title: FCS glc C646 rep 2

city: Zürich

first: Reinhard

last: Dechant

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH Zürich

data_processing:
Novaseq 6000 sequencer
Raw reads were first cleaned by removing adapter sequences, trimming low quality ends, and filtering reads with low quality (phred quality <20) using Trimmomatic (Version 0.36)
Read alignment was done using STAR (v2.7.0e)
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: .txt files with TPM data

source_name: RPE-1 cells

growth_protocol: Cells grown in RPMI 10%FCS 5 g/l, starved for FCS and glucose for 24h

extract_protocol:
total RNA was isolated using the RNeasy kit (Quiagen)
TruSeq Stranded mRNA kit (Illumina, Inc, California, USA)

treatment_protocol: Cells were stimulated in RPMI 10%FCS 5 g/l glucose for 4 hours with DMA (100µM), C646 (10µM), or solvent control (DMSO)


title: S17_LUHMES_diff_DopaNeuron_Rotenone_2

status: Public on Aug 11 2020

type: SRA

city: Rockville

first: David

middle: Lee

last: Gerhold

state: MD

address: 9800 Medical Center Drive

department: Division of Preclinical Innovation

country: USA

institute: NCATS/NIH

library_source: transcriptomic

data_processing:
Fastq-gz files were delivered from the NHLBI sequencing core. All processing was performed at the NIH HPC resource. Paired end sequence reads files, three file pairs from three lanes per sample, were aligned to the Ensembl GRCh38 Human Genome sequence using STAR aligner.
Alignment BAM files for each biological sample were merged to a single BAM file for each biological sample.
Merged BAM files, one per sample, were analyzed by htseq-count script (HTSeq) to produce raw count files.
Individual count files for all samples were combined to produce the raw, unnormalized count matrix (See Raw Matrix File).
DESeq was used to normalize read counts to produce a normalized count matrix (see Normalized Matrix File).
Differential expression tests and further analysis are described in the associated publication.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw unnormalized matrix file. A tab delimited text file containing Ensembl Gene ids and Gene Symbols, one row per gene, 24 columns of data, one per sample. Values are un-normalized read counts per gene in each sample.
Supplementary_files_format_and_content: Normalized matrix file. A tab delimited text file containing Ensembl Gene ids and Gene Symbols, one row per gene, 24 columns of data, one per sample. Values are DESeq normalized read counts per gene in each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: dopa-neurons exposed to 1uM ROT

growth_protocol: LUHMES cells were grown in culture vessels coated with 50mg/ml each poly-L-ornithine and human fibronectin in Advanced DMEM/F12 medium containing 2 mM L-glutamine, 1X N2-supplement and 40 ng/ml bFGF. LUHMES differentiation was induced by 1mg/ml tetracycline and 1 mM cAMP contained in advanced DMEM/F12 medium with 2 mM L-glutamine, 1X N2-supplement, and 2ng/ml GDNF (Schildknecht et al. 2009).

extract_protocol:
Initial extraction and polyA enrichment were performed in the NCATS laboratories. Total RNA samples were prepared from cultured cells using Qiaquick kit (Qiagen, Germantown, MD) and selected for polyA+ transcripts using the Qiagen Oligotex midi kit. The resulting samples were then depleted of ribosomal sequences using two rounds of RiboZero Gold™, Illumina Inc. TruSeq Protocol by the NHLBI-NIH sequencing core (NHLBI-NIH DNA Sequencing and Genomics Core, Bethesda, MD, https://www.nhlbi.nih.gov/science/dna-sequencing-and-genomics-core).
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq)
RNA-Seq library production (TruSeq) for Hiseq 3000

treatment_protocol: For gene expression assays, 3 x 10e5 cells were cultured per well in 12 well plates with 2 mL medium to enable RNA extraction. Toxicant stock solutions in DMSO were diluted with culture medium to make 10X working solutions for each concentration and added to the cells at 10% of the volume in each well. Control cells were treated with 1% DMSO to match treatments. Cells were treated with DMSO or a toxicant for 6h prior to commencing RNASeq sample preparation.

tag: cell line

value: Lund human mesencephalic (LUHMES) cell line

tag: cell type

value: Dopaminergic Neurons Differentiated from LUHMES Cells

tag: compound treatment

value: Rotenone

tag: compound name

tag: publication comp. abbr.

value: ROT

tag: toxicant dose

tag: teatment class

value: Toxicant

tag: cas#


title: S13_LUHMES_diff_DopaNeuron_Ziram_1

source_name: dopa-neurons exposed to 2uM Ziram

value: Ziram

value: Zinc dimethyldithiocarbamate


title: FCS glc DMA rep 2


title: nESCs WT rep12

city: Shanghai

first: Bi

last: Yan

address: Siping Road 1239

country: China

institute: Tongji university

description:
PolyA RNA
scRNA-seq

data_processing:
All sequenced reads were checked for quality control by using FastQC (v0.11.7) with default parameters.
Sequenced reads was removed adapters and low-quality sequence by using trim_galore (v0.4.2 ) with the default parameters.
The processed RNA-Seq reads were mapped to hg19 genome using STAR (v0.6.0). RefSeq genes were quantified to FPKM using Stringtie.
The processed RIP-Seq reads were mapped to hg19 genome using TopHat (v2.1.1) with default parameters.
FPKM for each sample and log2 fold change were calculated by using cuffdiff (v2.1.1).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *fpkm: Tab-delimited text files include FPKM values.

molecule: total RNA

source_name: pluripotent stem cells

growth_protocol: For cell culture, hiF-T were cultured in DMEM (Gibco) supplemented with 10% FBS (Gibco) and 2mM GlutaMAX (Millipore). Primed ESCs/iPSCs (pESCs/piPSCs) were cultured in hESM containing DMEM/F12 (Gibco) with 20% KnockOut SR (Gibco), 1% nonessential amino acids (Millipore), 2mM GlutaMAX (Millipore), Penicillin Streptomycin(Millipore),8 ng/ml bFGF (Peprotech). Naïve ESCs/iPSCs (nESCs/niPSCs) were cultured in 5iLAF medium containing DMEM/F12: Neurobasal (1:1) (Gibco), 1% N2 supplement (Gibco), 2% B27 supplement (Gibco), 0.5% KnockOut SR (Gibco), 1% nonessential amino acids (Millipore), 2mM GlutaMAX (Millipore), Penicillin Streptomycin(Millipore), 20ng/ml human LIF (Milipore), 8 ng/ml bFGF (Peprotech), 50 μg/ml BSA (Sigma) and the following cytokines and small molecules: PD0325901 (Selleck, 1 μM), SB590885 (Selleck, 0.5 μM), WH-4-023 (Selleck, 1 μM), Y-27632 (Selleck, 10 μM), and Activin A (Peprotech, 20 ng/ml) and passaged by Accutase (Sigma) every 4-5 days as previously reported. All hESCs were routinely cultured at 37 °C in 5% CO2, 5% O2.

extract_protocol:
For mRNA-seq, total RNAs were isolated from cells using TRizol (Invitrogen). To generate RNA sequencing libraries, KAPA Stranded mRNA-Seq Kit (KAPA) was used following the manufacturer’s instructions. For single cell RNAseq, cell clones were mechanically picked and washed with PBS supplemented with 0.5% BSA. Following the Covaris DNA shearing protocol for Smart-seq sequence library generation as previously described. Briefly, cells were lysed, RNAs with a polyadenylated tail were captured, reverse transcripted and preamplified.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: TJ-1# nESCs

tag: passages

tag: genotype/variation

value: Wild type


title: nESCs WT rep11

description:
PolyA RNA
scRNA-seq


title: S16_LUHMES_diff_DopaNeuron_Rotenone_1


title: S15_LUHMES_diff_DopaNeuron_Ziram_3


title: S21_LUHMES_diff_DopaNeuron_6-HD_3

source_name: dopa-neurons exposed to 1uM 6HD


title: FCS glc C646 rep 1


title: S14_LUHMES_diff_DopaNeuron_Ziram_2


title: nESCs WT rep9

description:
PolyA RNA
scRNA-seq


title: nESCs WT rep8

description:
PolyA RNA
scRNA-seq


title: FCS glc rep 3


title: S11_LUHMES_diff_DopaNeuron_MPP_2

source_name: dopa-neurons exposed to 5uM MPP

value: MPP


title: nESCs WT rep10

description:
PolyA RNA
scRNA-seq


title: S10_LUHMES_diff_DopaNeuron_MPP_1


title: S19_LUHMES_diff_DopaNeuron_6-HD_1


title: FCS glc rep 1


title: FCS glc rep 2


title: FCS glc DMA rep 3


title: S12_LUHMES_diff_DopaNeuron_MPP_3


title: nESCs WT rep4

description:
PolyA RNA
scRNA-seq


title: nESCs WT rep14

description:
PolyA RNA
scRNA-seq


title: nESCs WT rep5

description:
PolyA RNA
scRNA-seq


title: S8_LUHMES_diff_DopaNeuron_Paraquat_2

source_name: dopa-neurons exposed to 5uM PQ

value: Paraquat

value: PQ


title: nESCs WT rep7

description:
PolyA RNA
scRNA-seq


title: FCS glc C646 rep 3


title: S9_LUHMES_diff_DopaNeuron_Paraquat_3


title: starved rep 3


title: S7_LUHMES_diff_DopaNeuron_Paraquat_1


title: nESCs WT rep6

description:
PolyA RNA
scRNA-seq


title: starved rep 1


title: S6_LUHMES_diff_DopaNeuron_MS275_3

source_name: dopa-neurons exposed to 5uM MS5

value: Etinostat


title: 273-MAR0

city: Stanford

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

data_processing:
TrimGalore
STAR
featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: Raw read counts in TXT format

source_name: iPSC-ECs

growth_protocol: iPSCs were differentiated into endothelial cells (iPSC-ECs) using a monolayer chemically-defined methods.

extract_protocol:
RNA was then extracted using the miRNeasy Mini Kit with DNA digestion, and collected total RNA was used for RNA-sequencing.
RNA-seq construction protocol of Illumina.

treatment_protocol: iPSC-ECs (passage 3) were seeded into 6-well plates. 24 hours later, iPSC-Ecs were exposed to e-liquids with and without nicotine for up to 72 hours.

tag: treatment

value: E-cig liquid, Marcado with 0 mg/ml of nicotine

value: iPSC-ECs

tag: cell origin


title: APG nESCs WT rep1

description: PolyA RNA

value: APG TJ-1# nESCs


title: S3_LUHMES_diff_DopaNeuron_DMSO_3

source_name: dopa-neurons exposed to 1% (v/v), vehicle control DMSO

value: DMSO

value: Dimethyl Sulfoxide

value: 1% (v/v), vehicle control

value: Vehicle Control


title: nESCs WT rep3

description:
PolyA RNA
scRNA-seq


title: APG nESCs WT rep2

description: PolyA RNA


title: starved rep 2


title: nESCs WT rep1

description:
PolyA RNA
scRNA-seq


title: 273-MAR18

value: E-cig liquid, Marcado with 18 mg/ml of nicotine


title: FCS glc DMA rep 1


title: S5_LUHMES_diff_DopaNeuron_MS275_2

value: Lund human mesencephalic (LUHMES) cell line

value: Dopaminergic Neurons Differentiated from LUHMES Cells

value: Toxicant


title: S4_LUHMES_diff_DopaNeuron_MS275_1


title: APG nESCs AKD rep1

description: PolyA RNA

value: ALPPL2 knockdown


title: APG nESCs AKD rep2

description: PolyA RNA


title: S2_LUHMES_diff_DopaNeuron_DMSO_2


title: 273-RY0

value: E-cig liquid, RY4 with 0 mg/ml of nicotine


title: 273-RY18

value: E-cig liquid, RY4 with 18 mg/ml of nicotine


title: S1_LUHMES_diff_DopaNeuron_DMSO_1


title: T cell_mir24_sponge

city: Guangzhou

first: Jiang

last: Li

state: Guangdong

address: Dongfengdong Road NO.651, Yuexiu District

institute: State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.13 with parameters -p 8 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 -G hg19
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: T cells

growth_protocol: T cells were plated into OKT-3 (1 ug/mL) in 48-well plates in low-dose rhIL-2 (150 IU/ml) medium.

