title: PA-GFP Foxp3IRES-RFP_201


title: PA-GFP Foxp3IRES-RFP_199

status: Public on Jul 15 2021

type: SRA

city: New York

first: Johanne

last: Jacobsen

state: NY

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

library_source: transcriptomic

data_processing:
Raw FASTQ sequence files generated from Smartseq2 libraries were aligned to the mouse genome (v. mm10) with the annotated transcriptome (v. gencode M22) using STAR (v. 2.6). Subsequently, genome-mapped BAM files were processed using RSEM (v. 1.3.1) for gene quantification. The matrix of gene counts was used as input for analysis using the R package Seurat (v. 3.1.4.). To control unwanted sources of experimental variation, we eliminated any experiment-specific variables by regressing out the batch effect factors as described. Additionally, cells containing more than 10% of sequence reads aligned to mitochondrial genes were excluded before normalization.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files contains RSEM results for each cell.

molecule: total RNA

organism: Mus musculus

source_name: Germinal Centers

extract_protocol:
Single T cells were index-sorted into 96-well PCR plates containing 5 μl of TCL buffer (Qiagen) with 1% β-mercaptoethanol.
SmartSeq2: Libraries were prepared as previously described (Trombetta et al., 2014). Briefly, nucleic acids were extracted from sorted single cell using RNAClean XP SPRI beads (Beckman Coulter), and RNA was hybridized first using RT primer (/5BiosG/AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN) then reverse-transcribed into cDNA using TSO primer (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG) and RT maxima reverse transcriptase (Thermo Fisher Scientific). cDNA was amplified using ISPCR primer (AAGCAGTGGTATCAACGCAGAGT) and KAPA HiFi HotStart ReadyMix (Fisher Scientific), cleaned up using RNAClean XP SPRI beads three times, and tagmented using Nextera XT DNA Library Preparation Kit (Illumina). For each sequencing batch, up to four plates were barcoded at a time with Nextera XT Index Kit v2 Sets A-D (Illumina). Finally, dual-barcoded libraries were pooled and sequenced using the Illumina Nextseq 500.

tag: sequencing plate

tag: strain

value: PA-GFP Foxp3IRES-RFP

tag: experiment

tag: cell annotation


title: PA-GFP Foxp3IRES-RFP_200


title: ucMSC - H3 total - Young - Batch2

city: Houston

first: Weiwei

last: Dang

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

library_source: genomic

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low quality reads using Trim Galore version 0.4.4 with default parameters.
ChIP-seq reads were aligned to the hg19 genome assembly using using bowtie2 version 2.2.4 with default parameters.
Duplicated reads were removed using Picard with default parameters.
Peak calling was performed using MUSIC with default parameters, except that H3K9me3, H3K36me3 and H3K27me3 were performed using the get_motimal_broad_ERs model and peaks were called for the remaining datasets using get_optimal_punctate_ERs model.
Differentially bound regions were identified by comparing the changes between young and old data using the csaw R package version 3.11 with H3 total and input as internal control for histone markers and TBP, respectively.
Signal tracks were generated using H3 total or input as control. Deeptools bamCompare version 3.2.0 were used with paraeters: -p max --operation subtract -bs 10 --minMappingQuality 30 --extendReads --ignoreDuplicates --scaleFactors --blackListFileName blacklist.bed. scaleFactors were calucluated using SES method. black list regions of hg19 were downloaded from ENCODE website
Genome_build: hg19
Supplementary_files_format_and_content: normalized signal tracks in bigwig format
Supplementary_files_format_and_content: peak files in bed format

molecule: genomic DNA

organism: Homo sapiens

source_name: mesenchymal stem cells

growth_protocol: Human cord blood mesenchymal stem cells (hMSCs) were purchased from ATCC (PCS-500-010, lot #63216949). Cells were grown in low glucose DMEM (Life Technologies 11885-084) supplemented with 10% FBS (Life Technologies 16000-044, lot #1314735) and 1× penicillin/streptomycin (Life Technologies 15140-122) at 37ºC with 5% CO2 and 3% O2. Medium was replaced every 4 days in the absence of passaging. Cells were grown to ~70% confluence and split 1:4 as needed. Cell density was below the concentration needed for reliable detection with a hemocytometer (105 cells/mL), so the growth curve was estimated as 2 population doublings per passage.

extract_protocol:
Approximately 1 million PD12 and PD32 hMSCs were fixed in 1% formaldehyde at room temperature for 10 minutes. Following 3 washes in cold PBS, cell pellets were flash frozen on dry ice and store at -80ºC. Samples were thawed on ice and resuspended in 100uL RIPA with 10uM PFMS and 1× Halt Protease Inhibitor Cocktail (Thermo Fisher PI78439). Samples were sonicated to release chromatin with an average fragment length of 400bp in an EpiShear Multi-Sample sonicator (Active Motif 53062) using the following parameters: 5 minutes sonication, 30 second ON/OFF cycles, 50% amplitude at 4ºC. For each ChIP, 10uL of clarified lysate was added to 90uL of HBSS and used as input into the True MicroChIP Kit (Diagenode, C01010130); manufacturer’s instructions were followed beyond the fixation/sonication part of the protocol, using 2ug of each antibody. 2uL of clarified lysate was used as input and was treated as a sample starting from the reverse crosslinking step in the protocol. The ChIPed DNA was cleaned and concentrated using the Qiaquick PCR Purification Kit (Qiagen, 28104), following the manufacturer’s protocol with the following exception
Sequencing libraries were prepared using the MicroPlex Library Preparation Kit v2 (Diagenode, C05010014) following manufacturer’s instructions

treatment_protocol: Cells were cultured to PD12 and PD32.

tag: cell type

value: umbilical cord-derived mesenchymal stem cells (PCS-500-010, lot #63216949)

tag: cell passage

tag: chip antibody

value: histone Millipore #05-928, lot #2884434


title: ucMSC - H3 total - Young - Batch1

value: histone H3:Active Motif #61475


title: PA-GFP Foxp3IRES-RFP_198


title: PA-GFP Foxp3IRES-RFP_197

value: Tfr


title: ucMSC - input DNA - Old - Batch1


title: ucMSC - input DNA - Old - Batch2


title: PA-GFP Foxp3IRES-RFP_195

value: Filtered cell


title: PA-GFP Foxp3IRES-RFP_196


title: ucMSC - H3K9me3- Old - Batch2


title: PA-GFP Foxp3IRES-RFP_194


title: ucMSC - H3K4me1 - Young - Batch1


title: ucMSC - H3K4me3 - Old - Batch1


title: ucMSC - H3K4me1 - Old - Batch1


title: ucMSC - H3K36me3 - Old - Batch1


title: ucMSC - H3K27me3 - Old - Batch2


title: PA-GFP Foxp3IRES-RFP_190


title: PA-GFP Foxp3IRES-RFP_193


title: PA-GFP Foxp3IRES-RFP_189


title: ucMSC - H3K27ac - Old - Batch1


title: PA-GFP Foxp3IRES-RFP_188


title: ucMSC - TBP - Old - Batch1

value: TBP:Cell Signaling Technologies #440595, lot #1


title: ucMSC - H3 total - Old - Batch1


title: ucMSC - H3 total - Old - Batch2


title: PA-GFP Foxp3IRES-RFP_187


title: PA-GFP Foxp3IRES-RFP_185

value: CD4+ Resting


title: ucMSC - H3K27ac - Young - Batch1


title: KMS11_shM2 #1

city: Singapore

first: Jing Yuan

last: Chooi

address: 1E Kent Ridge Road

department: Yong Loo Lin School of Medicine

country: Singapore

institute: National University of Singapore

data_processing:
Trimming of adapter was performed with Trim Galore version 0.3.7. Most of the settings were set to default other then the specific ones found below with a brief description on their choice -q 20 –stringency 5 --paired
The trimmed reads data has to be mapped/aligned to a genome before any further analysis can take place. In this analysis, we are using STAR version 2.5.3 aligner to map the reads to the Ensembl Reference Sequence which is prepared by RNAEditor. The STAR aligner is used with default setting and the following optional setting changes --outSAMmapqUnique 60
The count matrix of gene expression is counted with featureCount found in the subread software package version 1.4.6.
Gene counting is performed with annotation GTF file packaged in RNAEditor with below setting. Reads which are marked as duplicate by the Picard software are also counted in this analysis as requested by user.
Differentially expressed genes (DEG) between conditions was analyzed with DEseq2.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample.

source_name: Myeloma Cells

growth_protocol: KMS11 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin and 100 mg/mL streptomycin. Cells were grown at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted with miRNeasy Mini Kit (Qiagen) according to manufacturer’s instruction.
Sequencing library was generated with 1 ug of total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina) according to manufacturer’s protocol.

treatment_protocol: Cells were infected with lentiviruses in the presence of 10 µg/mL polybrene (Sigma-Aldrich). Twenty four hours after infection, infection mixtures were replaced with normal growth medium. Cells were incubated at 37C in a humidified, 5% CO2 atmosphere for 72 h and subsequently collected for RNA extraction.

tag: genotype

value: NSD2 Knockdown

tag: cell line

value: Multiple myeloma cell line KMS11


title: PA-GFP Foxp3IRES-RFP_186


title: KMS11_control #1

value: Control


title: KMS11_shM2 #2


title: KMS11_control #2


title: PA-GFP Foxp3IRES-RFP_183


title: PA-GFP Foxp3IRES-RFP_182


title: PA-GFP Foxp3IRES-RFP_181


title: PA-GFP Foxp3IRES-RFP_192


title: PA-GFP Foxp3IRES-RFP_191


title: PA-GFP Foxp3IRES-RFP_180


title: PA-GFP Foxp3IRES-RFP_179


title: PA-GFP Foxp3IRES-RFP_178


title: PA-GFP Foxp3IRES-RFP_177


title: PA-GFP Foxp3IRES-RFP_184


title: PA-GFP Foxp3IRES-RFP_175


title: PA-GFP Foxp3IRES-RFP_176


title: PA-GFP Foxp3IRES-RFP_174

value: Cycling


title: PA-GFP Foxp3IRES-RFP_172


title: PA-GFP Foxp3IRES-RFP_173


title: PA-GFP Foxp3IRES-RFP_171


title: B (ptc+) 3

type: RNA

city: Washington

first: Xiaoyan

last: Zheng

state: District of Columbia

address: SEH, Suite 8840, 800 22nd Street NW

department: Anatomy and Cell Biology

institute: George Washington University School of Medicine and Health Sciences

description: Gene expression data from B cells

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on the Affymetrix GeneChip® Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with the multi-array average (RMA) for background correction followed by quantile normalization. Expression values were log2 transformed.

label: Biotin

organism: Drosophila melanogaster

source_name: Ptc expressing cells in the anterior (A) compartment flanking the A/P boundary of the wing imaginal discs

label_protocol: Biotinylated cRNA were prepared according to the standard protocol of the GeneChip® 3’ IVT Express Kit.

growth_protocol: Parental flies, embryos and larvae are grown at 25°C.

extract_protocol: Total RNA was extracted from sorted cells (RNeasy, Qiagen), quality was assessed with the Agilent Bioanalyzer 2100 (RIN > 7.0).

