title: dsRed Foxp3IRES-GFP_123


title: dsRed Foxp3IRES-GFP_118

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: dsRed Foxp3IRES-GFP

tag: experiment

tag: cell annotation

value: Filtered cell


title: dsRed Foxp3IRES-GFP_121


title: dsRed Foxp3IRES-GFP_143


title: dsRed Foxp3IRES-GFP_119

value: Tfr


title: dsRed Foxp3IRES-GFP_120


title: dsRed Foxp3IRES-GFP_122


title: dsRed Foxp3IRES-GFP_114


title: dsRed Foxp3IRES-GFP_115


title: dsRed Foxp3IRES-GFP_138


title: dsRed Foxp3IRES-GFP_116


title: dsRed Foxp3IRES-GFP_117


title: dsRed Foxp3IRES-GFP_113


title: dsRed Foxp3IRES-GFP_112


title: dsRed Foxp3IRES-GFP_131


title: dsRed Foxp3IRES-GFP_110


title: dsRed Foxp3IRES-GFP_109


title: dsRed Foxp3IRES-GFP_108


title: dsRed Foxp3IRES-GFP_111


title: dsRed Foxp3IRES-GFP_133


title: dsRed Foxp3IRES-GFP_105


title: dsRed Foxp3IRES-GFP_107


title: dsRed Foxp3IRES-GFP_106


title: dsRed Foxp3IRES-GFP_101


title: dsRed Foxp3IRES-GFP_104


title: dsRed Foxp3IRES-GFP_103


title: dsRed Foxp3IRES-GFP_99


title: dsRed Foxp3IRES-GFP_98


title: dsRed Foxp3IRES-GFP_97


title: dsRed Foxp3IRES-GFP_94


title: dsRed Foxp3IRES-GFP_93


title: dsRed Foxp3IRES-GFP_92


title: dsRed Foxp3IRES-GFP_89


title: dsRed Foxp3IRES-GFP_88


title: dsRed Foxp3IRES-GFP_95


title: dsRed Foxp3IRES-GFP_96


title: dsRed Foxp3IRES-GFP_86


title: dsRed Foxp3IRES-GFP_91


title: dsRed Foxp3IRES-GFP_90


title: dsRed Foxp3IRES-GFP_87


title: dsRed Foxp3IRES-GFP_84


title: dsRed Foxp3IRES-GFP_102


title: dsRed Foxp3IRES-GFP_80


title: dsRed Foxp3IRES-GFP_78


title: dsRed Foxp3IRES-GFP_83


title: dsRed Foxp3IRES-GFP_77


title: dsRed Foxp3IRES-GFP_76


title: dsRed Foxp3IRES-GFP_75


title: dsRed Foxp3IRES-GFP_100


title: dsRed Foxp3IRES-GFP_81


title: dsRed Foxp3IRES-GFP_82


title: dsRed Foxp3IRES-GFP_85


title: dsRed Foxp3IRES-GFP_73


title: dsRed Foxp3IRES-GFP_74


title: dsRed Foxp3IRES-GFP_71

value: Cycling


title: dsRed Foxp3IRES-GFP_70


title: dsRed Foxp3IRES-GFP_69


title: dsRed Foxp3IRES-GFP_65


title: dsRed Foxp3IRES-GFP_67


title: dsRed Foxp3IRES-GFP_68


title: dsRed Foxp3IRES-GFP_66


title: dsRed Foxp3IRES-GFP_63

value: CD4+ Resting


title: dsRed Foxp3IRES-GFP_64


title: dsRed Foxp3IRES-GFP_61


title: dsRed Foxp3IRES-GFP_79


title: dsRed Foxp3IRES-GFP_60


title: dsRed Foxp3IRES-GFP_62


title: dsRed Foxp3IRES-GFP_58


title: dsRed Foxp3IRES-GFP_56


title: dsRed Foxp3IRES-GFP_54


title: dsRed Foxp3IRES-GFP_59


title: dsRed Foxp3IRES-GFP_72


title: dsRed Foxp3IRES-GFP_55


title: dsRed Foxp3IRES-GFP_57


title: dsRed Foxp3IRES-GFP_47


title: dsRed Foxp3IRES-GFP_53


title: dsRed Foxp3IRES-GFP_44


title: dsRed Foxp3IRES-GFP_52


title: dsRed Foxp3IRES-GFP_49


title: dsRed Foxp3IRES-GFP_46


title: dsRed Foxp3IRES-GFP_50


title: dsRed Foxp3IRES-GFP_42


title: dsRed Foxp3IRES-GFP_37


title: dsRed Foxp3IRES-GFP_36


title: dsRed Foxp3IRES-GFP_35


title: dsRed Foxp3IRES-GFP_39


title: dsRed Foxp3IRES-GFP_45