extract_protocol:
Total RNA from lentivirus-transduced T cells was isolated using TRIzol reagent, and dissolved in RNase-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: OKT-3-stimulated T cells were forced exogenous miR-24 expression or blocked the endogenous miR-24 by introducing the miR-24 or miR-24-sponge lenti-virus into human T cell in vitro for 3 days

value: PBMC

value: mir24_sponge (blocked the endogenous miR-24)


title: T cell_mir24_sponge_cont

value: control (for mir24_sponge)


title: APG+ niPSCs rep1

description:
PolyA RNA
APG 2° niPSCs

value: APG secondary niPSCs

value: Wild type


title: 78-MAR0

value: E-cig liquid, Marcado with 0 mg/ml of nicotine

value: iPSC-ECs


title: T cell_mir24

value: mir24 (forced exogenous miR-24 expression)


title: 78-RY18


title: APG+ niPSCs rep2

description:
PolyA RNA
APG 2° niPSCs


title: 273-CTR

value: Vehicle


title: T cell_cont

value: control (for mir24)


title: APG+ 20d rep2

description:
PolyA RNA
APG 2° hiF-Ts

value: APG secondary hiF-Ts


title: nESCs WT rep2

description:
PolyA RNA
scRNA-seq

value: TJ-1# nESCs


title: 78-CTR


title: APG+ 20d rep1

description:
PolyA RNA
APG 2° hiF-Ts


title: 78-MAR18

value: E-cig liquid, Marcado with 18 mg/ml of nicotine


title: APG+ 24d rep1

description:
PolyA RNA
APG 2° hiF-Ts


title: APG+ 14d rep1

description:
PolyA RNA
APG 2° hiF-Ts


title: 78-RY0


title: mRNA_R2

city: Taipei

first: Ming-Jung

last: Liu

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Academia sinica

data_processing:
Adaptor sequences (CTGTAGGCACCATCAAT) were trimmed from the sequence reads.
Genome_build: The reference genome sequences (SL3.0) and gene annotation (ITAG3.2) of  Solanum Lycopersicum were retrieved from Sol Genomics Network
Supplementary_files_format_and_content: The processed data contians the number of reads of each nucleotide on the genome for 3 samples (LTM, CHX and mRNA). The "plus" and "minus"" indicated the strand direction of the seqeunced reads.

organism: Solanum lycopersicum

source_name: total RNA from leaves

growth_protocol: Tomato was grown in a growth chamber under 12-h light (8:00 to 20:00, 150 μmol m-2 s-1)/12-h dark cycle at 28ºC.

extract_protocol:
To purify the ribosome-protected fragments (RPFs) samples for cycloheximide  (CHX) datasets, the polysome complexes were isolated from the grounded plant powder with polysome extraction buffer (20 mM Hepes, 100mM KCl, 5 mM MgCl2, recipe from Gao et al. (2015)) containing 100 ug/ml CHX via 13,000g at 40C for 5 min and digested with RNase 1 to purify the RPFs. The purified RPFs were further resolved in 15% TBE-UREA polyacrylamide gel (Invitrogen) and excise the gels slides corresponding to the 26~32 nt region for library construction of CHX-treated samples  as described previously (Hsu et al., 2016). To purify the RNA samples for total RNA datasets, total RNAs was extracted from the aliquot of the polysome extract mentioned above via RNA clean kit (Zymo) and then input to Ribo-Zero rRNA depletion kit (Illumina) for the rRNA removal. To purify the RPFs for LTM datasets, the polysome complexes were isolated from the grounded powder of the LTM-treated plants with polysome extraction buffer via 13,000g at 40C for 5 min. The supernatant were then subjected to purimycin (PUR) treatment based a reported protocol (Gao et al., 2015) and then processed to RPF purification as described above.
The purified RNA fragments was used to construct a library for single 75-bp single-end  sequencing following the protocol described previously (Ingolia, N. T., et al., Science, 2009).
Ribosome profiling (LTM-seq and CHX-seq) for initiating and elongation ribosomes ; RNA-seq for total mRNA

treatment_protocol: True leaves of two weeks old plants were collected.

tag: tissue

value: Three-week-old leaves


title: CHX_R1

description: Ribosome-protected fragments

data_processing:
Library strategy: Ribo-seq
Adaptor sequences (CTGTAGGCACCATCAAT) were trimmed from the sequence reads.
Genome_build: The reference genome sequences (SL3.0) and gene annotation (ITAG3.2) of  Solanum Lycopersicum were retrieved from Sol Genomics Network
Supplementary_files_format_and_content: The processed data contians the number of reads of each nucleotide on the genome for 3 samples (LTM, CHX and mRNA). The "plus" and "minus"" indicated the strand direction of the seqeunced reads.

source_name: ribosome protected fragments from CHX-treated leaves

value: CHX


title: mRNA_R1


title: C2-MAR18


title: C2-MAR0


title: LTM_R2

description: Ribosome-protected fragments

source_name: ribosome protected fragments from LTM-treated leaves

value: LTM


title: APG+ 14d rep2

description:
PolyA RNA
APG 2° hiF-Ts


title: APG+ 0d rep2

description:
PolyA RNA
APG 2° hiF-Ts


title: C2-RY0

value: E-cig liquid, RY4 with 0 mg/ml of nicotine


title: APG+ 8d rep1

description:
PolyA RNA
APG 2° hiF-Ts


title: ACT88FGS>W1118 RU486+

city: College Station

first: Jason

last: Karpac

state: Texas

address: Reynolds Medical Building

department: Molecular and Cellular Medicine

institute: Texas A&M University Health Sciences Center

data_processing:
Sequence cluster identification, quality pre-filtering, base calling and uncertainty assessment were done in real time using Illumina's HCS and RTA software with default parameter settings.
Between 8 and 10 million (2X150) base pair reads were generated per library and mapped to the Drosophila genome (Release 6).
Expression was recorded as TPM (transcripts per kbp per million reads) followed by Log2 transformation.

organism: Drosophila melanogaster

source_name: Muscle

growth_protocol: In order to standardize metabolic results, fifty virgins were crossed to 10 males and kept in bottles for 2-3 days to lay enough eggs. Wet folded filters (GE healthcare, CAT No.10311843) were inserted in bottles after parental flies removed. Progeny of crosses was collected for 3–4 d after initial eclosion. Collected progeny were then transferred to new bottles to allow them mate for 2 d. All these flies were reared on diet (cornmeal-based) at 25°C and 65% humidity on a 12 hr light/dark cycle, unless otherwise indicated. Around 20 female flies were then separated into each vial with diet for 10 days at 25 °C and 65% humidity on a 12 hr light/dark cycle.

extract_protocol:
Intact fly thoraces (8) were dissected in PBS. Total RNA was extracted using Trizol reagent.
Total RNA was extracted using Trizol reagent and used as template to generate sample libraries for RNA sequencing (using the TruSeq Stranded Total RNA Library Prep Kit).

tag: genotype

value: Muscle - thorax

tag: age

value: 10 days

tag: gender

value: Female

tag: diet

value: high calorie diet


title: ciPSC-CM

description: abundance data: primates.read.counts.txt

data_processing:
ATAC-Seq reads alignment using Bowtie v2.2.6
Sort/remove duplicates using Sambamba v0.6.5
Convert to bam using Samtools v1.2.0
Count feature coverage around features using Deeptools v2.0.0
Count feature coverages using Rsubread v1.26.1
Trim reads/ quality control using Trim Galore v0.4.2
RNA-Seq reads alignment using STAR v2.5.3a
Count feature coverage around transcriptomic features using fetureCounts v1.5.0
Count feature coverages using igvtools v2.3.91
Detect differential regions using DESeq2 v1.16.1
Genome_build: hg19/panTro4/gorGor3/rheMac3/mm9
Supplementary_files_format_and_content: TDF format, read coverage

organism: Pan troglodytes

source_name: Chimpanzee iPSC-CM

growth_protocol: Pluripotent cells were grown on Matrigel-coated plates (1:100 Matrigel in E8 medium) using chemically defined E8 medium. The medium was changed daily and cells were passaged every 3-4 days using EDTA or Accutase. Cardiomyocytes were maintained in RPMI + B27+ with media change every other day.

extract_protocol:
For RNA-seq, RNA was isolated using miRNeasy kit (Qiagen) following the manufacture’s protocol. For ATAC-seq, 100,000 cells were centrifuged 500 g for 5 min at room temperature. The cell pellet was resuspended in 50 ml lysis buffer (10 mM Tris–Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.01% Igepal CA-630) and centrifuged immediately 500 g for 10 min at 4°C. The cell pellet was resuspended in 50 ml transposase mixture (25 ul 2×TD buffer, 22.5 μl dH2O, and 2.5 μl Illumina Tn5 transposase or with final concentration of 100 nM Atto-590-labeled in-house Tn5) and incubated at 37°C for 30 min. After transposition, the mixture was purified with the Qiagen Mini-purification kit and eluted in 10 ul Qiagen EB elution buffer. For transgenic BANCR embryos plasmid vector construction (pRP[Exp]-BetaMHC>hBANCR) and purification, pronuclear plasmid injection of FVB embryos, harvesting and genotyping of E16 embryos were performed by Cyagen Biosciences (Santa Clara, CA,USA). Total RNA was isolated from extracted embryo hearts that were plasmid positive (n=2) or negative (n=2).
Total RNA was submitted to a core facility (Stanford Functional Genomics) for library preparation and Illumina sequencing. For ATAC-seq, sequencing libraries were prepared following the original ATAC-seq protocol (Buenrostro, J. D. et al. Nat Methods 10, 1213-1218 (2013)). The HiChIP protocol was performed as previously described (Mumbach, M. R. et al. Nat Methods 13, 919-922 (2016)).

treatment_protocol: Cardiomyocytes were differentiated from human and NHP pluripotent cells. Briefly, differentiation medium consisted of RPMI-1640 media (11875-085, Life Technologies) supplemented with B27® minus insulin (A1895601, Life Technologies) (RPMI + B27-). To this medium, various small molecules were added over a week-long timetable as previously described. On the first day (D0) of differentiation, 6 µM CHIR 99021 (C-6556, LC Laboratories) was added. On D2, media was aspirated and replaced with RPMI + B27-. On D3, media was aspirated and replaced with 5 µM of IWR-1 (S7086, Selleck Chemicals) in RPMI + B27-. Media was replaced with RPMI + B27- on D5 and RPMI plus B27 supplemented with insulin (17504-044, Life Technologies) (RPMI + B27+) on D7.

value: iPSC-CM

value: male

tag: differentiation days


title: ciPSC

source_name: Chimpanzee iPSC

value: iPSC


title: CHX_R2

description: Ribosome-protected fragments


title: C2-CTR

tag: cell type

value: iPSC-ECs


title: ACT88FGS>W1118 ETH

value: Ethanol control


title: ACT88FGS>MEF2RNAi RU486+


title: LTM_R1

description: Ribosome-protected fragments


title: APG+ 8d rep2

description:
PolyA RNA
APG 2° hiF-Ts

value: Wild type


title: ACT88FGS>MEF2RNAi ETH


title: C2-RY18

value: E-cig liquid, RY4 with 18 mg/ml of nicotine


title: AR_KO_Bioreplicate_1_H3K4me3

status: Public on Aug 10 2020

city: Bethesda

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

library_source: genomic

data_processing:
RTA 1.13.48 and CASAVA 1.8.2. software used for basecalling and deplexing.
Raw sequence files generated per sample were quality inspected using the FastQC tool then adaptor clipped (TruSeq3-SE.fa:2:30:10) and trimmed to remove 5' nucleotide bias (HEADCROP:5) and low quality calls (TRAILING:20, SLIDINGWINDOW:4:20, MINLEN:15) using the Trimmomatic tool. Surviving reads per sample were then imported into v11 of the CLCbio Genomics Workbench (www.qiagenbioinformatics.com) and reference mapped by sample against the current instance of the human genome (GRCh38.82) using the "Map Reads To reference" tool supported therein using default parameters. Post mapping, alignment files were exported from the Workbench in Binary Alignment Map (BAM) format then sorted and indexed using samtools (http://samtools.sourceforge.net/). Peak calling on these sorted alignment files was then performed using macs2 (https://github.com/taoliu/MACS) via the "callpeak" command (-B -g hs -q 0.05 --broad --broad-cutoff 0.05). Peak calls returned were captured and saved in bed-formatted files.
Genome_build: GRCh38.82
Supplementary_files_format_and_content: One bed formatted file per non-Input sample is provided. These bed files describe the location of the peaks called in each of the non-Input samples.

