title: B7

status: Public on Jun 01 2022

city: Columbus

first: Phillip

middle: G.

last: Popovich

state: OH

address: 460 W 12th Ave

department: Department of Neuroscience

institute: The Ohio State University

description:
extract protocol 2, library construction protocol 2, library strategy 2
processed data file: counts.csv, metadata.csv

data_processing:
RNA-seq:
Reads were aligned to the mouse GRCm38 reference genome using STAR (v.2.4.0).
Read counts for RefSeq genes (mm10) were generated by HTSeq v.0.6.1.
Low-count genes were filtered and fragments per kilobase per million mapped reads (FPKM) values were generated
scRNA-seq:
Fastq sequence files were de-multiplexed, aligned, and annotated using the mouse ENSMBL database and Cell Ranger software.
Gene expression was counted using unique molecular identifier barcodes  and gene-cell matrices were constructed.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts, normalized gene counts, and FPKM values for every gene and every sample
Supplementary_files_format_and_content: Barcode, Matrix and Features files for Seurat Object generation

source_name: Single cell RNAseq

growth_protocol: 8-10 week old female mice were purchased from Jackson labs and housed under conventional conditions, 12 hr light cycle and free access to food and water. All procedures were performed in accordance with The Ohio State University Institutional Animal Care and Use Committee.

extract_protocol:
protocol 1: Mice were euthanized with 1.5x the surgical dose of ketamine and xylazine then perfused transcardially with DEPC buffer until the liver and blood were cleared. A 1 cm piece of spinal cord (centered on the T9 laminectomy site) was quickly dissected and homogenized in 1 ml of TRIzol reagent (ThermoFisher). RNA was extracted according to the manufacturers instructions. Briefly, the tissue lysate was centrifuged at 4°C for 5 mins at 12 000 g. The supernatant was incubated for 5 mins to dissociate nucleoproteins. Samples were incubated with 0.2 ml of chloroform for 2.5 mins then shaken vigorously for 15 sec.  Samples were centrifuged at 4°C for 15 mins at 12 000 g. The aqueous phase was collected and mixed with 0.5 ml of isopropanol with 2 ul of glycogen then stored at -20°C. Samples were centrifuged (4°C, 5 mins, 12 000 g) and the pellet resuspended in 75% ethanol. The sample was vortexed, centrifuged (4°C, 5 mins, 7 5 00 g), the supernatant removed and pellet dried for 5-10 mins. The pellet was resuspended in 20 μl RNAse free water and warmed to 55°C. RNA yield was determined using Nanodrop. RNA was purified using the QIAGEN RNeasy spin column steps according to manufacturers instructions. RNA quality and final yield was then measured using a RNA 6000 NanoAssay by Chip. Samples with RIN > 7 were included for analysis (average RIN = 8.6). Samples were stored at -80°C until sequencing.
protocol 2: Mice were euthanized with 1.5x the surgical dose of ketamine and xylazine. A 1 cm piece of unperfused, fresh spinal cords (centered on the T9 laminectomy site) was quickly dissected. Tissue was dissociated to a single cell suspension using a gentleMACS dissociator (Miltenyi) and mouse adult brain dissociation kit (Miltenyi, 130-107-677). Dissociated cells were passed through a sterile 70 μm filter to remove large particulate debris. Myelin debris was removed using myelin removal beads (Miltenyi, 130-096-733). Dead cells were removed using Viahance dead cell removal (BioPAL, #CP-50VQ02). Cells were diluted to 1000 cells/μl.
protocol 1: RNA-seq was carried out by the UCLA Technology Center for Genomics and Bioinformatics. The library was prepared using Nugen Ovation RNA Ultra Low Input (500 pg) + Kapa Hyper. The quantity and quality of cDNA were assessed using an Agilent 2100 Expert High Sensitivity DNA Assay. cDNA samples were sequenced at UCLA Technology Center for Genomics and Bioinformatics. Reads were aligned to the mouse GRCm38 reference genome using STAR (v.2.4.0). Read counts for RefSeq genes (mm10) were generated by HTSeq v.0.6.1. Low-count genes were filtered and fragments per kilobase per million mapped reads (FPKM) values were generated.
protocol 2: The single cell suspension and Chromium Single Cell 3’ V3 reagents (10X Genomics) were loaded into chips to collect individual cells encapsulated by gel beads in emulsion (GEMs) using the 10X Chromium Controller. cDNA and library amplification for an optimal signal was 13-16 cycles. Sequencing was conducted on HiSeq4000 (Novogene).

treatment_protocol: Mice are fed diet laced with PLX5622 (1200 ppm) (Plexxikon Inc.) or Vehicle chow for 2 weeks before undergoing a T9 contusion SCI or sham (laminectomy) surgery. Mice remain on diet until the end point at 7 or 28 days post-surgery.

value: Dissociated mouse spinal cord

value: Spinal cord cells

tag: mouse strain

value: Vehicle

tag: disease state

value: T9 SCI

tag: cell numbers

tag: time post injury

value: 28 dpi


title: HEK293T, IgG

status: Public on Jun 21 2022

type: SRA

city: Houston

first: Isaac

middle: B

last: Hilton

state: TX

address: 6500 Main St

department: Bioengineering

country: USA

institute: Rice University

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq (v2.17)
Reads were trimmed using Trim Galore (v0.6.6)
Aligned to the hg38 reference genome using Bowtie2 (v7.3.0)
Aligned reads were deduplicated using Picard MarkDuplicates (v2.23.8)
Deduplicated alignments were converted into a bedGraph file using bedtools (v2.30.0)
BedGraph files from biological replicates were then merged using bedops (v2.4.39)
Assembly: hg38
Supplementary files format and content: bedGraph (except for IgG control)
Library strategy: CUT&RUN-Seq

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HEK293T cells (ATCC, CRL-11268) were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco, 31-053-028) supplemented with 10% FBS (Sigma, F2442) and 1% penicillin/streptomycin (Gibco, 15140). Cell lines were maintained at 37 °C and 5% CO2.

extract_protocol:
CUT&RUN assays were carried out using the Epicypher CUTANA ChIC/CUT&RUN Kit (Epicypher 14-1048). Briefly, 5.0e5 transfected cells were harvested, immobilized on concanavalin A beads, and permeabilized in 0.01% digitonin cell permeabilization buffer. The cell-bead conjugate mixture was then divided equally into 2 aliquots and incubated in 50ul antibody buffer with either 0.5µg of anti-H3K27ac antibody (Abcam, 4279) or 0.5µg of control rabbit IgG antibody (Epicypher, 14-1048) overnight at 4°C. After washing the beads, pAG-MNase was added to the immobilized cells and the solution was incubated for 2 hours at 4°C to digest and release chromatin DNA
Libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® kit (NEB, E7645) by Azenta Life Sciences

tag: cell line

tag: cell type

value: Human embryonic kidney

tag: chip antibody

value: IgG (Epicypher, 14-1048)


title: B4

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: treatment

value: 7 dpi


title: HEK293T, H3K27ac, HS2, dCas9

value: H3K27ac (Abcam, ab4729)


title: B3


title: B8


title: HEK293T, H3K27ac, HBG1, dCas9-VPR


title: shNSD1_DMSO_R7

status: Public on May 09 2022

city: Memphis

first: Jacquelyn

middle: A

last: Myers

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children’s Research Hospital

description:
X1688046_YDR464
G401 loss NSD1 DMSO treated
G401_hg19_raw_count_FORGEO.txt

data_processing:
trim_galore v0.6.3 remove adapter sequences
alignment with STAR2.7.3a --twopassMode Basic
read counts quantified by RSEMv1.3.1
Genome_build: GRCh37
Supplementary_files_format_and_content: quantified read counts are provided in the txt format for every sample for gencode v19

growth_protocol: G401 cells were grown in McCoy's 5A media supplemented with 10% fetal bovine serum and 1% Glutamax (Gibco) at 37°C and 5% CO2.

extract_protocol:
Trizol and the DirectZol Mini Prep Plus kit (Zymo Research, R2070)
TruSeq Stranded mRNA Library Prep kit

treatment_protocol: G401 cells were engineered to express either GFP or SMARCB1 (B1) under doxycycline treatment and further transfected with either control (sgC) or NSD1 (sgN) targeting sgRNAs. Cells were then treated with 1ug/mL dox for 24h and collected for RNA extraction. For EZH2 inhibition studies, G401 cells stably expressing shCTRL or shNSD1 RNAs were treated for 72h with 1uM GSK126 and collected for RNA extraction.

tag: genotype

value: G401 loss NSD1

tag: agent

value: DMSO


title: shCTRL_GSK_R7

description:
X1688049_YDR467
G401 control EZH2i treated
G401_hg19_raw_count_FORGEO.txt

value: G401 control


title: shCTRL_DMSO_R6

description:
X1688044_YDR462
G401 control DMSO treated
G401_hg19_raw_count_FORGEO.txt


title: shCTRL_DMSO_R7

description:
X1688045_YDR463
G401 control DMSO treated
G401_hg19_raw_count_FORGEO.txt


title: HD8_HC_water

status: Public on Jun 22 2022

city: Lille

first: David

last: Blum

state: Cedex

address: 1 place de Verdun

department: Lille Neurosience & Cognition

country: France

institute: Inserm

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR [3] version 2.5.3a.
Gene expression quantication was performed from uniquely aligned reads using htseq-count version  0.6.1p1, with annotations from Ensembl version 90 and union mode.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text file with raw read counts per Ensembl Gene.

molecule: polyA RNA

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from dorsal hippocampal tissues using TRIzol reagent (Invitrogen) (n=4/group). Freshly dissected tissue was chopped, homogenized in 300 μL of TRIzol reagent, and frozen (20 minutes at -80°C), followed by 3-minutes centrifugation at 14000xg before chloroform/isoamyl extraction. The supernatant was used to precipitate RNA using isopropanol and RNase-free glycogen (30 minutes at 4°C). The pellet was washed once with 70% ethanol and resuspended in Milli-Q water. A new RNA precipitation was performed with 100% ethanol and 3 M NaOAC (overnight at -20°C). After two further 70% ethanol washes, pellet was air-dried and resuspended in 30 μL nuclease-free Milli-Q water, heated 6 minutes at 50°C, and RNA quantification was performed.
RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Two-three month-old mice were randomly assigned to the two following experimental groups: water (control group) and caffeine. The caffeine solution was kept in dark bottles thus protected from light and changed weekly. Treatment started at eight to nine weeks of age and lasted for two weeks. The chronic caffeine treatment in mice has been set in order to mimic the usual dose range of caffeine consumption in Humans. The selected caffeine dose of 0.3 g/L p.o., administered through drinking water at 0.3 g/L, has been previously shown to provide a significant benefit in neurodegenerative contexts (Arendash et al., 2006; Arendash et al., 2009; Laurent et al., 2014).