treatment_protocol: 200 pairs of wing imaginal discs were dissected from third instar larvae of the genotypes w; UAS-mCD8GFP/+; hh-Gal4/+ or w; UAS-mCD8GFP/+; ptc-Gal4/+. Discs were stored in Schneider's Drosophila Media plus 10% FBS on ice for less than two hours prior to cell dissociation. Discs were washed twice with 1 ml cell dissociation buffer. Elastase was diluted to 0.4 mg/ml in fresh cell dissociation buffer once discs were ready. Discs were incubated for 20 min at room temperature in 0.4 mg/ml elastase with stirring by a magnetic micro stirring bar. Undissociated tissue was spun out, cell viability was measured using the Beckman Vi-CELL Cell Viability Analyzer (>80%), and cells were immediately isolated using the BD FACSAria II system within the Stanford FACS facility. Dead cells labeled with propidium iodide were excluded during FACS, and purity of sorted cells was greater than 99% by post-sorting FACS analysis.

tag: tissue

value: Imaginal discs from wandering third instar larvae

value: w; ptc-Gal4/+; UAS-mCD8-GFP/+

tag: age

value: the wandering third instar larval stage


title: B (ptc+) 2

description: Gene expression data from B cells


title: PA-GFP Foxp3IRES-RFP_170


title: PA-GFP Foxp3IRES-RFP_168


title: PA-GFP Foxp3IRES-RFP_166


title: PA-GFP Foxp3IRES-RFP_167


title: PA-GFP Foxp3IRES-RFP_165


title: B (ptc+) 1

description: Gene expression data from B cells


title: A (hh-) 2

description: Gene expression data from A cells

source_name: Non-Hh expressing cells in the anterior (A) compartment of the wing imaginal discs

value: w; UAS-mCD8-GFP/+; hh-Gal4/+


title: A (hh-) 1

description: Gene expression data from A cells


title: PA-GFP Foxp3IRES-RFP_163


title: PA-GFP Foxp3IRES-RFP_162


title: PA-GFP Foxp3IRES-RFP_169


title: P (hh+) 3

description: Gene expression data from P cells

source_name: Hh expressing cells in the posterior (P) compartment of the wing imaginal discs


title: P (hh+) 2

description: Gene expression data from P cells


title: A (hh-) 3

description: Gene expression data from A cells


title: LB-HeLa-control-3 vs. LB-HeLa-stimulated-3

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA  * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan)  * Priming: 5xSSC, 0.1%SDS  * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul  * Hybridization: 45 min at 42C.  * Wash 2x: milliQ  * Wash: 5xSSC, 0.1%SDS  * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul)  * Hybridization: 16 hours at 42C.  * Wash 2x: 1xSSC, 0.2%SDS at 23C  * Wash 2x: 0.1xSSC, 0.2%SDS at 23C  * Wash 2x: 0.1xSSC at 23C  * Drying: blow with nitrogen for 3min at 30C

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. ImaGene feature extraction: Features were extracted using ImaGene software from BioDiscovery.

data_processing: Genes, no bg corr: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background subtraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve.

source_name: LB-HeLa-control

label_protocol: Robot amplification and labeling v1.0: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrophotometer (Molecular Devices), and a magnetic bead-locator (Beckman).  mRNA amplification protocol description:  * all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script.  * mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well.  * plate is incubated @ 70C for 10 mins, cooled to 48C.  * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAs Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and 1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well.  * plate is incubated @ 48C for 2 hours and cooled to room temperature.  * 106 ul water and subsequently mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul Ranse (Promega) is added and mixed in each well.  * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul .  * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems).  * Plate is incubated @37C for 4 hours.  * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturers protocol.   * Concentration is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot.  * Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C.    Labeling protocol description:   * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).   All subsequent steps are performed by the robot script :  * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ).  * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells.  * 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour.  * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes.  * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol.  * RNA concentration and labeling incorporation are measured (SpectraMax 190).  * 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C.  * Samples are stored at -20C until hybridization.

growth_protocol: Growth of cell lines: HeLa 57A cells, containing a stably transfected NF-κB luciferase reporter plasmid (Rodriguez et al., 1999), were routinely cultured in DMEM+10% FCS at 37C and 10% CO2.

extract_protocol: RNA extraction cell line: 1. Add 1 ml Trizol per 5x 106 cells in suspension (1 ml Trizol per 10 cm culture disk) and mix by pipetting, transfer to 1.5 ml eppendorf tube.   2. Incubate 5 min at room temperature.   3. Add chloroform (200 µl per ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature.   4. Centrifuge 20 min at 14000 rpm 4°C. After centrifugation, transfer the water-phase to a new 1.5-ml micro centrifuge tube.   5. add isopropanol to precipitate RNA. Use 0.5 ml per 1 ml Trizol. Mix by shaking, leave samples at RT for 10 minutes. Centrifuge at 14000 rpm for 15 min.   6. wash pellet with 75% ethanol. Centrifuge at 14000 rpm for 15 min. Carefully pipet off all ethanol (respin briefly and use a P20 for the last microliters). Airdry pellets briefly before dissolving in MilliQ water. Depending on pellet-size, this may take a while. Continue with RNeasy columns (Qiagen) for clean-up of RNA (maximal 100 µg/column)   7. Adjust each sample to a volume of 300 µl with sterile MilliQ water. Add 160 µl buffer RLT to the samples, and mix (= lysis buffer).   8. Add 240 µl ethanol (100% stored at -20 °C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipet and work as quick as possible). Next lysate, and so on.   9. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flowthrough, reuse collection tube. All centrifugation steps at room temperature! DNase treatment: D1. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm to wash. Discard the flow-through. Reuse the collection tube in step D3. D2. Prepare DNase I incubation mix (80 µl/reaction): add 10 µl DNase I stock solution to 70 µl Buffer RDD. Mix by gently inverting the tube. Buffer RDD is supplied with the RNase-Free DNase Set. Note: DNase I is especially sensitive to physical denaturation. Mixing should only be carried out by gently inverting the tube. Do not vortex. D3. Pipet the DNase I incubation mix (80 µl) directly onto the RNeasy silica-gel membrane, and place on the benchtop (20-30°C) for 15 min. Note: Make sure to pipet the DNase I incubation mix directly onto the RNeasy silica-gel membrane. DNase digestion will be incomplete if part of the mix sticks to the walls or the O-ring of the RNeasy column. D4. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm. Discard the flow-through and collection tube.   10. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 µl buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in next steps.  11. Pipet 500 µl buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube.   12. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane).   13. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipet 100 µl milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. Note: When small yields are expected, the elution volume can be lowered to a minimum of 35 µl milliQ.   14. Pipet the eluate of step 13 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. After elution, put all RNA-samples on ice. 15. Determine RNA concentration by measuring A260, and RNA intactness by Bioanalyzer. Snap-freeze and store eluate at -80 °C.

treatment_protocol: Treatment of cell lines: For the generation of the NF-κB activating periplasmic fraction (NAPF), C. jejuni 81116 were cultured in HI broth +0.05% glucose microaerophilic, shaking (160 rpm), 16 h at 42°C with a start OD550 of 0.0125 from an 5 h pre-culture. The bacteria were washed (15 min, 5,000 x g, 4°C), taken up in H2O (volume <15 start volume) and incubated (1 h, 20°C). After the incubation the supernatant was collected (2 min, 18,000 x g), filtered (0.22 µm filter), and fractionated to <3 kDa using a centricon concentrator. The NAPF was stored at -20°C until use. HeLa 57A cells were grown overnight in a 6-well plate and the next day without removing the FCS stimulated with 80 µl of NAPF (<3kDa) for 2 hours, after which cells were collected for RNA isolation. Untreated cells were taken along as control.

value: HeLa 57A

tag: treatment

value: control

source_name: LB-HeLa-stimulated

value: NAPF stimulated


title: PA-GFP Foxp3IRES-RFP_161

value: PA-GFP Foxp3IRES-RFP


title: LB-HeLa-stimulated-2 vs. LB-HeLa-control-2


title: LB-HeLa-control-1 vs. LB-HeLa-stimulated-1


title: P (hh+) 1

description: Gene expression data from P cells


title: LB-HeLa-stimulated-4 vs. LB-HeLa-control-4


title: DGM-12523_asthma_on_LAE

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: large airways

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: asthma

value: on

value: large airway epithelium


title: DGM-12681_asthma_on_LAE


title: DGM-12640_asthma_on_LAE


title: DGM-12649_asthma_on_LAE


title: DGM-12501_asthma_on_LAE


title: DGM-12602_asthma_on_LAE


title: PA-GFP Foxp3IRES-RFP_159


title: PA-GFP Foxp3IRES-RFP_158

value: Filtered cell


title: PA-GFP Foxp3IRES-RFP_164


title: DGM-12062_asthma_on_LAE


title: DGM-12366_asthma_on_LAE


title: PA-GFP Foxp3IRES-RFP_157


title: PA-GFP Foxp3IRES-RFP_156


title: DGM-12223_asthma_on_LAE


title: PA-GFP Foxp3IRES-RFP_155


title: DGM-12014_asthma_on_LAE


title: PA-GFP Foxp3IRES-RFP_153


title: DGM-11730_asthma_on_LAE


title: DGM-11955_asthma_on_LAE


title: PA-GFP Foxp3IRES-RFP_151


title: PA-GFP Foxp3IRES-RFP_154


title: DGM-11696_asthma_on_LAE


title: PA-GFP Foxp3IRES-RFP_152


title: DGM-11681_asthma_on_LAE


title: DGM-11641_asthma_on_LAE


title: DGM-11416_asthma_on_LAE


title: DGM-00199_asthma_on_LAE


title: PA-GFP Foxp3IRES-RFP_149


title: DGM-11562_asthma_on_LAE


title: DGM-00303_asthma_on_LAE


title: DGM-12687_asthma_off_LAE

value: off


title: PA-GFP Foxp3IRES-RFP_148


title: DGM-12688_asthma_off_LAE


title: PA-GFP Foxp3IRES-RFP_146


title: PA-GFP Foxp3IRES-RFP_147


title: PA-GFP Foxp3IRES-RFP_150


title: PA-GFP Foxp3IRES-RFP_143

value: Tfr


title: PA-GFP Foxp3IRES-RFP_142

value: CD4+ Resting


title: DGM-12680_asthma_off_LAE


title: PA-GFP Foxp3IRES-RFP_145


title: Dis3l2 P12 KO1

city: Bethesda

first: Zhengpin

last: Wang

state: MD

address: National Institutes of Health, 9000 Rockville Pike

department: Laboratory of Cellular and Developmental Biology

institute: NIDDK, NIH

data_processing:
removing adapter sequences with cutadapt
aligning the reads with hisat2 against Mus musculus genome sequence
using featurecounts to estimate the number of gene reads
using a R script to perform differential expression analysis
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: featurecounts output  and fastq files

source_name: P12 Testis_KO

growth_protocol: B6D2F1 mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Testes isolated from P12 aged control and knockout mice.

extract_protocol:
Testess were isolated, total RNA was isolated using a RNeasy Micro Kit.
The libraries were constructed by using a Universal RNA-Seq Library Preparation Kit (TECAN) per the manufacturer’s protocol in which double-strand cDNA was generated using a mixture of random and poly(T) priming, followed by fragmentation of double-stranded cDNA, end repair, adaptor ligation, strand selection, targeted transcript depletion with AnyDeplete, and PCR amplification to produce the final library.

