title: Input of ARID1-less H2.35 cells

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the GRCh38/mm10 genome assembly using default parameters in Bowtie2 (v 2.3.4.3)
The aligned reads were subsequently filtered for quality and uniquely mappable reads were retained for further analysis.
Peaks were called using HOMER version 4.9, peaks were called using findpeaks command with with '-sytle histone' and FDR set to 1e-3.
Genome_build: GRCh38/mm10
Supplementary_files_format_and_content: bigwig genome browser tracks

source_name: Input of ARID1-less H2.35 cells

growth_protocol: The H2.35 cell line was cultured in DMEM with 4% (vol/vol) FBS, 1x Pen/Strep and 200 nM Dexamethasone

extract_protocol:
WT H2.35 cells expressing a Dox-inducible scramble shRNA and the indicated 3xTy1-tagged proteins were used for control ChIP. ARID1B knockout H2.35 cells expressing a Dox-inducible ARID1A shRNA and the indicated 3xTy1-tagged proteins were used for ARID1-less ChIP. Expression of exogenous proteins was titrated by transfecting different amount of pT3 plasmids. Transfections that resulting similar expression levels with their endogenous counterparts were used. To do ChIP, cells were induced with 1μg/ml Dox for 3 days and crosslinked by addition of 2mM disuccinimidyl glutarate (0.5M DMSO stock) for 45 min, followed by addition of 1% formaldehyde (37% stock) for 10 min. Crosslinking was quenched by addition of final 125 mM glycine solution (2.5 M stock) to the medium for 5 min. The cells were washed with PBS twice, scraped and collected by centrifugation. Cell pellets were resuspended in RIPA-0 (10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.1% SDS, 1% Triton X-100, 0.25% sarkosyl, pH8.0) and sonicated until DNA to an average size of 200 bp. The sonicated lysates were cleared by centrifugation at 20,000g for 10 min and supplemented with NaCl to final concentration of 0.3 M. The lysates were then incubated with 5 μg Ty1 antibody overnight followed by incubation with 25 μl protein A/G Dynabeads for another 3 hours with rotation. After incubation, the beads were washed with 1 ml following buffers, twice with RIPA-0, twice with RIPA-0.3 (RIPA-0 supplemented with 0.3 M NaCl), twice with LiCl buffer (10 mM Tris-HCl, 1 mM EDTA, 0.5% sodium deoxycholate, 0.5% NP-40, 250 mM LiCl, pH 8.0), and twice with TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0). The DNA was eluted with 150 μl SDS elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0) followed by incubation at 65°C overnight. The eluted DNA was treated with 2 μl RNase A (0.5 μg/μl) for 30 min at 37 °C followed by 2 μl Protease K (20 mg/ml) for 2 hours at 37 °C, and purified using MinElute PCR purification kit (Qiagen).
The purified DNA was used for library preparation using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina Kit according to manufacturer's protocol.

value: mouse hepatocyte cell

value: ARID1B KO and ARID1A KD (ARID1-less)


title: 065_41BB_3_AS_AL

status: Public on Jun 10 2020

type: SRA

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

country: USA

institute: La Jolla Institute for Immunology

description: 200 cells bulk, full-transcriptome (Smart-seq2, Rosales et al.,  2018)

library_source: transcriptomic

data_processing:
RNA-seq data were mapped against the hg19 reference using TopHat (v1.2.1 (--library-type fr-unstranded --no-coverage-search) with FastQC (v0.11.2), Bowtie108 (v1.1.2), Samtools 0.1.18.0) and we employed Cutadapt (v1.3) was used to remove adapters. The RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site.
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s no -t exon -i gene_name,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
Genome_build: hg19
Supplementary_files_format_and_content: allergen_Tcells_raw_counts.txt.gz contains Transcript per Million normalized counts
Supplementary_files_format_and_content: allergen_Tcells_TPM.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

growth_protocol: Not applicable

extract_protocol:
Cells of interest were directly collected by sorting 200 cells into 0.2 ml PCR tubes (low-retention, Axygen) containing 8 μl of ice-cold lysis buffer (Triton X-100 [0.1 %, Sigma-Aldrich] containing RNase inhibitor (1:100, Takara). Once collected, tubes were vortexed for 10 seconds, spun for 1 minute at 3000 g and stored at -80 ˚C.
We followed the Samert-Seq2 protocol as described previously (Picelli et al.,2013; Rosales et al.,2018) with following modifications: (i) the pre-amplification PCR cycle for T cells was set at 22 cycles; (ii) to eliminate any traces of primer-dimers, the PCR pre-amplified cDNA product was purified using 0.8x Ampure-XP beads (Beckman Coulter) before using the DNA for sequencing library preparation. One ng of pre-amplified cDNA was used to generate barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina) in 8 µl reaction volume. Samples failing any quality control step (DNA quality assessed by capillary electrophoresis (Fragment analyzer, Advance analytical) and quantity (Picogreen quantification assay, Thermofisher) were eliminated from further downstream steps. Libraries were then pooled at equal molar concentration and sequenced using the HiSeq 2500 Illumina platform to obtain 50-bp single-end reads (HiSeq SBS Kit v4; Illumina).
50 bp single-end reads, full transcriptome, Hg10 human reference genome.

treatment_protocol: For each donor, PBMC cryovials were thawed, washed and, plated overnight in 6-well culture plates at a concentration of 10 x 106 cells/ml in 2 ml of serum-free TexMACS medium (Miltenyi Biotec) (5 % CO2, 37 ˚C). In presence of a blocking CD40 antibody (1 µg/ml; Miltenyi Biotec), cells were then stimulated by addition of HDM peptide pool (1 µg/ml; Hintz et al, 2015) for 6 h (Bacher et al.,2016). Subsequently, cells were stained with fluorescence-labeled antibodies and a biotinylated CD154 antibody (clone 5C8; Miltenyi Biotec). Anti-biotin microbeads (Miltenyi Biotec) were added to allow MACS-based enrichment of CD154+ cells using MS columns (Miltenyi Biotec). 5 % of cells were kept as control sample (‘input’) and used for FACS sorting of HDM– T cells and analysis of cell frequencies before enrichment. Positively selected cells (CD154+) were eluted from the column and used for FACS sorting of CD154+ memory CD4+ T cells. The flow-through from the MACS column was collected, stained with a biotinylated CD137 antibody (clone REA765; Miltenyi Biotec) and anti-biotin MicroBeads and applied to a second MS column. Positively selected cells (CD137+) were used for FACS sorting of CD137+ cells.

tag: tissue

value: Blood

tag: cell type

value: Memory CD4 T cells, Treg enriched:CD3+ CD4+ CD45RA- CD154- CD137Hi

tag: disease group

value: Asthmatic & Allergic to HDM


title: PNX-NaK-6

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

data_processing:
Reads were trimmed to remove adapters and low-quality base calls using Trimmomatic v0.38
Reads were aligned to the reference genome GRCm38 using HISAT2 v2.1.0
Count tables were generated using GenomicAlignments v1.16.0
Data were analyzed using DESeq2 v1.20.0. Raw and normalized count tables were exported as CSV files
Genome_build: GRCm38
Supplementary_files_format_and_content: raw_counts.csv: raw read counts per gene per sample
Supplementary_files_format_and_content: normalized_counts.csv: read counts per gene per sample, normalized by library size by DESeq2
Supplementary_files_format_and_content: fpkm.csv: FPKM values

molecule: total RNA

organism: Mus musculus

source_name: Adipose tissue

extract_protocol:
Total RNA was extracted from adipose tissue using RNeasy Protect Mini Kit (QIAGEN, Maryland)
Libraries were prepared from 1 ug total RNA per sample using the Truseq strand mRNA kit (Illumina , San Diego, CA) according to the manufacturers’ instructions.

treatment_protocol:
Mice underwent either 5/6 nephrectomy involving ligation of the left kidney leaving 1/3 functional and removal of the right kidney (PNX); or a sham operation (CTR) without ligation of the left kidney or removal of the right kidney.
Lentivirus (100µL, 2x109 TU/mL), with NaKtide or its counterpart Lenti-eGFP, driven by adiponectin promoter, was injected into the C57BL6 mice intraperitoneally (i.p.) in saline

tag: model (partial nephrectomy or sham operation)

value: PNX

tag: expressed protein

value: NaK


title: PNX-NaK-2


title: PNX-NaK-3


title: PNX-NaK-4


title: R21_2

city: Saint Louis

first: Bo

last: Zhang

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Raw reads were trimmed with cutadapt to remove low quality bases
Trimmed reads were aligned to mm10 using STAR_2.5.4b with gencode vM15 annotation
Aligned reads were quantified using featureCounts 1.6.3 from the subreads package
Quantified reads were corrected for batch effect using RUVr from the RUVSeq R package (v 1.16.1) according to the protocol described in the vignette using option k=3.
Genome_build: mm10
Supplementary_files_format_and_content: gene counts .txt file

source_name: 21 DPA, distal amputation

extract_protocol:
Frozen tissues were crushed with a pestle and the tissue lysates homogenized. Total RNA was isolated (RNeasy Mini Kit, QIAGEN) following the manufacturer’s protocol, depleted of ribosomal RNA via a hybridization method (Ribo-Zero Gold rRNA Removal Kit, Illumina), and purified with DNase treatment (Ambion DNA-free DNA Removal Kit, Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using 1 µg of total RNA per sample (average RNA integrity number of 8) and standard Illumina protocols.

tag: strain

tag: age

value: 10-12 weeks old

value: Hind limb digit tip (bone, cartilage, marrow, dermis, epidermis)

tag: treatment

value: distal amputation

tag: time

value: 21 DPA


title: 064_41BB_2_AS_AL


title: ChIP-seq of Brd9 in ARID1-less H2.35 cells [ARID1-less-Brd9-2]

city: DALLAS

first: Zixi

last: Wang

state: TX

address: 5323 HARRY HINES BLVD

department: CRI

institute: UT SOUTHWESTERN MEDICAL CENTER

library_source: genomic

molecule: genomic DNA

tag: cell line

tag: genotype/variation

tag: protein (cloned with a 3xty1 tag at the c-terminal and expressed)

tag: chip antibody


title: Genomic DNA from FC915

type: genomic

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: Control sample from FC915

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

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

data_processing: GenomeStudio methylation module v.1.9.0

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Kit according to standard instructions

tag: Sex

tag: disease

value: Control

tag: ige

value: PBMC


title: Genomic DNA from FC902

description: Control sample from FC902


title: R21_3


title: Genomic DNA from FC938

description: Control sample from FC938


title: Input of WT H2.35 cells

source_name: Input of WT H2.35 cells

value: WT


title: N14_4

source_name: 14 DPA, proximal amputation

value: proximal amputation

value: 14 DPA


title: 063_41BB_1_AS_AL


title: R21_1


title: ChIP-seq of Brd9 in ARID1-less H2.35 cells [ARID1-less-Brd9-1]


title: 062_41BB_12_AS_NA

value: Asthmatic & Non Allergic to HDM


title: R14_4

source_name: 14 DPA, distal amputation


title: CTR-NaK-6

value: Sham


title: ChIP-seq of ARID2 in ARID1-less H2.35 cells [ARID1-less-ARID2-4]

value: mouse hepatocyte cell

value: ARID1B KO and ARID1A KD (ARID1-less)


title: PNX-NaK-5


title: 061_41BB_11_AS_NA

value: Blood

value: Memory CD4 T cells, Treg enriched:CD3+ CD4+ CD45RA- CD154- CD137Hi


title: R14_3


title: CTR-NaK-5


title: ChIP-seq of ARID2 in ARID1-less H2.35 cells [ARID1-less-ARID2-3]


title: PNX-NaK-1

value: PNX


title: CTR-NaK-4

value: NaK


title: R14_2

value: 10-12 weeks old


title: ChIP-seq of ARID2 in ARID1-less H2.35 cells [ARID1-less-ARID2-2]


title: 060_41BB_10_AS_NA


title: 059_41BB_9_AS_NA


title: CTR-NaK-3


title: ChIP-seq of ARID2 in ARID1-less H2.35 cells [ARID1-less-ARID2-1]


title: CTR-NaK-2


title: 058_41BB_8_AS_NA


title: CTR-NaK-1


title: R12_3

source_name: 12 DPA, distal amputation

value: Hind limb digit tip (bone, cartilage, marrow, dermis, epidermis)

value: 12 DPA


title: R12_4

value: distal amputation


title: ChIP-seq of BAF45d in ARID1-less H2.35 cells [ARID1-less-BAF45d-1]


title: 073_41BB_17_AR

value: Non-Asthmatic & Allergic to HDM


title: ChIP-seq of BAF45d in ARID1-less H2.35 cells [ARID1-less-BAF45d-2]


