title: CLL_02_PostIbrutinib_1_2

value: chronic lymphocytic leukemia


title: Nr3

status: Public on Aug 10 2020

type: SRA

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

description: total RNA after removing rRNA

library_source: transcriptomic

data_processing:
bcl2fastq(v2.16.0.10) were used for base calling
Raw reads were first discarded if containing more than 2-N bases, then reads were processed by clipping adaptor, removing low quality bases, and discarding too short reads (less than 16nt). FASTX-Toolkit (Version 0.0.13) was used to get the clean reads.
After that, clean reads were aligned to the human GRCH38 genome by tophat2 (Kim et al., 2013). Aligned reads with more than one genome location were discarded due to their ambiguous location.
Uniquely localized reads were used to calculate reads number and FPKM value (FPKM represents fragments per kilobase and per million) for each gene according to reads and genes genome location.
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: tab-separate text file,the gene expression FPKM and Reads file

molecule: total RNA

organism: Homo sapiens

source_name: retina

extract_protocol:
Total RNA was extracted from tissue or cell samples by using TRIzol Reagent (Ambion) following the manufacturer’s instructions. RQ1 DNase (promega) was added to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agarose gel electrophoresis.
For each sample，50ng of total RNA was used for RNA-seq library preparation. Ribosomal RNAs were depleted with Ribo-Zero™ rRNA depletion kit for human (Epicentre) before used for directional RNA-seq library preparation. Purified RNA was fragmented ，and Reverse transcription was performed with random primer harboring adaptor sequence and a randomized hexamer，then synthesized DNA with Terminal-Tagging oligo cDNA using ScriptSeq™ v2 RNA-Seq Library Preparation Kit(epicentre). The cDNAs were purified and amplified. PCR products corresponding to 300-500 bps were purified, quantified and stored at -80°C until used for sequencing.

tag: disease

value: Normal retina

tag: tissue

value: retina


title: Nr2

description: total RNA after removing rRNA


title: CLL_02_PreIbrutinib_1_2

city: Columbus

first: Eileen

middle: Yifan

last: Hu

state: OH

address: Rm 449, 410 West 12th Ave

country: USA

institute: The Ohio State University

library_source: genomic

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.

molecule: genomic DNA

source_name: CD5+/CD19+ 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

tag: treatment/time-point

value: Pre-Ibrutinib

tag: cell type

tag: cell number

tag: extract protocol

value: No DNA isolation


title: Nr1

description: total RNA after removing rRNA


title: CLL_02_PreIbrutinib_1_1

value: CD5+/CD19+ tumor cells sorted from blood


title: ccRCC CD8 T cell + anti-CD3/CD28 + IL7

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

data_processing:
cell ranger2.2 (scRNAseq)
seurat/phate/monocle (scRNAseq)
fastqc for read quality (bulk RNAseq)
salmon quant (bulk RNAseq)
edgeR (bulk RNAseq)
fgsea (bulk RNAseq)
Genome_build: hg19 (scRNAseq)
Genome_build: hg38 (bulk RNAseq)
Supplementary_files_format_and_content: sparse matrix (scRNAseq)
Supplementary_files_format_and_content: quant.sf (bulk RNAseq)

molecule: polyA RNA

source_name: ccRCC CD8 T cell + anti-CD3/CD28 + IL7

extract_protocol:
10x Genomics Single Cell Protocols
Chromium Single Cell 5'
5' capture

value: ccRCC tumor

value: CD8 T cell

tag: treatment

value: anti-CD3/CD28 + IL7


title: Ip3

description: total RNA after removing rRNA

source_name: Retinal neovascular proliferative membrane

value: abbreviations of type I diabetes

value: whole part


title: CLL_01_PostIbrutinib_6_2

value: Post-Ibrutinib


title: ccRCC CD8 T cell + anti-CD3/CD28

source_name: ccRCC CD8 T cell + anti-CD3/CD28


title: RCC_13-CD8_48B

source_name: peripheral CD8 T cell

value: PMBC


title: CLL_01_PostIbrutinib_6_1


title: Ip1

description: total RNA after removing rRNA


title: Cells from human pancreatic islets of Langerhans [6929806060_R03C02]

type: genomic

city: Bruxelles

first: Jean-Valery

last: Turatsinze

address: Route de Lennik 808 CP618

department: Faculté de Medecine

country: Belgium

institute: Université Libre de Bruxelles

description:
6929806060_R03C02
Pancreatic islet cells

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

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

data_processing: GenomeStudio software v2010.2, Methylation module v1.7.0.

label: Cy5 and Cy3

source_name: Pancreatic islets of Langerhans

label_protocol: Standard Illumina protocol.

growth_protocol: After isolation, islets were incubated at 37°C in CMRL 1066 medium with 10% fetal calf serum for 24 h prior to shipment at room temperature in the same culture medium. Upon arrival, samples were recultured at 37°C in Ham's F-10 medium containing 10% fetal bovine serum (FBS), 2 mM GlutaMAX, 50 U/ml penicillin and 50 μg/ml streptomycin (GIBCO), 6.1 mM glucose, 50 μM 3-isobutyl-1-methylxanthine, 1% BSA (Sigma).

extract_protocol: Genomic DNA was extracted and purified from primary pancreatic cells using Qiagen QiaAMP Kit according to standard instructions. The recommended RNase treatment was performed.

treatment_protocol: Dissociation of human islets was achieved by incubation with accutase (Millipore) supplemented with 5 U/ml of DNase 1 at 37°C for 10-15 min. The dissociated cells were washed with 1% BSA in PBS and cultured in islet standard medium and followed by Newport Green labeling.

value: Dispersed primary pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [6929806060_R06C01]

description:
6929806060_R06C01
Pancreatic islet cells


title: Ip2

description: total RNA after removing rRNA


title: Cells from human pancreatic islets of Langerhans [7471147042_R04C01]

description:
7471147042_R04C01
Pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [6929806060_R04C01]

description:
6929806060_R04C01
Pancreatic islet cells


title: ccRCC CD8 T cell + IL7

source_name: ccRCC CD8 T cell + IL7


title: ccRCC CD8 T cell + anti-CD3

source_name: ccRCC CD8 T cell + anti-CD3


title: Cells from human pancreatic islets of Langerhans [6929742057_R01C01]

description:
6929742057_R01C01
Pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [6929806060_R01C02]

description:
6929806060_R01C02
Pancreatic islet cells


title: IIsp1

description: total RNA after removing rRNA

value: abbreviations of type II diabetes

value: surrounding part


title: CLL_01_PostIbrutinib_5_1

value: chronic lymphocytic leukemia


title: CLL_01_PostIbrutinib_4_2


title: IIsp2

description: total RNA after removing rRNA


title: peripheral CD8 T cell + anti-CD3/CD28

source_name: peripheral CD8 T cell + anti-CD3/CD28


title: peripheral CD8 T cell + anti-CD3/CD28 + IL7


title: CLL_01_PostIbrutinib_4_1


title: Cells from human pancreatic islets of Langerhans [6929806060_R02C01]

description:
6929806060_R02C01
Pancreatic islet cells


title: IIrp2

description: total RNA after removing rRNA

value: optic disc


title: IIrp1

description: total RNA after removing rRNA


title: peripheral CD8 T cell + anti-CD3

source_name: peripheral CD8 T cell + anti-CD3


title: CLL_01_PostIbrutinib_3_2


title: Cells from human pancreatic islets of Langerhans [6929742057_R05C02]

description:
6929742057_R05C02
Pancreatic islet cells


title: peripheral CD8 T cell + IL7

source_name: peripheral CD8 T cell + IL7


title: IIrbp2

description: total RNA after removing rRNA

value: hemal arch part and optic disc


title: Cells from human pancreatic islets of Langerhans [6929742028_R06C01]

description:
6929742028_R06C01
Pancreatic islet cells


title: CLL_01_PostIbrutinib_5_2

value: Blood


title: CLL_01_PostIbrutinib_3_1


title: CLL_01_PostIbrutinib_2_2


title: Human_AA_skin

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 500 Newton Road

department: Dermatology

institute: University of Iowa

data_processing:
Basecalls were converted into FASTQs using the Illumina bcl2fastq software by the University of Iowa Genomics Division
10x data was processed with the Cell Ranger pipeline, version 3.1
Genome_build: mm10 and GRCh38
Supplementary_files_format_and_content: tab-delimited tsv files for genes and cell barcodes, mtx single-cell expression matrix, csv of CDR3 contig sequences

source_name: CD45+ Immune Cells

extract_protocol:
CD45+ immune cell populations were flow sorted in parallel. Single-cell suspensions were processed with the Chromium Single Cell 5-prime Library & Gel Bead Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin

tag: condition

value: AA


title: naive CD14 cells S20

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

country: Germany

institute: Philipps-Universität Marburg

description: naive CD14 cells (rep 3)

data_processing:
RTA version 2.4.11 was used for basecalling
bcl2fastq version 2.18.0.2 was used for demultiplexing
Reads were mapped using the CLC genomics workbench version 10.01 and the GRCh38 human genome annotation with standard settings: mismatch cost = 2; insertion cost = 3; deletion cost = 3; length fraction = 0.8; similarity fraction = 0.8.
RPKMs were calculated for genes using the CLC genomics worbench version 10.01
Genome_build: hg38
Supplementary_files_format_and_content: text file with genes and abundance

source_name: Peripheral blood leukocytes

growth_protocol: PBMCs’ isolated monocytes from buffy-coats (1.8x105), diluted in 500 µL of cRPMI, were routinely seeded per well (day 0) on treated Costar 24-well plates and let adhere for 24h before adding 500 µL CSC-H460 (0.2x105 cells), thus starting day 1 of experimental time-lapse for assaying fusion event. Cells were recovered after four days (d4, 96 hours) by gently tip-scraping of wells and posterior measurement of surface markers expression by FACS was done.

extract_protocol:
High-Pure RNA isolation kit (Roche) was used to isolate total RNA from sorted fractions (co-cultured CD14+ monocytes, co-CD14; GFP+ tumour cells, GFP; CD14+GFP+ hybrids, CD14/GFP) and parallel PBMCs’ adherence-isolated monocytes, naïve-CD14.
Libraries were prepared using Vertis Biotech mRNA library generation protocols

treatment_protocol: Puromycin-dependent GFP-expressing H460 cells were achieved by infection with pGIPZ-shRNAmir-NS lentiviral vector. CSC-H460 were obtained by culture in non-treated Costar plates with selective DMEM/F-12 supplemented with 2 mmol/L L-Glutamine, 5 mmol/L Hepes, 0.4% BSA, N2 supplement and 20 ng/mL of EGF and bFGF.

value: macrophage

tag: precursor

value: CD14+ monocyte

tag: donor

value: healthy, unknown


title: SBMA_Bioreplicate_4

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

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 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) 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 (http://www.usadellab.org/cms/?page=trimmomatic). Surviving intact pairs of reads per library were next reference mapped against the current instance of the human genome (GRCh38.82) using the RNA-Seq tool supported in v11 of the CLCbio Genomics Workbench (www.qiagenbioinformatics.com). After, expression per known annotated gene (Homo_sapiens.GRCh38.82.chr.gtf) was enumerated and exported in Transcripts Per Kilobase Million (TPM) units.
Genome_build: GRCh38.82
Supplementary_files_format_and_content: One tab-delimited text file per sequenced library is provided. Each of these text files describes the gene expression observed in the sample in Transcript Per Kilobase Million (TPM) units.