title: dsRed Foxp3IRES-GFP_43


title: dsRed Foxp3IRES-GFP_34


title: dsRed Foxp3IRES-GFP_38


title: dsRed Foxp3IRES-GFP_41


title: dsRed Foxp3IRES-GFP_40


title: dsRed Foxp3IRES-GFP_33


title: dsRed Foxp3IRES-GFP_30


title: dsRed Foxp3IRES-GFP_48


title: dsRed Foxp3IRES-GFP_27


title: dsRed Foxp3IRES-GFP_31


title: dsRed Foxp3IRES-GFP_32


title: dsRed Foxp3IRES-GFP_29


title: dsRed Foxp3IRES-GFP_28


title: dsRed Foxp3IRES-GFP_51


title: dsRed Foxp3IRES-GFP_26


title: dsRed Foxp3IRES-GFP_24


title: dsRed Foxp3IRES-GFP_25


title: dsRed Foxp3IRES-GFP_20


title: dsRed Foxp3IRES-GFP_22


title: dsRed Foxp3IRES-GFP_23


title: dsRed Foxp3IRES-GFP_18


title: dsRed Foxp3IRES-GFP_19


title: dsRed Foxp3IRES-GFP_21


title: dsRed Foxp3IRES-GFP_17


title: dsRed Foxp3IRES-GFP_16


title: dsRed Foxp3IRES-GFP_15


title: dsRed Foxp3IRES-GFP_11


title: dsRed Foxp3IRES-GFP_12


title: dsRed Foxp3IRES-GFP_9


title: dsRed Foxp3IRES-GFP_13


title: dsRed Foxp3IRES-GFP_8


title: dsRed Foxp3IRES-GFP_10


title: dsRed Foxp3IRES-GFP_6


title: dsRed Foxp3IRES-GFP_5


title: dsRed Foxp3IRES-GFP_7


title: dsRed Foxp3IRES-GFP_2


title: dsRed Foxp3IRES-GFP_1


title: dsRed Foxp3IRES-GFP_3


title: PA-GFP Foxp3IRES-RFP_1020

value: PA-GFP Foxp3IRES-RFP


title: PA-GFP Foxp3IRES-RFP_1018


title: PA-GFP Foxp3IRES-RFP_1019


title: dsRed Foxp3IRES-GFP_4


title: PA-GFP Foxp3IRES-RFP_1021


title: PA-GFP Foxp3IRES-RFP_1017


title: PA-GFP Foxp3IRES-RFP_1014


title: PA-GFP Foxp3IRES-RFP_1013


title: PA-GFP Foxp3IRES-RFP_1010


title: PA-GFP Foxp3IRES-RFP_1009


title: dsRed Foxp3IRES-GFP_14


title: PA-GFP Foxp3IRES-RFP_1011


title: PA-GFP Foxp3IRES-RFP_1008


title: PA-GFP Foxp3IRES-RFP_1007


title: PA-GFP Foxp3IRES-RFP_1006


title: PA-GFP Foxp3IRES-RFP_1004


title: PA-GFP Foxp3IRES-RFP_1003


title: PA-GFP Foxp3IRES-RFP_1001


title: PA-GFP Foxp3IRES-RFP_1005


title: PA-GFP Foxp3IRES-RFP_1000


title: PA-GFP Foxp3IRES-RFP_1002


title: PA-GFP Foxp3IRES-RFP_999


title: PA-GFP Foxp3IRES-RFP_997


title: PA-GFP Foxp3IRES-RFP_996


title: PA-GFP Foxp3IRES-RFP_998


title: PA-GFP Foxp3IRES-RFP_1016


title: PA-GFP Foxp3IRES-RFP_994


title: PA-GFP Foxp3IRES-RFP_992


title: PA-GFP Foxp3IRES-RFP_993


title: PA-GFP Foxp3IRES-RFP_995


title: PA-GFP Foxp3IRES-RFP_991


title: PA-GFP Foxp3IRES-RFP_990


title: PA-GFP Foxp3IRES-RFP_989


title: PA-GFP Foxp3IRES-RFP_1012


title: PA-GFP Foxp3IRES-RFP_987


title: PA-GFP Foxp3IRES-RFP_986


title: PA-GFP Foxp3IRES-RFP_985


title: PA-GFP Foxp3IRES-RFP_984


title: PA-GFP Foxp3IRES-RFP_980


title: PA-GFP Foxp3IRES-RFP_982


title: PA-GFP Foxp3IRES-RFP_1015


title: PA-GFP Foxp3IRES-RFP_983


title: PA-GFP Foxp3IRES-RFP_988


title: PA-GFP Foxp3IRES-RFP_981


title: PA-GFP Foxp3IRES-RFP_979


title: PA-GFP Foxp3IRES-RFP_977


title: PA-GFP Foxp3IRES-RFP_976


title: PA-GFP Foxp3IRES-RFP_973


title: PA-GFP Foxp3IRES-RFP_974


title: PA-GFP Foxp3IRES-RFP_975


title: PA-GFP Foxp3IRES-RFP_972


