title: microRNA-seq from layer of hippocampus (ENCLB758TPE)

description:
https://www.encodeproject.org/experiments/ENCSR760SKT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation WT male mouse layer of hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR760SKT
assay title: microRNA-seq
assembly: mm10
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB758TPE
size range: <30

value: layer of hippocampus

value: tissue

value: Hippocampus from 6 mo C57BL/6 male

value: not collected

value: adult

value: 6 month

value: ENCBS604NYS at ENCODE; https://www.encodeproject.org/ENCBS604NYS/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: total RNA-seq from monocyte (ENCLB463TMR)

status: Public on Jun 15 2021

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR069PIG/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse monocyte 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR069PIG
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-12-01
lab: Ross Hardison, PennState
library encode accession: ENCLB463TMR
size range: 200-491
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

library_source: transcriptomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: total RNA

organism: Mus musculus

source_name: Mus musculus strain C57BL/6J adult (5-6 weeks) monocyte primary cell

value: monocyte

value: primary cell

tag: description

value: monocytes from peripheral blood

tag: biosample encode accession

tag: Sex

tag: dev stage

tag: age

value: 5-6 week

tag: lab

value: Ross Hardison, PennState

tag: source

value: David Bodine

tag: link

value: ENCBS648WVZ at ENCODE; https://www.encodeproject.org/ENCBS648WVZ/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: CCMV infected 6h, replicate 2

status: Public on Jun 01 2021

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al., doi: 10.1038/s41587-019-0201-4)
Sequencing reads were aligned to the hg19 version of the human genome, using standard parameter, using the Refseq gtf file downloaded from the UCSC genome browser, or the CCMV genome.
Reads were then quantified using quasR (Gaidatzis et al., doi: 10.1038/nbt.3269) and the above mentioned gtf file, or the CCMV annotation (accession number NC_003521).
Genome_build: hg19
Genome_build: CCMV NC_003521
Supplementary_files_format_and_content: readcounts

molecule: polyA RNA

organism:
Homo sapiens
Panine betaherpesvirus 2

source_name: Primary human lung fibroblasts (Fi301)

growth_protocol: Primary human lung fibroblasts (Fi301) cells were maintained in EMEM supplemented with 10% FCS, 2 mM Ultraglutamine, 0.15% sodium bicarbonate, 1 mM sodium pyruvate, 1x non-essential amino acids, 45 µg/ml gentamycine. Cells were cultured at 37°C and 5% CO2.

extract_protocol:
For RNA-sequencing, Cells were resuspended in Trizol (Invitrogen) and RNA extracted from Trizol.
RNA-sequencing libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New Engand Biolabs)
adapter sequence:  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

treatment_protocol: CCMV BAC virus was added to the cells in a MOI of 5 and incubated in a humidified 5% CO2 incubator at 37°C for 30 minutes. After incubation, fresh medium was added, plates were centrifuged at 1000 rcf for 30 minutes at 34°C and infection mix was subsequently replaced by fresh medium. Infected cells were harvested at the 6, 24, 48, 72 and 96 hours post infection.

tag: infection

value: CMV

tag: host cell type

value: Primary human lung fibroblasts (Fi301)

tag: harvesting timepoint


title: microRNA-seq from layer of hippocampus (ENCLB776ABC)

description:
https://www.encodeproject.org/experiments/ENCSR436GZP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation WT female mouse layer of hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR436GZP
assay title: microRNA-seq
assembly: mm10
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB776ABC
size range: <30

source_name: Mus musculus strain B6NCrl layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: Control hippo Female

value: unknown

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS177UPU at ENCODE; https://www.encodeproject.org/ENCBS177UPU/


title: microRNA-seq from adrenal gland (ENCLB301XTV)

description:
https://www.encodeproject.org/experiments/ENCSR424VMF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND4 female adrenals microRNA-seq from Mortazavi
experiment encode accession: ENCSR424VMF
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-02-13
lab: Ali Mortazavi, UCI
library encode accession: ENCLB301XTV
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (4 days) adrenal gland tissue

value: adrenal gland

value: B6Cast F1 PND4 Female 03 adrenal gland for Wold core

value: female

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS886BLQ at ENCODE; https://www.encodeproject.org/ENCBS886BLQ/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: CCMV infected 6h, replicate 1

value: CMV


title: microRNA-seq from layer of hippocampus (ENCLB469ETY)

description:
https://www.encodeproject.org/experiments/ENCSR751IHR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation 5xFAD male mouse layer of hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR751IHR
assay title: microRNA-seq
assembly: mm10
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB469ETY
size range: <30

source_name: Mus musculus strain B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax adult (8 months) layer of hippocampus tissue

value: 5xFAD hippo 8 mo Male

value: not collected

value: adult

value: 8 month

value: ENCBS329OHE at ENCODE; https://www.encodeproject.org/ENCBS329OHE/

value: Derived from ENCODE donor ENCDO835CXP; https://www.encodeproject.org/ENCDO835CXP/


title: NAFLD liver 96

status: Public on May 31 2021

city: Suita

first: Takahiro

last: Kodama

state: Osaka

address: 2-2 Yamadaoka

department: Department of Gastroenterology and Hepatology

country: Japan

institute: Osaka university, Graduate School of Medicine

data_processing:
Sequencing was performed on an Illumina HiSeq 3000 platform in a 100-base single-end mode.
Sequenced reads were mapped to the mouse reference genome sequences (hg19) using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.9.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: Liver

extract_protocol:
mRNA was extracted from frozen tissues with the RNeasy Plus Mini kit (Qiagen). Concentrations and quality were assessed using the Agilent Pico 6000 kit on the Bioanalyzer 2100.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit

tag: tissue

value: liver biopsy

tag: disease state

value: NAFLD

tag: disease subtype

value: NASH

tag: gender

value: F


title: NAFLD liver 98

value: M


title: total RNA-seq from monocyte (ENCLB753NUJ)

description:
https://www.encodeproject.org/experiments/ENCSR069PIG/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse monocyte 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR069PIG
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-12-01
lab: Ross Hardison, PennState
library encode accession: ENCLB753NUJ
size range: 200-594
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: monocyte

value: primary cell

value: monocytes from peripheral blood

value: 5-6 week

value: Ross Hardison, PennState

value: David Bodine

value: ENCBS994OHV at ENCODE; https://www.encodeproject.org/ENCBS994OHV/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: Bru-seq from IMR-90 (ENCLB043VGO)

description:
https://www.encodeproject.org/experiments/ENCSR103IHW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR103IHW
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB043VGO
size range: 400-500

source_name: Homo sapiens IMR-90 cell line

tag: line

value: cell line

value: female

tag: health state

value: unknown

value: embryonic

value: 16 week

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS812YZU at ENCODE; https://www.encodeproject.org/ENCBS812YZU/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/


title: microRNA-seq from layer of hippocampus (ENCLB356JLO)

description:
https://www.encodeproject.org/experiments/ENCSR659HKO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation 5xFAD female mouse layer of hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR659HKO
assay title: microRNA-seq
assembly: mm10
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB356JLO
size range: <30

source_name: Mus musculus strain B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax layer of hippocampus tissue

value: layer of hippocampus

value: tissue

tag: description

value: 5xFAD hippo het Female

value: not collected

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS251XQY at ENCODE; https://www.encodeproject.org/ENCBS251XQY/

value: Derived from ENCODE donor ENCDO835CXP; https://www.encodeproject.org/ENCDO835CXP/


title: CCMV infected 6h, replicate 3

value: CMV

value: Primary human lung fibroblasts (Fi301)


title: total RNA-seq from monocyte (ENCLB382RPQ)

description:
https://www.encodeproject.org/experiments/ENCSR069PIG/
***************
biological replicate number: 3
technical replicate number: 1
description: PSU mouse monocyte 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR069PIG
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-12-01
lab: Ross Hardison, PennState
library encode accession: ENCLB382RPQ
size range: 200-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: monocyte

value: primary cell

value: monocytes from peripheral blood

tag: biosample encode accession

value: adult

value: 5-6 week

value: Ross Hardison, PennState

value: David Bodine

value: ENCBS160KPE at ENCODE; https://www.encodeproject.org/ENCBS160KPE/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: NAFLD liver 85

value: liver biopsy

value: NAFLD

value: NASH

value: M


title: NAFLD liver 86

value: F


title: 161_Aged_High_scRNA-seq

city: Urbana

first: Mario

middle: Pietro Emilio

last: Vailati Riboni

state: IL

address: 1207 W Gregory Dr

department: Animal Science

description: single cell

data_processing:
Sequencing results were demultiplex using the mkfastq function in Cell Ranger v3.1.0, then a filtered reference was created using the mkgt function starting from the Mus musculus GRCm38.98 ensembl built. Only protein coding, antisense, long intergenic ncRNA, and Immunoglobulin (IG) and T cell receptor (TR) categories were the kept transcript biotypes.
Reads alignment, filtering, and barcode count was performed using the custom filtered reference via the cellranger count pipeline
Genome_build: Mus musculus GRCm38.98 ensembl built
Supplementary_files_format_and_content: Provided processed data are the output of Cell Ranger pipeline. Filtered matrix of count number per feature per cell, plus cells barcodes and feature list per sample. Barcodes and feaures are tsv, while matrixes are mtx

source_name: Whole Brain

growth_protocol: Adult (1-2 months old, raised in-house) and aged (21-22 months old,  obtained from the National Institute on Aging, Bethesda, MD), male and female C57BL/6J mice were used in the current experiment. Animals were kept under a reverse 12 h light:dark cycle and given ad libitum access to water and a nutritionally complete purified AIN-93M diet (Envigo, Indianapolis, IN) beginning two months before imposition of the experimental diets to establish a baseline microbiota for this diet under our conditions. To this end, during weekly cage changes, used bedding (e.g., litter and feces) from mice similarly aged was collected, homogenized, and mixed with clean bedding before being redistributed to each cage.

extract_protocol:
After collection, fresh whole brains were dissociated using the Adult Brain Dissociation kit (Miltenyi Biotec, Germany), for 30 min at 37oC. After filtration (70µm), debris and red blood cells were removed according to the kit protocol, and the obtained pellet was depleted of myelin and dead cells, using the Myelin Removal Beads v2 (Miltenyi Biotec, Germany), and the Dead Cell Removal Kit (Miltenyi Biotec, Germany), sequentially. Final pellets were eluted in 100µL of PBS with 4% BSA.
Single-cell 3’ cDNA libraries were prepared at the DNA Services laboratory of the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign. Single-cell 3’ cDNA libraries were prepared at the DNA Services laboratory of the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign. The four single-cell suspensions with an average viability of 75.5 ± 3.1 %, and concentration of 753 ± 121.3 cells/µL by AO/PI staining on the Nexcelom K2 (Nexcelom Bioscience, Lawrence, MA) were converted into individually barcoded cDNA libraries with the Single-Cell 3’ Chromium kit version 3 from 10X Genomics (Pleasanton, CA) following the manufacturer’s protocols. The target number of cells per library was 6000. On average 14.5 ± 2.2 µL of the cell suspensions were used for the preparation of the libraries. The 10X Chromium instrument separates thousands of single cells into Gel Bead Emulsions (GEMs) that add a barcode to the mRNA from each individual cell. Following ds-cDNA synthesis, individually-barcoded libraries compatible with the Illumina chemistry were constructed. The final libraries were quantitated on Qubit and the average size determined on the AATI Fragment Analyzer (Advanced Analytics, Ames, IA). Libraries were pooled evenly, and the final pool was diluted to 5nM concentration and further quantitated by qPCR on a Bio-Rad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA). The final library pool was sequenced on one lane of an Illumina NovaSeq 6000 S4 flowcell as paired-reads with 28 cycles for read 1, 8 cycles for the index read, and 150 cycles for read 2.