value: dorsal hippocampus

tag: group

value: Home cage (water)

tag: strain


title: shNSD1_DMSO_R8

description:
X1688047_YDR465
G401 loss NSD1 DMSO treated
G401_hg19_raw_count_FORGEO.txt


title: shCTRL_GSK_R6

description:
X1688048_YDR466
G401 control EZH2i treated
G401_hg19_raw_count_FORGEO.txt


title: HD9_HC_Caffeine

value: Home cage (caffeine)


title: shNSD1_GSK_R5

description:
X1688042_YDR460
G401 loss NSD1 EZH2i treated
G401_hg19_raw_count_FORGEO.txt


title: shCTRL_GSK_R5

description:
X1688041_YDR459
G401 control EZH2i treated
G401_hg19_raw_count_FORGEO.txt


title: shNSD1_GSK_R6

description:
X1688043_YDR461
G401 loss NSD1 EZH2i treated
G401_hg19_raw_count_FORGEO.txt


title: shCTRL_GSK_R4

description:
X1688040_YDR458
G401 control EZH2i treated
G401_hg19_raw_count_FORGEO.txt


title: B1

value: Sham

value: 7 and 28 d


title: shCTRL_DMSO_R4

description:
X1688036_YDR454
G401 control DMSO treated
G401_hg19_raw_count_FORGEO.txt


title: shCTRL_DMSO_R5

description:
X1688037_YDR455
G401 control DMSO treated
G401_hg19_raw_count_FORGEO.txt


title: shNSD1_DMSO_R5

description:
X1688038_YDR456
G401 loss NSD1 DMSO treated
G401_hg19_raw_count_FORGEO.txt


title: shNSD1_DMSO_R6

description:
X1688039_YDR457
G401 loss NSD1 DMSO treated
G401_hg19_raw_count_FORGEO.txt


title: shNSD1_GSK_R3

description:
X1688034_YDR452
G401 loss NSD1 EZH2i treated
G401_hg19_raw_count_FORGEO.txt


title: HEK293T, H3K27ac, HBG1, dCas9


title: shNSD1_DMSO_R3

description:
X1688032_YDR450
G401 loss NSD1 DMSO treated
G401_hg19_raw_count_FORGEO.txt


title: shNSD1_DMSO_R4

description:
X1688033_YDR451
G401 loss NSD1 DMSO treated
G401_hg19_raw_count_FORGEO.txt


title: shCTRL_GSK_R3

description:
X1688031_YDR449
G401 control EZH2i treated
G401_hg19_raw_count_FORGEO.txt


title: B2

description:
extract protocol 2, library construction protocol 2, library strategy 2
processed data file: counts.csv, metadata.csv

value: Dissociated mouse spinal cord


title: shCTRL_GSK_R2

description:
X1688030_YDR448
G401 control EZH2i treated
G401_hg19_raw_count_FORGEO.txt


title: shCTRL_DMSO_R2

description:
X1688028_YDR446
G401 control DMSO treated
G401_hg19_raw_count_FORGEO.txt


title: shNSD1_GSK_R1

description:
X1688025_YDR443
G401 loss NSD1 EZH2i treated
G401_hg19_raw_count_FORGEO.txt


title: shNSD1_DMSO_R2

description:
X1688026_YDR444
G401 loss NSD1 DMSO treated
G401_hg19_raw_count_FORGEO.txt


title: shCTRL_DMSO_R3

description:
X1688029_YDR447
G401 control DMSO treated
G401_hg19_raw_count_FORGEO.txt


title: shNSD1_DMSO_R1

description:
X1688024_YDR442
G401 loss NSD1 DMSO treated
G401_hg19_raw_count_FORGEO.txt


title: shCTRL_DMSO_R1

description:
X1688022_YDR440
G401 control DMSO treated
G401_hg19_raw_count_FORGEO.txt


title: B1_sgN_1_R3

description:
X2030412_YDR940
SMARCB1 expressing loss of NSD1
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt

value: SMARCB1 expressing loss of NSD1


title: B1_sgN_2_R3

description:
X2030415_YDR943
SMARCB1 expressing loss of NSD1
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt


title: shCTRL_GSK_R1

description:
X1688023_YDR441
G401 control EZH2i treated
G401_hg19_raw_count_FORGEO.txt


title: B1_sgC_2_R2

description:
X2030408_YDR936
SMARCB1 expressing; control
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt

value: SMARCB1 expressing; control


title: GFP_sgN_2_R2

description:
X2030402_YDR930
GFP expressing; loss NSD1
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt

value: GFP expressing; loss NSD1


title: B1_sgC_1_R2

description:
X2030405_YDR933
SMARCB1 expressing; control
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt


title: B1_sgC_2_R3

description:
X2030409_YDR937
SMARCB1 expressing; control
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt


title: B1_sgN_2_R2

description:
X2030414_YDR942
SMARCB1 expressing loss of NSD1
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt


title: B1_sgC_1_R3

description:
X2030406_YDR934
SMARCB1 expressing; control
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt


title: GFP_sgN_1_R3

description:
X2030400_YDR928
GFP expressing; loss NSD1
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt


title: B1_sgN_1_R2

description:
X2030411_YDR939
SMARCB1 expressing loss of NSD1
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt


title: GFP_sgN_2_R3

description:
X2030403_YDR931
GFP expressing; loss NSD1
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt


title: GFP_sgN_1_R2

description:
X2030399_YDR927
GFP expressing; loss NSD1
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt


title: GFP_sgC_1_R3

description:
X2030394_YDR922
GFP expressing; control
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt

value: GFP expressing; control


title: GFP_sgC_2_R3

description:
X2030397_YDR925
GFP expressing; control
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt


title: GFP_sgC_1_R2

description:
X2030393_YDR921
GFP expressing; control
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt


title: N3_4

status: Public on May 02 2022

city: Trondheim

first: Jing

last: Ye

address: Høgskoleringen 1

department: Department of Clinical and Molecular Medicine (IKOM)

country: Norway

institute: Norwegian University of Science and Technology (NTNU)

data_processing:
Low-quality reads include two types, and the reads meet anyone of the two conditions will be removed:  1) Unknown bases are more than 10%; 2) The ratio of bases whose quality was less than 20 was over 10%.  After filtering, the remaining reads are called "clean reads" and stored as FASTQ format
After filtering, the Clean data was then mapped to the reference genome by BSMAP, and then remove the duplication reads and merge the mapping results according to each library. Here we calculate the Mapping rate and bisulfite Conversion rate of each sample.
Methylation level was determined by dividing the number of reads covering each mC by the total reads covering that cytosine. We used Metilene to identify DMRs . Metilene is a software tool to annotate differentally  methylated regions ( DMRs ) and differentially methylated CpG sites (DMCs) from Methyl-seq data. metilene uses a circular binary segmentation and a 2D-KS test to call DMRs . Adjsuted p-values are calculated using the Bonferroni correction.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: xlsx - all identified DMRs sorted by chromosome

source_name: baseline

growth_protocol: animals housed in an SPF facility (55% humidity, 21°C, 12h/12h light cycle) until an age of 3-6 months; only male animals were used

extract_protocol:
Animals were killed by isoflurane overdose and neck dislocation. No perfusion was performed. The brain was taken out in <120s and immediately frozen in liquid nitrogen until further processing. Brains were cut at 8µm thickness and CA1 isolated using a commercially available laser dissection microscope (MMI instruments, Eching, Germany)
DNA was fragmented by sonication using a Bioruptor (Diagenode, Belgium) to a mean size of approximately 250 bp, followed by the blunt-ending, dA addition to 3'-end, finally, adaptor ligation (in this case of methylated adaptors to protect from bisulfite conversion), essentially according to the manufacturer’s instructions. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different Insert size fragments were excised from the same lane of a 2% TAE agarose gel. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. At last, Sequencing was performed using  the HighSeq4000 or other Illumina platforms.

treatment_protocol: "baseline" condition: no intervention, animals taken directly from home cage

value: brain

tag: brain region

tag: background strain


title: shNSD1_GSK_R2

description:
X1688027_YDR445
G401 loss NSD1 EZH2i treated
G401_hg19_raw_count_FORGEO.txt


title: N3_3


title: N3_2


title: wt3

value: wild type


title: wt1


title: wt2


title: ATAC pESC rep3

status: Public on Apr 29 2022

city: Shanghai

first: Tu

middle: zhi

last: fen

address: Tongji University Siping Road Campus

department: life science and technology

country: China

institute: Tongji University

description: ALPG-promoter-RFP/OCT4-ΔPE-GFP dual repoter

data_processing:
All sequenced reads were checked for quality control by using FastQC (v0.11.9) with default parameters.
Sequenced reads was removed adapters and low-quality sequence by using trim_galore (v0.6.6 )with the default parameters.
The processed RNA-Seq reads were mapped to hg38 genome using STAR (v2.5.2b). Refseq genes were quantified to FPKM using Stringtie.
The processed ATAC-Seq reads were mapped to hg38 genome using Bowtie2 (v2.4.1). MACS2(v2.2.7.1) was used to call peaks
Genome_build: hg38
Supplementary_files_format_and_content: text files of counts and FPKM values

source_name: pluripotent stem cells

growth_protocol: For primed-to-naive state transition and prolong culture , cells were cultured in 5iLAF medium containing DMEM/F12: Neurobasal (1:1) (ThermoFisher), 1% N2 supplement (ThermoFisher), 2% B27 supplement (ThermoFisher), 0.5% KnockOut SR (ThermoFisher), 1% nonessential amino acids (Millipore), 2mM GlutaMAX (Millipore), Penicillin Streptomycin (Millipore), 20 ng/ml human LIF (Milipore), 8 ng/ml bFGF (Peprotech), 50 mg/ml BSA (Sigma) and the following cytokines and small molecules: 1 mM PD0325901 (Selleck), 0.5 mM SB590885 (Selleck), 1 mM WH-4-023 (Selleck), 10 mM Y-27632 (Selleck), and 20 ng/ml Activin A (Peprotech). For TS induction, cells were cultured in TSC medium containing DMEM/F-12 supplemented with 0.3% BSA (Sigma), 0.2% FBS (ThermoFisher), 1% ITS-X supplement (ThermoFisher), 0.1 mM 2-mercaptoethanol (Millipore), 2mM GlutaMAX (Millipore), Penicillin Streptomycin (Millipore), 1.5 μg/ml l-ascorbic acid (Sigma), 5 μM Y27632 (Selleck), 2 μM CHIR99021 (Selleck), 0.5 μM A83-01 (Sigma), 1 μM SB431542 (Selleck), 50 ng/ml EGF (Peprotech) and 0.8 mM valproic acid (VPA) (Sigma). Medium were changed daily, and cells were passaged every 2-4 days using 0.5 mM EDTA (Invitrogen).

extract_protocol:
total RNAs were isolated from cells using TRizol (Invitrogen). To generate RNA sequencing libraries, KAPA Stranded mRNA-Seq Kit (KAPA) was used following the manufacturer’s instructions.
mRNA-seq and ATAC-seq libraries were prepared for sequencing using standard Illumina protocols
mRNA-seq and ATAC-seq

treatment_protocol: For primed-to-naive state transition, 2~3×105 dissociated single cells of RFP; GFP pESCs were seeded on the irradiated feeder layer in conventional ESC medium supplemented with Y-27632 (Selleck, 10 mM). Medium was then switched to 5iLAF medium on the second day, and was changed every day. Intermediate cells were collected at different time points during primed-to-naïve transition.

tag: source

value: H9 primed ESC

tag: library type

value: ATAC-seq

tag: condition

value: primed-to-naive transition


title: ATAC pESC rep1


title: ATAC day8 RFP-GFP- rep1


title: ATAC nESC rep1


title: ATAC nESC rep3


title: ATAC day8 RFP+GFP- rep3


title: ATAC day8 RFP+GFP- rep1


title: ATAC day10 RFP+GFP+ rep2


title: ATAC day8 RFP-GFP- rep2


title: ATAC day10 RFP+GFP+ rep1


title: ATAC day8 RFP-GFP- rep3


title: ATAC nESC rep2


title: ATAC day10 RFP+GFP- rep2


title: GFP_sgC_2_R2

description:
X2030396_YDR924
GFP expressing; control
ROBERTS-200044-STRANDED_RSEM_count_FORGEO.txt


title: pESC rep3

value: mRNA-seq


title: ATAC day10 RFP+GFP- rep1


title: ATAC day10 RFP+GFP- rep3


title: nESC rep2


title: ATAC day8 RFP+GFP- rep2


title: pESC rep1


title: pESC rep2


title: day8 RFP-GFP- rep3


title: ATAC pESC rep2


title: nESC rep1


title: day8 RFP+GFP- rep2


title: day10 RFP+GFP+ rep2


title: day8 RFP+GFP- rep1


title: day10 RFP+GFP+ rep1


title: day10 RFP+GFP- rep2


title: day10 RFP+GFP- rep1


title: RNA-seq: Healthy control subject 5 (CTL5)

status: Public on Apr 26 2022

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Datasets were processed and analyzed using an in-house automated pipeline (https://github.com/MarioPujato/NextGenAligner); the following steps describe briefly the characteristics of the NextGenAligner pipeline.
Basic quality control for raw sequencing reads was performed using FASTQC (version 0.11.2) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
The quality controlled reads were aligned to the reference human genome (hg19) using STAR (version 2.5.2a)(Dobin et. al., 2013).
Adapter sequences were removed using Trim Galore (version 0.4.2) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), a wrapper script that runs cutadapt (version 1.9.1) to remove the detected adapter sequence from the reads.
Aligned reads were then sorted using samtools (version 1.8)(Li et al., 2009) and duplicate reads were removed using picard (version 1.89) (https://broadinstitute.github.io/picard/).
The featureCounts function (Rsubread version: 3.5.3) was used to count reads (Liao et al. 2014) and create non-normalized gene counts.
Genome_build: hg19
Supplementary_files_format_and_content: Non-normalized gene counts in a tab separated text file. Columns are 1) gene name; 2) non-normalized read count.
Supplementary_files_format_and_content: Aligned reads in bigWig format

source_name: CD3/CD28 stimulated CD4+ T cells

extract_protocol:
Total RNA was extracted using the mirVANA Isolation Kit (Ambion) from stimulated CD4+ T cells of controls and AD subjects 45 hours post stimulation.
RNA (Transcriptome) libraries were prepared and sequenced at BGI Genomics (Shenzhen, China).