title: 057_41BB_7_AS_NA


title: 056_41BB_24_HC

value: Non-Asthmatic & Non-Allergic to HDM


title: R12_2


title: PNX-GFP-6

value: GFP


title: ChIP-seq of Brd9 in WT H2.35 cells [WT-Brd9-2]

source_name: ChIP-seq of Brd9 in WT H2.35 cells

value: WT


title: PNX-GFP-5


title: ChIP-seq of Brd9 in WT H2.35 cells [WT-Brd9-1]


title: PNX-GFP-4


title: R12_1


title: 055_Neg_6_AS_AL

value: Memory CD4 T cells:CD3+ CD4+ CD45RA- CD154- CD137-

value: Asthmatic & Allergic to HDM


title: 054_Neg_5_AS_AL


title: R14_1

value: 14 DPA


title: ChIP-seq of ARID2 in WT H2.35 cells [WT-ARID2-2]

source_name: ChIP-seq of ARID2 in WT H2.35 cells

value: mouse hepatocyte cell


title: sample_40

city: Fort Collins, CO

first: Sarah

middle: Tepler

last: Drobnitch

state: Colorado

address: C106 Plant Sciences

institute: Colorado State University

data_processing:
Reads were mapped to the S. bicolor genome (v.3.1.1) from the Joint Genome Institute (McCormick et al., 2018).
Assembly of the transcriptome was performed using the Tuxedo Protocol (Trapnell et al., 2012). The included versions of Bowtie, TopHat and Cufflinks were 2-2.3.4.2, 2.1.1, and 2.2.1 respectively. Default parameters were used, with the exception of the following: min-intron-length 4 and max-intron-length 1900.
Functional annotation was obtained for a subset of the transcriptome by BLASTing annotated S. bicolor genes to all members of the Poaceae in the NCBI Gene Database.
Differential analysis was performed using DESeq in R (v.3.6.1)
Genome_build: S. bicolor v. 3.1.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM counts for each sample as well as BLAST annotations

organism: Sorghum bicolor

source_name: fine root tissue

extract_protocol:
RNA from root tissue was extracted and sequenced by Amaryllis Nucleics (Oakland, CA) using the protocol of Townsley et al. (2015)
RNA-Seq libraries were prepared using a high-throughput Illumina RNA-Seq library extraction protocol (Kumar et al. 2012). The enriched libraries were then quantified on an Analyst Plate Reader (LJL Biosystems) using SYBR Green I reagent (Invitrogen). Once the concentration of libraries was determined, a single pool of all the RNA-Seq libraries within each block was made. The pooled libraries were run on a Bioanalyzer (Agilent, Santa Clara) to determine the average product size for each pool. Each pool was adjusted to a final concentration of 20 nM and sequenced on a single lane on an Illumina Hi-Seq 2000 flow cell as 50 bp single-end reads.

value: root

tag: genotype

value: control watering, low root pressure


title: sample_57

tag: tissue


title: N12_3

source_name: 12 DPA, proximal amputation

value: proximal amputation


title: ChIP-seq of ARID2 in WT H2.35 cells [WT-ARID2-1]

tag: cell type


title: PNX-GFP-3

value: PNX


title: 053_Neg_4_AS_AL

value: Blood

tag: disease group


title: PNX-GFP-2

tag: model (partial nephrectomy or sham operation)


title: 052_Neg_3_AS_AL


title: ChIP-seq of BAF45d in WT H2.35 cells [WT-BAF45d-2]

source_name: ChIP-seq of BAF45d in WT H2.35 cells


title: PNX-GFP-1

tag: expressed protein


title: 051_Neg_2_AS_AL


title: ChIP-seq of BAF45d in WT H2.35 cells [WT-BAF45d-1]


title: CTR-GFP-6

value: Sham


title: 050_Neg_1_AS_AL


title: mRNA seq of control liver (ARID1A f/f; ARID1B f/f; Alb-Cre-) [WT-7067]

description:
WT-7067
mRNA-seq
processed data file: RawCount_feature_inVivo_DKO_ARID1A_and_ARID1B.txt

data_processing:
Reads with phred quality scores less than 20 and read length less than 35bp after trimming were removed from further analysis using trimgalore version 0.4.1.
Quality-filtered reads were then mapped to the mouse reference genome GRCm38 (mm10) using the HISAT (version 2.1.0) aligner with default settings.
After mapping, rRNA reads were filtered from resulting .bam files according to their overlap with the coordinates of rRNA gene list obtained from UCSC genome browser site.
Mapped reads were counted using featureCounts (version 1.6.2) program to obtain raw read counts for each gene.
Genome_build: GRCh38/mm10
Supplementary_files_format_and_content: *.normalized.bigwig: bigWig genome browser tracks.
Supplementary_files_format_and_content: *txt: Tab-delimited text files include the raw counts from featureCounts.

source_name: liver

growth_protocol: All mice were handled in accordance with the guidelines of the Institutional Animal Care and Use Committee at UTSW.

extract_protocol:
Liver total RNA was extracted from BKO, DKO and corresponding WT using TRIzol reagent followed by purification using RNeasy Mini kit (Qiagen).
RNA-seq libraries were prepared with the Ovation RNASeq Systems 1-16 (Nugen).

value: Liver

value: ARID1A f/f; ARID1B f/f; Alb-Cre-


title: sample_39

value: deficit watering, mid root pressure


title: sample_12


title: ChIP-seq of Brg1 in WT H2.35 cells [WT-Brg1-2]

source_name: ChIP-seq of Brg1 in WT H2.35 cells


title: sample_7

value: deficit watering, low root pressure


title: CTR-GFP-5


title: 048_CD154Pos_24_HC

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+

value: Non-Asthmatic & Non-Allergic to HDM


title: CTR-GFP-4

value: GFP


title: 047_CD154Pos_23_HC


title: ChIP-seq of Brg1 in WT H2.35 cells [WT-Brg1-1]

value: WT


title: ChIP-seq of ARID1B in WT H2.35 cells [WT-ARID1B-2]

source_name: ChIP-seq of ARID1B in WT H2.35 cells


title: 046_CD154Pos_22_HC


title: 045_CD154Pos_21_HC


title: ChIP-seq of ARID1B in WT H2.35 cells [WT-ARID1B-1]


title: R210_444_10

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

data_processing:
Standard Illumina pipeline
Alignments of mRNA sequences to all 88,647 Glyma models, including splice variants, from the Williams 82 reference genome of G. max (Phytozome, Joint Genome Institutes; Wm82.a2.v1) were performed using the Bowtie program v.1 (Langmead et al., 2009).
Transcriptome data were normalized in RPKM (reads per kilobase of gene model size per million mapped reads) (Mortazavi et al., 2008).
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: One Excel file with RPKM values

organism: Glycine max

source_name: Immature cotyledon, 10-25mg fresh weight of whole seed

growth_protocol: Plants were grown in optimal greenhouse conditions. Tissues were harvested at stated fresh weight. Seed coats were separated from cotyledons by hand.

extract_protocol:
Total RNA was extracted from tissues using phenol:chloroform and a lithium chloride precipitation (Gonzalez and Vodkin 2007). Sequencing was performed by the Keck Center (University of Illinois) using an Illumina HiSeq2500 or HiSeq4000.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Jack plants were transformed with a custom 8333bp circular plasmid containing: hygromycin and ampicillin resistance genes, 5' and 3' soybean lectin segments; pyruvate dehydrogenase kinase from soybean, Exon 5 in both forward and reverse orientations with Intron 5 in between; 35S promoter region.

value: Immature cotyledon

tag: cultivar

value: Jack mutant

tag: transgenic status

value: Negative

tag: generation


title: CTR-GFP-1


title: R206_J410

value: Jack

value: Negative (control)


title: CTR-GFP-2


title: 044_CD154Pos_20_HC


title: R205_J210


title: R209_441_10

value: Positive


title: 043_CD154Pos_19_HC


title: TAM

city: Los Angeles

first: Quan

last: Lin

address: 635 Charles E Young Drive South

department: Department of Psychiatry and Behavioral Sciences, Intellectual Development and Disabilities Research Center

institute: University of California, Los Angeles

data_processing:
The raw sequence reads were analyzed by Cell Ranger (10x Genomics, version 2.1.1) with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: Filtered feature-barcode matrices (in HDF5 file format) generated after Cell Ranger pipeline

source_name: forebrain

extract_protocol:
The forebarins were dissociated in papain at a concentration of 2 mg/ml in Hibernate E-Ca (HE-Ca, BrainBits, LLC.) at 30°C for 10 minutes. The digested tissues were gently triturated 10 times with fire-polished pasture pipettes. The single cell suspension was filtered through a 40mm cell strainer, and then centrifuged at 200g for 5 minutes at room temperature.  The pellet was washed with PBS containing 0.04% bovine serum albumin (BSA).
Libraries were prepared using the Chromium v2 Single Cell 3′ Library and Gel Bead Kit (10x Genomics) according to the manufacturer’s specifications

treatment_protocol: 750µg of tamoxifen was injected to pregnant mice at embryonic day 10 (E10), and forebrains were collected at E12.

tag: strain

tag: age

value: embryonic day 12 (E12)

tag: treament

value: tamoxifen treatment


title: ChIP-seq of ARID1A in WT H2.35 cells [WT-ARID1A-1]

source_name: ChIP-seq of ARID1A in WT H2.35 cells

tag: cell line

value: mouse hepatocyte cell

tag: genotype/variation

tag: protein (cloned with a 3xty1 tag at the c-terminal and expressed)


title: ChIP-seq of ARID1A in WT H2.35 cells [WT-ARID1A-2]

tag: chip antibody


title: sample_5

value: root

tag: treatment


title: CTL-2

value: another hemisphere of control


title: R208_J4100

source_name: Immature cotyledon, 100-200mg fresh weight of whole seed


title: RMS2W_RH_63: Mouse, intraamygdala kainic acid (IAKA), Chronic, control

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

description: Ago2 IP RNA, small RNA seq

data_processing:
FASTX-Toolkit (0.0.13) was used to quality filter reads and cutadapt (1.2.1) was used to remove adaptor sequences
Using Bowtie (0.12.8), reads were mapped to miRNAs from miRBase v21 allowing zero mismatches, but allowing for non-templated 3’ A and T bases
Genome_build: Reference: mature miRNAs from miRBase v21
Supplementary_files_format_and_content: Text files with raw read counts for miRNAs in each sample

source_name: Hippocampus

extract_protocol:
Frozen hippocampal tissue is homogonized and immunoprecipitation is done using Ago2 antibody
Immunoprecitated RNA was prepared using TruSeq small RNA library prep

value: Hippocampus

tag: model

value: intraamygdala kainic acid (IAKA)

tag: period

value: Chronic, control


title: RMS2W_RH_62: Mouse, intraamygdala kainic acid (IAKA), Chronic, control

description: Ago2 IP RNA, small RNA seq

tag: tissue


title: CTL-1

value: one hemisphere of control


title: 042_CD154Pos_18_AR

source_name: PBMC

value: Blood

tag: cell type

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+

tag: disease group

value: Non-Asthmatic & Allergic to HDM


title: RMS2W_RH_36: Mouse, intraamygdala kainic acid (IAKA), Chronic, control

description: Ago2 IP RNA, small RNA seq


title: 041_CD154Pos_17_AR


title: R207_J2100

value: Immature cotyledon


title: CTR-GFP-3

source_name: Adipose tissue

tag: model (partial nephrectomy or sham operation)

value: Sham

tag: expressed protein

value: GFP


title: R211_441_100

tag: cultivar

value: Jack mutant

tag: transgenic status


title: 040_CD154Pos_24_HC

value: Non-Asthmatic & Non-Allergic to HDM


title: b_49x

city: Durham

first: Vincent

middle: Michael

last: Perez

state: NC

address: 25 Alexandria Wy

department: Translational reasearch

institute: Tempus AI

description: mRNA isolated using using Illumina TruSeq® RNA sample preparation kit

data_processing:
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and 125 bp/150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: GRCm38, mus_musculus_mm10
Supplementary_files_format_and_content: Excel with read count and FPKM

source_name: whole liver

growth_protocol: Mice were maintained on a their respective diets from the ages of 12 to 16 weeks. After 16 weeks, the mice were CO2 asphyxiated, sacrified, and dissected for organ harvesting.

