation for sequencing was performed with the NEBNext® Ultra™ II DNA Library Prep Kit and NEBNext® Multiplex Oligos for Illumina (New England Biolabs) according to manufacturer guidelines. Sequencing was performed on a NovaSeq 6000 platform (Illumina) with a single-end 100 bp format.

value: thyroid

value: Input

value: untreated

tag: totalreads


title: fca_smallintestine_input_rep2

value: small intestine, jejunum


title: fca_lung_input_rep1

source_name: lung

value: lung


title: fca_lung_input_rep2


title: fca_liver_input_rep2

value: liver, left lateral lobe


title: fca_kidney_input_rep1

source_name: kidney-cortex

value: kidney, cortex


title: fca_liver_input_rep1


title: fca_testis_input_rep2

source_name: testis

value: testis


title: DC05 at T3 2

description:
DC Patient DC05 Time Point T3 2
A0173.S0032

value: Sorted tetramer positive CD8+ lymphocytes

value: DC

value: M

tag: batch


title: fca_smallintestine_input_rep1


title: fca_kidney_input_rep2


title: fca_thyroid_input_rep2


title: fca_heart_input_rep1

value: heart, left ventricle


title: fca_liver_h3k27me3_rep2


title: fca_liver_ctcf_rep2

value: CTCF (Diagenode; C15410210)


title: 2047_Muscle_S4

city: St. Lucia

first: Antonio

last: Reverter

state: QLD

address: 306 Carmody Road

department: Agriculture and Food

institute: CSIRO

data_processing:
Illumina NextSeq 150 cycle (2X 75 bp).
ATAC-seq data processing and alignment was completed using the Harvard pipeline (https://informatics.fas.harvard.edu/atac-seq-guidelines.html).
Peak calling was performed using the tool Genrich v0.6.1 (available at https://github.com/jsh58/Genrich) including all biological replicates per tissue and parameters -j (ATAC-seq mode) -r (remove PCR duplicates) -e MT (to exclude mitochondrial chromosome) -p 0.01 (p-value).
To compare the three tissues and identify tissue-specific peaks we used bedtools interesct -v (v. 2.29.2)[64] for each pairwise contrast. By looking at the results of the multiple contrasts we defined peaks exclusive to one tissue as tissue-specific. Then, bedtools multiIntersectBed
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: tab-delimited text files conatining the nuber of peaks per tissue

organism: Bos indicus

source_name: Muscle

growth_protocol: Liver, hypothalamus and muscle samples were collected from three unrelated, post-pubertal Brahman heifers of similar age and weight as previously described (Fortes MRS, Nguyen LT, Weller MMDCA, Cánovas A, Islas-Trejo A, Porto-Neto LR, et al. Transcriptome analyses identify five transcription factors differentially expressed in the hypothalamus of post- versus prepubertal Brahman heifers. ) Heifers used in this study were managed, handled, and euthanized as per approval of the Animal Ethics Committee of the University of Queensland, Production and Companion Animal group (certificate number QAAFI/279/12). After slaughter, tissue samples were collected as fast as possible and stored at−80◦C.

extract_protocol:
Frozen tissue (20mg) was ground in liquid nitrogen using a mortar and pestle.
The pulverized tissue was transferred to a pre-chilled 2ml Dounce homogenizer containing 1ml cold 1 x homogenization buffer and homogenized with the pestle until a uniform suspension was seen (10-20 strokes).  The homogenate was filtered with a 40uM nylon cell strainer (BD Falcon) before layering onto the iodixanol solution.The ratio of nuclei to enzyme concentration was optimized for each sample by performing transposition reactions containing 50 000, 100 000 and 200 000 nuclei with 2.5ul of tagment enzyme in 50ul of transposition mix .The transposed DNA was amplified with custom primers . Amplified libraries were purified using Agencourt AMPure XP beads (Beckman Coulter) and quality controlled using a Bioanalyser High Sensitivity DNA Analysis kit (Agilent).

tag: breed

value: Brahman

value: Muscle


title: 2054_Liver_S1

source_name: Liver

treatment_protocol: After slaughter, tissue samples were collected as fast as possible and stored at−80◦C.