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from subjects' blood using Ficoll-Paque (GE Healthcare) density gradient separation. Untouched CD4+ T cells were then isolated using magnetic column separation (Miltenyi Biotec, CD4+ T cell isolation kit, human). The CD4+ T cells were stimulated with CD3/CD28 crosslinking as directed for 45 hours (Gibco, Dynabeads Human T-Activator CD3/CD28).

tag: case or control

value: Healthy control

tag: age

tag: Sex

value: Female

tag: ancestry

value: Caucasian


title: RNA-seq: Healthy control subject 2 (CTL2)


title: RNA-seq: Healthy control subject 6 (CTL6)


title: nESC rep3


title: RNA-seq: Healthy control subject 3 (CTL3)

value: African American


title: RNA-seq: Atopic Dermatitis subject 6 (AD6)

value: Atopic Dermatitis case


title: RNA-seq: Healthy control subject 1 (CTL1)

value: Male


title: RNA-seq: Atopic Dermatitis subject 2 (AD2)


title: RNA-seq: Healthy control subject 4 (CTL4)


title: WGS: Healthy control subject 1 (CTL1)

data_processing:
Sequencing reads were aligned, and variant calls were made simultaneously following the Genome Analysis Toolkit (GATK) Best Practices 3.3 using the GATK Unified Genotyper
Genome_build: hg19
Supplementary_files_format_and_content: Heterozygous variants called by GATK in bim format

extract_protocol: Whole genome sequencing was performed using DNBseq next generation sequencing technology

tag: cell type

value: CD4+ T cells


title: RNA-seq: Atopic Dermatitis subject 5 (AD5)


title: RNA-seq: Atopic Dermatitis subject 4 (AD4)


title: WGS: Healthy control subject 5 (CTL5)


title: RNA-seq: Atopic Dermatitis subject 3 (AD3)


title: WGS: Healthy control subject 6 (CTL6)


title: WGS: Healthy control subject 3 (CTL3)


title: WGS: Healthy control subject 4 (CTL4)


title: day8 RFP-GFP- rep1


title: WGS: Atopic Dermatitis subject 4 (AD4)


title: WGS: Atopic Dermatitis subject 3 (AD3)


title: day8 RFP-GFP- rep2


title: WGS: Atopic Dermatitis subject 2 (AD2)


title: WGS: Atopic Dermatitis subject 6 (AD6)


title: WGS: Atopic Dermatitis subject 1 (AD1)


title: WGS: Atopic Dermatitis subject 5 (AD5)


title: RNA-seq: Atopic Dermatitis subject 1 (AD1)


title: WGS: Healthy control subject 2 (CTL2)


title: NFKB1 ChIP-seq: Healthy control subject 3 (CTL3)

data_processing:
Datasets were processed and analyzed using an in-house automated pipeline (https://github.com/MarioPujato/NextGenAligner); the following steps describe briefly the characteristics of the NextGenAligner pipeline.
Basic quality control for raw sequencing reads was performed using FASTQC (version 0.11.2) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
The quality controlled reads were aligned to the reference human genome (hg19; chromosomes 1-22, X, Y, M)) using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012).
Adapter sequences were removed using Trim Galore (version 0.4.2) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), a wrapper script that runs cutadapt (version 1.9.1) to remove the detected adapter sequence from the reads.
Aligned reads were then sorted using samtools (version 1.8)(Li et al., 2009) and duplicate reads were removed using picard (version 1.89) (https://broadinstitute.github.io/picard/).
Peaks were called using MACS2 (version 2.1.0) (https://github.com/taoliu/MACS)(Zhang et al., 2008).
ENCODE blacklist regions (Amemiya et al., 2019) were removed using the hg19-blacklist.v2.bed.gz file available at https://github.com/Boyle-Lab/Blacklist/tree/master/lists.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks called by MACS2 in narrowPeak format
Supplementary_files_format_and_content: Aligned reads in bigWig format
Supplementary_files_format_and_content: For each pair, peaks enriched in the AD sample, the control sample, or common between them. Enrichment determined by MAnorm. Peaks are in narrowPeak format
Supplementary_files_format_and_content: Peaks that are present in 3 or more AD samples in bed format
Supplementary_files_format_and_content: Peaks that are present in 3 or more control samples in bed format

extract_protocol:
Cells were crosslinked and nuclei were sonicated as described previously (Lu et al. 2015).
Libraries were prepared via ChIPmentation (Schmidl et al. 2015).

value: Control

tag: chip antibody

value: NFKB1 (Cell Signaling, catalog number 12540S, lot number 2)


title: NFKB1 ChIP-seq: Healthy control subject 4 (CTL4)


title: NFKB1 ChIP-seq: Atopic Dermatitis subject 6 (AD6)


title: NFKB1 ChIP-seq: Healthy control subject 2 (CTL2)


title: NFKB1 ChIP-seq: Atopic Dermatitis subject 3 (AD3)


title: NFKB1 ChIP-seq: Healthy control subject 1 (CTL1)


title: NFKB1 ChIP-seq: Atopic Dermatitis subject 2 (AD2)


title: NFKB1 ChIP-seq: Healthy control subject 5 (CTL5)


title: NFKB1 ChIP-seq: Atopic Dermatitis subject 5 (AD5)


title: NFKB1 ChIP-seq: Atopic Dermatitis subject 4 (AD4)


title: NFKB1 ChIP-seq: Atopic Dermatitis subject 1 (AD1)


title: NFKB1 ChIP-seq: Healthy control subject 6 (CTL6)


title: ATAC-seq: Atopic Dermatitis subject 6 (AD6)

data_processing:
Datasets were processed and analyzed using an in-house automated pipeline (https://github.com/MarioPujato/NextGenAligner); the following steps describe briefly the characteristics of the NextGenAligner pipeline.
Basic quality control for raw sequencing reads was performed using FASTQC (version 0.11.2) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
The quality controlled reads were aligned to the reference human genome (hg19; chromosomes 1-22, X, Y, M) using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012).
Adapter sequences were removed using Trim Galore (version 0.4.2) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), a wrapper script that runs cutadapt (version 1.9.1) to remove the detected adapter sequence from the reads.
Aligned reads were then sorted using samtools (version 1.8)(Li et al., 2009) and duplicate reads were removed using picard (version 1.89) (https://broadinstitute.github.io/picard/).
Peaks were called using MACS2 (version 2.1.0) (https://github.com/taoliu/MACS)(Zhang et al., 2008).
ENCODE blacklist regions (Amemiya et al., 2019) were removed
Differential peaks were calculated using MAnorm (Shao et al. 2012) with threshold of log2 fold change greater than 1.5 and a p-value of less than 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks called by MACS2 in narrowPeak format
Supplementary_files_format_and_content: Aligned reads in bigWig format
Supplementary_files_format_and_content: For each pair, peaks enriched in the AD sample, the control sample, or common between them. Enrichment determined by MAnorm. Peaks are in narrowPeak format
Supplementary_files_format_and_content: Peaks that are present in 3 or more AD samples in bed format
Supplementary_files_format_and_content: Peaks that are present in 3 or more control samples in bed format

extract_protocol:
Transposase Tn5 with adapter sequences was used to cut accessible DNA (Buenrostro et al. 2015).
Accessible DNA with adaptor sequences were isolated, then libraries were prepared from 50,000 stimulated CD4+ T cells using the OMNI protocol (Corces et al. 2017).


title: C8_S18

status: Public on Apr 12 2022

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

description: Counts.matrix.csv

data_processing:
Qiagen adapters were removed (allowing 1 mismatch) and UMI sequences were retained with UMI tools version 0.5.4 (extract module). Reads shorter than 15bp were removed with Cutadapt version 2.1.
Reads in the fastq files were mapped with STAR version 2.6.0 (A.Dobin et al. 2013) against miRBase v22.1. The table of counts was obtained with FeatureCounts function in the package subread, version 1.6.4 (Y.Liao, GK.Smyth, and W.Shi 2014) and posterior counting of unique UMIs with UMI tools version 0.5.4 (count, default method “directional”).
For the differential gene expression analysis (DEG) genes having less than 3 counts in at least 2 samples were excluded from the analysis. Read counts were converted to log2-counts-per-million (logCPM) and the mean-variance relationship was modelled with precision weights using voom approach in limma package using a linear model design adjusting for the sum of risk factors.
Genome_build: miRBase v22.1
Supplementary_files_format_and_content: csv file containing the table of raw counts

source_name: small RNA from serum samples of Covid-19 patients

extract_protocol:
miRNeasy Serum/Plasma kit (QIAGEN)
NGS smallRNA libraries were prepared according to the manual QIAseq miRNA Library Kit Handbook for Illumina (QIAGEN) (Version 1.0, 12/18)

tag: mv

value: MV-

tag: batch

value: BATCH 2

tag: tobacco

tag: alcohol

tag: hta

tag: irc

tag: dm

tag: obesity

tag: hepatopaty

tag: psiquiatric

tag: active cancer

tag: hiv

tag: other

tag: exitus


title: ATAC-seq: Healthy control subject 4 (CTL4)

tag: case or control

tag: age

tag: Sex

tag: ancestry


title: ATAC-seq: Healthy control subject 5 (CTL5)

tag: cell type


title: ATAC-seq: Healthy control subject 2 (CTL2)


title: ATAC-seq: Atopic Dermatitis subject 4 (AD4)


title: ATAC-seq: Atopic Dermatitis subject 1 (AD1)


title: C7_S5

description: Counts.matrix.csv

tag: mv

tag: batch

value: BATCH 1

tag: tobacco


title: ATAC-seq: Healthy control subject 1 (CTL1)


title: ATAC-seq: Atopic Dermatitis subject 5 (AD5)


title: ATAC-seq: Atopic Dermatitis subject 3 (AD3)


title: ATAC-seq: Healthy control subject 3 (CTL3)


title: C9_S19

description: Counts.matrix.csv

tag: alcohol

tag: hta

tag: irc


title: C6_S4

description: Counts.matrix.csv

tag: dm

tag: obesity

tag: hepatopaty


title: C5_S3

description: Counts.matrix.csv

tag: psiquiatric

tag: active cancer

tag: hiv


title: C30_S16

description: Counts.matrix.csv

value: MV+

tag: other

tag: exitus


title: C26.REP_S27

description: Counts.matrix.csv

tag: age

tag: Sex

value: lupus inmunodepressed


title: C27_S24

description: Counts.matrix.csv


title: C4_S17

description: Counts.matrix.csv


title: C21_S23

description: Counts.matrix.csv


title: C25_S14

description: Counts.matrix.csv

value: renal transplant


title: ATAC-seq: Healthy control subject 6 (CTL6)

tag: cell type

tag: case or control

tag: ancestry


title: C23_S12

description: Counts.matrix.csv

tag: mv

tag: batch

tag: tobacco


title: C28.REP_S28

description: Counts.matrix.csv

tag: alcohol

tag: hta

tag: irc

value: behçet


title: C29_S15

description: Counts.matrix.csv

tag: dm

tag: obesity

tag: hepatopaty


title: C22_S11

description: Counts.matrix.csv

tag: psiquiatric

tag: active cancer

tag: hiv


title: ATAC-seq: Atopic Dermatitis subject 2 (AD2)