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:
RNA was extracted from cells using Trizol-Chloroform and purified using the Qiagen RNeasy Mini kit.
Libraries were prepared from 500 ng of total RNA using the TruSeq Stranded RiboZero Gold kit  (Cat. No. 20020599, Illumina, Inc.). Sequencing was paired-end (2x75bp) for a target depth of 100M read pairs per sample using an Illumina HiSeq 4000.

value: iPSC derived Motor Neuron (iMN)

tag: age

tag: gender

value: Male

tag: cag repeat length

tag: race

value: Caucasian

tag: sample group

value: Spinal and Bulbar Muscular Atrophy (SBMA)

tag: culture condition

value: DHT

tag: author reference id


title: Cells from human pancreatic islets of Langerhans [6929742028_R06C02]

description:
6929742028_R06C02
Pancreatic islet cells

value: Dispersed primary pancreatic islet cells


title: IIr2

description: total RNA after removing rRNA

tag: disease

value: abbreviations of type II diabetes

tag: tissue

value: retina


title: CLL_01_PostIbrutinib_2_1

tag: tumor type

value: chronic lymphocytic leukemia

tag: treatment/time-point

value: Post-Ibrutinib

value: CD5+/CD19+ tumor cells sorted from blood

value: No DNA isolation


title: IIrbp1

description: total RNA after removing rRNA

value: hemal arch part and optic disc


title: Cells from human pancreatic islets of Langerhans [6929742057_R05C01]

description:
6929742057_R05C01
Pancreatic islet cells

tag: cell type


title: Cells from human pancreatic islets of Langerhans [6929742038_R06C01]

description:
6929742038_R06C01
Pancreatic islet cells


title: IIr1

description: total RNA after removing rRNA


title: Cells from human pancreatic islets of Langerhans [7471147042_R02C02]

description:
7471147042_R02C02
Pancreatic islet cells


title: CLL_02_PostIbrutinib_4_1

value: Blood

tag: cell number

tag: extract protocol


title: SBMA_Bioreplicate_3


title: IIp3

description: total RNA after removing rRNA

value: whole part


title: SBMA_Bioreplicate_2


title: SBMA_Bioreplicate_1


title: IIp2

description: total RNA after removing rRNA


title: Cells from human pancreatic islets of Langerhans [7471147042_R01C01]

description:
7471147042_R01C01
Pancreatic islet cells


title: CLL_01_PreIbrutinib_1_2

value: Pre-Ibrutinib


title: CLL_01_PostIbrutinib_1_1


title: CLL_01_PostIbrutinib_1_2


title: AR_KO_Bioreplicate_3

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

value: "AR KO-3"


title: Cells from human pancreatic islets of Langerhans [6929806060_R02C02]

description:
6929806060_R02C02
Pancreatic islet cells


title: AR_KO_Bioreplicate_2

value: iPSC derived Motor Neuron (iMN)

value: Male

value: "AR KO-2"


title: CLL_01_PreIbrutinib_1_1


title: VKOR_plasmid_library

city: Seattle

first: Douglas

last: Fowler

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: plasmid DNA

data_processing:
Library strategy: barcoded variant screen
Libraries were sequenced on NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis software.
Sequencing reads were converted to fastq format and de-multiplexed with bcl2fastq. Barcode paired sequencing reads for all VKOR abundance and activity replicates were joined using PEAR software (https://cme.h-its.org/exelixis/web/software/pear/). FASTQ files from technical replicate amplification were concatenated for analysis with Enrich2.
The abundance and activity scores for VKOR were calculated as follows: The count for each variant in a bin was divided by the sum of counts recorded in that bin to obtain the frequency of each variant within that bin. This calculation was repeated for every bin in each replicate experiment. The summed counts of each variant in all four bins of an experiment was divided by the summed counts of all variants in all four bins of an experiment to obtain the total frequency value for each variant for each experiment. This total frequency value was used for filtering low-frequency variants out of the subsequent calculations. Next, a weighted average (w_ave) was calculated for each variant, with all weighted average values ranged from a value of 0.25 to 1. Finally, for each experiment, an abundance or activity score for each variant was obtained by subjecting the weighted average of each variant to min-max normalization, using the weighted average value of synonymous variants, which was given a score of 1, and the median weighted average value for non-terminal nonsense variants at positions 21 through 142, which was given an abundance score of 0. The final activity or abundance score for each variant was calculated by taking the mean of the min-max normalized scores across the replicate experiments in which it could have been observed. Only variants which were scored in two or more replicate experiments were retained in the analysis. A standard error for each score was calculated by dividing the standard deviation of the min-max normalized values for each variant by the square root of the number of replicate experiments in which it was observed. Lastly, the lower bound of the 95% confidence interval was calculated by multiplying the standard error with the 97.5 percentile value of a normal distribution and subtracting this product from the abundance score. The upper bound of the 95% confidence interval was calculated by instead adding the product with the score.
Genome_build: NONE
Supplementary_files_format_and_content: The VKOR_barcode_map.tsv.gz  processed data file is in gzip-compressed tab-separated text file format, containing the variant-barcode map determined by subassembly.

organism: synthetic construct

source_name: Escherichia coli plasmid library

growth_protocol: HEK 293 and HEK293T TetBxb1BFP cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/mL penicillin, 0.1 mg/mL streptomycin, and 2.5 μg/mL doxycycline.

extract_protocol:
Cells were collected, pelleted by centrifugation and stored at −20 °C. Genomic DNA was prepared using a DNEasy kit, according to the manufacturer’s instructions (Qiagen), with the addition of a 30 min incubation at 37 °C with RNAse in the re-suspension step.
Eight 50 μl first-round PCR reactions were each prepared with a final concentration of ~50 ng μl−1 input genomic DNA, 1 × Q5 High-Fidelity Master Mix and 0.25 μM of the KAM499/VKORampR 1.1 primers. The reaction conditions were 98 °C for 30 s, 98°C for 10 s, 65°C for 20 s, 72°C for 60 s, repeat 5 times, 72°C for 2 min, 4°C hold. Eight 50 μl reactions were combined, bound to AMPure XP (Beckman Coulter), cleaned and eluted with 21 μl water. Forty percent of the eluted volume was mixed with Q5 High-Fidelity Master Mix; VKOR_indexF_1.1 and one of the indexed reverse primers, PTEN_seq_R1a through PTEN_seq_R2a, were added at 0.25 μM each. These reactions were run with Sybr Green I on a BioRad MiniOpticon; reactions were denatured for 3 minutes at 95°C and cycled 20 times at 95°C for 15s, 60°C for 15s, 72°C for 15s with a final 3 min extension at 72°C. The indexed amplicons were mixed based in relative fluorescence units and run on a 1% agarose gel with Sybr Safe and gel extracted using a freeze and squeeze column (Bio-Rad). The product was quantified using Kapa Illumina Quant kit.


title: IIp4

description: total RNA after removing rRNA


title: IIp1

description: total RNA after removing rRNA


title: IInp3

description: total RNA after removing rRNA

value: nasal side


title: Cells from human pancreatic islets of Langerhans [6929742057_R04C02]

description:
6929742057_R04C02
Pancreatic islet cells

value: Dispersed primary pancreatic islet cells


title: Control_Bioreplicate_2

value: Wild Type

value: Asian

value: Control

value: DHT


title: IInp2

description: total RNA after removing rRNA

value: abbreviations of type II diabetes


title: Control_Bioreplicate_3


title: IIbp4

description: total RNA after removing rRNA

value: hemal arch


title: Control_Bioreplicate_4

value: Caucasian


title: AR_KO_Bioreplicate_1

value: "AR KO-1"


title: IInp1

description: total RNA after removing rRNA


title: Control_Bioreplicate_1


title: Cells from human pancreatic islets of Langerhans [6929806060_R01C01]

description:
6929806060_R01C01
Pancreatic islet cells


title: Untreated, biological rep3 [Het3 H]

type: RNA

first: Jill

last: Rafael-Fortney

address: 460 W. 12th Ave

department: Physiology & Cell Biology

hyb_protocol: Labeled cDNA targets were hybridized to Affymetrix GeneChip® Clariom D array, Mouse for 16 h at 45°C, rotating at 60 and and stained using the GeneChip Fluidics Station 450 rpm.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G

data_processing:
Arrays were normalized using the gene-level SST RMA algorithm in Expression Console software and comparisons were made in Transcriptome Analysis Console software (Affymetrix).
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: Biotin

organism: Mus musculus

label_protocol: cDNA was labeled and fragmented using the GeneChip WT PLUS Reagent Kit Affymetrix following the manufacturer’s instructions.

growth_protocol: Dystrophin-deficient, utrophin haplo-insufficient (utrn+/-; mdx) “Het” mice on a C57BL/10 background were bred in-house, genotyped and used in this study. Het mice were randomly assigned into treated and untreated groups.

extract_protocol: RNA was isolated with TRIzol reagent, DNase-treated using RQ1 DNase (Promega #M610) and further purified using RNeasy mini kit (Qiagen #74104) ; RNA integrity was analyzed with an Agilent 2100 Bioanalyzer (Agilent Technologies), and all samples had RNA integrity numbers above 7.3 and 260/280 ratios between 1.7 and 2.1.

treatment_protocol: Het treated mice were given a custom diet Teklad Rodent Chow #7912 containing 100 ppm (parts per million) finerenone (Bayer AG, Wuppertal, Germany). Untreated Het mice mice received Teklad Rodent Chow #7912 without medication. Mice were started on treatment at 4 weeks-of-age at weaning or left untreated and were all sacrificed at 20 weeks-of-age.

tag: strain background

tag: genotype/variation

tag: Sex

value: male

value: 20 weeks old

tag: treatment

value: none; untreated

value: heart ventricular tissues


title: Cells from human pancreatic islets of Langerhans [7471147018_R06C02]

description:
7471147018_R06C02
Pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [6929742038_R06C02]

description:
6929742038_R06C02
Pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [7471147046_R05C02]

description:
7471147046_R05C02
Pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [6929806060_R03C01]

description:
6929806060_R03C01
Pancreatic islet cells


title: Untreated, biological rep2 [Het2 H]

value: Dystrophin-deficient, utrophin haplo-insufficient (utrn+/-; mdx)

tag: age


title: IIbp3

description: total RNA after removing rRNA


title: Cells from human pancreatic islets of Langerhans [6929742038_R05C01]

description:
6929742038_R05C01
Pancreatic islet cells


title: Finerenone, biological rep3 [AF3 H]

value: finerenone


title: Untreated, biological rep1 [Het1 H]


title: Cells from human pancreatic islets of Langerhans [7471147018_R04C01]

description:
7471147018_R04C01
Pancreatic islet cells


title: Patient tumor [scRNA-Seq]

city: La Jolla

last: Li

state: California

address: 9500 Gilman Dr

department: Pediatrics

institute: University of California, San Diego

data_processing:
Basecalls performed using FastQC v0.11.8
RNA-seq reads and MeRIP reads were aligned to the mm10 genome assembly using STAR aligner version 2.6.
Data were filtered using cutadapt: Phred quality score > 30 and remove adapters
peaks were called using m6A viewer and MACS2 using the following configuration: m6Aviewer: p-value 0.05, min enrichment 2, fdr 0.05, Peak de-convolution running mode ; MACS2: fdr 0.05 with --call-summit option
Raw read gene counts are generated using htseq-count; normalized read gene counts are generated by DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt format: contains raw gene counts for RNA-seq samples, xlsx: contains normailzed gene expression by DESeq2; bigBed: contains common peaks detecting by both peak-calling tools

source_name: Patient tumor

extract_protocol: The freshly dissected tissue biopsies were digested to single-cell suspension and filtered with a 70μm nylon mesh. Dead cells were removed by dead cell removal kit (Stemcell technologies), and viable cells were counted.Cells were then washed with 0.04% RNase-free BSA in PBS and used for single cell RNA Seq.  Reverse transcription, cDNA amplification and library preparation were carried out following manufacturer’s protocols (Chromium Single Cell 3’ Library & Gel Bead Kit v2, 10X Genomics). Completed libraries were sequenced on an Illumina HiSeq 4000.

treatment_protocol: Cancer immunotherapy by PD-1 antibody and GVAX in mice

tag: tissue/cell type

value: tumor biopsies

tag: passages

value: fresh tumor from patient

tag: experiment type

value: scRNA-Seq


title: Cells from human pancreatic islets of Langerhans [6929806060_R04C02]

description:
6929806060_R04C02
Pancreatic islet cells

value: Dispersed primary pancreatic islet cells


title: Finerenone, biological rep2 [AF2 H]


title: oxic_6

city: Vienna

first: Lena

last: König

address: Althanstrasse 14

country: Austria

institute: University of Vienna

description:
whole symbiotic marine nematodes
rRNA-depleted RNA containing both nematode and symbiont RNA

data_processing:
Based on quality assessment of raw sequencing reads using FastQC (Andrews, 2010) and prinseq-lite (Schmieder and Edwards, 2011), reads were trimmed and filtered using Trimmomatic (Bolger et al., 2014) and prinseq-lite as follows:  18 nucleotides were removed from the 5-prime end (HEADCROP), Illumina adapters were removed (ILLUMINACLIP:TruSeq3-SE.fa:2:30:10), reads were trimmed when the average quality of a five-base sliding window dropped below a phred score of 20 (SLIDINGWINDOW:5:20), 3-prime poly-A tails were trimmed (-trim_tail_right 1), and only reads longer than 24 nucleotides were kept (MINLEN:25).
Trimmed reads were mapped to the symbiont (Ca. Thiosymbion oneisti) genome draft using BWA-backtrack (Li and Durbin, 2009) with default settings, only uniquely mapped reads were kept using SAMtools (Li et al., 2009), and the number of strand-specific reads per predicted gene were counted using HTSeq in the union mode of counting overlaps (Anders et al., 2014).
Genome_build: Ca. Thiosymbion oneisti GenBank accession JAAEFD000000000
Supplementary_files_format_and_content: txt files with 2 columns each; column 1 contains locus tag IDs (genes), column 2 contains read counts

organism: Laxus oneistus

source_name: Laxus oneistus associated with Ca. Thiosymbion oneisti

growth_protocol: Laxus oneistus individual worms were collected on multiple field trips (2016-2019) at approximately 1 m depth from sand bars off the Smithsonian Field Station, Carrie Bow Cay in Belize (16°48′11.01″N, 88°4′54.42″W). The nematodes were extracted from the sediment by gently stirring the sand and pouring the supernatant seawater through a 212 μm mesh sieve. The retained meiofauna was collected in a petri dish, and single worms of similar size (1-2 mm length, representing adult L. oneistus) were handpicked by forceps (Dumont 3, Fine Science Tools, Canada), under a dissecting microscope. Right after collection, the nematodes were incubated under four different conditions.

