title: QUADRIS2_CG006_rep3

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

institute: University of Wisconsin

description: library: 3DeltaAlpha (MATα pdr1Δ::natMX pdr3Δ::KI.URA3 snq2Δ::KI.LEU2 (y13206)) deletion library (Piotrowski et al., Nat Chem Biol. 2017)

data_processing:
Library strategy: BAR-seq
Barcode read counts were generated by identifying the deletion library gene up-tag using custom python scripts.

source_name: 3DeltaAlpha strains pool, 0.0390625 % QUADRIS-2, replicate 3

growth_protocol: Pooled yeast gene-knockout library was inoculated into 1.5 mL of SynBase or SynBase + 1% DMSO without (control) or with individual inhibitors at their defined IC30 concentration in 24-well plates at an OD600 = 0.1. Inoculated plates were grown in an anaerobic chamber (Coy Laboratory Products Inc.), containing 1-2% H2, 4-5% CO2 and 90-95% N2 at 30ºC for 24 hr, and then transferred into the identical fresh medium at OD600=0.1 for another 24 hr without shaking.

extract_protocol:
Cells were harvested and genomic DNA was extract using the MasterPure Yeast DNA Extraction Kit (Lucigen).
DNA barcodes were amplified using specific index and U2  primers (Sigma-Aldrich) and high-fidelity DNA polymerase (Phusion, Thermo Fisher) as previously described (Piotrowski et al, 2015).

treatment_protocol: Yeast cells were submitted either to control (non-inhibitor condition) or 45 different inhibitors individually.

tag: experiment day

tag: base media

value: 1x SynBase

tag: treatment

tag: control 1

tag: control 2


title: QUADRIS1_CG006_rep3

status: Public on Nov 01 2021

type: SRA

department: Genetics

country: USA

library_source: genomic

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: 3DeltaAlpha strains pool, 0.078125 % QUADRIS-1, replicate 3

tag: strain


title: QUADRIS1_CG006_rep2

source_name: 3DeltaAlpha strains pool, 0.078125 % QUADRIS-1, replicate 2


title: QUADRIS2_CG006_rep1

source_name: 3DeltaAlpha strains pool, 0.0390625 % QUADRIS-2, replicate 1


title: QUADRIS2_CG006_rep2

source_name: 3DeltaAlpha strains pool, 0.0390625 % QUADRIS-2, replicate 2


title: b001: replete_L_T4 D

city: Vancouver

first: Anwar

last: Alqattan

state: BC

address: 4200-6270 University Boulevard

department: Earth Ocean and Atmospheric Sciences/Oceanography

country: Canada

institute: University of British Columbia

library_source: transcriptomic

data_processing:
Trimmomatic version 0.36 was used to clip NEB adapter sequences, trim for minimum trailing quality of 30 and filter reads for minimum length of 32.
RSEM version 1.3.1 was used to quantify genes as defined on ASM309565v1
Genome_build: ASM309565v1
Supplementary_files_format_and_content: File containing RSEM gene-level expression estimates. Details at http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html#output

molecule: total RNA

organism: Dokdonia sp. Dokd-P16

source_name: Bacterial culture

extract_protocol:
Total RNA from filtered cultured samples was extracted using RNeasy PowerWater kit (Qiagen, Hilden, Germany) following the manufacturer's instructions. The integrity of RNA samples was assessed using Bio-analyzer 2100 with the Agilent RNA 6000 Pico Kit (Agilent Technologies). The concentration of RNA samples was measured using the Qubit HS RNA kit on the Qubit 4. Extracted total RNA samples were sent to genome Quebec, Canada (https://cesgq.com/home) for rRNA depletion, library preparation and sequencing.
For RNA-seq analyses, rRNA was removed by Ribo-Zero rRNA Removal kit (Illumina). After depletion of rRNA, RNA-seq libraries were generated with NEBNext UltraII directional RNA library prep kit for Illumina (New England Biolabs) following the manufacturer’s instructions. The libraries were sequenced with Illumina Novaseq to generate paired-ends 100 bp reads.

tag: iron bioavailability

value: replete

tag: media

value: L

tag: exposure time


title: QUADRIS1_CG006_rep1

source_name: 3DeltaAlpha strains pool, 0.078125 % QUADRIS-1, replicate 1


title: 18P2-65-39_S244

city: Rensselaer

first: Nathan

middle: C

last: Boles

state: NY

address: One Discovery Dr

institute: Neural Stem Cell Institute

data_processing:
After de-multiplexing fastq files were mapped with STAR aligner (version 2.7.0a)
A raw counts matrix was generated in R with the GenomicAlignments package.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-seperated file of raw counts with samples by column

organism: Mus musculus

source_name: meninges

extract_protocol:
Meninges were dissected from the anterior and posterior of the cortex of  C57BL/6 mice and a single cell suspension was generated. Cells were dispensed using the ICELL8 single cell system as single cells followed by reverse transcription and barcoding according to the manufacturer's protocol
RNA libraries were prepared for sequencing the 150 cycle Nextera DNA library preperation kit from Illumina.

tag: tissue

value: Posterior meninges

tag: age

value: 3 months


title: 18P2-65-36_S245


title: 18P2-65-66_S243

value: 18 months


title: MMS_CG006_rep2

source_name: 3DeltaAlpha strains pool, 0.01% MMS, replicate 2

value: 0.01% Methylmethane sulphonate (MMS)


title: 18P2-64-70_S246


title: 18P2-64-64_S247


title: 18P2-64-63_S248


title: MMS_CG005_rep1

source_name: 3DeltaAlpha strains pool, 0.01% MMS, replicate 1


title: 18P2-64-60_S249


title: Vanillin_CG005_rep3

source_name: 3DeltaAlpha strains pool, 5mM Vanillin, replicate 3

value: 1x SynBase + 1% DMSO

value: 5mM Vanillin


title: 18P2-64-41_S250


title: 18P2-64-23_S251


title: 18P2-64-14_S252


title: 18P2-63-20_S253


title: F46

city: Edmonton

first: Zhi

last: Zhu

state: Alberta

address: 116 St and 85 Ave

department: AFNS

institute: University of Alberta

data_processing:
Adapter sequence was removed and quality of reads was filtered using fastq-mcf with parameters quality score ³ 20 and length ³ 75.
The remaining reads were aligned to reference bovine genome UMD3.1 and assembled by software package TopHat2 (v2.0.9).
Samtools (v1.1) was used to sort BAM alignment files and then convert them to SAM format.
HTSeq-count (v0.6.1) was used to quantify the number of mapped reads per each bovine gene.
Genome_build: Bovine genome UMD3.1
Supplementary_files_format_and_content: Bam files were generated using TopHat2 (v2.0.9). Sam files were generated using Samtools (v1.1). Txt files were generated using HTSeq-count (v0.6.1).

organism: Bos taurus

source_name: subcutaneous backfat tissue

growth_protocol: Backfat tissue were from Angus, Charolais, and Kinsella composite, including high-RFIfat and low-RFIfat in each breed.

extract_protocol:
Backfat tissue were applied to isolate total RNA using RNeasy Lipid Tissue Mini Kit.
The isolated RNA from each sample was used to construct a cDNA library for RNA-seq according to the protocol of TruSeq Standed Total RNA Sample Prep Kit. Briefly, the steps included removement of rRNA using Ribo-Zero Gold rRNA Removal Kit (Epicentre Technologies), RNA fragmentation, and cDNA synthesis. The resulting double-stranded cDNA was subjected to end repair and addition of a single A base at 3’-end, followed by ligation of bar-coded adapters. To guarantee the high quality of libraries, cDNA was amplified by 15 cycles of PCR to check its size using Agilent 2200 TapeStation. And cDNA libraries were quantified with a Qubit fluorometer using a Qubit dsDNA HS Assay Kit.
The cDNA libraries with effective concentration (³ 2 nM) were sequenced in 4 lanes on Illumina HiSeqTM 4000 platform to obtain 100-bp paired-end reads (average phred quality score ≥ 33) at the McGill University and Genome Quebec Innovation Centre (Montreal, Quebec, Canada).

value: subcutaneous backfat tissue

tag: cell type

value: Adipocytes

tag: breed

value: Charolais

tag: phenotype

value: Low RFIfat (-1.03 kg)


title: F43

value: High RFIfat (1.10 kg)


title: F48

value: High RFIfat (0.72 kg)


title: F36

value: High RFIfat (0.69 kg)


title: 18P2-35-70_S254


title: F47

value: Low RFIfat (-0.96 kg)


title: 18P2-66-13_S242


title: 18P2-34-67_S258


title: F28

value: Angus

value: High RFIfat (1.64 kg)


title: F33

value: Low RFIfat (-1.00 kg)


title: Vanillin_CG004_rep2

source_name: 3DeltaAlpha strains pool, 5mM Vanillin, replicate 2


title: VanillicAcid_CG004_rep2

source_name: 3DeltaAlpha strains pool, 6.67mM Vanillic Acid, replicate 2

value: 6.67mM Vanillic Acid


title: MMS_CG006_rep3

source_name: 3DeltaAlpha strains pool, 0.01% MMS, replicate 3

value: 1x SynBase


title: VanillicAcid_CG005_rep3

source_name: 3DeltaAlpha strains pool, 6.67mM Vanillic Acid, replicate 3


title: 18P2-35-42_S256

value: Posterior meninges

value: 3 months


title: Vanillin_CG003_rep1

source_name: 3DeltaAlpha strains pool, 5mM Vanillin, replicate 1

value: 1x SynBase + 1% DMSO


title: F25

value: Low RFIfat (-1.01 kg)


title: 18P2-33-66_S259


title: 18P2-33-19_S260


title: VanillicAcid_CG003_rep1

source_name: 3DeltaAlpha strains pool, 6.67mM Vanillic Acid, replicate 1


title: 18P2-35-23_S257


title: F24

value: subcutaneous backfat tissue

value: Low RFIfat (-1.09 kg)


title: 18P2-32-47_S262


title: 18P2-32-16_S263


title: F23

value: Adipocytes

value: Low RFIfat (-1.13 kg)


title: 18P2-35-47_S255


title: 18P2-31-37_S264


title: 18P2-31-17_S265


title: SyringicAcid_CG004_rep2

source_name: 3DeltaAlpha strains pool, 15mM Syringic Acid, replicate 2

value: 15mM Syringic Acid


title: SyringicAcid_CG003_rep1

source_name: 3DeltaAlpha strains pool, 15mM Syringic Acid, replicate 1


title: F20

value: High RFIfat (1.17 kg)


title: F21

value: High RFIfat (1.14 kg)


title: F32

value: High RFIfat (0.75 kg)


title: Syringaldehyde_CG006_rep3

source_name: 3DeltaAlpha strains pool, 2.25 mM Syringaldehyde, replicate 3

value: 2.25 mM Syringaldehyde


title: 18P2-30-19_S266


title: Syringaldehyde_CG005_rep2

source_name: 3DeltaAlpha strains pool, 2.25 mM Syringaldehyde, replicate 2


title: 18P2-30-16_S267


title: F18

value: Angus

value: Low RFIfat (-0.75 kg)


title: MespCre E9.5 (WT95)

city: Bronx

first: Hiroko

last: Nomaru

address: 1300 Morris Park ave

institute: Albert Einstein College of Medicine

data_processing:
Cell Ranger (v 3.1.0) were used to align reads of scRNA-seq data to the mouse reference genome (mm10).
Supplementary_files_format_and_content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: pharyngeal mesoderm

extract_protocol:
After dissected out, the tissues were incubated in trypsin-EDTA. Then GFP positive DAPI negative cells were sorted and then the cells were loaded in a 10x Chromium instrument (10x Genomics, Pleasanton, CA) using Chromium Single Cell 3’ Library & Gel Bead Kit v2
RNA libraries were prepared for sequencing using standard 10xGenomics protocols
scRNA-seq

value: Swiss Webster

value: pharyngeal apparatus and heart

tag: developmental stage

tag: genotype


title: F16

value: Kinsella composite (Hereford x Angus crossbred)

value: Low RFIfat (-1.16 kg)


title: Syringaldehyde_CG004_rep1

source_name: 3DeltaAlpha strains pool, 2.25 mM Syringaldehyde, replicate 1

value: 1x SynBase + 1% DMSO


title: SyringicAcid_CG005_rep3

source_name: 3DeltaAlpha strains pool, 15mM Syringic Acid, replicate 3


title: Mesp1Cre-Tbx1cKO E9.5 (MKO)


title: 18P2-29-63_S269

source_name: meninges

value: Posterior meninges

value: 3 months


title: F14

value: subcutaneous backfat tissue

value: Low RFIfat (-1.77 kg)


title: 18P2-32-60_S261


title: SodiumGlyoxylate_CG005_rep3

source_name: 3DeltaAlpha strains pool, 0.1875 mM Sodium Glyoxylate, replicate 3

value: 1x SynBase

value: 0.1875 mM Sodium Glyoxylate


title: AngII_1

city: New York

first: Michele

last: Silvestro

address: 550 1st Avenue

department: Surgery

institute: New York University Langone Medical Center

description: re-analysis of GSE141732

data_processing:
Cell Ranger Single Cell Software Suite, version 1.3, was used to perform de-multiplexing, barcode and UMI processing, and single-cell 3′ gene counting (https://support.10xgenomics.com/single-cell-gene). Data analysis was performed using the ‘Seurat’ version 3.1.2 package, using R Studio Desktop, version 1.2.5033, and R, version R 3.0.1+. Quality control, metrics, data normalization, scaling, batch correction and dimension reductions were all performed using the Seurat package. Cells with mitochondrial transcript proportion <5% were kept for analysis, neighboring and clustering was performed on the most significant principal component analysis.
Supplementary_files_format_and_content: 10X Genomics format (barcodes.tsv; features.tsv; matrix.mtx)

source_name: Abdominal aorta

extract_protocol:
Dissected aortas were processed for digestion for 10 min at 37 °C in an enzymatic mix composed of type II collagenase (10 mg/ml, C6885, Sigma Aldrich) and elastase (1 mg/ml, LS002292, Worthington Biochemistry). Following the digestion, viable cells were enriched using a dead cell removal magnetic kit (130-090-101, Miltenyi Biotech; for non-pooled samples only) and cellular viability, assessed using 0.4% Trypan blue (1450013, Bio-Rad) on an automated cell counter (TC20, Bio-Rad).
15,000 of viable cells per sample (15,000 viable cells per pooled sample and 15,000 viable cells per hashtag in hastagged samples) were loaded on a 10x Genomics Chromium instrument to obtain individual gel beads in emulsion (GEMs). Chromium Single Cell 3′ Library & Gel Bead Kit v2, PN-120237, the Single Cell 3′ Chip Kit v2 PN-120236 and the i7 Multiplex Kit PN-120262, (10x Genomics) were used for library preparation. Illumina HiSeq 4000 as 2 x 150 paired-end reads was used for sequencing (>90% sequencing saturation).