tag: age


title: C24_S13

description: Counts.matrix.csv

tag: Sex

tag: other

tag: exitus


title: C20_S22

description: Counts.matrix.csv


title: C2_S2

description: Counts.matrix.csv


title: C16_S21

description: Counts.matrix.csv


title: C17.REP_S26

description: Counts.matrix.csv


title: C14_S8

description: Counts.matrix.csv


title: C18_S9

description: Counts.matrix.csv

value: dialisis


title: C12_S7

description: Counts.matrix.csv


title: C15_S20

description: Counts.matrix.csv


title: C19_S10

description: Counts.matrix.csv


title: C13.REP_S25

description: Counts.matrix.csv


title: MMTVRANK population luminal rep3

status: Public on Feb 24 2022

data_processing:
Alignment was made using STAR version 2.6.1b
The table of counts was obtained with FeatureCounts function in the package subread, version 1.5
Genome_build: Gencode release M17 based on the GRCm38.p6
Supplementary_files_format_and_content: txt file containing the table counts

extract_protocol:
Mammary gland were enzymatically disaggregated and live CD24 and CD49f were sorted using MoFlo Astrios.Total RNA from sorted cells was extracted using the RNAeasy Micro kit (Cat.No.74004).
SMARTer™Stranded Total RNA-seq Kit- Pico: following manufacturer protocol

tag: genotype

value: MMTVRANK

tag: cell type

value: sorted mammary epithelial cells

tag: cell subtype

value: luminal


title: WT population basal rep3

value: WT

value: basal


title: WT population basal rep2


title: WT population luminal rep3


title: MMTVRANK population basal rep3


title: WT population luminal rep2


title: MMTVRANK population luminal rep2


title: MMTVRANK population luminal rep1


title: WT population luminal rep1


title: MMTVRANK population basal rep1


title: WT population basal rep1


title: Sample.253160

status: Public on Jan 17 2022

data_processing:
Quality control performed using fastQC, fastQScreen and MultiQC
RNA-seq reads were aligned to the mm10 genome assembly using STAR version STAR version 2.5.3a
RNA-seq reads were mapped using featureCounts, the package version 1.5.1 (Y.Liao, GK.Smyth, and W.Shi 2014)
Differential gene expression analysis (DEG) was assessed with voom+limma in the limma package (ME.Ritchie and GK.Smyth 2015) and using R version 3.4.3
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: csv files containing the table counts

source_name: Brain

extract_protocol:
RNeasy Lipid Tissue Mini Kit (Qiagen)
Total Dual RNA-Seq PolyA

treatment_protocol: Each tissue sample was homogenized in 1ml of QIAzol Lysis Reagent

tag: area

value: Striatum

tag: genotipe

value: Non-Carrier

value: Old


title: Sample.254172

value: Hippocampus


title: Sample.252148

value: PFC


title: Sample.255184

value: Amygdala


title: Sample.251136


title: MMTVRANK population basal rep2


title: Sample.250124


title: C1_S1

description: Counts.matrix.csv

tag: mv

value: MV-

tag: batch

value: BATCH 1

value: Female

tag: tobacco

tag: alcohol

tag: hta


title: Sample.249112


title: Sample.248195


title: C11_S6

description: Counts.matrix.csv

value: Male

tag: irc

tag: dm

tag: obesity

tag: hepatopaty

tag: psiquiatric


title: Sample.244147

tag: age


title: Sample.247183


title: Sample.246171


title: Sample.245159


title: Sample.243135


title: Sample.240194


title: Sample.237158


title: Sample.238170


title: Sample.242123


title: Sample.239182


title: Sample.236146


title: Sample.241111


title: Sample.235134


title: Sample.233110


title: Sample.230169


title: Sample.231181


title: Sample.232193


title: Sample.225109


title: Sample.224192


title: Sample.223180


title: Sample.222168


title: Sample.227133


title: Sample.221156


title: Sample.220144


title: Sample.214167


title: Sample.217108


title: Sample.219132


title: Sample.213155


title: Sample.218120


title: Sample.216191


title: Sample.212143


title: Sample.209107


title: Sample.210119


title: Sample.234122


title: Sample.211131


title: Sample.207178

value: Young


title: Sample.208190


title: Sample.205154


title: Sample.203130


title: Sample.202118


title: Sample.228145


title: Sample.229157


title: Sample.204142


title: Sample.201106


title: Sample.226121


title: Sample.296189


title: Sample.293153


title: Sample.294165


title: Sample.292141


title: Sample.291129


title: Sample.295177


title: Sample.215179


title: Sample.288188


title: Sample.289105


title: Sample.287176


title: Sample.283128


title: Sample.280187


title: Sample.206166


title: Sample.278163


title: Sample.281104


title: Sample.286164


title: Sample.285152


title: Sample.282116


title: Sample.277151


title: Sample.279175


title: Sample.284140


title: Sample.290117


title: Sample.276139


title: Sample.273103


title: Sample.274115


title: Sample.271174


title: Sample.270162


title: Sample.272186


title: Sample.269150


title: Sample.268138


title: Sample.275127


title: Sample.264185


title: Sample.263173


title: Sample.265102


title: Sample.267126


title: Sample.259125


title: Sample.261149


title: Sample.260137


title: Sample.258113


title: shNC-rep2

status: Public on Dec 31 2021

city: Hangzhou City

first: HongKai

last: Shang

address: 388 Yuhangtang Road, Xihu District

institute: Zhejiang University

data_processing:
Trimmomatic version 3.6 [6] tool was used to clean up the reads by removing adapters and low-quality reads (quality value less than 20), and the reads with N ratio exceeding 10% or length less than 50bp were also removed.
Hisat2 software (v2.05) [7] was used for the alignment of clean reads to human genomic database (GRCH38, Gencode).
Human genome annotation in resulting files was mapped to corresponding read count by using featureCounts tools .
Further filtering was performed for different results according to Fragments Per Kilobase Of Exon Per Million Fragments Mapped (FPKM) method, and the genes with FPKM value less than 0.1 in any samples were removed.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: ovarian cancer cells

growth_protocol: The cells were cultured in RPMI1640 medium supplement with 10% fetal bovine serum and maintained in a condition of 37˚C and 5% CO2.

extract_protocol:
The total RNA was extracted from ovarian cancer cells using TRIzol (TaKaRa, Inc. Tokyo, Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SKOV3 cells were seeded in a 6-well plate at a density of 1x105/well and transfected with shNTPCR and negative control (NC) using lentiviral-mediated RNA interference methods. Primers of shRNA were synthesized from Genewiz biotechnology Inc. (Suzhou, China). The shNTPCR was inserted into pLKO.1-pure vector and validated by gene sequencing. SKOV3 cells were incubated for 72 h after transfection and then screened in a medium containing 0.5ug/ml puromycin for one week. The mRNA level of NTPCR was detected by RT‑qPCR analysis to explore the transfection efficiency.

tag: type

value: Ascites-derived  ovarian cancer cells

tag: strain

tag: treatment

value: untreated


title: Sample.262161


title: Sample.257101


title: shNTPCR-rep2

value: NTPCR down-regulation


title: shNC-rep3


title: Sample.266114


title: shNTPCR-rep3


title: shNC-rep1


title: shNTPCR-rep1


title: siOLFM2_72h-1

status: Public on Dec 28 2021

type: RNA

description: Gene expression data from treated human adipose tissue-derived and in vitro differentiated adipocytes (treatment of 72h with siRNAs against OLFM2 mRNA)

hyb_protocol: Sample was hybridized to Affymetrix Clariom S Human array using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

label: Biotin

label_protocol: 100ng of total RNA from each sample was processed and labelled according to manual GeneChip WT PLUS Reagent kit (P/N 703174 Rev. 2, Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: Total RNA was extracted following Qiagen protocol

tag: condition

value: OLFM2 KD (72h)


title: siPKP2_72h-2

description: Gene expression data from treated human adipose tissue-derived and in vitro differentiated adipocytes (treatment of 72h with siRNAs against PKP2 mRNA)

value: PKP2 KD (72h)


title: siOLFM2_72h-4

source_name: adipose tissue-derived and in vitro differentiated adipocytes


title: siPKP2_72h-1


title: siCTRL_72h-4

description: Gene expression data from treated human adipose tissue-derived and in vitro differentiated adipocytes (treatment of 72h with NTC)

value: Non-targeting control (NTC)


title: shPkp2_4

description: Gene expression data from infected human adipose tissue-derived and in vitro differentiated adipocytes (after 6d with shRNAs against PKP2 mRNA)

value: PKP2 KD (6d)


title: shOlfm2_3

description: Gene expression data from infected human adipose tissue-derived and in vitro differentiated adipocytes (after 6d with shRNAs against OLFM2 mRNA)

value: OLFM2 KD (6d)


title: shOlfm2_2


title: siOLFM2_72h-2


title: siCTRL_72h-2


title: shPkp2_1


title: siPKP2_72h-4


title: shOlfm2_1


title: shPkp2_2


title: MAJA69

description: Gene expression data

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  using Affymetrix GeneChip Scanner 3000 7G

label: biotin

source_name: Total RNA from FFPE samples_goodResp

label_protocol: A total of 50ng from each sample was processed and labelled according to the GeneChip 3’ IVT Pico Kit user guide

extract_protocol: Total RNA was isolated from 10-μm sections of FFPE tumors fixed on positively charged slides. After selection of tumor areas by macrodissection, cells were lysed and sheared by sonication with a S2 (Covaris Inc., Wobrun, MA), RNA was purified using the truXTRAC FFPE microTube RNA Kit (Covaris) following the manufacturer’s instructions, eluted in a final volume of 30 µl, and immediately quantified using the Qubit 3 Fluorometer (Thermo Fisher Scientific).

tag: tissue

value: FFPE tumor tissue

tag: cycles

tag: resonse

value: goodResp

tag: Sex

value: male


title: siCTRL_72h-3


title: MAJA66b

description: Gene expression data

source_name: Total RNA from FFPE samples_badResp

value: badResp


title: MAJA55

description: Gene expression data


title: shCtr_2

description: Gene expression data from infected human adipose tissue-derived and in vitro differentiated adipocytes (non-targeting control, 6d)


title: shCtr_3


title: shCtr_4


title: siCTRL_72h-1


title: MAJA75

description: Gene expression data

value: female


title: MAJA59

description: Gene expression data


title: shCtr_1


title: MAJA56

description: Gene expression data


title: MAJA62

description: Gene expression data


title: MAJA50

description: Gene expression data


title: MAJA48

description: Gene expression data


title: MAJA49

description: Gene expression data


title: V2320_150K

status: Public on Dec 17 2021

city: Oxford

first: Toluwalase

last: Awoyemi

state: Oxfordshire

address: John Radcliffe Hospital, Level 3

department: Nuffield Department's of Women's and reproductive health

country: United Kingdom

institute: University of Oxford

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed in OASIS 2 for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human reference genome, miRNAome and sRNAome stored in the OASIS database with STAR (2.4.1d). Novel miRNA were predicted and archived in the OASIS db using Bowtie (v1.0.0). Gene counts outputted from OASIS 2.0 were then imported into R
Gene count tables were analysed for differential expression with DESEQ2 in R
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with DESEQ2 normalised gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Placenta

extract_protocol:
For Placenta tissue, samples were mechanically homogenised, RNA was harvested using Rneasy mini kit. For STB-EVS, RNA was harvested with the miRCURY RNA isolation kit. Illumina TruSeq-stranded total RNA 20020597 was used with an equal amount of total RNA (depending on the sample type) for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Small STB-Evs

tag: diseases state (normal or pe)

value: PE

tag: maternal age

tag: maternal weight (kg)

tag: maternal height (cm)

tag: bmi

tag: parity

tag: gravidity

tag: no of preterm deliveries

tag: history of diabetes melitus

value: no

tag: smoking)

value: exsmoker

tag: highest blood pressure

tag: urine dipstick

tag: gestational age at diagnosis

tag: gestational age at delivery

tag: newborngender

value: M

tag: birth weight

tag: iugr

value: No


title: V2409_150K

tag: tissue

tag: diseases state (normal or pe)

