title: 2w4w_SS2_146818.66h [SLX-20544.i706_i511]


title: Yorkshire pig omental adipose tissue, lean, rep1

status: Public on Jun 20 2023

type: SRA

city: Chengdu

first: mailin

last: gan

state: Sichuan

address: No. 211, Huimin Road, Wenjiang District, Chengdu, Sichuan, China

country: China

institute: Sichuan Agricultural University

library_source: transcriptomic

data_processing:
Raw sequencing data generated form Illumina NextSeq 500 that pass the Illumina chastity filter are used to the following analysis.
Trimmed reads (trimmed 5', 3'-adaptor bases) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software
The abundance of tRF & tiRNA is evaluated using their sequencing counts and is normalized as counts per million of total aligned reads (CPM). For each tRF & tiRNA, estimated the expression level using the mapped reads number and given an ID. Then the tRF & tiRNA are filtered if CPM less than 20 in all samples.
The CPM value of tRF & tiRNA can be calculated with the formula:CPM =10^6Count/N
Assembly: tRNA sequences of cytoplasmic were downloaded from GtRNAdb. tRNA sequences of mitochondrial were predicted with tRNAscan-SE software.
Supplementary files format and content: An excel file contains the COUNT and CPM values of tsRNAs for each sample.

molecule: total RNA

organism: Sus scrofa

source_name: Omental adipose tissue sample

extract_protocol:
Total RNA extraction was performed using TRIzol reagent (TaKaRa, Japan) according to the manufacturer's instructions.Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, ~134-160 bp PCR amplified fragments were extracted and purified from the PAGE gel. And finally, the completed libraries were quantified by Agilent 2100 Bioanalyzer.
Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, ~134-160 bp PCR amplified fragments were extracted and purified from the PAGE gel. And finally, the completed libraries were quantified by Agilent 2100 Bioanalyzer.Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, ~134-160 bp PCR amplified fragments were extracted and purified from the PAGE gel. And finally, the completed libraries were quantified by Agilent 2100 Bioanalyzer.The libraries were denatured and diluted to a loading volume of 1.3ml and loading concentration of 1.8pM.

tag: tissue

value: Omental adipose tissue sample


title: ChIP-Input_DKO-rep1

city: Shanghai

first: Jiwei

last: Chen

address: 130 DongAn Road

institute: Fudan University

library_source: genomic

data_processing:
Raw reads were trimmed by Trim Galore v0.6.6 in paired-end mode.
Trimmed reads were aligned to human hg19 and mouse mm10 genome assemblies using Bowtie v2.4.4 with default parameters.
All unmapped reads, low mapping quality reads (MAPQ < 30), and PCR duplicates were removed using SAMtools v1.12 and MarkDuplicates function of Picard Tools v2.25.5.
Peaks were called using MACS2 v2.2.7.1 with option ‘nomodel’ and peak annotation was performed with R package ChIPseeker v1.28.3.
Normalized bigwig was generated with bamCoverage function from deepTools v3.5.1 using scale factors calculated according to the method in manuscript. Reads mapped to the ENCODE blacklist regions were removed using bedTools v2.30.0
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: The human DLD-1 cells were grown in McCoy's 5A medium (BasalMedia) supplemented with 10% fetal bovine serum (FBS, Yeasen), 1XPenicillin-Streptomycin (Gibco).

extract_protocol:
Cells were crosslinked with 1% formaldehyde at room temperature for 10 min. After quenching and cell lysis, chromatin was sonicated (Qsonica) to appropriate fragment (200-700bp). After sonication, the lysate was centrifuged at maximal speed for 15 min to collect the supernatant and mixed with 20% of lysate from mouse embryonic fibroblast (MEF) cells processed identically as spike-in for normalization.
The DNA samples were purified using Phenol/Chloroform DNA extraction method. Library preparation using the VAHTS Universal Plus DNA Library Prep Kit for Illumina.

tag: cell line

tag: cell type

value: Human colorectal cancer cell

tag: genotype

value: DKO

tag: chip antibody

value: Input

tag: treatment


title: 2w4w_SS2_146818.66h [SLX-20544.i704_i511]

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description:
Smart-Seq2 scRNA-Seq, see metadata for details
SLX20544_scB5Tom_2w_ss2_fcounts.txt

library_source: transcriptomic single cell

data_processing:
library strategy: Smart-Seq2 or 10x Genomics
Smart-Seq2 sequencing reads were aligned to the mouse genome (mm10) using the STAR aligner (version 2.7.3a) with default parameters. Reads mapping to exons were counted with featureCounts (version 2.0.0) using the ENSEMBL v93 annotation. For consistency only a single read was processed for each sample. 10x genomics reads were pre-processed using cellranger (version 3.1.0, reference genome and annotation version 3.0.0) with default settings
Assembly: mm10
Supplementary files format and content: Smart-Seq2 data: count matrices for each fastq file as produced by feature counts  10x Genomics data: annotated, filtered (default cellranger setting) cell x gene matrices in .h5 format (cellranger output file)

organism: Mus musculus

source_name: bone marrow

extract_protocol:
All steps in this section (unless otherwise indicated) were performed on ice, and centrifugation steps performed at 300g, 4°C for 5 min. 8-12 weeks old mice carrying the Hoxb5-Cre and the Rosa26-LoxP-STOP-LoxP-tdTomato constructs were treated with 7 daily injections of tamoxifen and sacrificed at indicated time points. Bone marrow cells were extracted from ilia, tibiae and femura by grinding with mortar and pestle in PBS supplemented with 2% Fetal Bovine Serum (cell buffer). The suspension was filtered through a 50µm filter, centrifuged and resuspended in 3 ml of cell buffer. Red blood cells were removed using the ammonium chloride solution: 5 ml of 0.8% Ammonium Chloride (StemCell Tech. 07800) was added to the suspension and incubated for 10 min with intermittent mixing. Afterwards cells were diluted with 7 ml of cell buffer, centrifuged and resuspended in 1 ml of cell buffer. Subsequently, lineage depletion was performed as follows: added 20 µl of the EasySep mouse haematopoietic progenitor cell isolation cocktail (Stem Cell Technologies 19856), incubated for 15 min, added 30 µl magnetic particles, incubated for 10 min, added 1.5 ml of cell buffer and placed tubes in a magnet, incubated for 3 min at room temperature and eluted cells twice (with additional 2.5 ml of cell buffer). Afterwards, cells were centrifuged, resuspended in 200 µl of cell buffer and stained with the antibody panel as follows: antibody mix was added, cells were incubated for 30 min, washed with 2 ml of cell buffer, centrifuged, reuspended in 200 µl cell buffer. For the secondary staining Streptavidin-BV510 was added, cells were washed with 2 ml of cell buffer, centrifuged and resuspended in 1000 µl of cell buffer supplemented with 7AAD. Afterwards cells were sorted with BD influx sorter into either 96 well plates containing 2.3 µl lysis buffer (for the Smart-Seq2 protocol) or 100 µl of PBS with 0.04% BSA in eppendorf tubes ('droplet buffer') when used for the 10x Genomics scRNA-Seq protocol. The Smart-Seq2 plates were vortexed, centrifuged at 800g for 2 min and stored at -80°C. Antibodies and fluorochromes used: Mouse haematopoietic progenitor cell isolation cocktail (Stem Cell Technologies 19856), CD48-APC (Thermo-Fischer 17-0481-82), c-Kit-APC/Cy7 (Biolegend 105826), Sca1-BV421 (Biolegend 108133) and CD150-PE/Cy7 (Biolegend 115914), Streptavidin-BV510 (Biolegend 405234), 7AAD (Thermo Fischer A1310).
Smart-Seq2:
When cell numbers were limiting single cells were profiled with a modified version of the Smart-Seq2 protocol rather than 10x Genomics kit. Single cells were sorted into 96-well plates with 2.3 µl lysis buffer containing 0.115 µl of SUPERase-In RNase Inhibitor at 20 U/µl concentration (ThermoFisher AM2694) and 0.23 µl of 10% Triton X-100 solution (Sigma 93443), plates were vortexed and stored at -80°C. After thawing 2 µl of the annealing solution (0.1 µl of ERCC RNA Spike-In solution (1:300,000 dilution) Thermo-Fisher 4456740), 0.02 µl of the oligo-dT primer (100 µM stock concentration) and 1 µl of dNTP (10 mM stock concentration)) was added. The plate was incubated at 72°C for 3 min, cooled down on ice and reverse transcription was performed by adding 5.7 µl of RT buffer (0.1 µl of Maxima H minus reverse transcriptase at 200 U/µl concentration (ThermoFischer EP0752), 0.25 µl of SUPERase-In RNAse Inhibitor at 20 U/µl concentration, 2 µl of the Maxima enzyme buffer, 0.2 µl of TSO oligo at 100 µM concentration, 1.875 µl of PEG 8000 solution (Sigma P1458) at 40% v/v concentration and 1.275 µl water) and incubation at 42°C for 90 min followed by incubation at 70°C for 15 min. Immediately after, cDNA was amplified by PCR by adding 1 µl of the Terra PCR Direct Polymerase (1.25 U/µl, Takara 639270), 25 µl of the Terra PCR Direct buffer and 1 µl of the ISPCR primer (10 µM stock concentration) to a total volume of 50 µl using the following PCR conditions: 98°C for 3 min, 98°C for 15 s, 65°C for 30 s, 68°C for 4 min (21 cycles), 72°C for 10 min. The amplified cDNA was purified using AMPure XP beads (Beckman A63882), quantified using the PicoGreen assay (ThermoFischer P7589) and used for Nextera library preparation. The libraries were generated using either a standard protocol (batch 7d) or modified protocol (batches 3d7d, 2w4w and 3dr2), see the corresponding metadata) described below. No obvious batch effects were observed among cells analysed with either of the protocols.
The standard Nextera protocol: cDNA was diluted to approximately 50-150 pg/µl and 1.25 µl of the solution was used, 2.5 µl of Tagment DNA buffer 1.25 µl of Amplicon Tagment Mix (Nextera XT kit, Illumina FC-131-1096) were added, samples were incubated at 55°C for 10 min, and the reaction was stopped by addition of 1.25 µl of NT buffer. Tagmentation products were amplified by PCR by adding 1.25 µl of each N and S primers (Illumina Nextera XT 96-index kit FC-131-1002) and 3.75 µl of NPM solution and using the following thermocycler settings: 72°C 3 min, 95°C 30 s, 12 cycles of 95°C 30s, 55°C 30s, 72°C 60s and a final extension at 72°C for 5 min.
The modified Nextera protocol follows the same principle as the standard Nextera protocol and includes the following steps: cDNA was diluted to approximately 50-150 pg/µl and 1.03 µl of the solution was used, 1.63 µl of Tagment DNA buffer and 0.6 µl Amplicon Tagment Mix was added, samples were incubated at 55°C for 10 min, the reaction was stopped by adding 0.82 µl of NT buffer. Tagmentation products were amplified by adding 1.23 µl of each N and S primers (as above but diluted 5 times), 2.3 µl of Phusion HF buffer (ThermoFischer F530L), 0.1 µl of dNTP (25 mM stock concentration), 0.07 µl of Phusion polymerase and 2.5 µl of water and using the following thermocycler settings: 72°C 3 min, 98°C 3 min s, 12 cycles of 98°C 10s, 55°C 30s, 72°C 30s and a final extension at 72°C for 5 min.
Libraries were sequenced using the Illumina Hiseq4000 or NovaSeq instruments, obtaining approximately 100-200 mln reads per 96 cells.
10X genomics:
For the 10x Genomics scRNA-Seq protocol up to 20,000 cells were pooled in pairs corresponding to male and female animals, centrifuged and resuspended in a volume of droplet buffer optimal for recovery of up to 10,000 cells and immediately processed with the 10x Genomics Single Cell 3' v3 protocol following the manufacturer's instructions.
Libraries were sequenced using the Illumina NovaSeq instrument, obtaining at least 20,000 reads per cells.