value: Abdominal aorta

value: Apolipoprotein E ko

tag: infused with

value: Angiotensin II


title: 18P2-29-70_S268

value: 18 months


title: 18P2-29-47_S270


title: AngII_hashtag1


title: PBS_pooled

value: PBS


title: AngII_2_pooled

description: re-analysis of GSE118237


title: SodiumGlyoxylate_CG004_rep2

source_name: 3DeltaAlpha strains pool, 0.1875 mM Sodium Glyoxylate, replicate 2

tag: experiment day


title: F11

source_name: subcutaneous backfat tissue

value: Adipocytes

value: Low RFIfat (-0.80 kg)


title: F10

value: Low RFIfat (-1.59 kg)


title: 18P2-29-43_S271


title: SodiumGlyoxylate_CG003_rep1

source_name: 3DeltaAlpha strains pool, 0.1875 mM Sodium Glyoxylate, replicate 1

tag: base media


title: 18P2-29-39_S272


title: PBS_hashtag


title: F9

value: Kinsella composite (Hereford x Angus crossbred)

value: High RFIfat (2.03 kg)


title: 18P2-29-22_S273


title: F8

value: High RFIfat (1.62 kg)


title: SodiumButyrate_CG005_rep3

source_name: 3DeltaAlpha strains pool, 0.1875 mM Sodium Butyrate, replicate 3

tag: treatment

value: 0.1875 mM Sodium Butyrate


title: SodiumButyrate_CG004_rep2

source_name: 3DeltaAlpha strains pool, 0.1875 mM Sodium Butyrate, replicate 2

tag: control 1


title: F7

value: High RFIfat (0.54 kg)


title: 18P2-29-14_S275

value: Posterior meninges


title: SodiumButyrate_CG003_rep1

source_name: 3DeltaAlpha strains pool, 0.1875 mM Sodium Butyrate, replicate 1

tag: control 2


title: 18P2-29-18_S274


title: 18P2-29-12_S276


title: SodiumAcetate_CG005_rep2

source_name: 3DeltaAlpha strains pool, 150 mM Sodium Acetate, replicate 2

tag: strain

value: 150 mM Sodium Acetate


title: SodiumAcetate_CG006_rep3

source_name: 3DeltaAlpha strains pool, 150 mM Sodium Acetate, replicate 3

value: 1x SynBase


title: 18P2-28-62_S277


title: F1

value: subcutaneous backfat tissue

value: High RFIfat (0.94 kg)


title: SodiumAcetate_CG004_rep1

source_name: 3DeltaAlpha strains pool, 150 mM Sodium Acetate, replicate 1


title: Ileal lamina propria CD4+ cells, EL-7

city: San Francisco

first: Margaret

last: Alexander

state: California

address: 513 Parnassus Ave

institute: UCSF

data_processing:
Data were analyzed for differential expression with DEseq2 (Love et al., 2014) in R with the attached RMD: RNAseq_GF_EL.Rmd
Genome_build: mm9
Supplementary_files_format_and_content: Features.csv (Matrix with raw gene counts for every gene and every sample)
Supplementary_files_format_and_content: deseq.results.csv (Matrix with deseq results)
Supplementary_files_format_and_content: RNAseq_GF_EL.Rmd (R markdown file of data processing steps)

source_name: Ileal lamina propria CD4+ cells

extract_protocol:
RNA was extracted with from isolated CD4+ cells from ileal lamina propria with Qiagen RNeasy Micro kit according to manufacturer's instructions
RNA library preparation with Universal plus mRNA kit and sequencing with HiSeq4000 by the UCSF Institute for Human Genetics core facility

value: Ileum

value: Ileal lamina propria CD4+ cells

tag: colonization status

value: E. lenta strain 2243 monocolonized


title: Ileal lamina propria CD4+ cells, GF-4

value: germ-free (GF)


title: Ileal lamina propria CD4+ cells, GF-3


title: Ileal lamina propria CD4+ cells, EL-6


title: Ileal lamina propria CD4+ cells, GF-5


title: Ileal lamina propria CD4+ cells, EL-8


title: SinapicAcid_CG005_rep3

source_name: 3DeltaAlpha strains pool, 1.5 mM Sinapic Acid, replicate 3

value: 1x SynBase + 1% DMSO

value: 1.5mM Sinapic Acid


title: Ileal lamina propria CD4+ cells, GF-2


title: SinapicAcid_CG004_rep2

source_name: 3DeltaAlpha strains pool, 1.5 mM Sinapic Acid, replicate 2


title: Ileal lamina propria CD4+ cells, EL-9


title: SinapicAcid_CG003_rep1

source_name: 3DeltaAlpha strains pool, 1.5 mM Sinapic Acid, replicate 1


title: 18P2-28-20_S280

value: 18 months


title: 18P2-28-39_S278

value: 3 months


title: 18P2-28-14_S281


title: SAP rep3, IP

city: Chengdu

first: jun

last: wu

state: Sichuan

address: 270 Tianhuan Road, Rongdu Avenue, Chengdu City, Sichuan Province

department: Laboratory of Basic Medicine

country: China

institute: The General Hospital of Western Theater Command

description:
CircRNA Expression Profiling.xlsx
Methylated_RNA_sites.xlsx

data_processing:
Library strategy: MeRIP-seq
Basecalls performed using CASAVA version 1.8
The high quality reads of circRNA were aligned to the reference genome/transcriptome with STAR software and circRNAs were detected and identified with DCC software.
Use the circBase database and Circ2Traits to annotate the identified circRNA.
The methylated sites in each sample were identified using MACS software.
Differentially methylated sites were identified using diffReps software.
Genome_build: MM10
Supplementary_files_format_and_content: The circRNA expression profile file includes junction reads, Normalized Intensity and Annotations. Methylated_RNA_sites file includes methylation sites, methylated RNA, enrichment information and annotations.

source_name: pancreatic tissues

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) from the homogenized pancreatic tissues of the control and SAP groups that contained three mice respectively. The concentration of extracted RNA was measured at OD260nm and 280nm by NanoDrop ND-2000 instrument (Thermo Fisher Scientific, Waltham, MA, USA). We assessed the integrity of RNA using denaturing agarose gel electrophoresis. The OD A260/A280 ratio between 1.8 and 2.0 is set as the RNA purity standard.
Firstly, the rRNAs in total RNA were removed using Ribo-Zero rRNA Removal Kits (Illumina, USA) according to the manufacturer’s instructions. Next, the fragmented RNA was incubated with the anti-m6A antibody for 2 hours in IPP buffer at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours. Then, bound RNA was eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Thermo Fisher) by following the manufacturer’s instruction. The immunoprecipitated RNA and input RNA were used to construct library by RNA library kit (NEBNext® Ultra™ RNA Library Prep Kit)

treatment_protocol: Before the operation, the mice were divided into control group and SAP group randomly (3 mice per group) and were fasted overnight but had free access to water. 5% isoflurane was used to anesthetize mice by induction box prior to surgery. Then, 4% sodium taurocholate salt was slowly retrogradely injected into the biliopancreatic duct with a micro infusion pump to induce SAP. All mice were sacrificed 24 hours after the model was established, and the blood samples and pancreatic tissues were collected for further analysis.

value: pancrease

tag: group

value: SAP

tag: antibody


title: NAO_CG005_rep3

source_name: 3DeltaAlpha strains pool, 5 uM NAO, replicate 3

value: 5 uM Nonyl-acridine orange (NAO)


title: 18P2-27-68_S282

source_name: meninges

tag: tissue


title: SAP rep2, IP


title: SAP rep3, input


title: 18P2-27-60_S283

tag: age


title: NAO_CG003_rep1

source_name: 3DeltaAlpha strains pool, 5 uM NAO, replicate 1


title: NAO_CG004_rep2

source_name: 3DeltaAlpha strains pool, 5 uM NAO, replicate 2


title: 18P2-27-19_S284


title: SAP rep2, input


title: SAP rep1, IP


title: 18P2-28-23_S279


title: Mycobutanil_CG003_rep1

source_name: 3DeltaAlpha strains pool, 13.25 ug/mL Mycobutanil, replicate 1

value: 13.25 ug/mL Mycobutanil


title: 18P2-27-17_S285

value: Posterior meninges


title: Methylglyoxal_CG006_rep3

source_name: 3DeltaAlpha strains pool, 7.5 mM Methylglyoxal, replicate 3

value: 7.5 mM Methylglyoxal


title: control rep2, IP

value: control


title: Mycobutanil_CG005_rep3

source_name: 3DeltaAlpha strains pool, 13.25 ug/mL Mycobutanil, replicate 3

value: 1x SynBase


title: 18P1-71-56_S286


title: 18P1-71-30_S287


title: Mycobutanil_CG004_rep2

source_name: 3DeltaAlpha strains pool, 13.25 ug/mL Mycobutanil, replicate 2


title: SAP rep1, input


title: control rep1, IP


title: Methylglyoxal_CG005_rep2

source_name: 3DeltaAlpha strains pool, 7.5 mM Methylglyoxal, replicate 2


title: 18P1-70-55_S289


title: control rep3, IP


title: control rep3, input


title: 18P1-70-30_S290


title: control rep2, input


title: MBO_CG004_rep2

source_name: 3DeltaAlpha strains pool, 1.5% MBO, replicate 2

value: 1.5% 2-Methyl-3-buten-2-ol (MBO)


title: 18P1-69-52_S291


title: control rep1, input


title: 18P1-69-33_S292


title: BHB3

city: Guangzhou

first: Zirong

last: Lan

address: 253 Industrial Avenue

institute: Zhujiang Hospital, Southern Medical University

data_processing:
The sequencing data was filtered with SOAPnuke by removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%
Removing reads whose unknown base ratio is more than 5%，afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2(v2.0.4)
Bowtie2(v2.2.5) was applied to align the clean reads to the reference coding gene set
The expression level of gene was calculated by RSEM (v1.2.12).
Genome_build: GCF_000001405.39_GRCh38.p13
Supplementary_files_format_and_content: xls file includes FPKM, TPM values and read counts for each sample

organism: Homo sapiens

source_name: vascular smooth muscle cells

extract_protocol:
Total RNA of human vascular smooth muscle cells were extracted using TRIzol regents and RNA quality was determined using Agilent 2100 Bioanalyser.
mRNA molecules were purified from total RNA using oligo (dT)-attached magnetic beads. Then, mRNA molecules were fragmented into small pieces using fragmentation reagent after reaction a certain period in proper temperature. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesis cDNA was subjected to end-repair and then was 3'-adenylated. Adapters were ligated to the ends of these 3'-adenylated cDNA fragments. PCR was used to amplify the cDNA fragments with adapters from previous step. PCR products were purified with Ampure XP Beads (AGENCOURT), and dissolved in EB solution. Library was validated on the Agilent Technologies 2100 Bioanalysers.

treatment_protocol: Human vascular smooth muscle cells were cultured in calcifying medium (CM) in the presence of β-hydroxybutyrate (BHB).