value: Never

value: F

value: yes


title: V2446_150K

tag: maternal age

tag: maternal weight (kg)

value: Trace


title: V2441_150K

tag: maternal height (cm)

tag: bmi


title: MAJA42

description: Gene expression data

tag: cycles

tag: resonse

tag: Sex

tag: age


title: V2492_150K

tag: parity

tag: gravidity

tag: no of preterm deliveries

tag: history of diabetes melitus

tag: smoking)

tag: highest blood pressure


title: V2506_150K

tag: urine dipstick

tag: gestational age at diagnosis

tag: gestational age at delivery

tag: newborngender

tag: birth weight

tag: iugr


title: V2442_150K

tag: tissue

tag: diseases state (normal or pe)

tag: maternal age

tag: maternal weight (kg)

tag: maternal height (cm)

tag: bmi


title: MAJA35

description: Gene expression data

tag: cycles

tag: resonse

tag: Sex

tag: age


title: MAJA22

description: Gene expression data


title: MAJA13

description: Gene expression data


title: MAJA2

description: Gene expression data


title: MAJA36

description: Gene expression data


title: MAJA8

description: Gene expression data


title: V2373_150K

value: NP

tag: parity

tag: gravidity

tag: no of preterm deliveries

tag: history of diabetes melitus

tag: smoking)

tag: highest blood pressure


title: V2367_150K

tag: urine dipstick

tag: gestational age at diagnosis

tag: gestational age at delivery

tag: newborngender

tag: birth weight

tag: iugr


title: V2368_150K

tag: tissue

tag: diseases state (normal or pe)

tag: maternal age

tag: maternal weight (kg)

tag: maternal height (cm)

tag: bmi


title: V2481_150K

tag: parity

tag: gravidity


title: V2545_150K

tag: no of preterm deliveries

tag: history of diabetes melitus


title: V2409_10K

value: Medium/Large STB-EVs

tag: smoking)

tag: highest blood pressure


title: V2320_10K

tag: urine dipstick

tag: gestational age at diagnosis


title: V2441_10K

tag: gestational age at delivery

tag: newborngender


title: V2442_10K

tag: birth weight

tag: iugr


title: V2440_150K

tag: tissue

tag: diseases state (normal or pe)


title: V2446_10K

tag: maternal age

tag: maternal weight (kg)


title: V2506_10K

tag: maternal height (cm)

tag: bmi


title: V2508_10K

tag: parity

tag: gravidity

value: nonsmoker

value: Yes


title: V2492_10K

tag: no of preterm deliveries

tag: history of diabetes melitus


title: V2373_10K

tag: smoking)

tag: highest blood pressure


title: V2367_10K

tag: urine dipstick

tag: gestational age at diagnosis


title: V2368_10K

tag: gestational age at delivery

tag: newborngender


title: V2440_10K

tag: birth weight

tag: iugr


title: V2481_10K

tag: tissue

tag: diseases state (normal or pe)


title: V2508_150K

tag: maternal age

tag: maternal weight (kg)


title: V2409_PLAC

value: Placenta

tag: maternal height (cm)

tag: bmi


title: V2441_PLAC

tag: parity

tag: gravidity


title: V2442_PLAC

tag: history of diabetes melitus


title: V2373_PLAC

tag: no of preterm deliveries

tag: smoking)


title: V2508_PLAC

tag: highest blood pressure

tag: urine dipstick


title: V2367_PLAC

tag: gestational age at diagnosis

tag: gestational age at delivery


title: V2440_PLAC

tag: newborngender

tag: birth weight


title: V2368_PLAC

tag: tissue

tag: iugr


title: V2481_PLAC

tag: diseases state (normal or pe)

tag: maternal age


title: V2545_PLAC

tag: maternal weight (kg)

tag: maternal height (cm)


title: V2506_PLAC

tag: bmi

tag: parity


title: mRNA_V2409_150K

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using HISAT2 on usegalaxy.org with default settings (Galaxy Version 2.2.1+galaxy0) and features were counted with featureCounts (Galaxy Version 2.0.1+galaxy1)
Gene count tables were analysed for differential expression with DESEQ2 in R
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with DESEQ2 normalised gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

tag: disease state (normal or pe)

tag: gravidity

tag: history of diabetes melitus


title: mRNA_V2441_150K

tag: no of preterm deliveries

tag: smoking)

tag: highest blood pressure


title: mRNA_V2320_150K

tag: urine dipstick

tag: gestational age at diagnosis

tag: gestational age at delivery


title: mRNA_V2446_150K

tag: tissue

tag: newborngender

tag: birth weight


title: mRNA_V2442_150K

tag: maternal age

tag: iugr


title: mRNA_V2506_150K

tag: maternal weight (kg)

tag: maternal height (cm)


title: mRNA_V2508_150K

tag: bmi

tag: parity


title: V2545_10K

tag: diseases state (normal or pe)

tag: gravidity


title: V2446_PLAC

tag: no of preterm deliveries

tag: history of diabetes melitus


title: V2492_PLAC

tag: smoking)

tag: highest blood pressure


title: mRNA_V2368_150K

tag: disease state (normal or pe)

tag: urine dipstick

tag: gestational age at diagnosis


title: mRNA_V2440_150K

tag: tissue

tag: gestational age at delivery

tag: newborngender


title: mRNA_V2373_150K

tag: maternal age

tag: birth weight

tag: iugr


title: mRNA_V2481_150K

tag: maternal weight (kg)

tag: maternal height (cm)

tag: bmi


title: mRNA_V2367_150K

tag: parity

tag: gravidity


title: mRNA_V2545_150K

tag: no of preterm deliveries

tag: history of diabetes melitus


title: mRNA_V2320_10K

tag: smoking)

tag: highest blood pressure


title: mRNA_V2409_10K

tag: disease state (normal or pe)

tag: urine dipstick


title: mRNA_V2446_10K

tag: tissue

tag: gestational age at diagnosis


title: mRNA_V2441_10K

tag: gestational age at delivery

tag: newborngender


title: mRNA_V2442_10K

tag: maternal age

tag: birth weight


title: mRNA_V2508_10K

tag: maternal weight (kg)

tag: iugr


title: mRNA_V2367_10K

tag: maternal height (cm)

tag: bmi


title: mRNA_V2373_10K

tag: parity

tag: gravidity


title: mRNA_V2506_10K

tag: no of preterm deliveries

tag: history of diabetes melitus


title: mRNA_V2368_10K

tag: smoking)

tag: highest blood pressure


title: mRNA_V2440_10K

tag: disease state (normal or pe)

tag: urine dipstick


title: mRNA_V2492_10K

tag: tissue

tag: gestational age at diagnosis


title: mRNA_V2481_10K

tag: gestational age at delivery

tag: newborngender


title: mRNA_V2545_10K

tag: maternal age

tag: birth weight


title: mRNA_V2492_150K

tag: maternal weight (kg)

tag: iugr


title: mRNA_V2446_PLAC

tag: maternal height (cm)

tag: bmi


title: mRNA_V2409_PLAC

tag: parity

tag: gravidity


title: mRNA_V2442_PLAC

tag: history of diabetes melitus


title: mRNA_V2492_PLAC

tag: no of preterm deliveries

tag: smoking)


title: mRNA_V2506_PLAC

tag: disease state (normal or pe)

tag: highest blood pressure


title: mRNA_V2508_PLAC

tag: tissue

tag: urine dipstick


title: mRNA_V2368_PLAC

tag: gestational age at diagnosis

tag: gestational age at delivery


title: mRNA_V2367_PLAC

tag: maternal age

tag: newborngender


title: mRNA_V2373_PLAC

tag: maternal weight (kg)

tag: birth weight


title: mRNA_V2545_PLAC

tag: maternal height (cm)

tag: iugr


title: culture_1

status: Public on Dec 14 2021

city: Würzburg

first: Robert

address: Josef-Schneider-Str. 11

department: Department of Neurology

country: Germany

institute: University Hospital Würzburg

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 1.17 (cutadapt parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of trimmed reads to mouse genome using STAR (Dobin et al., 2013)  v2.7.2b with default parameters based on RefSeq annotation version 108.20200622 for GRCm38.p6
Calculation of read counts on exon level summarized for each gene (RefSeq annotation version 108.20200622 for GRCm38.p6) using featureCounts v1.6.4 from the Subread package (Liao et al., 2014). Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (command line parameters: -s 2 -t exon -M -O --fraction).
Genome_build: GRCm38.p6 (primary assembly and mitochondrion)
Supplementary_files_format_and_content: Character (TAB) seperated value file containing mRNA abundance measurements

source_name: cultured, cortical astrocytes

growth_protocol: Primary mouse cortical glial cells were prepared from P4 wt CD1 mice. Pieces of the frontal cortex were dissected bilaterally and collected in Hank’s buffered saline solution (HBSS). After three steps of trituration, glial cells were cultivated in basal glial medium (1:1 mixture of DMEM/F12 with 10% FCS, 5% HS, 1% penicillin/streptomycin, 0.45% glucose) containing B27 (1:50) and 10 ng/ml EGF (PeproTech). Cells were cultured in a poly-D L‑ornithine hydrobromide (PORN, 0.5 mg/ml)-coated 75 cm2 culture flask at 37°C, 5% CO2 atmosphere. After 3 days, cells were washed with PBS to remove cell debris and cell clumps. At day in vitro 6, cells were seeded on PORN-coated 3.5 cm cell culture dishes at a density of 200.000 cells per dish. RNA preparation was performed after 3 days. For standardization of cell culture coniditions, cell medium was removed and cells were kept in serum-free Ham’s medium for 60 min. Finally, total RNA was prepared with the Qiagen RNA Mini kit.

extract_protocol:
Total RNA was extracted from cell cultures using the Qiagen RNA Mini Kit.
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was >9.3. DNA libraries suitable for sequencing were prepared from 500 ng of total RNA with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions (½ volume). After 14 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated ~275 bp by electrophoresis on Agilent DNA 1000 Bioanalyzer microfluidic chips.

treatment_protocol: For standardization, all four cell samples were washed and kept in fresh Ham's medium for one hour.

value: cortex

tag: treatment

value: Ham's medium, 1h

tag: developmental stage

value: early postnatal, P4

tag: strain


title: Scrambled_siRNA_3

status: Public on Dec 05 2021

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: North Carolina State University

data_processing:
Fastq reads were demultiplexed using Illumina bcl2fastq v2.19.1.403
Paired-end sequencing reads (75 bp) were mapped using STAR 2.7.9a to the human genome assembly 38 (Hg38) with gencode version 38 annotation.
Genes with at least 3 sample counts greater than 20 raw reads were retained
Normalized gene counts were calculated using Limma 3.42.2 Voom mean-variance transformation
Linear contrast: E2D of normalized counts between CUX1 siRNA treated samples vs scrambled siRNA treated samples, was calculated using Limma 3.42.2
Genome_build: hg38
Supplementary_files_format_and_content: Tab separated table with columns containing raw gene counts, normalized gene counts, and linear contrast effects for each sample and linear contrast

source_name: Primary human arterial ECs

growth_protocol: Primary human arterial ECs (Cat#: CC-2535) and human arterial VSMCs (Cat#: CC-2571) were purchased from Lonza. HMC3 (Cat#: ATCC CRL-3304) and HTP-1 (Cat#: ATCC TIB-202) were purchased from ATCC. All cells were free of mycoplasma. ECs were cultured in basal medium EGM-2, VSMCs in SmGM-2 supplemented with Bullet Kit (Lonza), HMC3 in DMEM/F12 mix (1:1), and HTP-1 in RPMI-1640. All media were supplemented with 10% fetal bovine serum. All cells were cultured at 37ºC in 5% CO2

extract_protocol:
Total RNA was extracted from the scrambled siRNA knockdown and the CUX1 siRNA knockdown ECs at passage 10 using an RNeasy Mini kit (Qiagen Cat#74104). All samples were quantified and assayed to confirm minimum RINs of at least 9.3 using an Agilent Bioanalyzer (High Sensitivity DNA Kit, Cat#5067-4626). 1 µg total RNA per sample underwent mRNA capture and was then fragmented at 94 ºC for 6 min.
Sequencing library was prepared according to the manufacturer’s protocol using 10 cycles of final amplification (KAPA mRNA HyperPrep Kit, Cat#KK8580 and KAPA UDI Adapter Kit, Cat#KK8727). Next generation sequencing was performed on Illumina NextSeq500 (75 bp paired end) to a targeted depth of ~20M reads/sample.