treatment_protocol: Mice were treated with tamoxifen to induce a persistent fluorescent label, cells were harvested at indicated time intervals

value: bone marrow

value: Lin-negative, (cKit OR Sca1)-positive

value: WT


title: ECS+SST WT cells - Rep 1

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

country: USA

institute: New York University, NYU Langone Medical Center

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped to mm10 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig

source_name: Somatosensory cortex S1

extract_protocol:
Animals were placed un light sediation and perfused with ice cold ACSF, brains were harvested, S1 cortex was dissected and subjected to light pronase digestion prior to  mechanical dissociation with flame polished pipettes. Samples were filtered and subjected to FACS to isolate SST interneurons from the cortex.
The NYU Genome Technology Center constructed the libraries followed their standard protocol

treatment_protocol: Samples with 'ECS+' were extracted from animals who had been subjected to electroconvulsive shock, permitting in vivo activity-dependent changes within select neurons

value: SST interneuron

tag: strain

value: Swiss Webster+C57BL/6+C57BL/6J-A

tag: age


title: ChIP-Input_CTR-rep2

value: CTR


title: 2w4w_SS2_146818.66h [SLX-20544.i703_i511]


title: SST WT cells - Rep 1


title: ECS+SST conditionaldoubleKO Nova1Nova2 - Rep 4

value: conditionaldoubleKO Nova1Nova2


title: ChIP-Input_CTR-rep1


title: ECS+SST conditionaldoubleKO Nova1Nova2 - Rep 3


title: ChIP-H3K4me1_WT


title: 2w4w_SS2_146818.66h [SLX-20544.i702_i511]


title: 2w4w_SS2_146818.66h [SLX-20544.i701_i511]


title: ChIP-H3K27ac_WT


title: ECS+SST conditionaldoubleKO Nova1Nova2 - Rep 2


title: 2w4w_SS2_146818.66h [SLX-20544.i715_i510]


title: ECS+SST conditionaldoubleKO Nova1Nova2 - Rep 1


title: Rh30 sgDNAJC17 repl C

city: San Francisco

first: Amit

middle: J

last: Sabnis

state: CA

address: 1550 4th Street

institute: University of California, San Francisco

data_processing:
Sequence reads were trimmed using Trimmomatic v.0.36.
Reads were mapped to the GRCh38 reference genome from ENSEMBL using STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: GRChg38
Supplementary files format and content: tab-delimited text file containing raw counts for individual genes for each sample

growth_protocol: Cells were grown in RPMI-1640 with 10% FBS and 1x penicillin/streptomycin in a 37 degree C incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using RNEasy kits (Qiagen).  Between 2 to 10 micrograms of RNA were used for library preparation.
After poly-A selection for mRNA enrichment, libraries were prepared using Illumina kits.

treatment_protocol: Cells were transduced with lentiviral particles using 1x polybrene, followed by selection with puromycin for 72 hours.

value: Rhabdomyosarcoma

value: parental


title: Rh30 +JC17-RRM sgDNAJC17 repl A


title: Rh30 sgDNAJC17 repl B


title: Rh30 +JC17-RRM sgDNAJC17 repl C


title: Rh30 +JC17-RRM sgDNAJC17 repl B


title: 2w4w_SS2_146818.66h [SLX-20544.i714_i510]


title: Rh30 sgDNAJC17 repl A


title: SST conditionalKO Nova2 - Rep 4

value: conditionalKO Nova2


title: CUTTag-XRN2_DKO

data_processing:
library strategy: CUT&Tag
Adapters and low-quality reads were trimmed and resulting reads were aligned to human hg19 genome using Bowtie v2.4.4 with default parameters.
For quantitative comparison, the reads were also aligned to the E. coli genome by Bowtie v2.4.4 with the options ‘--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant -I 10 -X 700’.
Duplicated reads were removed with Picard Tools v2.25.5 and reads were shifted to compensate for the offset in tagmentation site relative to the Tn5 binding site using the alignmentSieve function of deepTools v3.5.1. Reads counts adjusted to total reads aligned to E. coli genome using deepTools v3.5.1
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
DLD-1 cells were harvested by Accutase (Thermo Fisher Scientific) to avoid over-digestion. For a single R-loop CUT&Tag, half a million cells were typically used to obtain sufficient DNA extraction for library construction. The cells were centrifuged (600 g, 3 min) at room temperature, washed twice with 800 μl of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1x protease inhibitor), and finally resuspended with 100 μl of wash buffer in low-retention PCR tubes. The concanavalin A (ConA)-coated magnetic beads (Smart-Lifesciences) were activated in advance and resuspended with the same volume of the binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 10 μl of activated ConA beads were added to 5 x105 cells with incubation for 10 minutes under gentle rotation. The bead-bound cells were magnetized to remove the liquid with a pipettor and resuspended in 50 μl of antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1x protease inhibitor, 0.05% digitonin, 0.01% NP-40, 2 mM EDTA). Next, 1 μg of S9.6 (Active Motif) was added to combine DNA-RNA hybrid by rotating at 4 °C overnight. 10 μg of RNase H (ThermoFisher Scientific) was added with S9.6 to cleavage DNA-RNA hybrid in negative control. The bead-bound cells were washed three times by dig-wash buffer (antibody buffer without 2 mM EDTA) to remove the unbound antibody. Mix pAG-Tn5 adapter complex in dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1 x protease inhibitors, 0.01% digitonin, 0.01% NP-40) to a final concentration of 0.2 μM. The bead-bound cells were resuspended in 100 μl of pAG-Tn5 mix and incubated at room temperature for 1 h followed by removing the supernatant. After adequate washing, the tagmentation reaction was performed in 40 μl of tagmentation buffer (10 mM TAPS-KOH pH 8.3, 10 mM MgCl2, 1% DMF) at 37 °C for 1 h. Next, 1.5 μl of 0.5 M EDTA, 0.5 μl of 10% SDS and 1 μl of 20 mg mL-1 protease K were added to stop the reaction. Following 1 h incubation at 55 °C, DNA extraction was purified using VAHTS DNA Clean Beads (Vazyme), and eluted in 10 μl of 0.1% Tween-20. The eluent is mixed with10 U of Bst 2.0 WarmStart DNA polymerase (NEB) and 1 x Q5 polymerase reaction buffer (NEB) in a 20-μl reaction system. The reaction was completed at 65 °C for 30 minutes and then at 80 °C for 20 minutes to inactivate the Bst 2.0 WarmStart DNA polymerase.
The purified DNA was amplified by Q5 high-fidelity DNA polymerase (NEB) with a universal i5 primer and a uniquely barcoded i7 primer. The exact PCR cycles were estimated by qPCR before amplification. PCR amplification with 13-14 cycles should yield enough quantity of library for sequencing. After library size-selection with 0.56-0.85 VAHTS DNA Clean Beads with library sizes ranging from 200 to 700 bp, the products were then either analyzed by qPCR or subjected to sequence on NovaSeq 6000 platform (Mingma Technologies Co., Ltd.)

tag: antibody


title: CUTTag-XRN2_CTR


title: 2w4w_SS2_146818.66h [SLX-20544.i712_i510]


title: Rh30 sgCTL repl C

value: sgCTL


title: SST conditionalKO Nova2 - Rep 3


title: CUTTag-Rloop_Vector-shNonT-rep2

value: Vector-shNonT

value: Rloop


title: Choroid plexus HFD 4

city: Copenhagen

first: Søren

middle: Norge

last: Andreassen

state: Region Hovedstaden

address: Blegdamsvej 3

department: Department of Neuroscience

country: Denmark

institute: University of Copenhagen

data_processing:
QC quality control and adapter removal was done by Novogene (UK) Company Limited.
Mapping to reference genome (rattus norvegicus Rnor_6.0.104) using STAR (v. 2.7.2a) (--sjdbOverhang 100 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --quantMode TranscriptomeSAM)
Abundance quantified by RSEM (v. 1.3.3) (--bam --paired-end --forward-prob 0)
Assembly: Rnor_6.0 (rn6) v.104
Supplementary files format and content: tab-delimited text files for gene abundance for each samples in TPM and FPKM

organism: Rattus norvegicus

source_name: Choroid plexus

extract_protocol:
Extraction was performed by Novogene (UK) Company Limited.
Done by Novogene (UK) Company using NEB Next® Ultra™ RNA Library Prep Kit, and sequenced on Illumina NovaSeq 6000, paired-end 150 bp, 12Gb output.

value: Wistar

value: 27 weeks

tag: Sex

value: Female

value: Choroid plexus

tag: animals pooled

value: High fat diet


title: CUTTag-Rloop_Vector-shNonT-rep1

value: Human colorectal cancer cell


title: Rh30 sgCTL repl B


title: 2w4w_SS2_146818.66h [SLX-20544.i711_i510]

value: bone marrow

value: Lin-negative, (cKit OR Sca1)-positive

value: WT


title: 2w4w_SS2_146818.66h [SLX-20544.i710_i510]


title: SST conditionalKO Nova2 - Rep 2

value: SST interneuron

value: Swiss Webster+C57BL/6+C57BL/6J-A


title: ES8 +JC17-RRM sgDNAJC17 repl C

value: Ewing sarcoma


title: SST conditionalKO Nova2 - Rep 1


title: CUTTag-Rloop_Vector-shINTS11-rep2


title: Rh30 sgCTL repl A

value: Rhabdomyosarcoma

value: parental


title: 2w4w_SS2_146818.66h [SLX-20544.i707_i510]


title: SST conditionaldoubleKO Nova1Nova2 - Rep 4

value: conditionaldoubleKO Nova1Nova2


title: ES8 +JC17-RRM sgDNAJC17 repl B


title: CUTTag-Rloop_Vector-RNaseH1

value: Vector


title: SST conditionaldoubleKO Nova1Nova2 - Rep 3


title: ES8 +JC17-RRM sgDNAJC17 repl A


title: SST conditionaldoubleKO Nova1Nova2 - Rep 2


title: 2w4w_SS2_146818.66h [SLX-20544.i705_i510]


title: ES8 sgDNAJC17 repl B


title: SST conditionaldoubleKO Nova1Nova2 - Rep 1


title: ES8 sgDNAJC17 repl C


title: CUTTag-Rloop_RNaseH1

value: CTR

value: Rloop


title: 2w4w_SS2_146818.66h [SLX-20544.i703_i510]


title: 2w4w_SS2_146818.66h [SLX-20544.i704_i510]


title: ES8 sgDNAJC17 repl A


title: 2w4w_SS2_146818.66h [SLX-20544.i702_i510]


title: CUTTag-Rloop_INTS11-WT-OE-shNonT-rep2


title: CUTTag-Rloop_INTS11-WT-OE-shINTS11-rep2


title: SST conditionalKO Nova1 - Rep 4

value: conditionalKO Nova1


title: CUTTag-Rloop_INTS11-WT-OE-shNonT-rep1


title: SST conditionalKO Nova1 - Rep 3


title: CUTTag-Rloop_Vector-shINTS11-rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i701_i510]


title: ES8 sgCTL repl C

value: sgCTL


title: 2w4w_SS2_146818.66h [SLX-20544.i706_i510]


title: SST conditionalKO Nova1 - Rep 2


title: 2w4w_SS2_146818.66h [SLX-20544.i715_i508]


title: SST conditionalKO Nova1 - Rep 1


title: CUTTag-Rloop_INTS11-E203Q-OE-shNonT-rep2


title: 2w4w_SS2_146818.66h [SLX-20544.i714_i508]


title: CUTTag-Rloop_INTS11-E203Q-OE-shNonT-rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i712_i508]


title: ES8 sgCTL repl A


title: 2w4w_SS2_146818.66h [SLX-20544.i711_i508]


title: CUTTag-Rloop_INTS11-E203Q-OE-shINTS11-rep2


title: ZIKV_MOI-1_mock_1

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

data_processing:
rRNA was removed using Bowtie2 (version 2.2.5)
Reads then were mapped to the human genome (NCBI 37.1) using STAR (2.4.2)
gene counts with ht-seq (0.6.0)
Assembly: NCBI 37.1
Supplementary files format and content: text files with counts

source_name: Testis

growth_protocol: Human Sertoli cells (hSeC) purchased from Lonza (MM-HSE-2305) were propagated in DMEM/F-12 media (ratio of 1:1) with HEPES, L-Gln, 100 units/mL Pen-Strep, and 5% untreated FBS. Full procedure described in doi: 10.1128/JVI.00623-17

extract_protocol:
Total RNA was purified from ZIKV (PRVABC59)-infected hSeC at 12, 24, 48, and 72 hours after infection as well as from mock-infected hSeC at 24 hours (control), in triplicates for each time point using RNeasy kit (QIAGEN)
Total RNA-seq libraries were constructed from 100 ng Total RNA input using the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) with TruSeq HT Adapters.