molecule: genomic DNA

source_name: iPSC

growth_protocol: Human iPSCs were transfected with the hNIL construct as previously described (Fernandopulle et al., 2018). Briefly, iPSCs were grown to 80% confluency, then digested with accutase solution into single cells. Cells were passaged on matrigel coated plates in E8 Flex media supplemented with 10 μM ROCK inhibitor (Tocris). 3 μg of total DNA (hNIL donor construct and each of the site- specific TALEN or CRISPER/cas9) was added using Lipofectamine Stem (ThermoFisher). 48 hours later, transfected iPSCs were dissociated with accutase and re-plated sparsely onto matrigel coated dishes in E8 flex and 10 μM ROCK inhibitor. Differentiation was performed as previously described (Fernandopulle et al., 2018). In brief stably transfected iPSCs with the hNIL cassette were plated at 30,000 cells/cm2 on a Matrigel-coated surface in E8 Flex medium (ThermoFisher) containing 10 μM ROCK inhibitor. 24 hours later, cells were induced with Neural Induction Medium (NIM): DMEM/F12, B27(1x), N2 (1x), NEAA (1x), GlutaMax(1x), compound E (0.2 μg/mL), ROCK inhibitor (10 μM), doxycycline 2 μg/mL, DHT (10 nM). After 48 hours of doxycycline treatment, motor neurons were dissociated with accutase to single cells and re-plated 50,000 cells/cm2 on PDL/Laminin coated surfaces in Neural Differentiation Medium (NDM): DMEM/F12:Brainphys neuronal medium, B27(1x), N2 (1x), NEAA (1x), GlutaMax(1x), compound E (0.2 μg/mL), ROCK inhibitor (10 μM), doxycycline (2 μg/mL), Laminin (1 μg/mL), BDNF (10 ng/mL), GDNF (10 ng/mL), NT3 (10 ng/mL) and DHT (10 nM). On day 4 onward, half of cell culture medium was removed and replaced by Neuron medium (NM): Brain phys neuronal medium, B27(1x), N2 (1x), NEAA (1x), GlutaMax(1x), compound E (0.2 μg/mL), ROCK inhibitor (10 μM), doxycycline (2 μg/ml), Laminin (1 μg/ml), BDNF (10 ng/mL), GDNF (10 ng/mL), NT3 (10 ng/mL) and DHT (10 nM).

extract_protocol:
iMNs were first treated with 1% formaldehyde for 10 min n 37o C, followed by 0.125 M glycine in PBS. iMNs were then resuspended in RIPA buffer supplemented with EDTA-free protease inhibitor (ROCHE). After, cells were sonicated using TC12x24 tube on Covaris S2, duty cycle 20%, intensity 5, cycle/burst 200, 60s x 30 cycles. For immunoprecipitation, Dynabeads Protein A was incubated with 10 μg ChIP-antibody for 45 min at RT on a shaker. The pre-cleared chromatin was transferred into the antibody-bound beads and incubated on a tube rotator overnight in 4o C. Following overnight incubation, samples were washed for 10 min with rotation at 4o C with 2x RIPA buffer, 2x RIPA + 0.3 M NaCl, 2x LiCl buffer. After the last wash beads were re-suspended with TE (pH8) +10% SDS supplemented with 20 mg/mL proteinase K and incubated at 65o C for 4 hours in a shaker. The supernatant was collected using a magnet and DNA was purified using phenol/chloroform/isoamyl alcohol. The DNA concentration was measured using Pico-Green dsDNA assay kit (ThermoFisher).
Libraries were constructed from 10 ng of ChIP DNA using Ovation Ultralow System V2 1-96 using 15 cycles of PCR amplification.  These libraries were then purified twice using Ampure XP PCR Purification Beads (Agencourt). Following purification, libraries were pooled then quantitated by qPCR. The balance of the pool was subsequently checked by performing a MiSeq run of 25 cycles plus index read using a MiSeq Nano kit, version 2. The percentage of each library in the pool was determined from the demultiplexing and was used to optimize the pool balance prior to final single-end (1x50bp) sequencing using an Illumina HiSeq 2500.

value: iPSC derived Motor Neuron (iMN)

tag: chip antibody

value: H3K4me3 (Abcam, ab8550)

tag: donor

value: Male

tag: cag repeat length

tag: race

value: Caucasian

tag: sample group

value: Androgen Receptor (AR) Knock-Out (KO) - H3K4me3

tag: culture condition

value: DHT

tag: author reference id


title: APG+ 0d rep1

description:
PolyA RNA
APG 2° hiF-Ts

value: APG secondary hiF-Ts

tag: passages

tag: genotype/variation


title: Control_Bioreplicate_1

data_processing:
RTA 1.13.48 and CASAVA 1.8.2. software used for basecalling and deplexing.
Raw sequence files generated per sample were quality inspected using the FastQC tool then adaptor clipped (TruSeq3-PE-2.fa:2:30:10) and trimmed to remove 5' nucleotide bias (HEADCROP:15) and low quality calls (TRAILING:20, SLIDINGWINDOW:4:20, MINLEN:15) using the Trimmomatic tool. Surviving reads per sample were then imported into v11 of the CLCbio Genomics Workbench (www.qiagenbioinformatics.com) and reference mapped by sample against the current instance of the human genome (GRCh38.82) using the "Map Reads To reference" tool supported therein using default parameters. Post mapping, alignment files were exported from the Workbench in Binary Alignment Map (BAM) format then sorted and indexed using samtools (http://samtools.sourceforge.net/). Peak calling was next performed on two separate combinations of the sorted alignment files using macs2 (https://github.com/taoliu/MACS) via the "callpeak" command (-B -f BAMPE -g hs -q 0.05 --broad --broad-cutoff 0.05). For the first combination, sorted alignment files representing Wild Type Control were collectively passed using the "-t" parameter and the sorted alignment file representing AR KO passed using the "-c" parameter. For the second combination, sorted alignment files representing SBMA were collectively passed using the "-t" parameter and the the sorted alignment file representing AR KO again passed using the "-c" parameter. Peak calls returned were captured and saved in tab-deliminated files.
Genome_build: GRCh38.82
Supplementary_files_format_and_content: Two tab-delimited text files are provided; one describing the location of peaks called in Control samples vs AR KO and the other describing the peaks called in SBMA samples vs AR KO.

extract_protocol:
iMNs were first treated with 1% formaldehyde for 10 min n 37o C, followed by 0.125 M glycine in PBS. iMNs were then resuspended in RIPA buffer supplemented with EDTA-free protease inhibitor (ROCHE). After, cells were sonicated using TC12x24 tube on Covaris S2, duty cycle 20%, intensity 5, cycle/burst 200, 60s x 30 cycles. For immunoprecipitation, Dynabeads Protein A was incubated with 10 μg ChIP-antibody for 45 min at RT on a shaker. The pre-cleared chromatin was transferred into the antibody-bound beads and incubated on a tube rotator overnight in 4o C. Following overnight incubation, samples were washed for 10 min with rotation at 4o C with 2x RIPA buffer, 2x RIPA + 0.3 M NaCl, 2x LiCl buffer. After the last wash beads were re-suspended with TE (pH8) +10% SDS supplemented with 20 mg/mL proteinase K and incubated at 65o C for 4 hours in a shaker. The supernatant was collected using a magnet and DNA was purified using phenol/chloroform/isoamyl alcohol. The DNA concentration was measured using Pico-Green dsDNA assay kit (ThermoFisher).
Libraries were constructed from 10 ng of ChIP DNA using used the Illumina Nextera XT kit. These libraries were then purified twice using Ampure XP PCR Purification Beads (Agencourt). Following purification, libraries were pooled then quantitated by qPCR. The balance of the pool was subsequently checked by performing a MiSeq run of 25 cycles plus index read using a MiSeq Nano kit, version 2. The percentage of each library in the pool was determined from the demultiplexing and was used to optimize the pool balance prior to final paired-end (2x50bp) sequencing using an Illumina HiSeq 2500.

value: anti-AR Santa cruz (SC-816)

value: Wild Type

value: Control


title: Control_Bioreplicate_1_Input

value: none (input)

value: Control - Input


title: Control_Bioreplicate_3

value: Asian


title: AR_KO_Bioreplicate_1_H3K27ac

value: H3K27ac (Abcam, ab4729)

value: Androgen Receptor (AR) Knock-Out (KO) - H3K27ac


title: CG114_C9MJ6ANXX_GTGAAA_L007

city: Nedlands

first: Anya

last: Jones

state: Western Australia

address: Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute, The University of Western Australia

data_processing:
The Illumina bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data.
FASTQC (Andrews Trop Med Int Health. 2011) was employed for pre-alignment quality control (QC) of raw sequence data. Raw sequencing reads were aligned to the human reference genome (hg19; Pertea Nat Protocol. 2016) using HISAT2 (Kim Nat Methods. 2015), and summarised as gene-level counts employing summariseOverlaps (Anders Nat Protoc. 2013), followed by post-alignment QC with SAMStat (Lassmann Bioninformatics. 2011). Genes with an official HUGO Gene Nomenclature Committee (HGCN) symbol were retained.
Genome_build: hg19
Supplementary_files_format_and_content: PBMC_raw_counts.txt

extract_protocol:
Total RNA was extracted from viable PBMC employing TRizol (Ambion, Life Technologies) followed by RNeasy MinElute (Qiagen, Hilden, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: PBMC were cultured for 24hrs in sera-free AIM-V medium (Life Technologies, Mulgrave Australia) supplemented with 50 uM 2-mercaptoethanol (Invitrogen, Mulgrave, Australia) in sextuplicate with RV-A or RV-C peptide pools or without stimulus (unstimulated control).

tag: sampleID

tag: gender (f=female, m=male)

value: F

tag: age at visit (years)

tag: asthma status (1=yes, 0=no)

tag: atopic (1=yes, 0=no)

tag: rv-a positive (1=yes, 0=no)

tag: rv-b positive (1=yes, 0=no)

tag: rv-c positive (1=yes, 0=no)

tag: peptide treatment

value: negControl

value: Peripheral blood mononuclear cells (PBMC)


title: SBMA_Bioreplicate_3

tag: cell type

value: iPSC derived Motor Neuron (iMN)

tag: chip antibody

tag: donor

tag: age

tag: gender

value: Spinal and Bulbar Muscular Atrophy (SBMA)


title: SBMA_Bioreplicate_2

value: Male

tag: cag repeat length

tag: race

value: Caucasian

tag: sample group

tag: culture condition

tag: author reference id


title: SBMA_Bioreplicate_1

value: DHT


title: Input

description: Input

value: Input


title: CG109_C9MJ6ANXX_AGTCAA_L007

source_name: non-asthmatic control_RV-A peptide pool_PBMC

tag: sampleID

tag: gender (f=female, m=male)

tag: age at visit (years)

value: Pool A


title: Control_Bioreplicate_2

value: anti-AR Santa cruz (SC-816)

value: Wild Type


title: Tissue specific expression analysis [Stem_BR2]

type: RNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression in STEM as compared to whole plant

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 50th percentile shift  method

organism: Calotropis procera

source_name: Stem replicate two

label_protocol: The microarray hybridization and scanning were performed at the Agilent certified microarray facility of Genotypic Technology, Bengaluru, India. The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Calotropis procera seeds were allowed to germinate in soilrite: vermiculite mix (3:1). Individual germinated seedlings were transferred in pots (soilrite: vermiculite mix (3:1)) and grown in green house (16/8 day light condition) for 3 months.

extract_protocol: RNA was prepared using standard TRIzol method. The concentration and purity of the RNA extracted were evaluated using the Nanodrop Spectrophotometer (Thermo Scientific; 1000).  The integrity of the extracted RNA were analysed on the Bioanalyzer (Agilent; 2100). We considered RNA to be of good quality based on the 260/280 values (Nanodrop), rRNA 28S/18S ratios and RNA integrity number (RIN) (Bioanalyzer).