value: calcifying medium supplemented with 8mM β-hydroxybutyrate


title: MBO_CG003_rep1

source_name: 3DeltaAlpha strains pool, 1.5% MBO, replicate 1


title: 18P1-69-31_S293


title: 18P1-71-26_S288


title: Control_CP1

city: Mumbai

first: Shubha

last: Tole

state: Maharashtra

address: B304 TIFR Homi Bhabha road

department: Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

data_processing:
HISAT2
SAM tools
Feature Counts
DESEQ2
Genome_build: mm10
Supplementary_files_format_and_content: Normalised counts using feature counts

source_name: Control Choroid plexus

growth_protocol: Preganant dams were harvested for embryos 14 days post vaginal plug

extract_protocol: Trizol

value: Choroid plexus

value: Control


title: CM3

growth_protocol: Human vascular smooth muscle cells were cultured in calcifying medium (CM)

value: calcifying medium


title: LevulinicAcid_CG006_rep3

source_name: 3DeltaAlpha strains pool, 10mM Levulinic Acid, replicate 3

value: 10mM Levulinic Acid


title: GOF_CP1

source_name: Wnt Gain of function Chorid plexus

value: Lmx1acre;Beta-catenin GOF


title: GOF_hippocampus1

source_name: Wnt Gain of function Hippocampus

value: Hippocampus


title: 18P1-68-27_S295

value: 18 months


title: LevulinicAcid_CG004_rep1

source_name: 3DeltaAlpha strains pool, 10mM Levulinic Acid, replicate 1


title: 18P1-67-7_S296


title: LevulinicAcid_CG005_rep2

source_name: 3DeltaAlpha strains pool, 10mM Levulinic Acid, replicate 2


title: Methylglyoxal_CG004_rep1

source_name: 3DeltaAlpha strains pool, 7.5 mM Methylglyoxal, replicate 1


title: 18P1-67-51_S297

source_name: meninges


title: IBA_CG005_rep3

source_name: 3DeltaAlpha strains pool, 0.75% IBA, replicate 3

value: 0.75% Isobutanol (IBA)


title: CM2


title: IBA_CG004_rep2

source_name: 3DeltaAlpha strains pool, 0.75% IBA, replicate 2


title: MBO_CG005_rep3

source_name: 3DeltaAlpha strains pool, 1.5% MBO, replicate 3


title: Control_hippocampus1

source_name: Control Hippocampus


title: Low Wnt NC cells 1

city: Irvine

first: Thomas

middle: F

last: Schilling

state: CA

address: 4462 Natural Sciences II

department: Developmental and Cell Biology

institute: University of California Irvine

data_processing:
reads were mapped using STAR
Quantification of reads was performed using RSEM. TPMs were calculated for each sample and used for downstream analysis
Differential expression was performed in R using edgeR in R
Genome_build: GRCz11
Supplementary_files_format_and_content: .txt file contains TPMs for each sample

organism: Danio rerio

source_name: FACS sorted NC cells

extract_protocol:
Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II.
Libraries were constructed according to the Smart-seq2 protocol.

tag: Stage

value: 24 hpf

tag: cell type

value: NC cell

tag: wnt status

value: Low Wnt


title: DG17X066057_chicken_blood_responder327

type: genomic

first: Graham

last: Plastow

address: 1400 College Plaza, 8215 - 112 Street

department: Agricultural, Food & Nutritional Science

hyb_protocol: Extracted DNA is prepped for hybridization according to the Axiom User guide. Once prepped, the hyb ready sample is transferred to a hybridization tray that is included in the GeneTitan® MC Consumables Kit. The Array is then clamped to the hyb tray that contains the hyb ready samples and is incubated for 23.5-24 hours in a 48℃ oven.

scan_protocol: An external lamp is used to illuminate the array pegs. The assay is scanned and imaged creating .DAT file for each sample. The .DAT file will automatically undergo a gridding process that will align with the control probs and generate .CEL files that will be used in the Axiom Analysis Suite.

data_processing:
Axiom Analysis Suite version 5 were used with the default settings, except for the QC call rate threshold which we change from 95% to 97%.  Samples were run through the best practices workflow which excludes samples that don’t meet the QC criteria.
The primary data are provided as a matrix table with row names and column names. Each row represents an animal, with SampleName as the row name. Each column represents a SNP, with Affymetrix Probeset ID as the column name. Each cell represents a diploid genotype coded as A/G/C/T. Missing genotype is coded as "--"

label: Biotin or FAM depending on channel

organism: Gallus gallus

source_name: responder

label_protocol: We have probes in the hybridization cocktail that have a specific attached hapten (either Biotin or FAM depending on channel) that are bound to the gDNA/oligo/probeset conjugate during hybridization. The signal is then amplified by a combination of anti-hapten and antibody-hapten conjugate that create a sandwich/layering effect during the staining process.

extract_protocol: Genomic DNA isolated using Dneasy Blood and Tissue Kit (Qiagen) following the manufacturer's protocol.

treatment_protocol: A fraction of each blood sample from day 35 birds was supplemented with EDTA (to a final concentration of 10 mM) to prevent agglutination. Samples were frozen immediately and were kept at -80°C until further use.

value: responder

value: Blood


title: BHB2


title: 18P1-67-24_S298

value: Posterior meninges


title: 18P1-66-6_S299


title: DG17X066143_chicken_blood_responder325


title: High Wnt NC cells 3

value: High Wnt


title: 18P1-68-4_S294


title: GVL_CG005_rep3

source_name: 3DeltaAlpha strains pool, 1.5% GVL, replicate 3

value: 1x SynBase

value: 1.5% Gamma-Valerolactone (GVL)


title: 18P1-66-55_S300


title: BHB1

source_name: vascular smooth muscle cells

value: calcifying medium supplemented with 8mM β-hydroxybutyrate


title: DG17X066137_chicken_blood_responder321


title: 18P1-66-51_S301


title: DG17X066056_chicken_blood_responder318


title: 18P1-66-3_S302

value: 3 months


title: GVL_CG003_rep1

source_name: 3DeltaAlpha strains pool, 1.5% GVL, replicate 1


title: Low Wnt NC cells 2


title: CM1

value: calcifying medium


title: Furfural_CG005_rep3

source_name: 3DeltaAlpha strains pool, 8 mM Furfural, replicate 3

value: 8 mM Furfural


title: High Wnt NC cells 1


title: 18P1-66-11_S303


title: High Wnt NC cells 2


title: DG17X066113_chicken_blood_responder316


title: astrocytes ischemic preconditioning rep1

city: Shijiazhuang City

first: Min

last: Zhang

address: 361 Zhongshan East Road, Shijiazhuang, 050017, People’s Republic of China

institute: Hebei Medical univercity

data_processing:
Illumina Novaseq 6000 software used for basecalling.
Fastx-toolkit software was used to clean and filter the original sequence, the filtered sequences are called clean reads
Hisat2 was used for sequence alignment. Its alignment algorithm is called Spliced Maping algorithm, which can partition and map the read that cannot be fully matched. It is suitable for the alignment of eukaryotic genomes containing introns
Circos software package was used to compare the reads from the sequencing results of each sample to the specific location of the genome and display them in the form of ring graph
We used the concept of FPKM to characterize the expression levels of different genes. Trimmed fragments from each subsequent gene segment were counted using Stringtie software, trimmed with TMM (mean of M values) algorithm, and trimmed with FPKM values from each gene
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: astrocytes cells

growth_protocol: Primary cerebral cortices were taken from neonatal Wistar rats (< 24 h) and digested with papain and deoxyribonuclease. Then the cells were mechanically separated and suspended in DMEM/F12 containing 10% fetal bovine serum. As for the astrocytes, the cell suspension was seeded into cell culture flasks, and then renewed every 3 days. On the 6th–8th day, astrocytes were sub-cultured. After the astrocytes were sub-cultured and plated for 2–3 days, coverslips containing astrocytes were placed on top of the neuron cultures and were cultured for approximately 6–8 days. The astrocytes on coverslips were separated from neurons by paraffin dots, and both cell types were immersed in the neurobasal medium supplemented with 2% B-27 and 1% penicillin-streptomycin. Co-cultures were incubated in a normoxic incubator for 48 h

extract_protocol:
Trizol reagent was used to extract total RNA from slides
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Co-cultures were rinsed with 1*PBS and then incubated in glucose-free DMEM in a hypoxic incubator containing 94% N2, 1% O2, and 5% CO2 for 45 min. Then, cells were placed into normal medium under normoxic conditions for another 24 h, which was considered reoxygenation

value: wistar rat

value: rat cerebral cortical

value: OGD for 45 min


title: astrocytes ischemic preconditioning rep2


title: IBA_CG003_rep1

source_name: 3DeltaAlpha strains pool, 0.75% IBA, replicate 1

value: 0.75% Isobutanol (IBA)


title: Furfural_CG004_rep2

source_name: 3DeltaAlpha strains pool, 8 mM Furfural, replicate 2


title: 18P1-65-58_S304

value: 18 months


title: DG17X066069_chicken_blood_responder315


title: 18P1-65-53_S305


title: Furfural_CG003_rep1

source_name: 3DeltaAlpha strains pool, 8 mM Furfural, replicate 1


title: astrocytes control rep2

value: untreated


title: DG17X066060_chicken_blood_responder314


title: GVL_CG004_rep2

source_name: 3DeltaAlpha strains pool, 1.5% GVL, replicate 2


title: DG17X066141_chicken_blood_responder320


title: astrocytes control rep1


title: DG17X066135_chicken_blood_responder313


title: FeruloylAmide_CG006_rep3

source_name: 3DeltaAlpha strains pool, 2 mM Feruloyl Amide, replicate 3

value: 1x SynBase + 1% DMSO

value: 2 mM Feruloyl Amide


title: 18P1-65-52_S306

source_name: meninges


title: 18P1-65-30_S307


title: DG17X066117_chicken_blood_responder311

value: responder

value: Blood


title: DG17X066105_chicken_blood_responder312


title: DG17X066115_chicken_blood_responder310


title: FerulicAcid_CG006_rep3

source_name: 3DeltaAlpha strains pool, 0.9375 mM Ferulic Acid, replicate 3

value: 0.9375 mM Ferulic Acid


title: 18P1-65-24_S309

value: Posterior meninges


title: 18P1-65-27_S308


title: 18P1-65-1_S310


title: DG17X066062_chicken_blood_responder309


title: FerulicAcid_CG005_rep2

source_name: 3DeltaAlpha strains pool, 0.9375 mM Ferulic Acid, replicate 2


title: 18P1-65-0_S311


title: FerulicAcid_CG004_rep1

source_name: 3DeltaAlpha strains pool, 0.9375 mM Ferulic Acid, replicate 1


title: DG17X066145_chicken_blood_responder308


title: EtOH_CG005_rep3

source_name: 3DeltaAlpha strains pool, 4% Ethanol, replicate 3

value: 1x SynBase

value: 4% Ethanol


title: DG17X066055_chicken_blood_responder305


title: FeruloylAmide_CG005_rep2

source_name: 3DeltaAlpha strains pool, 2 mM Feruloyl Amide, replicate 2


title: EtOH_CG004_rep2

source_name: 3DeltaAlpha strains pool, 4% Ethanol, replicate 2


title: 18P1-64-4_S313


title: 18P1-64-7_S312


title: DG17X066101_chicken_blood_responder304

source_name: responder


title: FeruloylAmide_CG004_rep1

source_name: 3DeltaAlpha strains pool, 2 mM Feruloyl Amide, replicate 1


title: EtOH_CG003_rep1

source_name: 3DeltaAlpha strains pool, 4% Ethanol, replicate 1


title: No.10 Periodontal ligament

type: RNA

city: Itabashi-ku, Tokyo

first: Shigehiro

last: Abe

address: 30-1 Oyaguchikami-cho

department: Oral Surgery

country: Japan

institute: Nihon University

description: Gene expression of sphere-forming cells

hyb_protocol: cRNA was added to a hybridization buffer and hybridized to a SurePrint G3 Human GE Microarray 8X60k v3 (Agilent Technologies) for 17 h using standard protocols.

scan_protocol: The chips were washed and subsequently scanned using the Agilent Microarray Scanner (Agilent Technologies).

data_processing: Raw data were analyzed using the Feature Extraction Software (v.11.5.1.1) (Agilent Technologies).

source_name: Human Periodontal ligament

label_protocol: 100 ng of total RNA was reverse transcribed into cRNA using the Low Input Amp Labeling kit (Agilent Technologies, Santa Clara, CA).

extract_protocol: Total RNA was extracted from cells by using RNeasy® Mini Kit (Qiagen, Hilden, Germany). RNA quality was assessed by using a 2100 Bioanalyzer (Agilent, Santa Clara, CA) and a NanoDrop™ spectrophotometer (Thermo, Waltham, Massachusetts).

treatment_protocol: Total RNA of sphere-forming APDCs, PDLCs and OMSCs obtained from three patients was used for the microarray analysis.