treatment_protocol: Cells were infected at MOI 1 for 1 hr at 37 °C followed by 2 washes and replaced with fresh media. Full procedure described 10.1128/JVI.00623-17

value: Testis

value: Low-passage primary human Sertoli cells (hSeC) purchased from Lonza (MM-HSE-2305)

value: Sertoli

value: Mock

tag: replicate

value: Rep 1


title: CUTTag-Rloop_INTS11-E203Q-OE-shINTS11-rep1

value: Human colorectal cancer cell


title: ZIKV_MOI-1_mock_3

value: Rep 3


title: CUTTag-Rloop-IgG_CTR


title: 2w4w_SS2_146818.66h [SLX-20544.i710_i508]

value: bone marrow

value: Lin-negative, (cKit OR Sca1)-positive

value: WT


title: ZIKV_MOI-1_72H_3

value: ZIKV infected MOI-1

tag: time point


title: CUTTag-Rloop_INTS11-WT-OE-shINTS11-rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i706_i508]


title: 2w4w_SS2_146818.66h [SLX-20544.i707_i508]


title: CUTTag-Rloop_dTAG-6h-rep2


title: CUTTag-Rloop_dTAG-6h-rep1


title: HST3/4-LOG (for HST3/4), 1

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

description:
for GEO hst3 hst4 data plus controls.txt
lane8071_ACAGTG_PC_1_hst3_4_log_1_L001_R64-1-1_2Micron_hisat2.bam

data_processing:
After adapter and quality trimming using Trim Galore (v0.6.6), RNA-seq data was mapped to yeast genome R64-1-1 using HISAT2 v2.1.0 (Kim et al., 2019) by the Babraham Institute Bioinformatics Facility. Mapped data was imported into SeqMonk v1.47.0
Assembly: R64-1-1
Supplementary files format and content: Quantified for log2 total reads mapping to the antisense strand of annotated open reading frames (opposite strand specific libraries) including probes to the rDNA intergrenic regions. Read counts were adjusted by Size Factor normalisation for the full set of quantified probes.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: yeast cell

extract_protocol:
[Sample collection protocol]  All cells were grown in YPD media (2% peptone, 1% yeast extract, 2% glucose) at 30°C with shaking at 200 rpm. Media components were purchased from Formedium and media was sterilised by filtration. MEP experiments were performed as described with modifications (Cruz et al., 2018): cells were inoculated in 4 ml YPx (where x is the sugar) and grown for 6-8 hours then diluted in 25 ml YPD and grown for 16-18 hours to 0.2-0.6x107 cells/ml in 50 ml Erlenmeyer flasks. 0.125x107 cells per aged culture were harvested by centrifugation (15 s at 13,000 g), washed twice with 125 µl PBS and re-suspended in 125 µl of PBS containing ~3 mg/ml Biotin-NHS (Pierce 10538723). Cells were incubated for 30 min on a wheel at room temperature, washed once with 125 µl PBS and re-suspended in 125 µl YPD then inoculated in 125 ml YPD at 1x104 cells/ml in a 250 ml Erlenmeyer flask (FisherBrand FB33132) sealed with Parafilm. 1 µM β-estradiol (from stock of 1 mM Sigma E2758 in ethanol) was added after 2 hours. An additional 0.125x107 cells were harvested from the log phase culture while biotin labelling reactions were incubating at room temperature. Cells were harvested by centrifugation for 1 min, 4600 rpm, immediately fixed by resuspension in 70% ethanol and stored at -80°C.
Percoll gradients (1-2 per sample depending on harvest density) were formed by vortexing 1 ml Percoll (Sigma P1644) with 110 µl 10x PBS in 2 ml tubes and centrifuging 15 min at 15,000 g, 4 °C. Ethanol fixed cells were defrosted and washed once with 1 volume of cold PBSE (PBS + 2 mM EDTA) before resuspension in ~100 µl cold PBSE per gradient and layering on top of the pre-formed gradients. Gradients were centrifuged for 4 min at 2,000 g, 4 °C, then the upper phase and brown layer of cell debris removed and discarded. 1 ml PBSE was added, mixed by inversion and centrifuged 1 min at 2,000 g, 4 °C to pellet the cells, which were then re-suspended in 1 ml PBSE per time point (re-uniting samples where split across two gradients). 25 µl Streptavidin microbeads (Miltenyi Biotech 1010007) were added and cells incubated for 5 min on a wheel at room temperature. Meanwhile, 1 LS column per sample (Miltenyi Biotech 1050236) was loaded on a QuadroMACS magnet and equilibrated with cold PBSE in 4 °C room. Cells were loaded on columns and allowed to flow through under gravity, washed with 1 ml cold PBSE and eluted with 1 ml PBSE using plunger. Cells were re-loaded on the same columns after re-equilibration with ~500 µl PBSE, washed and re-eluted, and this process repeated for a total of three successive purifications. After addition of Triton X-100 to 0.01% to aid pelleting, cells were split into 2 fractions in 1.5 ml tubes, pelleted 30 s at 20,000 g, 4 °C, frozen on N2 and stored at -70 °C.
Cells were re-suspended in 50 µl Lysis/Binding Buffer (from mirVANA kit, Life Technologies AM1560), and 50 µl 0.5 µm zirconium beads (Thistle Scientific 11079105Z) added. Cells were lysed with 5 cycles of 30 s 6500 ms-1 / 30 s ice in an MP Fastprep bead beater or for 3 min at power 12 in a Bullet Blender (ThermoFisher) in cold room, then 250 µl Lysis/Binding buffer added followed by 15 µl miRNA Homogenate Additive and cells were briefly vortexed before incubating for 10 minutes on ice. 300 µl acid phenol : chloroform was added, vortexed and centrifuged 5 min at 13,000 g, room temperature before extraction of the upper phase. 400 µl room temperature ethanol and 2 µl glycogen (Sigma G1767) were added and mixture incubated for 1 hour at -30 °C before centrifugation for 15 minutes at 20,000 g, 4 °C. The pellet was washed with cold 70% ethanol and re-suspended in 10 µl water. 1 µl RNA was glyoxylated and analyzed on a BPTE mini-gel, and RNA was quantified using a PicoGreen RNA kit (Life Technologies R11490) or Qubit® RNA HS Assay Kit. 150 ng RNA was used to prepare libraries using the NEBNext Ultra II Directional mRNAseq kit with poly(A)+ purification module (NEB E7760, E7490) as described with modifications: Reagent volumes for elution from poly(T) beads, reverse transcription, second strand synthesis, tailing and adaptor ligation were reduced by 50%; libraries were amplified for 13 cycles using 2 µl each primer per 50 µl reaction before two rounds of AMPure bead purification at 0.9x and elution in 11 µl 0.1x TE prior to quality control using a Bioanalyzer HS DNA ChIP (Agilent) and quantification using a KAPA Library Quantification Kit (Roche).

value: yeast cell

value: MEP diploid wild type (for HST3/4)

tag: media

value: YPD

value: log


title: HST3/4-48h (for HST3/4), 1

description:
for GEO hst3 hst4 data plus controls.txt
lane8071_CAGATC_PC_3_hst3_4_aged_1_L001_R64-1-1_2Micron_hisat2.bam


title: ES8 sgCTL repl B

value: Ewing sarcoma

value: parental


title: 2w4w_SS2_146818.66h [SLX-20544.i705_i508]


title: HST3/4-LOG (for HST3/4), 2

description:
for GEO hst3 hst4 data plus controls.txt
lane8199_GCCAAT_2_hst3_4_log_2_L001_R64-1-1_2Micron_hisat2.bam


title: CUTTag-Rloop_dTAG-24h-rep2

value: Rloop


title: ZIKV_MOI-1_72H_1

value: Testis

value: Low-passage primary human Sertoli cells (hSeC) purchased from Lonza (MM-HSE-2305)


title: WT-48h (for HST3/4)

description:
for GEO hst3 hst4 data plus controls.txt
lane8071_CTAGCT_PC_23_wt_aged_batch_4_L001_R64-1-1_2Micron_hisat2.bam


title: WT-LOG (for HST3/4)

description:
for GEO hst3 hst4 data plus controls.txt
lane8071_CCAACA_PC_21_wt_log_batch_4_L001_R64-1-1_2Micron_hisat2.bam


title: ZIKV_MOI-1_48H_3

value: Sertoli


title: 2w4w_SS2_146818.66h [SLX-20544.i704_i508]


title: ZIKV_MOI-1_mock_2

value: Mock

value: Rep 2


title: HST3/4-48h (for HST3/4), 2

description:
for GEO hst3 hst4 data plus controls.txt
lane8199_ACTTGA_4_hst3_4_aged_2_L001_R64-1-1_2Micron_hisat2.bam


title: CUTTag-Rloop_dTAG-24h-rep1

value: Human colorectal cancer cell


title: ZIKV_MOI-1_48H_2


title: ZIKV_MOI-1_72H_2


title: 2w4w_SS2_146818.66h [SLX-20544.i703_i508]

value: bone marrow


title: CUTTag-Rloop_DMSO-RNaseH1-rep2

value: CTR


title: MUS81-48h, 1

description:
for GEO mus81 data plus controls.txt
lane8444_GTAGAG_6-A_41-MUS81-48h_L001_R64-1-1_2Micron_hisat2.bam

value: MEP diploid mus81 mutant


title: ZIKV_MOI-1_48H_1

value: ZIKV infected MOI-1

value: Rep 1


title: 2w4w_SS2_146818.66h [SLX-20544.i701_i508]

value: Lin-negative, (cKit OR Sca1)-positive

value: WT


title: CUTTag-Rloop_DMSO-RNaseH1-rep1


title: ZIKV_MOI-1_24H_2


title: MUS81-24h, 2

description:
for GEO mus81 data plus controls.txt
lane8444_ATGTCA_4-A_41-MUS81-24h_L001_R64-1-1_2Micron_hisat2.bam

value: yeast cell

value: YPD


title: ZIKV_MOI-1_24H_3

value: Rep 3


title: MUS81-24h, 1

description:
for GEO mus81 data plus controls.txt
lane8444_GAGTGG_10-A_42-MUS81-24h_L001_R64-1-1_2Micron_hisat2.bam


title: CUTTag-Rloop_DMSO-rep2

value: Rloop

value: DMSO


title: 2w4w_SS2_146818.66h [SLX-20544.i714_i507]


title: MUS81-LOG, 2

description:
for GEO mus81 data plus controls.txt
lane8444_GTTTCG_8-A_42-MUS81-LOG_L001_R64-1-1_2Micron_hisat2.bam

value: log


title: MUS81-LOG, 1

description:
for GEO mus81 data plus controls.txt
lane8444_AGTCAA_2-A_41-MUS81-LOG_L001_R64-1-1_2Micron_hisat2.bam


title: ZIKV_MOI-1_24H_1

value: Testis

value: Low-passage primary human Sertoli cells (hSeC) purchased from Lonza (MM-HSE-2305)

value: Sertoli


title: 2w4w_SS2_146818.66h [SLX-20544.i715_i507]


title: CUTTag-Rloop_DMSO-rep1

value: Human colorectal cancer cell


title: MUS81-48h, 2

description:
for GEO mus81 data plus controls.txt
lane8444_ATGAGC_12-A_42-MUS81-48h_L001_R64-1-1_2Micron_hisat2.bam


title: CUTTag-Rloop_DKO-rep1

value: DKO


title: CUTTag-Rloop_DKO-rep2


title: ZIKV_MOI-1_12H_2

value: Rep 2


title: ZIKV_MOI-1_12H_3


title: 2w4w_SS2_146818.66h [SLX-20544.i711_i507]

value: bone marrow


title: WT-48h (for MUS81), 1

description:
for GEO mus81 data plus controls.txt
lane8444_CCGTCC_5-A_41-WT-48h_L001_R64-1-1_2Micron_hisat2.bam

value: MEP diploid wild type (for MUS81)


title: ZIKV_MOI-1_12H_1

value: ZIKV infected MOI-1

value: Rep 1


title: 2w4w_SS2_146818.66h [SLX-20544.i702_i508]

value: Lin-negative, (cKit OR Sca1)-positive

value: WT


title: 2w4w_SS2_146818.66h [SLX-20544.i710_i507]


title: CUTTag-Rloop_CTR-rep2

value: CTR


title: WT-24h (for MUS81), 2

description:
for GEO mus81 data plus controls.txt
lane8444_AGTTCC_3-A_41-WT-24h_L001_R64-1-1_2Micron_hisat2.bam

value: yeast cell

value: YPD


title: H3K27ac_HiChIP.OIS.Rep2.Batch3

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

data_processing:
Alignment: data were aligned using bowtie2 through the HiC-Pro pipeline (default parameters, hg19 assembly)
Filtering: unpaired mates and multi-mappers were filtered out through the HiC-Pro pipeline (default parameters)
Mate classification: aligned mate-pairs were classified into unique, valid, and cis- interactions using the HiC-Pro pipeline (default parameters)
Loop identification: contact maps were constructed at default resolution and genomic binning, and maps were ICE adjusted through HiC-Pro (default parameters).
Enhancer clique identification: in-house R scripts were used to identify connected graphs of cis-looped anchor points and to assign genes to these cliques by loops at their promoters.
Assembly: GRCh37/hg19
Supplementary files format and content: BED files show the hg19 coordinates of each looped anchor point, or "node," identified in either proliferating or OIS cells
Supplementary files format and content: Tab-separated values files (*clique.hg19.tsv) show enhancer cliques, with (i) the clique ID, (ii) the # anchors, (iii) the gene targets, separated by semicolons, and (iv) the anchor points/nodes, separated by semicolons, in columns 1-4 respectively. If a clique targets no genes, the gene column has "nonpromoter."

growth_protocol: Primary IMR90 fibroblasts were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, and 100 μg/mL streptomycin (Invitrogen). Cells were routinely tested for mycoplasma. The cells were cultured under physiological oxygen (3%), and were used within population doubling of 35.

extract_protocol:
The HiChIP experiments were carried out following the protocol previously described (Mumbach et al, Nature Methods, 2016), using the H3K27ac antibody (Abcam, ab4729). Briefly, 10 million cells were crosslinked using 1% formaldehyde for 10 minutes, and then sonicated for 6 minutes. After the immunoprecipitation step, DNA were purified and then quantified using Qubit. The amount of Tn5 used and the number of PCR cycles were determined as previously described based on Qubit quantification. After PCR amplification, size selection was performed using Ampure beads.
Libraries were sequenced in paired-end mode on a NextSeq 550 instrument.

treatment_protocol: Retrovirus from retroviral vector encoding HRasV12 was used to infect cells. Following hygromycin selection, cells were cultured for 7 or more days.