value: Liver


title: 2047_Liver_S5


title: 2054_Hypothalamus_S2

source_name: Hypothalamus

value: Hypothalamus


title: fca_liver_h3k4me3_rep2

value: H3K4me3 (Diagenode; C15410003)


title: fca_liver_ctcf_rep1


title: 2047_Hypothalamus_S4


title: 2054_Muscle_s2


title: 2057_Muscle_S9


title: fca_heart_input_rep2

value: Input


title: 2057_Liver_s8


title: 2057_Hypothalamus_s7


title: fca_testis_input_rep1

value: untreated


title: fca_liver_h3k4me3_rep1


title: fca_kidney_h3k4me3_rep2


title: fca_liver_h3k27me3_rep1


title: fca_kidney_h3k27me3_rep2


title: fca_thyroid_ctcf_rep2

value: thyroid


title: fca_kidney_h3k27ac_rep1

value: H3K27ac (Diagenode; C15410196)


title: fca_kidney_ctcf_rep1


title: fca_kidney_h3k27ac_rep2


title: fca_kidney_h3k27me3_rep1


title: fca_kidney_ctcf_rep2


title: fca_thyroid_h3k4me3_rep2


title: fca_thyroid_h3k27me3_rep1


title: fca_thyroid_h3k4me3_rep1


title: fca_thyroid_ctcf_rep1


title: fca_thyroid_h3k27me3_rep2


title: fca_testis_ctcf_rep2


title: fca_testis_h3k4me3_rep2


title: fca_testis_h3k27me3_rep2


title: fca_testis_h3k27me3_rep1


title: fca_thyroid_h3k27ac_rep2


title: fca_testis_h3k27ac_rep1


title: fca_testis_h3k4me3_rep1


title: fca_testis_ctcf_rep1


title: fca_thyroid_h3k27ac_rep1


title: fca_smallintestine_ctcf_rep2

value: small intestine, jejunum


title: fca_liver_h3k27ac_rep1

value: liver, left lateral lobe


title: fca_smallintestine_h3k4me3_rep2


title: fca_smallintestine_h3k27me3_rep2


title: fca_kidney_h3k4me3_rep1

value: kidney, cortex


title: fca_smallintestine_h3k27ac_rep2


title: fca_liver_h3k27ac_rep2


title: fca_smallintestine_ctcf_rep1


title: fca_smallintestine_h3k27ac_rep1


title: fca_lung_ctcf_rep2

value: lung


title: fca_smallintestine_h3k27me3_rep1


title: fca_lung_h3k27ac_rep2


title: fca_lung_h3k27me3_rep2


title: fca_lung_h3k27me3_rep1


title: fca_lung_ctcf_rep1


title: fca_testis_h3k27ac_rep2

value: testis


title: Control EEVs

city: Dallas

first: Chengsong

last: Zhu

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

data_processing:
Fastqs were generated with bcl2fastq2 2.19.0, and reads were trimmed with Trim Galore! v0.6.6. FastQC v0.11.9, FASTX v0.0.14, and miRTrace v1.0.1 were used for QC purposes.
Bowtie v1.3.0 was used for alignment against mature miRNAs and miRNA precursors (GRCh37).
Processing of alignments was done with Samtools v1.12, miRNA annotation was done with mirtop 0.4.23 and miRDeep2 v2.0.1.2.
Genome_build: GRCh37
Supplementary_files_format_and_content: raw_counts
Supplementary_files_format_and_content: normalized_CPM

source_name: cultured endothelial cells

growth_protocol: HUVEC were cultured in EBM2 complete growth medium, containing 2% v/v serum, to confluency

extract_protocol: miRNA was isolated from EVs using mirVana  miRNA isolation kit (Thermo Fisher)

treatment_protocol: Cells were incubated with serum-free EBM2 medium for 2 h, and then treated wirth control vehicle or FVIIa (100 nM) for 24 h. The EEVs were islated from the culture supernate by spinning 21,000g for 1 hour. Evs were quantified using Nano sight 300.

value: human umbilical vein endothelila cells

tag: time point

value: 24 h treatment

tag: agent

value: control vehicle


title: FVIIa-released EEVs

value: Factor VIIa


title: fca_smallintestine_h3k4me3_rep1


title: fca_heart_h3k27me3_rep2

value: heart, left ventricle


title: fca_heart_ctcf_rep2

value: CTCF (Diagenode; C15410210)