tag: individual

value: patient no.10

tag: gender

value: Female

value: Periodontal ligament

value: PDLCs


title: No.10 Apical papilla

description: Gene expression of sphere-forming cells

source_name: Human Apical papilla

value: Apical papilla

value: APDCs


title: DG17X066151_chicken_blood_responder302


title: 18P1-64-0_S314


title: 18P1-63-6_S315

value: 3 months


title: No.2 Oral mucosa

description: Gene expression of sphere-forming cells

source_name: Human Oral mucosa

value: patient no.2

value: Oral mucosa

value: OMSCs


title: No.10 Oral mucosa

description: Gene expression of sphere-forming cells


title: No.2 Periodontal ligament

description: Gene expression of sphere-forming cells


title: No.2 Apical papilla

description: Gene expression of sphere-forming cells


title: EMIMCl_CG005_rep3

source_name: 3DeltaAlpha strains pool, 50mM EMIM-Cl, replicate 3

value: 50mM 1-ethyl-3-methylimidazolium chloride (EMIM-Cl)


title: DG17X066084_chicken_blood_responder301

value: responder


title: EMIMCl_CG004_rep2

source_name: 3DeltaAlpha strains pool, 50mM EMIM-Cl, replicate 2


title: 18P1-63-55_S316


title: DG17X066109_chicken_blood_responder300

value: Blood


title: S3

city: Shanghai

first: Ruiting

last: Li

state: Shanghai

address: 600 Yishan Rd

institute: Shanghai Sixth People's Hospital

data_processing:
Clean data was generated by trimming the adaptor and filtering rRNAs using Seqtk (https://github.com/lh3/seqtk)
Clean reads were mapped to human genome (GRCh38) with Hisat2(version:2.0.4)
The uniquely mapped fragments of genes were counted by Stringtie(version:1.3.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include counts for each gene in each sample

source_name: HAEC

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using VAHTS mRNA-seq V2 Library Prep Kit for Illumina

tag: sample type

value: primary

value: aorta


title: EMIMCl_CG003_rep1

source_name: 3DeltaAlpha strains pool, 50mM EMIM-Cl, replicate 1

tag: experiment day

value: 1x SynBase


title: No.9 Oral mucosa

description: Gene expression of sphere-forming cells

value: patient no.9


title: No.9 Periodontal ligament

description: Gene expression of sphere-forming cells


title: DG17X066088_chicken_blood_responder299


title: No.9 Apical papilla

description: Gene expression of sphere-forming cells


title: 18P1-63-48_S317

source_name: meninges

value: Posterior meninges


title: DMSO_CG006_rep3

source_name: 3DeltaAlpha strains pool, 2.5% DMSO, replicate 3

tag: base media

value: 2.5% Dimethyl Sulfoxide (DMSO)


title: S1


title: S2


title: 18P1-35-9_S319


title: L3


title: DMSO_CG005_rep2

source_name: 3DeltaAlpha strains pool, 2.5% DMSO, replicate 2

tag: treatment


title: DMSO_CG004_rep1

source_name: 3DeltaAlpha strains pool, 2.5% DMSO, replicate 1

tag: control 1


title: 18P1-35-56_S320


title: L2


title: L1


title: 18P1-35-52_S321


title: CV_CG005_rep3

source_name: 3DeltaAlpha strains pool, 15 uM CV, replicate 3

value: 15 uM Crystal Violet (CV)

tag: control 2


title: CV_CG004_rep2

source_name: 3DeltaAlpha strains pool, 15 uM CV, replicate 2

tag: strain


title: DG17X066091_chicken_blood_responder293


title: 18P1-35-4_S322


title: C2


title: 18P1-63-33_S318


title: DG17X066100_chicken_blood_responder298


title: 18P1-35-3_S323


title: 18P1-34-10_S324


title: C1


title: CoumaroylAmide_CG006_rep3

source_name: 3DeltaAlpha strains pool, 3mM Coumaroyl Amide, replicate 3

value: 1x SynBase + 1% DMSO

value: 3mM Coumaroyl Amide


title: DG17X066123_chicken_blood_responder296

source_name: responder


title: CoumaroylAmide_CG005_rep2

source_name: 3DeltaAlpha strains pool, 3mM Coumaroyl Amide, replicate 2


title: TIVE_rep3 [miRNA-seq]

city: Boston

first: Soo Mi

last: Lee

state: MA

address: 3 BLACKFAN CIRCLE, CLS 417

department: Pathology

institute: BIDMC/Harvard Medical School

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase v22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80). Differential expression analysis was performed using DESeq2 v1.26.0.
Supplementary_files_format_and_content: excel,expression profiles

source_name: TIVE cells

growth_protocol: LTC and TIVE cell lines were cultured in Medium 199 (Sigma-Aldrich) supplemented with 15% FBS, 200 mM L-glutamine (Gibco), 1% penicillin-streptomycin (Gibco) and 30 mg endothelial cell growth supplement from bovine neural tissue (ECGS) (Sigma-Aldrich).

extract_protocol:
Total RNA was isolated using mirVana miRNA isolation Kit following the manufacturer's protocol.
Approximately 1 μg of total RNA were used to prepare small RNA library according to Illumina’s TruSeq small RNA sample preparation protocol (Illumina, San Diego, CA, USA). Then the libraries were sequenced by Illumina’s HiSeq 2500 following the vector’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

tag: tissue source

value: Human umbilical cord

tag: cell type source

value: Human umbilical vein endothelial cells

value: uninfected parental cells (TIVE) cells.


title: DG17X066147_chicken_blood_responder290

tag: group


title: DG17X066086_chicken_blood_responder291

tag: tissue


title: TIVE_rep2 [miRNA-seq]


title: 18P1-33-4_S325

tag: age

value: 3 months


title: DG17X066076_chicken_blood_responder289


title: DG17X066085_chicken_blood_responder295


title: DG17X066152_chicken_blood_responder286


title: CoumaroylAmide_CG004_rep1

source_name: 3DeltaAlpha strains pool, 3mM Coumaroyl Amide, replicate 1


title: 18P1-33-26_S326


title: DG17X066094_chicken_blood_responder294


title: 18P1-33-1_S327


title: CoumaricAcid_CG006_rep3

source_name: 3DeltaAlpha strains pool, 3.33mM Coumaric Acid, replicate 3

value: 3.33mM Coumaric Acid


title: DG17X066068_chicken_blood_responder285


title: Low Wnt NC cells 3

source_name: FACS sorted NC cells

tag: genotype

tag: Stage

value: 24 hpf

value: NC cell

value: Low Wnt


title: TIVE_rep1 [miRNA-seq]

tag: cell type


title: C3

value: primary


title: CV_CG003_rep1

source_name: 3DeltaAlpha strains pool, 15 uM CV, replicate 1


title: LTC_rep3 [miRNA-seq]

source_name: LTC cells

value: Kaposi’s sarcoma-associated herpesvirus (KSHV)-infected human endothelial cells (LTC)


title: CoumaricAcid_CG005_rep2

source_name: 3DeltaAlpha strains pool, 3.33mM Coumaric Acid, replicate 2


title: DG17X066099_chicken_blood_responder284

value: responder

value: Blood


title: 18P1-32-58_S328

value: Posterior meninges


title: LTC_rep2 [miRNA-seq]


title: 18P1-32-5_S329


title: LTC_rep1 [miRNA-seq]


title: CoumaricAcid_CG004_rep1

source_name: 3DeltaAlpha strains pool, 3.33mM Coumaric Acid, replicate 1


title: CinnamicAcid_CG006_rep3

source_name: 3DeltaAlpha strains pool, 0.375mM Cinnamic Acid, replicate 3

value: 0.375mM Cinnamic Acid


title: DG17X066139_chicken_blood_responder281


title: DG17X066082_chicken_blood_responder282


title: 18P1-32-48_S330

source_name: meninges


title: TIVE

description: processed data file: comparison_1.xlsx

data_processing:
Single-end reads were mapped to the human genome (Ensembl GRCh37) using Bowtie2 v2.2.9. The abundance of gene expression was estimated using RSEM v1.3.0 and the differential expression analysis was performed using edgeR v3.12.1.
Paired-end reads were mapped to the human genome (Ensembl GRCh38) using HISAT2 v2. The abundance of gene expression was estimated using StringTie v1.3.4 and edgeR v3.30.3, and the differential expression analysis was performed using edgeR v3.30.3.
Genome_build: GRCh37;GRCh38
Supplementary_files_format_and_content: excel,expression profiles

extract_protocol:
Total RNA was extracted using mirVana miRNA isolation Kit following the manufacturer's protocol. Quality control was performed with Agilent Bioanalyzer.
RNA libraries were prepared according to the Illumina's TruSeq stranded mRNA sample preparation protocol or Illumina's TruSeq small RNA sample preparation protocol (Illumina, San Diego, CA, USA).

tag: library construction method

value: Illumina TruSeq small RNA sample preparation

tag: reference assembly


title: CinnamicAcid_CG005_rep2

data_processing:
Library strategy: BAR-seq
Barcode read counts were generated by identifying the deletion library gene up-tag using custom python scripts.

source_name: 3DeltaAlpha strains pool, 0.375mM Cinnamic Acid, replicate 2

extract_protocol:
Cells were harvested and genomic DNA was extract using the MasterPure Yeast DNA Extraction Kit (Lucigen).
DNA barcodes were amplified using specific index and U2  primers (Sigma-Aldrich) and high-fidelity DNA polymerase (Phusion, Thermo Fisher) as previously described (Piotrowski et al, 2015).

value: 1x SynBase + 1% DMSO


title: 18P1-31-29_S331


title: LTC

description: processed data file: comparison_1.xlsx

value: Kaposi's sarcoma-associated herpesvirus (KSHV)-infected human endothelial cells (LTC)


title: CinnamicAcid_CG004_rep1

source_name: 3DeltaAlpha strains pool, 0.375mM Cinnamic Acid, replicate 1


title: 18P1-30-6_S332


title: DG17X066064_chicken_blood_responder280


title: CaffeicAcid_CG005_rep3

source_name: 3DeltaAlpha strains pool, 7.5mM Caffeic Acid, replicate 3

value: 7.5mM Caffeic Acid


title: 18P1-30-5_S333


title: CaffeicAcid_CG004_rep2

source_name: 3DeltaAlpha strains pool, 7.5mM Caffeic Acid, replicate 2


title: 18P1-30-31_S334


title: DG17X066096_chicken_blood_responder278


title: DG17X066075_chicken_blood_responder277


title: 293T138_HSV2_PAR-CLIP

city: Hangzhou

first: Dongli

last: Pan

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

description:
small RNA
Control cells, infected with HSV-2 for 4 hours

data_processing:
Reads were trimmed to discard adapters and low-quality reads and reads less than 20 base long using fastx_clipper (http://hannonlab.cshl.edu/fastx_toolkit/).
Using the “grep” command to retain only reads that contain this sequence CACCAGC (binding site of the miR-138 seed region). These reads were aligned with the human genome (assembly version hg19) or HSV-2 strain HG52 (GenBank accession number NC_001798.2) using Tophat2 (https://ccb.jhu.edu/software/tophat/index.shtml)
For human reads, counts of reads aligned to 5’ UTR, CDS and 3’ UTR of each transcript were determined by Htseq-count (https://htseq.readthedocs.io/).  For viral reads, counts of reads aligned to each viral trancript were determined by Htseq-count
Genome_build: Human genome build hg19, HSV-2 strain HG52 (GenBank accession number NC_001798.2)
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts of sequencing reads for each viral gene

source_name: 293T138 cells derived from 293T cells

extract_protocol:
RNA crosslinked and immunoprecipitate with Agonaute was extracted according to standard PAR-CLIP protocol (Danan, C., Manickavel, S., and Hafner, M. (2016). PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites. Methods in molecular biology 1358, 153-173.)
RNA libraries were prepared for sequencing using TruSeq Small RNA Library Preparation Kit (Illumina)
PAR-CLIP followed by RNAseq

treatment_protocol: Cells were infected with wild-type HSV-2 (strain 186) for 4  hours (MOI = 1) before PAR-CLIP

value: Kidney

value: transduced with lentivirus expressing miR-138

tag: cell line


title: M70+IL-12_TGFB

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform or on the BGISeq500 platform for single end ChIP-seq data
Processing by the Babraham Bioinformatics Facility used the ClusterFlow fastq_hisat2 pipeline, comprising adapter and quality trimming using Trim Galore v0.6.0 using default single end parameters followed by mapping to the mouse GRCm38 genome guided by gene models from Ensembl release 70 using hisat2 v2.1.0.  Hisat2 mapping parameters were --dta --sp 1000, 1000. Data was imported into SEQMONK (version 1.44.0) as RNA-seq data with a minimum mapping quality of 20.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimed text files showing log2RPM values per gene for each sample

source_name: CD3/CD28 activated CD4+ T cell

extract_protocol:
RNA was collected using Qiagen Micro RNEasy kit according to manufacturer's instructions.
RNA was processed and RNA-Seq libraries generated using Illumina Tru-Seq mRNA Stranded Kit A according to manufacturer's instructions.

treatment_protocol: CD45RA+CD27+ CD4+ T cells were sorted from human peripheral blood and cultured in complete media for 3 days in the presence of anti-CD3/CD28 activator beads in the presence/absence of IL-12+TGFB.