treatment_protocol: After the initial two months (now adult 3-4 months old, and aged 23-24 months old), mice were switched to a modified AIN-93M diet with 1% cellulose plus either 0 (Low Fiber), or 5% (High Fiber) inulin (Envigo, Indianapolis, IN).

tag: strain

value: Aged

tag: treatment

value: High fiber

value: Whole Brain


title: microRNA-seq from cerebral cortex (ENCLB374SLS)

description:
https://www.encodeproject.org/experiments/ENCSR036UMN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation 5xFAD female mouse cerebral cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR036UMN
assay title: microRNA-seq
assembly: mm10
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB374SLS
size range: <30

source_name: Mus musculus strain B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax cerebral cortex tissue

value: cerebral cortex

value: tissue

value: 5xFAD cortex het Female

tag: Sex

value: not collected

tag: dev stage

value: unknown

tag: age

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS354HBB at ENCODE; https://www.encodeproject.org/ENCBS354HBB/

value: Derived from ENCODE donor ENCDO835CXP; https://www.encodeproject.org/ENCDO835CXP/


title: NAFLD liver 83

value: liver biopsy

value: NAFL


title: NAFLD liver 97

value: NAFLD

value: NASH


title: NAFLD liver 93

value: F


title: NAFLD liver 94

value: M


title: NAFLD liver 79


title: NAFLD liver 76


title: 135_Adult_Low_scRNA-seq

institute: University of Illinois at Urbana-Champaign

description: single cell

value: Adult

value: Low fiber


title: microRNA-seq from cerebral cortex (ENCLB714LQX)

description:
https://www.encodeproject.org/experiments/ENCSR059NOB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation WT female mouse cerebral cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR059NOB
assay title: microRNA-seq
assembly: mm10
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB714LQX
size range: <30

source_name: Mus musculus strain B6NCrl cerebral cortex tissue

value: cerebral cortex

value: Control cortex Female

tag: lab

tag: source

tag: link

value: ENCBS093QAO at ENCODE; https://www.encodeproject.org/ENCBS093QAO/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: NAFLD liver 77


title: NAFLD liver 88


title: NAFLD liver 89


title: NAFLD liver 91


title: NAFLD liver 72


title: NAFLD liver 92


title: NAFLD liver 73


title: NAFLD liver 70


title: NAFLD liver 69


title: NAFLD liver 82


title: NAFLD liver 87


title: NAFLD liver 81


title: NAFLD liver 64


title: NAFLD liver 65


title: NAFLD liver 84


title: NAFLD liver 61


title: NAFLD liver 74


title: NAFLD liver 75


title: NAFLD liver 95


title: NAFLD liver 90


title: NAFLD liver 54


title: NAFLD liver 78


title: NAFLD liver 68


title: NAFLD liver 52


title: NAFLD liver 49


title: NAFLD liver 80


title: NAFLD liver 63


title: NAFLD liver 67


title: NAFLD liver 71


title: NAFLD liver 46


title: NAFLD liver 59


title: NAFLD liver 51


title: NAFLD liver 58


title: NAFLD liver 43


title: NAFLD liver 40


title: NAFLD liver 66


title: NAFLD liver 55


title: NAFLD liver 41


title: NAFLD liver 53


title: NAFLD liver 42


title: NAFLD liver 48


title: NAFLD liver 57


title: NAFLD liver 47


title: NAFLD liver 39


title: NAFLD liver 62


title: NAFLD liver 38


title: NAFLD liver 33


title: NAFLD liver 31


title: NAFLD liver 50


title: NAFLD liver 56


title: NAFLD liver 45


title: NAFLD liver 32


title: NAFLD liver 44


title: NAFLD liver 25


title: NAFLD liver 35


title: NAFLD liver 37


title: NAFLD liver 24


title: NAFLD liver 21


title: NAFLD liver 18


title: NAFLD liver 20


title: NAFLD liver 28


title: NAFLD liver 30


title: NAFLD liver 26


title: NAFLD liver 60


title: NAFLD liver 29


title: NAFLD liver 22


title: NAFLD liver 19


title: NAFLD liver 16


title: NAFLD liver 23


title: NAFLD liver 10


title: NAFLD liver 6


title: NAFLD liver 34


title: NAFLD liver 17


title: NAFLD liver 36


title: NAFLD liver 5


title: NAFLD liver 1


title: NAFLD liver 4


title: NAFLD liver 15


title: HiChIP SMC1A A673 STAG2 KO Replicate 1

status: Public on May 13 2021

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

description: L22-2809_GT17-05034_AGGCAGAA-ATAGAGAG_S1

library_source: genomic

data_processing:
HiChIP raw reads were aligned to hg19 human reference genome using HiC-Pro v2.10 (Servant et al., 2015). Each of the four replicate samples was sequenced to a depth > 150M reads. Moreover, each sample passed stringent quality control with a minimum of 23% of all reads mapping to intrachromosomal loci. Replicate samples were merged.   High-confidence loop calls were inferred on th emerged replicates using hichipper (Lareau and Aryee, 2018) using the  union of   SMC1A ChIP-Seq peaks from both the WT and STAG2 KO cell lines (144,863 genomic regions).     Long range interactions spanning two anchor regions, termed DNA loops, were derived from linked paired-end reads that overlapped restriction fragments containing  the SMC1A anchors. In total, 1,836,186 interactions spanning pairs of 102,398 genomic loci were observed among the four samples. As a majority of these interactions represent background proximity ligation,  stringent filtering was performed to identify putative biologically functional DNA loops.
We called a set of 56,219 loops naive to any additional genetic or epigenetic annotation that met stringent criteria. These loops contained at least four reads with paired-end tags (PETs) in two or more replicates and were statistically-significant at a distance-dependent P-value of 1% and FDR of 1% based on the per-loop measures from the loop proximity bias correction algorithm originally implemented in Mango (Phanstiel et al., 2015). The set of 56,219 stringently filtered loops served as a basis for differential loop calling between the wild-type and STAG2 KO mutant cell lines. To identify loops with significant changes in contact coverage (either decrease or increase) in A673 with STAG2 KO compared to STAG2 WT cells, differential loops were called at using the diffloop (Lareau et al., 2018) package  with the cutoffs |abs(fold change contact coverage)|≥2 and P-value ≤0.05.
Loop edges were annotated for their overlap with gene promoter regions and with ChIP-Seq binding sites for  H3K27ac enhancers and EWS/FLI1. Loop were annotated for TSS+/-5kb promoter region landing  for hg19 genes, and separately for expressed hg19 genes, in accordance with the 5kb resolution of our  HiChIP data.   Enhancer-Promoter loops were defined as the significant loops connecting a H3K27ac enhancer binding site on one anchor and a landing gene promoter (TSS+/-5kb region) on the opposite anchor.  Enhancers were identified in the H3K27ac A673 ChIP-Seq data in this study as the H3K27ac binding sites outside the TSS+/-3kb regions. Loop anchors were fully annotated with the hosted  enhancer binding sites and gene targets.
EWS/FLI1 status was assigned to the significant loops that host a EWS/FLI1 binding site (ChIP-Seq peak) on one anchor and a gene promoter (TSS+/-5kb) region on the opposite anchor. Thus, an  EWS/FLI1  loop intermediates the "long interactions" between any of the  EWS/FLI1 binding sites on one anchor to any of the gene promoter regions on the opposite anchor. For the purpose of the  EWS/FLI1 loop annotation, we defined  a consensus of 11,519 ChIP-Seq EWS/FLI1 binding sites  on A673 cells  by intersecting  the  peaks identified in the A673 EWS/FLI1 ChIP-Seq high coverage data  in this study (macs2, FDR =0.01) with the union of the  EWS/FLI1  peaks   identified  in  two published  A673 EWS/FLI1 ChIP-Seq studies  (Riggi et al., 2014; Tomazou et al., 2015).  Based on the consensus EWS/FLI1 peaks we identified 8,957 EWS/FLI1 loops. The  anchors of the EWS/FLI1 loops were annotated with  the EWS/FLI1 ChIP-Seq binding sites and gene promoter landing regions  and with the STAG2 KO vs. WT differential status information for the host loop and for the gene. The fully annotated collection of all 23,580 EWS/FLI1 binding site – promoter long interactions harbored by the 8,957 EWS/FLI1 loops is available.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: (1) tab separated text: *.mango   per replicate sample  list of all unfiltered interactions as produced by hichipper. Shown:  anchor1 genomic position, anchor2 genomic position, # PETs (reads) per sample, per-loop FDR measures from the loop proximity bias correction algorithm originally implemented in Mango  (2) excel.xlsx: annotated list of all high confidence interactions (mango P < 0.01, mango FDR < 0.01). Legend provided.  (3) excel xlsx: annotated list of all differential interactions (|diffloop fold change|> 2, difloop P-value < 0.05). Legend provided.  (4) WashU Epigenome Browser long interaction files (bgzipped *.gz and indexed *gz.tbi format),  separately for STAG2 WT  and STAG2 KO samples, for the  high confidence loops,  respectively, for the differential (STAG2 KO vs. STAG2 WT) loops in the following categories:  All, Enhancer-Promoter, EWS/FLI1, EWS/FLI1 & Enhancer-Promoter.