extract_protocol:
RNA was isolated using standard QIAzol protocol (Cat No./ID 79306). After RNA isolation, we cleaned up the RNA using the Qiagen RNeasy kit following the manufacturer’s protocol (Cat No./ID 74104). Quality control checks of the RNA were performed to define purity and concentration. We used a nanodrop to assess the quantity and quality for each sample, ensuring the quantity was between 50-250ng/µl and the 260/280 was between 1.95-2.10. We ensured no RNA degradation occurred using Agarose Gel Electrophoresis for each sample. Lastly, before sequencing Novogene performed additional quality and quantity assessments of the RNA samples using an Agilent 2100 instrument and gel electrophoresis.
RNA-Seq libraries were prepared using Illumina TruSeq® RNA sample preparation kit as per the manufacturer’s protocol. Library construction, additional quality assessment, and sequencing were performed by Novogene Corporation, Ltd. Library concentration was quantified with a Qubit 2.0 fluorometer from Life Technologies and samples diluted to 1ng/µL before checking insert size using a bioanalyzer (Agilent 2100 Bioanalyzer) and quantifying to greater accuracy using qPCR. Using paired-end sequencing at a depth of 40 million reads or greater per sample was completed on final libraries.

treatment_protocol: Liver slices (70mg) snap frozen in RNAlater® were thawed on ice, transferred to a 2mL tubes with 1mL of QIAzol, and thoroughly homogenized.

tag: strain

value: liver

value: 16 Weeks

tag: Sex

value: male

tag: genotype

value: wt control

tag: diet

value: ketogenic diet (KD)

tag: hours fasted


title: RMS_DOFS_RH_97: Mouse, intraamygdala kainic acid (IAKA), Day of first seizure, control

description: Ago2 IP RNA, small RNA seq

value: Hippocampus

value: Day of first seizure, control


title: b_51

tag: age


title: MRP8_RH_31: Rattus norvegicus, perforant pathway stimulation (PPS), Control

description: Ago2 IP RNA, small RNA seq

organism: Rattus norvegicus

value: Sprague-Dawley

value: perforant pathway stimulation (PPS)

value: Control


title: b_85

value: control-ketogenic diet (CD)


title: RMS_DOFS_RH_44: Mouse, intraamygdala kainic acid (IAKA), Day of first seizure, control

description: Ago2 IP RNA, small RNA seq

value: intraamygdala kainic acid (IAKA)


title: RMS_DOFS_RH_96: Mouse, intraamygdala kainic acid (IAKA), Day of first seizure, control

description: Ago2 IP RNA, small RNA seq


title: 038_CD154Pos_22_HC

value: Blood

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+


title: MRP8_RH_20: Rattus norvegicus, perforant pathway stimulation (PPS), Control

description: Ago2 IP RNA, small RNA seq


title: R212_444_100

value: Immature cotyledon

value: Negative

tag: generation


title: 039_CD154Pos_23_HC

value: Non-Asthmatic & Non-Allergic to HDM


title: b_87

value: liver


title: RMS72_RH_55: Mouse, intraamygdala kainic acid (IAKA), 72 hours, control

description: Ago2 IP RNA, small RNA seq

value: 72 hours, control


title: b_11

value: 16 Weeks

value: male


title: 037_CD154Pos_21_HC


title: RMS72_RH_54: Mouse, intraamygdala kainic acid (IAKA), 72 hours, control

description: Ago2 IP RNA, small RNA seq


title: MRP7_RH_75: Rattus norvegicus, perforant pathway stimulation (PPS), Chronic

description: Ago2 IP RNA, small RNA seq

value: Chronic


title: MRP7_RH_43: Rattus norvegicus, perforant pathway stimulation (PPS), Chronic

description: Ago2 IP RNA, small RNA seq

value: Hippocampus


title: MRP8_RH_17: Rattus norvegicus, perforant pathway stimulation (PPS), Control

description: Ago2 IP RNA, small RNA seq


title: RMS72_RH_47: Mouse, intraamygdala kainic acid (IAKA), 72 hours, control

description: Ago2 IP RNA, small RNA seq


title: 035_CD154Pos_19_HC


title: 036_CD154Pos_20_HC


title: b_827

value: ketogenic diet (KD)


title: RMS48_RH_028: Mouse, intraamygdala kainic acid (IAKA), 48 hours, control

description: Ago2 IP RNA, small RNA seq

value: 48 hours, control


title: MRP7_RH_37: Rattus norvegicus, perforant pathway stimulation (PPS), Chronic

description: Ago2 IP RNA, small RNA seq

value: Sprague-Dawley

value: perforant pathway stimulation (PPS)


title: 034_CD154Pos_18_AR

value: Non-Asthmatic & Allergic to HDM


title: b_812

value: control-ketogenic diet (CD)


title: MRP6_RH_74: Rattus norvegicus, perforant pathway stimulation (PPS), Day of first seizure

description: Ago2 IP RNA, small RNA seq

value: Day of first seizure


title: b_830


title: 033_CD154Pos_17_AR

value: Blood

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+


title: RMS48_RH_027: Mouse, intraamygdala kainic acid (IAKA), 48 hours, control

description: Ago2 IP RNA, small RNA seq

value: intraamygdala kainic acid (IAKA)


title: 032_CD154Pos_16_AR


title: b_2

value: wt control


title: MRP5_RH_6: Rattus norvegicus, perforant pathway stimulation (PPS), 16 days

description: Ago2 IP RNA, small RNA seq

value: 16 days


title: RMS24_RH_023: Mouse, intraamygdala kainic acid (IAKA), 24 hours, control

description: Ago2 IP RNA, small RNA seq

value: 24 hours, control


title: 030_CD154Pos_14_AR


title: RMS48_RH_026: Mouse, intraamygdala kainic acid (IAKA), 48 hours, control

description: Ago2 IP RNA, small RNA seq


title: 031_CD154Pos_15_AR


title: RMS24_RH_019: Mouse, intraamygdala kainic acid (IAKA), 24 hours, control

description: Ago2 IP RNA, small RNA seq


title: b_807

value: liver

value: 16 Weeks


title: RMS24_RH_016: Mouse, intraamygdala kainic acid (IAKA), 24 hours, control

description: Ago2 IP RNA, small RNA seq


title: b_806

value: male


title: 029_CD154Pos_13_AR


title: 028_CD154Pos_6_AS_AL

value: Asthmatic & Allergic to HDM


title: b_805

value: ketogenic diet (KD)


title: RMS1_RH_64: Mouse, intraamygdala kainic acid (IAKA), 1 hour, control

description: Ago2 IP RNA, small RNA seq

value: Hippocampus

value: 1 hour, control


title: 027_CD154Pos_5_AS_AL


title: b_804


title: RMS1_RH_043: Mouse, intraamygdala kainic acid (IAKA), 1 hour, control

description: Ago2 IP RNA, small RNA seq


title: b_802


title: RMS1_RH_039: Mouse, intraamygdala kainic acid (IAKA), 1 hour, control

description: Ago2 IP RNA, small RNA seq


title: MRP4_RH_5: Rattus norvegicus, perforant pathway stimulation (PPS), 10 days

description: Ago2 IP RNA, small RNA seq

value: Sprague-Dawley

value: perforant pathway stimulation (PPS)

value: 10 days


title: b_38


title: MRP4_RH_9: Rattus norvegicus, perforant pathway stimulation (PPS), 10 days

description: Ago2 IP RNA, small RNA seq


title: 026_CD154Pos_4_AS_AL


title: b_43


title: MRP4_RH_4: Rattus norvegicus, perforant pathway stimulation (PPS), 10 days

description: Ago2 IP RNA, small RNA seq


title: MRP6_RH_64: Rattus norvegicus, perforant pathway stimulation (PPS), Day of first seizure

description: Ago2 IP RNA, small RNA seq

value: Day of first seizure


title: MRP6_RH_69: Rattus norvegicus, perforant pathway stimulation (PPS), Day of first seizure

description: Ago2 IP RNA, small RNA seq


title: 025_CD154Pos_3_AS_AL

value: Blood


title: 024_CD154Pos_16_AR

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+

value: Non-Asthmatic & Allergic to HDM


title: RMK2W_RH_76: Mouse, intraamygdala kainic acid (IAKA), Chronic

description: Ago2 IP RNA, small RNA seq

value: intraamygdala kainic acid (IAKA)

value: Chronic


title: RMK2W_RH_106: Mouse, intraamygdala kainic acid (IAKA), Chronic

description: Ago2 IP RNA, small RNA seq


title: MRP5_RH_28: Rattus norvegicus, perforant pathway stimulation (PPS), 16 days

description: Ago2 IP RNA, small RNA seq

value: 16 days


title: 022_CD154Pos_14_AR


title: MRP5_RH_19: Rattus norvegicus, perforant pathway stimulation (PPS), 16 days

description: Ago2 IP RNA, small RNA seq


title: 023_CD154Pos_15_AR


title: b_789

value: liver


title: MRP3_RH_2: Rattus norvegicus, perforant pathway stimulation (PPS), 72 hours

description: Ago2 IP RNA, small RNA seq

value: 72 hours


title: RMK2W_RH_101: Mouse, intraamygdala kainic acid (IAKA), Chronic

description: Ago2 IP RNA, small RNA seq


title: b_797

value: 16 Weeks

value: male


title: RMK_DOFS_RH_95: Mouse, intraamygdala kainic acid (IAKA), Day of first seizure

description: Ago2 IP RNA, small RNA seq


title: MRP3_RH_1: Rattus norvegicus, perforant pathway stimulation (PPS), 72 hours

description: Ago2 IP RNA, small RNA seq


title: MRP2_RH_16: Rattus norvegicus, perforant pathway stimulation (PPS), 24 hours

description: Ago2 IP RNA, small RNA seq

value: 24 hours


title: RMK_DOFS_RH_85: Mouse, intraamygdala kainic acid (IAKA), Day of first seizure

description: Ago2 IP RNA, small RNA seq

value: Hippocampus


title: RMK_DOFS_RH_94: Mouse, intraamygdala kainic acid (IAKA), Day of first seizure

description: Ago2 IP RNA, small RNA seq


title: 021_CD154Pos_13_AR


title: 020_CD154Pos_6_AS_AL

value: Asthmatic & Allergic to HDM


title: b_779

value: ketogenic diet (KD)


title: MRP2_RH_15: Rattus norvegicus, perforant pathway stimulation (PPS), 24 hours

description: Ago2 IP RNA, small RNA seq

value: Sprague-Dawley

value: perforant pathway stimulation (PPS)


title: b_800


title: RMK72_RH_92: Mouse, intraamygdala kainic acid (IAKA), 72 hours

description: Ago2 IP RNA, small RNA seq


title: 018_CD154Pos_4_AS_AL


title: MRP3_RH_3: Rattus norvegicus, perforant pathway stimulation (PPS), 72 hours

description: Ago2 IP RNA, small RNA seq


title: MRP2_RH_11: Rattus norvegicus, perforant pathway stimulation (PPS), 24 hours

description: Ago2 IP RNA, small RNA seq


title: b_48

value: wt control

value: control-ketogenic diet (CD)


title: 019_CD154Pos_5_AS_AL

value: Blood

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+


title: MRP1_RH_36: Rattus norvegicus, perforant pathway stimulation (PPS), 1 hour

description: Ago2 IP RNA, small RNA seq

value: 1 hour


title: b_795


title: RMK72_RH_60: Mouse, intraamygdala kainic acid (IAKA), 72 hours

description: Ago2 IP RNA, small RNA seq

value: intraamygdala kainic acid (IAKA)


title: b_44


title: b_786


title: 017_CD154Pos_3_AS_AL


title: MRP1_RH_26: Rattus norvegicus, perforant pathway stimulation (PPS), 1 hour

description: Ago2 IP RNA, small RNA seq


title: 016_CD154Pos_2_AS_AL


title: b_771


title: RMK48_RH_050: Mouse, intraamygdala kainic acid (IAKA), 48 hours

description: Ago2 IP RNA, small RNA seq

value: 48 hours


title: RMK48_RH_049: Mouse, intraamygdala kainic acid (IAKA), 48 hours

description: Ago2 IP RNA, small RNA seq


title: b_770

value: liver


title: 015_CD154Pos_1_AS_AL


title: 4X  3

city: Beijing

first: Luming

last: Zou

state: PR

address: Haidian strict, Xiang Mountain South Road, Xiang Mountain South Village 20#

department: Institute of Botany

country: China

institute: University of Chinese Academy of Sciences

data_processing:
The reads were trimmed using FASTX-Toolkit (version 0.11.5)
The clean reads were mapped to the grape genome by using tophat (version 2.0.14) with default parameters.
Ragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks (version 2.2.1).
Genome_build: 12X grape genome of IGGP
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample ...

organism: Vitis vinifera

source_name: tip buds

growth_protocol: All the 2X and 4X vines received standard fertilization, irrigation, pruning and pests and diseases control.