extract_protocol:
RNA was extracted using the NucleoSpin RNA XS Kit (Macherey-Nagel). Briefly, sets of 50 worms in RNA storage solution were thawed and the worms were transferred into 90 µl lysis buffer RA1 containing Tris (2-carboxyethyl) phosphine (TCEP) according to the manufacturer. The remaining RNA storage solution was centrifuged to collect any detached bacterial cells (10 min, 4°C, 16,100 x g), pellets were resuspended in 10 µl lysis buffer RA1 (plus TCEP) and then added to the worms in lysis buffer. To further disrupt cells, suspensions were vortexed for two minutes followed by three cycles of freeze (-80°C) and thaw (37°C), and homogenization using a pellet pestle (Sigma-Aldrich) for 60 s with a 15 s break after 30 s. Any remaining biological material on the pestle tips was collected by rinsing the tip with 100 µl lysis buffer RA1 (plus TCEP). Lysates were applied to NucleoSpin Filters and samples were processed as suggested by the manufacturer, including an on-filter DNA digest. RNA was eluted in 20 µl RNase-free water. To remove any residual DNA, a second DNase treatment was performed using the Turbo DNA-free Kit (Thermo Fisher Scientific), RNA was then dissolved in 17 µl RNase-free water, and the RNA quality was assessed using a Bioanalyzer (Agilent). To check whether all DNA was digested, real-time quantitative PCR using the GoTaq qPCR Master Mix (Promega) was performed targeting a 158 bp stretch of the sodB gene using primers specific for the symbiont (sodB-F: GTGAAGGGTAAGGACGGTTC, sodB-R: AATCCCAGTTGACGATCTCC, 10 µM per primer). Different concentrations of genomic Ca. T. oneisti DNA were used as positive controls. The program was as follows: 1x 95°C for 2 min, 40x 95°C for 15 s and 60°C for 1 min, 1x 95°C for 15 s, 55°C to 95°C over 20 min. Next, bacterial and eukaryotic rRNA was removed using the Ribo-Zero Gold rRNA Removal Kit (Epidemiology) (Illumina) following the manufacturer’s instructions, but volumes were adjusted for low input RNA (Alberti et al., 2014). In short, 125 µl of Magnetic Beads Solution, 32.5 µl Magnetic Bead Resuspension Solution, 2 µl Ribo-Zero Reaction Buffer and 4 µl Ribo-Zero Removal Solution were used per sample. RNA was cleaned up via ethanol precipitation, dissolved in 9 µl RNase-free water, and rRNA removal was evaluated using the Bioanalyzer RNA Pico Kit (Agilent).
Strand-specific, indexed cDNA libraries were prepared using the SMARTer Stranded RNA-Seq Kit (Takara Bio USA). Library preparation was performed according to the instructions, with 8 µl of RNA per sample as input, 3 min fragmentation time, two rounds of AMPure XP Beads (Beckman Coulter) clean-up before amplification, and 18 PCR cycles for library amplification. The quality of the libraries was assessed via the Bioanalyzer DNA High Sensitivity Kit (Agilent). Libraries were sequenced on an Illumina HiSeq 200 instrument (single-read, 100 nt) at the next generation sequencing facility of the Vienna BioCenter Core Facilities (VBCF, https://www.viennabiocenter.org/facilities/). Demultiplexing was provided by the VBCF.

treatment_protocol: Batches of 50 freshly collected L. oneistus individuals per condition were incubated for 24 h in the dark in 13 ml-exetainers (Labco, Lampeter, Wales, UK) fully filled with 0.2 µm-filtered seawater. Moreover, different oxygen concentrations were applied: (1) high oxygen (exetainers were kept open and submerged in an aquarium constantly bubbled with air), (2) hypoxic (exetainers were kept open and were exposed to air), (3) anoxic (exetainers were kept inside polyethylene glove bags (AtmosBag; Sigma-Aldrich) that were flushed with N2 gas, together with incubation media and all vials, for at least 1 h before closing), and (4) anoxic with 11 µM sulfide (Na2S*9H2O) added ((exetainers were kept inside polyethylene glove bags (AtmosBag; Sigma-Aldrich) that were flushed with N2 gas, together with incubation media and all vials, for at least 1 h before closing). After the 24 h incubations, each set of 50 worms was quickly transferred into 2 ml RNA storage solution (13.3 mM EDTA disodium dihydrate pH 8.0, 16.6 mM sodium citrate dihydrate, 3.5 M ammonium sulfate, pH 5.2), kept at 4°C overnight, and finally stored in liquid nitrogen until RNA extraction.

tag: incubation condition

value: oxic

tag: replicate


title: IIbp1

description: total RNA after removing rRNA

tag: disease


title: IIbp2

description: total RNA after removing rRNA

tag: tissue


title: oxic_5


title: Bp4

description: total RNA after removing rRNA

value: branch retinal vein occlusion


title: oxic_4


title: Cells from human pancreatic islets of Langerhans [6929742057_R06C02]

description:
6929742057_R06C02
Pancreatic islet cells


title: R120G

city: Cinicnnati

first: Katherine

middle: E

last: Yutzey

address: 240 Albert Sabin Way

department: Divison of Molecular Cardiovascular Biology

institute: Cinicnnati Children's Hospital Medical Center

description: run2375_lane12_read*_indexD701-D504=R120G

data_processing:
Fastq files were trimmed to remove adapter and low quality sequences using Cutadapt
Trimmed reads were mapped to the reference Rattus norvegicus (Rn6) using TopHat
Quantification was done using Cufflinks
Genome_build: Rat Rn6
Supplementary_files_format_and_content: Tab-delimited text files for FPKM

organism: Rattus norvegicus

source_name: Neonatal rat ventricle myocytes

growth_protocol: Neonatal rat ventricular myocytes were primarily isolated and cultured in DMEM+10%FBS. After AdCryABR120G infection, cells were cultured in DMEM+2%FBS for 5 days prior to RNA extraction.

extract_protocol:
Total RNA was extracted and pooled from NRVMs per group using RNAzol reagent (Molecular Research Center; RN190) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using Illumina Truseq stranded mRNA protocol

treatment_protocol: NRVMs were infected with CryABR120G adenovirus and either siUbe2v1 or AdUbe2v1. Five days later, cells were collected. Each group was in triplicate.

value: Sprague-Dawley

value: Neonatal Day 1-2

value: AdCryABR120G infection

tag: cell type source

value: Primarily isolated from heart

value: Neonatal rat ventricle myocytes (NRVMs)


title: RSIV1

description: run2375_lane12_read*_indexD702-D503=Rsiv1

value: AdCryABR120G infection with siUbe2v1 transfection


title: RADV1

description: run2375_lane12_read*_indexD703-D502=Radv1

value: Coinfection with AdCryABR120G and AdUbe2v1


title: anoxic_5

value: anoxic, without added sulfide


title: CTR

value: Untreated


title: Cells from human pancreatic islets of Langerhans [6929793139_R06C02]

description:
6929793139_R06C02
Pancreatic islet cells


title: Bp2

description: total RNA after removing rRNA


title: Bp3

description: total RNA after removing rRNA


title: pre-infusion CAR-NKT (mixed samples)

city: Houston

first: Leonid

last: Metelitsa

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Cell count matrices were produced using the Cell Ranger Single-Cell Software Suite (V 3.1.0) with a human transcriptome reference (GRCh38) with the following modifications:  (1) The GD2-CAR construct sequence was added. (2) In order to avoid an erroneous cross-mapping of the GD2-CAR ScFv transcripts to Immunoglubulin (IG) genes, the IG sequences were removed from the reference.
Genome_build: GRCh38
Supplementary_files_format_and_content: Data analysis was done using Seurat (V 3.1.1). Seurat code is publicly available. Product. Matrix containing raw counts generating using Seurat v3.1.5 samples were dehashed and singlets were extracted by applying HTODemux (1) on CLR-normalized data with 0.95 as the positive quantile.
Cell hashing was performed as follows:
Run1 - patient 1 - Biolegend TotalSeq-C hashtag 1
Run1 - patient 2 - Biolegend TotalSeq-C hashtag 2
Run1 - patient 3 - Biolegend TotalSeq-C hashtag 6
Run2 - patient 1 - Biolegend TotalSeq-C hashtag 1 and 2
Run2 - patient 2 - Biolegend TotalSeq-C hashtag 3 and 5
Run2 - patient 3 - Biolegend TotalSeq-C hashtag 6 and 7

source_name: pre-infusion CAR-NKT from three cancer patients

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from peripheral blood leukapheresis products using Ficoll gradient purification, and NKTs were isolated utilizing a special lot of anti-iNKT microbeads (Miltenyi Biotech) and the CliniMACS instrument (Miltenyi Biotech). Enriched NKTs were then stimulated with alpha-galactocylceramide (GlycoSyn)-pulsed PBMCs and cultured with IL-2 and IL-21 (NCI, 200U/mL and CellGenix, 10ng/mL respectively). Cells were transduced with retroviral particles encoding the GD2-CAR-IL15 construct in RetroNectin-coated plates (Takara Bio) for 72 hours then washed, replated, and cultured at 38C for 9-15 days.

extract_protocol:
Samples were processed twice with the 10x Genomics V(DJ) v1.1 kit
10x Genomics V(DJ) v1.1

tag: individual

value: Patients 1-3

value: CAR engineered NKT cells

value: 6-12 years old

tag: gender

value: male

tag: disease state

value: Stable disease, Partial response


title: anoxic_4


title: Cells from human pancreatic islets of Langerhans [6929793122_R01C01]

description:
6929793122_R01C01
Pancreatic islet cells

tag: cell type

value: Dispersed primary pancreatic islet cells


title: PCM_27908_LPS4

status: Public on Aug 09 2020

city: Chicago

first: Luis

middle: B

last: Barreiro

state: IL

address: 900 East 57th Street

department: Genetic Medicine

institute: Chicago University

data_processing:
Reads were trimmed from Illumina adapter sequence from the ends of the reads and remove bases with quality scores < 20
STAR software was used to align the reads to reference genomes
Gene expression estimates were obtained by summing the number of reads that mapped uniquely to each species annotated genome using HTSeq-count
Genome_build: hg19 for human; CHIMP2.1.4 for chimpanzee; MMUL 1.0 for macaque; PapAnu2.0 for olive baboon species.
Supplementary_files_format_and_content: cram files of aligned reads to species genomes

organism: Papio anubis

source_name: Baboon whole blood stimulation

growth_protocol: 1 ml of species blood was incubated in Truculture tube pre prepared with stimulant (lipopolysaccharide or gardiquimod) or negative control (endotoxin-free water)

extract_protocol:
RBC lysis and RNA extraction of total white blood cells was carried out after stimulation
Messenger RNA (mRNA) was 491 isolated by magnetic bead and converted into RNA libraries using the Illumina TruSeq RNA 492 Library preparation kit v2 according to the manufacturer’s instructions

treatment_protocol: TruCulture tubes + species blood were incubated for 4 and 24 hours time points

value: whole blood

value: LPS

tag: time points

value: M

tag: individual id


title: PCF_28589_LPS4

tag: Sex

value: F


title: PCF_26198_LPS4

tag: treatment


title: PCM_27908_NC4

value: NC


title: PCM_28740_LPS4


title: PCM_28740_NC4


title: PCF_28285_NC4


title: PCF_28285_LPS4


title: Finerenone, biological rep1 [AF1 H]

tag: strain background

tag: genotype/variation

value: Dystrophin-deficient, utrophin haplo-insufficient (utrn+/-; mdx)

tag: age

value: 20 weeks old

value: finerenone

value: heart ventricular tissues


title: Cells from human pancreatic islets of Langerhans [6929793139_R05C01]