tag: population doubling

value: Abcam ab4729

value: OIS


title: 2w4w_SS2_146818.66h [SLX-20544.i707_i507]


title: CUTTag-Rloop_CTR-rep1

value: Rloop


title: CUTTag-rH2AX_sgCtr-rep2

value: sgCtr


title: 2w4w_SS2_146818.66h [SLX-20544.i706_i507]


title: H3K27ac_HiChIP.OIS.Rep2.Batch2


title: WT-24h (for MUS81), 1

description:
for GEO mus81 data plus controls.txt
lane8444_CGTACG_9-A_42-WT-24h_L001_R64-1-1_2Micron_hisat2.bam


title: WT-LOG (for MUS81), 2

description:
for GEO mus81 data plus controls.txt
lane8444_GTGAAA_7-A_42-WT-LOG_L001_R64-1-1_2Micron_hisat2.bam

value: log


title: 2w4w_SS2_146818.66h [SLX-20544.i712_i507]

description:
Smart-Seq2 scRNA-Seq, see metadata for details
SLX20544_scB5Tom_2w_ss2_fcounts.txt


title: CUTTag-rH2AX_sgCtr-rep1

value: Human colorectal cancer cell


title: 2w4w_SS2_146818.66h [SLX-20544.i705_i507]


title: H3K27ac_HiChIP.OIS.Rep1.Batch2


title: CUTTag-rH2AX_INTS2KO-rep2


title: WT-48h (for MUS81), 2

description:
for GEO mus81 data plus controls.txt
lane8444_ACTGAT_11-A_42-WT-48h_L001_R64-1-1_2Micron_hisat2.bam


title: 2w4w_SS2_146818.66h [SLX-20544.i703_i507]


title: CUTTag-rH2AX_DKO-rep2

value: DKO


title: H3K27ac_HiChIP.OIS.Rep1.Batch1


title: XIIr<>V 48h  (diploid)

description:
for GEO new translocations.txt
lane8444_GGCTAC_6-48h-JH1726_L001_R64-1-1_2Micron_hisat2.bam

value: MEP diploid a/a Tom70-GFP (no I-SceI) XII<>V translocation diploid


title: CUTTag-rH2AX_INTS2KO-rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i704_i507]

value: bone marrow


title: XIIr<>V 24h  (diploid)

description:
for GEO new translocations.txt
lane8444_CAGATC_4-24h-JH1726_L001_R64-1-1_2Micron_hisat2.bam


title: H3K27ac_HiChIP.Pro.Rep2.Batch3

value: Control


title: XIIr<>V log  (diploid)

description:
for GEO new translocations.txt
lane8444_TGACCA_2-LOG-JH1726_L001_R64-1-1_2Micron_hisat2.bam


title: 2w4w_SS2_146818.66h [SLX-20544.i702_i507]


title: H3K27ac_HiChIP.Pro.Rep2.Batch2


title: CUTTag-rH2AX_DKO-rep1


title: 2w4w_SS2_146818.66h [SLX-20544.i701_i507]


title: wt GST-V-U 48h  (diploid)

description:
for GEO new translocations.txt
lane8444_ACTTGA_5-48h-JH1725_L001_R64-1-1_2Micron_hisat2.bam

value: MEP diploid a/a Tom70-GFP (no I-SceI) ADE2 pGST-V-U diploid


title: H3K27ac_HiChIP.OIS.Rep2.Batch1


title: CUTTag-rH2AX_CTR-rep2


title: H3K27ac_HiChIP.Pro.Rep2.Batch1


title: wt GST-V-U 24h  (diploid)

description:
for GEO new translocations.txt
lane8444_ACAGTG_3-24h-JH1725_L001_R64-1-1_2Micron_hisat2.bam


title: 2w4w_SS2_146818.66h [SLX-20544.i715_i506]


title: WT-LOG (for MUS81), 1

description:
for GEO mus81 data plus controls.txt
lane8444_CTTGTA_1-A_41-WT-LOG_L001_R64-1-1_2Micron_hisat2.bam

value: MEP diploid wild type (for MUS81)


title: H3K27ac_HiChIP.Pro.Rep1.Batch2


title: 2w4w_SS2_146818.66h [SLX-20544.i712_i506]

value: Lin-negative, (cKit OR Sca1)-positive


title: CUTTag-MTR4_DKO


title: 2w4w_SS2_146818.66h [SLX-20544.i714_i506]

value: WT


title: HFF-tert dox-inducible amiRNA2 8 hpi, +PAA, HSV-1, strain F, US1 deleted, 5ug/ml dox for 24 h, rep2

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

description:
ICP22_plus_dox_rep2
SSRP1 KD

data_processing:
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.7.9
Number of read fragments per gene were determined using featureCounts and gene annotations from Ensembl (version 87 for GRCh37). HSV-1 gene annotations were obtained from GenBank (GenBank accession code: JN555585).
Assembly: GRCh37/hg19
Supplementary files format and content: gene read counts (tsv)

source_name: HFF-tert (telomerase-immortalized), transduced with lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA2)

growth_protocol: Human fetal foreskin fibroblasts transduced with the indicated vectors were cultured in DMEM supplements with 10% FBS, P/S with 1 ug/ml puromycin (no doxycycline).

extract_protocol:
Total RNA was prepared using Trizol + DirectZOL microprep kit (Zymo Research).
TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat
76bp single-end, NextSeq500

treatment_protocol: For the experiment cells were seeded in medium without puromycin but containing 5 ug/ml doxycycline (where indicated) for 24 h prior to harvest. Expression of amiRNA against SSRP1 or of the proteins HA-ICP22 and V5-ICP27 was induced by adding 5 μg/ml doxycycline for 24 h. KCl at a final concentration of 200 mM was added to conditioned medium 24 h after doxycycline induction and cells were harvested by scraping 2 h later.

value: foreskin

value: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line

tag: transduction

tag: time post_infection

value: 8 hpi, +PAA

tag: infection

value: HSV-1, strain F, US1 deleted

value: 5ug/ml doxycycline for 24 h, 350 ug/ml PAA supplemented upon removal of inoculum (8h treatment)


title: H3K27ac_HiChIP.Pro.Rep1.Batch1

tag: cell line

value: Abcam ab4729


title: wt GST-V-U log (diploid)

description:
for GEO new translocations.txt
lane8444_TTAGGC_1-LOG-JH1725_L001_R64-1-1_2Micron_hisat2.bam

tag: cell type

value: yeast cell

value: YPD


title: CUTTag-MTR4_CTR

value: Human colorectal cancer cell

tag: genotype

value: CTR


title: HFF-tert dox-inducible amiRNA1 8 hpi, +PAA, HSV-1, strain F, US1 deleted, 5ug/ml dox for 24 h, rep1

description:
ICP22_plus_dox_rep1
SSRP1 KD

source_name: HFF-tert (telomerase-immortalized), transduced with lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA1)

tag: tissue


title: CT27, Stem, K4me3

city: Kansas City

first: Boryana

last: Koseva

state: MO

address: 2420 Pershing Road

department: CMRI

institute: Children's Mercy Hospital

data_processing:
PhiX  reads were removed using HTStream's (Version 1.3.2) hts_SeqScreener with default parameters.
Duplicates were removed using HTStream's (Version 1.3.2) hts_SuperDeduper (-e 250000).
Adapter sequences were trimmer using HTStream's (Version 1.3.2) hts_AdapterTrimmer (-p 4).
N's were removed using HTStream's (Version 1.3.2) hts_Ntrimmer.
Base quality trimming was performed using HTStream's (Version 1.3.2) hts_QWindowTrim (-w10 -q 20).
Reads shorted than 50bp were remvoed using HTStream's (Version 1.3.2) hts_LengthFilter (-n -m 50).
Reads were aligned to the human genome (GRCh38) using BWA mem (0.7.17-r1188).
Alignments in the ENCODE blacklisted regions were removed using Bedtools (Version 2.30.0).
Peaks were called using MACS3 callpeak (Version 3.0.0a6) with the following parameters: -B -q 0.01.
Assembly: GRCh38.86
Supplementary files format and content: tab-separated narrowPeak files containing coordinates and scores for discovered peaks by MACS3

extract_protocol:
ChIP was performed on a hTSC line,TSCT-1 (CT27), established in our previous study (Okae et al. Cell Stem Cell 2018) using the ChIP Reagents (NIPPON GENE).
The ChIP-seq library was constructed using the Ovation Ultralow System V2 (NuGEN) and sequenced on the Illumina HiSeq 2500 platform (Illumina).
The puromycin resistant gene (PuroR) and Cas9 were PCR amplified from the pGIPZ vector (Open Biosystems) and Alt-R S.p. Cas9 Expression Plasmid (IDT), respectively. PuroR, a T2A element, and Cas9 were cloned into the CS-CA-MCS plasmid (kindly provided by H. Miyoshi, RIKEN BioResource Center, Ibaraki, Japan) using the In-Fusion HD Cloning kit (Takara). The resulting vector was designated as pCS-CA-PuroR-T2A-Cas9. The kanamycin/neomycin resistance gene and the pUC origin were amplified from pCAG-HIVgp (kindly provided by H. Miyoshi), and the human U6 (hU6) promoter was amplified from the pCS-hU6 vector2. The kanamycin/neomycin resistance gene, the pUC origin, the hU6 promoter, 3xFLAG, and a loxP sequence were assembled using the NEBuilder HiFi DNA Assembly Cloning Kit (NEB). An sgRNA targeting the last exon of SNAI1 (target sequence: 5′-CAC CAA GAG TCC GGC TGC TC-3′), a loxP sequence, and a gRNA target sequence (5′-CCC GAG CAG CCG GAC TCT TGG TG-3′; the PAM sequence is underlined), were inserted between the hU6 promoter and 3xFLAG to generate pU6-sgSNAI1-loxP-FLAG-loxP. The Cre recombinase gene was amplified from the Cre Vector (Santa Cruz) and cloned into the pCS-3G vector2 to generate pCS-3G-Cre. Sequences of the primers used for the vector construction are shown in Supplemental Table. pCS-CA-PuroR-T2A-Cas9 was cotransfected with pCMV-VSV-G-RSV-Rev and pCAG-HIVgp (kindly provided by H. Miyoshi) into 293T cells and lentivirus expressing PuroR-T2A-Cas9 was prepared. The lentivirus was transduced into TSCT-1 cells, and Cas9-expressing cells were selected by 2 mg/ml puromycin for two days. The pU6-sgSNAI1-loxP-FLAG-loxP vector was transfected into the Cas9-expressing TSCT-1 cells using an electroporator (CUY21Vitro-EX; BEX) with the following setting: Poration pulse [125 V, 10 ms]; Driving pulse [20 V, 50 ms, 5 pulses]. After 200 mg/ml G418 selection for 5 days, lentivirus expressing Cre was transduced into the cells to delete the kanamycin/neomycin resistant gene, the hU6 promoter, and the sgRNA sequence. Then, single-cell cloning was performed, and clones with an in-frame insertion of 3xFLAG were identified by Sanger sequencing. This knock-in strategy is based on homology-independent targeted integration3. One of the obtained clones had a homozygous in-frame insertion of 3xFLAG (Supplemental Figure) and was used for ChIP-seq.
ChIP was performed on the clone with 3xFLAG-tagged SNAI1 using the ChIP Reagents (NIPPON GENE) and an anti-FLAG antibody (Sigma, Clone #M2). Immunoprecipitation was carried out in IP buffer containing 400 mM NaCl instead of 150 mM to reduce the background signal. The sequencing adapters were a mixture of two adapters (Adapter-T and Adapter-C) in equal amounts4. Adapter-T with a 3’-T overhang was prepared by annealing (5’-CTA CAC GAC GCT CTT CCG ATC TT-3’) and (5’-AGA TCG GAA GAG CAC ACG TCT GAA-3’; 5’ phosphorylated). Adapter-C with a 3’-C overhang was prepared by annealing (5’- CTA CAC GAC GCT CTT CCG ATC TC-3’) and (5’-AGA TCG GAA GAG CAC ACG TCT GAA-3’; 5’ phosphorylated). Adapter-C was added to increase the ligation efficiency. The ChIP-seq library was constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and sequenced on the Illumina HiSeq 2500 platform (Illumina).