tag: strain background

value: B6D2F1 inbred

value: Dis3l2 KO

value: postnatal day 12 (P12)

value: Testis


title: PA-GFP Foxp3IRES-RFP_144


title: PA-GFP Foxp3IRES-RFP_139


title: PA-GFP Foxp3IRES-RFP_141


title: DGM-12669_asthma_off_LAE


title: PA-GFP Foxp3IRES-RFP_140


title: Dis3l2 P12 WT3

source_name: P12 Testis_WT

value: Dis3l2 WT


title: Dis3l2 P12 KO2


title: DGM-12561_asthma_off_LAE


title: DGM-12426_asthma_off_LAE


title: DGM-12367_asthma_off_LAE


title: PA-GFP Foxp3IRES-RFP_138


title: DGM-12529_asthma_off_LAE


title: DGM-12567_asthma_off_LAE


title: DGM-12461_asthma_off_LAE


title: DGM-12349_asthma_off_LAE


title: Q2: MYB5OE

city: Gif-sur-Yvette

first: Pierre

middle: M

last: Jacob

address: Bâtiment 630, Rue Noetzlin

country: France

data_processing:
Reads were trimmed using CLC genomics workbench v10, quality score limit of 0.05 and maximum ambiguities 2, automatic read through adaptor trimming.
Reads were mapped using CLC genomics workbench v10 RNAseq analysis tool with mismatch cost 2, insertion cost 3, deletion cost 3, length fraction 0.8, similarity fraction 0.95.
Statistical analysis of differential gene expression was performed in CLC genomics workbench v10 using the differential expression for RNA-seq tool with Col-0 as control
Genome_build: TAIR10
Supplementary_files_format_and_content: Total count and normalized gene expression (RPKM, TPM and CPM) values for each sample and each gene

organism: Arabidopsis thaliana

growth_protocol: in vitro, half MS basal salt mixture, pH=5,8

extract_protocol:
Rneasy plant qiagen kit.
NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®

treatment_protocol: no treatment

value: 6 days old whole seedlings

tag: genotype/variation

value: MYB5 OE

tag: growth conditions

value: 8h photoperiod, 22C, in vitro 1/2 MS agar


title: U2: TT2OE

value: TT2 OE


title: S2: Col 0

source_name: Col 0

value: WT


title: Dis3l2 P12 WT2


title: Dis3l2 P12 KO3


title: Dis3l2 P12 WT1


title: DGM-12340_asthma_off_LAE

value: asthma


title: O2: TT2OE


title: DGM-12192_asthma_off_LAE


title: PA-GFP Foxp3IRES-RFP_137

value: PA-GFP Foxp3IRES-RFP


title: R2: TT2OE


title: PA-GFP Foxp3IRES-RFP_136


title: P2: Col 0


title: PA-GFP Foxp3IRES-RFP_135


title: N2: MYB5OE


title: PA-GFP Foxp3IRES-RFP_134


title: sufR-Complemented  DETA-NO treated- rep3 [comp_NO_3]

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

data_processing:
Illumina HiSeq-2500 for sequencing
BWA (0.7.12-r1039) was used for indexing the reference genome and aligning the reads (q >= 20)
SAMTOOLS (0.1.19-96b5f2294a) was used to filter out multiply mapped reads
BEDTOOLS(2.25.0) was used to calculate the read counts per gene
Normalisation and differential gene expression analysis was done using DESeq2 (genes with atleast 10 reads in each sample were selected for each comparative analysis)
Genome_build: Reference genome used : Mycobacterium tuberculosis H37Rv, accession number : NC_000962.3
Supplementary_files_format_and_content: tab delimited .txt files containing raw reads count (raw_data_counts.txt) and normalised read count (normalised_CPM.txt)

organism: Mycobacterium tuberculosis H37Rv

source_name: sufR-Complemented  DETA-NO treated

growth_protocol: The Mycobacterium tuberculosis H37Rv (Mtb) , MtbΔsufR, sufR-comp were grown in Middlebrook 7H9 broth medium supplemented with 0.2% glycerol, 0.5% BSA, 0.2% dextrose, and 0.085% NaCl (ADS) with 0.05% Tween 80 to an O.D.600 of 0.4 at 37 degrees Celcius at 180 rpm.

extract_protocol:
After 4 h post-exposure with DETA-NO, total RNA extraction was conducted using the FastRNA® Pro Blue Kit (MP Biomedicals) in accordance with the manufacturer’s instruction and further purified using RNeasy spin columns (Qiagen) as described (Mishra et al.,2017 ). Following purification and removal of genomic DNA, the RNA was quantified and assessed for purity by a 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). RNA samples with an RIN (RNA Integrity Number) value >8 were processed further for sequencing. Ribosomal RNA (16s and 23s rRNA) was removed by hybridization with magnetic beads-coupled oligonucleotide (MicrobExpress Kit, Life Technologies) and concentration of enriched mRNA was quantified by QuBit RNA HS Assay Kit (Life Technologies).
Libraries were prepared according to Illumina's instructions accompanying the NEBNext® Ultra™ II Directional RNA Library Prep kit (Catalog no-E7765L).In brief fragmentation and random priming of samples was done for 15 nanograms of mRNA for each sample. First and second strand cDNA synthesis was carried out using NEBNextUltra Dirctional RNA library prep kit for Illumina according to manufacturer’s protocol. Equimolar quantities of all libraries were pooled and sequenced in a highthroughput run on the Illumina HiSeq 2500 sequencer using 1X50 bp single-end reads and a 1% PhiX spike-in control.  .

treatment_protocol: Exponentially grown bacterial culture was exposed to 0.5 mM DETA/NO for 4 h at 37 degrees Celcius. Untreated counterpart was treated with same volume of 0.01M NaOH used to disolved DETA-NO.The experiment was carried out with three independent biological replicates.

value: sufR complemented

value: DETA-NO treated

value: log phase bacteria grown in 7H9 media


title: sufR-Complemented  DETA-NO treated- rep1 [comp_NO_1]


title: sufR-Complemented  DETA-NO treated- rep2 [comp_NO_2]


title: PA-GFP Foxp3IRES-RFP_132


title: sufR-Complemented  untreated control- rep1 [comp_UT_1]

source_name: sufR-Complemented  untreated control

value: Untreated control


title: PA-GFP Foxp3IRES-RFP_131


title: MtbΔsufR DETA-NO treated- rep3 [KO_NO_3]

source_name: MtbΔsufR DETA-NO treated

value: sufR knockout


title: sufR-Complemented  untreated control- rep3 [comp_UT_3]


title: PA-GFP Foxp3IRES-RFP_133


title: PA-GFP Foxp3IRES-RFP_130


title: M2: Col 0


title: DGM-12208_asthma_off_LAE

value: off

value: large airway epithelium


title: DGM-12183_asthma_off_LAE


title: MtbΔsufR DETA-NO treated- rep1 [KO_NO_1]


title: sufR-Complemented  untreated control- rep2 [comp_UT_2]


title: DGM-12127_asthma_off_LAE


title: PA-GFP Foxp3IRES-RFP_129


title: MtbΔsufR DETA-NO treated- rep2 [KO_NO_2]


title: MtbΔsufR untreated control- rep2 [KO_UT_3]

source_name: MtbΔsufR untreated control


title: PA-GFP Foxp3IRES-RFP_128


title: DGM-12019_asthma_off_LAE


title: Mtb DETA-NO treated- rep3 [WT_NO_3]

source_name: Mtb DETA-NO treated

value: wild type


title: MtbΔsufR untreated control- rep1 [KO_UT_2]


title: DGM-12020_asthma_off_LAE


title: DGM-12021_asthma_off_LAE


title: DGM-11907_asthma_off_LAE


title: PA-GFP Foxp3IRES-RFP_127

source_name: Germinal Centers


title: Mtb DETA-NO treated- rep2 [WT_NO_2]


title: DGM-11803_asthma_off_LAE


title: DGM-11936_asthma_off_LAE


title: Mtb DETA-NO treated- rep1 [WT_NO_1]


title: Mtb untreated control- rep3 [WT_UT_3]

source_name: Mtb untreated control


title: PA-GFP Foxp3IRES-RFP_126


title: PA-GFP Foxp3IRES-RFP_160


title: PA-GFP Foxp3IRES-RFP_125

value: CD4+ Resting


title: Mtb untreated control- rep2 [WT_UT_2]


title: PA-GFP Foxp3IRES-RFP_124

value: Tfr


title: Berlin_Monocyte_Berlin/Monocyte

type: genomic

first: Michael

last: Corley

address: 413 East 69th Street

department: Medicine, Division of Infectious Diseases

institute: Weill Cornell Medicine

description:
Berlin_Monocyte
Berlin/Monocyte

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol.

scan_protocol: Illumina Infinium HumanMethylationEPIC protocol. Scanned using Illumina HiScan System.

data_processing:
IDAT Data loaded into R using The Chip Analysis Methylation Pipeline (ChAMP) and normalized using BMIQ method.
matrix_processed.txt includes normalized average beta values.

label: Cy5 and Cy3

source_name: Monocyte

label_protocol: Illumina Infinium protocol. Cy5 and Cy3.

extract_protocol: Genomic DNA was extracted from FACS sorted cells in RLT buffer using the Qiagen Allprep Universal DNA/RNA kit according to manufacturer's instructions. DNA was bisulfite converted using the Zymo EZ DNA methylation kit.

value: FACS sorted Monocyte

tag: gender

value: Male

tag: disease state

value: Berlin

tag: individual


title: Mtb untreated control- rep1 [WT_UT_1]