title: PA-GFP Foxp3IRES-RFP_971


title: PA-GFP Foxp3IRES-RFP_970


title: PA-GFP Foxp3IRES-RFP_965


title: PA-GFP Foxp3IRES-RFP_966


title: PA-GFP Foxp3IRES-RFP_969


title: PA-GFP Foxp3IRES-RFP_968


title: PA-GFP Foxp3IRES-RFP_963


title: PA-GFP Foxp3IRES-RFP_962


title: PA-GFP Foxp3IRES-RFP_961


title: PA-GFP Foxp3IRES-RFP_960


title: PA-GFP Foxp3IRES-RFP_959


title: PA-GFP Foxp3IRES-RFP_957


title: PA-GFP Foxp3IRES-RFP_958


title: PA-GFP Foxp3IRES-RFP_956


title: PA-GFP Foxp3IRES-RFP_978


title: PA-GFP Foxp3IRES-RFP_954


title: PA-GFP Foxp3IRES-RFP_955


title: PA-GFP Foxp3IRES-RFP_953


title: PA-GFP Foxp3IRES-RFP_952


title: PA-GFP Foxp3IRES-RFP_951


title: PA-GFP Foxp3IRES-RFP_950


title: PA-GFP Foxp3IRES-RFP_947


title: PA-GFP Foxp3IRES-RFP_945


title: PA-GFP Foxp3IRES-RFP_964


title: PA-GFP Foxp3IRES-RFP_943


title: PA-GFP Foxp3IRES-RFP_946


title: PA-GFP Foxp3IRES-RFP_944


title: PA-GFP Foxp3IRES-RFP_941


title: PA-GFP Foxp3IRES-RFP_942


title: PA-GFP Foxp3IRES-RFP_939


title: PA-GFP Foxp3IRES-RFP_937


title: PA-GFP Foxp3IRES-RFP_935


title: PA-GFP Foxp3IRES-RFP_933


title: PA-GFP Foxp3IRES-RFP_940


title: PA-GFP Foxp3IRES-RFP_936


title: PA-GFP Foxp3IRES-RFP_938


title: PA-GFP Foxp3IRES-RFP_932


title: PA-GFP Foxp3IRES-RFP_931


title: PA-GFP Foxp3IRES-RFP_930


title: PA-GFP Foxp3IRES-RFP_929


title: PA-GFP Foxp3IRES-RFP_926


title: PA-GFP Foxp3IRES-RFP_927


title: PA-GFP Foxp3IRES-RFP_949


title: PA-GFP Foxp3IRES-RFP_925


title: PA-GFP Foxp3IRES-RFP_924


title: PA-GFP Foxp3IRES-RFP_948


title: PA-GFP Foxp3IRES-RFP_928


title: PA-GFP Foxp3IRES-RFP_923


title: PA-GFP Foxp3IRES-RFP_922


title: PA-GFP Foxp3IRES-RFP_920


title: PA-GFP Foxp3IRES-RFP_967


title: PA-GFP Foxp3IRES-RFP_919


title: PA-GFP Foxp3IRES-RFP_917


title: PA-GFP Foxp3IRES-RFP_915


title: PA-GFP Foxp3IRES-RFP_914


title: PA-GFP Foxp3IRES-RFP_921


title: PA-GFP Foxp3IRES-RFP_934


title: PA-GFP Foxp3IRES-RFP_913


title: PA-GFP Foxp3IRES-RFP_911


title: PA-GFP Foxp3IRES-RFP_912


title: PA-GFP Foxp3IRES-RFP_909


title: PA-GFP Foxp3IRES-RFP_910


title: PA-GFP Foxp3IRES-RFP_908


title: PA-GFP Foxp3IRES-RFP_906


title: PA-GFP Foxp3IRES-RFP_907


title: PA-GFP Foxp3IRES-RFP_905


title: PA-GFP Foxp3IRES-RFP_904


title: PA-GFP Foxp3IRES-RFP_900


title: PA-GFP Foxp3IRES-RFP_903


title: PA-GFP Foxp3IRES-RFP_899


title: PA-GFP Foxp3IRES-RFP_898


title: PA-GFP Foxp3IRES-RFP_901


title: PA-GFP Foxp3IRES-RFP_897


title: PA-GFP Foxp3IRES-RFP_896


title: PA-GFP Foxp3IRES-RFP_895


title: PA-GFP Foxp3IRES-RFP_918


title: PA-GFP Foxp3IRES-RFP_916


title: PA-GFP Foxp3IRES-RFP_890


title: PA-GFP Foxp3IRES-RFP_885


title: PA-GFP Foxp3IRES-RFP_892


title: PA-GFP Foxp3IRES-RFP_887


title: PA-GFP Foxp3IRES-RFP_891


title: PA-GFP Foxp3IRES-RFP_886


title: PA-GFP Foxp3IRES-RFP_902


title: PA-GFP Foxp3IRES-RFP_877


title: PA-GFP Foxp3IRES-RFP_880


title: PA-GFP Foxp3IRES-RFP_881


title: PA-GFP Foxp3IRES-RFP_883