tag: source

value: human trophoblast stem cell

tag: cell state

value: stem state trophoblast cell

tag: chip antibody

value: H3K4me3 (MBL, Clone #CMA304)


title: 2w4w_SS2_146818.66h [SLX-20544.i711_i506]

value: bone marrow

tag: treatment


title: 2w4w_SS2_146818.66h [SLX-20544.i710_i506]


title: 2w4w_SS2_146818.66h [SLX-20544.i707_i506]


title: HFF-tert dox-inducible amiRNA2 8 hpi, +PAA, HSV-1, strain F, US1 deleted, no dox, rep2

description:
ICP22_minus_dox_rep2
SSRP1 KD

value: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA2)

value: no doxycycline, 350 ug/ml PAA supplemented upon removal of inoculum (8h treatment)


title: 2w4w_SS2_146818.66h [SLX-20544.i706_i506]

value: Lin-negative, (cKit OR Sca1)-positive

value: WT


title: CUTTag-rH2AX_CTR-rep1

tag: antibody


title: CT27, Stem, K27ac

value: H3K27ac (MBL, Clone #CMA309)


title: CT27, Input


title: 2w4w_SS2_146818.66h [SLX-20544.i705_i506]


title: 2w4w_SS2_146818.66h [SLX-20544.i704_i506]


title: HFF-tert dox-inducible amiRNA1 8 hpi, +PAA, HSV-1, strain F, 5ug/ml dox for 24 h, rep1

description:
Wt_plus_dox_rep1
SSRP1 KD

value: foreskin

value: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line

value: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA1)

value: 8 hpi, +PAA

value: HSV-1, strain F


title: HFF-tert dox-inducible amiRNA1 8 hpi, +PAA, HSV-1, strain F, US1 deleted, no dox, rep1

description:
ICP22_minus_dox_rep1
SSRP1 KD

value: HSV-1, strain F, US1 deleted


title: HFF-tert dox-inducible amiRNA2 8 hpi, +PAA, HSV-1, strain F, 5ug/ml dox for 24 h, rep2

description:
Wt_plus_dox_rep2
SSRP1 KD

value: 5ug/ml doxycycline for 24 h, 350 ug/ml PAA supplemented upon removal of inoculum (8h treatment)


title: CT27, EVT, K4me3

value: extravillous trophoblast cell


title: CT27,EVT, K27ac

value: human trophoblast stem cell


title: CUTTag-IgG_DKO

value: Human colorectal cancer cell

value: DKO

value: IgG


title: HFF-tert dox-inducible amiRNA2 8 hpi, +PAA, HSV-1, strain F, no dox, rep2

description:
Wt_minus_dox_rep2
SSRP1 KD

value: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA2)


title: CUTTag-IgG_DMSO-rep2

value: CTR

value: DMSO


title: CUTTag-IgG_DMSO-rep1


title: CUTTag-IgG_sgCtr

value: sgCtr


title: CUTTag-IgG_Vector

value: Vector


title: CUTTag-IgG_CTR-rep2


title: 2w4w_SS2_146818.66h [SLX-20544.i703_i506]

value: bone marrow

value: Lin-negative, (cKit OR Sca1)-positive

value: WT


title: THP-1 cells, nano extracellular vesicles, 1

city: Auckland

first: Xinyi

last: Sun

address: 85 Park Road, Grafton

country: New Zealand

institute: the university of auckland

data_processing:
Illumina Bcl2FastQsoftware used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
The clean reads were compared to the miRbase22 and Rfam database to identify known miRNA and other non-coding RNAs.
The raw count for known miRNAs were summarized and then normalized using reads per million mapped reads (RPM).
Total clean reads were also mapped to the human reference genome hg38 using the bowtie.The mapped reads were further annotated to the repeats and exon regions based on the genome annotation.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPM values for each Sample.

source_name: THP-1 cells

growth_protocol: THP-1 monocyte cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Exosomal RNA was extracted by the MagZol (Magen) according to the manufacturer’s protocol
Briefly, rRNAs were removed fromExosomal RNA using QIAseqFastSelect RNA Removal Kit（QIAGEN，Germany）and fragmented to approximately 200bp. Subsequently, the RNAfragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA LibraryPrep Kit for Illumina (NEB, USA)

treatment_protocol: the culture medium of THP-1 cells was centrifuged sequentially at 2000 g for five minutes to remove tissue debris. And the conditioned media was centrifugated at 20,000 g for one hour to collect micro-EVs. The conditioned media wasfurther centrifugated at 100,000 g for one hour to collect nano-EVs (Avanti J30I Ultracentrifuge, JA 30.50 Ti fixed angle rotor, Beckman Coulter, NZ).

value: THP-1 cells

value: human leukemia monocytic cell line

value: extracellular vesicles extraction


title: THP-1 cells, nano extracellular vesicles, 2


title: HFF-tert dox-inducible amiRNA1 8 hpi, +PAA, HSV-1, strain F, no dox, rep1

description:
Wt_minus_dox_rep1
SSRP1 KD

value: foreskin

value: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line

value: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA1)

value: 8 hpi, +PAA

value: HSV-1, strain F

value: no doxycycline, 350 ug/ml PAA supplemented upon removal of inoculum (8h treatment)


title: THP-1 cells, nano extracellular vesicles, 3


title: THP-1 cells, micro extracellular vesicles, 3


title: 2w4w_SS2_146818.66h [SLX-20544.i701_i506]


title: HFF-tert dox-inducible amiRNA2 Mock, +PAA, 8 hpi, Mock, 5ug/ml dox for 24 h, rep2

description:
Mock_plus_dox_rep2
SSRP1 KD

value: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA2)

value: Mock, +PAA, 8 hpi

value: Mock

value: 5ug/ml doxycycline for 24 h, 350 ug/ml PAA supplemented upon removal of inoculum (8h treatment)


title: CUTTag-EXOSC10_DKO

value: Human colorectal cancer cell

value: DKO


title: THP-1 cells, micro extracellular vesicles, 2


title: 2w4w_SS2_146818.66h [SLX-20544.i715_i505]

value: bone marrow

value: Lin-negative, (cKit OR Sca1)-positive


title: HFF-tert dox-inducible amiRNA1 Mock, +PAA, 8 hpi, Mock, 5ug/ml dox for 24 h, rep1

description:
Mock_plus_dox_rep1
SSRP1 KD


title: CUTTag-EXOSC10_CTR

value: CTR


title: THP-1 cells, micro extracellular vesicles, 1

value: THP-1 cells

value: human leukemia monocytic cell line

value: WT


title: CUTTag-DIS3_DKO


title: HFF-tert dox-inducible amiRNA2 Mock, +PAA, 8 hpi, Mock, no dox, rep2

description:
Mock_minus_dox_rep2
SSRP1 KD

value: foreskin

value: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line


title: 2w4w_SS2_146818.66h [SLX-20544.i702_i506]


title: HFF-tert dox-inducible amiRNA1 Mock, +PAA, 8 hpi, Mock, no dox, rep1

description:
Mock_minus_dox_rep1
SSRP1 KD

value: lentivirus containing an inducible artificial miRNA against SSRP1 (amiRNA1)


title: 2w4w_SS2_146818.66h [SLX-20544.i712_i505]


title: GBM8401, siINTS9 2

city: Taipei

first: YAO FENG

last: LI

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 11490, Taiwan

department: Pathology

country: Taiwan

institute: National Defense Medical Center

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each Sample

growth_protocol: U87MG cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using total RNA using TRIzol reagent (Invitrogen) and assessed its quality at 260/280 nm and 260/230 nm, and RIN ranged from 9.6 to 10.0
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: U87MG cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics supplemented 100mM metformin with  in humidified atmosphere with 5% CO2 at 37C

value: glioblastoma

value: IDH mutant


title: CUTTag-IgG_CTR-rep1

value: IgG


title: GBM8401, siINTS9 1


title: HFF-tert dox-inducible ICP27, 5ug/ml dox for 24h, no KCl, rep2

description:
ICP27_dox_rep2
ICP22/27 OE, salt stress

source_name: HFF-tert (telomerase-immortalized), transduced with lentivirus containing an inducible ICP27 cassette and rtTA3

value: 5ug/ml doxycycline for 24h, no KCl


title: HFF-tert dox-inducible ICP27, no dox, no KCl, rep2

description:
ICP27_no_dox_rep2
ICP22/27 OE, salt stress

value: lentivirus containing an inducible ICP27 cassette and rtTA3

value: no doxycycline, no KCl


title: GBM8401, siINTS9 3


title: 2w4w_SS2_146818.66h [SLX-20544.i710_i505]


title: ATAC-seq_DKO-rep2

data_processing:
After trimming the adaptors and low-quality reads, the remaining reads were aligned to human hg19 using Bowtie v2.4.4 with parameters ‘-N 1 -L 25 -X 2000 --no-mixed --no-discordant’. For spike-in normalization, the reads were also aligned to the E. coli genome by Bowtie v2.4.4 with the options ‘--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant -I 10 -X 700’.
Mitochondrial reads and PCR duplicates were then filtered using the SAMtools v1.12 and Picard Tools v2.25.5.
Finally, reads were shifted to compensate for the offset in tagmentation site relative to the Tn5 binding site using the alignmentSieve function of deepTools v3.5.193 with the ‘--ATACshift’ option. Read counts were adjusted to total reads aligned to E. coli genome using deepTools v3.5.1.
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
DNA was isolated with PCR clear-up.
Libraries were prepared according to Vazyme's instructions accompanying the TruePrep DNA Library Prep Kit.

value: Human colorectal cancer cell


title: HFF-tert dox-inducible ICP27, no dox, no KCl, rep1

description:
ICP27_no_dox_rep1
ICP22/27 OE, salt stress


title: ATAC-seq_DKO-rep1

value: DKO


title: 2w4w_SS2_146818.66h [SLX-20544.i707_i505]

value: bone marrow


title: HFF-tert dox-inducible ICP27, 5ug/ml dox for 24h, no KCl, rep1

description:
ICP27_dox_rep1
ICP22/27 OE, salt stress


title: GBM8401, control 3

value: Scramble siRNA


title: GBM8401, control 1


title: GBM8401, control 2


title: HFF-tert dox-inducible ICP22, no dox, no KCl, rep2

description:
ICP22_no_dox_rep2
ICP22/27 OE, salt stress

source_name: HFF-tert (telomerase-immortalized), transduced with lentivirus containing an inducible ICP22 cassette and rtTA3


title: 2w4w_SS2_146818.66h [SLX-20544.i714_i505]

value: Lin-negative, (cKit OR Sca1)-positive


title: 2w4w_SS2_146818.66h [SLX-20544.i705_i505]


title: F209-1_Bcell_Smoker

city: Research Triangle Park

first: Douglas

middle: A.

last: Bell

state: NC

address: PO Box 12233

department: Immunity Inflammation and Disease Lab

institute: National Institute of Environmental Health Sciences

data_processing:
75 bp paired-end sequencing was performed on NovaSeq 6000 platform using S1 flow cell (Illumina).
Raw sequencing reads in FASTQ files sequenced to 26-119 million reads
Aligned with STAR version 2.6.0c
Gene read counts obtained using featureCounts from the Subread package version 1.5.1 using release 41 of the GENCODE annotation
Assembly: hg38
Supplementary files format and content: counts: 1st column = Gene symbol, 2nd column = Gene read counts

source_name: Peripheral blood

extract_protocol:
Granulocytes were isolated directly from whole blood using anti-CD15+ antibody–coated magnetic beads following the protocol (Invitrogen). Density gradient centrifugation using Histopaque-1077 Ficoll medium and Accuspin™ Tubes (Sigma-Aldrich) was used to isolate the mononuclear layer of CD19+ B cells using antibody-coated magnetic beads (Invitrogen). RNA was harvested using RNeasy mini plus kit (Qiagen).
Aliquots of RNA (375 ng) were used to generate poly-adenylated RNA libraries with TruSeq Stranded Total RNA Ribo-Zero Human Gold kit (Illumina). Samples were indexed with NEXTfle-96 RNA-Seq Barcodes (Bioo-scientific, Austin, TX).

tag: sample id

value: Peripheral blood

value: Peripheral blood CD19+ B cell

tag: variable-condition

value: smoking

tag: covariate


title: F199-1_Bcell_nonSmoker

value: nonsmoking


title: CUTTag-DIS3_CTR

value: CTR


title: IPF-LC_3

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed fastq files
100bp single-end reads were trimmed using Trim Galore 0.5.0 (Cutadapt 1.18 parameters -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC).
Trimmed reads were aligned to the mm10 reference using STAR 2.6.0a.  Annotations for mm10 were from UCSC and obtained from iGenomes (Illumina).
Alignments were collapsed to UMIs using collapse_UMI_bam from Lexogen.
Gene counting was carried out using featureCounts (subReads R package).
Supplementary files format and content: genes_counts.txt and genes_cpm.txt are tab-delimited matrices provides as genes by samples.  Raw read counts are in genes_counts.txt and counts per million normalized counts are in genes_cpm.txt.  Gene IDs are mouse gene symbols.

source_name: lung

extract_protocol:
RNA was isolated from total lung tissue using the Qiagen RNA isolation kit according to manufacturer protocol. RNA was stored in 30µl of RNase/DNase free water and quantified using the NanoDrop 2000c (Thermofisher).
Total RNA quality was assessed using the Tapestation 4200 (Agilent). 500ng of DNase-treated total RNA was used to generate QuantSeq 3’ mRNA FWD (Lexogen).

treatment_protocol: Female C57B/L6-albino mice aged 6-8 weeks were randomized into 4 different experimental cohorts: (1) control mice not receiving bleomycin or LLC-1 Luc+ cells, (2) mice that received two doses of 0.5mg/kg and 1 mg/kg bleomycin in 50 µl saline (double oropharyngeal aspiration schedule at day 0 and day 4) to induce fibrosis, (3) mice wherein LLC-1 Luc+ cells were injected at a concentration of 1x10^6 cells per mouse intravenously through the tail vein and (4) mice where LLC-1 Luc+ cells were implanted intravenously (IV) into bleomycin pre-conditioned mice. Since the bleomycin model exhibits two distinct phases, the inflammatory (2 weeks) and the fibrotic (2 weeks) phase, LLC-1 Luc+ cells were injected 2 weeks post instillation during the fibrotic phase.