title: fca_heart_h3k4me3_rep2


title: fca_heart_h3k27ac_rep1


title: fca_heart_h3k27me3_rep1


title: fca_lung_h3k4me3_rep2


title: fca_heart_h3k4me3_rep1


title: UO_AH_132

city: Aurora

first: Neelanjan

last: Mukherjee

state: CO

department: BMG/RBI

institute: University of Colorado School of Medicine

data_processing:
Reads were first mapped to rRNA sequences using bowtie v1.0.1 (https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.0.1/bowtie-1.0.1-linux-x86_64.zip/download) (Langmead et al., 2009). Reads that did not map to rRNA were subject to downstream analysis.
To quantify transcript expression we used using RSEM v 1.2.11 (http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.2.11.tar.gz) (Li and Dewey, 2011) using the gencodev25 transcripts.
We used mirUtils (https://github.com/abattenhouse/mirutils/blob/master/mirUtils) to calculate miRNA counts from smallRNA-seq data.
Code will be available at https://github.com/rnabioco/rnaroids
Genome_build: hg38 and mm10

growth_protocol: H295R cells were cultured in DMEMF-12 (Life Technologies, 31330038) supplemented with 10% cosmic calf serum (HyClone, SH30087.03), 1% ITS+ premix (Corning, 354352) and 1% Pen/Strep (Thermofisher, #15070063).

extract_protocol:
NEXTflex smallRNA-Seq v2
RNA was extracted with TRIzol. For metabolic labeling, samples treated with 4-thiouridine and labeled RNA was biotinylated and purified using streptavidin as described previously (Methods Mol Biol. 2013;1064:91-100. doi: 10.1007/978-1-62703-601-6_6). All paired end RNA-seq was performed using the specificied BIOO scientific library prepartion protocol. Ribosome profiling was performed as described in (10.1038/nmeth.3688) and libraries were constructed using the specified BIOO scientific kit, which was also used for smallRNA sequencing.

treatment_protocol: Cells were treated with either 100 nM Angiotensin (Sigma-Aldrich, A2900) or 10uM Forskolin (Sigma-Aldrich, F6886). For metabolic labeling, 4-thiouridine was added 20 minutes before sample collection.

value: Ang

tag: time

tag: barcode#


title: fca_lung_h3k27ac_rep1

tag: tissue

tag: chip antibody


title: UO_AH_127

description:
H295R_expression.txt
ribosome profiling

tag: treatment


title: UO_AH_137


title: UO_AH_136


title: UO_AH_129

description:
H295R_expression.txt
ribosome profiling


title: UO_AH_131


title: UO_AH_133


title: UO_AH_135


title: UO_AH_128

description:
H295R_expression.txt
ribosome profiling


title: UO_AH_125

description:
H295R_expression.txt
ribosome profiling


title: fca_heart_h3k27ac_rep2


title: UO_AH_126

description:
H295R_expression.txt
ribosome profiling


title: UO_AH_123


title: UO_AH_122


title: UO_AH_121


title: UO_AH_120


title: UO_AH_130


title: UO_AH_119


title: fca_lung_h3k4me3_rep1

value: H3K4me3 (Diagenode; C15410003)


title: UO_AH_118


title: UO_AH_117


title: UO_AH_113


title: UO_AH_114


title: UO_AH_116


title: fca_heart_ctcf_rep1


title: UO_AH_115


title: UO_AH_112

value: Ctrl


title: UO_AH_124

description:
H295R_expression.txt
ribosome profiling


title: UO_AH_110


title: UO_AH_134


title: UO_AH_111


title: UO_AH_106


title: UO_AH_108


title: UO_AH_109


title: UO_AH_107


title: UO_AH_071

extract_protocol:
NEXTflex RD qRNA-seq
RNA was extracted with TRIzol. For metabolic labeling, samples treated with 4-thiouridine and labeled RNA was biotinylated and purified using streptavidin as described previously (Methods Mol Biol. 2013;1064:91-100. doi: 10.1007/978-1-62703-601-6_6). All paired end RNA-seq was performed using the specificied BIOO scientific library prepartion protocol. Ribosome profiling was performed as described in (10.1038/nmeth.3688) and libraries were constructed using the specified BIOO scientific kit, which was also used for smallRNA sequencing.