title: PA-GFP Foxp3IRES-RFP_884


title: Rat_TS_Knockdown_Sample_3

city: Kansas City

first: Khursheed

last: Iqbal

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

data_processing:
Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in reads per kb of exon per million reads mapped.
A false discovery rate of 0.05 was used as a cutoff for significant differential expression.
Functional patterns of transcript expression were analyzed using Ingenuity Pathway Analysis (Qiagen).
Genome_build: rat reference genome (Ensembl Rnor_5.0.78)

organism: Rattus norvegicus

source_name: rat trophoblast stem cells

growth_protocol: Rat TS cells were transduced with shControl or shSUV39h2 lentiviral supernatant and incubated for 24 h. Media was changed 24 h post-transduction and selected with puromycin dihydrochloride (5mg/mL, cat. no. A11138-03, Thermo-Fisher) for two days. Cells recovered for 1-3 days in complete human TS medium prior to splitting for EVT differentiation. RNA was isolated on the eighth day of differentiation.

extract_protocol:
Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with a HiSeq2000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility. Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA). mRNA abundance was expressed in reads per kb of exon per million reads mapped.  A false discovery rate of 0.05 was used as a cutoff for significant differential expression (euglycemia vs hyperglycemia).

tag: cell type

value: rat trophoblast stem cells

tag: shRNA

value: Suv39h2 shRNA


title: PA-GFP Foxp3IRES-RFP_878


title: PA-GFP Foxp3IRES-RFP_875


title: PA-GFP Foxp3IRES-RFP_876


title: Rat_TS_Knockdown_Sample_1


title: Rat_TS_Control_Sample_2

value: Control shRNA


title: PA-GFP Foxp3IRES-RFP_873


title: Rat_TS_Control_Sample_3


title: PA-GFP Foxp3IRES-RFP_893


title: PA-GFP Foxp3IRES-RFP_894


title: PA-GFP Foxp3IRES-RFP_889


title: PA-GFP Foxp3IRES-RFP_872


title: PA-GFP Foxp3IRES-RFP_888


title: Rat_TS_Control_Sample_1


title: PA-GFP Foxp3IRES-RFP_871


title: PA-GFP Foxp3IRES-RFP_870


title: PA-GFP Foxp3IRES-RFP_869


title: PA-GFP Foxp3IRES-RFP_879


title: R-3

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR-2.5.2b aligner
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: Femur

extract_protocol:
A 5 mm region below the growth plate of the distal metaphyseal femur was cut out from the radiated (R) and non-radiated (NR) legs. After removal of muscle tissue, the bone samples were homogenized and total RNA was isolated using RNeasy Mini Columns (QIAGEN, Valencia, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols
TruSeq Stranded mRNA (TSMRN)

tag: tissue

value: Femur

tag: date

value: day 21 post-radiation

tag: group

value: R-radiated


title: Adult mouse oviduct

city: montreal

first: Yojiro

last: Yamanaka

state: Quebec

address: 1160 Pine Avenue West, room 416

department: Human Genetics

country: Canada

institute: McGill University (Goodman Cancer Research Centre)