value: CD3/CD28 activated CD4+ T cell

tag: cytokines

value: IL-12 + TGFB

value: 70 years


title: CaffeicAcid_CG003_rep1

city: Madison

first: Audrey

last: Gasch

address: 425G Henry mall

institute: University of Wisconsin

source_name: 3DeltaAlpha strains pool, 7.5mM Caffeic Acid, replicate 1

tag: experiment day

tag: base media


title: 293Tcontrol_HSV2_PAR-CLIP

description:
small RNA
293T cells overexpressing miR-138, infected with HSV-2 for 4 hours

source_name: 293Tcontrol cells derived from 293Tcontrol cells infected

tag: treatment

value: control


title: DG17X066009_chicken_blood_responder240

source_name: responder


title: DG17X066023_chicken_blood_responder233


title: 18P1-29-27_S336

first: Nathan

last: Boles

address: One Discovery Dr

data_processing:
After de-multiplexing fastq files were mapped with STAR aligner (version 2.7.0a)
A raw counts matrix was generated in R with the GenomicAlignments package.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-seperated file of raw counts with samples by column

extract_protocol:
Meninges were dissected from the anterior and posterior of the cortex of  C57BL/6 mice and a single cell suspension was generated. Cells were dispensed using the ICELL8 single cell system as single cells followed by reverse transcription and barcoding according to the manufacturer's protocol
RNA libraries were prepared for sequencing the 150 cycle Nextera DNA library preperation kit from Illumina.

value: 18 months


title: 18P1-29-48_S335


title: DG17X066020_chicken_blood_responder232


title: BMIMCl_CG005_rep3

source_name: 3DeltaAlpha strains pool, 8mM BMIM-Cl, replicate 3

value: 1x SynBase

value: 8mM 1-butyl-3-methylimidazolium chloride (BMIM-Cl)

tag: control 1

tag: control 2


title: 18P1-29-24_S337


title: BMIMCl_CG003_rep1

source_name: 3DeltaAlpha strains pool, 8mM BMIM-Cl, replicate 1

tag: strain


title: 18P1-29-11_S338


title: BMIMCl_CG004_rep2

source_name: 3DeltaAlpha strains pool, 8mM BMIM-Cl, replicate 2


title: M67a-

value: 67 years


title: DG17X066008_chicken_blood_responder228

value: responder

value: Blood


title: DG17X066013_chicken_blood_responder231


title: M67a+IL-12_TGFB


title: DG17X066025_chicken_blood_responder226


title: M66-

value: 66 years


title: M66+IL-12_TGFB


title: BenzoicAcid_CG006_rep3

source_name: 3DeltaAlpha strains pool, 0.125mM Benzoic Acid, replicate 3

value: 0.125mM Benzoic Acid


title: 18P1-28-53_S340

value: Posterior meninges

value: 3 months


title: BenzoicAcid_CG005_rep2

source_name: 3DeltaAlpha strains pool, 0.125mM Benzoic Acid, replicate 2

value: 1x SynBase + 1% DMSO


title: DG17X066168_chicken_blood_responder223


title: M63d+IL-12_TGFB

value: 63 years


title: DG17X066017_chicken_blood_responder221


title: 18P1-28-52_S341


title: M70-


title: Benomyl_CG005_rep3

source_name: 3DeltaAlpha strains pool, 10 ug/mL Benomyl, replicate 3

value: 10 ug/mL Benomyl


title: BenzoicAcid_CG004_rep1

source_name: 3DeltaAlpha strains pool, 0.125mM Benzoic Acid, replicate 1


title: M60b+IL-12_TGFB

value: CD3/CD28 activated CD4+ T cell

value: 60 years


title: M63d-


title: DG17X066163_chicken_blood_responder218


title: 18P1-27-4_S343

source_name: meninges


title: Benomyl_CG004_rep2

source_name: 3DeltaAlpha strains pool, 10 ug/mL Benomyl, replicate 2


title: M60b-


title: 18P1-29-10_S339


title: 18P1-27-29_S344


title: AzelaicAcid_CG005_rep3

source_name: 3DeltaAlpha strains pool, 10mM Azelaic Acid, replicate 3

value: 10mM Azelaic Acid


title: M59+IL-12_TGFB

value: IL-12 + TGFB

value: 59 years


title: Benomyl_CG003_rep1

source_name: 3DeltaAlpha strains pool, 10 ug/mL Benomyl, replicate 1

value: 1x SynBase


title: DG17X066158_chicken_blood_responder214


title: 18P1-27-1_S345

value: 18 months


title: M59-


title: 18A2-62-45_S346

value: Anterior meninges


title: DG17X066164_chicken_blood_responder213

value: responder


title: AzelaicAcid_CG004_rep2

source_name: 3DeltaAlpha strains pool, 10mM Azelaic Acid, replicate 2


title: 18A2-62-37_S347


title: AzelaicAcid_CG003_rep1

source_name: 3DeltaAlpha strains pool, 10mM Azelaic Acid, replicate 1


title: 18P1-27-6_S342


title: DG17X066032_chicken_blood_responder212

value: Blood


title: Acetovanillone_CG006_rep3

source_name: 3DeltaAlpha strains pool, 3mM Acetovanillone, replicate 3

value: 3mM Acetovanillone


title: M38b-

source_name: CD3/CD28 activated CD4+ T cell

value: 38 years


title: 18A2-62-36_S348


title: DG17X066030_chicken_blood_responder211


title: DG17X066027_chicken_blood_responder209


title: M38a+IL-12_TGFB


title: Acetovanillone_CG005_rep2

source_name: 3DeltaAlpha strains pool, 3mM Acetovanillone, replicate 2


title: 18A2-62-22_S349


title: M38a-


title: DG17X066022_chicken_blood_responder216

source_name: responder


title: Acetovanillone_CG004_rep1

source_name: 3DeltaAlpha strains pool, 3mM Acetovanillone, replicate 1


title: DG17X066172_chicken_blood_responder208


title: DG17X066021_chicken_blood_responder215


title: 18A2-61-64_S350


title: DG17X066173_chicken_blood_responder207


title: 18A2-61-39_S351


title: Acetosyringone_CG005_rep3

source_name: 3DeltaAlpha strains pool, 5mM Acetosyringone, replicate 3

value: 5mM Acetosyringone


title: M31f-

value: 31 years


title: M31f+IL-12_TGFB


title: Acetosyringone_CG004_rep2

source_name: 3DeltaAlpha strains pool, 5mM Acetosyringone, replicate 2

value: 1x SynBase + 1% DMSO


title: 18A2-59-66_S352


title: M38b+IL-12_TGFB


title: DG17X066029_chicken_blood_responder206


title: M28+IL-12_TGFB

value: 28 years


title: Acetosyringone_CG003_rep1

source_name: 3DeltaAlpha strains pool, 5mM Acetosyringone, replicate 1


title: M28-


title: 18A2-59-64_S353


title: DG17X066007_chicken_blood_responder205


title: Acetamide_CG006_rep3

source_name: 3DeltaAlpha strains pool, 250mM Acetamide, replicate 3

value: 250mM Acetamide


title: 18A2-59-40_S354


title: 18A2-59-22_S355


title: M25+IL-12_TGFB

value: CD3/CD28 activated CD4+ T cell

value: 25 years


title: Acetamide_CG005_rep2

source_name: 3DeltaAlpha strains pool, 250mM Acetamide, replicate 2


title: DG17X066161_chicken_blood_responder204


title: DG17X066026_chicken_blood_responder200


title: M25-


title: DG17X066181_chicken_blood_responder201


title: 18A2-58-67_S356


title: 45Methylimidazole_CG006_rep3

source_name: 3DeltaAlpha strains pool, 3.33mM 4(5)-Methylimidazole, replicate 3

value: 3.33mM 4(5)-Methylimidazole


title: DG17X066035_chicken_blood_responder198


title: 18A2-58-65_S357

source_name: meninges


title: Acetamide_CG004_rep1

source_name: 3DeltaAlpha strains pool, 250mM Acetamide, replicate 1


title: M25a-


title: DG17X066167_chicken_blood_responder194


title: 18A2-57-61_S358


title: 45Methylimidazole_CG004_rep1

source_name: 3DeltaAlpha strains pool, 3.33mM 4(5)-Methylimidazole, replicate 1


title: M25a+IL-12_TGFB

value: IL-12 + TGFB


title: 45Methylimidazole_CG005_rep2

source_name: 3DeltaAlpha strains pool, 3.33mM 4(5)-Methylimidazole, replicate 2


title: 18A2-57-60_S359


title: MDA-MB-435S siScr control 3

city: Bethesda

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Trimmomatic (version 0.30)
STAR (version 2.4.2a)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files (read counts per gene).

source_name: melanoma

growth_protocol: MDA-MB-435S cells were grown in DMEM supplemented with 10% FBS  and 1% Penicilin-streptomycin

extract_protocol:
Total RNA was isolated using GeneJet kit (ThermoScientific K0731).
Twenty-four mRNA samples were pooled and sequenced on two lanes of HiSeq2500 with Illumina TruSeq V4 chemistry (library protocol: mRNA RS-122-2201) and paired-end sequencing.

treatment_protocol: MDA-MB-435 cells were transfected with two independent control oligos (siNS and siScr) or CEBPD (siCEBPD1 and siCEBPD2) targeting oligos. 48h post transfection, cells were treated with Vehicle (DMSO) or Tg (100nM) for 6h. The experiment was set up as three biological replicates. RNA was isolated and processed for RNAseq analysis

value: melanoma cell line

tag: transfection

value: siScr

value: Vehicle (DMSO)


title: MDA-MB-435S siScr Tg 3

value: Tg (100nM) for 6h


title: 26Dimethylpyrazine_CG006_rep3

source_name: 3DeltaAlpha strains pool, 37.5mM 2,6-Dimethylpyrazine, replicate 3

value: 1x SynBase

value: 37.5mM 2,6-Dimethylpyrazine


title: MDA-MB-435S siScr Tg 2


title: 18A2-56-69_S361

city: Rensselaer

institute: Neural Stem Cell Institute

value: Anterior meninges

value: 18 months


title: 26Dimethylpyrazine_CG004_rep1

source_name: 3DeltaAlpha strains pool, 37.5mM 2,6-Dimethylpyrazine, replicate 1


title: MDA-MB-435S siScr control 2


title: 18A2-56-15_S363


title: DG17X066144_chicken_blood_responder171

city: Edmonton

institute: University of Alberta

tag: group

value: responder

value: Blood


title: MDA-MB-435S siScr Tg 1

tag: tissue


title: DG17X066179_chicken_blood_responder189


title: 18A2-57-23_S360

tag: age

value: 3 months


title: DG17X066132_chicken_blood_responder173


title: 26Dimethylpyrazine_CG005_rep2

source_name: 3DeltaAlpha strains pool, 37.5mM 2,6-Dimethylpyrazine, replicate 2


title: DG17X066038_chicken_blood_responder172


title: 24Dimethylimidazole_CG004_rep2

source_name: 3DeltaAlpha strains pool, 6mM 2,4-Dimethylimidazole, replicate 2

value: 6mM 2,4-Dimethylimidazole


title: 18A2-55-61_S365


title: 18A2-56-61_S362


title: 18A2-54-70_S366


title: DG17X066122_chicken_blood_responder170

source_name: responder


title: 22Dipyridyl_CG004_rep2

source_name: 3DeltaAlpha strains pool, 18.125 ug/mL 2,2'-Dipyridyl, replicate 2

value: 18.125 ug/mL 2,2'-Dipyridyl


title: MDA-MB-435S siScr control 1


title: DG17X066061_chicken_blood_responder169


title: MDA-MB-435S siNS Tg 2

value: siNS


title: 18A2-56-12_S364


title: DG17X066127_chicken_blood_responder166


title: MDA-MB-435S siNS Tg 3


title: 24Dimethylimidazole_CG003_rep1

source_name: 3DeltaAlpha strains pool, 6mM 2,4-Dimethylimidazole, replicate 1


title: MDA-MB-435S siNS control 3


title: 18A2-54-18_S368


title: 5HMF_CG006_rep3

source_name: 3DeltaAlpha strains pool, 3.33mM 5-HMF, replicate 3

value: 3.33mM 5-Hydroxymethylfurfural (5-HMF)