molecule: genomic DNA

source_name: A673 clones with STAG2 knocked-out

extract_protocol:
HiChIP was performed on the A673 clonal lines sgNT-1c4 and sgSTAG2-1c6 in duplicate based on a previously published protocol (Mumbach et al., 2016) with a few adaptations which were performed as previously described (Weintraub et al., 2017). The A673 clonal lines sgNT-1c4 and sgSTAG2-1c6 were tested with duplicates for each line crosslinked on separate occasions. The SMC1A antibody used in the ChIP experiments was by Bethyl A300-055A. Libraries were sequenced 100x100 on an Illumina Hi-Seq 2500 platform.
HiChIP was performed as described in (Mumbach et al., 2016) with a few modifications. Ten million cells were cross-linked for 10 min at room temperature with 1% formaldehyde in growth media and quenched in 0.125 M glycine. After washing twice with ice-cold PBS, the supernatant was aspirated and the cell pellet was flash-frozen in liquid nitrogen and stored at -80°C. Cross-linked cell pellets were thawed on ice, resuspended in 800 µL of ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, and 0.2% IGEPAL CA-630 with 1× cOmplete protease inhibitor (Roche, 11697498001)), and incubated at 4°C for 30 minutes with rotation. Nuclei were pelleted by centrifugation at 2500 rcf. for 5 min at 4°C and washed once with 500 µL of ice-cold Hi-C lysis buffer. After removing the supernatant, nuclei were resuspended in 100 µL of 0.5% SDS and incubated at 62°C for 10 minutes. SDS was quenched by adding 335 µL of 1.5% Triton X-100 and incubating for 15 minutes at 37°C. After the addition of 50 µL of 10X NEB Buffer 2 (NEB, B7002) and 375 U of MboI restriction enzyme (NEB, R0147), chromatin was digested at 37°C for 2 hours with rotation. Following digestion, MboI enzyme was heat-inactivated by incubating the nuclei at 62°C for 20 min. To fill in the restriction fragment overhangs and mark the DNA ends with biotin, 52 µL of fill-in master mix, containing 37.5 µL of 0.4 mM biotin-dATP (Invitrogen, 19524016), 1.5 µL of 10 mM dCTP (Invitrogen, 18253013), 1.5 µL of 10 mM dGTP (Invitrogen, 18254011), 1.5 µL of 10 mM dTTP (Invitrogen, 18255018), and 10 µL of 5 U/µL DNA Polymerase I, Large (Klenow) Fragment (NEB, M0210), was added and the tubes were incubated at 37°C for 1 hour with rotation. Proximity ligation was performed by addition of 947 µL of ligation master mix, containing 150 µL of 10X NEB T4 DNA ligase buffer (NEB, B0202), 125 µL of 10% Triton X-100, 7.5 µL of 20 mg/mL BSA (NEB, B9000), 10 µL of 400 U/µL T4 DNA ligase (NEB, M0202), and 655.5 µL of water, and incubation at room temperature for 4 hours with rotation. After proximity ligation, nuclei were pelleted by centrifugation at 2500 rcf. for 5 minutes and resuspended in 1 mL of ChIP sonication buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS with protease inhibitor). Nuclei were sonicated using a Covaris S220 for 6 minutes with the following settings: fill level 8, duty cycle 5, peak incidence power 140, cycles per burst 200. Sonicated chromatin was clarified by centrifugation at 16,100 rcf. for 15 min at 4°C and supernatant was transferred to a tube. 60 µL of protein G magnetic beads were washed three times with sonication buffer, resuspended in 50 µL of sonication buffer. Washed beads were then added to the sonicated chromatin and incubated for 1 hour at 4°C with rotation. Beads were then separated on a magnetic stand and the supernatant was transferred to a new tube. 7.5 µg of SMC1A antibody (Bethyl A300-055A) was added to the tube and the tube was incubated overnight at 4°C with rotation. The next day, 60 µL of protein G magnetic beads were washed three time in 0.5% BSA in PBS and washed once with sonication buffer before being resuspended in 100 µL of sonication buffer and added to each sample tube. Samples were incubated for 2 hours at 4°C with rotation. Beads were then separated on a magnetic stand and washed three times with 1 mL of high salt sonication buffer (50 mM HEPES-KOH pH 7.5, 500 mM NaCl, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS) followed by three times with 1 mL of LiCl wash buffer (20 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, 0.1% SDS) and once with 1 mL of TE with salt (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 50 mM NaCl). Beads were then resuspended in 200 µL of elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS) and incubated at 65°C for 15 minutes to elute. To purify eluted DNA, RNA was degraded by the addition of 2.5 µL of 33 mg/mL RNase A (Sigma, R4642) and incubation at 37°C for 2 hours. Protein was degraded by the addition of 10 µL of 20 mg/mL proteinase K (Invitrogen, 25530049) and incubation at 55°C for 45 minutes. Samples were then incubated at 65°C for 5 hours to reverse crosslinks. DNA was then purified using Zymo DNA Clean and Concentrate 5 columns (Zymo, D4013) according to manufacturer’s protocol and eluted in 14 µL water. The amount of eluted DNA was quantified by Qubit dsDNA HS kit (Invitrogen, Q32854).
Tagmentation of ChIP DNA was performed using the Illumina Nextera DNA Library Prep Kit (Illumina, FC-121-1030). First, 5 µL of streptavidin C1 magnetic beads (Invitrogen, 65001) was washed with 1 mL of tween wash buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA pH 8.0, 1 M NaCl, 0.05% Tween-20) and resuspended in 10 µL of 2X biotin binding buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 2 M NaCl). 54.19 ng purified DNA was added in a total volume of 10 µL of water to the beads and incubated at room temperature for 15 minutes with agitation every 5 minutes. After capture, beads were separated with a magnet and the supernatant was discarded. Beads were then washed twice with 500 µL of tween wash buffer, incubating at 55°C for 2 minutes with shaking for each wash. Beads were resuspended in 25 µL of Nextera Tagment DNA buffer. To tagment the captured DNA, 3.5 µL of Nextera Tagment DNA Enzyme 1 was added with 21.5 µL of Nextera Resuspension Buffer and samples were incubated at 55°C for 10 minutes with shaking. Beads were separated on a magnet and supernatant was discarded. Beads were washed with 500 µL of 50 mM EDTA at 50°C for 30 minutes, then washed three times with 500 µL of tween wash buffer at 55°C for 2 minutes each, and finally washed once with 500 µL of 10 mM Tris-HCl pH 7.5 for 1 minute at room temperature. Beads were separated on a magnet and supernatant was discarded. To generate the sequencing library, PCR amplification of the tagmented DNA was performed while the DNA is still bound to the beads. Beads were resuspended in 15 µL of Nextera PCR Master Mix, 5 µL of Nextera PCR Primer Cocktail, 5 µL of Nextera Index Primer 1, 5 µL of Nextera Index Primer 2, and 20 µL of water. DNA was amplified with 8 cycles of PCR. After PCR, beads were separated on a magnet and the supernatant containing the PCR amplified library was transferred to a new tube, purified using the Zymo DNA Clean and Concentrate-5 (Zymo D4003T) kit according to manufacturer’s protocol, and eluted in 14 µL water. Purified HiChIP libraries were size selected to 300-700 bp using a Sage Science Pippin Prep instrument according to manufacturer’s protocol and subject to paired-end sequencing on an Illumina HiSeq 2500. SMC1A libraries were initially sequenced with 100×100 bp paired-end sequencing.

tag: cell line

tag: cell type

value: Ewing sarcoma cell line

tag: genotype/variation

value: STAG2 knocked-out (sg16)

tag: chip antibody

value: SMC1A (Bethyl A300-055A)


title: HiChIP SMC1A A673 STAG2 WT Replicate 2

description: L22-2808_GT17-05037_CGTACTAG_ATAGAGAG_S2

source_name: A673 clones with STAG2 wild type

extract_protocol:
HiChIP was performed on the A673 clonal lines sgNT-1c4 and sgSTAG2-1c6 in duplicate based on a previously published protocol (Mumbach et al., 2016) with a few adaptations which were performed as previously described (Weintraub et al., 2017). The A673 clonal lines sgNT-1c4 and sgSTAG2-1c6 were tested with duplicates for each line crosslinked on separate occasions. The SMC1A antibody used in the ChIP experiments was by Bethyl A300-055A. Libraries were sequenced 100x100 on an Illumina Hi-Seq 2500 platform.
HiChIP was performed as described in (Mumbach et al., 2016) with a few modifications. Ten million cells were cross-linked for 10 min at room temperature with 1% formaldehyde in growth media and quenched in 0.125 M glycine. After washing twice with ice-cold PBS, the supernatant was aspirated and the cell pellet was flash-frozen in liquid nitrogen and stored at -80°C. Cross-linked cell pellets were thawed on ice, resuspended in 800 µL of ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, and 0.2% IGEPAL CA-630 with 1× cOmplete protease inhibitor (Roche, 11697498001)), and incubated at 4°C for 30 minutes with rotation. Nuclei were pelleted by centrifugation at 2500 rcf. for 5 min at 4°C and washed once with 500 µL of ice-cold Hi-C lysis buffer. After removing the supernatant, nuclei were resuspended in 100 µL of 0.5% SDS and incubated at 62°C for 10 minutes. SDS was quenched by adding 335 µL of 1.5% Triton X-100 and incubating for 15 minutes at 37°C. After the addition of 50 µL of 10X NEB Buffer 2 (NEB, B7002) and 375 U of MboI restriction enzyme (NEB, R0147), chromatin was digested at 37°C for 2 hours with rotation. Following digestion, MboI enzyme was heat-inactivated by incubating the nuclei at 62°C for 20 min. To fill in the restriction fragment overhangs and mark the DNA ends with biotin, 52 µL of fill-in master mix, containing 37.5 µL of 0.4 mM biotin-dATP (Invitrogen, 19524016), 1.5 µL of 10 mM dCTP (Invitrogen, 18253013), 1.5 µL of 10 mM dGTP (Invitrogen, 18254011), 1.5 µL of 10 mM dTTP (Invitrogen, 18255018), and 10 µL of 5 U/µL DNA Polymerase I, Large (Klenow) Fragment (NEB, M0210), was added and the tubes were incubated at 37°C for 1 hour with rotation. Proximity ligation was performed by addition of 947 µL of ligation master mix, containing 150 µL of 10X NEB T4 DNA ligase buffer (NEB, B0202), 125 µL of 10% Triton X-100, 7.5 µL of 20 mg/mL BSA (NEB, B9000), 10 µL of 400 U/µL T4 DNA ligase (NEB, M0202), and 655.5 µL of water, and incubation at room temperature for 4 hours with rotation. After proximity ligation, nuclei were pelleted by centrifugation at 2500 rcf. for 5 minutes and resuspended in 1 mL of ChIP sonication buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS with protease inhibitor). Nuclei were sonicated using a Covaris S220 for 6 minutes with the following settings: fill level 8, duty cycle 5, peak incidence power 140, cycles per burst 200. Sonicated chromatin was clarified by centrifugation at 16,100 rcf. for 15 min at 4°C and supernatant was transferred to a tube. 60 µL of protein G magnetic beads were washed three times with sonication buffer, resuspended in 50 µL of sonication buffer. Washed beads were then added to the sonicated chromatin and incubated for 1 hour at 4°C with rotation. Beads were then separated on a magnetic stand and the supernatant was transferred to a new tube. 7.5 µg of SMC1A antibody (Bethyl A300-055A) was added to the tube and the tube was incubated overnight at 4°C with rotation. The next day, 60 µL of protein G magnetic beads were washed three time in 0.5% BSA in PBS and washed once with sonication buffer before being resuspended in 100 µL of sonication buffer and added to each sample tube. Samples were incubated for 2 hours at 4°C with rotation. Beads were then separated on a magnetic stand and washed three times with 1 mL of high salt sonication buffer (50 mM HEPES-KOH pH 7.5, 500 mM NaCl, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS) followed by three times with 1 mL of LiCl wash buffer (20 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, 0.1% SDS) and once with 1 mL of TE with salt (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 50 mM NaCl). Beads were then resuspended in 200 µL of elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS) and incubated at 65°C for 15 minutes to elute. To purify eluted DNA, RNA was degraded by the addition of 2.5 µL of 33 mg/mL RNase A (Sigma, R4642) and incubation at 37°C for 2 hours. Protein was degraded by the addition of 10 µL of 20 mg/mL proteinase K (Invitrogen, 25530049) and incubation at 55°C for 45 minutes. Samples were then incubated at 65°C for 5 hours to reverse crosslinks. DNA was then purified using Zymo DNA Clean and Concentrate 5 columns (Zymo, D4013) according to the manufacturer’s protocol and eluted in 14 µL water. The amount of eluted DNA was quantified by Qubit dsDNA HS kit (Invitrogen, Q32854).
Tagmentation of ChIP DNA was performed using the Illumina Nextera DNA Library Prep Kit (Illumina, FC-121-1030). First, 5 µL of streptavidin C1 magnetic beads (Invitrogen, 65001) was washed with 1 mL of tween wash buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA pH 8.0, 1 M NaCl, 0.05% Tween-20) and resuspended in 10 µL of 2X biotin-binding buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 2 M NaCl). 54.19 ng purified DNA was added in a total volume of 10 µL of water to the beads and incubated at room temperature for 15 minutes with agitation every 5 minutes. After capture, beads were separated with a magnet and the supernatant was discarded. Beads were then washed twice with 500 µL of tween wash buffer, incubating at 55°C for 2 minutes with shaking for each wash. Beads were resuspended in 25 µL of Nextera Tagment DNA buffer. To tagment the captured DNA, 3.5 µL of Nextera Tagment DNA Enzyme 1 was added with 21.5 µL of Nextera Resuspension Buffer and samples were incubated at 55°C for 10 minutes with shaking. Beads were separated on a magnet and supernatant was discarded. Beads were washed with 500 µL of 50 mM EDTA at 50°C for 30 minutes, then washed three times with 500 µL of tween wash buffer at 55°C for 2 minutes each, and finally washed once with 500 µL of 10 mM Tris-HCl pH 7.5 for 1 minute at room temperature. Beads were separated on a magnet and supernatant was discarded. To generate the sequencing library, PCR amplification of the tagmented DNA was performed while the DNA is still bound to the beads. Beads were resuspended in 15 µL of Nextera PCR Master Mix, 5 µL of Nextera PCR Primer Cocktail, 5 µL of Nextera Index Primer 1, 5 µL of Nextera Index Primer 2, and 20 µL of water. DNA was amplified with 8 cycles of PCR. After PCR, beads were separated on a magnet and the supernatant containing the PCR amplified library was transferred to a new tube, purified using the Zymo DNA Clean and Concentrate-5 (Zymo D4003T) kit according to manufacturer’s protocol, and eluted in 14 µL water. Purified HiChIP libraries were size selected to 300-700 bp using a Sage Science Pippin Prep instrument according to manufacturer’s protocol and subject to paired-end sequencing on an Illumina HiSeq 2500. SMC1A libraries were initially sequenced with 100×100 bp paired-end sequencing.