value: For

tag: ercc

value: y


title: UO_AH_073


title: UO_AH_067


title: UO_AH_057


title: UO_AH_056


title: UO_AH_054


title: UO_AH_055


title: UO_AH_069


title: UO_AH_075


title: PLC3

city: Dublin

first: Jianghui

last: Meng

address: Glasnevin Avenue

country: Ireland

institute: Dublin City University

data_processing:
Primary image processing was performed on the NextSeq500 instrument using Real Time Analysis 2.4.11 Software (RTA).
Primary data analysis was performed using the bcl2fastq2.15 software package.
Image and signal processing, such as template generation, imaging and base calling, was carried out by the Illumina NextSeq500 inherited NCS and RTA software packages applying the FastQ only processing pipeline.
During sequencing every base is assigned with a quality score according to its probability for correctness. Raw clusters are determined as well.They are checked for quality issues and low quality clusters, with e. g. mixed fragment content,  are filtered out during the processing.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated RPKM=total exon read count/mapped reads [millions]*exon length [kb]
Genome_build: hg19-GRCh37.p13
Supplementary_files_format_and_content: RPKM

source_name: human skin keratinocytes

growth_protocol: phKCs provided by Lonza were cultured in the KBM-Gold™ plus SingleQuot KCs supplement (Lonza).

extract_protocol:
The frozen cell pellet samples were dissolved in 6 ml Buffer RLT. Total RNA was isolated using the Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions including on-column Dnase digestion. In order not to overload the silica column,  isolation was performed with 10 million cells (1/10 of the lysate=600 microliters). Total RNA was eluted in 30 microliters RNase-free water.
Library preparation with the TruSeq Stranded mRNA HT technology, according to the manufacturer's protocol. The protocol started with an RNA fragmentation step using divalent cations. Samples were then introduced into a reverse transcription to generate first strand cDNA. In the second strand cDNA synthesis dUTP is incorporated instead of dTTP, to avoid amplification by the DNA polymerase in the subsequent PCR and thus guarantee strandedness. 3'-ends were adenylated and sequencing adapters were ligated. Those comprise sequencing primer- and flow cell-binding sites, as well as indices for multiplexed sequencing of pooled libraries. Adapter-ligated fragments were amplified during a limited-cycle PCR reaction.

treatment_protocol: Three samples of phKCs from 3 different human healthy donors were treated with 20 µg/ml poly(I:C) for 2 h before cell pellet were harvested and entrusted to IMGM Laboratories GmbH (Martinsried, Germany) for RNA-Seq using NextSeq500 next generation sequencing system.

tag: development stage

value: Adults

value: Skin

tag: passage


title: Control 3


title: UO_AH_083


title: Control 1


title: Gut epithelial cells KO-rep7

city: safed

first: Evan

last: Elliott

state: safed

address: 8 henrietta szold

country: Israel

institute: Bar Ilan University

data_processing:
Base calling was done by Illumina Basespace (version 2)
Fastq files were then analyzed by Deseq2 to produce read calls
aligned to mouse genome mm10
Deseq2 was used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: expr.txt (text file including values for each sample)

source_name: Gut epithelial cells KO

extract_protocol:
Gut epithelial cells were extracted, RNA was extracted from them using qiagen RNAeasy micro kit
library was prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module & NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® sequencing

tag: strain

tag: genotype

tag: age

value: 8 weeks old

value: gut

tag: cell type

value: epithelial cells


title: Gut epithelial cells KO-rep6


title: PLC 1


title: UO_AH_065


title: Gut epithelial cells KO-rep3


title: UO_AH_319

extract_protocol:
NEXTflex smallRNA-Seq v3
RNA was extracted with TRIzol. For metabolic labeling, samples treated with 4-thiouridine and labeled RNA was biotinylated and purified using streptavidin as described previously (Methods Mol Biol. 2013;1064:91-100. doi: 10.1007/978-1-62703-601-6_6). All paired end RNA-seq was performed using the specificied BIOO scientific library prepartion protocol. Ribosome profiling was performed as described in (10.1038/nmeth.3688) and libraries were constructed using the specified BIOO scientific kit, which was also used for smallRNA sequencing.


title: UO_AH_317


title: UO_AH_318


title: UO_AH_320


title: UO_AH_070


title: Gut epithelial cells KO-rep1


title: Gut epithelial cells KO-rep2


title: Gut epithelial cells WT-rep5

source_name: Gut epithelial cells WT

value: wild type


title: UO_AH_312


title: Gut epithelial cells WT-rep3


title: UO_AH_314


title: UO_AH_316


title: Gut epithelial cells WT-rep2


title: PLC2


title: UO_AH_310


title: UO_AH_309


title: Control 2


title: Gut epithelial cells WT-rep4


title: Gut epithelial cells WT-rep1


title: UO_AH_308

extract_protocol:
NEXTflex RD qRNA-seq w/ qPCR
RNA was extracted with TRIzol. For metabolic labeling, samples treated with 4-thiouridine and labeled RNA was biotinylated and purified using streptavidin as described previously (Methods Mol Biol. 2013;1064:91-100. doi: 10.1007/978-1-62703-601-6_6). All paired end RNA-seq was performed using the specificied BIOO scientific library prepartion protocol. Ribosome profiling was performed as described in (10.1038/nmeth.3688) and libraries were constructed using the specified BIOO scientific kit, which was also used for smallRNA sequencing.