tag: tissue

value: Stem tissue


title: Tissue specific expression analysis [Stem_BR1]

description: Gene expression in stem as compared to whole plant

source_name: Stem replicate 1


title: Tissue specific expression analysis [Whole plant_BR2]

description: Gene expression in  whole plant

source_name: Whole plant replicate two

value: Whole plant tissue


title: Tissue specific expression analysis  [Leaf_BR1]

description: Gene expression in leaf as compared to whole plant

source_name: Leaf replicate 1

value: Leaf tissue


title: SBMA_Bioreplicate_1_Input

value: none (input)

value: Spinal and Bulbar Muscular Atrophy (SBMA) - Input


title: AR_KO_Bioreplicate_1_H3K4me1

value: H3K4me1 (Millipore, 07-436)

value: Androgen Receptor (AR) Knock-Out (KO) - H3K4me1


title: SBMA_Bioreplicate_1_H3K4me3

value: H3K4me3 (Abcam, ab8550)

value: Spinal and Bulbar Muscular Atrophy (SBMA) - H3K4me3


title: SBMA_Bioreplicate_1_RNAPolII

value: iPSC derived Motor Neuron (iMN)

value: RNAPolII (Abcam, ab5095)

value: Spinal and Bulbar Muscular Atrophy (SBMA) - RNAPolII


title: SBMA_Bioreplicate_1_H3K4me1

value: Male

value: Caucasian

value: Spinal and Bulbar Muscular Atrophy (SBMA) - H3K4me1

value: DHT


title: CG107_C9MJ6ANXX_GGCTAC_L007

source_name: asthmatic_RV-C peptide pool_PBMC

value: F

tag: asthma status (1=yes, 0=no)

tag: atopic (1=yes, 0=no)

tag: rv-a positive (1=yes, 0=no)

tag: rv-b positive (1=yes, 0=no)

value: Pool C

value: Peripheral blood mononuclear cells (PBMC)


title: CG108_C9MJ6ANXX_CTTGTA_L007

tag: rv-c positive (1=yes, 0=no)

tag: peptide treatment

value: negControl

tag: cell type


title: CG110_C9MJ6ANXX_AGTTCC_L007

source_name: non-asthmatic control_RV-C peptide pool_PBMC


title: CG104_C9MJ6ANXX_ACTTGA_L007

value: M


title: CG103_C9MJ6ANXX_CAGATC_L007

value: Pool A


title: Tissue specific expression analysis [Root_BR2]

description: Gene expression in root as compared to whole plant

source_name: Root replicate two

value: Root tissue


title: Tissue specific expression analysis [Whole plant_BR1]

description: Gene expression in whole plant

source_name: Whole plant replicate 1

value: Whole plant tissue


title: Tissue specific expression analysis [Leaf_BR2]

source_name: Leaf replicate two

value: Leaf tissue


title: CG100_C9MJ6ANXX_TGACCA_L007

source_name: asthmatic_RV-A peptide pool_PBMC


title: Control_Bioreplicate_1_H3K4me3

tag: chip antibody

value: H3K4me3 (Abcam, ab8550)

tag: donor

tag: age

tag: gender

value: Wild Type

value: Control - H3K4me3


title: CG113_C9MJ6ANXX_GTCCGC_L007


title: CG099_C9MJ6ANXX_TTAGGC_L007

source_name: non-asthmatic control_negControl_PBMC


title: AR_KO_Bioreplicate_1

value: iPSC derived Motor Neuron (iMN)

value: anti-AR Santa cruz (SC-816)

tag: cag repeat length

tag: race

tag: sample group

value: Androgen Receptor (AR) Knock-Out (KO)

tag: culture condition

value: "AR KO"


title: CG098_C9MJ6ANXX_CGATGT_L007

tag: sampleID

tag: gender (f=female, m=male)

tag: age at visit (years)


title: Control_Bioreplicate_1_H3K4me1

value: H3K4me1 (Millipore, 07-436)

value: Male

value: Caucasian

value: Control - H3K4me1

value: DHT

tag: author reference id


title: CG112_C9MJ6ANXX_CCGTCC_L007

value: F

tag: asthma status (1=yes, 0=no)

tag: atopic (1=yes, 0=no)

tag: rv-a positive (1=yes, 0=no)

value: Peripheral blood mononuclear cells (PBMC)


title: CG111_C9MJ6ANXX_ATGTCA_L007

tag: rv-b positive (1=yes, 0=no)

tag: rv-c positive (1=yes, 0=no)

tag: peptide treatment

value: negControl


title: SBMA_Bioreplicate_1_H3K27ac

tag: cell type

tag: chip antibody

value: H3K27ac (Abcam, ab4729)

tag: donor

value: Spinal and Bulbar Muscular Atrophy (SBMA) - H3K27ac


title: CG093_C9MJ6ANXX_CGTACG_L006


title: CG090_C9MJ6ANXX_GTGAAA_L006


title: CG089_C9MJ6ANXX_GTCCGC_L006

value: Pool C


title: CG094_C9MJ6ANXX_GAGTGG_L006

value: M

value: Pool A


title: CG102_C9MJ6ANXX_GCCAAT_L007


title: CG106_C9MJ6ANXX_TAGCTT_L007


title: CG101_C9MJ6ANXX_ACAGTG_L007


title: Tissue specific expression analysis [Root_BR1]

source_name: Root replicate 1

tag: tissue

value: Root tissue


title: CG096_C9MJ6ANXX_ATTCCT_L007


title: CG105_C9MJ6ANXX_GATCAG_L007


title: CG095_C9MJ6ANXX_ACTGAT_L006


title: CG091_C9MJ6ANXX_GTGGCC_L006


title: CG085_C9MJ6ANXX_AGTCAA_L006


title: CG087_C9MJ6ANXX_ATGTCA_L006


title: CG084_C9MJ6ANXX_CTTGTA_L006


title: CG097_C9MJ6ANXX_ATCACG_L007


title: CG083_C9MJ6ANXX_GGCTAC_L006


title: CG081_C9MJ6ANXX_GATCAG_L006


title: CG082_C9MJ6ANXX_TAGCTT_L006


title: CG080_C9MJ6ANXX_ACTTGA_L006


title: CG086_C9MJ6ANXX_AGTTCC_L006


title: CG092_C9MJ6ANXX_GTTTCG_L006


title: CG079_C9MJ6ANXX_CAGATC_L006


title: CG078_C9MJ6ANXX_GCCAAT_L006


title: CG088_C9MJ6ANXX_CCGTCC_L006


title: CG077_C9MJ6ANXX_ACAGTG_L006


title: CG076_C9MJ6ANXX_TGACCA_L005


title: CG075_C9MJ6ANXX_TTAGGC_L005


title: 20180518_CentrumOnkologii02_7MS_09

city: Warszawa

first: Filip

last: Ambrozkiewicz

state: Mazowieckie

address: ul.Roentgena 5

department: Genetics

country: Poland

institute: Centrum Onkologii -  Instytut im. Marii Skłodowskiej - Curie

hyb_protocol: Hybridization was performed on the nCounter Prep Station, and miRNA was detected with an nCounter Digital Analyzer.

data_processing: Data were processed and analyzed with nSolver™ Analysis Software 4.0.

label: miRNA tag

source_name: Stool

label_protocol: miRNA was screened using 100 ng miRNA,  as recommended, and analyzed with nCounter human v2 miRNA expression assay kits, which allow detection of 800 human miRNAs

extract_protocol: Fecal miRNA was isolated from stool samples (approximately 200 mg) using mirVana miRNA Isolation Kits, according to the manufacturer’s protocol.

tag: diseasee status

value: Crohn Disease

tag: activity

value: Non-active


title: 20180518_CentrumOnkologii02_4K_01

scan_protocol: Hybridization was performed on the nCounter Prep Station, and miRNA was detected with an nCounter Digital Analyzer.

value: Control

value: K


title: 20180518_CentrumOnkologii02_4MS_11

value: Active


title: 20180518_CentrumOnkologii02_3MS_08


title: CG072_C9MJ6ANXX_ATTCCT_L005


title: CG073_C9MJ6ANXX_ATCACG_L005


title: CG074_C9MJ6ANXX_CGATGT_L005


title: 20180518_CentrumOnkologii02_5K_02


title: CG071_C9MJ6ANXX_ACTGAT_L005


title: 20180518_CentrumOnkologii02_1SK_04


title: 20180518_CentrumOnkologii02_19MS_12


title: CG070_C9MJ6ANXX_GAGTGG_L005


title: CG069_C9MJ6ANXX_CGTACG_L005


title: CG068_C9MJ6ANXX_GTTTCG_L005


title: 20180518_CentrumOnkologii02_18MS_07


title: 20180518_CentrumOnkologii02_6K_03


title: 20180518_CentrumOnkologii02_12MS_10


title: 20180518_CentrumOnkologii02_10MS_05


title: CG067_C9MJ6ANXX_GTGGCC_L005


title: 20180518_CentrumOnkologii02_15MS_06


title: CG066_C9MJ6ANXX_GTGAAA_L005


title: CG065_C9MJ6ANXX_GTCCGC_L005


title: CG064_C9MJ6ANXX_CCGTCC_L005


title: 20180517_CentrumOnkologii01_6MS_11


title: 20180517_CentrumOnkologii01_5MS_12


title: 20180517_CentrumOnkologii01_3K_03


title: 20180517_CentrumOnkologii01_2SK_05


title: 20180517_CentrumOnkologii01_2MS_10


title: CG062_C9MJ6ANXX_AGTTCC_L005


title: 20180517_CentrumOnkologii01_2K_02


title: CG063_C9MJ6ANXX_ATGTCA_L005


title: 20180517_CentrumOnkologii01_20MS_06


title: 20180517_CentrumOnkologii01_1K_01


title: R42-RACK7 KO-rep2

first: jiao

last: fangfang

address: DongAn Road 131

institute: fudan university

description: R42 gene_fpkm_anno.txt

data_processing:
the nascent RNA-seq reads were mapped to the human genome (hg19) using Bowtie2 (version 2.3.4.3)
the mRNA-seq reads were mapped to human transcripts (Ensembl, Release 91) and genome (hg19) databases using the software Hisat2
Differentially expressed genes are calculated by ballgown program (version 2.12.0) and DESeq program (version 1.32.0)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

source_name: pediatric glioblastomas from the cerebral cortex

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug total RNA were captured by NEBNext Oligo d(T) 25 beads (NEB, USA) , sheared to fragements of ~250bp, and reverse transcripted by NEBNext RNA first and second Strand Synthesis Module(NEB, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: genotype

value: RACK7 CRISPR/Cas9 knock-out

tag: tumor

value: pediatric glioblastomas


title: CG056_C9MJ6ANXX_ACTTGA_L004

tag: sampleID

tag: gender (f=female, m=male)


title: CG060_C9MJ6ANXX_CTTGTA_L005

value: F

tag: age at visit (years)


title: 20180517_CentrumOnkologii01_15SK_04


title: CG059_C9MJ6ANXX_GGCTAC_L005

tag: asthma status (1=yes, 0=no)

value: Peripheral blood mononuclear cells (PBMC)


title: R42-RACK7 KO-rep1

description: R42 gene_fpkm_anno.txt


title: 20180517_CentrumOnkologii01_13MS_08


title: R42-WT H3.3-rep2

description: R42 gene_fpkm_anno.txt

value: wildtype


title: CG058_C9MJ6ANXX_TAGCTT_L005

tag: atopic (1=yes, 0=no)


title: R42-rep2

description: R42 gene_fpkm_anno.txt

value: heterozygous H3.3G34R mutation


title: CG057_C9MJ6ANXX_GATCAG_L004

tag: rv-a positive (1=yes, 0=no)

value: negControl


title: CG055_C9MJ6ANXX_CAGATC_L004

tag: rv-b positive (1=yes, 0=no)


title: 20180517_CentrumOnkologii01_14MS_07


title: R42-WT H3.3-rep1

description: R42 gene_fpkm_anno.txt


title: CG054_C9MJ6ANXX_GCCAAT_L004

tag: rv-c positive (1=yes, 0=no)


title: CG052_C9MJ6ANXX_TGACCA_L004

tag: peptide treatment


title: CG051_C9MJ6ANXX_TTAGGC_L004

tag: cell type


title: CG061_C9MJ6ANXX_AGTCAA_L005


title: R6-RACK7 KO-rep2

description: R6 gene_fpkm_anno.txt


title: 20180517_CentrumOnkologii01_17MS_09


title: CG050_C9MJ6ANXX_CGATGT_L004

value: Pool C


title: CG053_C9MJ6ANXX_ACAGTG_L004


title: TR3

city: Beijing

first: Jiangcheng

last: Shi

address: 38 Xueyuan Road

institute: Peking University

data_processing:
cDNA library construction and sequencing were performed by BGI Genomics using BGISEQ-500 sequencer
Filtering and trimming the reads
Clean reads were mapped to the Mus musculus genome sequence (GCF_000001635.26_GRCm38.p6 )
The miRNA expression values were calculated
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include expression values for each Sample

organism: Mus musculus

source_name: right testicle

growth_protocol: All animals were bred, housed locally at 24°C ±2°C, and were acclimated to standard laboratory conditions (12L:12D cycle) with free access to rodent feed and water.

extract_protocol:
Total RNA was extracted using RNApure High-purity Total RNA Rapid Extraction Kit (Spin-column; BioTeke Corporation, Beijing, China) according to the manufacture’s recommendations.
RNA libraries were prepared for sequencing using standard BGI-500 protocols

tag: strain

value: right testicle

tag: Sex

value: Male

tag: age

value: 8-12 weeks old


title: R6-RACK7 KO-rep1

description: R6 gene_fpkm_anno.txt

tag: tissue


title: TR1


title: TL3

source_name: left testicle

value: left testicle


title: CG049_C9MJ6ANXX_ATCACG_L004

source_name: non-asthmatic control_RV-A peptide pool_PBMC

value: Pool A


title: TL2


title: LR3

source_name: right lung

value: right lung


title: CG044_C9MJ6ANXX_GTTTCG_L004


title: R42-rep1

description: R42 gene_fpkm_anno.txt


title: R6-WT H3.3-rep2

description: R6 gene_fpkm_anno.txt


title: CG045_C9MJ6ANXX_CGTACG_L004


title: R6-WT H3.3-rep1

description: R6 gene_fpkm_anno.txt


title: LL2

source_name: left lung

value: left lung


title: R6-rep2

description: R6 gene_fpkm_anno.txt


title: R6-rep1

description: R6 gene_fpkm_anno.txt


title: Control_Bioreplicate_1_H3K27ac

source_name: iPSC

value: iPSC derived Motor Neuron (iMN)

tag: chip antibody

value: H3K27ac (Abcam, ab4729)

tag: donor

tag: gender

tag: cag repeat length

value: Wild Type

tag: race

value: Caucasian

tag: sample group

value: Control - H3K27ac

tag: culture condition

value: DHT

tag: author reference id


title: LR1


title: TR2


title: LR2


title: CG042_C9MJ6ANXX_GTGAAA_L004

tag: sampleID

tag: gender (f=female, m=male)

value: M

tag: age at visit (years)

tag: asthma status (1=yes, 0=no)

tag: atopic (1=yes, 0=no)

tag: rv-a positive (1=yes, 0=no)

value: Peripheral blood mononuclear cells (PBMC)


title: LL3

tag: strain

tag: Sex


title: CG043_C9MJ6ANXX_GTGGCC_L004

value: F

tag: rv-b positive (1=yes, 0=no)

tag: rv-c positive (1=yes, 0=no)

tag: peptide treatment

tag: cell type


title: ER3

source_name: right eye

tag: tissue

value: right eye

tag: age


title: LL1


title: ER2


title: CG041_C9MJ6ANXX_GTCCGC_L004

source_name: asthmatic_RV-C peptide pool_PBMC

value: Pool C


title: R42-WT H3.3-input

description: 1% ChIP input

data_processing:
The software used to collect and analyze the ChIP-seq data was Bowtie2.2.5.
The ChIP-Seq profiles were normalized to 1 million total tag numbers and peaks were called by MACS2.1.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include peak data for each Sample ...