tag: strain

tag: age

value: 6-8 weeks old

tag: Sex

value: female

value: lung

value: LCC-1 luciferase cells

value: bleomycin


title: 2w4w_SS2_146818.66h [SLX-20544.i711_i505]

value: WT


title: ATAC-seq_CTR-rep2


title: IPF-LC_2


title: 2w4w_SS2_146818.66h [SLX-20544.i704_i505]


title: IPF-LC_1


title: 2w4w_SS2_146818.66h [SLX-20544.i703_i505]


title: HFF-tert dox-inducible ICP22, no dox, 200mM KCl for 2h, rep1

description:
ICP22_no_dox_KCl_rep1
ICP22/27 OE, salt stress

value: foreskin

value: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line

tag: transduction

value: lentivirus containing an inducible ICP22 cassette and rtTA3

tag: time post_infection

value: no doxycycline, 200mM KCl for 2h


title: 2w4w_SS2_146818.66h [SLX-20544.i702_i505]

value: bone marrow


title: F198-1_Bcell_Smoker


title: LC_3


title: ATAC-seq_CTR-rep1

tag: cell line

value: Human colorectal cancer cell


title: 2w4w_SS2_146818.66h [SLX-20544.i706_i505]

tag: cell type

value: Lin-negative, (cKit OR Sca1)-positive


title: 2w4w_SS2_146818.66h [SLX-20544.i701_i505]

tag: genotype


title: HFF-tert dox-inducible ICP22, no dox, 200mM KCl for 2h, rep2

description:
ICP22_no_dox_KCl_rep2
ICP22/27 OE, salt stress

tag: tissue

tag: infection


title: F189-1_Bcell_Smoker

value: Peripheral blood

value: Peripheral blood CD19+ B cell


title: HFF-tert dox-inducible ICP22, 5ug/ml dox for 24h, no KCl, rep2

description:
ICP22_dox_rep2
ICP22/27 OE, salt stress

value: 5ug/ml doxycycline for 24h, no KCl


title: F175-1_Bcell_Smoker

value: smoking


title: HFF-tert dox-inducible ICP22, 5ug/ml dox for 24h, no KCl, rep1

description:
ICP22_dox_rep1
ICP22/27 OE, salt stress


title: 2w4w_SS2_146818.66h [SLX-20544.i715_i503]


title: LC_1

value: 6-8 weeks old


title: HFF-tert dox-inducible ICP22, no dox, no KCl, rep1

description:
ICP22_no_dox_rep1
ICP22/27 OE, salt stress

value: no doxycycline, no KCl


title: F173-1_Bcell_Smoker


title: HFF-tert dox-inducible ICP22, 5ug/ml dox for 24h, 200mM KCl for 2h, rep2

description:
ICP22_dox_KCl_rep2
ICP22/27 OE, salt stress

value: 5ug/ml doxycycline for 24h, 200mM KCl for 2h


title: IPF_3

value: female

value: lung


title: HFF-tert dox-inducible ICP22, 5ug/ml dox for 24h, 200mM KCl for 2h, rep1

description:
ICP22_dox_KCl_rep1
ICP22/27 OE, salt stress


title: IPF_2

value: bleomycin


title: F169-1_Bcell_nonSmoker

value: nonsmoking


title: F192-1_Bcell_nonSmoker


title: F152-1_Bcell_Smoker


title: LC_2

value: LCC-1 luciferase cells


title: HFF-tert, doxycycline-inducible ICP27, no treatment, rep2

data_processing:
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.7.9
Assembly: GRCh37/hg19
Supplementary files format and content: bedGraph

extract_protocol:
Infected cells were harvested by scraping at the indicated time points, washed, lysed with mild lysis buffer according to the published OMNI-ATAC-seq protocol, incubated with Tn5 transposase (tagmentase) for 30 minutes, lysed in Qiagen's PB buffer, DNA purified according to the MinElute protocol.
Libraries were prepared using Illumina-compatible primers (like Nextera primers but custom sets with dual-unique barcodes). Initially, quantitative PCR was performed to judge how many cycles are required for optimal library preparation.
36bp paired-end, NextSeq 500 (Illumina)

treatment_protocol: For the experiment cells were seeded in medium without puromycin but containing 5 ug/ml doxycycline for 24 h prior to harvest. Expression of HA-ICP22 and V5-ICP27 was induced by adding 5 μg/ml doxycycline for 24 h. KCl at a final concentration of 200 mM was added to conditioned medium 24 h after doxycycline induction and cells were harvested by scraping 2 h later.

value: foreskin

value: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line

value: lentivirus containing an inducible ICP27 cassette and rtTA3

value: no treatment


title: HFF-tert, doxycycline-inducible ICP27, no treatment, rep1


title: F151-1_Bcell_Smoker


title: HFF-tert, doxycycline-inducible ICP27, 5ug/ml doxycycline for 24h, no  KCl, rep2

value: 5ug/ml doxycycline for 24h, no  KCl


title: F148-1_Bcell_Smoker

value: Peripheral blood


title: 2w4w_SS2_146818.66h [SLX-20544.i710_i503]

description:
Smart-Seq2 scRNA-Seq, see metadata for details
SLX20544_scB5Tom_2w_ss2_fcounts.txt

value: bone marrow

value: Lin-negative, (cKit OR Sca1)-positive

value: WT


title: 2w4w_SS2_146818.66h [SLX-20544.i707_i503]


title: HFF-tert, doxycycline-inducible ICP27, 5ug/ml doxycycline for 24h, no  KCl, rep1


title: control_2

value: 6-8 weeks old


title: F142-1_Bcell_nonSmoker

value: Peripheral blood CD19+ B cell


title: 2w4w_SS2_146818.66h [SLX-20544.i706_i503]


title: HFF-tert, doxycycline-inducible ICP22, no doxycycline, no KCl, rep2

value: lentivirus containing an inducible ICP22 cassette and rtTA3

value: no doxycycline, no KCl


title: 2w4w_SS2_146818.66h [SLX-20544.i714_i503]


title: control_1

value: female

value: lung


title: RNA-seq_Th1_Ets1-SE-KO_Ets1-RV_Rep2B_Rep2T

first: Golnaz

last: Vahedi

address: 421 Curie Blvd

department: Department of Genetics

institute: University of Pennsylvania

data_processing:
RNA-seq libraries were pair-end sequenced by Illumina NextSeq 550. RNA-seq samples were aligned by STAR_2.5.0a_alpha with parameters '--outSAMtype BAM SortedByCoordinate --outWigType wiggle read1_5p --outWigStrand Stranded --outWigNorm RPM --quantMode GeneCounts'.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files with read count

source_name: Th1 cells

extract_protocol:
Cells were washed with 1 x PBS (Corning, cat# 21031CV) and lysed with 350 μl RLT Plus buffer (Qiagen) supplemented with 10% 2-mercaptoethanol (Sigma, cat# M6250), vortexed briefly, snap-frozen on dry ice, and stored at -80°C. Subsequently, total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, cat# 74034).
Libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara). Indexed libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent). Paired end sequencing (38 bp+38 bp) was performed on a NextSeq 550 or on NovaSeq (61bp+61bp) following the manufacturer's protocol.

treatment_protocol: Spleen of mice were dissociated through a 70µM mesh filter (Falcon) in RPMI 1640 (Corning), red blood cells were depleted using ACK lysis buffer (Gibco, Invitrogen). Naive CD4+ T cells were selected using negative selection beads (StemCell, Cat# 19765). For in vitro polarization, flat bottom 96-well plates were coated with 2 mg/mL of anti-CD3 (Clone: 145-2C11, BioLegend, Cat#100302) in PBS overnight at 4°C or 4 hrs at 37°C. For Th1 polarization, naive CD4+ T cells were cultured in RPMI 1640 medium (Invitrogen), supplemented with 10% fetal bovine serum (Fisher Scientific), 1mM sodium pyruvate (Gibco), 1% non-essential amino acids (Gibco), 1X GlutaMAX (Gibco), 1% HEPES (Gibco), 1% penicillin-streptomycin and 0.1% 2-Mercaptoethanol (Gibco).  For Th1 polarization, 0.2x106 naive CD4+ T cells were cultured in presence of 10 ng/mL of recombinant IL-12 (BioLegend, Cat#577002), 1 ng/mL of recombinant IL-2 (BioLegend, Cat#575402) and 1 mg/mL of soluble anti-CD28 (Clone: 37.51, BD Biosciences, Cat# 553294) for 6 days at 37°C.

value: Spleen

value: Ets1-retrovirus transduced


title: 2w4w_SS2_146818.66h [SLX-20544.i712_i503]

data_processing:
library strategy: Smart-Seq2 or 10x Genomics
Smart-Seq2 sequencing reads were aligned to the mouse genome (mm10) using the STAR aligner (version 2.7.3a) with default parameters. Reads mapping to exons were counted with featureCounts (version 2.0.0) using the ENSEMBL v93 annotation. For consistency only a single read was processed for each sample. 10x genomics reads were pre-processed using cellranger (version 3.1.0, reference genome and annotation version 3.0.0) with default settings
Assembly: mm10
Supplementary files format and content: Smart-Seq2 data: count matrices for each fastq file as produced by feature counts  10x Genomics data: annotated, filtered (default cellranger setting) cell x gene matrices in .h5 format (cellranger output file)

extract_protocol:
All steps in this section (unless otherwise indicated) were performed on ice, and centrifugation steps performed at 300g, 4°C for 5 min. 8-12 weeks old mice carrying the Hoxb5-Cre and the Rosa26-LoxP-STOP-LoxP-tdTomato constructs were treated with 7 daily injections of tamoxifen and sacrificed at indicated time points. Bone marrow cells were extracted from ilia, tibiae and femura by grinding with mortar and pestle in PBS supplemented with 2% Fetal Bovine Serum (cell buffer). The suspension was filtered through a 50µm filter, centrifuged and resuspended in 3 ml of cell buffer. Red blood cells were removed using the ammonium chloride solution: 5 ml of 0.8% Ammonium Chloride (StemCell Tech. 07800) was added to the suspension and incubated for 10 min with intermittent mixing. Afterwards cells were diluted with 7 ml of cell buffer, centrifuged and resuspended in 1 ml of cell buffer. Subsequently, lineage depletion was performed as follows: added 20 µl of the EasySep mouse haematopoietic progenitor cell isolation cocktail (Stem Cell Technologies 19856), incubated for 15 min, added 30 µl magnetic particles, incubated for 10 min, added 1.5 ml of cell buffer and placed tubes in a magnet, incubated for 3 min at room temperature and eluted cells twice (with additional 2.5 ml of cell buffer). Afterwards, cells were centrifuged, resuspended in 200 µl of cell buffer and stained with the antibody panel as follows: antibody mix was added, cells were incubated for 30 min, washed with 2 ml of cell buffer, centrifuged, reuspended in 200 µl cell buffer. For the secondary staining Streptavidin-BV510 was added, cells were washed with 2 ml of cell buffer, centrifuged and resuspended in 1000 µl of cell buffer supplemented with 7AAD. Afterwards cells were sorted with BD influx sorter into either 96 well plates containing 2.3 µl lysis buffer (for the Smart-Seq2 protocol) or 100 µl of PBS with 0.04% BSA in eppendorf tubes ('droplet buffer') when used for the 10x Genomics scRNA-Seq protocol. The Smart-Seq2 plates were vortexed, centrifuged at 800g for 2 min and stored at -80°C. Antibodies and fluorochromes used: Mouse haematopoietic progenitor cell isolation cocktail (Stem Cell Technologies 19856), CD48-APC (Thermo-Fischer 17-0481-82), c-Kit-APC/Cy7 (Biolegend 105826), Sca1-BV421 (Biolegend 108133) and CD150-PE/Cy7 (Biolegend 115914), Streptavidin-BV510 (Biolegend 405234), 7AAD (Thermo Fischer A1310).
Smart-Seq2:
When cell numbers were limiting single cells were profiled with a modified version of the Smart-Seq2 protocol rather than 10x Genomics kit. Single cells were sorted into 96-well plates with 2.3 µl lysis buffer containing 0.115 µl of SUPERase-In RNase Inhibitor at 20 U/µl concentration (ThermoFisher AM2694) and 0.23 µl of 10% Triton X-100 solution (Sigma 93443), plates were vortexed and stored at -80°C. After thawing 2 µl of the annealing solution (0.1 µl of ERCC RNA Spike-In solution (1:300,000 dilution) Thermo-Fisher 4456740), 0.02 µl of the oligo-dT primer (100 µM stock concentration) and 1 µl of dNTP (10 mM stock concentration)) was added. The plate was incubated at 72°C for 3 min, cooled down on ice and reverse transcription was performed by adding 5.7 µl of RT buffer (0.1 µl of Maxima H minus reverse transcriptase at 200 U/µl concentration (ThermoFischer EP0752), 0.25 µl of SUPERase-In RNAse Inhibitor at 20 U/µl concentration, 2 µl of the Maxima enzyme buffer, 0.2 µl of TSO oligo at 100 µM concentration, 1.875 µl of PEG 8000 solution (Sigma P1458) at 40% v/v concentration and 1.275 µl water) and incubation at 42°C for 90 min followed by incubation at 70°C for 15 min. Immediately after, cDNA was amplified by PCR by adding 1 µl of the Terra PCR Direct Polymerase (1.25 U/µl, Takara 639270), 25 µl of the Terra PCR Direct buffer and 1 µl of the ISPCR primer (10 µM stock concentration) to a total volume of 50 µl using the following PCR conditions: 98°C for 3 min, 98°C for 15 s, 65°C for 30 s, 68°C for 4 min (21 cycles), 72°C for 10 min. The amplified cDNA was purified using AMPure XP beads (Beckman A63882), quantified using the PicoGreen assay (ThermoFischer P7589) and used for Nextera library preparation. The libraries were generated using either a standard protocol (batch 7d) or modified protocol (batches 3d7d, 2w4w and 3dr2), see the corresponding metadata) described below. No obvious batch effects were observed among cells analysed with either of the protocols.
The standard Nextera protocol: cDNA was diluted to approximately 50-150 pg/µl and 1.25 µl of the solution was used, 2.5 µl of Tagment DNA buffer 1.25 µl of Amplicon Tagment Mix (Nextera XT kit, Illumina FC-131-1096) were added, samples were incubated at 55°C for 10 min, and the reaction was stopped by addition of 1.25 µl of NT buffer. Tagmentation products were amplified by PCR by adding 1.25 µl of each N and S primers (Illumina Nextera XT 96-index kit FC-131-1002) and 3.75 µl of NPM solution and using the following thermocycler settings: 72°C 3 min, 95°C 30 s, 12 cycles of 95°C 30s, 55°C 30s, 72°C 60s and a final extension at 72°C for 5 min.
The modified Nextera protocol follows the same principle as the standard Nextera protocol and includes the following steps: cDNA was diluted to approximately 50-150 pg/µl and 1.03 µl of the solution was used, 1.63 µl of Tagment DNA buffer and 0.6 µl Amplicon Tagment Mix was added, samples were incubated at 55°C for 10 min, the reaction was stopped by adding 0.82 µl of NT buffer. Tagmentation products were amplified by adding 1.23 µl of each N and S primers (as above but diluted 5 times), 2.3 µl of Phusion HF buffer (ThermoFischer F530L), 0.1 µl of dNTP (25 mM stock concentration), 0.07 µl of Phusion polymerase and 2.5 µl of water and using the following thermocycler settings: 72°C 3 min, 98°C 3 min s, 12 cycles of 98°C 10s, 55°C 30s, 72°C 30s and a final extension at 72°C for 5 min.
Libraries were sequenced using the Illumina Hiseq4000 or NovaSeq instruments, obtaining approximately 100-200 mln reads per 96 cells.
10X genomics:
For the 10x Genomics scRNA-Seq protocol up to 20,000 cells were pooled in pairs corresponding to male and female animals, centrifuged and resuspended in a volume of droplet buffer optimal for recovery of up to 10,000 cells and immediately processed with the 10x Genomics Single Cell 3' v3 protocol following the manufacturer's instructions.
Libraries were sequenced using the Illumina NovaSeq instrument, obtaining at least 20,000 reads per cells.