title: 39_CD4_postART_HIV+/CD4

description:
39_CD4_postART
HIV+/CD4

source_name: CD4+ T cell

value: FACS sorted CD4+ T cell

value: HIV+

tag: time point

value: Post ART


title: PA-GFP Foxp3IRES-RFP_123

tag: sequencing plate

tag: strain

value: PA-GFP Foxp3IRES-RFP

tag: experiment

tag: cell annotation


title: Berlin_CD4_Berlin/CD4

description:
Berlin_CD4
Berlin/CD4

tag: cell type


title: 401_CD4_postART_HIV+/CD4

description:
401_CD4_postART
HIV+/CD4


title: 400_CD4_postART_HIV+/CD4

description:
400_CD4_postART
HIV+/CD4


title: PA-GFP Foxp3IRES-RFP_122


title: 276_CD4_postART_HIV+/CD4

description:
276_CD4_postART
HIV+/CD4


title: 211_CD4_postART_HIV+/CD4

description:
211_CD4_postART
HIV+/CD4


title: 207_CD4_postART_HIV+/CD4

description:
207_CD4_postART
HIV+/CD4


title: PA-GFP Foxp3IRES-RFP_121


title: 404_CD4_postART_HIV+/CD4

description:
404_CD4_postART
HIV+/CD4


title: PA-GFP Foxp3IRES-RFP_120


title: 391_CD4_postART_HIV+/CD4

description:
391_CD4_postART
HIV+/CD4


title: 389_CD4_postART_HIV+/CD4

description:
389_CD4_postART
HIV+/CD4


title: PA-GFP Foxp3IRES-RFP_119


title: PA-GFP Foxp3IRES-RFP_118


title: 212_CD4_postART_HIV+/CD4

description:
212_CD4_postART
HIV+/CD4


title: 366_CD4_postART_HIV+/CD4

description:
366_CD4_postART
HIV+/CD4


title: PA-GFP Foxp3IRES-RFP_117


title: DGM-11701_asthma_off_LAE

value: asthma


title: DGM-11694_asthma_off_LAE


title: 379_CD4_postART_HIV+/CD4

description:
379_CD4_postART
HIV+/CD4


title: DGM-11716_asthma_off_LAE


title: DGM-11667_asthma_off_LAE


title: DGM-11639_asthma_off_LAE


title: DGM-11666_asthma_off_LAE


title: DGM-11569_asthma_off_LAE


title: 161_CD4_postART_HIV+/CD4

description:
161_CD4_postART
HIV+/CD4


title: 210_CD4_postART_HIV+/CD4

description:
210_CD4_postART
HIV+/CD4


title: DGM-11212_asthma_off_LAE


title: DGM-11456_asthma_off_LAE


title: PA-GFP Foxp3IRES-RFP_116

value: Filtered cell


title: DGM-11482_asthma_off_LAE


title: DGM-11197_asthma_off_LAE


title: DGM-11632_asthma_off_LAE


title: 48_CD4_postART_HIV+/CD4

description:
48_CD4_postART
HIV+/CD4


title: 45_CD4_postART_HIV+/CD4

description:
45_CD4_postART
HIV+/CD4


title: 25_CD4_postART_HIV+/CD4

description:
25_CD4_postART
HIV+/CD4


title: 269_CD4_postART_HIV+/CD4

description:
269_CD4_postART
HIV+/CD4


title: 24_CD4_postART_HIV+/CD4

description:
24_CD4_postART
HIV+/CD4


title: PA-GFP Foxp3IRES-RFP_115


title: PA-GFP Foxp3IRES-RFP_114


title: 22_CD4_postART_HIV+/CD4

description:
22_CD4_postART
HIV+/CD4


title: 17_CD4_postART_HIV+/CD4

description:
17_CD4_postART
HIV+/CD4


title: DGM-11178_asthma_off_LAE


title: PA-GFP Foxp3IRES-RFP_113


title: 400_Mono_postART_HIV+/Monocyte

description:
400_Mono_postART
HIV+/Monocyte


title: 404_Mono_postART_HIV+/Monocyte

description:
404_Mono_postART
HIV+/Monocyte


title: 401_Mono_postART_HIV+/Monocyte

description:
401_Mono_postART
HIV+/Monocyte


title: PA-GFP Foxp3IRES-RFP_112


title: DGM-00775_asthma_off_LAE


title: DGM-10192_asthma_off_LAE


title: 391_Mono_postART_HIV+/Monocyte

description:
391_Mono_postART
HIV+/Monocyte


title: PA-GFP Foxp3IRES-RFP_111


title: 389_Mono_postART_HIV+/Monocyte

description:
389_Mono_postART
HIV+/Monocyte


title: 39_Mono_postART_HIV+/Monocyte

description:
39_Mono_postART
HIV+/Monocyte


title: 269_Mono_postART_HIV+/Monocyte

description:
269_Mono_postART
HIV+/Monocyte


title: 212_Mono_postART_HIV+/Monocyte

description:
212_Mono_postART
HIV+/Monocyte


title: PA-GFP Foxp3IRES-RFP_109


title: 379_Mono_postART_HIV+/Monocyte

description:
379_Mono_postART
HIV+/Monocyte


title: PA-GFP Foxp3IRES-RFP_110


title: PA-GFP Foxp3IRES-RFP_108


title: 366_Mono_postART_HIV+/Monocyte

description:
366_Mono_postART
HIV+/Monocyte


title: 276_Mono_postART_HIV+/Monocyte

description:
276_Mono_postART
HIV+/Monocyte


title: 211_Mono_postART_HIV+/Monocyte

description:
211_Mono_postART
HIV+/Monocyte


title: 210_Mono_postART_HIV+/Monocyte

description:
210_Mono_postART
HIV+/Monocyte


title: 207_Mono_postART_HIV+/Monocyte

description:
207_Mono_postART
HIV+/Monocyte


title: 161_Mono_postART_HIV+/Monocyte

description:
161_Mono_postART
HIV+/Monocyte


title: PA-GFP Foxp3IRES-RFP_107


title: 48_Mono_postART_HIV+/Monocyte

description:
48_Mono_postART
HIV+/Monocyte


title: DGM-12267_NS_LAE

value: healthy controls (nonsmokers)


title: DGM-12179_NS_LAE


title: DGM-12177_NS_LAE


title: DGM-12203_NS_LAE


title: DGM-00745_asthma_off_LAE


title: PA-GFP Foxp3IRES-RFP_105


title: 25_Mono_postART_HIV+/Monocyte

description:
25_Mono_postART
HIV+/Monocyte


title: DGM-12094_NS_LAE


title: 45_Mono_postART_HIV+/Monocyte

description:
45_Mono_postART
HIV+/Monocyte


title: 24_Mono_postART_HIV+/Monocyte

description:
24_Mono_postART
HIV+/Monocyte


title: DGM-12201_NS_LAE


title: 22_Mono_postART_HIV+/Monocyte

description:
22_Mono_postART
HIV+/Monocyte


title: PA-GFP Foxp3IRES-RFP_104


title: DGM-12087_NS_LAE


title: 17_Mono_postART_HIV+/Monocyte

description:
17_Mono_postART
HIV+/Monocyte


title: 50_Mono_Visit1_HIV+/Monocyte

description:
50_Mono_Visit1
HIV+/Monocyte


title: 39_Mono_Visit1_HIV+/Monocyte

description:
39_Mono_Visit1
HIV+/Monocyte


title: PA-GFP Foxp3IRES-RFP_103


title: PA-GFP Foxp3IRES-RFP_102


title: PA-GFP Foxp3IRES-RFP_106


title: 401_Mono_Visit1_HIV+/Monocyte

description:
401_Mono_Visit1
HIV+/Monocyte


title: PA-GFP Foxp3IRES-RFP_101


title: 391_Mono_Visit1_HIV+/Monocyte

description:
391_Mono_Visit1
HIV+/Monocyte


title: 389_Mono_Visit1_HIV+/Monocyte

description:
389_Mono_Visit1
HIV+/Monocyte


title: PA-GFP Foxp3IRES-RFP_100


title: 379_Mono_Visit1_HIV+/Monocyte

description:
379_Mono_Visit1
HIV+/Monocyte


title: 269_Mono_Visit1_HIV+/Monocyte

description:
269_Mono_Visit1
HIV+/Monocyte


title: PA-GFP Foxp3IRES-RFP_99


title: 212_Mono_Visit1_HIV+/Monocyte

description:
212_Mono_Visit1
HIV+/Monocyte


title: DGM-12053_NS_LAE


title: DGM-12050_NS_LAE


title: DGM-12027_NS_LAE


title: DGM-11961_NS_LAE


title: DGM-11962_NS_LAE


title: DGM-12044_NS_LAE


title: PA-GFP Foxp3IRES-RFP_97


title: 366_Mono_Visit1_HIV+/Monocyte

description:
366_Mono_Visit1
HIV+/Monocyte


title: 276_Mono_Visit1_HIV+/Monocyte

description:
276_Mono_Visit1
HIV+/Monocyte


title: 404_Mono_Visit1_HIV+/Monocyte

description:
404_Mono_Visit1
HIV+/Monocyte


title: 211_Mono_Visit1_HIV+/Monocyte

description:
211_Mono_Visit1
HIV+/Monocyte


title: 400_Mono_Visit1_HIV+/Monocyte

description:
400_Mono_Visit1
HIV+/Monocyte


title: 207_Mono_Visit1_HIV+/Monocyte

description:
207_Mono_Visit1
HIV+/Monocyte


title: 210_Mono_Visit1_HIV+/Monocyte

description:
210_Mono_Visit1
HIV+/Monocyte


title: PA-GFP Foxp3IRES-RFP_95


title: DGM-11921_NS_LAE


title: 48_Mono_Visit1_HIV+/Monocyte

description:
48_Mono_Visit1
HIV+/Monocyte


title: 161_Mono_Visit1_HIV+/Monocyte

description:
161_Mono_Visit1
HIV+/Monocyte


title: DGM-11956_NS_LAE


title: 45_Mono_Visit1_HIV+/Monocyte

description:
45_Mono_Visit1
HIV+/Monocyte


title: PA-GFP Foxp3IRES-RFP_98


title: 25_Mono_Visit1_HIV+/Monocyte

description:
25_Mono_Visit1
HIV+/Monocyte


title: PA-GFP Foxp3IRES-RFP_94


title: PA-GFP Foxp3IRES-RFP_96


title: PA-GFP Foxp3IRES-RFP_93


title: 50_CD4_Visit1_HIV+/CD4

description:
50_CD4_Visit1
HIV+/CD4


title: 22_Mono_Visit1_HIV+/Monocyte

description:
22_Mono_Visit1
HIV+/Monocyte


title: 39_CD4_Visit1_HIV+/CD4

description:
39_CD4_Visit1
HIV+/CD4


title: DGM-11852_NS_LAE


title: PA-GFP Foxp3IRES-RFP_92


title: DGM-11867_NS_LAE


title: 24_Mono_Visit1_HIV+/Monocyte

description:
24_Mono_Visit1
HIV+/Monocyte


title: DGM-11893_NS_LAE


title: 401_CD4_Visit1_HIV+/CD4

description:
401_CD4_Visit1
HIV+/CD4


title: PA-GFP Foxp3IRES-RFP_91


title: DGM-11657_NS_LAE


title: PA-GFP Foxp3IRES-RFP_90


title: 379_CD4_Visit1_HIV+/CD4

description:
379_CD4_Visit1
HIV+/CD4


title: 276_CD4_Visit1_HIV+/CD4

description:
276_CD4_Visit1
HIV+/CD4


title: DGM-11435_NS_LAE


title: 211_CD4_Visit1_HIV+/CD4

description:
211_CD4_Visit1
HIV+/CD4


title: 17_Mono_Visit1_HIV+/Monocyte

description:
17_Mono_Visit1
HIV+/Monocyte


title: PA-GFP Foxp3IRES-RFP_89


title: 400_CD4_Visit1_HIV+/CD4

description:
400_CD4_Visit1
HIV+/CD4


title: PA-GFP Foxp3IRES-RFP_88


title: 404_CD4_Visit1_HIV+/CD4

description:
404_CD4_Visit1
HIV+/CD4


title: PA-GFP Foxp3IRES-RFP_87


title: 389_CD4_Visit1_HIV+/CD4

description:
389_CD4_Visit1
HIV+/CD4


title: 391_CD4_Visit1_HIV+/CD4

description:
391_CD4_Visit1
HIV+/CD4


title: PA-GFP Foxp3IRES-RFP_86


title: 366_CD4_Visit1_HIV+/CD4

description:
366_CD4_Visit1
HIV+/CD4


title: 210_CD4_Visit1_HIV+/CD4

description:
210_CD4_Visit1
HIV+/CD4


title: 269_CD4_Visit1_HIV+/CD4

description:
269_CD4_Visit1
HIV+/CD4


title: 25_CD4_Visit1_HIV+/CD4

description:
25_CD4_Visit1
HIV+/CD4


title: 161_CD4_Visit1_HIV+/CD4

description:
161_CD4_Visit1
HIV+/CD4


title: PA-GFP Foxp3IRES-RFP_84


title: 207_CD4_Visit1_HIV+/CD4

description:
207_CD4_Visit1
HIV+/CD4


title: 24_CD4_Visit1_HIV+/CD4

description:
24_CD4_Visit1
HIV+/CD4


title: 45_CD4_Visit1_HIV+/CD4

description:
45_CD4_Visit1
HIV+/CD4


title: 22_CD4_Visit1_HIV+/CD4

description:
22_CD4_Visit1
HIV+/CD4


title: DGM-11378_NS_LAE


title: PA-GFP Foxp3IRES-RFP_82


title: DGM-01635_NS_LAE


title: DGM-11224_NS_LAE


title: 212_CD4_Visit1_HIV+/CD4

description:
212_CD4_Visit1
HIV+/CD4


title: PA-GFP Foxp3IRES-RFP_85


title: DGM-11374_NS_LAE


title: DGM-02007_NS_LAE


title: 29A_Mono_Control/Monocyte

description:
29A_Mono
Control/Monocyte

value: Control/HIV-


title: BO161N

city: Brussels

first: Geneviève

middle: Marie Henriette

last: Dom

address: 808 route de Lennik

department: Faculté de médecine

country: Belgium

institute: Université libre de Bruxelles

hyb_protocol: Gene expression analysis using the Human Genome U133 plus 2.0 arrays.