title: MDA-MB-435S siNS Tg 1


title: DG17X066116_chicken_blood_responder167


title: 18A2-54-15_S369


title: DG17X066040_chicken_blood_responder165


title: DG17X066148_chicken_blood_responder163


title: 18A2-54-42_S367


title: 24Dimethylimidazole_CG005_rep3

source_name: 3DeltaAlpha strains pool, 6mM 2,4-Dimethylimidazole, replicate 3


title: 22Dipyridyl_CG003_rep1

source_name: 3DeltaAlpha strains pool, 18.125 ug/mL 2,2'-Dipyridyl, replicate 1


title: 22Dipyridyl_CG005_rep3

source_name: 3DeltaAlpha strains pool, 18.125 ug/mL 2,2'-Dipyridyl, replicate 3


title: DG17X066131_chicken_blood_responder164


title: MDA-MB-435S siNS control 1


title: 5HMF_CG005_rep2

source_name: 3DeltaAlpha strains pool, 3.33mM 5-HMF, replicate 2


title: 18A2-26-41_S370

source_name: meninges


title: MDA-MB-435S siCEBPD2 Tg 3


title: 18A2-26-22_S371


title: 5HMF_CG004_rep1

source_name: 3DeltaAlpha strains pool, 3.33mM 5-HMF, replicate 1


title: DG17X066067_chicken_blood_responder161


title: MDA-MB-435S siNS control 2


title: MDA-MB-435S siCEBPD2 control 3


title: DG17X066083_chicken_blood_responder168


title: DG17X066106_chicken_blood_responder160


title: 18A2-25-69_S372


title: 18A2-25-64_S373


title: MDA-MB-435S siCEBPD2 Tg 2


title: DG17X066128_chicken_blood_responder159


title: 4OHBenzoicAcid_CG005_rep2

source_name: 3DeltaAlpha strains pool, 6mM 4-OH-Benzoic Acid, replicate 2

value: 1x SynBase + 1% DMSO

value: 6mM 4-OH-Benzoic Acid


title: MDA-MB-435S siCEBPD2 control 2

value: melanoma cell line


title: 4OHBenzoicAcid_CG004_rep1

source_name: 3DeltaAlpha strains pool, 6mM 4-OH-Benzoic Acid, replicate 1


title: MDA-MB-435S siCEBPD2 Tg 1

source_name: melanoma


title: 18A2-25-39_S374


title: 18A2-24-65_S375


title: DG17X066039_chicken_blood_responder153


title: 18A2-24-22_S376


title: 4OHBenzaldehyde_CG004_rep1

source_name: 3DeltaAlpha strains pool, 4mM 4-OH-Benzaldehyde, replicate 1

value: 4mM 4-OH-Benzaldehyde


title: DG17X066133_chicken_blood_responder150


title: 18A2-23-67_S377


title: 4OHBenzaldehyde_CG005_rep2

source_name: 3DeltaAlpha strains pool, 4mM 4-OH-Benzaldehyde, replicate 2


title: DG17X066118_chicken_blood_responder148


title: 4OHBenzoicAcid_CG006_rep3

source_name: 3DeltaAlpha strains pool, 6mM 4-OH-Benzoic Acid, replicate 3


title: MDA-MB-435S siCEBPD1 Tg 2


title: 18A2-23-20_S379


title: MDA-MB-435S siCEBPD1 control 3

value: Vehicle (DMSO)


title: DG17X066102_chicken_blood_responder147


title: 4OHAcetophenone_CG006_rep3

source_name: 3DeltaAlpha strains pool, 5mM 4-OH-Acetophenone, replicate 3

value: 5mM 4-OH-Acetophenone


title: 18A2-23-13_S380


title: DG17X066077_chicken_blood_responder158

source_name: responder


title: 4OHBenzaldehyde_CG006_rep3

source_name: 3DeltaAlpha strains pool, 4mM 4-OH-Benzaldehyde, replicate 3


title: DG17X066089_chicken_blood_responder143


title: MDA-MB-435S siCEBPD1 Tg 1

value: Tg (100nM) for 6h


title: DG17X066130_chicken_blood_responder157


title: 18A2-22-60_S381


title: DG17X066114_chicken_blood_responder138


title: MDA-MB-435S siCEBPD2 control 1


title: 2Methylimidazole_CG005_rep3

source_name: 3DeltaAlpha strains pool, 3.75mM 2-Methylimidazole, replicate 3

value: 3.75 mM 2-Methylimidazole


title: MDA-MB-435S siCEBPD1 Tg 3


title: 2Methylimidazole_CG004_rep2

source_name: 3DeltaAlpha strains pool, 3.75mM 2-Methylimidazole, replicate 2


title: MDA-MB-435S siCEBPD1 control 1


title: 18A2-22-40_S382

value: Anterior meninges


title: DG17X066093_chicken_blood_responder136


title: 2Methylimidazole_CG003_rep1

source_name: 3DeltaAlpha strains pool, 3.75mM 2-Methylimidazole, replicate 1


title: 4OHAcetophenone_CG005_rep2

source_name: 3DeltaAlpha strains pool, 5mM 4-OH-Acetophenone, replicate 2


title: 18A2-23-39_S378


title: Control4_CG006

source_name: 3DeltaAlpha strains pool, untreated


title: 18A2-22-39_S383


title: 18A2-22-19_S384

value: 18 months


title: ChIP_Input

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

data_processing:
Data were filtered and trimmed using BBmap (BBDuk)
The sequenced reads aligned to the human reference genome (hg38 assembly) using Bowtie2
Peaks were called using HOMER (findPeaks) to identify SMARCB1 binding sites (peaks) or H3K27Ac enriched sites compared to corresponding input samples in shCon and shSMARCB1 cells with a false discovery rate (FDR)-adjusted p value cutoff of 0.001.
The identified peaks were annotated according to the known gene database (RefSeq) using HOMER (annotatePeaks.pl)
Genome_build: hg38
Supplementary_files_format_and_content: bed files were generated using Homer

source_name: SK-Hep1 cell line

growth_protocol: SK-Hep1 cell line was maintained in DMEM (Welgene, korea) supplemented with 10% fetal bovine serum (FBS; welgene) and 100 units/mL of penicillin– streptomycin (Invitrogen, Carlsbad, CA). All cells were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
50 μg DNA, sheared by a sonication (the DNA fragment size was 200 to 500 bp), was pre-cleared with protein A magnetic beads (Upstate Biotechnology; cat. #16-661) and then 50 μg DNA was precipitated by SMARCB1 (abcam #12167) and H3K27Ac (abcam #ab4729).
The construction of library was performed using NEBNext® UltraTM DNA Library Prep Kit for Illumina (New England Biolabs, UK) according to the manufacturer’s instructions. Briefly, the chipped DNA was ligated with adaptors. After purification, PCR reaction was done with adaptor-ligated DNA and index primer for multiplexing sequencing. Library was purified by using magnetic beads to remove all reaction components. The size of library was assessed by Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands). High-throughput sequencing was performed as paired-end 100 sequencing using HiSeq 2500 (Illumina, Inc., USA).

treatment_protocol: Infected derivative cells stably expressing shRNA were selected in the presence of 1.25 μg/mL puromycin.

value: Human hepatic adenocarcinoma cell line

tag: chip antibody


title: DG17X066059_chicken_blood_responder135

value: responder

value: Blood


title: DG17X066136_chicken_blood_responder131


title: ChIP_H3K27ac_shSMARCB1

value: H3K27Ac (abcam #ab4729)


title: Control3_CG006


title: ChIP_H3K27ac_shCon


title: MDA-MB-435S siCEBPD1 control 2


title: 4OHAcetophenone_CG004_rep1

source_name: 3DeltaAlpha strains pool, 5mM 4-OH-Acetophenone, replicate 1


title: 18A2-21-62_S385

source_name: meninges


title: DG17X066112_chicken_blood_responder129


title: ChIP_SMARCB1

value: SMARCB1 (abcam #12167)


title: Control2_CG006

value: 1x SynBase


title: 18A2-21-61_S386


title: DG17X066155_chicken_blood_non-responder323

source_name: non-responder

value: non-responder


title: DG17X066111_chicken_blood_non-responder319


title: Control4_CG005

value: 1x SynBase + 1% DMSO


title: IRF3

first: Shi

last: Jiao

address: 320 Yue Yang Road

institute: Shanghai Institutes of Biological Sciences

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie version 0.12.8.
peaks were called using MACS version 1.4.2 and Different peaks were caculated by DiffBind in R with the Fold change >=2 and p value <0.05.
Genome_build: mm10
Supplementary_files_format_and_content: peaks files were generated by MACS version 1.4.2 20120305. Fold_enrichment reprensent fold change. Fold change >=2 and p value <0.05.

growth_protocol: HGC-27 cells (30% confluent) are cultured in dishes with DMEM medium contained 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and transcriptional factor-DNA complexes were isolated with antibody.
Libraries were constructed according to standard Illumina protocols.

value: gastric cancer cells

tag: confluence

value: IRF3 (santa cruz, sc-9082)


title: YAP

tag: cell type


title: DG17X066149_chicken_blood_non-responder307


title: 18A2-20-47_S389


title: PATIENT_46_DAY_1

city: Roskilde

first: Sara

middle: Kehlet

last: Watt

state: .No State

address: Sygehusvej 6, 3

country: Denmark

institute: Zealand University Hospital, Roskilde

hyb_protocol: According to standard Affymetrix HTA protocol

data_processing: Background correction, rma normalizaion and gene expression index calculation of probe intensities were done in Affymetrix Expression Console software

label: biotin

source_name: patient undergoing laparoscopic surgery for colon cancer stage I-III UICC

label_protocol: The GeneChip™ WT PLUS Reagent Kit was used to convert 500 ng purified total RNA to biotin-labeled cDNA

extract_protocol: Total RNA was extracted using Paxgene Blood RNA kit (Qiagen, Franklin Lakes, NJ, USA)

treatment_protocol: Blood samples were taken on the day prior to surgery and on day 1 and 10-14 day(s) after surgery, and were collected in Paxgene tubes (Preanalytix, Hombrechtikon, Switzerland) stored at -80⁰C until analysis. After sampling, tubes were stored at room temperature for 24 hours, then at -20⁰C for one day, and finally transferred to -80⁰C

value: blood

tag: diagnosis

value: colon cancer stage I-III UICC


title: Control3_CG005


title: 18A2-21-40_S388


title: Control2_CG005


title: DG17X066097_chicken_blood_non-responder297


title: 18A2-20-42_S390


title: Control1_CG005


title: PATIENT_46_DAY_10

scan_protocol: According to standard Affymetrix HTA protocol


title: Control4_CG004


title: DG17X066073_chicken_blood_non-responder292


title: DG17X066107_chicken_blood_non-responder303


title: PATIENT_44_DAY_10


title: 18A2-19-44_S392


title: 18A2-20-39_S391

value: 3 months


title: PATIENT_44_DAY_-1


title: DG17X066054_chicken_blood_non-responder283


title: 18A2-21-43_S387


title: PATIENT_44_DAY_1


title: Control1_CG006


title: Control3_CG004


title: 18A2-18-69_S393


title: Control2_CG004


title: 18A2-18-21_S394


title: PATIENT_43_DAY_10


title: DG17X066058_chicken_blood_non-responder317


title: PATIENT_43_DAY_1


title: PATIENT_46_DAY_-1


title: DG17X066081_chicken_blood_non-responder279


title: Control4_CG003


title: 18A1-62-58_S396


title: Control1_CG004


title: DG17X066170_chicken_blood_non-responder242


title: 18A2-18-13_S395


title: DG17X066182_chicken_blood_non-responder244


title: Control3_CG003


title: DG17X066024_chicken_blood_non-responder230


title: PATIENT_43_DAY_-1


title: Control2_CG003


title: 18A1-62-51_S397


title: DG17X066019_chicken_blood_non-responder229


title: PATIENT_41_DAY_1


title: 18A1-62-50_S398


title: DG17X066033_chicken_blood_non-responder225


title: 18A1-61-0_S400


title: DG17X066018_chicken_blood_non-responder227


title: Control1_CG003


title: PATIENT_39_DAY_10


title: PATIENT_41_DAY_-1


title: 18A1-60-34_S401


title: PATIENT_39_DAY_1


title: DG17X066165_chicken_blood_non-responder224


title: PATIENT_39_DAY_-1


title: RAD27 knockout Pol3 R484V

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: RAD27 knockout Pol3 R484V

data_processing:
Library strategy: DNA-seq
Reads were filtered by Cutadapt v 1.18 to remove low quality reads and sequencing adapters
Processed reads were aligned to the SacCer3 reference genome by novoalign v3.02.07
samtools mpile up was used to generate pileup of each genome location
VarScan v2.3.27 was used to call somatic mutations using the sample  WT-30 DNA
Somatic muations were filtered to keep only 0% allele freq in WT-30 sample
Genome_build: SacCer3
Supplementary_files_format_and_content: Filtered somatic mutations in text file

source_name: yeast cells cultured in 30 degree

growth_protocol: Yeast cells were grown at 30 degree in YPD medium overnight. They are diluted in fresh YPD medium and incubated for 4 hours at 30 or 37 degree and harvested for DNA or RNA isolation.