title: UO_AH_082


title: UO_AH_081


title: Gut epithelial cells KO-rep5


title: UO_AH_313


title: Gut epithelial cells KO-rep4


title: UO_AH_080


title: UO_AH_304


title: UO_AH_079


title: UO_AH_078


title: UO_AH_302


title: UO_AH_305


title: UO_AH_076


title: UO_AH_074


title: UO_AH_306


title: UO_AH_300


title: UO_AH_315


title: UO_AH_072


title: UO_AH_077


title: UO_AH_299


title: UO_AH_066


title: UO_AH_068


title: UO_AH_298


title: UO_AH_311


title: UO_AH_064


title: UO_AH_296

description:
H295R_expression.txt
metabolic labeling


title: UO_AH_307


title: UO_AH_063


title: UO_AH_295

description:
H295R_expression.txt
metabolic labeling


title: UO_AH_293

description:
H295R_expression.txt
metabolic labeling


title: UO_AH_060


title: UO_AH_061


title: UO_AH_292

description:
H295R_expression.txt
metabolic labeling


title: UO_AH_291

description:
H295R_expression.txt
metabolic labeling


title: UO_AH_303


title: UO_AH_062


title: UO_AH_289

description:
H295R_expression.txt
metabolic labeling


title: UO_AH_059


title: UO_AH_058


title: UO_AH_297


title: UO_AH_286

description:
H295R_expression.txt
metabolic labeling


title: UO_AH_294

description:
H295R_expression.txt
metabolic labeling


title: UO_AH_287

description:
H295R_expression.txt
metabolic labeling


title: UO_AH_288

description:
H295R_expression.txt
metabolic labeling


title: UO_AH_278

description:
H295R_expression.txt
ribosome profiling


title: UO_AH_276

description:
H295R_expression.txt
ribosome profiling


title: UO_AH_285

description:
H295R_expression.txt
metabolic labeling


title: UO_AH_277

description:
H295R_expression.txt
ribosome profiling


title: UO_AH_275

description:
H295R_expression.txt
ribosome profiling


title: UO_AH_301


title: UO_AH_269

description:
H295R_expression.txt
ribosome profiling


title: UO_AH_274

description:
H295R_expression.txt
ribosome profiling


title: UO_AH_273

description:
H295R_expression.txt
ribosome profiling


title: UO_AH_272

description:
H295R_expression.txt
ribosome profiling


title: UO_AH_270

description:
H295R_expression.txt
ribosome profiling


title: UO_AH_162


title: UO_AH_268

description:
H295R_expression.txt
ribosome profiling


title: UO_AH_159

description:
H295R_expression.txt
metabolic labeling


title: UO_AH_160

description:
H295R_expression.txt
metabolic labeling


title: UO_AH_161


title: UO_AH_163


title: UO_AH_023

source_name: adrenal gland

extract_protocol:
NEXTflex dirRNA-Seq
RNA was extracted with TRIzol. For metabolic labeling, samples treated with 4-thiouridine and labeled RNA was biotinylated and purified using streptavidin as described previously (Methods Mol Biol. 2013;1064:91-100. doi: 10.1007/978-1-62703-601-6_6). All paired end RNA-seq was performed using the specificied BIOO scientific library prepartion protocol. Ribosome profiling was performed as described in (10.1038/nmeth.3688) and libraries were constructed using the specified BIOO scientific kit, which was also used for smallRNA sequencing.