scan_protocol: Standard Affymetrix protocol.

data_processing: CEL file data were subjected to normalisation by RMA, and gene annotations were done using Carlson M.: hgu133plus2.db: Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2) R package version 3.2.

source_name: Human adult

label_protocol: Affymetrix 3’IVT plus labelling kit.

growth_protocol: The tissues were collected at the time of operations and / or autopsies and frozen.

extract_protocol: Total RNA extraction was performed using QIAzol reagent (Qiagen) and miRNeasy Mini kit (Qiagen). RNA quality and purity were measured using spectrophotometry. RNA integrity was verified using an automated gel electrophoresis system (Experion, Bio-Rad).

treatment_protocol: Frozen thyroid tissues were ground in liquid nitrogen and extracted with Trizol (Invitrogen).

value: thyroid normal tissues adjacent to thyroid cancer

tag: developmental stage

value: adult

tag: age/ age at operation


title: DGM-00056_NS_LAE

tag: tissue

value: large airway epithelium


title: PA-GFP Foxp3IRES-RFP_81


title: 17_CD4_Visit1_HIV+/CD4

description:
17_CD4_Visit1
HIV+/CD4


title: DGM-01620_NS_LAE

tag: treatment


title: DGM-00696_NS_LAE

tag: smoking status


title: BO160N


title: 23A_Mono_Control/Monocyte

description:
23A_Mono
Control/Monocyte


title: 48_CD4_Visit1_HIV+/CD4

description:
48_CD4_Visit1
HIV+/CD4


title: PA-GFP Foxp3IRES-RFP_83


title: PA-GFP Foxp3IRES-RFP_80


title: DGM-01270_NS_LAE


title: 17A_Mono_Control/Monocyte

description:
17A_Mono
Control/Monocyte


title: 21A_Mono_Control/Monocyte

description:
21A_Mono
Control/Monocyte


title: BO159N


title: PA-GFP Foxp3IRES-RFP_79


title: 16A_Mono_Control/Monocyte

description:
16A_Mono
Control/Monocyte


title: 15A_Mono_Control/Monocyte

description:
15A_Mono
Control/Monocyte


title: PA-GFP Foxp3IRES-RFP_78


title: Adult_D210_3

city: HeFei

first: Zhang

last: Fei

address: 130 Changjiang West Road, Shushan Distric

country: China

institute: Anhui Agricultural University

data_processing:
Firstly, Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
We used Bowtie2 and Tophat2 to map reads to the genome of species. Remaining reads (unmapped reads) were still mapped to genome using tophat-fusion.
CIRCExplorer was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion and CIRCExplorer.
All samples were generated unique circular RNAs. The differentially expressed circRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by edgeR.
Genome_build: Sus_scrofa.Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include srpbm and count values for each Sample …

organism: Sus scrofa

source_name: Testis

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
Approximately 5 mg of total RNAs was used to deplete ribosomal RNAs according to the manuscript of the Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, USA). Then left RNAs were treated with Rnase R (Epicentre Inc, Madison, WI, USA) to remove linear RNAs and to enrich circRNAs. After removing ribosomal and linear RNAs, the enriched circRNAs were fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA,which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP.. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs,The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the 150bp paired-end sequencing on an Illumina Hiseq 4000 (LC Bio, China) following the vendor's recommended protocol.

value: Adult

tag: tisssue

value: Testis

tag: age

value: post natal day 210

tag: breed

value: Landrace


title: PA-GFP Foxp3IRES-RFP_77

value: CD4+ Resting


title: 14A_Mono_Control/Monocyte

description:
14A_Mono
Control/Monocyte

value: FACS sorted Monocyte

tag: gender

value: Male


title: Adult_D210_2


title: PA-GFP Foxp3IRES-RFP_76


title: Adult_D210_1


title: Young_D30_3

value: Piglet

value: post natal day 30


title: PA-GFP Foxp3IRES-RFP_75

value: PA-GFP Foxp3IRES-RFP


title: Young_D30_2


title: PA-GFP Foxp3IRES-RFP_73

value: Tfr


title: 29A_CD4_Control/CD4

description:
29A_CD4
Control/CD4

value: FACS sorted CD4+ T cell

tag: disease state


title: Young_D30_1


title: 17A_CD4_Control/CD4

description:
17A_CD4
Control/CD4

tag: individual


title: 23A_CD4_Control/CD4

description:
23A_CD4
Control/CD4


title: 21A_CD4_Control/CD4

description:
21A_CD4
Control/CD4


title: PA-GFP Foxp3IRES-RFP_71


title: D14-2

city: Harbin

first: Jingli

last: Yang

address: Hexing Road 51

institute: Northeast Forestry University

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
The reference genomes and the annotation file were downloaded from Larix kaempferi single-molecule long read isoform sequence library. Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Genome_build: Lo.gene.fasta.transdecoder.cds.fa (Larix kaempferi single-molecule long read isoform sequence library)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Larix kaempferi

source_name: upper part of seedling

growth_protocol: Thirty days following emergence, transferred to15 cm pots (one plant per pot) filled with a 1:1 mixture. All experiments were grown in a greenhouse (12-h-light/12-h-dark, at 25 ± 1°C and 70 ± 10% humidity), keep soil water content at ≥ 70% field capacity (FC).

extract_protocol:
Upper part of  Larix kaempferi seedling (3 cm) were harvested, flash frozen on dry ice
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Four-month-old of L. kaempferi seedlings grown in the greenhouse into two groups, the drought treatment group was no watering for 14 d (D14), while normally watered seedlings were used as control group (CK).

value: upper part of seedling

value: four month

tag: stress

value: drought treatment


title: PA-GFP Foxp3IRES-RFP_72

tag: sequencing plate


title: D14-3


title: 16A_CD4_Control/CD4

description:
16A_CD4
Control/CD4

value: Control/HIV-


title: BO158N

value: thyroid normal tissues adjacent to thyroid cancer

value: adult


title: 11A_Mono_Control/Monocyte

description:
11A_Mono
Control/Monocyte


title: BO157N


title: BO103N

value: UNK


title: PA-GFP Foxp3IRES-RFP_70

tag: strain


title: BO75N


title: 15A_CD4_Control/CD4

description:
15A_CD4
Control/CD4


title: CK-3

value: control group


title: PA-GFP Foxp3IRES-RFP_74

tag: experiment


title: BO73N


title: PA-GFP Foxp3IRES-RFP_69

tag: cell annotation


title: PoolNB

value: thyroid:pool of normal tissues adjacent to thyroid cancer

value: mixed adults


title: CLONT

value: thyroid pool of normal tissues


title: TH FOE18

source_name: Human fetus

value: thyroid

value: fetus

value: ~7.5 gestation week


title: TH FOE15

value: ~10 gestation week


title: 11A_CD4_Control/CD4

description:
11A_CD4
Control/CD4

tag: cell type

value: Male


title: CK-2


title: TH FOE13

tag: developmental stage

value: ~7 gestation week


title: PA-GFP Foxp3IRES-RFP_68

value: PA-GFP Foxp3IRES-RFP

value: CD4+ Resting


title: CK-1

value: upper part of seedling

value: four month


title: 14A_CD4_Control/CD4

description:
14A_CD4
Control/CD4

value: FACS sorted CD4+ T cell

value: Control/HIV-


title: PA-GFP Foxp3IRES-RFP_67

value: Tfr


title: TH FOE14

tag: age/ age at operation


title: D14-1

tag: tissue

value: drought treatment


title: PA-GFP Foxp3IRES-RFP_66


title: stage 5 HH, 6 somites and 35 somites

city: Boston

first: Charlene

middle: Guillot

last: (Ryan)

state: MA

address: 60 Fenwood Road

department: Pathology

institute: Brigham and Women's hospital

description: For detailed information about samples, see the README_samples_information.txt on the Series record

data_processing:
Barcoding, sequencing and mapping of single-cell transcriptomes: Single-cell transcriptomes were barcoded using the inDrops pipeline using V3 sequencing adapters as previously reported 21. Following within-droplet reverse transcription, emulsions consisting of about 3000 cells were broken, frozen at −80 °C, and prepared as individual RNA-seq libraries. inDrops libraries were sequenced on an Illumina NextSeq 500 using the NextSeq 75 High Output Kits using standard Illumina sequencing primers and 61 cycles for read 1 and 14 cycles for read 2, 8 cycles each for index read 1 and index read 2. Raw sequencing data (FASTQ files) were processed using the inDrops.py bioinformatics pipeline available at https://github.com/indrops/indrops. Transcriptome libraries were mapped to Gallus gallus transcriptome built from the GRCg6a (GCA_000002315.5) genome assembly. Bowtie version 1.1.1 was used with parameter –e 200.
Processing of scRNA-seq data: Single-cell counts matrices were processed and analyzed using ScanPy (1.4.3) and custom Python scripts 24 (Code Availability). Low-complexity cell barcodes, which can arise from droplets that lack a cell but contain background RNA, were filtered in two ways. First, inDrops data were initially filtered to only include transcript counts originating from abundantly sampled cell barcodes. This determination was performed by inspecting a weighted histogram of unique molecular identifier–gene pair counts for each cell barcode, and manually thresholding to include the largest mode of the distribution. Second, low-complexity transcriptomes were filtered out by excluding cell barcodes associated with <400 expressed genes. Transcript unique molecular identifier counts for each biological sample were then reported as a transcript × cell table, adjusted by a total-count normalization, log-normalized, and scaled to unit variance and zero mean. Unless otherwise noted, each dataset was subset to the 1,000 most highly variable genes, as determined by a bin-normalized overdispersion metric.
Low-dimensional embedding and clustering: Processed single-cell data were projected into a 50-dimensional PCA subspace, (k = 10 except 35 somite k=15) nearest-neighbor graph using Euclidean distance and 50 PCA dimensions and visualized using UMAP (Uniform Manifold Approximation and Projection) representation.  Clustering was performed using Louvain community detection algorithms.
Genome_build: GRCg6a (GCA_000002315.5) genome assembly
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Gallus gallus

source_name: Epiblast / Tailbud

extract_protocol:
Single-cell dissociation protocols were optimized to achieve >90% viability and minimize doublets before sample collection. To generate the samples, 4 embryos were harvested for each stage and cells were dissociated and captured on an inDrops21 setup on the same day. For stage 5HH and 6-somite samples, the anterior half of the PS including the Hensen’s Node and the posterior region of the neural plate were dissected. 2 tailbud regions and 2 posterior ends (including the last somite formed, the PSM and posterior neural tube and the tail bud) were dissected to generate the 35-somite sample. For single cell dissociation, the dissected tissue was briefly rinsed in cold PBS, and incubated in Accutase (Gibco) for 10 to 25 min at 37 °C followed by mechanical dissociation. The cell suspension was analyzed with a hemocytometer to assess the quality of the dissociation and evaluate cell density. Dissociated cells were centrifuged at 350g for 5 min at 4 °C and resuspended at a concentration of 250,000 cells per microliter in 0.25% BSA in PBS. 2× 3,000 cells were sequenced per sample. Two biological replicates were collected per sample and the sequencing data from both samples were combined for data analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Epiblast / Tailbud