description:
6929793139_R05C01
Pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [6929793129_R01C02]

description:
6929793129_R01C02
Pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [6929793122_R02C01]

description:
6929793122_R02C01
Pancreatic islet cells


title: PCM_28740_NC24


title: PCM_28740_GARD4

value: GARD


title: PCM_28740_LPS24


title: PCM_27908_LPS24


title: PCM_28740_GARD24


title: PCM_27908_GARD24


title: PCF_28285_NC24


title: PCM_26322_LPS4


title: PCF_28285_GARD4


title: PCF_28285_LPS24


title: PCF_28075_LPS24


title: PCM_26800_GARD24


title: PCF_28075_NC24


title: PCM_27908_GARD4


title: PCF_28075_NC4


title: PCF_28075_GARD4


title: Cells from human pancreatic islets of Langerhans [6929793129_R03C01]

description:
6929793129_R03C01
Pancreatic islet cells


title: PCM_26800_LPS24


title: PCF_28285_GARD24


title: PCM_26800_NC24


title: PCM_27908_NC24


title: Cells from human pancreatic islets of Langerhans [6929793129_R01C01]

description:
6929793129_R01C01
Pancreatic islet cells


title: PCM_26800_GARD4


title: PCM_26322_NC24


title: Cells from human pancreatic islets of Langerhans [6929793122_R05C01]

description:
6929793122_R05C01
Pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [6929793122_R06C02]

description:
6929793122_R06C02
Pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [6929793122_R04C01]

description:
6929793122_R04C01
Pancreatic islet cells


title: PCM_26322_GARD24


title: Cells from human pancreatic islets of Langerhans [6929793122_R02C02]

description:
6929793122_R02C02
Pancreatic islet cells


title: PCM_26322_LPS24


title: PCF_26198_NC24


title: PCM_26322_NC4


title: PCF_28589_GARD24


title: PCF_28589_LPS24


title: PCF_28589_NC4


title: PCF_28589_NC24


title: PCM_26322_GARD4


title: PCF_26198_GARD24


title: PCF_28589_GARD4


title: PCF_26198_LPS24


title: HSM_101043_LPS4

source_name: Human whole blood stimulation


title: HSM_101053_GARD24


title: HSM_101053_LPS24


title: HSM_101043_GARD4


title: HSF_100753_LPS24


title: HSF_100753_GARD4


title: HSF_100443_GARD24


title: HSF_100243_NC24


title: HSF_100443_NC4


title: HSF_100243_NC4


title: HSF_100443_LPS4


title: HSF_100243_LPS24


title: HSF_100243_GARD4


title: PCF_28075_GARD24


title: HSM_101053_LPS4


title: HSM_101053_NC4


title: HSM_100633_NC24


title: HSF_100443_LPS24


title: HSF_100443_GARD4


title: HSM_100633_GARD24


title: HSF_100753_NC4


title: HSF_100243_GARD24


title: PCF_26198_NC4


title: HSM_101043_NC4


title: HSM_101043_GARD24


title: HSM_100633_NC4


title: HSM_100633_GARD4


title: HSM_100633_LPS24


title: HSM_100633_LPS4


title: HSM_101043_LPS24


title: HSM_101043_NC24


title: HSM_101053_NC24


title: HSF_100753_GARD24


title: HSF_100753_NC24


title: HSF_100243_LPS4


title: HSF_100753_LPS4


title: HSF_100443_NC24


title: Hypothalamus, E12 Foxd1 CreGFP/+; Ctnnb1 Ex3/+ (2)

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

data_processing:
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Seurat and Scanpy were used to perform downstream analysis following the standard pipeline using cells with more than 500 genes and 1000 UMI counts. Clusters were annotated based on previous literature, and differential gene expression test was performed in each cluster, between treatment groups.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx (scRNA-Seq count matrix), barcodes.tsv (scRNA-Seq barcodes list) , genes.tsv (scRNA-Seq genes list), log2cpm*.rds (log2cpm matrix of aggregated dataset), tSNE.rds (tSNE data of aggregated dataset), umap.rds (UMAP data of aggregated dataset)

source_name: Hypothalamus

extract_protocol:
scRNA-Seq - following the manufacturer's (10x Genomics)
scRNA-Seq (Illumina NextSeq500)

tag: strain

value: CD1 & C57BL/6J

value: Hypothalamus

value: embryonic 12 days

tag: genotype

value: mutant


title: Hypothalamus, E12 Foxd1 CreGFP/+; Ctnnb1 Ex3/+ (1)


title: Hypothalamus, E12 Foxd1 Cre/+

value: wild type


title: Hypothalamus, E12 Foxd1 CreGFP/-; Dlx1/2 lox/lox (2)


title: Hypothalamus, E12 Nkx2.2 Cre/Cre (1)


title: Hypothalamus, postnatal P45 time point (2)

value: postnatal 45 days


title: Hypothalamus, E12 Nkx2.2 Cre/+


title: Hypothalamus, postnatal P14 time point

value: postnatal 14 days


title: Hypothalamus, E12 Nkx2.1 CreERT2/CreERT2 (2)


title: Hypothalamus, E12 Nkx2.2 Cre/Cre (2)


title: Hypothalamus, postnatal P8 time point

value: postnatal 8 days


title: Hypothalamus, E12 Foxd1 CreGFP/-; Dlx1/2 lox/lox (1)


title: Hypothalamus, E12 Foxd1 CreGFP/-; Dlx1/2 lox/+


title: HSM_101053_GARD4

value: whole blood


title: Hypothalamus, embryonic E16 time point (2)

value: embryonic 16 days


title: Hypothalamus, postnatal P4 time point

value: postnatal 4 days


title: Hypothalamus, postnatal P45 time point (1)


title: Hypothalamus, E12 Nkx2.1 CreERT2/+


title: Hypothalamus, embryonic E16 time point (1)


title: Hypothalamus, embryonic E15 time point (2)

value: embryonic 15 days


title: Hypothalamus, embryonic E13 time point

value: embryonic 13 days


title: Hypothalamus, embryonic E12 time point


title: Hypothalamus, embryonic E15 time point (1)


title: Hypothalamus, embryonic E11 time point

value: embryonic 11 days


title: Hypothalamus, embryonic E10 time point

value: embryonic 10 days


title: Hypothalamus, E12 Nkx2.1 CreERT2/CreERT2 (1)


title: 322_Input_E32C_girl_IVF-FET.1

first: Yong

last: Peng

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

data_processing:
For duplicated reads that aligned to the same position with the same orientation, only the read with highest mapping quality was retained to prevent potential PCR bias by using picard (http://broadinstitute.github.io/picard/). The nonredundant reads with no more than 2% mismatches that uniquely mapped to the reference genome were retained for further analyses.
The MACS2 peak caller (version 2.1.0) with the parameter settings “--keep-dup=1, --broad” was used to identify peaks of histone modifications.
The R/Bioconductor package DiffBind, which employs DESeq2 or edgeR to identify differential peaks (DPs) with q-values < 0.05 and fold changes > 2 for H3K4me1, H3K4me3, H3K27ac, and H3K27me3, respectively, was also used. The shared outputs of the DESeq2 and edgeR methods were taken as the final DPs.
human GRCh38/hg38

source_name: input

growth_protocol: Genomic DNA (gDNA) was extracted from stored whole blood samples using the QIAmp DNA Blood Mini Kit (Qiagen, cat.: 51106), according to manufacturer’s instruction and stored in -80 ℃ if not used immediately.

extract_protocol:
Before read mapping, adapters, low-quality bases in the reads and reads smaller than 50 bases were removed with Trimmomatic to optimize the paired-end alignments.
The remaining reads were aligned to the Homo sapiens reference genome (human GRCh38/hg38) using the Burrows-Wheeler Aligner (BWA) with the default parameters in paired-end mode.

treatment_protocol: Briefly, isolated nuclei were sonicated into fragments of an average of 200–500 bp using an M220 Focused-ultrasonicator (Covaris) with the following parameters: burst, 200; cycle, 20%; and intensity, 8. After centrifugation (13000 rpm for 10 min at 4°C), sheared chromatin in supernatant was precleared by incubating the samples with protein A Dynabeads (Invitrogen, cat.: 10002D) at 4°C for 1 h with rotation.

value: input


title: 331_Input_E25C_girl_ICSI-ET.1


title: 431_Input_E15C_boy_ICSI-ET.1


title: 421_Input_E35C_boy_IVF-FET.1


title: 321_Input_E14C_girl_IVF-FET.1


title: 2_Input_E65D_girl_CTRL.1


title: Hypothalamus, embryonic E18 time point

value: embryonic 18 days


title: 241_Input_E45D_boy_ICSI-FET.1


title: 31_Input_E95D_girl_ICSI-ET.1


title: 31_Input_E95C_girl_ICSI-ET.1


title: 2_Input_E65C_girl_CTRL.1


title: 232_Input_E115C_boy_ICSI-ET.1


title: 212_Input_E69D_girl_IVF-ET.1


title: 212_Input_E69C_boy_IVF-ET.1


title: Hypothalamus, embryonic E14 time point

value: embryonic 14 days


title: 211_Input_E18D_boy_IVF-ET.1


title: 241_Input_E45C_girl_ICSI-FET.1


title: 202_Input_E114D_girl_CTRL.1


title: 211_Input_E18C_girl_IVF-ET.1


title: 202_Input_E114C_boy_CTRL.1


title: 201_Input_E98D_boy_CTRL.1


title: 231_Input_E111D_boy_ICSI-ET.1


title: 231_Input_E111C_girl_ICSI-ET.1


title: 201_Input_E98C_girl_CTRL.1


title: 232_Input_E115D_girl_ICSI-ET.1


title: 1_Input_E103D_girl_CTRL.1


title: 1_Input_E103C_girl_CTRL.1


title: 11_Input_E29D_girl_IVF-ET.1


title: 11_Input_E29C_girl_IVF-ET.1


title: 111_Input_E113D_boy_IVF-ET.1


title: 102_Input_E56C_boy_CTRL.1


title: 111_Input_E113C_boy_IVF-ET.1


title: 101_Input_E24D_boy_CTRL.1


title: 102_Input_E56D_boy_CTRL.1


title: 92_A62F_father_ICSI-FET

data_processing:
Paired-end 150-nucleotide (nt) RRBS reads were generated with a HiSeq X Ten sequencer. Before read mapping, adapters, low-quality bases in the reads and reads smaller than 50 bases were removed with Trim Galore (www.bioinformat-ics.babraham.ac.uk/projects/trim_galore) and Cutadapt63 to optimize the paired-end alignments.
The remaining reads were aligned to the Homo sapiens reference genome (human GRCh38/hg38) using Bismark (version 0.18.1) with the parameter “--bowtie2”.
The uniquely mapped reads with less than 2% mismatch were retained for further analyses. Bisulfite conversion efficiency was estimated by aligning the reads to the spiked-in phage λ genome.
Then, the number of reads supporting C (methylated) and supporting T (unmethylated) for each covered CpG site was determined with the Bismark methylation extractor. Only the CpG sites with greater than fivefold read coverage (>=6) were passed to the script “bismark2bedGraph” in Bismark to generate a bedGraph file as well as a coverage file, both of which were sorted by chromosomal position.
DMRs between any two groups of RRBS samples were identified with the R/Bioconductor package methylKit, which uses logistic regression to calculate p-values.
human GRCh38/hg38
Bismark coverage file (CpG sites with with reads number >= 6)

source_name: umbilical cord blood

extract_protocol:
Genomic DNA (gDNA) was extracted from stored whole blood samples using the QIAmp DNA Blood Mini Kit (Qiagen, cat.: 51106), according to manufacturer’s instruction and stored in -80 ℃ if not used immediately.
In brief, approximately 0.3% unmethylated lambda DNA (dam-; dcm-) (Thermo Scientific, cat.: SD0021) was spiked into 500 ng of high-quality gDNA, and the mixture was digested by MspI (Thermo Scientific, cat.: ER0541). After purification with Agencourt AMPure XP beads (Agencourt, cat.: A63881), the digested DNA was end-repaired and tailed with deoxyadenosine using Klenow Fragment exo- (Thermo Scientific, cat.: EP0422). Then, NEBNext adapters (NEB, cat.: E7335) were ligated overnight with T4 DNA ligase at a high concentration (NEB, cat.: M0202M) with subsequent digestion by Uracil-Specific Excision Reagent (USER) enzyme (NEB, cat.: M5505L).