value: STAG2 wild-type (sgNT)


title: Single Cell RNA-Seq of the Female Embryonic Day 14.5 Genital Tubercle_1_1

status: Public on May 26 2021

city: Gainesville

first: Martin

middle: J

last: Cohn

state: Fl

address: 2033 Mowry rd

department: Molecular Genetics and Microbiology

institute: Univerisity of Florida

data_processing:
Raw scRNA-Seq data was demultiplexed into FASTQ files, aligned (mouse genome mm10), filtered, and UMIs and barcodes were counted using default settings in CellRanger (v3.1 10x Genomics).
Aligner : Star
Used_Spike_Ins : False
Protocol_Reference : 10x Genomics:Chromium Single Cell 3' v3
Transcriptome_Model : RefSeq
Genome_build: mm10

source_name: Genital tubercle

extract_protocol: The genital tubercles were then dissected from the body and placed into 1.3mg/ml collagenase XI (Sigma-Aldrich, C7657-25MG) on ice. Collagenase XI was made by first dissolving 13mg into 1ml TESCA buffer at 37°C for 5 minutes and then further diluting to 1.3mg/ml in 10% inactivated fetal bovine serum/ Dulbecco’s phosphate-buffered saline. The genital tubercles were chopped into small pieces using forceps while in 500μl collagenase XI on ice. The entire 500μl of collagenase XI and tissue was collected and placed into a 1.5ml microcentrifuge tube for remainder of digestion.  Cells were agitated at 37°C for 30 mins and tritrated with a glass pipettes every 5 mins. After digestion, cells were centrifuged at 500rpm for 5 minutes at 4°C, then were was resuspended in 100ul of magnesium and calcium free 1xPBS with 0.04% bovine serum albumin, filtered through a 40μm strainer (Flowmi Bel-Art H13680-0040), and placed on ice.

tag: tissue

value: Genital tubercle

tag: phenotype

value: Wild Type

value: Female

tag: Stage


title: Single Cell RNA-Seq of the Male Embryonic Day 14.5 Genital Tubercle_1_1

value: Male


title: NAFLD liver 13

value: liver biopsy

tag: disease state

value: NAFLD

tag: disease subtype

value: NAFL

tag: gender


title: HiChIP SMC1A A673 STAG2 WT Replicate 1

description: L22-2807_GT17-05036_TAAGGCGA_ATAGAGAG_S1

treatment_protocol: The SMC1A antibody used in the ChIP experiments was by Bethyl A300-055A.


title: HiChIP SMC1A A673 STAG2 KO Replicate 2

description: L22-2810_GT17-05035_TCCTGAGC-ATAGAGAG_S2


title: CUT&RUN H3K18ac XL-500K K562 cells

status: Public on May 06 2021

city: Durham

first: Bryan

last: Venters

state: NC

address: 6 Davis Drive

institute: EpiCypher

description: H3K18ac K562 cells

data_processing:
Library strategy: CUT&RUN
Base-calling: illumina software
Adapter Trimming: none
Alignment: Paired-end fastq files were aligned to the hg19 reference genome using the Bowtie2 algorithm (PMID: 22388286).
Filtering: Only uniquely aligned reads were retained, and blacklist regions (PMID: 31249361) were filtered out for subsequent analyses.
Peak Calliing: Peaks were called using SEACR (Sparse Enrichment Analysis of CUT&RUN) (PMID: 31300027).
Genome_build: hg19

source_name: K562 cells

growth_protocol: K562 cells were maintained (1–10 × 10^5 cell/ml) in T25 flasks in IMDM + 10% FBS  +  1% Pen/Strep

extract_protocol:
CUTANA protocol v1.5.1; optimized version of PMID: 29651053
NEBNext Ultra II DNA Library Prep kit (New England Biolabs #E7645S)
Cleavage under targets and Release using nuclease

treatment_protocol: Native cells except 500K cells for H3K18ac CUT&RUN were crosslinked with 0.1% formaldehyde for 1 minute at room temperature, and then quenched with 125 mM glycine.

value: K562 human immortalised myelogenous leukemia cell line

tag: treatment

value: 0.1% Formaldehyde, 1 minute

tag: antibody

value: anti-H3K18ac Invitrogen #PA5-85523, lot UG2799523D


title: NAFLD liver 11

value: M


title: NAFLD liver 27


title: NAFLD liver 9


title: NAFLD liver 12


title: NAFLD liver 14


title: CUT&RUN BPTF 500K K562 cells

description: BPTF K562 cells

value: untreated

value: anti-FALZ/BPTF Bethyl #A300-973A, lot 2


title: NAFLD liver 2


title: NAFLD liver 3


title: CUT&RUN H3K4me3 500K K562 cells

description: H3K4me3 K562 cells

value: anti-H3K4me3 ThermoFisher #PA5-27029, lot SG2419844A


title: NAFLD liver 8


title: Data_ProbeOnly_001_noRCA_3

status: Public on May 04 2021

city: Uppsala

first: Rachel Yuan

last: Nong Mikkelsen

address: Biomedical Center (BMC)

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample6

data_processing:
reference: NAR-2014-Mikkelsen-gku511-42-14.pdf
Genome_build: synthetic DNA probe library 130106_UUProbe_carrier_fullTileAmp_rev.dat.txt

organism: synthetic construct

source_name: solid phase magnetic-bead RCA assay

extract_protocol: Solid phase assay: 25 amol of capture probes were immobilized of 1e7 MyOne T1 beads for each 25 microliter reaction following manufactural instruction and blocked by blocking buffer (1 mg/ml BSA, 1 mM biotin, 0.1 ug/ul salmon sperm DNA in 1x PBS) at room temperature (RT) for 30 min on an end-to-end table rotator, collected and stored at 4˚C in storage buffer (1x PBS and 0.1% BSA) after 2x washing by washing buffer (1x PBS, 0.05% Tween20) at RT. Assay was started by probe preparation that 0,2 uM probes and 20 uM protection oligo were incubated in 10 ul 1x NEB4 buffer and 0.5 ug/ul BSA for 30-60 min at 37˚C and diluted 1:20 in blocking buffer. 25 ul of probes mix were adding to 25e7 beads and incubate at RT for 60 min. A multi-step enzymatic treatment were then carried out on beads in 25 ul of: 1) 0,5 U/ul MlyI, 5 uM protection oligo, 0.5 ug/ul BSA, 1x NEB4 buffer by incubation at 37˚C for 30 min; 2) 0,5 U/ul Nb.BtsI or Nb.BbvCI or ddH2O, 0.5 ug/ul BSA, 1x NEB4 buffer by incubation at 37˚C for 30 min; 3), 0.05 U/ul UNG, 0,5 ug/ul BSA, 1x NEB4 buffer by incubation at 37˚C for 30 min; 4) 0,3 U/ul T4 DNA ligase, 0.5 mM ATP (Thermo Scientific R0441), 0.5 ug/ul BSA, 1x NEB4 buffer by incubation at 37˚C for 30 min; 5) 0,5 U/ul phi29 DNA polymerase, 0.25 mM dNTP, 1x phi29 buffer by incubation at 37˚C for 30 min; with 2x washing by washing buffer at RT. Sequencing library preparation were performed with a NEB High Fidelity DNA polymerase and high concentration PCR primers. Resulted products were sequenced at a HiSeq2000 sequencer with its rapid run program.

tag: probes

value: 0.01 uM probes

tag: amplification

value: no RCA amplification

tag: protection

value: protection oligo


title: Data_ProbeOnly_01_noProt_RCA_1

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample10

value: 0.1 uM probes

value: RCA amplification

value: no protection oligo


title: NAFLD liver 7

tag: age


title: Data_ProbeOnly_01_RCA_1

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample7


title: CUT&RUN IgG negative control 500K K562 cells

description: IgG K562 cells

value: CUTANA™ Rabbit IgG CUT&RUN Negative Control Antibody EpiCypher 13-0042, lot 20036001-52


title: Data_ProbeOnly_01_noProt_RCA_2

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample11


title: Data_ProbeOnly_001_noRCA_1

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample4


title: Data_ProbeOnly_001_RCA_2

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample2


title: Data_ProbeOnly_01_RCA_3

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample9


title: Data_ProbeOnly_001_RCA_1

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample1


title: Data_ProbeOnly_01_RCA_2

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample8


title: Data_Target_01_noRCA_3

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample36


title: Data_ProbeOnly_001_RCA_3

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample3


title: Data_Target_01_noRCA_2

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample35


title: Data_Target_01_noProt_RCA_1

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample28


title: Data_Target_01_noProt_noRCA_3

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample33


title: Data_Target_001_noRCA_2

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample23


title: Data_Ctrl

description:
-
probe
sample37

source_name: control assay


title: Data_Target_01_noProt_noRCA_2

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample32


title: Data_Target_01_noProt_noRCA_1

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample31


title: Data_Target_01_RCA_3

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample27


title: Data_Target_01_noProt_RCA_3

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample30


title: Data_Target_01_noRCA_1

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample34


title: Data_ProbeOnly_001_noRCA_2

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample5


title: Data_ProbeOnly_01_noRCA_1

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample16


title: Data_Target_001_RCA_1

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample19


title: Data_Target_01_noProt_RCA_2

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample29


title: Data_Target_001_RCA_3

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample21


title: Data_ProbeOnly_01_noRCA_2

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample17


title: LELab ChIP seq TLS3059 anti FLAG replicate1

status: Public on May 01 2021

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

data_processing:
For analysis of ChIP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command:bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage at each nucleotide position was computed using BEDTools (Quinlan and Hall, 2010) using the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. Finally, ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) using custom R scripts.
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Files ending with _coverage.txt: tab-delimited text file of nucleotide-resolution coverage from ChIP-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

organism: Caulobacter vibrioides

source_name: Caulobacter crecentus CB15N

growth_protocol: Cultures of Caulobacter (TLS3050 and TLS3059) were grown at 30oC in PYE and supplemented with antibiotics, as necessary, at appropriate concentrations. To deplete wild-type non-tagged ParB, exponential-phase cells were washed off xylose and re-introduced to PYE+0.2% glucose for an additional 5 hours. After 4 hours, vanillate was added to induce the expression of flag-parB (WT) or flag-parB (E102A) for an hour. After an hour, formadehyde (1% final concentration) were added to fix cells for ChIP-seq.