tag: samples number

tag: biological replicates


title: SG AdNTF3-Tg

city: Atlanta

first: Bingzhong

last: Xue

state: Georgia

address: 50 Decatur St SE

department: Biology

institute: Georgia State University

data_processing:
raw reads are filtered into clean reads which will be aligned to the reference sequences.
The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio.
Genes and isoforms expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). FPKM method is used in calculated expression level
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: sympathetic ganglia

extract_protocol:
T1-T4 Sympathetic ganglia were removed, flash frozen in liquid nitrogen, and RNA was harvested using Tri-reagent.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 or other sequencer when necessary

value: T1-T4 sympathetic ganglia

tag: genotype

value: 12 week


title: PA-GFP Foxp3IRES-RFP_65


title: SG WT_2

value: WT

tag: age


title: SG TRKC+/-

value: TRKC+/-


title: Kidney IRLacz rep4

city: 武汉

first: 汉

last: 朱

state: 湖北

address: 1095 解放大道， 武汉 430030， 中国

institute: 肾

data_processing:
cDNA quantity and labeling efficiency was checked using Agilent 2100 Bioanalyzer and ABI StepOne Plus Real-Time PCR System, and sequenced using the Illumina HiSeq platform
The filter software soapnuke (v1.5.2) was used for filtering raw reads, and the RNA seq reads gene comparison was carried out by HISAT (hierarchical indexing for shared alignment of scripts) software (v2.0.4).
Stringtie (v1.0.4) was used to reconstruct the transcripts of each sample, then cuffmerge was used to integrate the reconstruction information of all samples, and then cuffcompare was used to compare the integrated transcripts with the reference annotation information to define the new transcripts.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Kidney

extract_protocol:
Kidneys were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Agilent 2100 Bioanalyzer was used.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Kidney


title: SG WT_1


title: Kidney IRLacz rep3

address: 1095 解放大道， 武汉 430030， 中国


title: PA-GFP Foxp3IRES-RFP_64

value: Filtered cell


title: Kidney IRLacz rep2

address: 1095 解放大道， 武汉 430030， 中国


title: Kidney IRLacz rep1

address: 1095 解放大道， 武汉 430030， 中国


title: TH FOE12

value: thyroid

value: fetus

value: ~11 gestation week


title: PA-GFP Foxp3IRES-RFP_63

value: PA-GFP Foxp3IRES-RFP

value: CD4+ Resting


title: TH FOE8

value: ~9 gestation week


title: 10mMKO_VTreg

city: Shanghai

first: Bin

last: Li

address: South Chongqing Road 208

institute: Shanghai Institue of Immunology

description: 10mMKO_VTreg vs 10mWT_VTreg

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008)
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: adipose tissue

extract_protocol:
LN Tregs (from 4-month old Foxp3Cre mice) and adipose Tregs (from 4-month-old Foxp3Cre, 4-month-old obese Foxp3Cre, 10-month old Foxp3Cre and 10-month-old Med23fl/fl;Foxp3Cre mice) were sorted from indicated mice. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adipose tissue

value: 10-month old


title: 10mWT_VTreg

description: 10mMKO_VTreg vs 10mWT_VTreg


title: TH FOE6

value: ~8 gestation week


title: TH FOE5


title: TH FOE2


title: Kidney IRLac rep5

address: 1095 解放大道， 武汉 430030， 中国


title: PA-GFP Foxp3IRES-RFP_61

first: Johanne

last: Jacobsen

data_processing:
Raw FASTQ sequence files generated from Smartseq2 libraries were aligned to the mouse genome (v. mm10) with the annotated transcriptome (v. gencode M22) using STAR (v. 2.6). Subsequently, genome-mapped BAM files were processed using RSEM (v. 1.3.1) for gene quantification. The matrix of gene counts was used as input for analysis using the R package Seurat (v. 3.1.4.). To control unwanted sources of experimental variation, we eliminated any experiment-specific variables by regressing out the batch effect factors as described. Additionally, cells containing more than 10% of sequence reads aligned to mitochondrial genes were excluded before normalization.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files contains RSEM results for each cell.

extract_protocol:
Single T cells were index-sorted into 96-well PCR plates containing 5 μl of TCL buffer (Qiagen) with 1% β-mercaptoethanol.
SmartSeq2: Libraries were prepared as previously described (Trombetta et al., 2014). Briefly, nucleic acids were extracted from sorted single cell using RNAClean XP SPRI beads (Beckman Coulter), and RNA was hybridized first using RT primer (/5BiosG/AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN) then reverse-transcribed into cDNA using TSO primer (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG) and RT maxima reverse transcriptase (Thermo Fisher Scientific). cDNA was amplified using ISPCR primer (AAGCAGTGGTATCAACGCAGAGT) and KAPA HiFi HotStart ReadyMix (Fisher Scientific), cleaned up using RNAClean XP SPRI beads three times, and tagmented using Nextera XT DNA Library Preparation Kit (Illumina). For each sequencing batch, up to four plates were barcoded at a time with Nextera XT Index Kit v2 Sets A-D (Illumina). Finally, dual-barcoded libraries were pooled and sequenced using the Illumina Nextseq 500.


title: TH FOE7

value: ~10 gestation week


title: Kidney IRLac rep4

address: 1095 解放大道， 武汉 430030， 中国


title: TH FOE1


title: Rep5_WT

city: San Francisco

first: Jason

last: Fernandes

state: CA

address: 600 16th Street, Genentech Hall, Room S574, MC 2280

institute: UCSF

description:
HIV-1 RNA
Viral RNA harvested and sequenced after spread

data_processing:
Library strategy: Amplicon-Sequencing
FASTQs were generated using bcl2fastq v2.17.1.14
Codons were counted using countDMS
Genome_build: HIV-1 NL4-3
Supplementary_files_format_and_content: tab

organism: Human immunodeficiency virus 1

growth_protocol: SupT1 human T-cell lines were maintained in RPMI (supplemented with 25 mM HEPES pH 7.4, 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin/streptomycin) at 37°C and 5% CO2.

extract_protocol:
RNA was extracted from virions by ZR-96 Viral RNA extraction kits (Zymo) and eluted in 15 ul water. cDNA was amplified from 5uL of extracted RNA using the iScript Advanced (BioRad) cDNA synthesis.
PCR amplicons were made from DNA using primers specific to the Env LLP-2 region

treatment_protocol: We infected SupT1 cells at low MOI (multiplicity of infection) with each library individually and measured the change in allele frequencies after approximately 6 generations of viral spread (Figure 3A)

tag: source

value: SupT1 human T cell line

tag: treatment

value: Post-selection


title: Rep4_WT


title: PA-GFP Foxp3IRES-RFP_60

address: 1230 York Avenue

institute: The Rockefeller University


title: Rep6_WT


title: Rep3_WT


title: Kidney IRLac rep3

address: 1095 解放大道， 武汉 430030， 中国


title: PA-GFP Foxp3IRES-RFP_59

value: Tfr


title: Kidney IRLac rep2

address: 1095 解放大道， 武汉 430030， 中国


title: PA-GFP Foxp3IRES-RFP_58


title: Rep2_WT


title: PA-GFP Foxp3IRES-RFP_62


title: 4mWT_VTreg2

description: 4mWT_VTreg vs 4mWT_LNTreg

value: 4-month old


title: PA-GFP Foxp3IRES-RFP_57


title: Rep1_WT


title: 4mHFDWT_VTreg1

description: 4mHFDWT_VTreg vs 4mWT_LNTreg


title: 4mWT_LNTreg

description: 4mWT_VTreg vs 4mWT_LNTreg

source_name: Lymph nodes

value: Lymph nodes


title: Kidney IRLac rep1

address: 1095 解放大道， 武汉 430030， 中国

value: Kidney


title: Rep6_L776


title: Kidney IR rep5

address: 1095 解放大道， 武汉 430030， 中国


title: PA-GFP Foxp3IRES-RFP_55


title: PA-GFP Foxp3IRES-RFP_56


title: Rep5_L776


title: Kidney IR rep4

address: 1095 解放大道， 武汉 430030， 中国


title: PA-GFP Foxp3IRES-RFP_54


title: Kidney IR rep2

address: 1095 解放大道， 武汉 430030， 中国


title: PA-GFP Foxp3IRES-RFP_53


title: FVFneg_CD_Rep2

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

country: Germany

institute: Helmholtz Zentrum München German Research Center for Environmental Health

description: Gene expression data from FACS purified FVF-negative crypt cells, control diet, biological replicate 2

hyb_protocol: According to the Affymetrix expression protocol

data_processing: Expression data were RMA normalized using the Expression Console (v.1.3.0.187, Affymetrix) with standard settings including median polish and sketch-quantile normalisation

label_protocol: Ovation Pico WTA System V2 in combination with the Encore Biotin Module (Nugen)

growth_protocol: All animal experiments were carried out in compliance with the German Animal Protection Act, the guidelines of the Society of Laboratory Animals (GV-SOLAS) and Federation of Laboratory Animal Science Associations (FELASA). Mice were housed in groups of two to four animals at 23±1°C, with constant humidity and on a 12 hours light–dark cycle with free access to water and food.

extract_protocol: miRNeasy Mini Kit (Qiagen)

treatment_protocol: 10-12 weeks old male mice were randomized into test groups matched based on body weight, with similar variance, and given ad libitum access to either an obesogenic high-fat diet with sucrose (HFHSD) [58 % kcal from fat, 25 % kcal from carbohydrates, 17% kcal from protein (Research Diets Inc., USA, # D12331)] or a control diet (CD) [11 % kcal from fat, 64 % kcal from carbohydrates, 25 % kcal from protein (ssniff Spezialdiäten GmbH, E15051-04)] for a period of 11-13 weeks. For isolation of small intestinal crypts, small intestines were removed and washed with cold PBS. Villi were scraped off with a glass slide. The remaining tissue was cut into 2-cm pieces, washed several times with cold PBS and incubated in 2 mM EDTA/PBS for 35 min at 4 °C on a tube roller. Subsequently, crypts were harvested by rigorous shaking and filtered through a 70-µm mesh to remove villous fragments. For single cell preparation, isolated crypts were incubated with TrypLE (Life technologies, #12605) for 5 min on ice and then 5 min at 37 °C and treated with 10 µg/ml DNase in crypt complete medium (DMEM/F-12 containing 10 % FCS) for 5 min at 37 °C. Single cell suspension was achieved by gentle repeated pipetting. Cells were washed twice with FACS buffer (2 % FCS in PBS) and pelleted at 300xg, 5 min, 4 °C. For flow cytometry, cells were collected in 1-2 ml FACS buffer (2 % FCS, 2 mM EDTA in PBS) supplemented with 10 µM Rock-inhibitor (Sigma-Aldrich, #Y0503) and passed through the 40 µm cell strainer caps of FACS tubes.