description: Single cell RNA

data_processing:
Raw sequencing data for each sample was converted to matrices of expression counts using the Cell 1000 Ranger software provided by 10X genomics (version 2.0.2)
Raw BCL files from the Illumina HiSeq were demultiplexed into paired-end, gzip-compressed FASTQ files for each channel using Cell Ranger’s mkfastq. Using Cell Ranger’s count, reads were aligned to the mouse reference transcriptome (mm10), and transcript counts quantified for each annotated gene within every cell.
The resulting UMI count matrix (genes × cells) were then provided as input to Seurat suite (version 2.3.4). Cells were first filtered to remove those that contain less than 200 genes detected and those in which > 10% of the transcript counts were derived from mitochondrial-encoded genes. Mean UMIs and genes detected in each cell were 3696 and 1546 for adult and 5499 and 2253 for P4 datasets
Clustering was performed using the “FindClusters” function and integrated t-SNE visualization for 1010 all cells. Cluster-specific gene markers were identified using Seurat’s FindMarkers with cutoffs avg_logFC > 0.5 and FDR < 0.05 unless otherwise stated. For the combined analysis, OVA or P4 samples were merged into one 10x combined object using canonical correlation analysis (CCA), followed by scaling data (ScaleData function) and finding variable genes (FindVariableGenes function).
CCA subspaces were aligned using CCA dimensions 1-20, which was followed by clustering 1015 (FindClusters function) and integrated t-SNE visualization for all cells. Cluster-specific gene markers were identified using Seurat’s FindMarkers with cutoffs avg_logFC > 0.5 and FDR < 0.05. GO-term filtering was conducted using the Mouse Genome Informatic (MGI) database.
Genome_build: mm10
Supplementary_files_format_and_content: UMI count matrix
Supplementary_files_format_and_content: clusters

source_name: Adult mouse oviduct cells

extract_protocol:
Single cells were isolated by enzymatic dissociation followed by FACS sorting to remove dead cells and enrich epithelial cells using Epcam and CD45 antibodies
Libraries were constructed using the Chromium Single Cell 3' (10X genomics V2)

tag: Stage

value: estrus


title: Rat_TS_Knockdown_Sample_2


title: PA-GFP Foxp3IRES-RFP_874


title: R-2


title: R-1


title: P4 mouse oviduct

description: Single cell RNA

source_name: P4 mouse oviduct cells


title: PA-GFP Foxp3IRES-RFP_867


title: NR-2

value: NR-Non-radiated


title: PA-GFP Foxp3IRES-RFP_865


title: PA-GFP Foxp3IRES-RFP_866


title: PA-GFP Foxp3IRES-RFP_868


title: PA-GFP Foxp3IRES-RFP_882


title: NR-1


title: PA-GFP Foxp3IRES-RFP_864


title: PA-GFP Foxp3IRES-RFP_863


title: PA-GFP Foxp3IRES-RFP_862


title: PA-GFP Foxp3IRES-RFP_861


title: PA-GFP Foxp3IRES-RFP_860


title: PA-GFP Foxp3IRES-RFP_859


title: CMV+ TX Rep 3

city: Columbus

first: Masako

last: Shimamura

state: OH

address: 700 Childrens Drive

department: Infectious Diseases Medicine

institute: Nationwide Children's Hospital

data_processing:
Each sample was aligned to the GRCm38.p4 assembly of the mouse reference from NCBI (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.24/) using version 2.6.0c of the RNA-Seq aligner STAR (http://bioinformatics.oxfordjournals.org/content/29/1/15).
Features were identified from the GFF file that came with the assembly from NCBI.
Feature coverage counts were calculated using HTSeq (https://htseq.readthedocs.io/en/release_0.10.0/).
Differentially expressed features were calculated using DESeq2 (http://genomebiology.com/2014/15/12/550) and custom scripts developed in-house to perform RNA-Seq analysis.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: Excel spreadsheet containing read counts for each sample and differential expression data for each feature.

source_name: Allografts

extract_protocol:
Kidneys or allografts were snap frozen on dry ice and RNA was isolated using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cyclosporine A was injected subcutaneously once daily at 10mg/kg/day in transplant recipients (Tissue= Allografts).