extract_protocol:
We isolated total RNA from above ground samples (100mg per sample) using Sigma RNA Mini-Prep following the manufacturer's instructions (Zymo Research Corporation, Irvine, CA, USA) and the extracted RNA were treated with DNAse (Applied Biosystems/Ambion, Austin, TX, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genome size


title: b_7


title: 4X  2


title: RMK48_RH_048: Mouse, intraamygdala kainic acid (IAKA), 48 hours

description: Ago2 IP RNA, small RNA seq

tag: model


title: b_4


title: 014_CD154Pos_12_AS_NA

value: Asthmatic & Non Allergic to HDM


title: 013_CD154Pos_11_AS_NA


title: 4X  1


title: 012_CD154Pos_10_AS_NA


title: b_1

value: 16 Weeks


title: RMK24_RH_018: Mouse, intraamygdala kainic acid (IAKA), 24 hours

description: Ago2 IP RNA, small RNA seq

tag: period


title: b_9

tag: tissue

value: male


title: b_6


title: 011_CD154Pos_9_AS_NA

tag: cell type


title: 2X  1


title: RMK72_RH_59: Mouse, intraamygdala kainic acid (IAKA), 72 hours

description: Ago2 IP RNA, small RNA seq

value: 72 hours


title: 010_CD154Pos_8_AS_NA

tag: disease group


title: RMK24_RH_017: Mouse, intraamygdala kainic acid (IAKA), 24 hours

description: Ago2 IP RNA, small RNA seq

value: Hippocampus

value: 24 hours


title: 2X  2


title: RMK1_RH_66: Mouse, intraamygdala kainic acid (IAKA), 1 hour

description: Ago2 IP RNA, small RNA seq


title: 2X  3


title: 009_CD154Pos_7_AS_NA


title: b_5


title: 47-JPP rep2

city: Burnaby

first: Amy

middle: H.

last: Lee

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

country: Canada

institute: Simon Fraser University

data_processing:
Fastq sequence quality was assessed using FastQC v0.11.6 and MultiQC v1.6
Fastq reads were aligned to the Bos taurus genome using STAR v2.6.1d
Read counts were generated using htseq-count (HTSeq 0.11.2)
Genome_build: Bos taurus genome ARS-UCD1.2 (Ensembl release 95.12)
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads counts per gene for each sample

organism: Bos taurus

source_name: bovine_gutloop_MAP gc86_Jej_PP

growth_protocol: Gut loops were surgically created in 10-14 day old healthy, male Holstein calves and inoculated with PBS or MAP gc86

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen). QC performed using Agilent 2100 Bioanalyzer
mRNA enrichment was done using the NEBNext Poly(A) mRNA magnetic isolation module
Strand-specific cDNA libraries were generated from poly-adenylated mRNA using the KAPA stranded RNA-Seq Library Preparation Kit. Adapters for multiplexing were ligated, followed by amplification and purification using Agencourt Ampure XP beads.

treatment_protocol: Tissues were collected immediately after euthanization and preserved in RNALater

tag: breed

value: Holstein

tag: treatment/infection

value: Mycobacterium avium ssp. Paratuberculosis (MAP) gc86 infection


title: RMK1_RH_029: Mouse, intraamygdala kainic acid (IAKA), 1 hour

description: Ago2 IP RNA, small RNA seq


title: MRP1_RH_24: Rattus norvegicus, perforant pathway stimulation (PPS), 1 hour

description: Ago2 IP RNA, small RNA seq

value: Sprague-Dawley

value: perforant pathway stimulation (PPS)


title: RMK1_RH_030: Mouse, intraamygdala kainic acid (IAKA), 1 hour

description: Ago2 IP RNA, small RNA seq


title: RMK24_RH_022: Mouse, intraamygdala kainic acid (IAKA), 24 hours

description: Ago2 IP RNA, small RNA seq


title: 008_CD154Pos_2_AS_AL

value: Asthmatic & Allergic to HDM


title: 47-JLN rep2

source_name: bovine_gutloop_MAP gc86_Jej_LN


title: 007_CD154Pos_1_AS_AL

value: Blood


title: VMS4W_LH_3: Mouse, pilocarpine (PILO), Chronic, control

description: Ago2 IP RNA, small RNA seq

value: NMRI

value: pilocarpine (PILO)

value: Chronic, control


title: VMS4W_LH_2: Mouse, pilocarpine (PILO), Chronic, control

description: Ago2 IP RNA, small RNA seq


title: 006_CD154Pos_12_AS_NA

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+


title: VMS4W_LH_1: Mouse, pilocarpine (PILO), Chronic, control

description: Ago2 IP RNA, small RNA seq


title: 43-JejLN rep2

value: PBS


title: 42-JPP rep2


title: 43-IleLN rep2


title: VMS_DOFS_LH_3: Mouse, pilocarpine (PILO), Day of first seizure, control

description: Ago2 IP RNA, small RNA seq

value: Day of first seizure, control


title: 003_CD154Pos_9_AS_NA

value: Asthmatic & Non Allergic to HDM


title: 004_CD154Pos_10_AS_NA


title: 42-JLN rep2

value: male


title: VMS_DOFS_LH_2: Mouse, pilocarpine (PILO), Day of first seizure, control

description: Ago2 IP RNA, small RNA seq


title: 002_CD154Pos_8_AS_NA


title: 001_CD154Pos_7_AS_NA


title: 41-JejPP rep2


title: VMS72_LH_5: Mouse, pilocarpine (PILO), 72 hours, control

description: Ago2 IP RNA, small RNA seq

value: 72 hours, control


title: VMS_DOFS_LH_1: Mouse, pilocarpine (PILO), Day of first seizure, control

description: Ago2 IP RNA, small RNA seq

value: Hippocampus


title: 43-JejPP rep2


title: I17-1310-08: NIPBL ChIP clone 2.5 (c2 in manuscript)

city: Rotterdam

first: Eskeatnaf

last: Mulugeta

address: Wytemaweg 80

department: Cell Biology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam (Erasmus MC)

data_processing:
The quality of DNA sequence was investigated using FASTQC (version 0.11.2), and, when necessary trimmomatic (version 0.32) was used to remove low-quality reads and regions. Quality controlled sequence was aligned to Human genome (hg19) using bowtie (version 1.0.0), and samtools (version 0.1.19) was used to remove reads with mapping quality less than 30, and to keep only aligned reads. Duplicated reads were removed, after alignment, using Picard (version 1.97). Peaks were called using MACS (macs 2) and Peaks were filtered using P-value. UCSC tracks were generated after duplicate removal, using HOMER (version 4.3) and deeptools (version 3.0.2). Heatmaps were generated using Deeptools (version 3.0.2) and NGS plot (version 2.61). Peaks were annotated to specific regions using ChIPseeker (Bioconductor package version 1.14.2).
Supplementary_files_format_and_content: bed file, peaks

source_name: HEK293T cells

growth_protocol: Cells were grown in DMEM with 10% FCS and antibiotics (penicillin, streptomycine).

extract_protocol:
Cells at 70–80% confluence were crosslinked with 1% formaldehyde for 10 minutes and quenched with 125 mM glycine. After washing with PBS, cells were resuspended in lysis buffer (50 mM Tris-HCl pH 8.0, 1% SDS, 10 mM EDTA, 1 mM PMSF and Complete Protease Inhibitor (Roche)) and sonicated (Diagenode Bioruptor, Seraing, Belgium) to around 500 bp DNA fragments. Debris were removed by centrifugation and the lysate was diluted 1:4 with IP dilution buffer (20 mM Tris-HCl pH 8.0, 0.15 M NaCl, 2 mM EDTA, 1% TX-100, protease inhibitors) and precleared with Affi-Prep Protein A support beads (Bio-Rad). The respective antibodies were incubated with the lysate overnight at 4ºC, followed by 2 hours incubation at 4ºC with blocked protein A Affiprep beads (Bio-Rad) (blocking solution: 0.1 mg/ml BSA). Beads were washed with washing buffer I (20 mM Tris-HCl pH 8.0, 0.15 M NaCl, 2 mM EDTA, 1% TX-100, 0.1% SDS, 1 mM PMSF), washing buffer II (20 mM Tris-HCl pH 8.0, 0.5 M NaCl, 2 mM EDTA, 1% TX-100, 0.1% SDS, 1 mM PMSF), washing buffer III (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium desoxycholate) and TE-buffer (10 mM Tris-HCl pH 8.0,1 mM EDTA). Beads were eluted twice (25 mM Tris-HCl pH 7.5, 5 mM EDTA, 0.5% SDS) for 20 minutes at 65ºC. The eluates were treated with proteinase K and RNase for 1 hour at 37ºC and decrosslinked at 65ºC overnight. The samples were further purified by phenol-chloroform extraction and ethanol-precipitated. The pellet was dissolved in TE buffer.
For sequencing, the DNA libraries were prepared using the NEXTFlex ChIP-Seq kit (BioO Scientific, Austin, TX, USA). These libraries were sequenced according to the Illumina TruSeq v3 protocol on an Illumina HiSeq2500 sequencer (Illumina, San Diego, CA, USA). Single reads were generated of 50 base pairs in length.

value: HEK293T cells

tag: genotype/variation

value: CRISPR edited cell line


title: 41-JejLN rep2

value: Holstein


title: peripheral blood_HC_rep1-2

type: RNA

city: Nanjing

first: Ming

last: Li

address: NO.138Xianlin Road

institute: Nanjing University of Chinese Medicine

description: LncRNA and mRNA expresssion data from peripheral blood in healthy donors

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 2 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: peripheral blood_HC_rep1-2

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA from peripheral blood was extracted using TRIzol (Invitrogen, USA) according to the protocol of manufacturer. Subsequently, total RNA was evaluated by agarose gel electrophoresis and quantified with a NanoDrop spectrophotometer (NanoDrop, USA).

treatment_protocol: whole blood from RA patients and healthy donors were instantly immersed in liquid nitrogen and preserved at -80 ℃.

value: whole blood

tag: gender

value: female

tag: diagnosis

value: healthy control


title: 005_CD154Pos_11_AS_NA

value: Blood


title: VMS72_LH_4: Mouse, pilocarpine (PILO), 72 hours, control

description: Ago2 IP RNA, small RNA seq

tag: strain

value: NMRI


title: peripheral blood_RA_rep1-2

description: LncRNA and mRNA expresssion data from peripheral blood in RA patients

source_name: peripheral blood_RA_rep1-2

value: rheumatoid arthritis


title: I17-1310-06: Input clone N10 (c1 in manuscript)


title: 41-IlePP rep2

tag: Sex


title: SAMPLE 24: UEC001-009  d0

city: Fort Worth

first: Yu-Chieh

address: 3500 Camp Bowie Blvd

department: Pharmaceutical Sciences

institute: University of North Texas Health Science Center

description:
200638460068_I
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: RSN normalization in R

extract_protocol: RNA was extracted with Ambion MirVana Isolation Kit

value: cerebral organoids, urine epithelial cell derived


title: peripheral blood_HC_rep1-1

source_name: peripheral blood_HC_rep1-1


title: 41-IleLN rep2


title: VMS72_LH_3: Mouse, pilocarpine (PILO), 72 hours, control

description: Ago2 IP RNA, small RNA seq

value: pilocarpine (PILO)


title: SAMPLE 25: UEC001-010  d0

description:
200647720006_E
replicate 1


title: VMS48_LH_6: Mouse, pilocarpine (PILO), 48 hours, control

description: Ago2 IP RNA, small RNA seq

value: 48 hours, control


title: I17-1310-03: Input HEK293T wt

value: unmodified cell line


title: I17-1310-05: NIPBL ChIP clone N10 (c1 in manuscript)


title: 40-IPP rep2

source_name: bovine_gutloop_MAP gc86_Ile_PP

value: Mycobacterium avium ssp. Paratuberculosis (MAP) gc86 infection


title: VMS48_LH_5: Mouse, pilocarpine (PILO), 48 hours, control

description: Ago2 IP RNA, small RNA seq


title: SAMPLE 23: WA09 d0

description:
200723220017_F
replicate 3

source_name: WA09 d0

value: cerebral organoids, WA09 derived


title: 40-ILN rep2

source_name: bovine_gutloop_MAP gc86_Ile_LN

value: male


title: I17-1310-02: NIPBL ChIP HEK293T wt


title: SAMPLE 21: WA09 d80

description:
200757770055_I
replicate 1


title: SAMPLE 20: WA09 d40

description:
200641620005_B
replicate 2


title: VMS24_LH_6: Mouse, pilocarpine (PILO), 24 hours, control

description: Ago2 IP RNA, small RNA seq

value: Hippocampus

value: 24 hours, control


title: peripheral blood_RA_rep1-1

source_name: peripheral blood_RA_rep1-1


title: SAMPLE 19: WA09 d40

description:
200647720006_H
replicate 1


title: SAMPLE 22: WA09 d80

description:
200757770055_D
replicate 2


title: VMS48_LH_4: Mouse, pilocarpine (PILO), 48 hours, control

description: Ago2 IP RNA, small RNA seq


title: 39-JejPP rep2

value: PBS


title: VMS24_LH_5: Mouse, pilocarpine (PILO), 24 hours, control

description: Ago2 IP RNA, small RNA seq


title: 39-JejLN rep2

value: Holstein


title: 39-IleLN rep2


title: VMS24_LH_1: Mouse, pilocarpine (PILO), 24 hours, control

description: Ago2 IP RNA, small RNA seq


title: I17-1066-05: SMC3 ChIP HEK293T wt

value: HEK293T cells


title: 37-JPP rep2


title: VMS1_LH_5: Mouse, pilocarpine (PILO), 1 hour, control

description: Ago2 IP RNA, small RNA seq

value: 1 hour, control


title: I17-1066-08: Input clone N10 (c1 in manuscript)

value: CRISPR edited cell line


title: SAMPLE 16: WA09 d15

description:
200647720006_D
replicate 2


title: VMS1_LH_4: Mouse, pilocarpine (PILO), 1 hour, control

description: Ago2 IP RNA, small RNA seq


title: SAMPLE 17: WA09 d20

description:
200647720011_B
replicate 1


title: WS-N2A (scrambled #3)