tag: status

value: ZFP36L2 KO


title: UO_AH_267

description:
H295R_expression.txt
ribosome profiling


title: UO_AH_158

description:
H295R_expression.txt
metabolic labeling


title: UO_AH_021


title: UO_AH_022


title: UO_AH_019


title: UO_AH_020


title: UO_AH_017

value: ZFP36L2 WT


title: UO_AH_018


title: UO_AH_015


title: UO_AH_014


title: UO_AH_016


title: UO_AH_290

description:
H295R_expression.txt
metabolic labeling


title: GDT_minus_IL2

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
Illumina bcl2fastq v2.18.0.12 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR 2.6.0.a with default parameters.
The HTSeq software (v.0.6.0) was applied to generate the count matrix, with default parameters. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR 3.28.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: read_counts.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: gammadelta T cells

growth_protocol: Freshly sorted by FACS murine gammadelta T cells were activated with plate-bound anti-CD3 and soluble anti-CD28 antibodies in the presence of recombinant mouse IL-2 [100U/ml].

extract_protocol: Total RNA was extracted from cultured cells using the RNeasy Mini kit.

treatment_protocol: Gammadelta T cells expanded with IL-2 [100U/ml] for 5 days.

value: spleen

value: gammadelta T cells

value: freshly isolated


title: Egr1_rep3

city: Ikoma

first: Taito

last: Matsuda

country: Japan

institute: Nara Institute of Science and Technology

data_processing:
RNA-seq was performed with 50-bp single-end sequencing by an Illumina Hiseq 2500. Obtained reads were processed with FASTX tool kit to remove short (<20bp) and low quality (quality score<20) reads, followed by trimming of the adaptor sequence.
RNA-seq: Processed reads were mapped to the mouse genome (mm10) using TopHat/Bowtie2.
RNA-seq: DESeq2 package was used for differential gene expression analysis.
Supplementary_files_format_and_content: TXT files indicating TPM values of each sample
ATAC-seq was performed with 50-bp single-end sequencing by an Illumina Hiseq 2500. Obtained reads were processed with FASTX tool kit to remove short (<20bp) and low quality (quality score<20) reads, followed by trimming of the adaptor sequence.
ATAC-seq: Processed reads were mapped to the mouse genome (mm10)  using Bowtie2.
ATAC-seq: Open chromatin regions were analyzed using MACS software.
Supplementary_files_format_and_content: BigWig files indicating alignment of each sample
ChIP-seq was performed with 50-bp single-end sequencing by an Illumina Hiseq 2500. Obtained reads were processed with FASTX tool kit to remove short (<20bp) and low quality (quality score<20) reads, followed by trimming of the adaptor sequence.
ChIP-seq: Processed reads were mapped to the mouse genome (mm10)  using Bowtie2.
ChIP-seq: Egr1-occupied regions were identified using MACS software.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files indicating alignment of each sample

source_name: Neural stem/progenitor cells

growth_protocol: For in vitro experiments, we prepared mouse NSCs with multipotency and self-renewal capacity derived from mouse cortex at embryonic day 11 and passaged more than 20 times. Mouse NSCs were cultured with NSC medium, which iconsists of Dulbecco’s modified eagle’s medium (DMEM)/F-12 containing N2 supplement with 20 ng/ml basic fibroblast growth factor (bFGF),  20 ng/ml epidermal growth factor (EGF) and 0.1 mg/ml penicillin/streptomycin/fungizone.

extract_protocol:
Dentate gyrus were dissected from control or MDZ-exposed Nestin-EGFP mice at P10 and 8w and then EGFP-positive cells were isolated by FACS. mRNAs were isolated from the cells for the construction of sequencing libraries using Dynabeads mRNA DIRECT Micro Kit (Invitrogen) following the manufacturer's protocol. A cDNA library was constructed by 50,000 cells isolated from one mouse at P10. Three to five mice (approximately 30,000 cells) were used for cDNA library preparation from 8w mice.  For overexpression of Egr1, cultured mouse NSCs were infected with M2rtTa-expressing lentivirus constructs together with or without Flag-tagged Egr1-expressing lentivirus constructs (Control or Egr1) and then isolated mRNA for the construction of sequencing libraries using Dynabeads mRNA DIRECT Micro Kit.
Purified mRNAs were subjected to cDNA library construction using a NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocols.

treatment_protocol: For in vivo experiments, dH2O or MDZ (10 mg/kg) was intraperitoneally administered to Nestin-EGFP mice on P7, 8 and 9. MDZ-exposed mice were housed with or without running wheel (RUN).