value: Allografts

tag: age

value: 5 months 17 days

tag: genotype

value: wild type

tag: treatment

value: Cyclosporine A


title: CMV+ TX Rep 4

value: 5 months 24 days


title: CMV+ TX Rep 1

value: 5 months 3 days


title: CMV- TX Rep 4

value: 6 months 1 day


title: CMV+ TX Rep 2

value: 5 months 10 days


title: CMV- TX Rep 3

value: 4 months 24 days


title: PA-GFP Foxp3IRES-RFP_857

value: PA-GFP Foxp3IRES-RFP

value: CD4+ Resting


title: CMV- TX Rep 2

value: 4 months 17 days


title: PA-GFP Foxp3IRES-RFP_856


title: NR-3

value: Femur


title: PA-GFP Foxp3IRES-RFP_855

value: Filtered cell


title: PA-GFP Foxp3IRES-RFP_851


title: CMV+ NO TX Rep 3

source_name: Kidneys

value: BALB/cJ

value: Kidneys

value: 10 months 6 days


title: CMV+ NO TX Rep 2


title: PA-GFP Foxp3IRES-RFP_853


title: PA-GFP Foxp3IRES-RFP_854


title: PA-GFP Foxp3IRES-RFP_850


title: PA-GFP Foxp3IRES-RFP_852


title: CMV- NO TX Rep2


title: PA-GFP Foxp3IRES-RFP_848


title: PA-GFP Foxp3IRES-RFP_849


title: CMV- NO TX Rep1


title: PA-GFP Foxp3IRES-RFP_846

value: Tfr


title: PA-GFP Foxp3IRES-RFP_847


title: PA-GFP Foxp3IRES-RFP_839


title: PA-GFP Foxp3IRES-RFP_845


title: PA-GFP Foxp3IRES-RFP_843


title: PA-GFP Foxp3IRES-RFP_844


title: PA-GFP Foxp3IRES-RFP_841


title: PA-GFP Foxp3IRES-RFP_842


title: PA-GFP Foxp3IRES-RFP_858


title: PA-GFP Foxp3IRES-RFP_840


title: PA-GFP Foxp3IRES-RFP_837


title: CMV- TX Rep 1

value: Allografts

value: 4 months 10 days


title: PA-GFP Foxp3IRES-RFP_838


title: PA-GFP Foxp3IRES-RFP_836


title: PA-GFP Foxp3IRES-RFP_835


title: PA-GFP Foxp3IRES-RFP_834


title: CMV+ NO TX Rep 1

value: wild type


title: CMV- NO TX Rep3


title: PA-GFP Foxp3IRES-RFP_833


title: PA-GFP Foxp3IRES-RFP_832


title: PA-GFP Foxp3IRES-RFP_830


title: ChIP-seq_∆YY1_IAA_RAD21_ChIP

city: Berkeley

first: Xavier

last: Darzacq

state: CA

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

library_source: genomic

data_processing:
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)

molecule: genomic DNA

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:
Cells were cross-linked 7’ at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by PBS-glycine (0.125 M final). Cells were washed twice with ice-cold PBS, scraped, centrifuged for 10’ and pellets were flash-frozen. Cell pellets were thawed and resuspended in cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, and 0.5% NP-40, 1 ml/15 cm plate) w/ protease inhibitors and incubated for 10’ on ice. Lysates were centrifuged for 10’ at 4000 rpm and nuclear pellets resuspended in 6 volumes of sonication buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 0.1% SDS) w/ protease inhibitors, incubated on ice for 10’, and sonicated to obtain DNA fragments below 2000 bp in length (Covaris S220 sonicator, 20% Duty factor, 200 cycles/burst, 150 peak incident power, 10-20 cycles 50” on and 30" off). Sonicated lysates were cleared by centrifugation and chromatin (400 ug per antibody) was diluted in RIPA buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl) w/ protease inhibitors to a final concentration of 0.8 ug/ul, precleared with Protein G sepharose (GE Healthcare) for 2 hours at 4°C and immunoprecipitated overnight with 4 ug of specific antibodies. About 4% of the precleared chromatin was saved as input. Immunoprecipitated DNA was purified with the Qiagen QIAquick PCR Purification Kit, eluted in 36 ul of 0.1X TE (1 mM Tris-HCl pH 8.0, 0.01 mM EDTA) and analyzed by qPCR together with 2% of the input chromatin prior to ChIP-seq library preparation.
ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7645) according to manufacturer instructions with a few modifications. 20 ng of ChIP input DNA (as measured by Nanodrop) and 25 ul of the immunoprecipitated DNA were used as a starting material and the recommended reagents’ volumes were cut in half. The NEBNext Adaptor for Illumina was diluted 1:10 in Tris/NaCl, pH 8.0 (10 mM Tris-HCl pH 8.0, 10 mM NaCl) and the ligation step extended to 30’. After ligation, a single purification step with 0.9X volumes of Agencourt AMPure XP PCR purification beads (Beckman Coulter A63880) was performed, eluting DNA in 22 ul of 10 mM Tris-HCl pH 8.0. 20 l of the eluted DNA were used for the library enrichment step, performed with the KAPA HotStart PCR kit (Roche Diagnostics KK2502) in 50 ul of total reaction volume (10 ul 5X KAPA buffer, 1.5 ul 10 mM dNTPs, 0.5 ul 10 uM NEB Universal PCR primer, 0.5 ul 10 uM NEB index primer, 1 ul KAPA polymerase, 16.5 ul nuclease-free water and 20 ul sample). Samples were enriched with 9 PCR cycles (98 'C, 45”; [98 'C, 15”; 60 'C, 10”] x 9; 72 'C, 1’; 4 'C, hold), purified with 0.9 volumes of AMPure XP PCR purification beads and eluted with 33 ul of 10 mM Tris-HCl pH 8.0. Library concentration, quality and fragment size were assessed by Qubit fluorometric quantification (Qubit™ dsDNA HS Assay Kit, InvitrogenTM Q32851) qPCR and Fragment analyzer™. 12 multiplexed libraries were pooled and sequenced in one lane on the Illumina HiSeq4000 sequencing platform (50-bp, single end-reads)