extract_protocol:
Genomic DNA was isolated by cell lysis followed by protein digestion by proteinase K. After phenol/chloroform extraction, genomic DNA was isolated by ethanol preciptation and washed with 70% ethanol. Total RNA is extracted by Trizol.
Kapa HyperPrep DNA Kit

tag: genetic background

value: RAD27 knockout Pol3 R484V

tag: growth temperature

value: 30 degree


title: DG17X066180_chicken_blood_non-responder222


title: 18A1-59-34_S403

value: Anterior meninges


title: PATIENT_41_DAY_10


title: DG17X066169_chicken_blood_non-responder220


title: PATIENT_37_DAY_10


title: 18A1-59-56_S402

value: 18 months


title: WT-37 DNA

description: WT-37 DNA

source_name: yeast cells cultured in 37 degree 4h

value: wildtype

value: 37 degree


title: Rad27KO-37-DNA

value: RAD27 knockout


title: DG17X066031_chicken_blood_non-responder217

value: Blood


title: PATIENT_37_DAY_-1


title: 18A1-59-28_S405


title: DG17X066016_chicken_blood_non-responder219


title: Revertant-30-DNA

value: RAD27 knockout/suppressor mutations


title: RAD27 knockout Pol3 S847Y

description: RAD27 knockout Pol3 S847Y

value: RAD27 knockout Pol3 S847Y


title: 18A1-61-57_S399


title: PATIENT_35_DAY_10


title: DG17X066175_chicken_blood_non-responder202

value: non-responder


title: Rad27KO-30-DNA


title: 18A1-58-53_S406


title: RAD27 knockout Pol3 ITD

description: RAD27 knockout Pol3 ITD

value: RAD27 knockout Pol3 ITD


title: DG17X066174_chicken_blood_non-responder199


title: PATIENT_35_DAY_1


title: 18A1-57-51_S408


title: 18A1-57-9_S407


title: PATIENT_35_DAY_-1


title: 18A1-59-30_S404


title: PATIENT_37_DAY_1


title: WT-30 DNA

description: WT-30 DNA


title: 27737-Rad27KO2-37

data_processing:
Sequenced were trimmed to remove Illumina adapters and poly(A) tail
The trimmed reads were mapped back to the Saccharomyces cerevisiae S288C (baker's yeast) genome assembly R64 (SacCer3) using STAR software (v. 020201)
Htseq count was used generate gene expression counts
Genome_build: SacCer3
Supplementary_files_format_and_content: read counts in tab delimited file

source_name: yeast cells cultured in 37 degree, 4h

extract_protocol:
Genomic DNA was isolated by cell lysis followed by protein digestion by proteinase K. After phenol/chloroform extraction, genomic DNA was isolated by ethanol preciptation and washed with 70% ethanol. Total RNA is extracted by Trizol.
RNA-seq libraries were prepared using Kapa mRNA HyperPrep following manufecturer's recommendation


title: PATIENT_34_DAY_10


title: RAD27 knockout Pol3 R470G

description: RAD27 knockout Pol3 R470G

value: RAD27 knockout Pol3 R470G


title: 18A1-57-0_S409


title: 18A1-56-59_S410


title: 27736-Rad27KO1-37


title: DG17X066011_chicken_blood_non-responder196


title: DG17X066015_chicken_blood_non-responder195


title: DG17X066176_chicken_blood_non-responder197


title: 27741-Rad27KO2-30


title: DG17X066177_chicken_blood_non-responder192


title: 27740-Rad27KO1-30


title: PATIENT_34_DAY_-1


title: PATIENT_34_DAY_1


title: 18A1-56-55_S411


title: 18A1-56-50_S412


title: DG17X066012_chicken_blood_non-responder191


title: PATIENT_33_DAY_10


title: 27733-WT2-37


title: PATIENT_33_DAY_1


title: 18A1-56-35_S413


title: DG17X066010_chicken_blood_non-responder190


title: 27732-WT1-37


title: 18A1-56-34_S414


title: DG17X066046_chicken_blood_non-responder176


title: DG17X066063_chicken_blood_non-responder175


title: 27739-WT-2-30


title: PATIENT_29_DAY_1


title: PATIENT_29_DAY_10


title: 18A1-56-1_S416


title: PATIENT_29_DAY_-1


title: DG17X066052_chicken_blood_non-responder162


title: 18A1-56-3_S415


title: 27738-WT1-30


title: DG17X066041_chicken_blood_non-responder155


title: 18A1-55-56_S418


title: HEK293T cells-RA1 transfected-rep1

city: Changsha

first: Junyi

last: Song

email: 283693514@qq.com, songjunyi@nudt.edu.cn

address: Deya Road 109

institute: National University of Defense Technology

data_processing:
In this project, we sequence 6 samples used DNBSEQ platform
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads need to be filtered before the data analysis for reliability analysis results.
We used HISAT to align the clean reads to the reference genome.
Genome_build: Reference Genome Version: GCF_000001405.39_GRCh38.p13
Supplementary_files_format_and_content: gene_expression.txt represents FPKMs, TPMs, read_counts

source_name: HEK293T cells

growth_protocol: HEK293T cells plated in 10cm dishes (90% DMEM+10% FBS+P-S), when the convergence reached ~70%m we carried out the transfection assays, then the cells were cultivated for another 24hr. Harvest the cells by trypsin treatment.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Stantard Lipo3000 protocol

tag: cell line

value: HEK293T cells

tag: genotype

value: RfA1 expression


title: 18A1-55-27_S419


title: DG17X066138_chicken_blood_non-responder174

data_processing:
Axiom Analysis Suite version 5 were used with the default settings, except for the QC call rate threshold which we change from 95% to 97%.  Samples were run through the best practices workflow which excludes samples that don’t meet the QC criteria.
The primary data are provided as a matrix table with row names and column names. Each row represents an animal, with SampleName as the row name. Each column represents a SNP, with Affymetrix Probeset ID as the column name. Each cell represents a diploid genotype coded as A/G/C/T. Missing genotype is coded as "--"

extract_protocol: Genomic DNA isolated using Dneasy Blood and Tissue Kit (Qiagen) following the manufacturer's protocol.


title: DG17X066134_chicken_blood_non-responder154


title: HEK293T cells-GFP transfected-rep3

value: control


title: PATIENT_28_DAY_1

value: blood

value: colon cancer stage I-III UICC


title: PATIENT_33_DAY_-1


title: 18A1-55-6_S417


title: PATIENT_28_DAY_10


title: 18A1-54-6_S420


title: DG17X066053_chicken_blood_non-responder152


title: PATIENT_28_DAY_-1


title: HEK293T cells-GFP transfected-rep2


title: DG17X066104_chicken_blood_non-responder151


title: 18A1-54-2_S421


title: PATIENT_27_DAY_10


title: DG17X066146_chicken_blood_non-responder149


title: PATIENT_27_DAY_1


title: HEK293T cells-RA1 transfected-rep2


title: 18A1-26-8_S422


title: PATIENT_27_DAY_-1


title: Control planarians - rep2

first: Stephen

middle: M

last: Fuchs

address: 4 Blackfan Circle

institute: Institute for protein innovation

data_processing:
Analysis was done on linux cluster. Reads were mapped to Dugesia japonica transcriptome (Chan et al 2016, Data in Brief) using bowtie2 v2.2.3 with parameters --very-sensitive. Counts files were generated using sort | uniq -c command.
Counts files were subjected to principal component analysis and 2 replicates from each group (AO_1_counts.txt, AO_2_counts.txt, ctrl_2_counts.txt, ctrl_3_counts.txt) were used for downstream analysis.
Differential expression analysis was done using DESeq2 package and results were adjusted to q-value < 0.01
Genome_build: Published transcriptome - Chan et al, 2016, doi: 10.1016/j.dib.2016.11.022
Supplementary_files_format_and_content: Processed data files contain contig names from the reference transcriptome (Chan et al, 2016, doi: 10.1016/j.dib.2016.11.022) and respective counts.
Supplementary_files_format_and_content: CSV file containing reference contig names, baseMean, log2FoldChange, lfcSE, stat, pvalue and padj sorted by log2FoldChange

organism: Dugesia japonica

source_name: Intact planarians

growth_protocol: Planarian colony was maintained at 20 °C in the dark in PolandSpring water and fed with liver paste once a week. Planarians were starved for at least 7 days prior to the start of the experiment.

extract_protocol:
Total RNA was extracted using Trizol and 1-bromo-3-chloropropane and precipitated with isopropanol. RNA extracts were then treated with DNaseI to remove potential DNA contamination.
mRNA was enriched using NEBNext Ply(A) mRNA Magnetic Isolation Module, mRNA was fragmented at 94 °C for 15 minutes and used as input for library preparation. Library was prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina as per manufacturer's protocol.

treatment_protocol: 90 mM AdOx stock solution was prepared freshly in 0.14 M HCl as per manufacturers' instructions and diluted in PolandSpring to desired concentration. Control water was prepared dilution of the mock stock solution containing 0.14 HCl. For AdOx treatment planarians of 1cm in size were placed into 100uM AdOx-containing PolandSpring water (10 planarians/8mL) and kept in that solution for 1 month. Control planrians of matched size were kept in control water for 1 month in the same conditions.

tag: number of individuals

value: 6 individuals

value: Control - HCl


title: PATIENT_25_DAY_1


title: 18A1-26-24_S424

value: Anterior meninges

value: 18 months


title: 18A1-26-29_S423


title: DG17X066049_chicken_blood_non-responder145


title: Control planarians - rep3

tag: treatment


title: 18A1-24-9_S425


title: PATIENT_25_DAY_-1


title: DG17X066108_chicken_blood_non-responder142


title: Control planarians - rep1


title: DG17X066042_chicken_blood_non-responder141


title: 18A1-24-5_S427


title: AdOx-adapted planarians - rep3

value: Adenosine dialdehyde (AdOx)


title: DG17X066124_chicken_blood_non-responder140


title: AdOx-adapted planarians - rep2


title: 18A1-24-57_S426


title: HEK293T cells-RA1 transfected-rep3


title: PATIENT_23_DAY_10


title: AdOx-adapted planarians - rep1


title: PATIENT_23_DAY_1


title: 18A1-24-49_S428


title: DG17X066126_chicken_blood_non-responder146


title: HEK293T cells-GFP transfected-rep1


title: 18A1-24-2_S429


title: KOD1-KO-Small-RNA-sample

city: Tsukuba

first: Kiong

last: Ho

address: 1-1-1 Tennodai

institute: University of Tsukuba

data_processing:
fastQC was used to verify the presence of adaptor sequence, adaptor was trimed where necessary using cutadapt. Aligning Reads to T.Kodakarensis genome reference using bowtie2. The reads per kilo-base per million mapped reads (RPKM) was calculated using FeatureCount. A custom perl script was used to identify RNA-Seq reads containing circular junction sequences.
Genome_build: NC_006624.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Thermococcus kodakarensis KOD1

source_name: Thermococcus kodakarensis KOD1

growth_protocol: MA-YT-P medium (1L), which contains 0.8 x Marine Art SF1reagent (Osaka Yakken Co. Ltd., Osaka, Japan), 5 g of yeast extract (Y), 5 g of trypton (T) and 5 g of sodium pyruvate (P), was used. Cells from each of the WT and tk1545 KO strains were harvested when the absorbance at 600 nm reached ~0.7 (late-log phase).

extract_protocol:
T. kodakarensis total RNA was isolated from WT and tk1545KO cultures using TRIZOL reagent (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Tk1545 Knockout

tag: rna resouce

value: small length transcripome RNA


title: PATIENT_25_DAY_10


title: DG17X066120_chicken_blood_non-responder134

last: Plastow

address: 1400 College Plaza, 8215 - 112 Street

value: Blood


title: KOD1-KO-Total-RNA-sample

value: Whole transcripome RNA


title: PATIENT_23_DAY_-1


title: KOD1-WT-Small-RNA-sample

value: WT


title: PATIENT_21_DAY_10


title: PATIENT_21_DAY_1


title: DG17X066065_chicken_blood_non-responder130

value: non-responder


title: DG17X066119_chicken_blood_non-responder132


title: 18A1-23-8_S431

value: 3 months


title: 18A1-24-11_S430


title: KOD1-WT-Total-RNA-sample


title: L02-HBx3

city: Nanjing

first: Chuqian

last: Zheng

state: Jiangsu

address: 87 Dingjiaqiao, Gulou District

department: Department of Medical Genetics and Developmental Biology, School of Medicine

institute: Southeast University

description: F

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: HG19
Supplementary_files_format_and_content: Matrix tables with raw gene counts, log2FC for every gene and every sample

extract_protocol:
Remove the medium, wash the cells 3 times with PBS, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver cells

value: HBx expression


title: 18A1-23-6_S433


title: 18A1-23-7_S432


title: PATIENT_21_DAY_-1


title: 18A1-23-29_S434


title: PATIENT_19_DAY_10


title: PATIENT_19_DAY_1


title: DG17X066142_chicken_blood_non-responder139

first: Graham


title: L02-HBx2

description: D


title: L02-HBx1

description: B


title: PATIENT_19_DAY_-1


title: L02-vector3

description: E

value: control


title: 18A1-23-28_S435


title: PATIENT_17_DAY_10

value: blood


title: 18A1-23-10_S436


title: H880

city: Dallas

first: Yuqing

last: Zhang

state: TX

address: 6000 Harry Hines Blvd

institute: UTSouthwestern Medical Center

hyb_protocol: Total RNA from each sample was hybridized to the CodeSet nCounter PanCancer Immune Profiling Panel, Mouse.

scan_protocol: The scanning was processed on the NanoString Technologies nCounter Sprint Profiler.

data_processing:
We used the nSolver Analysis Software 4.0 (NanoString Technologies).
Samples were normalized based on the geometric means of the supplied positive controls and the panel of housekeeping genes.

label: NanoString nCounter probes

source_name: KPfC pancreatic tumor

growth_protocol: 0.5 × 10^6 KPfC BMF-A3 cells were implanted orthotopically into WT C57BL/6 mice. Ultrasound was done on a cohort of animals to confirm tumor burden before therapy was initiated.

extract_protocol: KPfC tumor tissues from orthotopic endpoint experiment were lysed in RLT lysis buffer and purified according to the manufacturer’s instructions (QIAGEN). Quality control was performed with Agilent Bioanalyser.