value: C57Bl/6; Foxa2-Venus fusion (FVF)

tag: gender

value: male

value: crypt cells

tag: fvf status

value: negative

tag: diet

value: control diet


title: Rep3_L776


title: FVFneg_CD_Rep1

description: Gene expression data from FACS purified FVF-negative crypt cells, control diet, biological replicate 1

scan_protocol: According to the Affymetrix expression protocol


title: Rep4_L776


title: Kidney IR rep3

address: 1095 解放大道， 武汉 430030， 中国


title: Kidney IR rep1

address: 1095 解放大道， 武汉 430030， 中国


title: Rep2_L776


title: PA-GFP Foxp3IRES-RFP_51

city: New York

tag: sequencing plate

value: PA-GFP Foxp3IRES-RFP

value: CD4+ Resting


title: Kidney sham rep5

address: 1095 解放大道， 武汉 430030， 中国

tag: strain


title: PA-GFP Foxp3IRES-RFP_52

tag: experiment


title: Rep1_L776


title: FVFlow_CD_Rep3

description: Gene expression data from FACS purified FVF-low crypt cells, control diet, biological replicate 3

value: low


title: Kidney sham rep4

address: 1095 解放大道， 武汉 430030， 中国


title: PA-GFP Foxp3IRES-RFP_50

tag: cell annotation

value: Filtered cell


title: FVFlow_CD_Rep2

description: Gene expression data from FACS purified FVF-low crypt cells, control diet, biological replicate 2

tag: cell type


title: FVFlow_CD_Rep1

description: Gene expression data from FACS purified FVF-low crypt cells, control diet, biological replicate 1


title: Kidney sham rep3

address: 1095 解放大道， 武汉 430030， 中国


title: FVFhigh_CD_Rep1

description: Gene expression data from FACS purified FVF-high crypt cells, control diet, biological replicate 1

value: high


title: Kidney sham rep2

address: 1095 解放大道， 武汉 430030， 中国


title: Rep5_L775


title: PA-GFP Foxp3IRES-RFP_49


title: Rep4_L775


title: FVFhigh_CD_Rep2

description: Gene expression data from FACS purified FVF-high crypt cells, control diet, biological replicate 2


title: PA-GFP Foxp3IRES-RFP_48


title: FVFneg_HFHSD_Rep3

description: Gene expression data from FACS purified FVF-negative crypt cells, high-fat high-sugar diet, biological replicate 3

value: high-fat high-sugar diet


title: FVFneg_HFHSD_Rep2

description: Gene expression data from FACS purified FVF-negative crypt cells, high-fat high-sugar diet, biological replicate 2


title: Rep3_L775

value: SupT1 human T cell line


title: Kidney sham rep1

address: 1095 解放大道， 武汉 430030， 中国


title: PA-GFP Foxp3IRES-RFP_47


title: Rep2_L775

value: Post-selection


title: PA-GFP Foxp3IRES-RFP_46

value: Tfr


title: anti-PPAR-γ Cut-and-run Seq

description: Cut-and-run assay with anti-PPAR-γ antibody

data_processing:
Library strategy: CUT&RUN
Reads were aligned to the mouse genome mm10 using Bowtie2 v2.2.5.
Uniquely aligned reads were extracted using SAMtools v1.1 and sorted and indexed using SAMtools. Sam files were further transformed into Bam or Bam.bai format with SAMtools. Integrative Genomics Viewer (IGV) was used to visualize Bam and Bam.bai files.
Genome_build: mm10
Supplementary_files_format_and_content: MACS peaks/summits files

source_name: adipose Treg cells

growth_protocol: Murine adipose TCRβ+CD4+CD25hiYFP+ Tregs were sorted from SVF pellets on a BD FACS ARIA III sorter (BD Biosciences), and cells were further subjected to Cut-and-run assay.

extract_protocol:
Murine TCRβ+CD4+CD25hiYFP+ adipose Treg cells were sorted from 4-month old male Foxp3Cre mice. Treg cells were washed and bound to Concanavalin A-coated magnetic beads, then permeabilized with Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and protease inhibitor) containing 0.05% digitonin (Dig Wash), and incubated with specific primary antibody overnight at 4℃. Cell-bead slurry was washed twice with Dig Wash, incubated with Protein A-MNase (pA-MN) for 1 hour at 4℃, then washed twice more with Dig Wash. Slurry was then placed on an ice-cold block and incubated with Dig Wash containing 2 mM CaCl2 to activate pA-MN digestion. After an antibody-specific incubation period, one volume of 2× Stop Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 0.05 mg/mL glycogen, 5 μg/mL RNase A, 2 pg/mL heterologous spike-in DNA) was added to stop the reaction, and fragments were released by 30-minute incubation at 37℃. Samples were centrifuged 5 minutes at 16000xg, and supernatant was recovered. DNA was extracted via the DNA Purification Buffers and Spin Columns (CUT&RUN, Cell Signaling Technology, Cat#14209). Resulting DNA was subjected to sequencing. anti-HIF-1α (Novus, Cat#NB100-105) and anti-PPAR-γ (Abcam, Cat#ab41928) antibodies were used.
Finally, DNA libraries were amplified and further sequenced on the Illumina Hiseq x10 platform.

treatment_protocol: No treatment

tag: Sex

value: adipose tissue

value: 4-month old


title: Rep6_L775


title: Rep1_L775


title: FVFneg_HFHSD_Rep1

description: Gene expression data from FACS purified FVF-negative crypt cells, high-fat high-sugar diet, biological replicate 1


title: anti-HIF-1α Cut-and-run Seq

description: Cut-and-run assay with anti-HIF-1α antibody


title: PA-GFP Foxp3IRES-RFP_45


title: Rep6_L774


title: HIF-1α-KO

description:
Bulk rna sequencing of  HIF-1α-KO adipose Treg cells
SC2003LBLY01

data_processing:
Raw data of fastq format were firstly processed through in-house perl scripts. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0). The P values were adjusted using the Benjamini & Hochberg method.
Genome_build: mm8
Supplementary_files_format_and_content: xls file include differentially expressed genes between WT and HIF-1α-KO adipose Treg cells

extract_protocol:
Adipose Tregs were sorted from Foxp3Cre and Hif1afl/fl;Foxp3Cre mice. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the Construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.
Libraries were further sequenced on the Illumina Hiseq x Ten platform. On average about 200 million 150bp paired end reads were generated per sample.


title: FVFlow_HFHSD_Rep1

description: Gene expression data from FACS purified FVF-low crypt cells, high-fat high-sugar diet, biological replicate 1


title: FVFlow_HFHSD_Rep2

description: Gene expression data from FACS purified FVF-low crypt cells, high-fat high-sugar diet, biological replicate 2


title: FVFhigh_HFHSD_Rep2

description: Gene expression data from FACS purified FVF-high crypt cells, high-fat high-sugar diet, biological replicate 2


title: Rep5_L774

description:
HIV-1 RNA
Viral RNA harvested and sequenced after spread


title: FVFhigh_HFHSD_Rep3

description: Gene expression data from FACS purified FVF-high crypt cells, high-fat high-sugar diet, biological replicate 3


title: Rep4_L774


title: WT

description:
Bulk rna sequencing of WT adipose Treg cells
SC2003LBLY02


title: PA-GFP Foxp3IRES-RFP_42


title: adipose Treg cells scATAC-Seq

description: DNA peaks

data_processing:
Fastq files were processed using Cell Ranger ATAC v1.0 (10x Genomics) based on mm10 reference genome.
We utilized functions in the Seurat v3 package to pre-process the scATAC-seq data. We retained cells with over 5,000 peaks, and peaks detected in at least 100 cells. We therefore obtained 4,677 adipose Treg cells after filtering. We next performed latent semantic indexing (lsi) on the scATAC-seq dataset to reduce dimensionality. To link the scATAC-seq accessibility peaks to genes, we summed peaks intersecting the gene body and 2 kilobase upstream region to give a gene activity score for each gene in each cell. Finally, the created gene activity matrix was used as an input for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tsv mtx and bed files include barcodes, fragments, matrix and peaks information for each cell

growth_protocol: Murine adipose TCRβ+CD4+CD25hiYFP+ Tregs were sorted from SVF pellets on a BD FACS ARIA III sorter (BD Biosciences), and cells were further subjected to sequencing

extract_protocol:
Briefly, the isolated nuclei suspension was diluted and incubated with transposition mix for a targeted nuclei recovery. The single-cell GEMs (Gel Bead in emulsion) were further captured on the chromium Chip E (10X Genomics 1000082). Following GEM incubation, clean up was performed using Dynabeads MyOne Silane beads (10X Genomics 2000048) and SPRIselect reagent (Beckman Coulter B23318).
Finally, scATAC-seq libraries were amplified and further sequenced on the Illumina Hiseq x10 platform. On average about 150bp paired end reads were generated.

value: Treg


title: PA-GFP Foxp3IRES-RFP_43


title: YR90d3

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Genome_build: Oncorhynchus mykiss Omyk_1.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Oncorhynchus mykiss

source_name: dorsal skin_90 day

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phenotype

value: yellow mutant

value: dorsal skin

value: 90 day


title: single-cell RNA sequencing dataset [TF]

data_processing:
Data were analyzed using the Cell Ranger Pipeline.
We next utilized Seurat package to normalize and scale the single-cell gene expression data.
The corrected expression matrix was used as an input for further analysis.
Genome_build: mm8
Supplementary_files_format_and_content: csv and tsv files include paired TCR clonotypes, barcodes, features and matrix information for each cell

extract_protocol:
Cells were then encapsulated in one lane of a 10x Chromium instrument, Libraries were constructed with a Single Cell 5′ Reagent Kit. And TCR transcripts can be enriched with a Single Cell V(D)J Reagent Kit.
Libraries were further sequenced on the Illumina Hiseq x10 platform. On average about 200 million 150bp paired end reads were generated per sample.

tag: genotype/variation

tag: tissue

value: TCRBeta+CD4+CD25+YFP+ adipose Treg cells


title: YR90d2


title: PA-GFP Foxp3IRES-RFP_41


title: single-cell TCR sequencing dataset [TC]


title: YR1d3

source_name: dorsal skin_1 day

value: 1 day


title: Rep2_L774


title: YR1d2


title: PA-GFP Foxp3IRES-RFP_44

value: PA-GFP Foxp3IRES-RFP


title: PA-GFP Foxp3IRES-RFP_39

value: CD4+ Resting


title: Rep1_L774


title: PA-GFP Foxp3IRES-RFP_38


title: YR1d1


title: Rep6_D773


title: FVFhigh_HFHSD_Rep1

description: Gene expression data from FACS purified FVF-high crypt cells, high-fat high-sugar diet, biological replicate 1

value: C57Bl/6; Foxa2-Venus fusion (FVF)

value: male

value: crypt cells


title: Rep5_D773


title: PA-GFP Foxp3IRES-RFP_37

value: Filtered cell


title: DCCO high dose rep5

city: Ste anne de bellevue

first: Jessica

last: Head

state: QC

address: 21111 Lakeshore Road

country: Canada

institute: McGill University

description: DCCO_KO_abundance_table_all_birds_Seq2Fun2.txt

data_processing:
Seq2Fun used for quantification of protein-coding genes
Seq2Fun starts the raw reads quality check and employs the translated search and does not require transcriptome de novo assembly. In brief, each pair of reads was first trimmed by both ends with an average base quality 20 in a sliding window size 4, followed by poly(G) trimming. The sequencing errors were corrected on the overlapped region of the read pair before ploy(A) removal. The overlapped read pair was joined to form a single end clean read. For the translated search, the clean read was translated to amino acid fragments using all possible reading frames from both directions. Length filtering was performed on the fragments and only the longest were kept for searching. The fragment homology searching was  performed using FMI based on Burrows-Wheeler transform data structure in Seq2Fun GREEDY mode. The gene abundance tables were generated by summarizing all the read-gene pairs. The protein sequences used by Seq2Fun for JQ and DCCO were retrieved from the KEGGREST database, consisting of 370644 protein sequences representing 36448 ortholog genes from 24 birds species (Tenenbaum and Maintainer 2020). The Gene Entrez IDs were used to retrieve Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog (KO) IDs.
Differential gene expression analysis was performed using EdgeR.
Genes were first filtered for low counts using minimum counts per million threshold of 0.5, then differentially expressed genes were identified between each treatment group (medium or high dose) and the control based on the combination of fold-change expression (log2FC ≥ 1) and adjusted p-value based on a false discovery rate (FDR < 0.05).
Genome_build: KEGGREST database with 24 bird species
Supplementary_files_format_and_content: tab delimited txt file with gene abundance counts for every gene and every sample

organism: Phalacrocorax auritus

source_name: embryonic liver

growth_protocol: Eggs were incubated at 37oC and 60% humidity

extract_protocol:
Individual liver samples were homogenized in buffer RLT using a TissueLyser II (Qiagen, Toronto, ON, CA), and RNA extracted using the RNeasy® Mini QIAcube Kit (Qiagen, Toronto, ON, CA) following the manufacturer’s protocol. An extra DNAse I digestion step was included in order to eliminate genomic DNA contamination. Total RNA concentration and purity was spectrophotometrically measured using the QIAxpert.
Library preparation and mRNA sequencing was performed by the Genome Quebec Innovation Centre (Montreal. QC). Libraries were sequenced to produce paired-end 101 bp reads using Illumina HiSeq 4000.