extract_protocol:
Cells were lysed with lysis buffer and the whole cell lysate was sonicated with a Biorupter sonicator (Diagenode). The RACK7-DNA complexes were isolated with RACK7 antibody.
The sequencing libraries for ChIP-seq were prepared from 2-5ng of DNA using the KAPA Hyper Prep Kits (KAPA, KK8504) according to the manufacturer’s instructions. Completed ChIP-seq libraries were qualified by Bioanalyzer 2100 (Agilent).

tag: chip antibody

tag: genotype

value: wildtype

tag: tumor

value: glioblastomas


title: CG040_C9MJ6ANXX_CCGTCC_L004

tag: sampleID


title: R42-WT H3.3-RACK7

description: RACK7 ChIP-seq


title: R6-WT H3.3-RACK7

description: RACK7 ChIP-seq


title: EL3

source_name: left eye

value: left eye

value: Male

value: 8-12 weeks old


title: EL2


title: TL1

value: left testicle


title: R6-WT H3.3-input

description: 1% ChIP input


title: CG038_C9MJ6ANXX_AGTTCC_L003

source_name: non-asthmatic control_RV-C peptide pool_PBMC

tag: gender (f=female, m=male)


title: WT39-RACK7-rep

description: RACK7 ChIP-seq


title: CG039_C9MJ6ANXX_ATGTCA_L004

tag: age at visit (years)

value: negControl


title: CG037_C9MJ6ANXX_AGTCAA_L003

tag: asthma status (1=yes, 0=no)

value: Pool A


title: Th17 WT1

city: Indianapolis

first: Mark

middle: H

last: Kaplan

state: IN

address: 635 Barnhill Dr. MS 420

department: Microbiology and Immunology

institute: Indiana University

description: Th17 WT1

data_processing:
Libraries were sequenced with 2×50 bp paired-end configuration on an Illumina NovaSeq 6000.
Illumina adapter sequences and low-quality base calls were trimmed off the paired-end reads with Trim Galore v0.4.3.
The resulting high-quality reads were aligned to the mouse reference genome mm10 using bowtie2.
Duplicate reads were discarded with Picard.
Reads mapped to mitochondrial DNA together with low mapping quality reads were excluded from further analysis.
Peaks were detected with MACS2 (version 2.1.0) with parameters "-f BAMPE --nolambda -broad".
Genome_build: UCSC mm10
Supplementary_files_format_and_content: broadPeak BED files were generated from MACS2

growth_protocol: Naïve T cells culture under Th2, Th9 and Th17 condition

extract_protocol:
Cells were washed by 1X PBS and re-suspended in cold PBS. Collected cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2 and 0.1% IGEPAL CA-630)  and the nuclei were pelleted and resuspended in Tn5 enzyme and transposase buffer (Illumina Nextera® DNA library preparation kit, FC-121-1030).
The resulting ATAC-seq libraries were sequenced on Illumina NovaSeq 6000 at CMG of Indiana University School of Medicine and paired-end 50 bp reads were generated

value: spleen

tag: treated

value: in vitro culture


title: Th2 WT3

description: Th2 WT3


title: R42-RACK7-rep

description: RACK7 ChIP-seq

value: heterozygous H3.3G34R mutation


title: Th2 WT1

description: Th2 WT1


title: CG035_C9MJ6ANXX_GGCTAC_L003

tag: atopic (1=yes, 0=no)

tag: rv-a positive (1=yes, 0=no)


title: Th17 WT3

description: Th17 WT3

tag: strain


title: Th9 WT3

description: Th9 WT3


title: R42-input-rep

description: 1% ChIP input


title: WT39-input-rep

description: 1% ChIP input


title: CG036_C9MJ6ANXX_CTTGTA_L003

tag: rv-b positive (1=yes, 0=no)


title: CG033_C9MJ6ANXX_GATCAG_L003

tag: rv-c positive (1=yes, 0=no)


title: R6-RACK7-rep

description: RACK7 ChIP-seq


title: EL1

tag: Sex


title: R6-input-rep

description: 1% ChIP input


title: CG032_C9MJ6ANXX_ACTTGA_L003

tag: peptide treatment

tag: cell type


title: WT39-RACK7

description: RACK7 ChIP-seq


title: CG031_C9MJ6ANXX_CAGATC_L003


title: WT39-input

description: 1% ChIP input


title: P28_V1_Dlx6pos

city: Cambridge

first: Kathryn

last: Allaway

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Disease

institute: Broad Institute

data_processing:
Raw sequencing data were passed through the Cell Ranger ATAC pipeline (10X Genomics, v1.1.0). FASTQ files were generated from BCL files using cellranger-atac mkfastq.
Read filtering, alignment, and barcode counting were performed using cellranger-atac count.
Genome_build: mm10
Supplementary_files_format_and_content: The fragments.tsv.gz file contains  a tabular file where each line represents a unique ATAC-seq fragment. Duplicate reads are collapsed into a single fragment record.
Supplementary_files_format_and_content: The singlecell.csv file contains QC information associated with each barcode for cell-calling.

source_name: primary visual cortex

extract_protocol:
Male hemizygous Dlx6a-Cre mice (Jax stock #008199) were crossed with female homozygous INTACT mice (flox-Sun1-eGFP, Jax stock #021039) to yield Dlx6a-Cre::INTACT offspring for scATAC-seq experiments. Brains from P28 Dlx6aCre::INTACT mice were harvested, sectioned coronally on a mouse brain slicer (Zivic Instruments), and regions of interest were dissected in ice-cold ACSF. Tissue was then transferred to a dounce homogenizer containing Lysis Buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, and 0.01% IGEPAL CA630, 0.001% Digitonin). Tissue was homogenized with 10 strokes of pestle A, 10 strokes of pestle B, and incubated for 5 min on ice before being filtered through a 30 μm filter and centrifuged at 500xg for 10 min at 4C. The pellet was resuspended in 1% BSA for sorting for GFP+ nuclei on a Sony SH800S cell sorter. Nuclei were sorted into Diluted Nuclei Buffer (10X Genomics).
scATAC-seq libraries were prepared using the Chromium Single Cell ATAC Solution (10X Genomics). Libraries were sequenced using a Nova-Seq S1 100 cycle kit (Illumina).

tag: age

tag: genotype/variation

tag: tissue

value: primary visual cortex

value: cortical interneurons


title: CG030_C9MJ6ANXX_GCCAAT_L003

value: Peripheral blood mononuclear cells (PBMC)


title: CG034_C9MJ6ANXX_TAGCTT_L003

value: M


title: HUVEC_AdGFP_rep2

city: Durham

first: Christopher

last: Kontos

state: NC

address: 180A CARL Bldg, 213 Research Dr

department: Cardiology

institute: Duke University

description: Gene expression data from HUVEC overexpressing GFP

hyb_protocol: After processing, samples were hybridized to GeneChip™ HG-U133A_2 (Affymetrix, Santa Clara, CA, USA) in an Affymetrix GeneChip hybridization Oven 645, washed in Affymetrix GeneChip Fluidics Station 450, and scanned with Affymetrix GeneChip Scanner 7G according to standard Affymetrix GeneChip hybridization, wash, and stain protocols.

scan_protocol: Affymetrix scanning protocol according to manufacturer, Affymetrix GeneChip Command Console Scan Control 3.2.3.1515 and Expression Console version 1.2.0.20

data_processing: Partek Genomics Suite 6.5 (Partek Inc., St. Louis, MO) was used to perform data analysis. Robust multi-chip analysis (RMA) normalization was done on the entire data set.

label: biotin

source_name: HUVEC infected with AdGFP

label_protocol: Total RNA was processed and labeled using the Ambion WT expression labeling kit per manufacturer instructions.

growth_protocol: Human umbilical vein endothelial cells (HUVEC) were isolated as described (PMCID: PMC2576276) and cultured in endothelial growth medium (EGM, Lonza CC-3124) supplemented with fetal bovine serum to a final concentration of 10% and 1x antibiotic-antimycotic (Gibco 15240).

extract_protocol: Total RNA was isolated from 1x10^6 cells using the RNeasy kit (Qiagen 74104) following manufacturer instructions and including the optional on-column DNase I digestion step (Qiagen 79254).

treatment_protocol: HUVEC were infected with approximately 5x10^8 pfu/ml adenovirus encoding human Caskin2 variant 1 or GFP overnight in growth medium and allowed to recover for 24 hours in fresh growth medium prior to RNA extraction.

value: human umbilical vein endothelial cell (HUVEC)

value: adenovirus encoding GFP


title: Th9 WT1

description: Th9 WT1


title: R6-RACK7

description: RACK7 ChIP-seq

tag: chip antibody

tag: genotype

tag: tumor


title: R42-RACK7

description: RACK7 ChIP-seq


title: D5: pure pancreatic macrophages (CD45+CD11b+F4/80+) from mice in RAP on d5

first: jinghua

last: wu

state: Shanghai

address: 160 Pujian Rd, Shanghai 200127,China

department: Stem Cell Research Center

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

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

extract_protocol:
Pancreases under RAP were removed. Macropaheges were isolated and sorted by FACSAriaⅡ to get pure macrophages (CD45+CD11b+F4/80+) and RNA was harvested using Trizol reagent. 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® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Balb/c

value: pancreas

value: wild type

tag: treatment

value: post RAP on D5


title: HUVEC_AdGFP_rep1


title: CG027_C9MJ6ANXX_TTAGGC_L003

tag: sampleID

tag: gender (f=female, m=male)

value: F

tag: age at visit (years)

tag: asthma status (1=yes, 0=no)


title: HUVEC_AdCaskin2_rep3

description: Gene expression data from HUVEC overexpressing human Caskin2 variant 1

source_name: HUVEC infected with AdCaskin2

value: adenovirus encoding human Caskin2 variant 1


title: CG029_C9MJ6ANXX_ACAGTG_L003

tag: atopic (1=yes, 0=no)

tag: rv-a positive (1=yes, 0=no)

value: Pool C


title: HUVEC_AdCaskin2_rep2


title: D7: pure pancreatic macrophages (CD45+CD11b+F4/80+) from mice in RAP on d7

tag: strain

value: post RAP on D7


title: HUVEC_AdGFP_rep3


title: D4: pure pancreatic macrophages (CD45+CD11b+F4/80+) from mice in RAP on d4

value: post RAP on D4


title: R42-input

description: 1% ChIP input

value: glioblastomas


title: HUVEC_AdCaskin2_rep1


title: AB5075 adeB::T26ΔadeIJK rep P4a

city: Norman

first: Justyna

middle: Weronika

last: Adamiak

state: OK

address: 101 Stephenson Parkway

department: Chemistry and Biochemistry

institute: University of Oklahoma

data_processing:
Raw data for each sample was analyzed using CLC Genomics Workbench version 12.0.1 software (QIAGEN Aarhus, Denmark), with default settings, based on their proprietary algorithms.
Pairwise comparison of the expression results was performed using the total mapping results for deletion mutants vs wild type.
Differential gene lists were created with 2-fold expression cutoff and significant p-values of <0.05 to identify genes that were up- or down-regulated under each condition.
Genome_build: Raw sequence reads were mapped to the A. baumannii AB5075-UW genome (Accession# CP008706.1)
Supplementary_files_format_and_content: txt files with RPKM values for each sample
Supplementary_files_format_and_content: fastq raw data for each sample

organism: Acinetobacter baumannii

source_name: bacterial cells

growth_protocol: Cells were grown in LB broth until mid-exponential phase (OD600 = 0.5-0.6)