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
TrimGalore for qc and adapter trimming
STAR Aligner for read alignment
Cufflinks for differential expression analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Results from Cuffdiff

growth_protocol: 143B osteosarcoma cells were cultured in α-MEM supplemented with 10% serum, antibiotics and glutamine (complete media) were cultured using standard protocols. Cells were passaged upon reaching >80% confluency at 10^6 cells per 100mm dish

extract_protocol:
Cells were scraped in TRIzol reagent total RNA was isolated using phenol-chloroform extraction using Invitrogen PureLink RNA Mini Kit (#12183018A)
RNA sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina). This protocol provides strand specific data while simultaneously removing both cytoplasmic and mitochondrial rRNA. Libraries were sequenced on the HiSeq 2500 instruments and 50 million 50 base pair single end reads were produced per sample. Data was extracted, de-convoluted based on dual index reads and analyzed using CLC Genomics Workbench software (Qiagen).

treatment_protocol: Cells were lifted and plated at 4 x 10^5 cells per 100mm dishes, and cultured overnight. Media was changed to complete media containing hexadimethrine bromide and infected with lentiviral shJAB1 particles at MOI = 5. The following day media was changed to complete media, and after 24hrs cells were selected after 72hrs in complete media containing 0.5µg/mL puromycin.

value: Immortalized

value: Bone osteosarcoma

tag: passage

tag: treatment

value: shRNA scrambled control


title: I17-1066-04: Input HEK293T wt


title: WS-N1B (scrambled #2)


title: VMS1_LH_2: Mouse, pilocarpine (PILO), 1 hour, control

description: Ago2 IP RNA, small RNA seq

value: NMRI


title: SAMPLE 18: WA09 d20

description:
200641620077_J
replicate 2


title: VMP4W_LH_3: Mouse, pilocarpine (PILO), Chronic

description: Ago2 IP RNA, small RNA seq

value: pilocarpine (PILO)

value: Chronic


title: SAMPLE 13: WA09 d6

description:
200638460067_H
replicate 1

source_name: WA09 d6


title: WS-N1A (scrambled #1)


title: SAMPLE 15: WA09 d15

description:
200641620005_E
replicate 1


title: I17-1066-01: SMC3 ChIP clone N10 (c1 in manuscript)


title: SAMPLE 14: WA09 d6

description:
200647720011_H
replicate 2


title: 37-JLN rep2

tag: age


title: WS-D2 (KD #2)

value: shRNA silencing


title: 35-JLN rep2

value: Mycobacterium avium ssp. Paratuberculosis (MAP) gc86 infection


title: VMP4W_LH_2: Mouse, pilocarpine (PILO), Chronic

description: Ago2 IP RNA, small RNA seq


title: VMP4W_LH_1: Mouse, pilocarpine (PILO), Chronic

description: Ago2 IP RNA, small RNA seq


title: 36-IPP rep2


title: 34-ILN rep2


title: WS-E1 (KD #3)


title: SAMPLE 12: WA09 d0

description:
200647720006_C
replicate 2

value: cerebral organoids, WA09 derived


title: SAMPLE 10: UEC715-501  d80

description:
200757770055_J
replicate 2

value: cerebral organoids, urine epithelial cell derived


title: 35-JPP rep2

value: male


title: Input in ERRg KO2

city: Philadelphia

first: Tomoya

last: Sakamoto

state: PA

address: Smilow Center for Translational Research 11th FL (Room 11-172) 3400 Civic Center Blvd Bldg 421

department: Cardiovascular Institute

institute: University of Pennsylvania

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie2
Peaks were called using findPeaks command in the Homer package
Genome_build: hg38

source_name: ERRgamma KO hiPSC-CMs

growth_protocol: hiPSC were cultured in TeSR-E8 (StemCell Technologies) and differentiated toward cardiomyocytes with the method published by Dr. Joseph Wu (Nat Methods. 2014 Aug;11(8):855-60. PMID: 24930130). ERRg KO iPSCs were generated by pSpCas9n(BB)-2A-Puro plasmids (PX462, Addgene plasmid # 48141) containing distinct sgRNAs against ERRg.

extract_protocol:
Lysates were clarified from sonicated nuclei and ERRg-DNA complexes were isolated with the antibody.
Libraries were prepared according to NuGen The Ovation® Ultralow Library System V2 (Part# 0801-0303) with 2 mg DNA sample.

tag: genotype

value: ERRgamma KO

value: hiPSC-derived cardioyocytes

tag: day

tag: chip antibody


title: VMP_DOFS_LH_2: Mouse, pilocarpine (PILO), Day of first seizure

description: Ago2 IP RNA, small RNA seq

source_name: Hippocampus

value: Hippocampus

tag: model

tag: period

value: Day of first seizure


title: SAMPLE 9: UEC715-501  d80

description:
200761430033_J
replicate 1

tag: cell type


title: SAMPLE 11: WA09 d0

description:
200641620077_G
replicate 1


title: SAMPLE 8: UEC715-501  d40

description:
200757770055_C
replicate 2


title: SAMPLE 7: UEC715-501  d40

description:
200757770055_L
replicate 1


title: 33-JejPP rep2

value: Holstein

value: PBS

tag: tissue


title: Input in ERRg KO1


title: VMP_DOFS_LH_1: Mouse, pilocarpine (PILO), Day of first seizure

description: Ago2 IP RNA, small RNA seq


title: 33-JejLN rep2

tag: breed


title: Input in WT2

source_name: Wild type hiPSC-CMs

value: wild type


title: WS-D1 (KD #1)

value: Immortalized

value: Bone osteosarcoma


title: VMP72_LH_5: Mouse, pilocarpine (PILO), 72 hours

description: Ago2 IP RNA, small RNA seq

value: NMRI

value: 72 hours


title: Input in WT1


title: 33-IlePP rep2

tag: treatment/infection


title: VMP72_LH_3: Mouse, pilocarpine (PILO), 72 hours

description: Ago2 IP RNA, small RNA seq

value: pilocarpine (PILO)


title: ERRg ChIP-Seq in ERRg KO2

value: ERRg (generated with collaborator)


title: 31-JejPP rep2


title: 33-IleLN rep2


title: SAMPLE 5: UEC715-501  d15

description:
200761430033_H
replicate 1


title: ERRg ChIP-Seq in ERRg KO1


title: VMP72_LH_1: Mouse, pilocarpine (PILO), 72 hours

description: Ago2 IP RNA, small RNA seq


title: TT2 mESC - input DNA

city: Villeurbanne

first: rita

last: rebollo

address: Bat. 406/Louis Pasteur, 20, avenue Albert Einstein

country: France

institute: BF2i UMR INRA-INSA de Lyon

data_processing:
Raw reads were filtered for low quality, and adapter sequences were trimmed with Trimmomatic
Clean reads were mapped against the reference genome C57BL/6J, (mm10, Accession: GCA_000001635.6/GRCm38.p4) with Bowtie2
We excluded reads with multiple mappings and reads that aligned with  more than 2 mismatches.
Peak calling was performed for each bowtie2 bam file against their controls using MACS2 software and FDR cutoff of 0.01
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraphs were generated in MACS2
Peak files refer to narrow peaks generated in MACS2

source_name: TT2 mouse embryonic stem cells

growth_protocol: C3H/HeJ mES cells (Jackson laboratory, C3H/HeJ-PRX-C3H #2) were cultured on irradiated feeders (MEFs) (CF-1 mouse embryonic fibroblasts), and maintained on mES cell media and passaged every day. TT2 ES cells (C57BL/6 x CBA F1) were cultured on mES cell media on gelatinized plates and passaged every 48–72 hours. mES cell media is composed of DMEM supplemented with 15% FBS (HyClone), 20 mM HEPES, 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 100 units/ml penicillin, 0.05 mM streptomycin, leukemia inhibitory factor (LIF) and 2mM glutamine. MEFs were cultured on DMEM supplemented with 10% FBS, and irradiated at early passages.

extract_protocol:
Chromatin immunoprecipitation was performed as previously described (Karimi et al Cell Stem Cell 2011) . Ten million TT2 and feeder depleted C3H/HeJ cells were harvested for nChIP-seq using antibodies against H3K4me3 (Abcam ab1012, 5 uL) and H3K9me3 (Active Motif 39161, 5 μl).
Illumina library construction was performed as described in Brind'Amour et al, Nature communications, 2015.

value: embryonic stem cells


title: VMP48_LH_6: Mouse, pilocarpine (PILO), 48 hours

description: Ago2 IP RNA, small RNA seq

value: 48 hours


title: 31-JejLN rep2


title: VMP48_LH_5: Mouse, pilocarpine (PILO), 48 hours

description: Ago2 IP RNA, small RNA seq


title: ERRg ChIP-Seq in WT2


title: 31-IlePP rep2


title: TT2 mESC - H3K4me3

value: H3K4me3 (Abcam ab1012, 5L)


title: SAMPLE 4: UEC715-501  d6

description:
200761430033_C
replicate 2

value: cerebral organoids, urine epithelial cell derived


title: SAMPLE 2: UEC715-501  d0

description:
200761430033_F
replicate 2


title: SAMPLE 1: UEC715-501  d0

description:
200761430033_K
replicate 1


title: VMP48_LH_4: Mouse, pilocarpine (PILO), 48 hours

description: Ago2 IP RNA, small RNA seq


title: ERRg ChIP-Seq in WT1


title: C3H/HeJ mESC - H3K9me3

source_name: C3H/HeJ mouse embryonic stem cells

value: H3K9me3 (Active Motif 39161, 5 μl)


title: 31-IleLN rep2

value: male


title: VMP24_LH_6: Mouse, pilocarpine (PILO), 24 hours

description: Ago2 IP RNA, small RNA seq

value: Hippocampus

value: 24 hours


title: 29-JPP rep2

value: Holstein

value: Mycobacterium avium ssp. Paratuberculosis (MAP) gc86 infection


title: C3H/HeJ mESC - H3K4me3


title: 28-IPP rep2


title: VMP24_LH_4: Mouse, pilocarpine (PILO), 24 hours

description: Ago2 IP RNA, small RNA seq


title: MRP8_RH_20: Rat, perforant pathway stimulation (PPS), Control

data_processing:
Sequencing data were quality controlled and adapter trimmed using Trim Galore
Filtered data were mapped to the rat genome Rn6 using TopHat2
Cufflinks was used to assemble transcripts from the mapped reads guided by gene annotation from Ensembl Release 87
Cuffmerge, cuffquant and cuffdiff (part of the cufflinks software package) were used to quantify transcript abundance in each sample and to perform differential expression analysis of genes and gene isoforms
Genome_build: rn6
Supplementary_files_format_and_content: Output from cuffdiff "gene_exp.diff". This shows gene names, expression and significance metrics

extract_protocol:
RNA is purified from frozen hippocampal tissue using Trizol
rRNA depleted using the Ribo-Zero Magnetic Kit. Libraries generated using ScriptSeq v2 kit (Illumina)

value: Sprague-Dawley

value: perforant pathway stimulation (PPS)

value: Control

value: hippocampus


title: 29-JLN rep2


title: SAMPLE 3: UEC715-501  d6

description:
200757770055_B
replicate 1


title: VMP24_LH_5: Mouse, pilocarpine (PILO), 24 hours

description: Ago2 IP RNA, small RNA seq

value: NMRI


title: RNAseq WT shScram rep 3

city: Seattle

first: Elise

middle: Y

last: Cai

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

description:
total mRNA
tot_WS3
RNAseq in vivo

data_processing:
fastx_clipper (-a AGATCGGAAGAGCACACGTCT)( -l 20) and fastx_trimmer were used to clip adapter and trim
bowtie to align to 45SpreRNA, norRNA reads were then used to align
tophat2 to align to mm10
raw counts for CDS were obtained using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: .txt file, raw counts

source_name: Epidermal basal cells

extract_protocol:
E18.5 epidermis extracted as described in Sendoel et al, Nature, 2017: CHX treatment, followed by dispase/CHX treatment to separate epidermis from dermis, trypsin/CHX to obtain single cell suspension.
Ribosome profiling protocol as described in Ingolia et al, Nature protocols, 2012.