value: umbilical cord blood

value: father

tag: art type

value: ICSI-FET


title: 101_Input_E24C_boy_CTRL.1


title: 92_A62M_mother_ICSI-FET

value: mother


title: 92_A62D_boy_ICSI-FET

value: boy


title: 91_W871M_mother_ICSI-FET


title: 91_W871F_father_ICSI-FET


title: 91_W871C_boy_ICSI-FET


title: 82_W1647M_mother_ICSI-ET

value: ICSI-ET


title: 91_W871D_boy_ICSI-FET


title: 83_W1719D_boy_ICSI-ET


title: 83_W1719C_boy_ICSI-ET


title: 83_W1719F_father_ICSI-ET


title: 82_W1647D_boy_ICSI-ET


title: 82_W1647F_father_ICSI-ET


title: 82_W1647C_boy_ICSI-ET


title: 81_W1579M_mother_ICSI-ET


title: 73_W1398M_mother_IVF-FET

value: IVF-FET


title: 73_W1398C_boy_IVF-FET


title: 73_W1398D_boy_IVF-FET


title: 72_W1733F_father_IVF-FET


title: 81_W1579C_boy_ICSI-ET


title: 72_W1733M_mother_IVF-FET


title: 73_W1398F_father_IVF-FET


title: PCM_26800_NC4

value: whole blood

value: NC

value: M


title: 71_W1365C_boy_IVF-FET


title: 71_W1365D_boy_IVF-FET


title: 63_W779M_mother_IVF-ET

value: IVF-ET


title: 71_W1365M_mother_IVF-FET


title: 92_A62C_boy_ICSI-FET


title: 71_W1365F_father_IVF-FET


title: 81_W1579D_boy_ICSI-ET


title: 81_W1579F_father_ICSI-ET


title: 63_W779F_father_IVF-ET


title: 63_W779C_boy_IVF-ET


title: 62_W58M_mother_IVF-ET


title: 63_W779D_boy_IVF-ET


title: 62_W58F_father_IVF-ET


title: 62_W58C_boy_IVF-ET


title: 61_E113M_mother_IVF-ET


title: 72_W1733D_boy_IVF-FET


title: 61_E113D_boy_IVF-ET


title: 61_E113F_father_IVF-ET


title: 72_W1733C_boy_IVF-FET


title: 61_E113C_boy_IVF-ET


title: 6_A32D_girl_CTRL

value: girl

value: CTRL


title: 6_A32C_girl_CTRL


title: 56_E117D_boy_CTRL


title: 55_A33D_boy_CTRL


title: 56_E117C_boy_CTRL


title: 54_A29C_boy_CTRL


title: 53_E123M_mother_CTRL


title: 53_E123F_father_CTRL


title: 53_E123D_boy_CTRL


title: 53_E123C_boy_CTRL


title: 52_E56M_mother_CTRL


title: 52_E56F_father_CTRL


title: 52_E56D_boy_CTRL


title: 52_E56C_boy_CTRL


title: 51_E24M_mother_CTRL


title: 51_E24F_father_CTRL


title: 51_E24D_boy_CTRL


title: 62_W58D_boy_IVF-ET


title: 5_A15C_girl_CTRL


title: 83_W1719M_mother_ICSI-ET


title: 42_A59M_mother_ICSI-FET


title: 5_A15D_girl_CTRL


title: 51_E24C_boy_CTRL


title: 42_A59F_father_ICSI-FET


title: 41_W845M_mother_ICSI-FET


title: 41_W845C_girl_ICSI-FET


title: 41_W845D_girl_ICSI-FET


title: 54_A29D_boy_CTRL


title: 42_A59C_girl_ICSI-FET


title: 42_A59D_girl_ICSI-FET


title: 55_A33C_boy_CTRL


title: 41_W845F_father_ICSI-FET


title: 4_E103C_girl_CTRL


title: 4_E103M_mother_CTRL


title: 34_W89D_girl_ICSI-ET


title: 34_W89C_girl_ICSI-ET


title: 4_E103D_girl_CTRL


title: 33_W1276D_girl_ICSI-ET


title: 33_W1276F_father_ICSI-ET


title: 33_W1276M_mother_ICSI-ET


title: 33_W1276C_girl_ICSI-ET


title: 32_W655F_father_ICSI-ET


title: 32_W655D_girl_ICSI-ET


title: 32_W655C_girl_ICSI-ET


title: 31_E95F_father_ICSI-ET


title: 31_E95D_girl_ICSI-ET


title: 31_E95C_girl_ICSI-ET


title: 32_W655M_mother_ICSI-ET


title: 3_E8M_mother_CTRL


title: 4_E103F_father_CTRL


title: 292_W1531F_father_ICSI-FET


title: 3_E8D_girl_CTRL


title: 293_W1656C_boy_ICSI-FET


title: 292_W1531M_mother_ICSI-FET


title: 3_E8C_girl_CTRL


title: 293_W1656M_mother_ICSI-FET


title: 293_W1656F_father_ICSI-FET


title: 291_W618M_mother_ICSI-FET


title: 282_W928M_mother_ICSI-ET


title: 282_W928F_father_ICSI-ET


title: 282_W928C_boy_ICSI-ET


title: 281_W766M_mother_ICSI-ET


title: 291_W618F_father_ICSI-FET


title: 281_W766F_father_ICSI-ET


title: 274_E35M_mother_IVF-FET


title: 31_E95M_mother_ICSI-ET


title: 274_E35F_father_IVF-FET


title: 274_E35C_boy_IVF-FET


title: 273_W104M_mother_IVF-FET


title: 3_E8F_father_CTRL


title: 273_W104C_boy_IVF-FET


title: 272_W88M_mother_IVF-FET


title: 271_W1149F_father_IVF-FET


title: 271_W1149M_mother_IVF-FET


title: 272_W88F_father_IVF-FET


title: 292_W1531C_boy_ICSI-FET


title: 271_W1149C_boy_IVF-FET


title: 291_W618C_boy_ICSI-FET


title: 263_W1452F_father_IVF-ET


title: 262_W76M_mother_IVF-ET


title: 263_W1452C_boy_IVF-ET


title: 263_W1452M_mother_IVF-ET


title: 261_E23M_mother_IVF-ET


title: 262_W76C_boy_IVF-ET


title: 281_W766C_boy_ICSI-ET


title: 262_W76F_father_IVF-ET


title: 261_E23C_boy_IVF-ET


title: 261_E23F_father_IVF-ET


title: 253_A91C_boy_CTRL


title: 252_A87F_father_CTRL


title: 252_A87C_boy_CTRL


title: 252_A87M_mother_CTRL


title: 253_A91F_father_CTRL


title: 251_E16M_mother_CTRL


title: 273_W104F_father_IVF-FET


title: 251_E16C_boy_CTRL


title: 242_W39F_father_ICSI-FET


title: 242_W39C_girl_ICSI-FET


title: 241_W1699C_girl_ICSI-FET


title: 24_W28M_mother_IVF-FET


title: 241_W1699M_mother_ICSI-FET


title: 24_W28F_father_IVF-FET


title: 24_W28D_girl_IVF-FET


title: 24_W28C_girl_IVF-FET


title: 253_A91M_mother_CTRL


title: 234_W200F_father_ICSI-ET


title: 234_W200C_girl_ICSI-ET


title: 232_W924F_father_ICSI-ET


title: 233_W934C_girl_ICSI-ET


title: 232_W924M_mother_ICSI-ET


title: 233_W934F_father_ICSI-ET


title: 251_E16F_father_CTRL


title: 232_W924C_girl_ICSI-ET


title: 231_W808C_girl_ICSI-ET


title: 242_W39M_mother_ICSI-FET


title: 231_W808M_mother_ICSI-ET


title: 23_W811M_mother_IVF-FET


title: 23_W811C_girl_IVF-FET


title: 23_W811F_father_IVF-FET


title: 23_W811D_girl_IVF-FET


title: 223_E32F_father_IVF-FET


title: 223_E32M_mother_IVF-FET


title: 223_E32C_girl_IVF-FET


title: 241_W1699F_father_ICSI-FET


title: 222_W857M_mother_IVF-FET


title: 234_W200M_mother_ICSI-ET


title: 222_W857C_girl_IVF-FET


title: 221_E14M_mother_IVF-FET


title: 221_E14F_father_IVF-FET


title: 222_W857F_father_IVF-FET


title: 221_E14C_girl_IVF-FET


title: 22_W1785M_mother_IVF-FET


title: 233_W934M_mother_ICSI-ET


title: 22_W1785F_father_IVF-FET


title: 22_W1785D_girl_IVF-FET


title: 231_W808F_father_ICSI-ET


title: 213_W1694F_father_IVF-ET


title: 213_W1694C_girl_IVF-ET


title: 213_W1694M_mother_IVF-ET


title: 212_W81F_father_IVF-ET


title: 211_W53F_father_IVF-ET


title: 212_W81C_girl_IVF-ET


title: 21_A42F_father_IVF-FET


title: 21_A42M_mother_IVF-FET


title: 211_W53M_mother_IVF-ET


title: 203_A92M_mother_CTRL


title: 211_W53C_girl_IVF-ET


title: 21_A42C_girl_IVF-FET


title: 203_A92F_father_CTRL


title: 21_A42D_girl_IVF-FET


title: 203_A92C_girl_CTRL


title: 202_E13M_mother_CTRL


title: 202_E13F_father_CTRL


title: 202_E13C_girl_CTRL


title: 143_A28M_mother_ICSI-FET


title: 2_BS20M_mother_CTRL


title: 201_E12C_girl_CTRL


title: 2_BS20F_father_CTRL


title: 201_E12F_father_CTRL


title: 142_W774M_mother_ICSI-FET


title: 143_A28D_girl_ICSI-FET


title: 201_E12M_mother_CTRL


title: 212_W81M_mother_IVF-ET


title: 142_W774D_girl_ICSI-FET


title: 142_W774F_father_ICSI-FET


title: 143_A28C_boy_ICSI-FET


title: 141_E45D_boy_ICSI-FET


title: 141_E45M_mother_ICSI-FET


title: 22_W1785C_girl_IVF-FET


title: 135_A19F_father_ICSI-ET


title: 141_E45F_father_ICSI-FET


title: 141_E45C_girl_ICSI-FET


title: 134_E115F_father_ICSI-ET


title: 143_A28F_father_ICSI-FET


title: 134_E115M_mother_ICSI-ET


title: 135_A19C_boy_ICSI-ET


title: 135_A19D_girl_ICSI-ET


title: 142_W774C_boy_ICSI-FET


title: 134_E115D_girl_ICSI-ET


title: 134_E115C_boy_ICSI-ET


title: 133_W1636F_father_ICSI-ET


title: 133_W1636M_mother_ICSI-ET


title: 133_W1636D_girl_ICSI-ET


title: 132_W1507M_mother_ICSI-ET


title: 132_W1507F_father_ICSI-ET


title: 132_W1507D_girl_ICSI-ET


title: 131_W1191F_father_ICSI-ET


title: 131_W1191M_mother_ICSI-ET


title: 131_W1191C_girl_ICSI-ET


title: 13_E29F_father_IVF-ET


title: 135_A19M_mother_ICSI-ET


title: 13_E29D_girl_IVF-ET


title: 123_W1387D_girl_IVF-FET


title: 124_W1458M_mother_IVF-FET


title: 124_W1458D_boy_IVF-FET


title: 123_W1387F_father_IVF-FET


title: 122_W1524F_father_IVF-FET


title: 122_W1524M_mother_IVF-FET


title: 123_W1387C_boy_IVF-FET


title: 13_E29C_girl_IVF-ET


title: 124_W1458F_father_IVF-FET


title: 123_W1387M_mother_IVF-FET


title: 131_W1191D_boy_ICSI-ET


title: 121_W839M_mother_IVF-FET


title: 122_W1524C_girl_IVF-FET


title: 132_W1507C_boy_ICSI-ET


title: 122_W1524D_boy_IVF-FET


title: 13_E29M_mother_IVF-ET


title: 121_W839D_girl_IVF-FET


title: 121_W839F_father_IVF-FET


title: 121_W839C_boy_IVF-FET