extract_protocol:
Total RNA was isolated from cells using hot phenol method. High quality total RNA was further processed by removing 23S and 16S rRNAs using the MicrobExpress bacterial mRNA enrichment kit (Life Technologies, USA). Final concentrations and purity grades of the samples were determined using Bioanalyzer 2100 (Agilent, USA). Samples with the amount at least 0.5-1 µg were used for library construction and RNA sequencing.
Libraries of depleted RNA were prepared using the Illumina TruSeq RNA LT v2 kit according to the manufacturer's instructions. RNA libraries were prepared for sequencing using Illumina protocols

value: double knockout mutant


title: AB5075 adeB::T26ΔadeIJK rep P4b


title: CG026_C9MJ6ANXX_CGATGT_L003

tag: rv-b positive (1=yes, 0=no)

tag: rv-c positive (1=yes, 0=no)


title: R6-input

description: 1% ChIP input

value: heterozygous H3.3G34R mutation


title: CG025_C9MJ6ANXX_ATCACG_L003

tag: peptide treatment

value: Pool A

tag: cell type


title: ER1

value: right eye

tag: Sex

value: Male

tag: age

value: 8-12 weeks old


title: D1: pure pancreatic macrophages (CD45+CD11b+F4/80+) from mice in RAP on d1

tag: tissue

value: post RAP on D1


title: AB5075 ΔadeIJK rep P3a

tag: genotype

value: single knockout mutant


title: D0: pure pancreatic macrophages (CD45+CD11b+F4/80+) from mock mice in RAP

value: Balb/c

value: pancreas


title: CG028_C9MJ6ANXX_TGACCA_L003

source_name: asthmatic_RV-A peptide pool_PBMC

value: Peripheral blood mononuclear cells (PBMC)


title: AB5075 ΔadeIJK rep P3b


title: CG019_C9Y62ANXX_GTGGCC_L003

value: M


title: Small intestine, Erk1/2-KO rep3

first: Jiwei

last: Chen

address: 500 Dongchuan Rd.

institute: East China Normal University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat v2.1.0.
Raw counts of all genes were estimated by the program “htseq-count” in HTSeq software (version 0.6.0). The number of reads were normalized by R package DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized count for each Sample

source_name: Small intestine

extract_protocol:
Small intestine were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Small intestine

value: post natal day 14


title: AB5075 adeB::T26 rep P2b


title: D3: pure pancreatic macrophages (CD45+CD11b+F4/80+) from mice in RAP on d3

value: wild type

value: post RAP on D3


title: CG020_C9MJ6ANXX_GTTTCG_L003

value: Pool C


title: Small intestine, Erk1/2-KO rep1


title: AB5075 adeB::T26 rep P2a


title: CG018_C9Y62ANXX_GTGAAA_L003

value: F

value: negControl


title: CG017_C9Y62ANXX_GTCCGC_L003


title: Small intestine, Erk1/2-KO rep2


title: RAD21 Stag2-KO siStag1 Rep2

city: Chapel Hill

first: Jill

last: Dowen

address: 250 Bell Tower Drive

institute: University of North Carolina at Chapel Hill

description: Samples were split across two lanes on the sequencer. These were treated as technical replicates and "L1" and "L2" were concatenated for each sample. This was paired-end and only the first read of the pair was used for analysis (samples with "R1")

data_processing:
Any samples that were split scross sequencing lanes were treated as technical replicates and "L1" and "L2" were concatenated for each sample. If the sample was paired-end, only the first read of the pair was used for analysis (samples with "R1"). If more than 50bp reads were acquired, only the first 50bp were used in analysis.
Alignment: reads were aligned to a hybrid mm10+hg38 genome with  bowtie v 1.2.2 with parameters -v 2 -p 24 -S -m 1 --best --strata
PCR Duplicate Removal: duplicates removed with samtools v 1.9 fixmate -m followed by markdup -r -s
Peak Calling: peaks were called using MACS (v 2016-02-15) with parameters -f BED -g mm -q 0.01
Spike-In Normalization Factor: reads mapping to each genome (mouse and human) were counted. Normalization factor = 1/(number human reads / 1,000,000)
Coverage File Generation: bigwig files were generated using bedtools (v 2.26) genomecov with parameters -bga -g mm10.chrom.sizes -scale (Normalization Factor) followed by ucsctools (v 320) bedGraphToBigWig
Genome_build: Custom built bowtie index of Mus musculus build mm10 plus Homo sapiens build hg38
Supplementary_files_format_and_content: For each ChIP sample, a BigWig coverage track of merged replicates is provided for viewing in UCSC genome browser.

source_name: mESC v6.5_RAD21 Stag2-KO siStag1

growth_protocol: Murine embryonic stem cells (v6.5, male) were grown on gelatinized tissue culture dishes under standard ESC conditions as previously described (Whyte et al., 2012).

extract_protocol:
mESCs were crosslinked in 1% formaldehyde for 5 minutes before quenching with 2.5M glycine. Before chromatin extraction, 5% of HEK293T cells was added to the mESC samples to be later used as a spike-in normalization for the indicated experiments. Crosslinked cells were lysed using Lysis Buffer 1 and Lysis Buffer 2 before washing and resuspension in Shearing Buffer. Sonication of nuclei was performed on a Covaris E220 with the following settings: Duty Factor 5, PIP/W 140, and 200 cycles per burst for 12 minutes. Chromatin fragments of 200-1000 base pairs were generated. The antibodies were incubated with 30uL Protein G Dynabeads for 6 hours prior to addition of chromatin. The chromatin in shearing buffer was spiked with NaCL and Triton X-100 to be in a ChIP buffer. Chromatin from 1 x 10^7 cells was added to antibody conjugated beads and incubated rotating overnight at 4C. Beads were then washed with ChIP Buffer and Wash Buffers 1, 2, and 3. Chromatin was eluted and crosslinks were reversed overnight via incubation at 65C and addition of 5ul Proteinase K. The next day, DNA was purified using a Zymo ChIP DNA Clean and Concentrate kit. Sequencing libraries were prepared using Kapa Hyper Prep Kit.
Sequencing libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA).

treatment_protocol: As indicated, cells were counted and 5 x 10^5 were plated per well in 6-well plates. Each well was treated with 50nM of siRNA or siGLO transfection control using DharmaFECT (Dharmacon, Lafayette, CO) transfection reagent following manufacturer’s instructions: siGLO (D-001630-01-0) and siStag1 (M-041989-01-0005). Cell were harvested after 48 hours for crosslinking.

tag: cell line

value: Mouse embryonic stem cells

tag: genotype/variation

value: Stag2 knockout

tag: chip antibody

value: Bethyl A300-080A


title: RAD21 Stag2-KO siStag1 Rep1


title: Small intestine, WT rep3


title: CG021_C9MJ6ANXX_CGTACG_L003

source_name: non-asthmatic control_negControl_PBMC

tag: sampleID

tag: gender (f=female, m=male)


title: Small intestine, WT rep2


title: AB5075 WT rep P1a

value: parent


title: CG015_C9Y62ANXX_ATGTCA_L003

tag: age at visit (years)

tag: asthma status (1=yes, 0=no)


title: Small intestine, WT rep1


title: CG014_C9Y62ANXX_AGTTCC_L003

tag: atopic (1=yes, 0=no)

tag: rv-a positive (1=yes, 0=no)


title: RAD21 WT siStag1 Rep2

source_name: mESC v6.5_RAD21 WT siStag1


title: CG013_C9Y62ANXX_AGTCAA_L003

source_name: non-asthmatic control_RV-A peptide pool_PBMC

tag: rv-b positive (1=yes, 0=no)

value: Pool A


title: RAD21 Stag2-KO siGLO Rep1

source_name: mESC v6.5_RAD21 Stag2-KO siGLO


title: BKO_THRAP3_eCLIP_IP2

city: La Jolla

last: Perelis

email: mperelis@ucsd.edu, perelis@gmail.com

address: Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Dr., Room 3805/Yeo Lab

institute: University of California San Diego

description:
RNA immunoprecipitated using THRAP3 antibody
eCLIP-seq to identify RNA binding sites for THRAP3 in Bmal1 knockout beta cells.

data_processing:
Base calling with Real Time Analysis version 2.4.11
ChIP-seq: alignment with bowtie2 v2.2.4, eCLIP-seq:alignment with STAR v2.4.0i
ChIP-seq: peak calling with Homer
eCLIP-seq: data processing with Clipper
Genome_build: mm10
Supplementary_files_format_and_content: Bed files containing genomic coordinates of ChIP-seq peaks and genome browser-compatible bigwig files used to view and analyze eCLIP-seq data

growth_protocol: cultured in DMEM supplemented with 15% FBS, 1% L-glutamine, and 1% penicillin/streptomycin

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA or protein-RNA complexes were isolated with antibody.
ChIP-seq libraries were generated using NEBNext Ultra II library kits and eCLIP using Illumina Trueseq-based library construction strategy

treatment_protocol: Cells used for ChIP-seq were crosslinked with formaldehyde and for eCLIP-seq were crosslinked with UV irradiation

tag: strain background

value: derived from insulinoma from transgenic mice

tag: mutations

value: CRISPR-CAS9 mediated deletion of Exon 8 in Bmal1

tag: passages

value: 5-15 passages

tag: antibody

value: THRAP3 antibody, Novus Biologicals, Cat. # NB100-40848, lot A1


title: BKO_THRAP3_eCLIP_input2

tag: cell type


title: BKO_THRAP3_eCLIP_input1


title: RAD21 WT siStag1 Rep1


title: CG012_C9Y62ANXX_CTTGTA_L003

value: M

tag: rv-c positive (1=yes, 0=no)

tag: peptide treatment

value: Peripheral blood mononuclear cells (PBMC)


title: BKO_THRAP3_eCLIP_IP1


title: AB5075 WT rep P1b

tag: strain

tag: genotype


title: RAD21 WT siGLO Rep2

source_name: mESC v6.5_RAD21 WT siGLO

tag: cell line

tag: genotype/variation

tag: chip antibody


title: CG011_C9Y62ANXX_GGCTAC_L003

tag: sampleID

tag: gender (f=female, m=male)

tag: age at visit (years)


title: 8P-2

city: Hefei

first: Peijie

last: Zhou

state: Anhui

address: Lujiang road

department: Department of Radiation Oncology, The First Affiliated Hospital of USTC

institute: University of Science and Technology of China

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

source_name: luminal cells

extract_protocol:
prostate were removed, frozen on dry ice, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: prostate epithelium

tag: age

value: post natal 8 weeks


title: 8P-4


title: 8P-3


title: RAD21 WT siGLO Rep1

value: wild type


title: CG016_C9Y62ANXX_CCGTCC_L003

tag: asthma status (1=yes, 0=no)

tag: atopic (1=yes, 0=no)

tag: rv-a positive (1=yes, 0=no)

tag: rv-b positive (1=yes, 0=no)


title: RAD21 Stag2-KO siGLO Rep2

tag: cell type


title: 8C-2


title: 8C-4


title: BKO_THRAP3_ChIPseq_Input

tag: strain background

tag: mutations

tag: passages


title: STAG2 Stag1-KO Rep1

description: Only the first 50 bp were used for subsequent analysis.

source_name: mESC v6.5_STAG2 Stag1-KO

value: Stag1 knockout

value: Bethyl A300-0159A


title: 8C-3

tag: strain

tag: genotype


title: CG010_C9Y62ANXX_TAGCTT_L003

tag: rv-c positive (1=yes, 0=no)

tag: peptide treatment


title: STAG2 Stag1-KO Rep2

tag: cell line

tag: genotype/variation

tag: chip antibody


title: CG009_C9Y62ANXX_GATCAG_L003

tag: sampleID

tag: gender (f=female, m=male)

value: F

tag: age at visit (years)

value: negControl


title: BKO_THRAP3_ChIPseq_rep1

description:
DNA immunoprecipitated using THRAP3 antibody
ChIP-seq to identify DNA binding sites for THRAP3 in Bmal1 knockout beta cells.

tag: antibody


title: CG008_C9Y62ANXX_ACTTGA_L003

tag: asthma status (1=yes, 0=no)

tag: atopic (1=yes, 0=no)

tag: rv-a positive (1=yes, 0=no)

value: Pool C


title: 14P-3

source_name: basal cells

tag: tissue

tag: age


title: STAG1 Stag2-KO Rep2

source_name: mESC v6.5_STAG1 Stag2-KO

tag: cell type

value: Mouse embryonic stem cells

value: Stag2 knockout

value: Bethyl A300-0157A


title: STAG1 Stag2-KO Rep1


title: 14P-1

tag: strain


title: 14P-2

tag: genotype


title: WT_THRAP3_eCLIP_input1

tag: strain background

value: derived from insulinoma from transgenic mice

tag: mutations

tag: passages


title: WT_THRAP3_eCLIP_input2


title: BKO_THRAP3_ChIPseq_rep2

value: CRISPR-CAS9 mediated deletion of Exon 8 in Bmal1


title: CG006_C9Y62ANXX_GCCAAT_L003

tag: rv-b positive (1=yes, 0=no)

tag: rv-c positive (1=yes, 0=no)

tag: peptide treatment


title: WT_THRAP3_eCLIP_IP1

description:
RNA immunoprecipitated using THRAP3 antibody
eCLIP-seq to identify RNA binding sites for THRAP3 in wild type beta cells.