treatment_protocol: E9.5 HrasG12V and WT mouse epidermis was transduced by in utero injection with shScrambled control or shEif2b5

value: Epidermis

value: WT


title: MRP8_RH_31: Rat, perforant pathway stimulation (PPS), Control


title: MRP8_RH_17: Rat, perforant pathway stimulation (PPS), Control


title: C3H/HeJ mESC - input DNA

value: embryonic stem cells


title: MRP7_RH_75: Rat, perforant pathway stimulation (PPS), Chronic

value: Chronic


title: 28-ILN rep2


title: RNAseq WT shScram rep 2

description:
total mRNA
tot_WS2
RNAseq in vivo


title: VMP1_LH_6: Mouse, pilocarpine (PILO), 1 hour

description: Ago2 IP RNA, small RNA seq

value: pilocarpine (PILO)

value: 1 hour


title: MRP7_RH_43: Rat, perforant pathway stimulation (PPS), Chronic


title: RNAseq WT shScram rep 1

description:
total mRNA
tot_WS1
RNAseq in vivo


title: VMP1_LH_5: Mouse, pilocarpine (PILO), 1 hour

description: Ago2 IP RNA, small RNA seq


title: MRP7_RH_37: Rat, perforant pathway stimulation (PPS), Chronic


title: 47-JPP rep1

source_name: bovine_gutloop_MAP gc86_Jej_PP


title: VMP1_LH_4: Mouse, pilocarpine (PILO), 1 hour

description: Ago2 IP RNA, small RNA seq


title: RNAseq Hras shScram rep 3

description:
total mRNA
tot_HS3
RNAseq in vivo


title: RNAseq Hras shScram rep 2

description:
total mRNA
tot_HS2
RNAseq in vivo


title: 16-WGE200x-48h-4

city: Morgantown

first: Nik

last: Kovinich

address: 1194 Evansdale Drive

department: Plant and Soil Sciences

institute: West Virginia University

data_processing:
QC checks were conducted upon receiving the raw data from the sequencing facility using FastQC software
Ribosomal RNA (rRNA) contamination, adapter sequences and/or low expressed genes were filtered out from the raw high-throughput RNA Sequencing data
clean reads were mapped/aligned to soybean (Glycine max) reference genome (Gmax_275_V2.0.fa, https://phytozome.jgi.doe.gov/pz/portal.html) using STAR RNA-seq Aligner with default parameters based on the current gene annotation
Only the paired mapped reads were considered for further analyses and the number of reads per gene was calculated using Feature Counts to count only reads which mapped concordantly
Differentially expressed genes (DEGs) were identified using DESeq2 package which is based in Negative Binomial Distribution
Multiple hypothesis correction was carried out to obtain an adjusted P value at 0.05 with Benjamini Hochberg procedure which is a powerful tool to decrease the false discovery rate (FDR). Principle component analysis, heatmap and clustering of the samples were also conducted to check the robustness of the analysis
Genome_build: Gmax_275_V2.0.fa, https://phytozome.jgi.doe.gov/pz/portal.html
Supplementary_files_format_and_content: Microsoft Excel Worksheet, DeSeq results annotated

source_name: seed

extract_protocol:
Total RNA from soybean seeds was extracted using the Spectrum Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO, USA) following the manufacturer’s protocol with some modification as described previously (Farrell et al., 2017).
The mRNA stranded library prep kit from KAPA Biosystems and 750 ng of total RNA were used to build each library following manufacturers recommended protocol with nine cycles of PCR.
RNA-seq: 100 bp paired-end reads were generated with the Illumina HiSeq1500 system.

tag: cultivar

value: WGE

tag: hours after treatment

value: seed


title: 47-JLN rep1

source_name: bovine_gutloop_MAP gc86_Jej_LN

value: male


title: R243_N1_10

source_name: Immature cotyledon, 10-25mg fresh weight of whole seed

value: Immature cotyledon

value: Jack mutant

tag: transgenic status

value: Negative

tag: generation


title: 15-WGE200x-48h-3


title: R239_A1_10


title: RNAseq Hras shScram rep 1

description:
total mRNA
tot_HS1
RNAseq in vivo

tag: strain


title: R241_J3_10

value: Jack

value: Negative (control)


title: RNAseq Hras shEif2b5 rep 3

description:
total mRNA
tot-HE3
RNAseq in vivo


title: 13-WGE200x-48h-1


title: 14-WGE200x-48h-2


title: RNAseq Hras shEif2b5 rep 2

description:
total mRNA
tot-HE2
RNAseq in vivo


title: R224_N7_10

value: Positive


title: 42-JPP rep1

value: Holstein

tag: Sex

value: Mycobacterium avium ssp. Paratuberculosis (MAP) gc86 infection


title: RNAseq Hras shEif2b5 rep 1

description:
total mRNA
tot-HE1
RNAseq in vivo

value: Epidermis


title: R223_N5_10


title: 42-JLN rep1


title: 12-H2O-48h-4_S59

tag: treatment


title: 43-IleLN rep1

tag: age

value: PBS


title: R222_A8_10


title: 10-H2O-48h-2_S58


title: 43-JejPP rep1


title: 41-JejPP rep1


title: 41-JejLN rep1


title: R221_A4_10


title: Rib. Prof. WT shScram rep 3

description:
Ribosome footprint
RP_WS3
Ribosome profiling in vivo

tag: genotype

value: WT


title: Rib. Prof. WT shScram rep 2

description:
Ribosome footprint
RP_WS2
Ribosome profiling in vivo


title: 43-JejLN rep1


title: 36-ILN rep2


title: Rib. Prof. WT shScram rep 1

description:
Ribosome footprint
RP_WS1
Ribosome profiling in vivo


title: VMP_DOFS_LH_3: Mouse, pilocarpine (PILO), Day of first seizure

description: Ago2 IP RNA, small RNA seq

value: NMRI

value: Hippocampus

value: Day of first seizure


title: 9-H2O-48h-1_S52


title: 41-IlePP rep1


title: HR-W82-WGE200x1d-4_S8

source_name: hairy root

value: WGE

value: hairy root


title: R226_488_10


title: R225_487_10


title: 41-IleLN rep1

value: male


title: Rib. Prof. Hras shScram rep 2

description:
Ribosome footprint
RP_HS2
Ribosome profiling in vivo


title: 11-H2O-48h-3_S53

value: seed


title: HR-W82-WGE200x1d-3_S7


title: R244_N3_100

source_name: Immature cotyledon, 100-200mg fresh weight of whole seed

value: Immature cotyledon

value: Jack mutant


title: HR-W82-WGE200x1d-2_S6


title: Rib. Prof. Hras shScram rep 1

description:
Ribosome footprint
RP_HS1
Ribosome profiling in vivo


title: R240_A1_100

value: Negative


title: 40-IPP rep1

source_name: bovine_gutloop_MAP gc86_Ile_PP


title: HR-W82-WGE200x1d-1_S5


title: 40-ILN rep1


title: Rib. Prof. Hras shEif2b5 rep 3

description:
Ribosome footprint
RP-HE3
Ribosome profiling in vivo


title: R242_J3_100

value: Jack

value: Negative (control)


title: 39-JejPP rep1

value: Holstein


title: HR-W82-H20-1d-4_S4


title: HR-W82-H20-1d-3_S3


title: Rib. Prof. Hras shEif2b5 rep 2

description:
Ribosome footprint
RP-HE2
Ribosome profiling in vivo


title: R230_N7_100

value: Positive


title: Rib. Prof. Hras shEif2b5 rep 1

description:
Ribosome footprint
RP-HE1
Ribosome profiling in vivo

value: Epidermis


title: Rib. Prof. Hras shScram rep 3

description:
Ribosome footprint
RP_HS3
Ribosome profiling in vivo


title: HR-W82-H20-1d-2_S2


title: R229_N5_100


title: 39-IleLN rep1

value: PBS


title: 37-JPP rep1

value: Mycobacterium avium ssp. Paratuberculosis (MAP) gc86 infection


title: pks1-deuteron-2

city: Washington

first: Zachary

last: Schultzhaus

state: DC

address: 4555 Overlook Avenue SW

institute: Naval Research Laboratory

data_processing:
Used Salmon version 0.8.1, with default parameters, for transcript alignnment and quantification using an index prepared from the Exophiala dermatitidis transcriptome obtained from Mycocosm (https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Exode1)
Used DEseq2 from the Bioconductor software package (version 3.0, default parameters) on RStudio (version 3.1) to perform  differential expression analysis, which provided fold change data and significance values for each transcript.
Supplementary_files_format_and_content: quant.sf.txt (Salmon_output)
Genome_build: https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Exode1

organism: Exophiala dermatitidis

source_name: pks1 deuteron irradiated_fungal cells

growth_protocol: Fungal cells grew in YPD for 48 hours at 30C

extract_protocol:
RiboPure™ RNA Purification Kit for yeast (ThermoFisher)
iIllumina RNA-seq library standard protocol

treatment_protocol: Cells were irradiated with 1000 Gy gamma radiation (Co60)

value: pks1 mutant

value: deuteron irradiated


title: R228_A6_100


title: HR-W82-H20-1d-1_S1


title: R227_A4_100


title: pks1-deuteron-1


title: pks1-deuteron-control-2

source_name: pks1 deuteron control_fungal cells

value: deuteron control


title: MMC-PLUS-3

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description: mitomyclin C (MMC) exposed

data_processing:
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1).
The reference genome for the Acinetobacter baumannii strain ATCC 17978 reference genome and two corresponding plasmids were downloaded from NCBI and stored as Ab.fa. The fasta headers for the three sequences were updated to “chromosome”, “pAB1” and “pAB2” to correspond to gene gtf files. The link to the reference genome and two plasmids are: http://www.ncbi.nlm.nih.gov/nuccore/CP000521 http://www.ncbi.nlm.nih.gov/nuccore/CP000522 http://www.ncbi.nlm.nih.gov/nuccore/CP000523.
A gene transfer format (GTF) annotation file for the Acinetobacter baumannii strain ATCC 17978 reference genome was downloaded from the Ensembl ftp site: ftp://ftp.ensemblgenomes.org/pub/release-26/bacteria//gtf/bacteria_1_collection/acinetobacter_baumannii_atcc_17978/.
Raw sequencing reads for each sample were aligned to the Acinetobacter baumannii genome using STAR versioon STAR_2.4.2a allowing for multi-mapped reads.
Differentially expressed genes were determined using cuffdiff v2.2.1.
Genome_build: ATCC 17978
Supplementary_files_format_and_content: The processed data file genes.fpkm_table contains the FPKM values for each sample normalized using reads mapped by STAR and normalized using cuffnorm.

organism: Acinetobacter baumannii ATCC 17978

source_name: purchased bacterial culture

growth_protocol: 3 ml overnight culture, grown at 37C at 250 rpm, was diluted 1:25 into 5 ml fresh minimal media+10uM succinate, and grown with shaking for two hours.

extract_protocol:
RNA extracted with Epicentre MasterPure RNA Purification kit. Further removal of contaminating DNA was performed using the Ambion DNA-free rigorous DNase treatment.
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gram-Negative Bacteria ribosomal depletion.

treatment_protocol: After two hours' growth, the culture was split and had 2 ug/mL mitomycin C (MMC) added to one sub-culture, and the other sub-culture had 0 MMC exposure.