title: 12_BS29M_mother_IVF-ET


title: 12_BS29F_father_IVF-ET


title: 12_BS29C_girl_IVF-ET


title: 12_BS29D_girl_IVF-ET


title: 114_E72F_father_IVF-ET


title: 114_E72M_mother_IVF-ET


title: 114_E72D_boy_IVF-ET


title: 114_E72C_girl_IVF-ET


title: 113_E101C_girl_IVF-ET


title: 112_E69M_mother_IVF-ET


title: 113_E101M_mother_IVF-ET


title: 113_E101D_boy_IVF-ET


title: 113_E101F_father_IVF-ET


title: 112_E69F_father_IVF-ET


title: 111_E18F_father_IVF-ET


title: 112_E69D_girl_IVF-ET


title: 11_BS18D_girl_IVF-ET


title: 111_E18D_boy_IVF-ET


title: 11_BS18M_mother_IVF-ET


title: 11_BS18C_girl_IVF-ET


title: 103_E98D_boy_CTRL


title: 111_E18C_girl_IVF-ET


title: 103_E98M_mother_CTRL


title: 103_E98F_father_CTRL


title: 103_E98C_girl_CTRL


title: 102_E54D_boy_CTRL


title: 102_E54F_father_CTRL


title: 101_E114M_mother_CTRL


title: 102_E54M_mother_CTRL


title: 102_E54C_girl_CTRL


title: 101_E114F_father_CTRL


title: 101_E114D_girl_CTRL


title: 101_E114C_boy_CTRL


title: 133_W1636C_boy_ICSI-ET


title: 112_E69C_boy_IVF-ET


title: 111_E18M_mother_IVF-ET


title: 1_BS2F_father_CTRL


title: 1_BS2M_mother_CTRL


title: 1_BS2D_girl_CTRL


title: 1_BS2C_girl_CTRL


title: 331_H3K27me3_E25C_girl_ICSI-ET

data_processing:
Before read mapping, adapters, low-quality bases in the reads and reads smaller than 50 bases were removed with Trimmomatic to optimize the paired-end alignments.
The remaining reads were aligned to the Homo sapiens reference genome (human GRCh38/hg38) using the Burrows-Wheeler Aligner (BWA) with the default parameters in paired-end mode.
For duplicated reads that aligned to the same position with the same orientation, only the read with highest mapping quality was retained to prevent potential PCR bias by using picard (http://broadinstitute.github.io/picard/). The nonredundant reads with no more than 2% mismatches that uniquely mapped to the reference genome were retained for further analyses.
The MACS2 peak caller (version 2.1.0) with the parameter settings “--keep-dup=1, --broad” was used to identify peaks of histone modifications.
The R/Bioconductor package DiffBind, which employs DESeq2 or edgeR to identify differential peaks (DPs) with q-values < 0.05 and fold changes > 2 for H3K4me1, H3K4me3, H3K27ac, and H3K27me3, respectively, was also used. The shared outputs of the DESeq2 and edgeR methods were taken as the final DPs.
human GRCh38/hg38
bigwig

source_name: PBMC

extract_protocol:
Genomic DNA (gDNA) was extracted from stored whole blood samples using the QIAmp DNA Blood Mini Kit (Qiagen, cat.: 51106), according to manufacturer’s instruction and stored in -80 ℃ if not used immediately.
Briefly, isolated nuclei were sonicated into fragments of an average of 200–500 bp using an M220 Focused-ultrasonicator (Covaris) with the following parameters: burst, 200; cycle, 20%; and intensity, 8. After centrifugation (13000 rpm for 10 min at 4°C), sheared chromatin in supernatant was precleared by incubating the samples with protein A Dynabeads (Invitrogen, cat.: 10002D) at 4°C for 1 h with rotation.

value: PBMC


title: 31_H3K27me3_E95D_girl_ICSI-ET


title: 11_BS18F_father_IVF-ET


title: 431_H3K27me3_E15C_boy_ICSI-ET


title: 421_H3K27me3_E35C_boy_IVF-FET


title: 322_H3K27me3_E32C_girl_IVF-FET


title: 31_H3K27me3_E95C_girl_ICSI-ET


title: 241_H3K27me3_E45D_boy_ICSI-FET


title: 241_H3K27me3_E45C_girl_ICSI-FET


title: 231_H3K27me3_E111D_boy_ICSI-ET


title: 231_H3K27me3_E111C_girl_ICSI-ET


title: 232_H3K27me3_E115D_girl_ICSI-ET


title: 321_H3K27me3_E14C_girl_IVF-FET


title: 212_H3K27me3_E69C_boy_IVF-ET


title: 232_H3K27me3_E115C_boy_ICSI-ET


title: 212_H3K27me3_E69D_girl_IVF-ET


title: 211_H3K27me3_E18C_girl_IVF-ET


title: 202_H3K27me3_E114D_girl_CTRL


title: 202_H3K27me3_E114C_boy_CTRL


title: 211_H3K27me3_E18D_boy_IVF-ET


title: 201_H3K27me3_E98D_boy_CTRL


title: 201_H3K27me3_E98C_girl_CTRL


title: 2_H3K27me3_E65D_girl_CTRL


title: 2_H3K27me3_E65C_girl_CTRL


title: 111_H3K27me3_E113D_boy_IVF-ET


title: 111_H3K27me3_E113C_boy_IVF-ET


title: 102_H3K27me3_E56C_boy_CTRL


title: 101_H3K27me3_E24D_boy_CTRL


title: 11_H3K27me3_E29C_girl_IVF-ET


title: 101_H3K27me3_E24C_boy_CTRL


title: 102_H3K27me3_E56D_boy_CTRL


title: 1_H3K27me3_E103D_girl_CTRL


title: 421_H3K27ac_E35C_boy_IVF-FET


title: 241_H3K27ac_E45D_boy_ICSI-FET


title: 31_H3K27ac_E95D_girl_ICSI-ET


title: 331_H3K27ac_E25C_girl_ICSI-ET


title: 232_H3K27ac_E115C_boy_ICSI-ET


title: 322_H3K27ac_E32C_girl_IVF-FET


title: 232_H3K27ac_E115D_girl_ICSI-ET


title: 241_H3K27ac_E45C_girl_ICSI-FET


title: 212_H3K27ac_E69C_boy_IVF-ET


title: 231_H3K27ac_E111C_girl_ICSI-ET


title: 321_H3K27ac_E14C_girl_IVF-FET


title: 31_H3K27ac_E95C_girl_ICSI-ET


title: 202_H3K27ac_E114C_boy_CTRL


title: 202_H3K27ac_E114D_girl_CTRL


title: 11_H3K27me3_E29D_girl_IVF-ET


title: 201_H3K27ac_E98D_boy_CTRL


title: 1_H3K27me3_E103C_girl_CTRL


title: 201_H3K27ac_E98C_girl_CTRL


title: 2_H3K27ac_E65D_girl_CTRL


title: 2_H3K27ac_E65C_girl_CTRL


title: 111_H3K27ac_E113D_boy_IVF-ET


title: MK108

city: Amherst

first: Minsoo

state: MA

address: 240 Thatcher Rd. N340B

department: BMB

institute: University of Massachusetts Amherst

description: mitochondrial DNA

data_processing:
Fastq  files were trimmed with Trim Galore!
Sequencing reads were aligned to the Arabidopsis thaliana (Col-0) mitochondrial genome (BK010421.1) using with Bowtie 2.
Peaks were called using MACS2 callpeak
Genome_build: BK010421.1
Supplementary_files_format_and_content: Peak text files

organism: Arabidopsis thaliana

source_name: Isolated mitochondria from whole seedlings

growth_protocol: Seedlings for mitochondria isolation were grown in 0.5x MS liquid media containing 0.5% sucrose with shaking. Plants were grown in controlled growth chambers at 22°C/18°C, 16-h-day/8-h-night cycle with fluorescent lamps (100 μmol m–2 s–1).

extract_protocol:
Mitochondria (500 ug protein equivalent) were crosslinked with formaldehyde, sonicated and immunoprecipitated with GFP-Trap (ChromoTek) to isolate SHOT1-DNA complexes.
Immunoprecipitated DNA samples were used to make libraries for sequencing following the manufacturer’s instructions (ACCEL-NGS 2S Plus DNA library kits, Swift Biosciences #21024). 151bp paired-end sequencing was performed using Illumina MiSeq.

treatment_protocol: Mitochondria were isolated from seedlings by a standard protocol with differental centrifugation and pvp-40 gradient.

value: whole seedlings

tag: developmental stage

tag: organelle isolation

value: Purified mitochondria

tag: dna-ip antibody

value: GFP-Trap


title: MK30

description: mitochondrial DNA

tag: tissue


title: 11_H3K27ac_E29D_girl_IVF-ET


title: 431_H3K27ac_E15C_boy_ICSI-ET


title: 231_H3K27ac_E111D_boy_ICSI-ET


title: 11_H3K27ac_E29C_girl_IVF-ET


title: Mito-GFP

description: mitochondrial DNA

value: Mito-GFP


title: 102_H3K27ac_E56C_boy_CTRL


title: 212_H3K27ac_E69D_girl_IVF-ET


title: 101_H3K27ac_E24C_boy_CTRL


title: 101_H3K27ac_E24D_boy_CTRL


title: 102_H3K27ac_E56D_boy_CTRL


title: 211_H3K27ac_E18C_girl_IVF-ET


title: 124_W1458C_girl_IVF-FET

value: umbilical cord blood


title: 1_H3K27ac_E103D_girl_CTRL


title: m40_Week_16_BFP_33-Hi

city: Stanford

first: Ravindra

last: Majeti

state: CA

address: 875 Blake Wilbur Dr Clinic F

institute: Stanford University

description: Barcoded CD34+ Cord Blood Cells engrafted into mouse and subsequently sequenced for barcode region

data_processing:
Library strategy: TRACE-seq
raw fastq files were trimmed, merged using PEAR, and aligned to a reference amplicon.
All bioinformatic steps were performed according to the TUBAseq pipeline.
Genome_build: FASTA file used for read alignment is available on the series record.
Supplementary_files_format_and_content: Barcode counts for samples were concatenated into count matrices for each experiment.

source_name: Human Cord Blood CD34+ Cells

growth_protocol: Cord blood cells were CD34 enriched, barcoded using the TRACEseq methodology, and engrafted into mice.

extract_protocol:
Genomic DNA was extracted.
Barcoded regions were amplified and libraries were prepared.

treatment_protocol: Mice were sacrificed and human cells were sorted into different cell populations.