value: 5-15 passages


title: STAG2 WT Rep2

source_name: mESC v6.5_STAG2 WT

tag: cell line

tag: genotype/variation

tag: chip antibody


title: CG007_C9Y62ANXX_CAGATC_L003

tag: sampleID

tag: gender (f=female, m=male)

tag: age at visit (years)

tag: asthma status (1=yes, 0=no)

value: Pool A


title: STAG2 WT Rep1


title: WT_THRAP3_eCLIP_IP2

tag: antibody

value: THRAP3 antibody, Novus Biologicals, Cat. # NB100-40848, lot A1


title: CG005_C9Y62ANXX_ACAGTG_L003

source_name: asthmatic_RV-C peptide pool_PBMC

value: M

tag: atopic (1=yes, 0=no)

tag: rv-a positive (1=yes, 0=no)

tag: cell type

value: Peripheral blood mononuclear cells (PBMC)


title: WT_THRAP3_ChIPseq_Input

tag: strain background


title: CG004_C9Y62ANXX_TGACCA_L003


title: STAG1 WT Rep2

source_name: mESC v6.5_STAG1 WT


title: 14C-2

tag: strain

tag: tissue

value: prostate epithelium

tag: age

value: post natal 8 weeks

tag: genotype


title: CG003_C9Y62ANXX_TTAGGC_L003

tag: rv-b positive (1=yes, 0=no)

tag: rv-c positive (1=yes, 0=no)

tag: peptide treatment


title: CG002_C9Y62ANXX_CGATGT_L003

source_name: non-asthmatic control_RV-C peptide pool_PBMC


title: WT_THRAP3_ChIPseq_rep2

description:
DNA immunoprecipitated using THRAP3 antibody
ChIP-seq to identify DNA binding sites for THRAP3 in wild type beta cells.

tag: mutations

tag: passages


title: sorted germcell ChIPseq_Ovary_Ph

city: Baltimore

first: Allan

middle: C

last: Spradling

address: 3520 San Martin Dr.

department: Embryology

institute: Carnegie Institution/HHMI

data_processing:
RNAseq: reads mapped with Hisat2.1.0, processed with Stringtie1.3.5
RNAseq: raw read counts per gene extracted with htseq0.10.0
ChIPseq: reads mapped with bowtie2.3.2
ChIPseq: MAPQ30 filtered with samtools1.6
ChIPseq: RPM normalized (additionally normalized to spike in if applicaple)
Genome_build: RNAseq: dmel6.02, Ensembl 81; ChIPseq: dmel6.02 (no spike in), dmel6.02/dpse3.0 (D. pseudoobscura spike-in), or dmel6.02/mm10 (mouse spike-in)
Supplementary_files_format_and_content: RNAseq: htseq are text files with raw readcounts, polyA_RNAseq_stringtieO.txt is txt file with TPMs for all genes/samples from stringtie

source_name: sorted germcell ChIPseq_whole ovary

growth_protocol: flies were grown on standard food plus wet yeast paste for 3-6 days

extract_protocol: FACS-purified Drosophila melanogaster germ cells were mixed with either FACS purified Drosophila pseudoobscura follicle cells, mouse embryonic fibroblasts, or in some cases, no spike-in. Sequences were mapped to the D.mel6.02 genome or a hybrid genome of D.mel6.02/D.pse3.0 or D.mel /M.m10 and MAPQ 30 filtered. The ratio of Spike-in to D.mel reads was used to normalize enrichment between IP samples and normalized genome wide read coverage was calculated with Bedtools and supplied as a bigWig file for each sample. Normalized read depth was also was also calculated for overlapping 5kb bins annotated with a 3 or 4 state chromatin model and supplied as a modified bed file.

tag: uas-rnai

tag: developmental stage

value: whole ovary

tag: chip antibody

value: Ph (Buchenau et al., 1998)

tag: spike-in normalization

tag: library construction

value: DNA libraries prepared with Takara Bio ThruPLEX DNA seq


title: CG001_C9Y62ANXX_ATCACG_L003

tag: sampleID

tag: gender (f=female, m=male)

value: F

tag: age at visit (years)

tag: asthma status (1=yes, 0=no)

tag: atopic (1=yes, 0=no)

tag: rv-a positive (1=yes, 0=no)


title: RNA-seq from Clock knockout BetaTC6 cells 2

data_processing:
Sequencing on Illumina NextSeq500 and basecalling by Real-Time Analysis (RTA) software version 2.4.11
Alignment to the mm10 genome using STAR version 2.5.0
mRNA quantitation using featureCounts version 1.5.3 and the option “–t exon” was specified to count mRNA features
Differential expression using DESeq2 version 1.22.1 specifying a false discovery cutoff of 0.01 for independent filtering
Genome_build: mm10
Supplementary_files_format_and_content: Transcripts per kilobase million (TPM) normalized count matrix of mapped reads, and DESeq2 outputs for Bmal1 and Clock knockout comparisons in ".csv" format

source_name: BetaTC6 cells from ATCC (CRL- 11506)

extract_protocol:
Tizol (sigma) and Directzol mini (Zymo)
NEBNext directional mRNA

tag: cell type

value: derived from insulinoma

value: CRISPR-CAS9 mediated deletion of Exons 6-7 in Clock


title: 14-C3

tag: strain

tag: tissue

tag: age

tag: genotype

value: wild type


title: RNA-seq from Clock knockout BetaTC6 cells 1

tag: mutations

tag: passages


title: RNA-seq from Clock knockout BetaTC6 cells 3


title: sorted germcell ChIPseq_GSC_pclGLKD_sortB_Pho

source_name: sorted germcell ChIPseq_FACS purified germ cell

tag: uas-rnai

value: Pcl

value: nos-Gal4, UASp-NLS-GFP

tag: developmental stage

value: bam ovary

tag: tissue/cell type

value: FACS-purified germ cells

value: Ph (Buchenau et al., 1998)o (Brown et al., 2003)


title: sorted germcell ChIPseq_Ovary_In

tag: chip antibody

value: Input

tag: spike-in normalization

tag: library construction


title: RNA-seq from Bmal1 knockout BetaTC6 cells 3

value: CRISPR-CAS9 mediated deletion of Exon 8 in Bmal1

value: 5-15 passages


title: RNA-seq from Bmal1 knockout BetaTC6 cells 2


title: sorted germcell ChIPseq_GSC_sortC_Ph


title: sorted germcell ChIPseq_GSC_pclGLKD_sortB_Ph


title: 14C-1

value: prostate epithelium


title: sorted germcell ChIPseq_GSC_pclGLKD_sortB_In


title: WTCHG_129189_07: pericycle-Pep1-rep3

city: Coventry

first: Patrick

last: Schafer

address: Gibbet Hill Road

department: Life Sciences

country: United Kingdom

institute: University of Warwick

data_processing:
Sequenced reads were mapped to Arabidopsis TAIR10 whole genome using tophat v2.0.14 with default parameters --library-type unstranded
Read counts were counted using htseq-count -f bam -s no -i Parent -t mRNA
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: read counts from htseq-count

organism: Arabidopsis thaliana

source_name: Root pericycle  - Pep1 treated

growth_protocol: Arabidopsis thaliana marker lines for 3 cell types, epidermis, cortex and pericycle (list constructs) plants were grown for 10 days on plates

extract_protocol:
For RNA-extraction, GFP-expressing protoplasts were sorted into Qiagen RLT  lysis  buffer  containing  1%  (v:v)  β-mercaptoethanol, mixed, and immediately frozen at -80 °C. At least 10,000 GFP-expressing protoplasts were sorted per experiment and treatment condition.  Sorting times were kept below 25 min.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Marker lines were treated with 1mM flg22, Pep1 or H2O as a mock and incubated for 1 hr

value: Root pericycle

tag: treatment

value: Pep1 treated


title: RNA-seq from Bmal1 knockout BetaTC6 cells 1


title: STAG1 WT Rep1

tag: cell line

value: Mouse embryonic stem cells

tag: genotype/variation

value: Bethyl A300-0157A


title: WTCHG_129190_05: pericycle-Pep1-rep1


title: RNA-seq from wild type BetaTC6 cells 3


title: WTCHG_129190_07: pericycle-Pep1-rep2


title: AML_U-09-0534_Bulk_Cells

city: Columbus

first: Eileen

middle: Yifan

last: Hu

state: OH

address: Rm 449, 410 West 12th Ave

institute: The Ohio State University

data_processing:
Data were collected and analyzed using the Torrent Server (4462616) with Torrent Suite 5.0 version and 5.6.0.
Variant alleles were called using a combination of the following software:  Variant Caller v.5.0.28 and v.5.6.8-1, IGV v5.01 (0), Ion Reporter v.4.6, Samtools v1.6, Bcftools v1.31 and Ensembl Variant Effect Predictor (VEP) v.92.03.
Genome_build: hg19
Supplementary_files_format_and_content: BAM and VCF files were generated for each sample with Torrent Suite versions 5.0 and 5.6.0 using a combination of the following software: Variant Caller v.5.0.28 and v.5.6.8-1, IGV v5.01 (0), Samtools v1.6, Bcftools v1.31 and Ensembl Variant Effect Predictor (VEP) v.92.03. Excel files showing quanitites of all variant allele frequencies wthin each sample were generated utilizing Ion Reproter version 4.6.

source_name: CD34+/CD38+ tumor cells sorted from blood

growth_protocol: Blood from CLL and AML patients were collected at The Ohio State University Comprehensive Cancer Center (Columbus, OH, USA). PBMCs were isolated using Ficoll density-gradient centrifugation, Ficoll-Paque Plus (GE Healthcare, Uppsala, Sweden) and cryopreserved. Cryopreserved patient primary PBMCs were thawed and briefly cultured in 37oC and 5% CO2 in RPMI 1640 supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2mM L-Glutamine (Invitrogen, Carlsbad, CA, USA), 56U/mL penicillin, and 56ug/mL streptomycin (Invitrogen) post isolation and before sorting. Cell sorting was performed using a BD Bioscience BD FACSAria™ Fusion flow cytometer with a blue, red, yellow-green, violet, and UV laser (BD Biosciences, San Jose, CA, USA). PBMCs from CLL and AML patients were selected and sorted for with the following antibody cocktail: Brilliant Violet 510 anti-human CD19 (Clone HIB19; #302242, Biolegend, San Diego, CA, USA), Alexa Fluor 700 anti-human CD3 (Clone UCHT1; #344822, Biolegend), PE/Cy7 anti-human CD5 (Clone UCHT2; #364008, Biolegend), PE anti-human CD45 (Clone HI30l; #555483, BD Biosciences), APC anti-human CD45 (Clone HI30; #561864, BD Biosciences), Pacific Blue anti-human Lineage Cocktail (#348805, Biolegend), and LIVE/DEAD Fixable Near-IR Dead Cell Stain (#L34975, Invitrogen, Carlsbad, CA, USA). CLL cells were identified as live, CD3-, CD45+, CD19+, and CD5+ cells. AML leukemic blasts were defined as CD45+ and Lin- cells. Briefly, cryopreserved or fresh mononuclear cells from CLL or AML patients were stained with antibody cocktail on ice for half an hour before being washed once and resuspended in DPBS at a concentration of 5 million cells/mL (Gibco, Grand Island, NY, USA). Cells were sorted through an 85um nozzle at a sheath pressure of 45 psi and a drop drive frequency of 60-70 kHz. A highly pure sorting modality (single-cell sorting for FACSAria Fusion) was used for cell numbers less than 1000 into PCR strip tubes. 4-way purity sorting was used for bulk samples (defined as >20000 cells) into 1.5mL Eppendorf tubes.