value: ddrR::lacZKanR mutant


title: R232_488_100

data_processing:
Standard Illumina pipeline
Alignments of mRNA sequences to all 88,647 Glyma models, including splice variants, from the Williams 82 reference genome of G. max (Phytozome, Joint Genome Institutes; Wm82.a2.v1) were performed using the Bowtie program v.1 (Langmead et al., 2009).
Transcriptome data were normalized in RPKM (reads per kilobase of gene model size per million mapped reads) (Mortazavi et al., 2008).
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: One Excel file with RPKM values

extract_protocol:
Total RNA was extracted from tissues using phenol:chloroform and a lithium chloride precipitation (Gonzalez and Vodkin 2007). Sequencing was performed by the Keck Center (University of Illinois) using an Illumina HiSeq2500 or HiSeq4000.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: 37-JLN rep1


title: MMC-PLUS-2

description: mitomyclin C (MMC) exposed


title: pks1-deuteron-control-1


title: 36-ILN rep1

source_name: bovine_gutloop_MAP gc86_Ile_LN


title: 39-JejLN rep1


title: R231_487_100


title: MMC-PLUS-1

description: mitomyclin C (MMC) exposed


title: pks1-proton-2

source_name: pks1 alpha irradiated_fungal cells

value: alpha irradiated


title: pks1-proton-1

source_name: pks1 proton irradiated_fungal cells

value: proton irradiated


title: 4X

description: methylation levels for each genomic site in 4X

data_processing:
The reads were trimmed using FASTX-Toolkit (version 0.11.5)
The clean reads were mapped to the grape genome by usingBimark (version 0.19) with default parameters.
The methylation level of individual cytosine was calculated by the ratio of mC and the total cytosines [mC/(mC+un-mC)]
Genome_build: 12X grape genome of IGGP
Supplementary_files_format_and_content: tab-delimited text file include methylation levels for each site

source_name: tip buds

extract_protocol:
The total DNA of 2X and 4X were extracted by using a Plant Genome DNA Purification Kit (Qiagen)
The total DNA were sent to Novogene (Beijing, China) for bisulfite treatment, library preparation and sent to Novogene (Beijing, China) for bisulfite treatment, library preparationfollow illumina instruction.

tag: genome duplication


title: MMC-MINUS-3

description: control


title: 35-JLN rep1

value: male


title: 35-JPP rep1


title: MMC-MINUS-2

description: control


title: pks1-alpha-2


title: 34-IPP rep1


title: pks1-alpha-1


title: 34-IPP rep2


title: 36-IPP rep1


title: SAMPLE 6: UEC715-501  d15

last: Wang

description:
200757770055_F
replicate 2

value: cerebral organoids, urine epithelial cell derived


title: 34-ILN rep1


title: 33-JejPP rep1


title: pks1-control-1

source_name: pks1 control_fungal cells

value: control


title: WT-deuteron-2

source_name: wild type deuteron irradiated_fungal cells

value: wild type

tag: strain info.


title: 2X

description: methylation levels for each genomic site in 2X


title: pks1-control-2


title: 33-JejLN rep1


title: 33-IlePP rep1


title: WT-deuteron-1


title: MMC-MINUS-1

description: control


title: 33-IleLN rep1


title: WT-deuteron-control-2

source_name: wild type deuteron control_fungal cells


title: 31-JejPP rep1


title: E5ind_dmso_5-10_rep2

city: Barcelona

first: Oriol

last: Llorà-Batlle

address: Carrer Rosselló 153, 1st floor

country: Spain

institute: ISGlobal

hyb_protocol: Hybridization performed as previously described (Painter, H. et al., 2013. PMID: 22990780).

scan_protocol: Microarrays images were obtained using the Agilent G2505C Microarray Scanner.

data_processing: Initial data processing of microarray data, including normalization, was performed using the GE2_1105_Oct12 extraction protocol in Agilent Feature Extraction 11.5.1.1 software. The next steps of the analysis were performed using Bioconductor in an R environment (R version 3.5.3). For each individual microarray, we calculated Cy3 and Cy5 background signal as the median of the 100 lowest signal probes for each channel. Probes with both Cy3 and Cy5 signals below three times the array background were excluded. Gene level log2(Cy5/Cy3) values and statistical estimation of parasite age were computed as described (Rovira-Graells et al., 2012). Genes with missing values or genes that in all samples had expression values within the lowest 20th percentile of intensity (Cy5 channel) were excluded from downstream analysis, including identification of differentially expressed genes, because differences in genes expressed at near-background levels are of low confidence.

organism: Plasmodium falciparum

source_name: E5ind, DMSO, 5-10 hpi

label_protocol: Test sample, Cy5; reference pool, Cy3. As previously described (Painter, H. et al., 2013. PMID: 22990780)

growth_protocol: Parasites were cultured in B+ erythrocytes at a 3 % haematocrit under standard culture conditions in RPMI-based media containing Albumax II without human serum, in a 5% CO2, 3% O2, balance N2 atmosphere. WR99210 selection was always maintained until the sychronization of the cultures.  Tight synchronization (5 h age window) was achieved by Percoll purification followed by sorbitol treatment 5 h later.

extract_protocol: RNA was purified using the TRIzol method following the manufacturer intructions.

treatment_protocol: Tightly synchronized E5ind cultures (0-5 h) were induced with 10 nM rapamycin (Rapa) for 1 h at 25-30 hpi or with DMSO as control (Dmso).

value: DMSO

source_name: E5 wild-type and E5ind reference pool

value: E5 and E5ind

tag: time-point

value: 6 samples of synchronized cultures covering the whole asexual cycle.


title: E5ind_dmso_15-20_rep2

source_name: E5ind, DMSO, 15-20 hpi


title: 31-JejLN rep1

value: Holstein


title: E5ind_dmso_40-45_rep2

source_name: E5ind, DMSO, 40-45 hpi


title: 9th week (Day60-1)

city: Tsukuba

first: Kenichiro

last: Shimatani

state: Ibaraki

address: 21, Miyukigaoka

country: Japan

institute: Astellas Pharma Inc

hyb_protocol: Following fragmentation, 2 μg of Single-Stranded cDNA was hybridized for 16 hr at 45˚C on Clariom S Array, Human. Arrays was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: Clariom S array was scanned using GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console Software 1.4 offered SST-RMA for gene level analysis using Thermo Fisher Scientific default analysis settings.

label: biotin

source_name: Gastrocnemius muscles of NOG mice at 9th week after ischemia operation

label_protocol: Biotinylated cDNA was prepared from 100 ng total RNA using GeneChip WT PLUS Reagent Kit（Thermo Fisher Scientific) following the manufacturer's instructions.

growth_protocol: Muscles were extracted at 1st week and 9th week after the hindlimb ischemia operation.

extract_protocol: Gastrocnemius muscles were homogenized with TissueLyser II (Qiagen) in RLT Buffer (Qiagen). The homogenates were centrifuged and the resulting supernatants were subjected to RNA purification using an RNeasy Fibrous Tissue Mini Kit (Qiagen).

treatment_protocol: Muscles were soaked in RLT buffer(Qiagen)

value: Gastrocnemius muscle

value: NOG mouse

tag: time

value: 9th week


title: E5ind_rapa_15-20_rep2

source_name: E5ind, rapa., 15-20 hpi

value: Rapamycin


title: 9th week (Day60-2)


title: 1st week (Day7-3)

source_name: Gastrocnemius muscles of NOG mice at 1st week after ischemia operation

value: 1st week


title: E5ind_rapa_5-10_rep2

source_name: E5ind, rapa., 5-10 hpi


title: 1st week (Day7-1)


title: 1st week (Day7-2)


title: Control-3

source_name: Intact gastrocnemius muscle

value: Control


title: OX_pBABE_BHLHE40-AS1_rep3

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: OX

hyb_protocol: 16 h to Affymetrix Human Clariom D arrays per manufacturer's protocol

scan_protocol: Affymetrix Scanner 3000 7G using AGCC software.

data_processing: CEL files were summarized using the SST RMA algorithm in Transcriptome Analysis Console v4.0.1.36 (Affymetrix) and the normalized data were subjected to one-way ANOVA with a Benjamin Hochberg False Discovery Rate correction included (p<0.05). A 2-fold change was used to select entities that were statistically and differentially expressed between the two conditions.

source_name: OX pBABE BHLHE40-AS1

label_protocol: Affymetrix Whole Transcript Sense Target labeling protocol

growth_protocol: MCF10A-pBABE and MCF10A-BHLHE40-AS1 cells were grown in MCF10A media for 48 hours prior to total RNA extraction

extract_protocol: Total RNA was extracted using Omega Bio-Tek E.Z.N.A.® Total RNA Kit according to the manufacturer's instructions.

treatment_protocol: The cell lines were treated identically, grown in standard growth media for 48 hours.

tag: sample type


title: WT-proton-2

source_name: wilde type proton irradiated_fungal cells


title: 31-IlePP rep1

data_processing:
Fastq sequence quality was assessed using FastQC v0.11.6 and MultiQC v1.6
Fastq reads were aligned to the Bos taurus genome using STAR v2.6.1d
Read counts were generated using htseq-count (HTSeq 0.11.2)
Genome_build: Bos taurus genome ARS-UCD1.2 (Ensembl release 95.12)
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads counts per gene for each sample

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen). QC performed using Agilent 2100 Bioanalyzer
mRNA enrichment was done using the NEBNext Poly(A) mRNA magnetic isolation module
Strand-specific cDNA libraries were generated from poly-adenylated mRNA using the KAPA stranded RNA-Seq Library Preparation Kit. Adapters for multiplexing were ligated, followed by amplification and purification using Agencourt Ampure XP beads.

value: PBS

tag: tissue


title: Control-2


title: 29-JPP rep1

source_name: bovine_gutloop_MAP gc86_Jej_PP

tag: breed

value: Mycobacterium avium ssp. Paratuberculosis (MAP) gc86 infection


title: E5ind_rapa_40-45_rep2

source_name: E5ind, rapa., 40-45 hpi


title: Control-1


title: OX_pBABE_BHLHE40-AS1_rep2

description: OX


title: WT-proton-1

value: proton irradiated


title: OX_pBABE_BHLHE40-AS1_rep1

description: OX


title: WT-alpha-1

source_name: wilde type alpha irradiated_fungal cells

value: alpha irradiated


title: WT-alpha-2


title: WT-deuteron-control-1

value: deuteron control


title: 29-JLN rep1

source_name: bovine_gutloop_MAP gc86_Jej_LN

value: male

tag: treatment/infection


title: WT-control-2

source_name: wild type control_fungal cells

value: wild type

value: control


title: Control_pBABE_rep3

description: control

source_name: Control pBABE


title: Control_pBABE_rep2

description: control


title: 28-IPP rep1

source_name: bovine_gutloop_MAP gc86_Ile_PP


title: E5ind_dmso_5-10_rep1

source_name: E5ind, DMSO, 5-10 hpi

value: DMSO

source_name: E5 wild-type and E5ind reference pool

value: E5 and E5ind


title: Control_pBABE_rep1

description: control


title: 31-IleLN rep1

value: Holstein


title: WT-control-1


title: 28-ILN rep1

source_name: bovine_gutloop_MAP gc86_Ile_LN


title: E5ind_rapa_15-20_rep1

value: 6 samples of synchronized cultures covering the whole asexual cycle.


title: E5ind_dmso_15-20_rep1

source_name: E5ind, DMSO, 15-20 hpi


title: E5ind_rapa_5-10_rep1


title: E5ind_dmso_40-45_rep1

source_name: E5ind, DMSO, 40-45 hpi


title: BJ APH r2 Late S

status: Public on Jun 09 2020

city: Jerusalem

first: Dan

last: Sarni

address: Givart Ram

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Reads are mapped to corresponding genome (HG38) using bowtie2.
Coverage data are calculated from mapped reads using samtools and bedtools
Base 2 log of early to late coverage ratio was calculated in 5kb windows
Log 2 ratio data were quantile normalized using R package preprocessCore
Data were loess smoothed and binned into 5kb windows
Genome_build: HG38
Supplementary_files_format_and_content: processed data are 5kb windows in HG38 genome.

source_name: BJ hTERT cell line

growth_protocol: Human foreskin fibroblasts BJ-hTERT cells were grown in DMEM supplemented with 10% fetal bovine serum, 1000,000 U l-1 penicillin and 100 mg l-1 streptomycin. The cells were tested and found negative for mycoplasma.

extract_protocol:
Genome-wide replication timing profiles were constructed as previously described (Marchal et al., 2018). Briefly, cells were pulse labeled with BrdU and separated into early and late S-phase fractions by flow cytometry.  From the total gemnomic DNA extracted from each fraction, BrdU-labeled DNA was enriched using anti-BrdU immunoprecipitation.
Sequencing libraries of BrdU-labeled DNA from early and late fractions were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).

treatment_protocol: Cells were treated with 200 nM Aphidicolin in growth media for 24 hours prior to BrdU labeling. BrdU was added to the media to a final concentration of 100 micomolar and incubated at 37°C for 2 hours.