title: F135-1_Bcell_nonSmoker

value: nonsmoking


title: 2w4w_SS2_146818.66h [SLX-20544.i705_i503]


title: 2w4w_SS2_146818.66h [SLX-20544.i704_i503]


title: HFF-tert, doxycycline-inducible ICP22, no doxycycline, no KCl, rep1

value: foreskin

value: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line


title: HFF-tert, doxycycline-inducible ICP22, no doxycycline, 200mM KCl for 2h, rep2

value: no doxycycline, 200mM KCl for 2h


title: IPF_1

value: bleomycin


title: RNA-seq_Th1_Ets1-SE-KO_Ets1-RV_Rep2B_Rep1T


title: RNA-seq_Th1_Ets1-SE-KO_Ets1-RV_Rep1B_Rep2T


title: 2w4w_SS2_146818.66h [SLX-20544.i711_i503]


title: control_3


title: 2w4w_SS2_146818.66h [SLX-20544.i703_i503]


title: F125-1_Bcell_Smoker

value: Peripheral blood

value: smoking


title: F147-1_Bcell_nonSmoker


title: HFF-tert, doxycycline-inducible ICP22, no doxycycline, 200mM KCl for 2h, rep1


title: F120-1_Bcell_nonSmoker


title: RNA-seq_Th1_Ets1-SE-KO_Ets1-RV_Rep1B_Rep1T


title: HFF-tert, doxycycline-inducible ICP22, 5ug/ml doxycycline for 24h, no KCl, rep2

value: 5ug/ml doxycycline for 24h, no KCl


title: 2w4w_SS2_146818.66h [SLX-20544.i702_i503]

value: bone marrow

value: Lin-negative, (cKit OR Sca1)-positive

value: WT


title: F108-1_Bcell_nonSmoker

value: Peripheral blood CD19+ B cell


title: 2w4w_SS2_146818.66h [SLX-20544.i701_i503]


title: RNA-seq_Th1_WT_Ets1-RV_Rep2B_Rep2T

value: Empty vector- retrovirus transduced


title: F093-1_Bcell_nonSmoker


title: HFF-tert, doxycycline-inducible ICP22, 5ug/ml doxycycline for 24h, 200mM KCl for 2h, rep2

value: lentivirus containing an inducible ICP22 cassette and rtTA3


title: 2w4w_SS2_146818.66h [SLX-20544.i715_i502]


title: F105-1_Bcell_nonSmoker


title: 2w4w_SS2_146818.66h [SLX-20544.i714_i502]


title: 2w4w_SS2_146818.66h [SLX-20544.i712_i502]


title: F077-1_Bcell_nonSmoker


title: RNA-seq_Th1_WT_Ets1-RV_Rep2B_Rep1T


title: RNA-seq_Th1_WT_Ets1-RV_Rep1B_Rep2T


title: HFF-tert, doxycycline-inducible ICP22, 5ug/ml doxycycline for 24h, 200mM KCl for 2h, rep1


title: RNA-seq_Th1_WT_Ets1-RV_Rep1B_Rep1T


title: F073-1_Bcell_nonSmoker


title: 2w4w_SS2_146818.66h [SLX-20544.i711_i502]


title: RNA-seq_Th1_Ets1-SE-KO_EV-RV_Rep2B_Rep1T


title: HFFF cells infected with HSV-1 WT (17), histone H3K36me3, replicate 2

description: DNA isolated with Zymo DNA Clean & Concentrator

data_processing:
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.7.9
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bedGraph

source_name: ChIPmentation

growth_protocol: HFFFs were cultured in DMEM supplements with 10% FBS and P/S. Cells were infected with WT HSV-1 (strain 17 or F) or ICP22-null mutant at an MOI of 10. Marked samples were treated with 350 µg/ml PAA throught the course of infection

extract_protocol:
Samples were processed according to the ChIPmentation protocol with few adjustments indicated in Materials and Methods (Schmidl C et al. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Methods. 2015)
See Schmidl C et al. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Methods. 2015, Oct;12(10):963-965. doi: 10.1038/nmeth.3542. Epub 2015 Aug 17. PMID: 26280331; PMCID: PMC4589892.
Paired-end sequencing

treatment_protocol: Cells were infected with WT HSV-1 for 15 min or ΔICP22 for 1 hour using an MOI of 10. After infection, cell culture media was replaced with fresh media in which the PAA was added. Samples were crosslinked and collected at the indicated time points and afterwards processed according to the ChIPmentation protocol.

value: Human fetal foreskin fibroblasts

value: no treatment

value: HSV-1 WT, strain 17


title: 2w4w_SS2_146818.66h [SLX-20544.i710_i502]


title: F072-1_Bcell_Smoker


title: F069-1_Bcell_Smoker


title: HFFF cells infected with HSV-1 WT (17), histone H3K36me3, replicate 1


title: RNA-seq_Th1_Ets1-SE-KO_EV-RV_Rep2B_Rep2T

value: Spleen

value: Ets1-retrovirus transduced


title: F068-1_Bcell_Smoker


title: RNA-seq_Th1_Ets1-SE-KO_EV-RV_Rep1B_Rep2T


title: HFFF cells mock infected, histone H3K36me3, replicate 3

value: mock


title: F067-1_Bcell_Smoker


title: HFF-tert, doxycycline-inducible ICP22, 5ug/ml doxycycline for 24h, no KCl, rep1

value: foreskin

value: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line


title: HFFF cells mock infected, histone H3K36me3, replicate 2


title: 2w4w_SS2_146818.66h [SLX-20544.i707_i502]


title: RNA-seq_Th1_Ets1-SE-KO_EV-RV_Rep1B_Rep1T


title: 2w4w_SS2_146818.66h [SLX-20544.i706_i502]


title: F061-1_Bcell_Smoker

value: Peripheral blood


title: RNA-seq_Th1_WT_EV-RV_Rep2B_Rep2T


title: 2w4w_SS2_146818.66h [SLX-20544.i705_i502]


title: 2w4w_SS2_146818.66h [SLX-20544.i704_i502]


title: RNA-seq_Th1_WT_EV-RV_Rep2B_Rep1T


title: F054-1_Bcell_Smoker

value: smoking


title: HFFF cells infected with HSV-1 WT (17), histone H3K27me3, replicate 2


title: 2w4w_SS2_146818.66h [SLX-20544.i703_i502]


title: RNA-seq_Th1_WT_EV-RV_Rep1B_Rep2T


title: HFFF cells infected with HSV-1 WT (17), histone H3K27me3, replicate 1


title: HFFF cells infected with HSV-1 WT (17), histone H3K36me3, replicate 3


title: F047-1_Bcell_nonSmoker

value: nonsmoking


title: 2w4w_SS2_146818.66h [SLX-20544.i702_i502]

value: bone marrow


title: RNA-seq_Th1_WT_EV-RV_Rep1B_Rep1T


title: HFFF cells mock infected, histone H3K27me3, replicate 2


title: 2w4w_SS2_146818.66h [SLX-20544.i701_i502]

value: Lin-negative, (cKit OR Sca1)-positive


title: F043-1_Bcell_nonSmoker


title: HFFF cells mock infected, histone H3K27me3, replicate 1


title: F037-1_Bcell_Smoker


title: HFFF cells infected with HSV-1 WT (17), histone H3, replicate 2


title: RNA-seq_Th1_Ets1-SE-KO_untransduced_Rep1B_Rep1T

value: un-transduced


title: RNA-seq_Th1_Ets1-SE-KO_untransduced_Rep2B_Rep1T


title: HFFF cells mock infected, histone H3K36me3, replicate 1


title: Hoxb5_Tom_16w_60c_60h_Tompos [SLX-20853_SITTE12_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20853_SITTE12_filtered_feature_bc_matrix.h5

value: WT


title: F031-1_Bcell_Smoker

value: Peripheral blood CD19+ B cell


title: Hoxb5_Tom_16w_60b_60f_Tompos [SLX-20853_SITTD12_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20853_SITTD12_filtered_feature_bc_matrix.h5


title: F026-1_Bcell_nonSmoker


title: RNA-seq_Th1_WT_untransduced_Rep2B_Rep1T


title: Hoxb5_Tom_16w_60b_60f_Tomneg [SLX-20853_SITTF12_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20853_SITTF12_filtered_feature_bc_matrix.h5


title: HFFF cells infected with HSV-1 WT (17), histone H3, replicate 1


title: F015-2_Bcell_nonSmoker


title: HFFF cells mock infected, histone H3, replicate 2


title: HFFF cells mock infected, histone H3, replicate 1


title: RNA-seq_Th2_Ets1-SE-KO_Rep1B_Rep3T

source_name: Th2 cells


title: F003-3_Bcell_nonSmoker


title: Hoxb5_Tom_7w_63b_63g_Tompos [SLX-20620_SITTF3_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20620_SITTF3_filtered_feature_bc_matrix.h5


title: Hoxb5_Tom_7w_63a_63f_Tompos [SLX-20620_SITTD3_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20620_SITTD3_filtered_feature_bc_matrix.h5


title: RNA-seq_Th2_Ets1-SE-KO_Rep1B_Rep2T


title: GFP-expressing HH-TERT cells, infected with BAC-derived WT HSV-1 strain 17, 8 hpi, replicate 2

source_name: Omin-ATAC-seq

growth_protocol: Telomerase-immortalized human foreskin fibroblasts (HFF-TERTs), which doxycycline-inducibly express GFP were cultured in DMEM supplemented with 10% FBS, non-essential amino acids and P/S. Cells were seeded a day prior to infected in complete medium supplemented with 5 ug/ml doxycyline and infected at 60-80% confluency 24h later (100000 cells/condition).

extract_protocol:
Infected cells were harvested by scraping at the indicated time points, washed, lysed with mild lysis buffer according to the published OMNI-ATAC-seq protocol, incubated with Tn5 transposase (tagmentase) for 30 minutes, lysed in Qiagen's PB buffer, DNA purified according to the MinElute protocol.
Libraries were prepared using Illumina-compatible primers (like Nextera primers but custom sets with dual-unique barcodes). Initially, quantitative PCR was performed to judge how many cycles are required for optimal library preparation.
35bp paired-end, NextSeq 500 (Illumina)

treatment_protocol: HFF-TERT cells were inoculated for 1 h with an MOI of 10 and the time of the experiment started after the inoculum was removed. 350 µg/ml PAA was added to indicated samples for the full duration of the experiment.