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

value: mIAA7-mScarletI-YY1 / osTir

value: 500 mM auxin in ethanol, 3 hrs

tag: chip antibody

value: SMC1A (Bethyl Laboratories Inc. A300-055A)


title: ChIP-seq_∆YY1_IAA_SMC1A_ChIP

value: SMC3 (Bethyl Laboratories Inc. A300-060A)


title: ChIP-seq_∆YY1_IAA_CTCF_ChIP

value: RAD21 (Abcam ab154769)


title: ChIP-seq_∆YY1_IAA_SMC3_ChIP

value: YY1 (Abcam ab38422 and ab109237)


title: PA-GFP Foxp3IRES-RFP_828

value: PA-GFP Foxp3IRES-RFP


title: ChIP-seq_∆YY1_IAA_CTCF_input

value: CTCF (Abcam ab128873 and EMD 07-729)


title: ChIP-seq_∆YY1_IAA_YY1_ChIP


title: ChIP-seq_∆YY1_UT_YY1_ChIP

value: Ethanol, 3 hrs


title: PA-GFP Foxp3IRES-RFP_826

value: Filtered cell


title: PA-GFP Foxp3IRES-RFP_824


title: PA-GFP Foxp3IRES-RFP_827


title: ChIP-seq_∆YY1_UT_SMC1A_ChIP


title: PA-GFP Foxp3IRES-RFP_825


title: PA-GFP Foxp3IRES-RFP_823


title: ChIP-seq_∆YY1_UT_RAD21_ChIP


title: ChIP-seq_∆YY1_UT_CTCF_ChIP


title: ChIP-seq_∆YY1_UT_CTCF_input


title: PA-GFP Foxp3IRES-RFP_822


title: ChIP-seq_∆YY1_UT_SMC3_ChIP


title: PA-GFP Foxp3IRES-RFP_821


title: PA-GFP Foxp3IRES-RFP_820

value: CD4+ Resting


title: ChIP-seq_∆WAPL_IAA_SMC3_ChIP

description: Homozygous cell line with endogenous WAPL loci tagged with an auxin-inducible degron

value: FLAG-Halo-CTCF / RAD21-SNAPf-V5 / HA-BFP-mAID-WAPL / osTir


title: ChIP-seq_∆WAPL_IAA_RAD21_ChIP


title: PA-GFP Foxp3IRES-RFP_831


title: ChIP-seq_∆WAPL_IAA_SMC1A_ChIP


title: PA-GFP Foxp3IRES-RFP_819


title: PA-GFP Foxp3IRES-RFP_818


title: ChIP-seq_∆WAPL_IAA_CTCF_ChIP


title: PA-GFP Foxp3IRES-RFP_817


title: ChIP-seq_∆WAPL_IAA_YY1_ChIP


title: ChIP-seq_∆WAPL_UT_YY1_ChIP


title: ChIP-seq_∆WAPL_UT_SMC3_ChIP


title: PA-GFP Foxp3IRES-RFP_815


title: PA-GFP Foxp3IRES-RFP_814


title: PA-GFP Foxp3IRES-RFP_812


title: ChIP-seq_∆WAPL_UT_SMC1A_ChIP


title: PA-GFP Foxp3IRES-RFP_813


title: ChIP-seq_∆WAPL_UT_CTCF_ChIP


title: ChIP-seq_∆WAPL_UT_CTCF_input


title: ChIP-seq_∆RAD21_IAA_SMC3_ChIP

description: Homozygous cell line with endogenous RAD21 loci tagged with an auxin-inducible degron