extract_protocol:
DNA was isolated using the Qiagen Cell Lysis and Protein Precipitation solutions. Detailed protocols are listed in the Supplementary Materials
Standard library construction for Illumina Hiseq2500 sequencing platform

treatment_protocol: cells were depleted of wild-type non-tagged ParB for 5 hours, then FLAG-ParB (E102A) were produced for an hour before formadehyde were added to 1% (final concentraation) to fix cells for ChIP-seq.

tag: developmental stage

value: mixed population, exponential phase

tag: genotype

value: CB15N parB::Pxyl-parB van::Pvan-1xflag-parB (E102A)

value: anti-FLAG


title: Data_ProbeOnly_01_noProt_noRCA_3

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample15


title: RNA_human_HD_UNSTIM_4

status: Public on Apr 29 2021

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

data_processing:
BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14, v2.18.0,  or v2.20.0.422).
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36).
Transcript quantification was performed by salmon (v0.10.2) using arguments '-l IU --gcBias' and tximport (v1.8.0 or v1.10.1) using the UCSC hg38 known gene transcript assembly.
Supplementary_files_format_and_content: Text files are raw estimated gene-level counts (1 count = 1 read pair) as quantified by salmon (v0.10.2) and imported by tximport (v1.8.0 or v1.10.1). Also provided are gene IDs (Entrez and Ensembl), gene names, gene descriptions, and chromosome (for human).

source_name: peripheral blood NK cells

extract_protocol:
RNA was isolated from sorted and stimulated cell populations using TRIzol (Invitrogen) or the PicoPure RNA Isolation Kit (Thermo Fisher)
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.705-2ng total RNA with RNA integrity numbers ranging from 6.5 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech catalog # 63488), with 12 cycles of amplification. Subsequently, 10ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 or HiSeq 2500 in Rapid mode in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit or HiSeq Rapid SBS Kit v2, respectively (Illumina).  An average of 37 million paired reads were generated per sample and the percent of mRNA bases per sample ranged from 42% to 70%.

treatment_protocol: Mouse NK cells were stimulated for 3 hr with combinations of 20 ng/mL recombinant mouse IL-2,  20 ng/ml recombinant mouse IL-15, 20 ng/ml recombinant mouse IL-12, 10 ng/ml recombinant mouse IL-18, and/or 100 IU recombinant mouse IFN-α. Human NK cells were stimulated with 100 U/ml recombinant human IL-2, 50 ng/ml recombinant human IL-15, 20 ng/ml recombinant human IL-12, 50 ng/ml recombinant human IL-18 and/or 1000 U/ml recombinant human IFN-α.

value: HD (healthy donor)

tag: cell type

value: ex-vivo NK cells

tag: condition

value: UNSTIM

tag: replicate


title: Data_ProbeOnly_01_noRCA_3

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample18


title: Data_Target_001_RCA_2

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample20


title: Data_Target_01_RCA_2

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample26


title: Data_Target_01_RCA_1

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample25


title: Data_ProbeOnly_01_noProt_noRCA_1

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample13


title: Data_ProbeOnly_01_noProt_noRCA_2

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample14


title: LELab ChIP seq TLS3050 anti FLAG replicate1

treatment_protocol: cells were depleted of wild-type non-tagged ParB for 5 hours, then FLAG-ParB (WT) were produced for an hour before formadehyde were added to 1% (final concentraation) to fix cells for ChIP-seq.

value: CB15N parB::Pxyl-parB van::Pvan-1xflag-parB (WT)


title: Data_Target_001_noRCA_3

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample24


title: LELab ChIP seq TLS3059 anti FLAG replicate2


title: Data_ProbeOnly_01_noProt_RCA_3

description:
MlyI, Nb.BtsI, Nb.BbvCI
probe only
one-step sample12


title: LELab ChIP seq TLS3050 anti FLAG replicate2


title: Q175_Glt1_12mo_33

status: Public on Apr 07 2021

type: RNA

city: Rochester

first: John

last: Mariani

state: NY

address: 601 Elmwood Avenue

department: Neurology

institute: University of Rochester

description: Gene expression from FACS isolated mouse striatum

hyb_protocol: Hybridization was processed according ot manufacturer instructions

scan_protocol: GeneChips were scanned according to manufacturer instructions

data_processing: Following import of raw data into R with the affy package (Gautier et al. 2004; R Core Team 2017) robust multiarray analysis (RMA) was utilized for pre-processing and normalization (Irizarry et al., 2003).  Probe annotations were fetched using biomaRt (Durinck et al. 2009) and probes targeting multiple ensembl IDs were removed.  Glt1 and Cd11b sample intensities were individually subset and analyzed for between timepoint differential expression using limma (Ritchie et al. 2015). An adjusted p-value of < 0.05 was deemed significant.

label: biotin

source_name: 12mo Glt1 Q175

label_protocol: Total RNA was labeled with biotin according to manufacturer instructions

extract_protocol:
[dissociation protocol]  The mice were euthanized with carbon dioxide, transcardially perfused with sterile Hank’s Balanced Salt Solution (HBSS), and the brain removed. The brains were immersed in ice-cold sterile HBSS for about 5 minutes to facilitate the microdissection. Under a dissecting microscope, the sub-ventricular zone was removed and discarded and the striata from each mouse was dissected and placed in sterile HBSS on ice. The striata from all the mice of the litter were pooled together as per genotype. The striatal tissues were transferred to a petri dish containing sterile HBSS then chopped into small pieces using sterile disposable scalpels, transferred into a sterile tube and then incubated in a papain/DNase dissociation solution at 37oC for 50 minutes. Minimum essential media plus 0.5% BSA (MEM-BSA) containing 5% serum was then added to inactivate the papain. The tissue was triturated by repeated pipetting in order to achieve a single cell suspension. The cells were then pelleted, resuspended into MEM-BSA and overlaid first onto a 90% Percoll gradient followed by a second 30% Percoll gradient and the solution centrifuged. The myelin and debris were removed from the tube and then the cells were resuspended into MEM-BSA plus donkey serum for flow cytometry analysis.
[facs protocol]  Flow cytometry analysis for astrocyte surface markers was performed on freshly dissociated striatal cells from wild-type or R6/2 mice. Cells were stained with primary antibodies against the astrocyte marker, GLT1 and the microglial marker, CD11b-PE (BD Biosciences). The primary antibodies, directly conjugated antibodies or their corresponding isotype controls were added to the cells and then incubated on ice for 15 minutes. 5 ml of MEM-BSA wash buffer was added to the cells and the cells were spun down. For the non-conjugated antibodies, the pelleted cells were resuspended in MEM-BSA plus 5% donkey serum and the appropriate secondary antibody, APC conjugated donkey anti-rabbit IgG, was added at a 1:200 dilution (Jackson ImmunoResearch). The samples were incubated on ice for 15 minutes and then washed with 5 ml of MEM-BSA wash buffer for 10 minutes. All samples were resuspended in MEM-BSA containing 20U/ml DNase to a concentration of 1-1.5x106 cells/ml and then passed over a 35 µm tube top cell strainer prior to flow cytometry. DAPI was added at 1 µg/ml. Flow cytometry analysis and FACS was performed on a BD FACSAria IIIU (Becton Dickinson, San Jose, CA). The cells were analyzed by forward and side scatter, for PE fluorescence through a 582 ± 15 nm band-pass filter, for APC fluorescence through a 660 ± 20 nm band-pass, and for DAPI fluorescence through a 450 ± 50 nm band-pass. Unstained cells were used to set the background fluorescence; a false positive rate of 0.5% was accepted. The GLT1+, CD11b+ and the GLT1-/CD11b- striatal cells isolated by FACS were pelleted, frozen on dry ice and stored at -80oC until the time of RNA extraction.
RNA was extracted from the pelleted/frozen cells using the Qiagen RNeasy Mini kit. An on column DNase treatment was performed and the RNA concentration was determined using a Nanodrop. A portion of the RNA was then used for bioanalysis to confirm the integrity of the RNA.

tag: tissue

value: Striatum

value: astrocytes

tag: facs markers


title: WT_CD11b_12mo_36

source_name: 12mo CD11b WT

value: WT

value: microglia


title: Q175_CD11b_12mo_33


title: WT_Neg_12mo_36

source_name: 12mo Neg WT

value: negative cells


title: WT_Neg_6mo_25

source_name: 6mo Neg WT


title: WT_Glt1_12mo_34

source_name: 12mo Glt1 WT


title: WT_Neg_12mo_34


title: Q175_CD11b_6mo_28

source_name: 6mo CD11b Q175


title: WT_Neg_12mo_37


title: WT_CD11b_12mo_34


title: Q175_Glt1_12mo_30


title: WT_Glt1_12mo_36


title: WT_CD11b_12mo_37


title: Data_Target_001_noRCA_1

description:
MlyI, Nb.BtsI, Nb.BbvCI
target
one-step sample22

value: 0.01 uM probes

value: no RCA amplification

value: protection oligo


title: Q175_Glt1_12mo_31


title: WT_Glt1_12mo_37


title: Q175_Neg_6mo_28

source_name: 6mo Neg Q175


title: Q175_CD11b_12mo_31


title: Q175_CD11b_12mo_30


title: Q175_Neg_12mo_31

source_name: 12mo Neg Q175


title: Q175_Neg_12mo_33


title: WT_Neg_6mo_22


title: WT_Neg_6mo_24


title: Q175_CD11b_6mo_26


title: Q175_Neg_12mo_30


title: Q175_CD11b_6mo_29


title: Q175_Neg_6mo_27


title: WT_CD11b_6mo_23

source_name: 6mo CD11b WT


title: 7k_2_TSB-D_planktonic

status: Public on Apr 03 2021

city: Minneapolis

first: Julia

last: Willett

state: MN

address: 689 23rd Avenue SE, 4-149 Micro Research Facility

institute: University of Minnesota

data_processing:
Library strategy: Tn-Seq
Reads were trimmed to remove Illumina adapter sequences using Trimmomatic and were mapped to the OG1RF reference genome (GenBank CP002621.1, NCBI RefSeq NC_017316.1) using Bowtie.
SMarT TnSeq analysis was performed using custom scripts and the Mesabi supercomputer at the Minnesota Supercomputing Institute.  The technical quality of the sequencing results was evaluated using the FastQC package produced by Babraham Bioinformatics (63).  We placed particular emphasis on the quality of the read tails as well as the presence of adapter contamination.  The cutadapt package was used to remove residual adapters and the primed transposon region from the sequenced forward reads (64).
The trimmed reads were then aligned to the E. faecalis OG1RF reference genome using bwa-mem (65).  Mapped reads not beginning or ending at a TA site were removed due to the potential for integrations independent of transposon activity.  Bedtools genomecov was used to quantify the number of integrations on a per position basis (66).
R and the package “sqldf,” which provides an SQL interface for R dataframes (67), were used to summarize the integration data at each TA site in the OG1RF genome.  These were filtered for the strains present in the SMarT TnSeq library using the 2D barcodes assigned to each transposon mutant stock tube.
Integration sites, matched between sample sets, were evaluated for a significant change in the proportion of integrations received using a Chi-squared test and a Monte Carlo-based method that models the effect of experimental replicates and determines whether the mean proportion parameter is significantly different for each gene between experimental conditions.  The Chi-squared results were filtered for significance (adjusted p < 0.05), and results with a significant p value that did not meet the highest confidence level from the Monte Carlo simulations (value = 1.19) were removed.
Genome_build: NC_017316

organism: Enterococcus faecalis OG1RF

source_name: total bacterial DNA

growth_protocol: Growth medium (either MM9-YEG or TSB-D) was inoculated with 6 x 108 – 2 x 109 CFU.  Batch cultures were grown without flow for 4-6 hours after which the peristaltic pump (Cole Parmer) was turned on at a flow rate of 8 mL/minute for 18-20 hours (total experiment time = 24 hours).