tag: mouse

value: Primary

tag: celltype

tag: barcoded


title: m40_Week_16_BFP_33-Mid


title: m38_Week_16_BFP_19-33-


title: m38_Week_16_BFP_33-Hi


title: m38_Week_16_BFP_33-Mid


title: 1_H3K27ac_E103C_girl_CTRL


title: 431_H3K4me3_E15C_boy_ICSI-ET


title: 421_H3K4me3_E35C_boy_IVF-FET


title: m34_Week_16_BFP_19+


title: m34_Week_16_BFP_19-33-


title: m34_Week_16_BFP_33-Hi


title: m40_Week_16_BFP_19+


title: m40_Week_16_BFP_19-33-


title: 322_H3K4me3_E32C_girl_IVF-FET


title: m34_Week_16_BFP_33-Mid


title: 321_H3K4me3_E14C_girl_IVF-FET


title: m31_Week_16_HBBbc_19


title: 31_H3K4me3_E95C_girl_ICSI-ET


title: 31_H3K4me3_E95D_girl_ICSI-ET


title: m31_Week_16_HBBbc_3410

value: HSPC


title: m38_Week_16_BFP_19+


title: m31_Week_16_HBBbc_33


title: 241_H3K4me3_E45D_boy_ICSI-FET

value: boy

value: ICSI-FET


title: 241_H3K4me3_E45C_girl_ICSI-FET


title: m29_Week_16_HBBbc_19


title: 232_H3K4me3_E115D_girl_ICSI-ET

value: ICSI-ET


title: m29_Week_16_HBBbc_33


title: m27_Week_16_HBBbc_19


title: 231_H3K4me3_E111D_boy_ICSI-ET


title: 231_H3K4me3_E111C_girl_ICSI-ET


title: 232_H3K4me3_E115C_boy_ICSI-ET


title: 212_H3K4me3_E69D_girl_IVF-ET


title: m27_Week_16_HBBbc_33


title: m23_Week_16_HBBbc_33


title: 331_H3K4me3_E25C_girl_ICSI-ET


title: m23_Week_16_HBBbc_19


title: 211_H3K4me3_E18C_girl_IVF-ET


title: m27_Week_16_HBBbc_3410


title: m23_Week_16_HBBbc_3410


title: 201_H3K4me3_E98D_boy_CTRL


title: 202_H3K4me3_E114D_girl_CTRL


title: 202_H3K4me3_E114C_boy_CTRL


title: 201_H3K4me3_E98C_girl_CTRL


title: m20_Week_16_HBBbc_3410


title: m18_Week_16_HBBbc_3410


title: m20_Week_16_HBBbc_19


title: m18_Week_16_HBBbc_33


title: 2_H3K4me3_E65D_girl_CTRL


title: m29_Week_16_HBBbc_3410


title: 2_H3K4me3_E65C_girl_CTRL


title: m18_Week_16_HBBbc_19


title: 111_H3K4me3_E113C_boy_IVF-ET


title: 111_H3K4me3_E113D_boy_IVF-ET


title: m15_Week_16_HBBbc_3410


title: m15_Week_16_HBBbc_19


title: 102_H3K4me3_E56C_boy_CTRL


title: 212_H3K4me3_E69C_boy_IVF-ET


title: m14_Week_16_HBBbc_3410


title: m14_Week_16_HBBbc_19


title: 211_H3K4me3_E18D_boy_IVF-ET


title: m14_Week_16_HBBbc_33


title: 11_H3K4me3_E29C_girl_IVF-ET


title: 102_H3K4me3_E56D_boy_CTRL


title: m13_Week_16_HBBbc_19


title: 101_H3K4me3_E24C_boy_CTRL


title: 101_H3K4me3_E24D_boy_CTRL


title: m20_Week_16_HBBbc_33


title: m13_Week_16_HBBbc_33


title: 1_H3K4me3_E103D_girl_CTRL


title: m7_Week_16_BFP_19-33-


title: m7_Week_16_BFP_19+


title: m15_Week_16_HBBbc_33


title: m7_Week_16_BFP_33-Hi


title: 11_H3K4me3_E29D_girl_IVF-ET


title: 331_H3K4me1_E25C_girl_ICSI-ET


title: 421_H3K4me1_E35C_boy_IVF-FET

value: IVF-FET


title: 431_H3K4me1_E15C_boy_ICSI-ET


title: m7_Week_16_BFP_33-Mid


title: 322_H3K4me1_E32C_girl_IVF-FET


title: m3_Week_16_BFP_19+


title: m3_Week_16_BFP_19-33-


title: m3_Week_16_BFP_33-Mid


title: 321_H3K4me1_E14C_girl_IVF-FET


title: 31_H3K4me1_E95C_girl_ICSI-ET


title: m3_Week_16_BFP_33-Hi


title: 31_H3K4me1_E95D_girl_ICSI-ET


title: m20_Week_12_Secondary_HBBbc_19

value: Secondary


title: m13_Week_16_HBBbc_3410


title: 1_H3K4me3_E103C_girl_CTRL


title: m20_Week_12_Secondary_HBBbc_HSPC


title: 241_H3K4me1_E45C_girl_ICSI-FET


title: 232_H3K4me1_E115D_girl_ICSI-ET


title: RMM_SD4_NC4

organism: Macaca mulatta

source_name: Macaque whole blood stimulation

value: whole blood

value: NC

tag: time points

value: M


title: 241_H3K4me1_E45D_boy_ICSI-FET


title: 231_H3K4me1_E111D_boy_ICSI-ET


title: 232_H3K4me1_E115C_boy_ICSI-ET


title: m7_Week_12_Secondary_BFP_33-Hi


title: m7_Week_12_Secondary_BFP_19+


title: RMM_OL11_LPS4

value: LPS

tag: individual id


title: 231_H3K4me1_E111C_girl_ICSI-ET

value: PBMC

value: girl


title: RMM_OL11_GARD4

value: GARD

tag: Sex


title: m7_Week_12_Secondary_BFP_19-33-


title: 212_H3K4me1_E69D_girl_IVF-ET

value: IVF-ET


title: RMM_OL11_NC24

tag: treatment


title: 212_H3K4me1_E69C_boy_IVF-ET


title: m3_Week_12_Secondary_BFP_33-Hi


title: m7_Week_12_Secondary_BFP_33-Mid


title: m20_Week_12_Secondary_HBBbc_33


title: RMF_MG6_LPS4

value: F


title: RMF_PE14_NC24


title: RMF_PE14_GARD24


title: m3_Week_12_Secondary_BFP_19+


title: RMF_MG6_NC4


title: 211_H3K4me1_E18D_boy_IVF-ET


title: RMF_25375_GARD4


title: 211_H3K4me1_E18C_girl_IVF-ET


title: RMM_SD4_GARD4


title: RMM_OL11_NC4


title: m3_Week_Secondary_12_BFP_19-33-


title: RMM_OL11_LPS24


title: m3_Week_12_Secondary_BFP_33-Mid


title: RMM_DH7_NC4


title: RMM_SD4_LPS24


title: RMM_OL11_GARD24


title: 202_H3K4me1_E114C_boy_CTRL

value: CTRL


title: RMM_DH7_LPS4


title: RMM_DH7_GARD4


title: 201_H3K4me1_E98D_boy_CTRL


title: 201_H3K4me1_E98C_girl_CTRL


title: RMF_PE14_LPS4


title: RMF_PE14_LPS24


title: RMF_PE14_GARD4


title: 2_H3K4me1_E65D_girl_CTRL


title: RMF_MG6_LPS24


title: RMF_25375_GARD24


title: 2_H3K4me1_E65C_girl_CTRL


title: RMF_MG6_GARD24


title: 111_H3K4me1_E113D_boy_IVF-ET


title: RMM_Sd4_NC24


title: RMM_Sd4_GARD24


title: RMF_25375_NC24


title: 202_H3K4me1_E114D_girl_CTRL


title: RMF_25375_LPS4


title: RMM_Sd4_LPS4


title: 111_H3K4me1_E113C_boy_IVF-ET


title: RMF_Pe14_NC4


title: 211_H3K27ac_E18D_boy_IVF-ET


title: RMM_DH7_LPS24


title: RMF_Mg6_NC24


title: 11_H3K4me1_E29D_girl_IVF-ET


title: EED 8

city: Beaverton

first: Hollis

last: Wright

state: OR

address: 505 NW 185th Avenue

department: DIvision of Neuroscience

institute: ONPRC/OHSU

description:
E8
28-day-old female rat stereotaxically injected with EED-overexpressing lentiviral construct at day 21 in MBH.
Processed data file: EED_raw_counts.xlsx

data_processing:
Initial basecalling using Illumina RTA 1.18.64.
Barcode and adapter sequence were removed using Trimmomatic v0.33 ILLUMINACLIP TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:10:34 HEADCROP:13
Alignment using Tophat2 v2.1 to rat rn6.
Splice junction mapping using Tophat2 v. 2.1.
Mapping to Ensembl build 83 using Bioconductor Rsubread package using default parameters except countMultiMappingReads = TRUE, AllowMultiOverlaps = TRUE.
Genome_build: rat rn6 (Rnor_6.0), Ensembl build 83 annotation
Supplementary_files_format_and_content: EED_raw_counts.xlsx: Excel file includes raw counts.

source_name: MBH, EED

extract_protocol:
MBH tissue was removed, flash frozen on dry ice and chromatin prepared for RNA sequencing before sending it to the OHSU Massively Parallel Sequencing Shared Resource for library preparation and sequencing using a HiSeq 2500 instrument. Four samples per lane were sequenced with a target density of 300 million reads per lane using a single-read 100 cycle protocol.
RNA-seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Stereotaxically injected with EED-overexpressing lentiviral construct or GFP-expressing lentiviral construct at day 21 in MBH.

tag: strain/background

value: Sprague Dawley

tag: gender

value: Female

value: 28 days

value: EED

value: MBH (medial basal hypothalamus)


title: EED 7

description:
E7
28-day-old female rat stereotaxically injected with EED-overexpressing lentiviral construct at day 21 in MBH.
Processed data file: EED_raw_counts.xlsx

tag: age


title: 111_H3K27ac_E113C_boy_IVF-ET

value: boy


title: 11_H3K4me1_E29C_girl_IVF-ET


title: 102_H3K4me1_E56D_boy_CTRL


title: RMF_Mg6_GARD4


title: RMF_25375_LPS24


title: HLyHLu_35_8w

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

hyb_protocol: Following fragmentation, 12.5 µg cRNA was hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChip was washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were quantified with Factor Analysis for Robust Microarray Summarization (FARMS), using the statistical language R (R-3.1.0) and Bioconductor 2.14.

label: biotin

source_name: Whole blood from healthy volunteer after ingesting high lycopene, high lutein beverage for 8 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng of total RNA.

extract_protocol: Total RNA was isolated from whole blood using the PAXgene® Blood RNA Kit (QIAGEN-PreAnalytix GmbH, Hombrechtikon, Switzerland).

treatment_protocol: Whole blood from the subjects was collected using PAXgene® Blood RNA Tube (Becton Dickinson, NJ, USA).

value: Male

tag: age (years)

tag: treatment group

value: high lycopene, high lutein

tag: time (weeks)

tag: subject id


title: HLyHLu_36_0w

source_name: Whole blood from healthy volunteer before ingesting high lycopene, high lutein beverage

value: whole blood


title: HLyHLu_36_8w


title: 102_H3K4me1_E56C_boy_CTRL

tag: art type


title: EED 4

description:
E4
28-day-old female rat stereotaxically injected with EED-overexpressing lentiviral construct at day 21 in MBH.
Processed data file: EED_raw_counts.xlsx


title: HLyHLu_22_8w


title: HLyHLu_18_8w


title: RMF_25375_NC4

value: NC


title: HLyHLu_22_0w


title: HLyHLu_18_0w


title: HLyHLu_08_0w


title: HLyHLu_35_0w


title: 101_H3K4me1_E24D_boy_CTRL


title: HLyHLu_08_8w


title: Control 7

description:
C7
28-day-old female rat stereotaxically injected with GFP-expressing lentiviral construct at day 21 in MBH.
Processed data file: EED_raw_counts.xlsx

source_name: MBH, control

value: GFP (control)


title: 101_H3K4me1_E24C_boy_CTRL

value: PBMC


title: PTM_4X0518_LPS24

organism: Pan troglodytes

source_name: Chimp whole blood stimulation

value: LPS

value: M


title: Control 5

description:
C5
28-day-old female rat stereotaxically injected with GFP-expressing lentiviral construct at day 21 in MBH.
Processed data file: EED_raw_counts.xlsx


title: 1_H3K4me1_E103D_girl_CTRL

value: girl


title: Control 3

description:
C3
28-day-old female rat stereotaxically injected with GFP-expressing lentiviral construct at day 21 in MBH.
Processed data file: EED_raw_counts.xlsx


title: 1_H3K4me1_E103C_girl_CTRL


title: PTM_4X0437_LPS24


title: EED 5

description:
E5
28-day-old female rat stereotaxically injected with EED-overexpressing lentiviral construct at day 21 in MBH.
Processed data file: EED_raw_counts.xlsx


title: PTM_4X0437_NC4


title: HLyHLu_07_0w


title: Control 2

description:
C2
28-day-old female rat stereotaxically injected with GFP-expressing lentiviral construct at day 21 in MBH.
Processed data file: EED_raw_counts.xlsx


title: PTF_4X0427_LPS4

value: F


title: 3_CTRL_A4D_boy

data_processing:
Before reads mapping, adapters, low-quality bases in the reads and reads smaller than 50 bases were removed with Trimmomatic to optimize the paired-end alignments.
The retained reads were mapped to the Homo sapiens reference genome (human GRCh38/hg38) using STAR with the default parameters.
The uniquely mapped reads with less than 2% mismatch were passed to StringTie for transcript assembly, and the transcripts per million (TPM) value was also generated for each gene.
Batch effects of TPM values were corrected with the R/Bioconductor package SVA.
Finally, the DEGs were called with DEseq2 with the criterion of an adjusted p-value<0.05.
Genome_build: human GRCh38/hg38
Supplementary_files_format_and_content: bigwig

extract_protocol:
Total RNA was prepared from fresh blood by QIAmp RNA Blood Mini Kit (Qiagen, Cat:52304), according to manufacturer’s instruction and stored in -80 ℃ if not used immediately.
mRNA libraries were constructed using NEBNext® UltraTM II RNA Library Prep Kit for Illumina® (NEB #E7770L/#E7775L) following the vendors protocol.