value: ICR

value: Cortex

value: Long term-cultured

value: Wild type


title: GDT_plus_IL2

value: IL-2 expanded


title: UO_AH_013


title: UO_AH_271

description:
H295R_expression.txt
ribosome profiling

value: For


title: UO_AH_012


title: UO_AH_011


title: Egr1_rep1


title: Egr1_rep2


title: Control_rep3


title: UO_AH_010


title: Control_rep2


title: UO_AH_008


title: UO_AH_006


title: UO_AH_007


title: UO_AH_005


title: RUN_MDZ_8w_RNAseq_rep3

value: Hippocampal dentate gyrus

value: Postnatal week 8

value: Nestin-EGFP


title: UO_AH_004


title: RUN_MDZ_8w_RNAseq_rep2


title: Control_rep1


title: BY4741 ΔP 7.2 mM P A-3

first: Paul

last: van Heusden

address: Sylviusweg 72

department: Institute of Biology

institute: Leiden University

data_processing:
CLC genomic workbench (Aarhus, Denmark) software was used for processing raw data.
Genome_build: FASTA sequence files of the 16 nuclear chromosomes and mitochondrial genome (S. cerevisiae S288c)(release: 03-Apr-2012)(www.yeastgenome.org).
Supplementary_files_format_and_content: Excel file with the number of reads (normalized to reads per million) aligning to each gene for all samples.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae BY4741 ΔP

growth_protocol: Strains were grown overnight at 30 °C in phosphate free YNB medium (Formedium) supplemented with 7.2 mM potassium phosphate and 50 mM KCl, supplemented with leucine, histidine, methionie and uracil. This culture was used to inoculate two times 50 ml of supplemented YNB medium containing 7.2 mM potassium phosphate and 50 mM KCl yielding A600nm 0.1. These cultures were grown to A600nm 0.5 and cells were isolated by centrifugation. Cells from one culture were washed twice with supplemented YNB medium containing 7.2 mM potassium phosphate and 50 mM KCl and resuspended in 50 ml supplemented YNB medium containing 7.2 mM potassium phosphate and 50 mM KCl. Cells from the other culture were washed twice with supplemented YNB medium lacking phosphate but containing 50 mM KCl and resuspended in 50 ml supplemented YNB medium lacking phosphate. Both cultures were incubated at 180 rpm at 30 °C. After 60 min the cultures were poured into plastic tubes and frozen in liquid nitrogen. Prior to RNA isolation, the frozen cultures were thawed on ice and cells were collected by centrifugation and transferred to Eppendorf tubes using ice-cold water.

extract_protocol:
RNA was isolated using the Ambion RiboPure yeast RNA Purification Kit (Life Technologies).
The Illumina TruSeq stranded RNA-seq library preparation kit is used and the purified mRNA is fragmented and converted to double-stranded cDNA. DNA adapters with sample-specific barcodes are ligated and a PCR amplification is performed. The library is size-selected using magnetic beads, resulting on average in libraries with insert size in the approximate range of 100-400 bp and sequenced on the Illumina HiSeq 2500.

value: 7.2 mM phosphate


title: BY4741 7.2 mM P A-1

source_name: Saccharomyces cerevisiae BY4741


title: rrp6 7.2 mMP -     D

source_name: Saccharomyces cerevisiae BY4741 ∆rrp6


title: spl2 0 mM P - 20

source_name: Saccharomyces cerevisiae BY4741 ∆spl2

value: 0 mM phosphate


title: rrp6 7.2mM P -   C


title: Egr1_ChIPseq

growth_protocol: We prepared mouse NSCs with multipotency and self-renewal capacity derived from mouse cortex at embryonic day 11 and passaged more than 20 times. Cultured mouse NSCs  were infected with Flag-tagged Egr1-expressing lentivirus constructs together with an M2rtTa-expressing lentivirus construct.  After 16-20 hours in medium containing lentivirus, the medium was replaced with medium for mouse NSCs, which consists of Dulbecco’s modified eagle’s medium (DMEM)/F-12 containing N2 supplement with 20 ng/ml basic fibroblast growth factor (bFGF),  20 ng/ml epidermal growth factor (EGF) and 0.1 mg/ml penicillin/streptomycin/fungizone.

extract_protocol:
Cells grown on 10-cm dishes were fixed with 1% formaldehyde-containing medium for 10 min and were quenched by glycine. Collected samples were then subjected to ChIP assay using the antibody against anti-Flag (SIgma).  Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina
Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs) following the manufacturer’s protocols..


title: BY4741 7.2 mM P - B


title: RUN_MDZ_8w_RNAseq_rep1


title: UO_AH_009


title: bmh1 -7.2 mM P - 2

source_name: Saccharomyces cerevisiae BY4741 ∆bmh1