extract_protocol:
Substrates were removed from the CDC biofilm reactor chamber and processed to remove adherent biofilm cells.  Biofilms from multiple substrates from each reactor were pooled in a conical tube, pelleted at 6371× g for 15 min, and frozen at -80 oC until further use.  Pellets were resuspended in 180 uL enzymatic lysis buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 1.2% Triton X-100) with 30 mg/mL lysozyme and 500 U/mL mutanolysin.  After 30 min incubation at 37 oC, 25 uL Proteinase K and 200 uL Buffer AL (DNeasy Blood and Tissue Kit, Qiagen) were added.  Tubes were incubated at 55 oC for 30 min, after which DNA was extracted using a DNeasy Blood and Tissue Kit following manufacturer’s instructions.
DNA was sheared and processed using the Illumina TruSeq Nano library preparation kit.  The libraries were normalized to 2 ng/μl, and 10 ng of each library was used as a PCR template to enrich for the mariner transposon junctions using a transposon-specific primer (mariner-seq) and the Illumina P7 primer.  1 μl of the enrichment PCR product was diluted 100-fold, and 10 μl of the diluted DNA was used as template for the indexing PCR (TruSeq P5 indexing primer + P7 primer).  The final libraries had unique combinations of P5 and P7 indexes suitable for multiplexed sequencing.  Libraries were quantified, normalized, and pooled.  The pooled library was cleaned using 1×SPRI beads (Ampure XP, Beckman Coulter) and eluted in 1:10 TE buffer (made from 1×TE buffer purchased from Fisher).  The amplicon size distribution of the pool was verified on a Bioanalyzer (Agilent) and the concentration of functional library molecules calculated using Kapa Library Quantification kit for Illumina.  The pool was sequenced using an Illumina HiSeq 2500 in 125-bp paired end output mode at the University of Minnesota Genomics Center.

tag: strain


title: 7k_1_TSB-D_input


title: 7k_2_TSB-D_biofilm


title: 7k_1_TSB-D_planktonic


title: WT_CD11b_6mo_22


title: 2k_1_TSB-D_input


title: 2k_1_TSB-D_planktonic


title: 2k_2_TSB-D_input


title: 2k_2_TSB-D_biofilm


title: WT_CD11b_6mo_25


title: 2k_1_TSB-D_biofilm


title: 2k_2_TSB-D_planktonic


title: 7k_2_M9_planktonic


title: 7k_1_TSB-D_biofilm


title: 7k_2_M9_input


title: 7k_2_M9_biofilm


title: 7k_1_M9_input


title: 7k_1_M9_biofilm


title: 2k_1_M9_planktonic


title: 2k_2_M9_biofilm


title: WT_Glt1_6mo_24

source_name: 6mo Glt1 WT


title: 2k_2_M9_input


title: Q175_Glt1_6mo_27

source_name: 6mo Glt1 Q175


title: WT_Glt1_6mo_23


title: 7k_2_TSB-D_input


title: 2k_2_M9_planktonic


title: Q175_Glt1_6mo_26


title: 2k_1_M9_input


title: Q175_Glt1_6mo_29


title: XVIVO_Week-8_iPSC-macrophages

status: Public on Apr 02 2021

city: Oxford

first: Alun

last: Vaughan-Jackson

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

data_processing:
Raw pair-end reads (150bp) were pre-processed using fastp 0.20.1 software with following additional parameters: --trim_poly_x, --correction, --detect_adapter_for_pe
Salmon 1.3.0 selective alignment was used for transcript mapping to a full decoy-aware transcriptome using the Gencode version 34 reference human transcriptome and GRCh38 primary assembly genome. Optional parameters used: --validateMappings, --seqBias, --gcBias, --dumpEq
The counts were imported, scaled to the average transcript length over samples and the library size (‘LengthScaledTPM’), and summarised to the gene level using the tximport package (v.1.16.0)
Lowly expressed genes with length-scaled abundance estimates less than 10 in 3 samples were filtered out with the default filtering function in the edgeR package
Differential expression was tested using limma-voom with time at harvesting macrophage precursor cells as a batch variable in the design matrix
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon quantification file (tar file), includes quant.sf with transcript length, effective length, estimated abundances and TPM values.

source_name: iPSC-derived macrophages

growth_protocol: iPSC-macrophages were differentiated as described in van Wilgenburg et al (2013) PLoS One. 8:8. with minor modifications (Vaughan-Jackson et al. (2020) BioRXiv) in 2 different media: X-VIVO-15 differentiation medium ( X-VIVO-15 (Lonza) supplemented with 2mM Glutamax, 100 U/mL penicillin and 100 μg/mL streptomycin, 50uM 2-mercaptoethanol, 25ng/mL IL-3 and 100ng/mL M-CSF) or a serum free, defined, open source medium we called OXM differentitaion medium (advanced DMEM-F12 (Gibco) supplemented with 2mM Glutamax, 100 U/mL penicillin and 100 μg/mL streptomycin, 15mM HEPES, 5ug/mL human insulin, 15uM Tropolone, 25ng/mL IL-3 and 100ng/mL M-CSF). Free-floating macrophage precursors were harvested from Differentiation Factories at 8, 10, and 12 weeks from the start of differentiation, and seeded in 6 well-plates at 1 million cells/well in macrophage media: either X-VIVO 15 macrophage medium (XVIVO differentiation medium with  2-ME and IL-3 removed) or OXM macrophage medium (OXM differentiation medium with Troplone and IL-3 removed), and incubated for 7 days at 37 °C/5% CO2, with a 50% media change on day 4.

extract_protocol:
Lysates were passed through QIAshredder columns (QIAGEN) and the total RNA extracted using a QIAGEN RNeasy Mini kit, according to the manufacturer’s protocol using on-column DNase treatment (QIAGEN). RNA samples were eluted in 50 µL of RNase-free water. The quantity and quality of RNA was measured by Nanodrop and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies), with measured RNA integrity (RIN) values ≥8.8.The mRNA fraction was selected from the total RNA for each sample before conversion to cDNA.
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

tag: cell line

tag: differentiation age

value: 8 weeks

tag: differentiation medium

value: XVIVO

tag: rin

value: iPSC-derived macrophages


title: XVIVO_Week-10_iPSC-macrophages

value: 10 weeks


title: 7k_1_M9_planktonic


title: OXM_Week-12_iPSC-macrophages

value: 12 weeks

value: OXM


title: XVIVO_Week-12_iPSC-macrophages


title: pCF10_P23IGR_pCIE_U_FLAG1

status: Public on Mar 16 2021

data_processing:
Sequenced reads were trimmed to remove adapter sequences and low-quality bases using the sliding-window option in Trimmomatic
RPKM and Expression values were calculated using Rockhopper
Genome_build: NC_006827

organism: Enterococcus faecalis

source_name: bacterial cellular RNA from pulldown

growth_protocol: E. faecalis strains were grown overnight in BHI (5 mL), and then diluted to an OD600 of ~0.03 in 200 mL BHI and grown without shaking to an OD600 of 0.1.

extract_protocol:
Cell lysates were prepared by suspending cells in 500 µL of TBS buffer with 5 µL of HALT protease inhibitor cocktail and 2 µL of superase.  Cells were added to a pre-chilled tube containing 500 µL of glass beads (0.1 mm) and disrupted by repeated cycles of maceration for 40 sec at 400 rpm with intervals on ice. TBS buffer (500 µL) was added and the slurry was vortexed for 30 sec, after which cell fragments and other material were pelleted by centrifugation 12,000 x g for 30 min at 4 °C. The supernatant was transferred to a pre-chilled tube, the volume was increased to 1 mL with cold TBS buffer, and 5 µL of superase inhibitor was added. An aliquot representing the input fraction was removed, and the remaining material was subjected to FLAG pull-downs by addition of 75 µL of anti-FLAG magnetic bead slurry to a 2.0 mL dolphin tube (Costar 3213).  The mixture was then placed on a nutator (rocker) for 2.0 h at 4 °C, after which time the resin was pelleted by centrifugation at 4,000 x g for 30 sec at 4 °C.  The supernatant was removed, and the resin washed 3 x with 1.5 mL of TBS buffer, with incubations on a nutator for 1 min and then subjected to magnetic bead pull-downs at 4 °C.  Material bound to the FLAG beads was eluted by addition of 15 µL 5 µg/µL 3xFLAG peptide solution and 250 µL of 3xFLAG elution buffer.  Ribosomal RNA was depleted using a MicrobeExpress kit.  All RNA samples were treated with Turbo DNase (ThermoFisher, rigorous method described by the manufacturer) and submitted to the University of Minnesota Genomics Center for Illumina library prep.
Pull-down samples were processed using the Illumina TruSeq stranded mRNA preparation kit. To retain small RNAs, size selection was not performed between library preparation and sequencing for pull-down samples. All samples were sequenced as paired-end reads on an Illumina HiSeq 2500 in high output mode (125 bp read length for whole-cell samples and 50 bp read length for pull-down samples). Sequencing files were trimmed to remove contaminating adapter sequences and low-quality bases using Trimmomatic.  Reads were mapped to the pCF10

treatment_protocol: cCF10 was added at a final concentration of 20 ng/mL and cultures were grown to an OD600 of 0.3.  Cells were pelleted by centrifugation at 16,000 x g at 4 °C for 5 min, washed once with 10 mL TBS buffer (50 mM Tris-HCl, pH 7.4; 150 mM NaCl), and resuspended in 1 mL TBS and transferred to a 1.5 mL eppendorf tube. Cells were pelleted by centrifugation at 16,000 x g at 4 °C for 5 min, the supernatant was removed, and the cell pellet was flash frozen in a dry ice-ethanol slurry and stored at -80 °C.

value: OG1RF pCF10


title: pCF10_P23IGR_pCIE_U


title: pCF10_P23IGR_pCIE_U_FLAG2


title: ETP-Lly 23

status: Public on Mar 15 2021

type: genomic

first: Xinjie

last: Xu

address: 200 2nd St SW

institute: Mayo Clinic

description: Affymetrix OncoScan

hyb_protocol: DNA was MIP annealed, gap-filled, cleaved, PCR amplified, fragmented by HaeIII digestion, the simultaneously labeled and hybridized to each array according to the manufacturer's instructions. Arrays were subsequently washed and stained using Affymetrix fluidics stations, according to manufacturer protocol.

scan_protocol: The Arrays were scanned using the Gene Chip Scanner 3000.

data_processing: The array image was acquired using Affymetrix GeneChip™ Command Console Software (AGCC version 4.0). Copy number values for individual SNPs were extracted and converted from paired CEL files into signal intensities using Affymetrix Chromosome Analysis Suite (ChAS) softwares.

source_name: Case 23

label_protocol: Labeling occurs during hybridization, as per manufacturer (Affymetrix).