treatment_protocol: For siRNA transient knockdown in human ECs, siRNAs for human CUX1 were purchased from Horizon Discovery, and knockdown was performed according to the manufacturer’s protocol. For CUX1 shRNA knockdown, lentiviruses were generated using the pLKO.1 puro vector (Addgene).

tag: cell type

value: Primary human arterial ECs

value: Scrambled siRNA


title: CUX1_siRNA_3

value: CUX1 siRNA


title: culture_2


title: culture_3


title: Scrambled_siRNA_1


title: WTP84_DG

status: Public on Nov 25 2021

data_processing:
Pair-end reads of 100bp were read via the BGISEQ-500 platform. Low quality reads were ltered using the BGI-internal software SOAPnuke (reads with adaptors, reads in which unknown bases are >10 and low-quality reads with threshold 15 were removed.
Genome mapping was done using the HISAT software. Transcripts were then reconstructed using StringTie and compared to reference using Cucompare. The coding potential of StringTie and compared to reference using Cucompare. The coding potential of novel transcripts was predicted using CPC. SNP and INDEL detection was done using GATK. Clean reads were mapped to Mus musculus (house mouse) genome assembly GRCm38 (mm10) from Genome Reference Consortium using Bowtie2 and gene expression levels were calculated using the RSEM software package
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: normalized counts FPKMs in .xlsx format

source_name: brain

growth_protocol: animals housed in an SPF facility (55% humidity, 21°C, 12h/12h light cycle); only male animals were used at an adult age, sex in pups not identifiable

extract_protocol:
Animals were killed by isoflurane overdose and neck dislocation. No perfusion was performed. The brain was taken out in <120s and immediately frozen using spray dry ice and subsequently transportet on dry ice. They were further processed the same day they were taken out using a "needle-scratch-method" isolating all hippocampal subfields.
library was constructed by BGI The final library was constructed making a single strand DNA circle. Rolling circle replication created DNA  nanoballs, which yields more fluorescent signal during sequencing. Pair-end reads of 100bp were read via the BGISEQ-500 platform.

treatment_protocol: only "baseline" condition: no intervention, animals taken directly from home cage

tag: genotype

value: wildtype pup

value: brain

tag: brain region

value: dentate gyrus


title: WTP84_CA3


title: Activated CD8 T cells replicate 2 [Activate_T_CD8_2]

status: Public on Dec 01 2021

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Libraries were sequenced with 50bp single end reads on an Illumina HiSeq3000.
The reads were mapped with STAR 2.5.3a to the human genome (hg38).
The counts for each gene were obtained using --quantMode GeneCounts in STAR commands, and the other parameters during alignment were set to default.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for each sample

source_name: Activated CD8 T cells

growth_protocol: All samples were isolated from human healthy donor peripheral nlood monunuclear cells provided by UCLA Virology Core

extract_protocol:
All samples were stored in RNA later stabilization solution and subsequently total RNA was extracted using RNA mini Kit (7326830, BioRad). cDNA was synthesized by using iScript cDNA Synthesis Kit (1708890, BioRad) and qPCR performed.
For RNA-sequencing, libraries were prepared by the Technology Center for Genomics & Bioinformatics at UCLA using Illumina TruSeq Stranded Total RNA Sample Prep kit and sequenced with 50bp single end reads on an Illumina HiSeq3000.

treatment_protocol: All samples were sorted using MACS microbeads or FACS flow sorting performed by UCLA FACS Core

value: human T cells

tag: cell subtype

value: Activated CD8 T cells


title: mRNA_V2440_PLAC

tag: tissue

tag: disease state (normal or pe)

tag: bmi

tag: parity

tag: gravidity

tag: no of preterm deliveries

tag: history of diabetes melitus

value: no

tag: smoking)

value: exsmoker

tag: highest blood pressure

value: M


title: Activated CD8 T cells replicate 1 [Activate_T_CD8_1]


title: Scrambled_siRNA_2


title: culture_4


title: WTP83_CA3


title: Activated CD8 T cells replicate 8 [Activate_T_CD8_8]


title: mRNA_V2441_PLAC

value: PE

tag: maternal age

tag: maternal weight (kg)

tag: maternal height (cm)

value: Never

tag: urine dipstick

value: Trace

tag: gestational age at diagnosis

tag: gestational age at delivery

tag: newborngender

value: F

tag: birth weight

tag: iugr

value: yes


title: WTP82_DG

tag: genotype

tag: tissue

tag: brain region


title: CUX1_siRNA_1

tag: cell type

tag: treatment


title: WTP83_CA1


title: WTP83_DG


title: WTP82_CA1


title: mRNA_V2481_PLAC

value: Placenta

tag: disease state (normal or pe)

value: NP

tag: bmi

tag: parity

tag: gravidity

tag: no of preterm deliveries

tag: history of diabetes melitus


title: WTP81_DG


title: CUX1_siRNA_2

value: Primary human arterial ECs


title: SM694_DG

value: Neil3-/- adult


title: WTP81_CA1

value: wildtype pup


title: WTP81_CA3

value: brain


title: WTP84_CA1


title: SM694_CA3


title: SM693_CA3


title: SM694_CA1


title: SM693_CA1


title: SM692_DG

value: dentate gyrus


title: SM627_CA3

value: wildtype adult


title: SM627_DG


title: SM627_CA1


title: SM692_CA3


title: WTP82_CA3


title: SM626_CA3


title: SM625_DG


title: N3P84_CA3

value: Neil3-/- pup


title: N3P84_DG


title: SM625_CA1


title: SM626_CA1


title: N3P83_DG


title: SM692_CA1


title: SM625_CA3


title: N3P83_CA3


title: N3P83_CA1


title: N3P82_DG


title: N3P82_CA3


title: SM693_DG


title: N3P81_DG


title: N3P82_CA1


title: SM626_DG


title: N3P81_CA1


title: FAC-sorted stimulated T cells, non-proliferating

status: Public on Nov 18 2021

data_processing:
Raw sequencing data were demultiplexed using the 10x Genomics cellranger (v4.0.0) commands mkfastq command.
Reads were aligned to the RheMac10 genome annotation, and UMI-collapsed using the 10x Genomics cellranger (v4.0.0) count command.
Raw gene expression matrices were normalized and scaled using the SCTransform20 method with the Seurat R package (v3.1.5).
Genome_build: RheMac10
Supplementary_files_format_and_content: H5 files contain gene expression matrices of UMI counts from single cells.

organism: Macaca mulatta

source_name: Peripheral Blood

extract_protocol:
Single cells were prepared and loaded onto the 10x Genomics Chromium controller for a targeted cell recovery of 10,000 cells based on the 10x Genomics Chromium Next GEM Single Cell VDJ User Guide. cDNA amplification was carried out at 13 cycles of amplification for all samples. Concentration of resulting amplification was assayed through the use of an Agilent Bioanalyzer 2100 instrument and High Sensitivity DNA Kit.
10x Genomics 5’ GEX library construction and subsequent analysis through sequencing was also performed according to the 10x Genomics User Guide.

value: Stimulated T cells

value: Mixed lymphocyte reaction

tag: facs marker

tag: fraction

value: Non-proliferating


title: Peripheral Blood Mononuclear cells - rep_2

value: Peripheral blood mononuclear cells

value: Untreated


title: N3P81_CA3


title: FAC-sorted stimulated B cells

value: Stimulated B cells


title: N3P84_CA1


title: B4-SM4-N

status: Public on Nov 01 2021

data_processing:
Pair-end reads of 100bp were read via the BGISEQ-500 platform. Low quality reads were ltered using the BGI-internal software SOAPnuke (reads with adaptors, reads in which unknown bases are >10 and low-quality reads with threshold 15 were removed.
Genome mapping was done using the HISAT software. Transcripts were then reconstructed using StringTie and compared to reference using Cucompare. The coding potential of StringTie and compared to reference using Cucompare. The coding potential of novel transcripts was predicted using CPC. SNP and INDEL detection was done using GATK. Clean reads were mapped to Mus musculus (house mouse) genome assembly GRCm38 (mm10) from Genome Reference Consortium using Bowtie2 and gene expression levels were calculated using the RSEM software package
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: normalized counts FPKMs in .txt format

source_name: learning condition

extract_protocol:
Animals were killed by isoflurane overdose and neck dislocation. No perfusion was performed. The brain was taken out in <120s and immediately frozen in liquid nitrogen until further processing. Brains were cut at 8µm thickness and CA1 isolated using a commercially available laser dissection microscope (MMI instruments, Eching, Germany)
library was constructed by BGI The library was constructed making a single strand DNA circle. Rolling circle replication created DNA  nanoballs, which yields more   uorescent signal during sequencing. Pair-end reads of  100bp were read via the BGISEQ-500 platform.

treatment_protocol: "baseline" condition: no intervention, animals taken directly from home cage; "learning" condition: animals trained in an open field test (50x50cm black plastic wall, white cue card, food cues) for 1 week 20min/day. On a test day, animals were sacrificed 20min after the last training period.

tag: background strain

tag: Sex

value: Male


title: A5-SM53-N

value: wild type


title: B6-SM31-N


title: FAC-sorted stimulated T cells, proliferating

value: Proliferating


title: A2-SM98-N


title: 1059

status: Public on Nov 17 2021

description: Transcriptome data from whole blood

hyb_protocol: Sample was hybridized to Affymetrix Human Gene 2.0 ST array using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the RMA algorithm and then limma was applied to calculate significant differential expression between samples

source_name: Total RNA from whole blood samples

label_protocol: a total of 100ng from each sample was processed and labelled according to manual GeneChip WT Pica Reagent kit (P/N 703174 Rev. 2, Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: RNA was extracted following Nucleospin RNA II kit (Macherey-Nagel) protocol

value: whole blood

tag: sample pair id

tag: iron status

tag: gender

tag: age

tag: hb

tag: logarithm pro-bnp

tag: left ventricular ejection fraction

tag: ischemic etiology

tag: creatinine clearance


title: B5-SM30-N

tag: genotype

tag: tissue

tag: brain region


title: 793

description: Transcriptome data from whole blood


title: 916

description: Transcriptome data from whole blood


title: 1008

description: Transcriptome data from whole blood


title: 875

description: Transcriptome data from whole blood


title: 1077

description: Transcriptome data from whole blood


title: 691

description: Transcriptome data from whole blood


title: 965

description: Transcriptome data from whole blood


title: 929

description: Transcriptome data from whole blood


title: 937

description: Transcriptome data from whole blood


title: 689

description: Transcriptome data from whole blood


title: 693

description: Transcriptome data from whole blood


title: A1-SM97-N


title: B3-SM3-F

source_name: spatial exploration

extract_protocol:
Animals were killed by isoflurane overdose and neck dislocation. No perfusion was performed. The brain was taken out in <120s and immediately frozen in liquid nitrogen until further processing. Brains were cut at 8µm thickness and CA1 isolated using a commercially available laser dissection microscope (MMI instruments, Eching, Germany)
library was constructed by BGI The library was con-  structed making a single strand DNA circle. Rolling circle replication created DNA  nanoballs, which yields more   fluorescent signal during sequencing. Pair-end reads of  100bp were read via the BGISEQ-500 platform.