treatment_protocol: For KPfC endpoint study, therapy was initiated at day 10 post tumor cell injection. Treatments consist of 8 groups: vehicle; TP-0903, 25 mg/kg, daily, oral gavage; gemcitabine, 25 mg/kg, ip, 3x/week; anti-PD1 antibody (clone: RMP14-1), 5 mg/kg, ip, twice per week; TP-0903+gemcitabine; TP-0903+anti-PD1; TP-0903+gemcitabine+anti-PD1; gemcitabine+anti-PD1. All mice were sacrificed on Day 35.

value: KPfC orthotopic pancreatic tumor


title: L02-vector2

description: C


title: H877


title: H779


title: 18A1-22-6_S437


title: H778


title: 18A1-22-4_S438


title: PATIENT_17_DAY_-1

value: colon cancer stage I-III UICC


title: 18A1-22-10_S439


title: D7_MORC3KO_IFNAR1KO_IFNAR2KO_rep3

city: Berkeley

first: Nir

last: Yosef

address: 629 Soda Hall

institute: University of California, Berkeley

description:
MG_D7_S43_L004
Replicate 3 for RNA-seq 5 days of trans-differentiation

data_processing:
Sequencing quality of fastq files was evaluated with FASTQC
RNA-seq reads were aligned to the reference genome (GRCh38.83) using Bowtie2
Transcript and gene counts were quantified using RSEM with the parameter ‘strandedness’ set to ‘reverse’.
Genome_build: GRCh38.83

molecule: polyA RNA

growth_protocol: BLaER1 cells were cultured in RPMI Medium 1640 supplemented with L-glutamine, sodium pyruvate, 100U/ml penicillin-streptomycin (Thermo Fisher) and 10% (v/v) FCS (Omega Scientific).

extract_protocol:
RNA from 2.8 million trans-differentiated BLaER1 monocytes was isolated using TRIzol™ Reagent (Thermo Fisher). DNA was removed with RQ1 RNase-free DNase (Promega) in the presence of RNasin plus Ribonuclease Inhibitor (Promega) and RNA isolated with Agencourt AMPure XP beads (Beckman Coulter).
mRNA-seq libraries were prepared from poly-A-enriched mRNA using a KAPA mRNA HyperPrep Kit (Roche) and sequenced on an Illumina Novaseq S4 150PE.

treatment_protocol: 1.4 million BLaER1 cells per well of a 6-well plate were trans-differentiated into monocytes for 5 days in medium containing 10 ng/ml of hrIL-3, 10 ng/ml hr-CSF-1 (M-CSF) (both PeproTech) and 100 nM β-Estradiol (Sigma-Aldrich).

value: IFNAR1-/- IFNAR2-/- MORC3-/-


title: PATIENT_16_DAY_10


title: PATIENT_17_DAY_1


title: H881


title: G869


title: L02-vector1

description: A


title: D6_MORC3KO_IFNB1KO_rep3

description:
MG_D6_S42_L004
Replicate 3 for RNA-seq 5 days of trans-differentiation

value: IFNB1-/- MORC3-/-


title: 18A1-21-49_S440

value: Anterior meninges

value: 18 months


title: PATIENT_16_DAY_1


title: G866


title: PATIENT_16_DAY_-1


title: 18A1-21-33_S441


title: D5_MORC3KO_rep3

description:
MG_D5_S41_L004
Replicate 3 for RNA-seq 5 days of trans-differentiation


title: D4_WT_rep3

description:
MG_D4_S40_L004
Replicate 3 for RNA-seq 5 days of trans-differentiation

source_name: WT


title: G862


title: G871


title: PATIENT_15_DAY_10


title: 18A1-21-28_S442


title: C4_MORC3KO_IFNAR1KO_IFNAR2KO_rep2

description:
MG_C4_S28_L004
Replicate 2 for RNA-seq 5 days of trans-differentiation


title: 18A1-19-52_S443


title: C3_MORC3KO_IFNB1KO_rep2

description:
MG_C3_S27_L004
Replicate 2 for RNA-seq 5 days of trans-differentiation


title: PATIENT_15_DAY_1


title: 18A1-19-32_S444


title: PATIENT_15_DAY_-1


title: F751


title: F752


title: 18A1-19-3_S445


title: C1_WT_rep2

description:
MG_C1_S25_L004
Replicate 2 for RNA-seq 5 days of trans-differentiation


title: PATIENT_14_DAY_10


title: 18A1-19-24_S446


title: PATIENT_14_DAY_1


title: PATIENT_14_DAY_-1


title: A12_MORC3KO_IFNB1KO_rep1

description:
MG_A12_S12_L004
Replicate 1 for RNA-seq 5 days of trans-differentiation


title: PATIENT_11_DAY_10


title: E784


title: F750


title: 18A1-18-7_S447


title: F786


title: 18A1-18-58_S448


title: 18A1-18-54_S449


title: B1_MORC3KO_IFNAR1KO_IFNAR2KO_rep1

description:
MG_B1_S13_L004
Replicate 1 for RNA-seq 5 days of trans-differentiation


title: E783


title: A11_MORC3KO_rep1

description:
MG_A11_S11_L004
Replicate 1 for RNA-seq 5 days of trans-differentiation


title: PATIENT_11_DAY_1


title: A10_WT_rep1

description:
MG_A10_S10_L004
Replicate 1 for RNA-seq 5 days of trans-differentiation


title: PATIENT_11_DAY_-1


title: 18A1-18-35_S450


title: E712


title: C2_MORC3KO_rep2

description:
MG_C2_S26_L004
Replicate 2 for RNA-seq 5 days of trans-differentiation


title: 18A1-18-32_S451


title: PATIENT_10_DAY_10


title: D3_IFNB1KO_E4ORF3_rep3

description:
MG_D3_S39_L004
Replicate 3 for RNA-seq 5 days of trans-differentiation

data_processing:
Sequencing quality of fastq files was evaluated with FASTQC
RNA-seq reads were aligned to the reference genome (GRCh38.83) using Bowtie2
Transcript and gene counts were quantified using RSEM with the parameter ‘strandedness’ set to ‘reverse’.
Genome_build: GRCh38.83
Supplementary_files_format_and_content: abundances_tpm, counts

treatment_protocol: 1.4 million BLaER1 cells per well of a 6-well plate were trans-differentiated into monocytes for 5 days in medium containing 10 ng/ml of hrIL-3, 10 ng/ml hr-CSF-1 (M-CSF) (both PeproTech) and 100 nM β-Estradiol (Sigma-Aldrich) and  stimulated with 1µg/ml doxycycline hyclate (Sigma-Aldrich) for 24h.


title: 18A1-18-10_S452


title: D2_IFNB1KO_ICP0_rep3

description:
MG_D2_S38_L004
Replicate 3 for RNA-seq 5 days of trans-differentiation


title: D774


title: D1_IFNB1KO_mCherry_rep3

description:
MG_D1_S37_L004
Replicate 3 for RNA-seq 5 days of trans-differentiation


title: PATIENT_10_DAY_1


title: D773


title: D757


title: E771


title: PATIENT_10_DAY_-1


title: C11_IFNAR1KO_IFNAR2KO_ICP0_rep3

description:
MG_C11_S35_L004
Replicate 3 for RNA-seq 5 days of trans-differentiation

value: IFNAR1-/- IFNAR2-/-


title: C12_IFNAR1KO_IFNAR2KO_E4ORF3_rep3

description:
MG_C12_S36_L004
Replicate 3 for RNA-seq 5 days of trans-differentiation


title: 3P_TTCAGAATCCT

value: Posterior meninges


title: E769


title: C10_IFNAR1KO_IFNAR2KO_mCherry_rep3

description:
MG_C10_S34_L004
Replicate 3 for RNA-seq 5 days of trans-differentiation


title: PATIENT_9_DAY_10


title: PATIENT_9_DAY_1


title: C791

value: Gemcitabine


title: C753


title: PATIENT_9_DAY_-1


title: C9_WT_E4ORF3_rep3

description:
MG_C9_S33_L004
Replicate 3 for RNA-seq 5 days of trans-differentiation


title: 3P_TCAATCAACCG


title: 3P_TTCGAGATCAT


title: PATIENT_8_DAY_10


title: 3P_TGGTTGGTACT


title: PATIENT_8_DAY_-1


title: PATIENT_3_DAY_10


title: B12_IFNB1KO_E4ORF3_rep2

description:
MG_B12_S24_L004
Replicate 2 for RNA-seq 5 days of trans-differentiation


title: C7_WT_mCherry_rep3

description:
MG_C7_S31_L004
Replicate 3 for RNA-seq 5 days of trans-differentiation


title: B11_IFNB1KO_ICP0_rep2

description:
MG_B11_S23_L004
Replicate 2 for RNA-seq 5 days of trans-differentiation


title: 3P_GTTCTAGGTAA


title: C795


title: 3P_GTTGGTACTAT


title: C8_WT_ICP0_rep3

description:
MG_C8_S32_L004
Replicate 3 for RNA-seq 5 days of trans-differentiation


title: D756


title: 3P_TCGTCTGAATG


title: PATIENT_3_DAY_1


title: 3P_GTAGAGTATAT


title: B10_IFNB1KO_mCherry_rep2

description:
MG_B10_S22_L004
Replicate 2 for RNA-seq 5 days of trans-differentiation


title: PATIENT_3_DAY_-1


title: B758


title: B780


title: B777


title: C870


title: B9_IFNAR1KO_IFNAR2KO_E4ORF3_rep2

description:
MG_B9_S21_L004
Replicate 2 for RNA-seq 5 days of trans-differentiation


title: 3P_GGTCGATCCAG


title: PATIENT_8_DAY_1


title: PATIENT_1_DAY_10


title: 3P_GTTGACTATAC


title: A890

value: Vehicle


title: B8_IFNAR1KO_IFNAR2KO_ICP0_rep2

description:
MG_B8_S20_L004
Replicate 2 for RNA-seq 5 days of trans-differentiation


title: B894


title: B7_IFNAR1KO_IFNAR2KO_mCherry_rep2

description:
MG_B7_S19_L004
Replicate 2 for RNA-seq 5 days of trans-differentiation


title: 3P_GGTCAGGAGGT


title: 3P_GGTAGAATATG


title: PATIENT_1_DAY_1


title: 3P_GTACGGCTTCT


title: B5_WT_ICP0_rep2

description:
MG_B5_S17_L004
Replicate 2 for RNA-seq 5 days of trans-differentiation

value: WT


title: PATIENT_1_DAY_-1


title: Motor neurons - Affected child clone 4

city: Cleveland

first: Ashleigh

last: Schaffer

state: OH

address: 2109 Adelbert Road

department: Department of Genetics and Genome Sciences and Center for RNA Science and Therapeutics

institute: Case Western Reserve University

description:
TotalRNAseq_A4
Mature d28 motor neurons differentiated from Affected patient, iPSC clone 4

data_processing:
Raw reads were aligned with STAR version 2.5.4b with settings "--outFilterMultimapNmax 1" to keep only unique alignments and "--sjdbOverhang 149" to maintain a readLength - 1 recommendation for splice junction overhangs during alignment.
Count files were generated with featureCounts version 1.6.1 using output BAM files above and gene annotations from Ensembl release 95. Stranded (reverse) and paired-end settings were used.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited genewise count files using Ensembl genome annotations release 95
Supplementary_files_format_and_content: Comma seaparated value genewise count matrix

source_name: iPSC-derived motor neurons

growth_protocol: Primary fibroblast cell lines were established from skin biopsies of affected children and an unaffected parent according to standard methods. Reprogramming of patient fibroblasts into induced pluripotent stem cells (iPSCs) was performed using the Epi5 Episomal iPSC Reprogramming Kit (ThermoFisher) with the following modifications. Electroporated fibroblasts were plated on Matrigel membrane matrix (Fisher). Reprogramming vectors were prepared in house and the medium was changed to StemFlex (ThermoFisher) at day 15. iPSC clones were selected for expansion and plated on vitronectin-coated plates. Motor neurons were differentiated from patient-derived iPSCs using a previously published protocol (Markmiller et a., Cell, 2018)

extract_protocol:
TRIzol
150bp paired-end sequencing was performed by Novogene with 2 ug of total RNA as starting material. Total RNA-seq utilized the dUTP protocol (Parkhomchuk et al., Nucleic Acids Res., 2009) after rRNA depletion with the RiboZero Gold kit.

tag: pch10 disease status

value: Affected


title: 3P_GAACCTGCGCT

value: 3 months


title: 3P_GATGAATTGAG


title: Motor neurons - Affected child clone 2

description:
TotalRNAseq_A2
Mature d28 motor neurons differentiated from Affected patient, iPSC clone 2


title: B6_WT_E4ORF3_rep2

description:
MG_B6_S18_L004
Replicate 2 for RNA-seq 5 days of trans-differentiation


title: A891


title: A799


title: A889


title: B4_WT_mCherry_rep2

description:
MG_B4_S16_L004
Replicate 2 for RNA-seq 5 days of trans-differentiation


title: Motor neurons - Affected child clone 1

description:
TotalRNAseq_A1
Mature d28 motor neurons differentiated from Affected patient, iPSC clone 1


title: A9_IFNB1KO_E4ORF3_rep1

description:
MG_A9_S9_L004
Replicate 1 for RNA-seq 5 days of trans-differentiation


title: 3P_CTTGCTCAATT


title: 3P_CTGGTCGAACC


title: A796