extract_protocol: DNA was isolated using the RecoverAll Total Nucleic Acid Isolation kit (Ambion/Applied Biosystems, Austin, TX) and quantitated with the PicoGreen assay (Invitrogen).

value: ETP-Lly


title: ETP-Lly 24

description: Affymetrix OncoScan

source_name: Case 24


title: OXM_Week-10_iPSC-macrophages


title: ETP-Lly 21

description: Affymetrix OncoScan

source_name: Case 21


title: ETP-Lly 22

description: Affymetrix OncoScan

source_name: Case 22


title: OXM_Week-8_iPSC-macrophages


title: non-ETP T-Lly 14

description: Affymetrix OncoScan

source_name: Case 14

value: non-ETP T-Lly


title: ETP-Lly 17

description: Affymetrix OncoScan

source_name: Case 17


title: ETP-Lly 20

description: Affymetrix OncoScan

source_name: Case 20


title: ETP-Lly 18

description: Affymetrix OncoScan

source_name: Case 18


title: ETP-Lly 16

description: Affymetrix OncoScan

source_name: Case 16


title: ETP-Lly 19

description: Affymetrix OncoScan

source_name: Case 19


title: non-ETP T-Lly 15

description: Affymetrix OncoScan

source_name: Case 15


title: non-ETP T-Lly 11

description: Affymetrix OncoScan

source_name: Case 11


title: non-ETP T-Lly 12

description: Affymetrix OncoScan

source_name: Case 12


title: non-ETP T-Lly 9

description: Affymetrix OncoScan

source_name: Case 9


title: 2k_1_M9_biofilm

source_name: total bacterial DNA


title: non-ETP T-Lly 10

description: Affymetrix OncoScan

source_name: Case 10


title: non-ETP T-Lly 6

description: Affymetrix OncoScan

source_name: Case 6


title: non-ETP T-Lly 7

description: Affymetrix OncoScan

source_name: Case 7


title: non-ETP T-Lly 8

description: Affymetrix OncoScan

source_name: Case 8


title: non-ETP T-Lly 4

description: Affymetrix OncoScan

source_name: Case 4


title: non-ETP T-Lly 3

description: Affymetrix OncoScan

source_name: Case 3


title: non-ETP T-Lly 5

description: Affymetrix OncoScan

source_name: Case 5


title: non-ETP T-Lly 1

description: Affymetrix OncoScan

source_name: Case 1


title: non-ETP T-Lly 2

description: Affymetrix OncoScan

source_name: Case 2


title: non-ETP T-Lly 13

description: Affymetrix OncoScan

source_name: Case 13


title: H3K27me3_24hpi_Rep3

status: Public on Mar 05 2021

city: Chicago

first: Mary

last: Hummel

address: 303 E. Chicago Ave

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to the reference genome using Bowtie2 version 2.2.6
bigWig files were created using HOMER
Genome_build: hg19
Genome_build: HCMV EF999921.1 [HCMV genome fa and gtf files for alignment of bigwig files are available at https://github.com/Mary-Hummel/HCMV-TB40-E-GFP-reference-genome.git]
Supplementary_files_format_and_content: bigWig files

organism:
Homo sapiens
Human betaherpesvirus 5

source_name: H3K27me3_24hpi GFP+ rep_3

growth_protocol: Kasumi-3 were grown in RPMI-1640 medium (ATCC 30-2001) supplemented with 20% fetal bovine serum (Corning) and 1,000 Units/ml Penicillin-Streptomycin (Gibco)

extract_protocol:
After fixation, cells were lysed and sonication with Covaris Focused-ultrasonicator at 10% Duty Cycle, 140 peak, 200 cycles per burst, 360 seconds. ChIP was performed by incubating the sonicated sample with Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb #8173, Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9733 (Cell Signaling Technologies), or Histone H3 Antibody #2650 (Cell Signaling Technologies)  and the protein A/G agarose beads. Beads were washed and eluted in 200μl of elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1.0% SDS). The eluates were de-cross-linked and the DNA purified using the Qiagen PCR purification kit.
Libraries were prepared with the KAPA HTP Library Preparation Kit multiplexed with NEXTflex DNA Barcodes (Bio Scientific) and size selected with AMPure XB beads (Beckman Coulter) to have fragments 250-450 bp in length. Library quality control was assessed using Bioanalyzer High Sensitivity DNA Analysis kit (Agilent) and sequencing was performed with Illumina NextSeq technology (50bp single- end reads).

treatment_protocol: Kasumi-3 were infected with TB40/E wtGFP strain of HCMV at MOI 1 or mock-infected. Extracellular virus was inactivated at 24 hours post infection. HCMV-infected cells were sorted for GFP expression and live cells. Mock-infected cells were sorted for live cells. Cells were then fixed with 1% of Formaldehyde in PBS fand quenched with 0.125 M glycine.

tag: treatment

value: live GFP+ infected, 24hpi

tag: chip antibody


title: H3_24hpi_Rep3

source_name: H3_24hpi GFP+ rep_3

value: Histone H3 Antibody (ChIP Formulated) #2650 (Cell Signaling Technologies)


title: H3_24hpi_Rep1

source_name: H3_24hpi GFP+ rep_1


title: H3K27me3_24hpi_Rep1

source_name: H3K27me3_24hpi GFP+ rep_1

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9733 (Cell Signaling Technologies)


title: H3K27Ac_24hpi_Rep2

source_name: H3K27Ac_24hpi GFP+ rep_2

value: Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb #8173 (Cell Signaling Technologies)


title: H3K27me3_24hpi_Rep2

source_name: H3K27me3_24hpi GFP+ rep_2


title: H3_24hpi_Rep2

source_name: H3_24hpi GFP+ rep_2


title: H3K27Ac_24hpi_Rep3

source_name: H3K27Ac_24hpi GFP+ rep_3


title: H3K27Ac_24hpi_Rep1

source_name: H3K27Ac_24hpi GFP+ rep_1


title: H3K27me3_mock_infected_cells_Rep2

source_name: H3K27me3_mock infected cells rep_2

value: live mock-infected, 24hpi


title: H3K27me3_mock_infected_cells_Rep3

source_name: H3K27me3_mock infected cells rep_3


title: H3K27Ac_mock-infected_cells_Rep3

source_name: H3K27Ac_mock-infected cells rep_3


title: input_24hpi_Rep2

source_name: input_24hpi GFP+ rep_2


title: H3K27me3_mock_infected_cells_Rep1

source_name: H3K27me3_mock infected cells rep_1


title: input_24hpi_Rep3

source_name: input_24hpi GFP+ rep_3


title: input_mock_infected_cells_Rep3

source_name: input_mock infected cells_ rep3


title: H3K27Ac_mock-infected_cells_Rep1

source_name: H3K27Ac_mock-infected cells rep_1


title: input_mock_infected_cells_Rep2

source_name: input_mock infected cells_ rep2


title: H3K27Ac_mock-infected_cells_Rep2

source_name: H3K27Ac_mock-infected cells rep_2


title: input_mock_infected_cells_Rep1

source_name: input_mock infected cells_ rep1


title: HFD7L-s102990-039

status: Public on Mar 01 2021

city: Leiden

first: Martine

middle: C

last: Morrison

address: Sylviusweg 71

department: MHR

country: Netherlands

institute: TNO

data_processing:
Base calling etc: see library construction protocol
Trimming of reads: removal of adapters and 3' regions with low base-quality was performed with software TRIMMOMATIC (bioportal)
Mapping of reads to the Mouse genome was performed with software STAR (bioportal)
Counting of reads on Mouse genome features/genes was performed with Htseq software (bioportal)
Identification of Differentially Expressed Genes was performed with software DESeq2 (bioportal)
Genome_build: Mus_musculus.GRCm_p4
Supplementary_files_format_and_content: .fastq.count files are tab delimited files per sample, containing #reads/gene per row. The last rows contain summaries (nofeature, ambiguous, toolowaQual, notaligned, alignmentnotunique) and should be omitted for further counts analysis.

growth_protocol: The animal experiment was performed in the AAALAC-accredited animal facility at TNO MetabolicHealth Research (Leiden, the Netherlands) in accordance with the rules and regulations set forward byhe Netherlands Law on Animal Experiments with ethical approval by an independent Animal Welfareody (IvD TNO; approval number 3682 / TNO-210). Animals were group-housed in makrolon cages2-4 mice/cage) in animal rooms with 50-60% relative humidity, temperature ~21 °C and a 7 am to pm light cycle. Male Ldlr-/-.Leiden mice (age 13-16 weeks) were obtained from the breeding colonyat TNO Metabolic Health Research (Leiden, the Netherlands). All animals were kept on a standardrodent maintenance diet until the start of the study (9 kcal% fat, 33 kcal% protein, 58 kcal%carbohydrate; R/M-H, Ssniff Specialdiäten, Soest, Germany). At the start of the study, one group ofmice (chow, n=10) was kept on this maintenance diet as a reference group. The rest of the mice (n=30)were switched to an energy-dense high-fat diet (HFD; 45 kcal% fat from lard, 20 kcal% protein, 35kcal% carbohydrate; D12451, Research diets, New Brunswick, NJ, USA) to induce obesity, metabolicdysfunction and NAFLD. This diet is characterised by a macronutrient composition that mimics humandiets23-25, and the natural cholesterol content of this diet was not further increased by addition ofsupraphysiological amounts of cholesterol.

extract_protocol:
RNA was isolated from snap-frozen liver tissue samples (left lobe, 24wk) from all mice using RNA-BeeTotal-RNA Isolation Kit (Bio-Connect, Huissen, the Netherlands). RNA concentration was determinedspectrophotometrically using Nanodrop 1000 (Isogen Life Science, De Meern, the Netherlands) andRNA quality was assessed using a 2100 Bioanalyzer (Agilent Technologies, Amstelveen, theNetherlands).
Next-generation RNA sequencing was performed on livers from all mice. For this, RNA was used to generate strand-specific cDNA libraries for Next Generation Sequencing according to the manufacturer's protocol by GenomeScan B.V. (Leiden, the Netherlands; using oligo-dT magnetic beads, mRNA fragmentation, NEBNext Ultra Directional RNA Library Prep Kit of Illumina NEB #E7420S/L resulting in 300-500bp amplified libraries/sample). Libraries were multiplexed, clustered, and sequenced on a NextSeq500 system (Illumina, San Diego, CA, USA, using 1.6 pM of DNA/sample and  NextSeq control software 2.0.2 and ) with a single-read 75 cycles sequencing protocol, 12 million reads per sample and indexing. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17.   Three mice were excluded as biological outliers (described below under statistical analysis), and one mouse (from the HFD + vehicle group) was excluded as a technical outlier (based on principal component analysis of the sequencing data), resulting in: n=10 chow, n=13 HFD+vehicle, n=13 HFD+HC-24 for further statistical analysis of the sequencing data. The number of differentially expressed genes (DEG)between groups was determined using an established statistical analysis procedure (DEseq2 pipeline40). These DEG were determined using a statistical cut-off of p<0.01 for the following two comparisons: HFD+vehicle vs chow; and HFD+HC-24 vs HFD+vehicle. Next, these DEG were used as an input for an upstream regulator analysis through Ingenuity Pathway Analysis suite (IPA; www.ingenuity.com,accessed 2017). This analysis integrates the expression of a multitude of genes downstream from predefined upstream regulators (e.g. transcription factors, signaling proteins, metabolites) thus allowing summation of multiple (small) gene expression changes to provide information on the predicted activation state of such an upstream regulator. A negative Z-score <-2 indicates a predicted reduction in activity based on the direction of gene expression changes of target genes. A positive Z-score>2 indicates activation of the upstream regulator.