value: male


title: B7-SM32-F


title: Splenocytes

source_name: Spleen

tag: cell type

value: Splenocytes

tag: treatment


title: B1-SM1-F


title: 706

description: Transcriptome data from whole blood


title: 1068

description: Transcriptome data from whole blood


title: R1804

source_name: homecage


title: A4-SM100-F


title: R1-1864


title: R2-1811


title: A3-SM99-F


title: R1902


title: A6-RW2068-F


title: OE_48h_3 [OE48h.3_S12]

status: Public on Oct 13 2021

description: Human adipocytes, doxycycline (dox)-inducible pTRIPz lentiviral system, 48h dox-induced

data_processing:
Raw sequencing reads in the fastq files were mapped with STAR version 2.5.3a to the Gencode release 29 based on the GRCh38.p12 reference human genome and Gencode release 17 based on the GRCm38.p6 reference mouse genome, with their corresponding GTF files.
Table counts was obtained with FeatureCounts function in the package subread, version 1.5.1
Genome_build: GRCh38.p12; GRCm38.p6
Supplementary_files_format_and_content: txt files containing the table counts obtained with FeatureCounts

growth_protocol: Mouse embryonic fibroblasts (MEFs) were isolated from Wt and miR-424(322)-/-/503-/- (miR-KO) E14 embryos. First, head, limbs, and intestinal organs were removed. Then, E14 embryos were cut into small pieces on a plate with PBS, transferred into a falcon with 0.25% Trypsin-EDTA (Gibco, 25300-054) and incubated 15 min at 37ºC. Then, the digested mixture was transferred into a new tube and centrifuged to eliminate non-disaggregated tissue at 200 rpm for 3 minutes. Cell density was measured using trypan blue (Sigma, T8154). Supernatants were diluted, plated and cultured with DMEM (Gibco, 31966047), 10% FBS (Gibco, 10270-106), and 50 IU/ml penicillin/streptomycin (Gibco, 15070063). Adipogenesis was induced in two days post-confluent miR-KO and Wt MEFs by means of 0.5 mM 3-isobutyl-1-methylxanthine (IBMX; Sigma, I7018), 1 µM dexamethasone (Sigma, D1756), 5 µg/ml insulin (Sigma, I3536), and 0.5 µM rosiglitazone (Acros Organics, 462410010) in DMEM containing 10% FBS. On day 4 and thereafter, IBMX, dexamethasone, and rosiglitazone were removed, and 5 µg/ml insulin was maintained for 4 additional days. Cryopreserved subcutaneous preadipocytes (SP-F-1) from Caucasian men and women of approximately same age and BMI, and culture and differentiation media were purchased (Zen-Bio, Inc.). To induce differentiation, confluent preadipocytes in preadipocyte medium (PM-1) were incubated with adipocyte differentiation medium (DM-2) for 7 days, according to manufacturer’s instructions. This media is composed of DMEM / Ham’s F-12 (1:1), HEPES, FBS, biotin, pantothenate, insulin, dexamethasone, IBMX, PPARγ agonist, penicillin, streptomycin, and amphotericin B. Thereafter, adipocytes were maintained in adipocyte maintenance medium (AM-1) for 7 days (DM-2 without dexamethasone, IBMX, and PPARγ agonist). During this process, the shape of preadipocytes evolves from the flattened form to rounded cells containing abundant lipid droplets, and are thus considered mature adipocytes (12th day and thereafter). Beyond day 14, differentiated adipocytes were maintained in adipocyte basal medium (BM-1), which contains the components necessary to support stability and activity of mature adipocytes (DMEM / Ham’s F-12 (1:1), HEPES, biotin, and pantothenate).

extract_protocol:
Total RNA was purified using the RNeasy Mini Kit (QIAgen, 74104). Concentration was measured by means of a NanoDrop 1000 Spectrophotometer (Thermo Scientific).
NGS libraries with polyA capture were prepared according to the manual NEBNext® Ultra™ II Directional RNA  Library Prep Kit for Illumina® (New England Biolabs) (Version 1.0, 4/17)

treatment_protocol: Conditional doxycycline (Dox)-inducible expression of the cluster miR-424(322)/503 was accomplished by means of lentiviral particles. These constructs were obtained by transfecting phoenix-packaging cells (ATCC, CRL-3213) with linear-jetPEI (Polyplus, 101-10N) in combination with control pTRIPz or our previously reported pTRIPz-miR-424(322)/503 system, and the pCMV-dR8.91 and pMD.G helper plasmids at a ratio of 2:1:1, respectively. Twenty-four hours after transfection, media supernatants were collected and lentiviral particles were concentrated using centrifugation columns (Sigma, UFC910024). Transduction of human preadipocytes with lentiviral particles carrying pTRIPz constructs was conducted as follows: pre-confluent (50-70%) preadipocytes cultured in PM-1 were incubated in PM-1 containing pT-miR-424/503 or pT-Control lentiviral particles (2:1) and 10 µg/ml Polybrene (Sigma, TR-1003) for 24 h. Twenty-four hours after, positive preadipocytes harbouring these constructs were enriched by 2 ng/ml Puromycin dihydrochloride (Sigma, P9620). To induce increased expression of miR-424(322) and miR-503, doxycycline (Alfa Aesar, J60579) (500 ng/ml final dilution) was added to the culture media for the indicated periods of time.

tag: condition

tag: genotype/variation

value: preadipocytes from subcutaneous adipose tissue and differentiated, modified and treated in vitro

tag: time point


title: OE_48h_2 [OE48h.2_S11]


title: MG_UKJ_30_7_brain_RNAseq 2

status: Public on Oct 19 2021

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

description:
sample_counts.txt
sample_rpkms.txt

data_processing:
Sequence information was extracted in FastQ format using CASAVA software 1.7 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome: GRCm38, and respective gene annotation (GRCm38.84)
Supplementary_files_format_and_content: The text files include raw counts (sample_counts.txt) and RPKM values (sample_rpkms.txt) of all genes for each sample.

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using Illumina's mRNA Sample Preparation Multiplex Kit following the manufacturer's instruction.

tag: strain

value: brain

value: 30 months

tag: Sex


title: OE_48h_1 [OE48h.1_S10]


title: OE_14d_3 [OE14d.3_S6]

description: Human adipocytes, doxycycline (dox)-inducible pTRIPz lentiviral system, 14d dox-induced


title: OE_14d_2 [OE14d.2_S5]


title: NTC_48h_3 [cnt48h.3_S9]

description: Human adipocytes, doxycycline (dox)-inducible pTRIPz lentiviral system, 48h non-targeting control

value: non-targeting control


title: PA_Wt_3 [M15_S3]

description: MEF-derived preadipocytes, Wt mice

value: Wt

value: MEF-derived preadipocytes from Wt embryos


title: NTC_48h_1 [cnt48h.1_S7]


title: NTC_48h_2 [cnt48h.2_S8]


title: NTC_14d_3 [cnt14d.3_S3]

description: Human adipocytes, doxycycline (dox)-inducible pTRIPz lentiviral system, 14d non-targeting control


title: NTC_14d_2 [cnt14d.2_S2]


title: PA_Wt_1 [M1_S1]

description: MEF-derived preadipocytes, Wt mice


title: OE_14d_1 [OE14d.1_S4]


title: PA_miR-KO_3 [M64_S9]

description: MEF-derived preadipocytes, miR-KO mice

value: miR-KO

value: MEF-derived preadipocytes from miR-KO embryos


title: PA_miR-KO_1 [M50_S7]

description: MEF-derived preadipocytes, miR-KO mice


title: MA_Wt_3 [M23_S6]

description: MEF-derived adipocytes, Wt mice

value: MEF-derived adipocytes from Wt embryos


title: PA_miR-KO_2 [M62_S8]

description: MEF-derived preadipocytes, miR-KO mice


title: MA_Wt_2 [M21_S4]

description: MEF-derived adipocytes, Wt mice


title: MA_miR-KO_2 [M58_S11]

description: MEF-derived adipocytes, miR-KO mice

value: MEF-derived adipocytes from miR-KO embryos


title: MA_miR-KO_3 [M71_S12]

description: MEF-derived adipocytes, miR-KO mice


title: MA_Wt_1 [M10_S5]

description: MEF-derived adipocytes, Wt mice


title: Burkitt lymphoma cell line MutuI

status: Public on Sep 23 2021

type: genomic

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Tecan Freedom Liquid Handling Sytem (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on iScanner (Illumina).

data_processing:
Genomic DNA extracted from cell lines was genotyped using Illumina Infinium Omni5-4 v1.1 BeadChip (HumanOmni5-4v1-1_A).
PLINK was used for data processing

source_name: Burkitt lymphoma cell line

label_protocol: 200ng of genomic DNA was amplified by  at 37°C. using amplification master mix (MSM) and primer/neutralization mix (RPM). After incubation the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from cells was performed using the DNeasy Blood and Tissue Kit from Qiagen (product number 69504).

tag: cell line

value: MutuI


title: MA_miR-KO_1 [M57_S10]

description: MEF-derived adipocytes, miR-KO mice


title: Burkitt lymphoma cell line Ramos

description: Genomic DNA extracted from cell lines was genotyped using Illumina Infinium Omni5-4 v1.1 BeadChip (HumanOmni5-4v1-1_A).

value: Ramos


title: EBV transformed lymphoblastoid cell line IB4

source_name: Lymphoblastoid cell line


title: EBV transformed lymphoblastoid cell line GM12878


title: EBNA2 ChIP-seq: GM12878 (B-Lymphocyte) LCL replicate 2

data_processing:
Datasets were processed and analyzed using an in-house automated pipeline (https://github.com/MarioPujato/NextGenAligner); the following steps describe briefly the characteristics of the NextGenAligner pipeline.
Basic quality control for raw sequencing reads was performed using FASTQC (version 0.11.2) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
The quality controlled reads were aligned to the reference human genome (hg19 and hg38) using bowtie2 (version 2.3.4.1) (Langmead and Salzberg, 2012).
Adapter sequences were removed using Trim Galore (version 0.4.2) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), a wrapper script that runs cutadapt (version 1.9.1) to remove the detected adapter sequence from the reads.
Aligned reads were then sorted using samtools (version 1.8) (Li et al., 2009) and duplicate reads were removed using picard (version 1.89) (https://broadinstitute.github.io/picard/).
Peaks were called using MACS2 (version 2.1.0) (https://github.com/taoliu/MACS) (Zhang et al., 2008).
ENCODE blacklist regions (Amemiya et al., 2019) were removed using the hg19-blacklist.v2.bed.gz file available at https://github.com/Boyle-Lab/Blacklist/tree/master/lists.
Pooled samples were created by combining the fastq files for replicates 1 and 2.
Genome_build: hg19 (GRCh37)
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Peaks called by MACS2 in narrowPeak format.
Supplementary_files_format_and_content: Aligned reads in bigWig format.

source_name: GM12878 (B-Lymphocyte) LCL

growth_protocol: Cells were cultured in 10% FBS supplemented RPMI 1640 medium for 2 weeks.

extract_protocol:
Cells were crosslinked and nuclei were sonicated as described previously (Lu et al. 2015).
Libraries were prepared via ChIPmentation (Schmidl et al. 2015).

value: GM12878 (B-Lymphocyte) LCL

tag: chip antibody

value: EBNA2 (Abcam; ab90543)


title: EBNA2 ChIP-seq: GM12878 (B-Lymphocyte) LCL replicate 1


title: HiChIP: EBNA2- (P3HR1) EBV infected Ramos B cells replicate 2

data_processing:
Library strategy: HiChIP
Pooled samples were created by combining the fastq files for replicates 1 and 2. Analyses were performed on the pooled samples only.
We used HiC-Pro (version: 2.11.0) to identify Hi-C contact maps (Servant et al. 2015).
We then used hichipper (version: 0.7.3) (http://aryeelab.org/hichipper) to correct the background, perform restriction site bias modeling and obtain looping information.
We identified differential looping events using the diffloop Bioconductor R package (1.6.0) (Lareau and Aryee 2018). Briefly, to calculate EBNA2-dependent differential looping, we first determined EBV-dependent chromatin looping by comparing EBVEBNA2+ looping events to uninfected looping events using diffloop (>1.5 fold, p-value < 0.05).
Genome_build: hg19
Genome_build: hg38
Supplementary_files_format_and_content: allValidPair files were created with HiC-Pro and contain 12 columns: 1) read name; 2) read 1 chromosome; 3) read 1 position; 4) read 1 strand; 5) read 2 chromosome; 6) read 2 position; 7) read 2 strand; 8) fragment size; 9) read 1 restriction fragment name; 10) read 2 restriction fragment name; 11) read 1 mapping quality; 12) read 2 mapping quality
Supplementary_files_format_and_content: mango.txt files (containing intrachromosomal loops) were generated using hichipper (version: 0.7.3) (http://aryeelab.org/hichipper) and contain 8 columns: 1) fragment 1 chromosome; 2) fragment 1 start; 3) fragment 1 end; 4) fragment 2 chromosome; 5) fragment 2 start; 6) fragment 2 end; 7) number of paired end tags supporting the interaction; 8) adjusted p-value
Supplementary_files_format_and_content: hic files (visualization files) were generated using the hicpro2juicebox.sh script from HiC-Pro (Servant et al. 2015) and KR normalized using Juicer Tools (https://github.com/aidenlab/juicer/wiki/Juicer-Tools-Quick-Start)

growth_protocol: Cells were cultured in 10% FBS supplemented RPMI medium 1640 for 2 weeks.