tag: cell line

value: BJ hTERT cell line

tag: s phase fraction

value: Late S phase fraction

tag: replicate

value: Aphidicolin


title: BJ NT r4 Late S

value: Non-treated


title: BJ APH r1 Late S


title: BJ APH r1 Early S

value: Early S phase fraction


title: BJ APH r4 Early S


title: BJ APH r3 Late S


title: BJ APH r3 Early S


title: BJ NT r4 Early S


title: BJ APH r2 Early S


title: BJ APH r4 Late S


title: BJ NT r3 Late S


title: BJ NT r3 Early S


title: BJ NT r1 Late S


title: BJ NT r2 Early S


title: myeloid progenitor cells, MT-HX-2

city: Tokyo

first: Shuhei

last: Asada

address: 4-6-1 Shirokanedai, Minato-ku

department: Cellular Therapy

institute: Institute of Medical Science, The University of Tokyo

description: ASXL1-MT+HHEX rep2

data_processing:
These libraries were sequenced on the Illumina HiSeq2500 System with 2×125 nucleotide paired-end reads according to the manufacturer’s protocol.
Derived reads were processed using cutadapt(1.8.1) to remove Illumina adaptor sequence.
Quality of reads was assessed using FastQC.
Processed reads were aligned to human hg19 reference transcripts using TopHat(2.1.1).
Aligned reads were counted at the gene level with featureCounts of subread-1.6.1 package to obtain gene expression profiles.
Genome_build: hg19
Supplementary_files_format_and_content: text files include FPKM values for each Sample

source_name: myeloid progenitor cells

growth_protocol: Cells were cultured in stemspan containing 10ng/ml human SCF, TPO, FLT3 ligand, GM-CSF, IL-3 and IL-6

extract_protocol:
Total RNA was prepared using RNeasy micro kit (QIAGEN).
RNA libraries were prepared using 500 ng total RNA with SureSelect Strand-Specific RNA Preparation Kit (Agilent) according to the manufacturer’s protocol.

value: cord blood

tag: cell type

value: myeloid progenitor cells

tag: transduced genes


title: myeloid progenitor cells, MT-HX-3

description: ASXL1-MT+HHEX rep3


title: myeloid progenitor cells, MT-HX-1

description: ASXL1-MT+HHEX rep1


title: E5ind_rapa_40-45_rep1

tag: strain

value: Rapamycin


title: myeloid progenitor cells, HHEX-3

description: HHEX rep3

value: HHEX


title: myeloid progenitor cells, HHEX-2

description: HHEX rep2


title: myeloid progenitor cells, HHEX-1

description: HHEX rep1


title: myeloid progenitor cells, ASXL-MT-2

description: ASXL1-MT rep2


title: myeloid progenitor cells, ASXL-MT-3

description: ASXL1-MT rep3


title: myeloid progenitor cells, ASXL-MT-1

description: ASXL1-MT rep1


title: myeloid progenitor cells, Mock-3

description: Mock rep3


title: BJ NT r2 Late S

tag: treatment


title: myeloid progenitor cells, Mock-1

description: Mock rep1


title: myeloid progenitor cells, Mock-2

description: Mock rep2


title: HEK 293T cells, HHEX-HA (ChIP-seq)

description: HHEX-HA ChIP

data_processing:
Basecalls performed using bcl2fastq 1.8.4
Sequenced reads were trimmed for adaptor sequence using Cutadapt 1.3, and mapped to human genome assembly hg19 using BWA 0.7.5.
Genome_build: hg19
Supplementary_files_format_and_content: tdf files were generated using IGVtools.

source_name: HEK 293T cells

extract_protocol:
The chromatin fraction was prepared according to the fanChIP method described in our previous report [Nucleic Acids Research  42:7 4241-4256 (2014)], and DNA/protein complexes were isolated by anti-HA antibody (3F10, Roche).
The fanChIP libraries were constructed using a TruSeq ChIP Sample Prep Kit [iIllumina] following the manufacturer's instructions. The quality and quantity of these libraries were checked using Agilent TapeStation D1000 and KAPA Library Quantification Kits [KAPA BioSystems] / Real-time PCR Systems Step One Plus [Applied Biosystems]. The libraries were sequenced on the Illumina HiSeq 2500 System with 50-bp single-end reads according to the manufacturer’s protocol at the core facility of Hiroshima University.

value: HEK 293T cells

value: HA-tagged HHEX

tag: chip antibody

value: HA (Roche, 3F10)


title: HEK 293T cells, input (ChIP-seq)

description: input DNA


title: HEK 293T cells, control-HA (ChIP-seq)

description: control-HA ChIP

tag: genotype

value: empty vector control


title: BJ NT r1 Early S


title: UACC62P_24h_N2

city: East Lansing

first: Sean

middle: Alexander

last: Misek

state: MI

address: 1355 Bogue Street

institute: Michigan State University

data_processing:
Basecalls performed with Illumina Real Time Analysis, RTA_v2.7.7
Demultiplexing and FastQ conversion with Illumina Bcl2fastq v2.19.0
Quality Control with FastQC v0.11.5
Read Trimming with Trimmomatic v0.33
Read Mapping with HISAT2 v2.1.0
Read Counting/Analysis with HTSeq v0.6.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include raw HTSeq counts for each sample

source_name: Melanoma Cell Line

growth_protocol: Cells were grown in DMEM + 10% FBS + 1% Anti/Anti and were passaged in 10-cm cell culture plates. To generate experimental samples the cells were seeded into 6-cm plates.

extract_protocol:
Total cellular RNA was harvested from the cell lines using the Qiagen Rneasy Mini Kit (Cat# 74104)
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit on a Perkin Elmer Sciclone G3 robot following manufacturer’s recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Caliper LabChipGX HS DNA assays. Libraries were pooled and run on two lanes, and sequencing was performed in a 1x50bp single end read format using HiSeq 4000 SBS reagents.

treatment_protocol: Cells were treated with 10 uM CCG-222740 or vehicle control for either 0, 2, 6, or 24 h.

tag: cell line name

value: melanoma

tag: treatment time (h)


title: UACC62R_24h_N1


title: UACC62P_6h_N2


title: UACC62R_2h_N1


title: UACC62P_2h_N2


title: UACC62P_2h_N1


title: UACC62R_24h_N2


title: UACC62P_6h_N1


title: UACC62R_6h_N1


title: 40_K562_ASTAR-RNA-5-9

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

description: 40_K562_ASTAR-RNA-5-9.FCH7W3GBBXY_L8_R1_ICGGAGCCT-CTCTCTAT

data_processing:
Libraries were mapped to hg19 genome using STAR allowing up to 2 mismatches. Only uniquely mapped reads were kept for further analysis.
Genes were quantified using Cuffquant.
Libraries were normalized using Cuffnorm.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimieted text table containing the FPKM for every gene in every single cell library

growth_protocol: K562 (ATCC® CCL-243™) were maintained in K562 medium, which is  composed of RPMI1640 medium with L- Glutamine (HyClone) supplemented with  10% Fetal Bovine Serum (Gibco), 200mM L-Glutamine (100X, Gibco), 10000  U/ml Penicillin-Streptomycin (100X, Gibco).

extract_protocol:
Single cell suspensions were harvested for ASTAR Scripts run using C1 Fluidigm Open App chips (10-17um).
The concentration of amplified cDNA was measured by high sensitivity bioanalyzer chips and diluted to required range of cDNA for following library preparation steps. ASTAR-mRNAseq libraries were prepared using Nextera XT DNA Library Preparation Kit (FC-131-1096) following “Using C1 to Generate Single-Cell cDNA Libraries for mRNA Sequencing” manual.


title: 40_K562_ASTAR-RNA-5-8

description: 40_K562_ASTAR-RNA-5-8.FCH7W3GBBXY_L8_R1_IGCGTAGTA-TCTCTCCG


title: 40_K562_ASTAR-RNA-5-40

description: 40_K562_ASTAR-RNA-5-40.FCH7W3GBBXY_L8_R1_ITAGCGCTC-TCTCTCCG


title: 40_K562_ASTAR-RNA-5-3

description: 40_K562_ASTAR-RNA-5-3.FCH7W3GBBXY_L8_R1_IGCGTAGTA-GTAAGGAG


title: 40_K562_ASTAR-RNA-5-5

description: 40_K562_ASTAR-RNA-5-5.FCH7W3GBBXY_L8_R1_IGCGTAGTA-AAGGAGTA


title: 40_K562_ASTAR-RNA-5-7

description: 40_K562_ASTAR-RNA-5-7.FCH7W3GBBXY_L8_R1_IGCGTAGTA-CGTCTAAT


title: 40_K562_ASTAR-RNA-5-6

description: 40_K562_ASTAR-RNA-5-6.FCH7W3GBBXY_L8_R1_IGCGTAGTA-CTAAGCCT


title: 40_K562_ASTAR-RNA-5-4

description: 40_K562_ASTAR-RNA-5-4.FCH7W3GBBXY_L8_R1_IGCGTAGTA-ACTGCATA


title: 40_K562_ASTAR-RNA-5-39

description: 40_K562_ASTAR-RNA-5-39.FCH7W3GBBXY_L8_R1_ITAGCGCTC-CGTCTAAT


title: 40_K562_ASTAR-RNA-5-37

description: 40_K562_ASTAR-RNA-5-37.FCH7W3GBBXY_L8_R1_ITAGCGCTC-AAGGAGTA


title: 40_K562_ASTAR-RNA-5-38

description: 40_K562_ASTAR-RNA-5-38.FCH7W3GBBXY_L8_R1_ITAGCGCTC-CTAAGCCT


title: 40_K562_ASTAR-RNA-5-36

description: 40_K562_ASTAR-RNA-5-36.FCH7W3GBBXY_L8_R1_ITAGCGCTC-ACTGCATA


title: 40_K562_ASTAR-RNA-5-35

description: 40_K562_ASTAR-RNA-5-35.FCH7W3GBBXY_L8_R1_ITAGCGCTC-GTAAGGAG


title: UACC62R_2h_N2


title: UACC62R_6h_N2


title: UACC62P_24h_N1


title: 40_K562_ASTAR-RNA-5-34

description: 40_K562_ASTAR-RNA-5-34.FCH7W3GBBXY_L8_R1_ITAGCGCTC-TATCCTCT


title: 40_K562_ASTAR-RNA-5-33

description: 40_K562_ASTAR-RNA-5-33.FCH7W3GBBXY_L8_R1_ITAGCGCTC-CTCTCTAT


title: 40_K562_ASTAR-RNA-5-32

description: 40_K562_ASTAR-RNA-5-32.FCH7W3GBBXY_L8_R1_IATGCGCAG-TCTCTCCG


title: 40_K562_ASTAR-RNA-5-31

description: 40_K562_ASTAR-RNA-5-31.FCH7W3GBBXY_L8_R1_IATGCGCAG-CGTCTAAT


title: 40_K562_ASTAR-RNA-5-30

description: 40_K562_ASTAR-RNA-5-30.FCH7W3GBBXY_L8_R1_IATGCGCAG-CTAAGCCT


title: 40_K562_ASTAR-RNA-5-2

description: 40_K562_ASTAR-RNA-5-2.FCH7W3GBBXY_L8_R1_IGCGTAGTA-TATCCTCT


title: 40_K562_ASTAR-RNA-5-27

description: 40_K562_ASTAR-RNA-5-27.FCH7W3GBBXY_L8_R1_IATGCGCAG-GTAAGGAG


title: 40_K562_ASTAR-RNA-5-23

description: 40_K562_ASTAR-RNA-5-23.FCH7W3GBBXY_L8_R1_ITACGCTGC-CGTCTAAT


title: 40_K562_ASTAR-RNA-5-26

description: 40_K562_ASTAR-RNA-5-26.FCH7W3GBBXY_L8_R1_IATGCGCAG-TATCCTCT


title: 40_K562_ASTAR-RNA-5-24

description: 40_K562_ASTAR-RNA-5-24.FCH7W3GBBXY_L8_R1_ITACGCTGC-TCTCTCCG


title: 40_K562_ASTAR-RNA-5-22

description: 40_K562_ASTAR-RNA-5-22.FCH7W3GBBXY_L8_R1_ITACGCTGC-CTAAGCCT


title: 40_K562_ASTAR-RNA-5-28

description: 40_K562_ASTAR-RNA-5-28.FCH7W3GBBXY_L8_R1_IATGCGCAG-ACTGCATA


title: 40_K562_ASTAR-RNA-5-18

description: 40_K562_ASTAR-RNA-5-18.FCH7W3GBBXY_L8_R1_ITACGCTGC-TATCCTCT


title: 40_K562_ASTAR-RNA-5-20

description: 40_K562_ASTAR-RNA-5-20.FCH7W3GBBXY_L8_R1_ITACGCTGC-ACTGCATA