value: umbilical cord blood

value: neonate

value: CTRL


title: PTM_4X0518_LPS4


title: HLyHLu_07_8w


title: InVitro-46_Day14_barcoded

description: Barcoded CD34+ Cord Blood Cells cultured in vitro and subsequently sequenced for barcode region

tag: cell type

value: cord blood cd34+

value: Barcoded


title: InVitro-45_Day14_barcoded


title: 3_CTRL_A4C_boy

tag: tissue


title: HLyHLu_01_8w


title: 2_CTRL_A18D_girl


title: InVitro-44_Day14_barcoded

tag: mouse


title: 2_CTRL_A18C_boy


title: 24_IVF-ET_A9D_girl

value: IVF-ET


title: HLyLLu_37_8w

source_name: Whole blood from healthy volunteer after ingesting high lycopene, low lutein beverage for 8 weeks

value: high lycopene, low lutein


title: HLyHLu_01_0w

value: Male


title: HLyLLu_37_0w

source_name: Whole blood from healthy volunteer before ingesting high lycopene, low lutein beverage


title: InVitro-41_Day14_barcoded


title: PTM_4X0518_GARD4

value: GARD


title: InVitro-40_Day14_barcoded


title: 24_IVF-ET_A9C_boy


title: PTF_4X0427_GARD4

value: whole blood


title: PTM_4X0437_GARD4


title: 23_ICSI-FET_A7D_girl

value: ICSI-FET


title: HLyLLu_33_8w


title: InVitro-38_Day14_barcoded


title: 23_ICSI-FET_A7C_boy


title: PTM_4X0429_LPS24


title: HLyLLu_33_0w


title: InVitro-37_Day14_barcoded


title: PTF_4X0421_GARD24


title: PTF_4X0421_NC4

value: NC


title: HLyLLu_30_8w


title: HLyLLu_30_0w


title: PTM_4X0429_GARD24


title: HLyLLu_15_8w


title: PTM_4X0518_NC24


title: InVitro-36_Day14_barcoded


title: 22_ICSI-ET_A19C_boy

value: ICSI-ET


title: HLyLLu_03_8w


title: PTF_4X0428_NC4


title: HLyLLu_15_0w


title: HLyLLu_03_0w


title: InVitro-43_Day14_unbarcoded

value: Unbarcoded


title: PTF_4X0428_LPS24

value: LPS


title: 21_IVF-ET_A12D_girl


title: PTF_4X0428_GARD4


title: InVitro-39_Day14_unbarcoded


title: 21_IVF-ET_A12C_girl


title: 1_CTRL_A15D_girl


title: 22_ICSI-ET_A19D_girl


title: InVitro-35_Day14_unbarcoded


title: InVitro-33_Day2_barcoded


title: PTF_4X0427_NC24


title: 1_CTRL_A15C_girl


title: InVitro-32_Day2_barcoded


title: PTF_4X0421_NC24


title: PTF_4X0427_LPS24


title: 108_ICSI-ET_V9D_girl


title: InVitro-31_Day2_barcoded


title: LLyHLu_31_8w

source_name: Whole blood from healthy volunteer after ingesting low lycopene, high lutein beverage for 8 weeks

value: low lycopene, high lutein


title: 108_ICSI-ET_V9C_girl


title: PTM_4X0518_GARD24

value: M


title: LLyHLu_27_0w

source_name: Whole blood from healthy volunteer before ingesting low lycopene, high lutein beverage


title: LLyHLu_27_8w


title: InVitro-29_Day2_barcoded


title: PTM_4X0518_NC4


title: InVitro-28_Day2_barcoded


title: LLyHLu_24_8w


title: 107_ICSI-FET_V7C_boy

value: umbilical cord blood


title: LLyHLu_24_0w


title: InVitro-42_Day14_barcoded


title: LLyHLu_31_0w


title: InVitro-27_Day2_barcoded


title: PTM_4X0437_NC24


title: PTM_4X0437_GARD24


title: 106_IVF-FET_A75D_boy

value: neonate

value: IVF-FET


title: InVitro-25_Day2_barcoded

value: cord blood cd34+


title: InVitro-24_Day2_barcoded

value: Barcoded


title: 105_IVF-ET_A60D_boy

value: IVF-ET


title: LLyHLu_19_0w


title: LLyHLu_19_8w


title: PTM_4X0437_LPS4


title: 106_IVF-FET_A75C_boy


title: PTM_4X0429_NC24


title: InVitro-22_Day2_barcoded


title: InVitro-23_Day2_barcoded


title: LLyHLu_11_0w


title: PTM_4X0429_GARD4


title: LLyHLu_05_8w


title: 107_ICSI-FET_V7D_girl


title: 105_IVF-ET_A60C_boy


title: InVitro-30_Day2_unbarcoded


title: PTM_4X0429_NC4


title: 103_IVF-FET_A58D_boy


title: 104_ICSI-FET_A59C_girl


title: InVitro-26_Day2_unbarcoded


title: PTM_4X0429_LPS4


title: PTF_4X0428_GARD24

value: F


title: LLyHLu_05_0w

value: Male


title: InVitro-21_Day2_unbarcoded


title: 104_ICSI-FET_A59D_girl


title: LLyHLu_11_8w


title: BC4_Plasmid

description: Sequencing of plasmid containing barcode region

source_name: Plasmid

tag: celltype


title: 103_IVF-FET_A58C_boy


title: 102_IVF-FET_A44D_boy


title: PTF_4X0428_LPS4


title: LLyLLu_34_0w

source_name: Whole blood from healthy volunteer before ingesting low lycopene, low lutein beverage

value: low lycopene, low lutein


title: LLyLLu_34_8w

source_name: Whole blood from healthy volunteer after ingesting low lycopene, low lutein beverage for 8 weeks

value: whole blood


title: BC4_AAV6

description: Barcoded AAV pool Sequenced for barcode region

source_name: Virus

tag: barcoded


title: 102_IVF-FET_A44C_girl

source_name: umbilical cord blood


title: BC2_Plasmid


title: 101_ICSI-ET_A37D_boy


title: LLyLLu_23_8w


title: PTF_4X0427_NC4

tag: time points


title: 101_ICSI-ET_A37C_boy


title: LLyLLu_21_0w


title: LLyLLu_21_8w


title: LLyLLu_23_0w


title: PTF_4X0428_NC24

tag: individual id


title: PTF_4X0421_LPS24

tag: Sex


title: PTF_4X0421_GARD4

tag: treatment

value: GARD


title: BC1_AAV6


title: PTF_4X0421_LPS4


title: 100_ICSI-FET_A28C_boy

value: ICSI-FET


title: LLyLLu_12_0w


title: optoWnt CHIR 1d ON 2d OFF

status: Public on Aug 08 2020

city: Philadelphia

first: Lukasz

last: Bugaj

state: PA

address: 390 Towne Building, 220 S. 33rd St

department: Bioengineering

institute: University of Pennsylvania

description: rawCounts.csv (B3)

data_processing:
Sequencing reads were aligned using the Bowtie 2 alignment tool. Reads were mapped to a Bowtie 2 index built from the Rattus norvegicus Rnor_6.0 reference genome downloaded from the Ensembl database (https://useast.ensembl.org/info/data/ftp/index.html).  Alignment was performed using the default preset options in “--local” mode.
Aligned reads were counted by processing the output .sam files with the featureCounts52 software through the Subread package in the R programming language (https://cran.r-project.org/). Within featureCounts, multi-mapped reads were counted (allowMultiOverlap == TRUE) and were assigned to the feature with the largest number of overlapping bases (largestOverlap == TRUE).
Feature counts (expressed genes) were analyzed using the edgeR53 library from the Bioconductor package.  Briefly, genes with fewer than 1 count per million in any sample were discarded from analysis.  The library sizes of the remaining genes were normalized for each sample using the upper quartile method.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: rawCounts.csv

source_name: rat neural stem cells

growth_protocol: Cultured rat hippocampal adult NSCs were transduced with optoWnt (MOI 0.5), were selected with 0.6 µg/mL puromycin, and were maintained on poly-ornithine and laminin (5 μg/mL, Life Technologies) coated polystyrene plates in Dulbecco’s Modified Eagle Medium (DMEM)/F12 (1:1, Life Technologies) high-glucose medium with N-2 supplement (Life Technologies) and stimulated with recombinant human FGF-2 (20 ng/mL, Peprotech). Cells were cultured at 37°C and 5% CO2.

extract_protocol:
RNA was extracted using RNAeasy kit and protocol (Qiagen).
The RNA library was prepared using QuantSeq3 kit (Lexogen) using the low RNA input protocol

treatment_protocol: OptoWnt-expressing NSCs were cultured in basal medium composed of DMEM/F12 (1:1) high glucose medium, N-2 supplement, and 0.5% FBS.  Cells were treated with either CHIR99021 (3 mM), Wnt 3a (100 ng/mL), or with light using custom LED arrays as described in the manuscript

tag: strain

value: Fisher 344

value: adult neural stem cell

tag: genotype

value: optoWnt

tag: b-catenin inducer

value: CHIR

tag: treatment profile

value: 1 day ON, 2 days OFF

tag: time point

value: 3 days


title: optoWnt Wnt 1d ON 2d OFF

description: rawCounts.csv (D3)


title: optoWnt Wnt 1d ON 1d OFF

description: rawCounts.csv (C3)

value: 1 day ON, 1 day OFF

value: 2 days


title: optoWnt CHIR 1d ON 1d OFF

description: rawCounts.csv (A3)


title: LLyLLu_12_8w

tag: gender

tag: age (years)

tag: treatment group

tag: time (weeks)


title: LLyLLu_04_8w

tag: tissue

tag: subject id


title: PTF_4X0427_GARD24


title: BC2_AAV6

tag: mouse

tag: celltype


title: optoWnt light 3d ON

description: rawCounts.csv (F2)

tag: cell type

value: light

value: 3 days ON


title: optoWnt light 1d ON 1d OFF

description: rawCounts.csv (G2)


title: optoWnt light 1d ON 2d OFF

description: rawCounts.csv (H2)


title: optoWnt light 1d ON

description: rawCounts.csv (E2)

value: 1 day ON

value: 1 day


title: optoWnt Wnt3a 3d ON

description: rawCounts.csv (C2)


title: optoWnt Wnt3a 5d ON

description: rawCounts.csv (D2)

value: 5 days ON

value: 5 days


title: BC1_Plasmid

tag: barcoded

value: Barcoded


title: LLyLLu_04_0w

value: whole blood

value: Male

value: low lycopene, low lutein


title: optoWnt CHIR 1d ON

description: rawCounts.csv (G1)

value: Fisher 344

value: adult neural stem cell


title: optoWnt Wnt3a 1d ON

description: rawCounts.csv (B2)

value: optoWnt


title: optoWnt CHIR 3d ON

description: rawCounts.csv (H1)

value: CHIR


title: optoWnt CHIR 5d ON

description: rawCounts.csv (A2)


title: 100_ICSI-FET_A28D_girl

value: umbilical cord blood

tag: age

value: neonate

tag: art type

value: ICSI-FET


title: optoWnt untreated 3d ON

description: rawCounts.csv (E1)

tag: strain

value: 3 days (baseline)

value: 3 days


title: wild-type untreated 5d ON

description: rawCounts.csv (C1)

tag: genotype

value: wild-type

value: 5 days (baseline)


title: wild-type untreated 3d ON

description: rawCounts.csv (B1)

tag: b-catenin inducer


title: optoWnt untreated 0d

description: rawCounts.csv (D1)

tag: treatment profile

value: 0 days (baseline)

value: 0 days


title: optoWnt untreated 5d ON

description: rawCounts.csv (F1)

tag: time point

value: 5 days


title: wild-type untreated 0d

description: rawCounts.csv (A1)


title: Mut_340

city: San Francisco

first: Samuel

last: Pleasure

address: 675 Nelson Rising Lane

institute: UCSF

data_processing:
Samples were sequenced, demultiplexed, aligned, and analyzed by the UCSF Functional Genomics Core Facility
sequenced reads were mapped to Ensembl Mouse GRCm38.78 using STAR_2.4.2a
Genome_build: Ensembl Mouse GRCm38.78
Supplementary_files_format_and_content: tab delimited text file containing samples and their raw (unnormalized ) read counts per gene.
Supplementary_files_format_and_content: tab delimited text file containing gene level differential expression tests

source_name: dorsal forebrain

extract_protocol:
Total RNA was extracted using Qiagen RNEasy Mini Kit (Qiagen) and prepared for RNAseq.
Illumina Truseq Stranded mRNA Library Prep Kit

value: mixed background with C57BL/6J

value: Emx1-cre/+;Sufu-fl/fl (Sufu-cKO)

tag: Sex

value: male


title: Mut_337


title: Cont_345

value: control (Sufu-fl/fl or Sufu-fl/+)


title: Cont_370


title: Mut_317


title: Cont_365


title: Day28_YFP+CD11b-_scRNA-Seq

city: Memphis

first: JIE

last: Lv

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

description: scRNA-seq from 10X genomics using 3’ v1 chemistry

data_processing:
Cell Ranger v2.1.1 (10X Genomics) was used to process raw sequencing data.
STAR aligner was used to align sequencing reads to the mouse transcriptome.
Genome_build: mm10

source_name: YFP+CD11b- cells of hindlimb muscle

extract_protocol:
tissue digestion and FACS sorted
RNA libraries were prepared for sequencing using standard Illumina protocols

value: YFP+CD11b- cells

value: hindlimb muscle

tag: treatment

value: Hindlimb ischemia surgery


title: Day0_YFP+CD11b-_scRNA-Seq


title: Cont_294