extract_protocol: HiChIP-seq libraries were prepared following Mumbach et al. (Mumbach et al. 2016).

treatment_protocol: Ramos B cells were infected with EBNA- (P3HR1) Epstein-Barr virus (EBV).

value: Ramos B cells

tag: infection

value: EBNA- (P3HR1) Epstein-Barr virus (EBV)

value: anti-H3K27ac antibody (Abcam ab4729)


title: HiChIP: EBNA2- (P3HR1) EBV infected Ramos B cells replicate 1


title: HiChIP: EBNA2+ (B95.8) EBV infected Ramos B cells replicate 2

treatment_protocol: Ramos B cells were infected with EBNA+ (B95.8) Epstein-Barr virus (EBV).

value: EBNA+ (B95.8) Epstein-Barr virus (EBV)


title: HiChIP: EBNA2+ (B95.8) EBV infected Ramos B cells replicate 1


title: NTC_14d_1 [cnt14d.1_S1]

value: preadipocytes from subcutaneous adipose tissue and differentiated, modified and treated in vitro


title: HiChIP: uninfected Ramos B cells replicate 2

source_name: Uninfected Ramos B cells


title: HiChIP: uninfected Ramos B cells replicate 1


title: ATAC-seq: EBNA2- (P3HR1) EBV infected Ramos B cells pooled replicates

data_processing:
The pooled sample was created by combining the fastq files for replicates 1 and 2.
Datasets were processed and analyzed using an in-house automated pipeline (https://github.com/MarioPujato/NextGenAligner); the following steps describe briefly the characteristics of the NextGenAligner pipeline.
Basic quality control for raw sequencing reads was performed using FASTQC (version 0.11.2) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
The quality controlled reads were aligned to the reference human genome (hg19 and hg38) using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012).
Adapter sequences were removed using Trim Galore (version 0.4.2) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), a wrapper script that runs cutadapt (version 1.9.1) to remove the detected adapter sequence from the reads.
Aligned reads were then sorted using samtools (version 1.8)(Li et al., 2009) and duplicate reads were removed using picard (version 1.89) (https://broadinstitute.github.io/picard/).
Peaks were called using MACS2 (version 2.1.0) (https://github.com/taoliu/MACS)(Zhang et al., 2008).
ENCODE blacklist regions (Amemiya et al., 2019) were removed
Differential peaks were calculated using MAnorm (Shao et al. 2012) with threshold of log2 fold change greater than 1.5 and a p-value of less than 0.05.
Genome_build: hg19; hg38
Supplementary_files_format_and_content: Peaks called by MACS2 in narrowPeak format
Supplementary_files_format_and_content: Aligned reads in bigWig format
Supplementary_files_format_and_content: EBNA2 dependent regions of open or closed chromatin in bed format

extract_protocol: ATAC-seq libraries were prepared using the standard protocol (Buenrostro et al. 2015).


title: ATAC-seq: uninfected Ramos B cells pooled replicates

tag: infection strain


title: ATAC-seq: EBNA2- (P3HR1) EBV infected Ramos B cells replicate 2

data_processing:
Datasets were processed and analyzed using an in-house automated pipeline (https://github.com/MarioPujato/NextGenAligner); the following steps describe briefly the characteristics of the NextGenAligner pipeline.
Basic quality control for raw sequencing reads was performed using FASTQC (version 0.11.2) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
The quality controlled reads were aligned to the reference human genome (hg19 and hg38) using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012).
Adapter sequences were removed using Trim Galore (version 0.4.2) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), a wrapper script that runs cutadapt (version 1.9.1) to remove the detected adapter sequence from the reads.
Aligned reads were then sorted using samtools (version 1.8)(Li et al., 2009) and duplicate reads were removed using picard (version 1.89) (https://broadinstitute.github.io/picard/).
Peaks were called using MACS2 (version 2.1.0) (https://github.com/taoliu/MACS)(Zhang et al., 2008).
ENCODE blacklist regions (Amemiya et al., 2019) were removed
Differential peaks were calculated using MAnorm (Shao et al. 2012) with threshold of log2 fold change greater than 1.5 and a p-value of less than 0.05.
Genome_build: hg19; hg38
Supplementary_files_format_and_content: Peaks called by MACS2 in narrowPeak format
Supplementary_files_format_and_content: Aligned reads in bigWig format
Supplementary_files_format_and_content: EBNA2 dependent regions of open or closed chromatin in bed format


title: ATAC-seq: EBNA2+ (B95.8) EBV infected Ramos B cells pooled replicates


title: PA_Wt_2 [M4_S2]

description: MEF-derived preadipocytes, Wt mice


title: ATAC-seq: EBNA2+ (B95.8) EBV infected Ramos B cells replicate 2


title: ATAC-seq: EBNA2- (P3HR1) EBV infected Ramos B cells replicate 1


title: ATAC-seq: uninfected Ramos B cells replicate 2


title: EBNA2 ChIP-seq: EBNA2+ (B95.8) EBV infected Ramos B cells replicate 2

source_name: Ramos B cells


title: RNA-seq: EBNA2- (P3HR1) EBV infected Ramos B cells replicate 1

data_processing:
Datasets were processed and analyzed using an in-house automated pipeline (https://github.com/MarioPujato/NextGenAligner); the following steps describe briefly the characteristics of the NextGenAligner pipeline.
Basic quality control for raw sequencing reads was performed using FASTQC (version 0.11.2) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
The quality controlled reads were aligned to the reference human genome (hg19 and hg38) using STAR (version 2.5.2a)(Dobin et. al., 2013).
Adapter sequences were removed using Trim Galore (version 0.4.2) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), a wrapper script that runs cutadapt (version 1.9.1) to remove the detected adapter sequence from the reads.
Aligned reads were then sorted using samtools (version 1.8)(Li et al., 2009) and duplicate reads were removed using picard (version 1.89) (https://broadinstitute.github.io/picard/).
The featureCounts function (Rsubread version: 3.5.3) was used to count reads (Liao et al. 2014) and create non-normalized gene counts.
DESeq2 (version 3.5.3) was used to calculate differential gene expression (Love et al. 2014).
Genome_build: hg19; hg38
Supplementary_files_format_and_content: Non-normalized gene counts in a tab separated text file. Columns are 1) gene name; 2) non-normalized read count.
Supplementary_files_format_and_content: Aligned reads in bigWig format
Supplementary_files_format_and_content: Differential genes identified by DESeq2 in a tab separated text file. Columns are 1) gene name; 2) log2FoldChange; 3) raw-pvalue; 4) adjusted p-value.

extract_protocol:
Total RNA was extracted using the mirVANA Isolation Kit (Ambion) from Ramos B cells.
RNA was depleted of ribosomal RNA and sequenced at Cincinnati Children’s Hospital Medical Center (CCHMC) DNA Sequencing and Genotyping Core Facility.

treatment_protocol: Cells were infected with EBV with EBNA+ strain (B95.8) and EBNA2- strain (P3HR1), respectively.


title: RNA-seq: EBNA2+ (B95.8) EBV infected Ramos B cells replicate 1


title: EBNA2 ChIP-seq: EBNA2+ (B95.8) EBV infected Ramos B cells replicate 1


title: RNA-seq: uninfected Ramos B cells replicate 1


title: RNA-seq: EBNA2+ (B95.8) EBV infected Ramos B cells replicate 2


title: RNA-seq: uninfected Ramos B cells replicate 2


title: ATAC-seq: EBNA2+ (B95.8) EBV infected Ramos B cells replicate 1


title: ATAC-seq: uninfected Ramos B cells replicate 1


title: C12 HttKO SH-Sy5Y rep 3

status: Public on Jun 19 2021

city: Boca Raton

first: Jianning

last: Wei

state: FL

address: 777 GLADES RD

department: Biomedical Science

institute: Florida Atlantic University

data_processing:
The final libraries were sequenced on the NextSeq 500 (Illumina) with paired-end 40bp reads.
The reads were subject to quality control which was comprised of the following steps:  1. Trimming of exogenous adapter sequences,  2. Removal of low quality bases from the ends of reads,  3. Removal of whole reads if the average quality was too low.
After quality control, the reads were mapped to the human genome (human-ENSEMBL-grch38.r91 : H.sapiens-ENSEMBL-GRCh38.r91 : downloaded February 16, 2018) using the star version 2.5.2a aligner and gene abundance was estimated with python version 2.7.11, and htseq version 0.11.0.
Genome_build: ENSEMBL-grch38release 91
Supplementary_files_format_and_content: tab-delimited text files include TPM values for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene and every sample

source_name: C12 HttKO SH-Sy5Y

growth_protocol: WT and HttKO SH-SY5Y cell lines were cultured at 37°C, 5% CO2 in a humidified incubator in Dulbecco's Modified Eagle Medium/F-12K (DMEM/F12K) medium supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic-antimycotic solution.

extract_protocol:
RNA was isolated from WT, B7 and C12 HttKO cells using Direct-ZolTM RNA miniprep Plus kit (Cat. #R2071, ZYMO RESEARCH) according to the manufacturer’s instruction. To reduce genomic DNA contamination, a 15 minute on-column DNase I treatment at room temperature was performed.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HttKO stable cell line were generated using the CRISPR-Cas9 genetic editing approach. Four sgRNA (1-4) and Cas9 2NLS at a molar ratio of 9:1 were used to form ribonucleoprotein complex at room temperature separately, which was then delivered to SH-SY5Y cells using the Neon electroporation system (1100V, 50ms width, 1 pulse). Forty-eight hours after electroporation, aliquots of cells were first analyzed for cleavage efficiency by mismatch cleavage assay. Based on the calculated cleavage efficiency, cells transfected with sgRNA2 were further serial-diluted to obtain single cell colony in 96-well plates. After colony expansion, colonies were first screened for Htt expression levels by western blot and positive clones were selected for further validation by Sanger sequencing. Two positive clones B7 and C12 were used for further RNA-seq analysis.

value: human neuroblastoma cell line SH-SY5Y

value: Htt-/-

tag: gene-editing

value: Ribonucleoprotein (RNP)-mediated CRISPR genome editing


title: WT SH-Sy5Y rep3

source_name: WT SH-Sy5Y

value: wild type


title: B7 HttKO SH-Sy5Y rep 3

source_name: B7 HttKO SH-Sy5Y


title: B7 HttKO SH-Sy5Y rep 2


title: C12 HttKO SH-Sy5Y rep 1


title: B7 HttKO SH-Sy5Y rep 1


title: WT SH-Sy5Y rep2


title: WT SH-SY5Y rep1

source_name: WT SH-SY5Y


title: C12 HttKO SH-Sy5Y rep 2


title: 139NT

status: Public on Sep 10 2021

description: Gene expression data from purified NK cells after 12h treatment with IL-2 (Donor 139)

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3, Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

source_name: Total RNA from purified NK cells after 12h treatment with IL-2 (200U/ml)

label_protocol: 100ng from each sample was processed and labelled according to manual GeneChip WT PLUS Reagent kit (P/N 703174 Rev. 2, Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: RNA was extracted following Quiagen protocol (RNeasy Micro Kit)

tag: individual

value: donor 139

value: NK cells

value: NT