extract_protocol:
For bulk tumor samples DNA was extracted from isolated CLL and AML cells using the Puregene Core kit A DNA extraction kit (# 158667, Qiagen, Maryland, USA) according to manufacturer recommendations for <1 million cells (Gentra Puregene Handbook).  DNA was quantified using spectrophotometric methods (Nanodrop 2000 from Thermo Scientific) using standard 260/280 OD ratios. 10ng of DNA from bulk samples are used for first step amplification. For low cell number samples (defined as <1000 sorted cells) DNA was prepared from sorted cells using the Single Cell Lysis Kit (#4458235, Invitrogen). Briefly, 9uL of Single Cell Lysis solution (no Dnase I) was directly added to sorted cell droplet. After incubating for 5 minutes at room temperature 1uL of Stop Solution was added to the reaction for 2 minutes at room temperature. 5uL of the total reaction is used for first step amplification.
Libraries were prepared with Ion AmpliSeq Library kit2.0 (4475345) with a custom designed panel of AmpliSeq primers (CLL: IAD14429, 304 amplicons, 2 pools, 31.66kb panel size, 99.63% coverage; AML: IAD145356, 129 amplicons, 2 pools, 15.32kb panel size, coverage 100%; Supplementary Table 1, 2). To run multiple samples on the same chip we used IonExpress barcode adapters (kit#4471250 and #4474009). Libraries were constructed by first amplifying genomic DNA preparations with individual primer pools. Amplification was completed on the GeneAmp PCR system 9700 Dual 96-well thermal cycler from Applied Biosystems, using the following protocol: Initial Hold 99oC-2min followed by 21 cycles for the CLL panel (99oC-15sec, 60oC-4min), 20 cycles for the AML panel (99oC-15sec, 60oC-4min), and a final hold of 10oC. Corresponding PCR product pools were then combined and barcoded with IonExpress barcode adapters. Barcoded PCR products were purified with Agencourt AMPure XP kit (A63881 Beckman Coulter, Indianapolis, Indiana). While bulk extracted DNA libraries were eluted with low TE at this point and directly quantified, libraries constructed with <1000 cells underwent an additional amplification cycle to equalize library amounts using the following protocol: Initial hold of 98oC-2min followed by 5 cycles  (99oC-15sec, 64oC-1min) and a final hold of 10oC. All libraries were quantified using real time PCR with Ion Library TAQMAN Quantitation kit 44688022 on the Applied Biosystems ViiA7 Real Time PCR System instrument to allow for optimal final dilution of library for template preparation.

value: Blood

tag: tumor type

value: acute myeloid leukemia

tag: cell number

tag: extract protocol

value: DNA isolated with Purgene Core Kit A


title: sorted germcell ChIPseq_GSC_sortC_Pho

value: DNA libraries prepared with Takara Bio ThruPLEX DNA seq


title: AML_U-09-0534_200_Cells

tag: tissue

tag: cell type

value: CD34+/CD38+ tumor cells sorted from blood

value: No DNA isolation


title: WT_THRAP3_ChIPseq_rep1

tag: strain background

value: derived from insulinoma from transgenic mice

tag: antibody

value: THRAP3 antibody, Novus Biologicals, Cat. # NB100-40848, lot A1


title: sorted germcell ChIPseq_GSC_sortC_In

value: nos-Gal4, UASp-NLS-GFP

value: bam ovary

value: FACS-purified germ cells


title: RNA-seq from wild type BetaTC6 cells 2

value: derived from insulinoma

tag: mutations

tag: passages

value: 5-15 passages


title: WTCHG_125416_03: pericycle-flg22-rep2

source_name: Root pericycle  - flg22 treated

value: Root pericycle

value: flg22 treated


title: AML_U-11-1361_Bulk_Cells


title: oneduplication2weeks_1

city: Athens

first: Niki

last: Chondrogianni

address: 48 Vassileos Constantinou Ave.

department: Institute of Chemical Biology

country: Greece

institute: National Hellenic Research Foundation

description:
3998405011_C_Grn.idat
replicate 1
HFL_1_D14_a

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using NEQC normalisation using limma in R

label: biotin, Cy3

source_name: HFL-1 cells

label_protocol: Performed with Illumina TotalPrep RNA Amplification Kit

growth_protocol: HFL-1 human embryonic fibroblasts were cultured in Dulbecco’s modified Eagle’s medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (Invitrogen, Carlsbad, CA, USA), 2mM glutamine and 1% non-essential amino acids (complete medium). HFL-1 cells were maintained at 37°C, 5% CO2 and 95% humidity.

extract_protocol: RNA was extracted with Trizol reagent (Invitrogen, Carlsbad, CA, USA)

treatment_protocol: We maintained human primary fetal lung fibroblasts (HFL-1) in culture from a young stage until they reached a senescent stage after 50 replication cycles. The cells were collected at three different time points while undergoing RS. In the first young stage the cells were replicating every 24 hours, in the second middle-aged stage the cells were replicating every 7 days and in the third stage the cells have not replicated for 14 days.

tag: age

value: Senescent


title: oneduplicationweek_1

description:
3998405011_B_Grn.idat
replicate 1
HFL_1_D7_a

value: Middle-aged


title: oneduplicationweek_2

description:
3998405012_B_Grn.idat
replicate 2
HFL_1_D7_b


title: oneduplication2weeks_2

description:
3998405012_C_Grn.idat
replicate 2
HFL_1_D14_b


title: sorted germcell ChIPseq_GSC_PclGLKD_sortA_H3K27me3

description:
processed data file:
4state_enrichment_counts.txt

tag: uas-rnai

value: Pcl

tag: developmental stage

tag: tissue/cell type

value: H3K27me3 (Cell Signaling C36B11 (#139619) Lot 14)

value: mouse embryonic fibroblast culture


title: oneduplicationday_1

description:
3998405011_A_Grn.idat
replicate 1
HFL_1_D1_a

value: Young


title: oneduplicationday_2

description:
3998405012_A_Grn.idat
replicate 2
HFL_1_D1_b


title: sorted germcell ChIPseq_GSC_PclGLKD_sortA_In

tag: chip antibody

value: Input

tag: spike-in normalization

tag: library construction

value: DNA libraries prepared with Takara Bio ThruPLEX DNA seq


title: AML_U-11-1361_300_Cells

value: Blood

value: acute myeloid leukemia

value: CD34+/CD38+ tumor cells sorted from blood

value: No DNA isolation


title: RNA-seq from wild type BetaTC6 cells 1


title: WTCHG_131167_05: pericycle-mock-rep3

source_name: Root pericycle  - mock treated

tag: treatment

value: mock treated


title: AML_U-12-0126_Bulk_Cells

tag: tumor type

value: DNA isolated with Purgene Core Kit A


title: WTCHG_125416_01: pericycle-flg22-rep1


title: sorted germcell ChIPseq_GSC_sortB_Pho

value: nos-Gal4, UASp-NLS-GFP

value: bam ovary

value: FACS-purified germ cells

value: Ph (Buchenau et al., 1998)o (Brown et al., 2003)


title: sorted germcell ChIPseq_GSC_sortB_In


title: AML_U-12-0126_300_Cells

tag: cell number


title: IgG-4_S12

data_processing:
Libraries were sequenced with 2×75bp paired-end configuration on an Illumina NextSeq 500
Illumina adapter sequences and low-quality base calls were trimmed off the paired-end reads with Trim Galore v0.4.3.
The resulting high-quality reads were aligned to the mouse reference genome mm10 using bowtie2.
Peaks were detected with MACS2 (version 2.1.0) with parameters "-f BAMPE --keep-dup all -B -q 0.01", peaks overlapped with the mm10 blacklist were removed.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: narrowPeak BED files were generated from MACS2

growth_protocol: Naïve T cells culture under Th9 and Th17 condition

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: IgG

tag: strain


title: IgG-3_S11


title: BATF-4_S10

value: BATF


title: AML_U-13-0667_Bulk_Cells

tag: tissue

tag: extract protocol


title: WTCHG_131167_01: pericycle-mock-rep1

value: Root pericycle


title: WTCHG_203839_08: epidermis-Pep1-rep3

source_name: Root epidermis - Pep1 treated

value: Root epidermis

value: Pep1 treated


title: AML_U-12-0905_Bulk_Cells

tag: cell type


title: IgG-2_S8

tag: antibody


title: WTCHG_125416_05: pericycle-flg22-rep3

value: flg22 treated


title: BATF-3_S9


title: AML_U-13-0667_300_Cells


title: sorted germcell ChIPseq_2CFC_H3K27me3

description:
processed data file:
3state_enrichment_counts.txt

value: white

value: otu-Gal4, mata-gal4, nos-gal4, UASz-tdTomato

value: 3-6 day old adult

value: FACS-purified 2C follicle cells

value: H3K27me3 (Cell Signaling C36B11 (#139619) Lot 14)

value: DNA libraries prepared with Takara Bio ThruPLEX DNA seq


title: IgG-1_S7


title: AML_U-12-0958_Bulk_Cells

value: Blood

value: acute myeloid leukemia

value: CD34+/CD38+ tumor cells sorted from blood

value: DNA isolated with Purgene Core Kit A


title: BATF-2_S6


title: Input-4-BN5_S4


title: BATF-1_S5


title: WTCHG_203839_06: epidermis-Pep1-rep2


title: sorted germcell ChIPseq_512CNC_wGLKD_Pse_In

value: FACS-purified 512C germ cells

value: Input

value: Drosophila pseudoobscura follicle cells


title: AML_U-12-0905_500_Cells

value: No DNA isolation


title: WTCHG_131167_03: pericycle-mock-rep2

value: Root pericycle

value: mock treated


title: AML_U-14-1295_Bulk_Cells


title: sorted germcell ChIPseq_512CNC_wGLKD_Pse_H3K27me2

value: H3K27me2 (Cell Signaling D18C8 (#9728) Lot 15)


title: sorted germcell ChIPseq_2CFC_In

value: white


title: WTCHG_203839_04: epidermis-Pep1-rep1

value: Root epidermis

value: Pep1 treated


title: WTCHG_203594_10: epidermis-flg22-rep3

source_name: Root epidermis - flg22 treated

value: flg22 treated


title: WTCHG_203594_07: epidermis-flg22-rep2


title: WTCHG_203594_05: epidermis-flg22-rep1


title: sorted germcell ChIPseq_GSC_sortA_H3K4me3

value: nos-Gal4, UASp-NLS-GFP

value: bam ovary

value: FACS-purified germ cells

value: H3K4me3 (Cell Signaling C42D8 (#9751) Lot 7)

value: mouse embryonic fibroblast culture


title: Input-1-BN2_S1


title: WTCHG_203594_03: epidermis-mock-rep2

source_name: Root epidermis - mock treated


title: Input-3-BN4_S3


title: WTCHG_203594_01: epidermis-mock-rep1


title: WTCHG_203839_01: epidermis-mock-rep3


city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

description: total RNA-seq from sample S12 CS status C. scindens (ATCC(R) 35704)  Mus musculus

data_processing:
Transcript-level quantitation with Salmon
Gene level summarization with txImport
Normalization with DESeq2
Differential expression with DESeq2
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: normalized gene level counts for GRCm38 genes

source_name: Granulocyte macrophage progenitors

growth_protocol: Five week old male CBA/J mice (Jackson Laboratories or RAG 1 KO mice (Jackson Laboratories) were housed in a specific pathogen?free facility in micro isolator cages and provided autoclaved food (Lab diet 5010) and water ad libitum. Specific pathogen free status was monitored quarterly. A sentinel mouse was removed from each room and was humanely euthanized for serologic evaluation, examination of pelage for fur mites, and examination of cecal contents for pinworms. The serologic assays, conducted in-house using CRL reagents, are MHV, EDIM, GD-7, MVM, MPV, and MNV, (Sendai, PVM, RPV/ KRV/H-1, M. pulmonis). In the final quarter, a comprehensive serology was performed which included the above agents plus K-virus, MCMV, MTV, LCM, Ectromelia, Polyomavirus, Reovirus-3, and mouse adenoviruses (K87 and FL). All procedures were approved by the Institutional Animal Care and Use Committee of the University of Virginia. All experiments were performed according to provisions of the USA Animal Welfare Act of 1996 (Public Law 89.544).

extract_protocol:
RNA was isolated  from approximately 17,000 sorted GMPs  utilizing the Qiagen RNeasy Micro Kit.
Ribosomal reduction was performed to concentrate for mRNA. Directional cDNA libraries were generated and samples sequenced in multiplex (50PE reads) using the Illumina HiSeq v4 platform. For library prep, the NEBNext(R) Ultra? Directional RNA Library Prep Kit for Illumina(R) and NEBNext(R) rRNA Depletion Kit (Human/Mouse/Rat) and alternate protocol for  low yield RNA and 15 PCR cycles of amplification was utilized. For sequencing, libraries were sequenced with the NGS NextSeq kit - 150 cycle High Output Kit, paired end 75x75 bp read.

treatment_protocol: CBA/J mice were colonized with bile acid 7?-dehydroxylating bacteria C. scindens (ATCC(R) 35704) over three weeks prior to intracecal infection with E. histolytica. Mice were gavaged with 100ul of overnight culture at an optical density of 1.4 at 600nm or media control (BHI, Anerobe Systems, AS-872) once per week.

tag: agent

value: C. scindens (ATCC(R) 35704)

value: CBA/J

tag: Sex

value: male


title: AML_U-18-1272_500_Cells

value: Blood

value: acute myeloid leukemia

value: CD34+/CD38+ tumor cells sorted from blood


title: AML_U-18-1272_Bulk_Cells

value: DNA isolated with Purgene Core Kit A