treatment_protocol: Dosing solutions were injected into the air cell of fertilized, un-incubated eggs, and included DMSO control, medium dose, and high dose. The high dose was selected to result in <20% embryonic mortality based on preliminary species-specific data. Nominal doses of chlorpyrifos were 0.4, 4.0, and 40 µg/g egg for both species and injected doses were also analytically determined from egg samples.

value: liver

value: embryo development day 16


title: Rep4_D773

value: SupT1 human T cell line

value: Post-selection


title: Rep3_L774


title: PA-GFP Foxp3IRES-RFP_36

source_name: Germinal Centers


title: Biopsy from post-op day 3 NEVKP kidney, biological rep3

city: Toronto

first: Markus

last: Selzner

state: Ontario

address: 200 Elizabeth St.,

institute: Toronto General Hospital Research Institute

description:
NEVKP 3
Gene expression data from porcine kidney, third post-op day following 30 mins warm ischemia, normothermic ex-vivo kidney perfusion x 8 hours then autotransplantation

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix WT Plus Kit. GeneChips were washed and stained using FS450_0002.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Microarray analysis was performed using packages sourced from the Bioconductor repository and implemented in the R statistical environment. Background correction and RMA (Robust Multi-Array)-based Log2 normalization were performed using ‘oligo’ (v1.48). The resultant expression set underwent interquartile range based filtering (variance cut-off 0.25) using ‘genefilter’ (v1.66.0) . Differential expression (DE) testing was performed between the various groups on the filtered dataset  using ‘limma’ (v3.34.14) followed by Benjamini and Hochberg correction for multiple testing. Initial probe-to-gene annotation for the entire dataset was performed using the Affymetrix annotation file.

source_name: Porcine kidney, third post-op day following 30 mins warm ischemia, normothermic ex-vivo kidney perfusion x 8 hours then autotransplantation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400ng total RNA.

growth_protocol: 30kg male Yorkshire pigs were obtained from Caughell farms (Fingal, Ontario). All care provided to these animals followed the “Principles of Laboratory Animal Care” created by the National society for Medical Research and the “Guide for the Care of Laboratory Animals” produced by the National Institutes of Health. Water and food were provided ad libitum while animals were housed in species-adapted housing.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: Following 30 minutes of warm ischemia, pig kidneys were removed, flushed and then 1) directly re-implanted (No Storage group); 2) subjected to static cold storage (SCS) x 8 hours followed by auto-transplantation (SCS group); or 3) subjected to Normothermic Ex-Vivo Kidney Perfusion (NEVKP) x 8 hours followed by auto-transplantation. Following auto-transplantation, the contralateral kidney was removed. The biopsies used for gene expression analysis were collected on Post-operative day 3.

value: Kidney biopsy

tag: breed

value: Yorkshire

value: NEVKP


title: YR90d1

value: yellow mutant

value: dorsal skin


title: PA-GFP Foxp3IRES-RFP_35


title: Biopsy from post-op day 3 NEVKP kidney, biological rep2

description:
NEVKP 2
Gene expression data from porcine kidney, third post-op day following 30 mins warm ischemia, normothermic ex-vivo kidney perfusion x 8 hours then autotransplantation


title: PA-GFP Foxp3IRES-RFP_40

value: Tfr


title: PA-GFP Foxp3IRES-RFP_34


title: DCCO high dose rep2


title: PA-GFP Foxp3IRES-RFP_33


title: Biopsy from post-op day 3 NEVKP kidney, biological rep1

description:
NEVKP 1
Gene expression data from porcine kidney, third post-op day following 30 mins warm ischemia, normothermic ex-vivo kidney perfusion x 8 hours then autotransplantation


title: DCCO high dose rep1


title: Rep3_D773


title: Rep6_R772


title: Rep2_D773


title: PA-GFP Foxp3IRES-RFP_32


title: Rep1_D773


title: DCCO medium dose rep5


title: Rep5_R772


title: Biopsy from post-op day 3 SCS kidney, biological rep1

description:
SCS 1
Gene expression data from porcine kidney, third post-op day following 30 mins warm ischemia, static cold storage x 8 hours then autotransplantation

source_name: Porcine kidney, third post-op day following 30 mins warm ischemia, static cold storage x 8 hours then autotransplantation

value: SCS


title: DCCO high dose rep4


title: Biopsy from post-op day 3 SCS kidney, biological rep3

description:
SCS 3
Gene expression data from porcine kidney, third post-op day following 30 mins warm ischemia, static cold storage x 8 hours then autotransplantation


title: PA-GFP Foxp3IRES-RFP_31

value: PA-GFP Foxp3IRES-RFP


title: DCCO medium dose rep4


title: DCCO high dose rep3


title: PA-GFP Foxp3IRES-RFP_30

value: CD4+ Resting


title: DCCO medium dose rep3


title: Micro-C_∆YY1_IAA_rep2

city: Berkeley

first: Xavier

last: Darzacq

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California, Berkeley

description:
Homozygous cell line with endogenous YY1 loci tagged with an auxin-inducible degron
YY1-AID_pool.mcool

data_processing:
Library strategy: Micro-C
ChIP-Seq quality check: FastQC
ChIP-Seq read alignment: Bowtie (-n 2, -m 1)
ChIP-Seq peak calling: MACS2 (--nomodel --extsize 300); merged inputs used as controls
ChIP-Seq heatmaps: deepTools (version 2.4.1) bamCoverage (--binSize 50 --normalizeTo1x 2150570000 --extendReads 300 --ignoreDuplicates -of bigwig) to normalize read numbers to 1x sequencing depth, obtaining read coverage per 50-bp bins across the whole genome (bigWig files). We then used the bigWig files to compute read numbers across 6 kb centered on  ChIP-Seq MACS2 peak summits (computeMatrix reference-point --referencePoint=TSS --upstream 3000 --downstream 3000 --missingDataAsZero --sortRegions=no). We sorted the output matrices by decreasing UT enrichment, calculated as the total number of reads within a MACS2 called ChIP-seq peak. Finally, heatmaps were created with the plotHeatmap tool (--averageTypeSummaryPlot=mean --colorMap='Blues' --sortRegions=no).
Micro-C allValidPairs were generated by HiC-Pro package (>2.10 version)
Micro-C mcool files were converted from allValidPairs by Cooler package
RNA-seq read alignment: STAR aligner
RNA-seq browser track: deepTools
mNET-seq read alignment: STAR aligner
mNET-seq browser track: deepTools
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-Seq bigWig files: read coverage per 50-bp bins across the whole genome (read numbers normalized to 1x sequencing depth; merged duplicates)
Supplementary_files_format_and_content: mcool file contains all valid Micro-C pairs stored in HDF5 format with mutiple resolutions
Supplementary_files_format_and_content: RNA-seq bigWig files: read coverage per 10-bp bins across the whole genome (read numbers normalized to TPM; merged duplicates; split strands)
Supplementary_files_format_and_content: mNET-seq bigWig files: read coverage per 10-bp bins across the whole genome (read numbers normalized to TPM; merged duplicates; split strands)

source_name: Embryonic stem cells

growth_protocol: JM8.N4 mESCs were grown on gelatin-coated plates in knock-out DMEM supplemented with 15% FBS, non-essential amino acids, glutamax, Penicillin-streptomycin, 2-mercapoethanol and LIF. mES cells were fed daily and passaged every 2-3 days by trypsinization.

extract_protocol:
Micro-C protocol was performed as the following steps: 1) digest crosslinked chromatin by MNase; 2) Repair fragment ends with biotin-dNTP; 3) Proximal ligation and purge unligated ends; 4) Purify ligated dinucleosomal DNA.
Purified DNA with biotin-dNTPs was captured by Dynabeads® MyOne™ Streptavidin C1. Standard library preparation protocol including end-repair, A-tailing, and adapter ligation was performed on beads with individual enzymes purchased from Lucigen or NEBnext UltraII kit. Sequencing library was amplified by Kapa HiFi PCR enzyme with lowest possible cycles to reduce PCR duplicates. Sequencing library was sequenced paired-end 50x50 in Illumina HiSeq 4000 sequencer.

treatment_protocol: Degron cell lines were treated for 3 hours with either ethanol only (control, untreated) or with 500 uM, ethanol-dissolved auxin.

tag: cell line

tag: genotype

value: mIAA7-mScarletI-YY1 / osTir

value: 500 mM auxin in ethanol, 3 hrs

tag: chip antibody


title: DCCO medium dose rep2

tag: age


title: Micro-C_∆YY1_IAA_rep1

tag: treatment


title: Biopsy from post-op day 3 No Storage kidney, biological rep3

description:
No Storage 3
Gene expression data from porcine kidney, third post-op day following 30 mins warm ischemia, flushing and then autotransplantation

source_name: Porcine kidney, third post-op day following 30 mins warm ischemia, flushing and then autotransplantation

value: male

value: No Storage


title: Rep3_R772

tag: source


title: Biopsy from post-op day 3 No Storage kidney, biological rep1

description:
No Storage 1
Gene expression data from porcine kidney, third post-op day following 30 mins warm ischemia, flushing and then autotransplantation


title: PA-GFP Foxp3IRES-RFP_29


title: Biopsy from post-op day 3 SCS kidney, biological rep2

description:
SCS 2
Gene expression data from porcine kidney, third post-op day following 30 mins warm ischemia, static cold storage x 8 hours then autotransplantation


title: Rep2_R772


title: DCCO medium dose rep1

value: liver


title: PA-GFP Foxp3IRES-RFP_28


title: Micro-C_∆YY1_UT_rep2

description:
Homozygous cell line with endogenous YY1 loci tagged with an auxin-inducible degron
YY1-UT_pool.mcool

value: Ethanol, 3 hrs


title: Rep1_R772

value: SupT1 human T cell line


title: DCCO control rep4

value: embryo development day 16


title: PA-GFP Foxp3IRES-RFP_27


title: PA-GFP Foxp3IRES-RFP_26


title: Rep6_L771

value: Post-selection


title: DCCO control rep3


title: PA-GFP Foxp3IRES-RFP_25


title: Rep5_L771


title: DCCO control rep2


title: Rep4_R772


title: Rep4_L771


title: PA-GFP Foxp3IRES-RFP_24


title: Rep3_L771


title: Biopsy from post-op day 3 No Storage kidney, biological rep2

description:
No Storage 2
Gene expression data from porcine kidney, third post-op day following 30 mins warm ischemia, flushing and then autotransplantation

value: Kidney biopsy

value: Yorkshire