value: HFF-TERT cells doxycycline-inducibly expressing GFP (control sample)

tag: virus strain

value: HSV-1(17+)Lox BAC derived WT virus

tag: agent

value: infected with parental BAC derived wt virus


title: RNA-seq_Th2_Ets1-SE-KO_Rep1B_Rep1T


title: PBMCs, Operational tolerant

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

description: Isolated Single Cell-RNA

data_processing:
Count matrices were generated using cellranger
Seurat objects were created using count matrices and the counts were normalized for library size
Seurat objects of normalized counts for all samples were integrated into one combined object
Assembly: hg38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: PBMC

extract_protocol:
Blood samples were diluted 1:1 with phosphate-buffered saline (PBS, Gibco) and layered onto the Ficoll Paque Plus (GE-healthcare) and centrifuged at 400g for 30 min, the buffy layer containing the peripheral blood mononuclear cells (PBMCs) were collected in 1.5mL centrifuge tubes. Cells were first isolated then washed twice in PBS by centrifugation at 10,000g for 4 min. Cell viability was determined using Trypan Blue and found to be greater than 9
Single-cell suspension samples were loaded on the Chromium platform (10X Genomics) for cell barcoding and library preparation was done using the Chromium Single Cell 5’ Reagent kit (10X Genomics) using the manufacturer’s instructions. Briefly, single-cell gel beads in emulsion (GEMs) generated from the Chromium controller were reverse transcribed to produce 10X barcoded cDNA. cDNA was then amplified, and the library generated.
Sequencing was performed on the Illumina NovaSeq6000 platform according to Illumina standard conditions with 10X Genomics recommended read parameters.

value: PBMC

tag: est. conc. of cells

tag: mean reads per cells

tag: fraction reads in cells (%)

tag: fraction of reads mapped to transcriptome (%)

tag: sample type

value: Tolerant (Tol)


title: GFP-expressing HH-TERT cells, infected with BAC-derived WT HSV-1 strain 17, 8 hpi, replicate 1


title: Hoxb5_Tom_11w_60a_57e_Tompos [SLX-20620_SITTC3_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20620_SITTC3_filtered_feature_bc_matrix.h5

source_name: bone marrow

tag: treatment


title: RNA-seq_Th2_WT_Rep1B_Rep3T

value: Spleen

tag: strain


title: RNA-seq_Th1_WT_untransduced_Rep1B_Rep1T


title: GFP-expressing HH-TERT cells, mock-infected, 8 hpi, replicate 2

value: mock infected


title: PBMCs, On immunosuppressants with stable graft function

description: Isolated Single Cell-RNA

value: Standard-of-care (SOC)


title: Hoxb5_Tom_11w_57b_57f_Tompos [SLX-20620_SITTA3_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20620_SITTA3_filtered_feature_bc_matrix.h5


title: RNA-seq_Th2_WT_Rep1B_Rep2T


title: RNA-seq_Th2_WT_Rep1B_Rep1T


title: Hoxb5_Tom_11w_57b_57f_Tomneg [SLX-20620_SITTB3_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20620_SITTB3_filtered_feature_bc_matrix.h5


title: GFP-expressing HH-TERT cells, infected with US1 deletion mutant HSV-1 strain 17, 8 hpi, replicate 2

value: HSV-1(17+)Lox BAC derived US1 deletion mutant

value: infected with US1 mutant


title: GFP-expressing HH-TERT cells, mock-infected, 8 hpi, replicate 1


title: PBMCs, Normal

description: Isolated Single Cell-RNA

value: Healthy Control (HC)


title: MDA-MB-231_GIV_KO_0_FBS_R2_S37

city: La Jolla, CA 92093

first: Pradipta

last: Ghosh

address: 9500 Gilman Drive (MC 0651)

department: Departments of Medicine and Cellular and Molecular Medicine

institute: University of California San Diego

data_processing:
RNASeq data was processed using kallisto (version 0.45.0). Gene-level TPM values and gene annotations were computed using a custom Perl Script.
Assembly: Homo sapiens genome build hsGRCh38_94
Supplementary files format and content: tab-delimited text file includes log2 of TPM values

growth_protocol: WT and GIV-KO MDA-MB231 cells grown in 0% and 10% serum concentration in p10 dishes (Corning) for 16 h prior to harvest

extract_protocol:
RNA extraction was done  using a kit (R2052, Zymo Research) as per manufacturer’s protocol
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: 0% and 10% serum concentration


title: RNA-seq_Th1_Ets1-SE-KO_Rep1B_Rep3T


title: MDA-MB-231_GIV_KO_10_FBS_R2_S43

value: 10percent serum concentration


title: Hoxb5_Tom_2w_66d_66g_Tompos [SLX-20428_SITTE4_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20428_SITTE4_filtered_feature_bc_matrix.h5

value: bone marrow


title: GFP-expressing HH-TERT cells, infected with US1 deletion mutant HSV-1 strain 17, 8 hpi, replicate 1


title: RNA-seq_Th1_Ets1-SE-KO_Rep1B_Rep2T


title: Hoxb5_Tom_7w_63a_63f_Tomneg [SLX-20620_SITTE3_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20620_SITTE3_filtered_feature_bc_matrix.h5

value: Lin-negative, (cKit OR Sca1)-positive


title: primary HFFF cells, infected with KOS 1.1 strain derived US1 knock-out,  PAA 350ug/ml, replicate 2

description: DNA isolated with MinElute PCR Purification Kit

source_name: Omni-ATAC-seq

growth_protocol: T-HF cells were cultured in DMEM supplements with 10% FBS and P/S. Expression of HA-ICP22 and HA-ICP22 + V5-ICP27 was induced by adding 5 μg/ml doxycycline for 48h. Salt stress was induced with the addition of 80 mM KCl. For the second experiment HFFF were cultured as described for THF cells. 100000 cells were infected at MOI 10 under PAA treatment for 8 h and harvested/processed according to the OMNI-ATAC-seq protocol

extract_protocol:
Samples were processed according to the Omni-ATAC-seq protocol (Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396)
See Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396
NextSeq 500 sequencing 35bp paired-end reads

treatment_protocol: 5 μg/mL DOX was added to indicated samples 48 hours prior to performing Omni-ATAC-seq. 80 mM KCl (salt stress) was added to indicated samples for 2 hours prior to Omni-ATAC-seq. No pre-treatment with doxycycline for the infections of HFFF cells was applied.

value: primary Human Foetal Foreskin Fibroblast cells

value: 350 ug'/ml PAA

tag: treatment 2

value: KOS 1.1 with US1 deletion


title: RNA-seq_Th1_Ets1-SE-KO_Rep1B_Rep1T


title: primary HFFF cells, infected with KOS 1.1 strain, PAA 350ug/ml, replicate 2

value: WT KOS 1.1


title: MDA-MB-231_parental_10_FBS_R1_S24

value: parental


title: MDA-MB-231_GIV_KO_10_FBS_R3_S46


title: primary HFFF cells, infected with KOS 1.1 strain derived US1 knock-out,  PAA 350ug/ml, replicate 1


title: RNA-seq_Th1_WT_Rep1B_Rep3T


title: Hoxb5_Tom_4w_61b_61h_Tomneg [SLX-20428_SITTA4_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20428_SITTA4_filtered_feature_bc_matrix.h5

value: WT


title: Hoxb5_Tom_4w_61b_61f_Tompos [SLX-20428_SITTC4_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20428_SITTC4_filtered_feature_bc_matrix.h5


title: Hoxb5_Tom_2w_66d_66g_Tomneg [SLX-20428_SITTB4_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20428_SITTB4_filtered_feature_bc_matrix.h5


title: RNA-seq_Th1_WT_Rep1B_Rep2T


title: MDA-MB-231_parental_0_FBS_R2_S12


title: F007-2_Bcell_Smoker

tag: sample id

value: Peripheral blood

value: Peripheral blood CD19+ B cell

tag: variable-condition

value: smoking

tag: covariate


title: MDA-MB-231_GIV_KO_10_FBS_R1_S33

tag: cell line


title: Hoxb5_Tom_3d7d_46e_46d_Tomneg [SLX-20264_SITTC7_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20264_SITTC7_filtered_feature_bc_matrix.h5

tag: cell type

tag: genotype


title: primary HFFF cells, Mock infected, PAA 350ug/ml, replicate 2

value: Mock


title: primary HFFF cells, infected with KOS 1.1 strain, PAA 350ug/ml, replicate 1


title: RNA-seq_Th1_WT_Rep1B_Rep1T

tag: tissue

value: Spleen


title: MDA-MB-231_parental_0_FBS_R1_S9


title: Hoxb5_Tom_4w_61c_61h_Tompos [SLX-20428_SITTD4_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20428_SITTD4_filtered_feature_bc_matrix.h5


title: MDA-MB-231_GIV_KO_0_FBS_R3_S18


title: RNA-seq_naive_CD4_Ets1-SE-KO_Rep1B_Rep1T

source_name: naive CD4+ T cells


title: primary HFFF cells, Mock-infected, PAA 350ug/ml, replicate 1


title: MDA-MB-231_parental_10_FBS_R2_S51


title: HA-ICP22 cells, salt stress, no DOX, replicate 2

value: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line

value: no treatment

value: 80 mM KCl


title: MDA-MB-231_parental_10_FBS_R3_S11

value: 10percent serum concentration


title: RNA-seq_naive_CD4_Ets1-SE-KO_Rep1B_Rep2T


title: Hoxb5_Tom_7d_54f_56a_Tompos [SLX-20391_SITTA4_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20391_SITTA4_filtered_feature_bc_matrix.h5

value: bone marrow


title: HA-ICP22 cells, salt stress, DOX, replicate 2

value: DOX (5 μg/mL)


title: RNA-seq_naive_CD4_WT_Rep1B_Rep2T


title: RNA-seq_naive_CD4_WT_Rep1B_Rep1T


title: Hoxb5_Tom_3d7d_46e_47c_Tompos [SLX-20264_SITTB7_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20264_SITTB7_filtered_feature_bc_matrix.h5

value: Lin-negative, (cKit OR Sca1)-positive


title: Hoxb5_Tom_7d_51f_38h_Tompos [SLX-20391_SITTB4_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-20391_SITTB4_filtered_feature_bc_matrix.h5


title: MDA-MB-231_GIV_KO_0_FBS_R1_S4


title: HA-ICP22 cells, salt stress, no DOX, replicate 1


title: Hoxb5_Tom_5mo_56e_58g_Tompos [SLX-19739_SIGAD9_10x]

description:
10X genomics scRNA-Seq, pool of 2 animals, male and female, see metadata for details
SLX-19739_SIGAD9_filtered_feature_bc_matrix.h5


title: HiC_PLN-CD4_HPAP-025_T1D_Rep1T

data_processing:
Raw reads for each HiChIP sample were processed with HiC-Pro (version v2.8.1) (Servant et al., 2015) to obtain putative interactions with default parameters except LIGATION_SITE = GAATAATC,GAATACTC,GAATAGTC,GAATATTC,GAATGATC,GACTAATC,GACTACTC,GACTAGTC,GACTATTC,GACTGATC,GAGTAATC,GAGTACTC,GAGTAGTC,GAGTATTC,GAGTGATC,GATCAATC,GATCACTC,GATCAGTC,GATCATTC,GATCGATC,GATTAATC,GATTACTC,GATTAGTC,GATTATTC,GATTGATC and GENOME_FRAGMENT generated for MboI restriction enzyme.
The valid pairs (allValidPairs file) from HiC-Pro were used to generate .hic file using Juicer tools (version 1.7.6) ‘pre’ command.
Valid pairs (VI), self-circle (SC) and dangling-end (DE) interactions in cis were used as input for significant interaction calling in ‘.bedpe’ format. Mango (version 1.2.0) step 4 identified putative significant interaction anchors by MACS peak calling (Zhang et al., 2008) with MACS_qvalue = 0.05 and MACS_shiftsize = 75. Mango step 5 identified significant interactions with default parameters except maxinteractingdist = 2000000 and MHT = found. In NOD mice, the BEDPE was shifted to BL6 coordinates with MMARGE (PMID: 29893919) utilizing the NOD VCF files (version 5) from the Mouse Genomes Project (PMID: 21921910).
Assembly: GRCm38
Supplementary files format and content: hic file obtained from Juicer tools.

source_name: CD4+ T cells

extract_protocol:
Hi-C libraries were generated on 1×106 cells using with Arima-HiC+ kit (Arima Genomics) following manufacturer's recommendations.
Library was prepared using Accel-NGS @S Plus DNA Library kit (21024 Swift Biosciences), according to the manufacturer’s recommendations. Libraries were validated for quality and size distribution using Qubit dsDNA HS Assay Kit (Invitrogen, cat# Q32851) and TapeStation 2200 (Agilent). Libraries were paired-end sequenced (66bp+66bp) on NovaSeq 6000 (Illumina).

value: Pancreatic Lymph Node


title: HA-ICP22 cells, salt stress, DOX, replicate 1