treatment_protocol: After 6 weeks of HFD feeding, these mice were matchedinto 2 groups based on body weight, blood glucose and plasma cholesterol levels. From that pointonwards, the HFD+vehicle control group was treated with vehicle (saline), and the HFD+HC-24 groupwas treated with HC-24 (Heel GmbH, Baden-Baden, Germany; full composition shown inSupplemental table 1). Both treatments were provided by intraperitoneal injection 3x weekly (Monday,Wednesday and Friday) at a dose of 1.5 ml/kg body weight.

tag: diet 0-24wk

value: HFD

tag: treatment 7-24wk)


title: HFD7L-s102990-038


title: HFD7L-s102990-037


title: HFD7L-s102990-040


title: HFD7L-s102990-036


title: HFD7L-s102990-034


title: HFD7L-s102990-033


title: HFD7L-s102990-035


title: input_24hpi_Rep1

source_name: input_24hpi GFP+ rep_1


title: HFD7L-s102990-029


title: HFD7L-s102990-032


title: HFD7L-s102990-031


title: HFD7L-s102990-030


title: HFD9L-s102990-025

value: vehicle


title: HFD9L-s102990-022


title: HFD7L-s102990-028


title: HFD9L-s102990-021


title: HFD9L-s102990-024


title: HFD9L-s102990-014


title: HFD9L-s102990-019


title: HFD9L-s102990-018


title: HFD9L-s102990-020


title: HFD9L-s102990-017


title: HFD9L-s102990-013


title: HFD9L-s102990-011


title: HFD9L-s102990-012


title: chow-s102990-010

value: chow


title: chow-s102990-009


title: chow-s102990-008


title: chow-s102990-007


title: hyperloaded rep 3

status: Public on Feb 26 2021

city: Neustadt

first: Claudia

last: Klein

address: Höltystr. 10

institute: Friedrich-Loeffler-Institut, Institute of Farm Animal Genetics

description: Sample 9

data_processing:
Base calling and demultiplexing of transcriptome sequencing reads were performed using the Consensus Assessment of Sequence and Variance (CASAVA) v 1.6 and Novobarcode software.
Reads were mapped to the porcine genome Sscrofa11.1 using JMP Genomics 7.1, allowing two mismatches per read.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Sus scrofa

source_name: ventral annulus fibrosus

extract_protocol:
Annuli fibrosi were flash frozen and RNA was extracted using the RNeasy Fibrous Tissue Mini Kit. The TruSeq RNA sample Prep v2 LS protocol  was used for preparation of mRNA libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: repetitive in vivo manual loads on porcine intervertebral disc

value: hyperloaded

value: ventral annulus fibrosus


title: chow-s102990-004


title: chow-s102990-005


title: chow-s102990-001


title: chow-s102990-006


title: chow-s102990-003


title: HFD9L-s102990-015


title: hyperloaded rep 1

description: Sample 7


title: control rep 6

description: Sample 6

value: control


title: sh-JMJD1C treated rep1

status: Public on Feb 09 2021

city: Luzhou

first: hong

middle: Chuan

last: Zhong

address: Luzhou Sichuan

country: China

institute: Neurosurgery Department, Affiliated Hospital of Southwest Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GENOME_hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: LN-229 glioblastoma cells

extract_protocol:
RNA was harvested using Trizol reagent. VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LN-229 glioblastoma cells


title: control-NC treated rep2


title: control-NC treated rep1


title: F22O5_Liver_RNA-Seq

status: Public on Jan 01 2021

city: Saint Martin d'Hères

first: Stéphane

last: REYNAUD

address: 2233 rue de la piscine

country: France

institute: Grenoble-Alpes University

data_processing:
Reads were filtered based on their length, pairing, and quality using Trimmomatic (v0.32.1)
Cleaned reads were mapped to the Xenopus genome (10.0 assembly) using HISAT2.
The Cufflinks (v0.0.7) tool was applied to HISAT2 alignments to enumerate the number of short reads overlapping the Ensembl annotated genes, for each library
The Cuffmerge (v0.0.6) toll was used to merge transcriptome
Cuffdiff (v0.0.7) toll was used for differential  gene expression  analysis

organism: Xenopus tropicalis

source_name: Liver

extract_protocol:
For each biological replicate, the RNAqueous®-4PCR Kit (Ambion, Austin USA) was used to extract the total RNA from 15 mg of liver according to manufacturer instructions
RNA-seq libraries were prepared using the TruSeq Stranded mRNA sample Prep kit (Illumina, San Diego, USA) and sequenced on an Illumina GAIIx sequencer as 75 bp reads

treatment_protocol: F0 generation exposure from the tadpole to the mature adult stage at a concentration (50 ng.L-1). F Females from F1 and F2 generation were not exposed.

tag: common name

value: tropical clawed frog

tag: generation and f0-treatment

value: F2 generation control

tag: Sex

value: female

value: Liver


title: F22O3_Liver_RNA-Seq


title: F22O4_Liver_RNA-Seq


title: F22O1_Liver_RNA-Seq


title: F12O3_Liver_RNA-Seq

value: F1 generation control


title: sh-JMJD1C treated rep3


title: F12O4_Liver_RNA-Seq


title: F12O2_Liver_RNA-Seq


title: F12O6_Liver_RNA-Seq


title: F12O1_Liver_RNA-Seq


title: chow-s102990-002


title: RF_pCF10dU_10

status: Public on Dec 24 2020

data_processing:
Sequenced reads were trimmed to remove adapter sequences and low-quality bases using the sliding-window option in Trimmomatic
RPKM and Expression values were calculated using Rockhopper
Genome_build: NC_006827
Supplementary_files_format_and_content: wig

source_name: total bacterial cellular RNA

growth_protocol: Overnight bacterial cultures of OG1RF(pCF10) and OG1RF(pCF10ΔprgU) were diluted 1:20 in BHI media and grown for 1 h at 37 °C.

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy kit.  Ribosomal RNA was depleted using a MicrobeExpress kit.  All RNA samples were treated with Turbo DNase (ThermoFisher, rigorous method described by the manufacturer) and submitted to the University of Minnesota Genomics Center for Illumina library prep.
Whole-cell RNA samples were prepared using a non-stranded TruSeq RNAv2 kit, and libraries were size selected to generate inserts of 200 bp. All samples were sequenced as paired-end reads on an Illumina HiSeq 2500 in high output mode (125 bp read length for whole-cell samples).

treatment_protocol: Cells were then induced with 10 ng/mL cCF10 followed by incubation for 1 h at 37 °C.

value: OG1RF pCF10

tag: pheromone

value: 10 ng/mL


title: F22O2_Liver_RNA-Seq


title: RF_pCF10_10


title: RF_pCF10dU_0


title: VE61728: patient with viral encephalitis (VE), patient#VE61728

status: Public on Dec 11 2020

city: Muenster

first: I-Na

last: Lu

state: NRW

address: Domagkstraße 20

department: Department of Pediatric Hematology and Oncology

institute: University Children's Hospital Münster

description: single-cell RNA seq data of a patient with viral encephalitis (VE), patient#VE61728

data_processing:
Raw bcl files were de-multiplexed using the cellranger mkfastq pipeline (cellranger v3.1.0)
Subsequent reads alignments and transcript counting was done individually for each sample using the cellranger count pipeline with standard parameters
 The cellranger aggr pipeline was employed to aggregate samples with mapping normalization to leave each sample with similar sequencing depth per cell.
Genome_build: GRCh38
Supplementary_files_format_and_content: Standard cellranger output format

source_name: CSF

extract_protocol:
CSF samples were collected into round bottom polypropylene tubes and then centrifuged for 10 min at 300 x g. The CSF supernatant was removed and CSF cells were resuspended in 5 ml of X-Vivo15 media (Lonza) and stored at 4°C. The samples were then transported to the laboratory of the Department of Neurology with Institute of Translational Neurology at the University Clinic Münster, Germany for scRNA-seq. Transport time of samples collected in Münster was 10-30 minutes. Transport time of samples collected in Essen was < 60 minutes. Cell suspensions were then centrifuged again for 5 min at 400 x g and then resuspended in 40 μl of media. Out of this volume, 6 μl were used for cell counting and the remaining volume was entirely used for scRNA-seq.
Four Neuro-COVID samples were processed with the Chromium Single Cell 5’ Library & Gel Bead Kit and barcoded, full-length VDJ segments from T cells were enriched from first-strand cDNA via PCR amplification with the Chromium Single Cell VDJ Enrichment Kit, Human T Cell (from 10X Genomics) following the manufacturer’s instructions. Further library preparation was performed using the Chromium Single Cell 5' Library Construction Kit (10X Genomics). Three Neuro-COVID samples were processed with the Chromium Single Cell 3’ Library & Gel Bead Kit and we developed a novel method to sequence antigen receptor information  from 3’ scRNA-seq libraries. The method allows removing the constant region of antigen receptors during enrichment, while maintaining their cell barcode and unique molecular identifier (UMI) information attached to the 3' of the cDNA molecules. In summary, the method involves self-circulating the cDNA library, enriching the VDJ region and re-linearizing. Each step maintains the VDJ region together with the cell barcode and UMI in the same molecule. Sample processing and library preparation was performed according to manufacturer instructions using AMPure XP beads (Beckman Coulter). Sequencing was either carried out on a local Illumina Nextseq 500 using the High-Out 75 cycle kit with a 26-8-0-57 read setup or commercially (Microanaly, China) on a NovaSeq 6000 using the 300 cycle kit with paired end 150 read setup. All the samples were sequenced with a sequencing depth >50,000 reads per cell.

value: CSF-derived leukocytes

tag: diagnosis

value: VE

tag: type of library

value: RNA expression

tag: subject id


title: control-NC treated rep3


title: sh-JMJD1C treated rep2


title: MS90896: patient with multiple sclerosis (MS), patient#MS90896

description: single-cell RNA seq data of a patient with multiple sclerosis (MS), patient#MS90896

tag: tissue

value: MS


title: MS79670: patient with multiple sclerosis (MS), patient#MS79670

description: single-cell RNA seq data of a patient with multiple sclerosis (MS), patient#MS79670


title: MS77654: patient with multiple sclerosis (MS), patient#MS77654

description: single-cell RNA seq data of a patient with multiple sclerosis (MS), patient#MS77654


title: MS76177: patient with multiple sclerosis (MS), patient#MS76177

description: single-cell RNA seq data of a patient with multiple sclerosis (MS), patient#MS76177


title: IIH32190: patient with idiopathic intracranial hypertension (IIH), patient#IIH32190

description: single-cell RNA seq data of a patient with idiopathic intracranial hypertension (IIH), patient#IIH32190 (previously uploaded in GSE138266)

value: IIH


title: VE48279: patient with viral encephalitis (VE), patient#VE48279

description: single-cell RNA seq data of a patient with viral encephalitis (VE), patient#VE48279


title: IIH45044: patient with idiopathic intracranial hypertension (IIH), patient#IIH45044

description: single-cell RNA seq data of a patient with idiopathic intracranial hypertension (IIH), patient#IIH45044 (previously uploaded in GSE138266)


title: IIH85037: patient with idiopathic intracranial hypertension (IIH), patient#IIH85037

description: single-cell RNA seq data of a patient with idiopathic intracranial hypertension (IIH), patient#IIH85037 (previously uploaded in GSE138266)


title: MS25719: patient with multiple sclerosis (MS), patient#MS25719

description: single-cell RNA seq data of a patient with multiple sclerosis (MS), patient#MS25719