value: FLAG-Halo-CTCF / RAD21-BFP-mAID-V5 / osTir


title: PA-GFP Foxp3IRES-RFP_809


title: PA-GFP Foxp3IRES-RFP_811

value: Tfr


title: ChIP-seq_∆RAD21_IAA_SMC1A_ChIP


title: PA-GFP Foxp3IRES-RFP_810


title: PA-GFP Foxp3IRES-RFP_808


title: ChIP-seq_∆RAD21_IAA_RAD21_ChIP


title: PA-GFP Foxp3IRES-RFP_807


title: ChIP-seq_∆RAD21_IAA_CTCF_ChIP


title: ChIP-seq_∆RAD21_IAA_CTCF_input


title: PA-GFP Foxp3IRES-RFP_806


title: PA-GFP Foxp3IRES-RFP_805


title: PA-GFP Foxp3IRES-RFP_804


title: ChIP-seq_∆WAPL_IAA_CTCF_input


title: ChIP-seq_∆RAD21_IAA_YY1_ChIP


title: PA-GFP Foxp3IRES-RFP_816


title: ChIP-seq_∆RAD21_UT_YY1_ChIP


title: ChIP-seq_∆RAD21_UT_SMC3_ChIP


title: PA-GFP Foxp3IRES-RFP_802


title: ChIP-seq_∆WAPL_UT_RAD21_ChIP


title: ChIP-seq_∆RAD21_UT_SMC1A_ChIP


title: ChIP-seq_∆RAD21_UT_RAD21_ChIP


title: PA-GFP Foxp3IRES-RFP_801


title: PA-GFP Foxp3IRES-RFP_800


title: ChIP-seq_∆RAD21_UT_CTCF_ChIP


title: PA-GFP Foxp3IRES-RFP_799


title: ChIP-seq_∆RAD21_UT_CTCF_input


title: PA-GFP Foxp3IRES-RFP_798


title: ChIP-seq_∆CTCF_IAA_SMC3_ChIP

description: Homozygous cell line with endogenous CTCF loci tagged with an auxin-inducible degron

value: FLAG-BFP-mAID-CTCF / RAD21-SNAPf-V5 / osTir


title: PA-GFP Foxp3IRES-RFP_797


title: ChIP-seq_∆CTCF_IAA_RAD21_ChIP


title: ChIP-seq_∆CTCF_IAA_SMC1A_ChIP


title: ChIP-seq_∆CTCF_IAA_CTCF_ChIP


title: PA-GFP Foxp3IRES-RFP_829


title: ChIP-seq_∆CTCF_IAA_CTCF_input


title: PA-GFP Foxp3IRES-RFP_793


title: PA-GFP Foxp3IRES-RFP_795


title: ChIP-seq_∆CTCF_IAA_YY1_ChIP


title: PA-GFP Foxp3IRES-RFP_794


title: PA-GFP Foxp3IRES-RFP_796


title: PA-GFP Foxp3IRES-RFP_792


title: ChIP-seq_∆CTCF_UT_YY1_ChIP


title: PA-GFP Foxp3IRES-RFP_803


title: PA-GFP Foxp3IRES-RFP_791


title: PA-GFP Foxp3IRES-RFP_790


title: ChIP-seq_∆CTCF_UT_SMC1A_ChIP


title: ChIP-seq_∆CTCF_UT_SMC3_ChIP


title: PA-GFP Foxp3IRES-RFP_789


title: PA-GFP Foxp3IRES-RFP_788


title: PA-GFP Foxp3IRES-RFP_787


title: PA-GFP Foxp3IRES-RFP_786


title: ChIP-seq_∆CTCF_UT_CTCF_ChIP


title: ChIP-seq_∆CTCF_UT_RAD21_ChIP


title: LSK_KO_3

city: Charlottesville

first: Golam

last: Mohi

state: Virginia

address: 1340 Jefferson Park Ave

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description:
DGE LSK BMT U2af1KOvsWT.txt
LSK BMT U2af1KOvsWT AS Events.xlsx

data_processing:
Raw reads were trimmed 50bp from both ends of the reads
Trimmed reads were aligned using HISAT2.1.0 to Mus musculus mm10
Aligned reads were converted to BAM via Samtools 1.10
Gene counts were generated using Stringtie
Differential gene expression was done using DESeq2
Alternative splicing events were identified using rMATS v4.1.0
Genome_build: mm10
Supplementary_files_format_and_content: Differential gene expression tab-delimited text files between U2af1KO and WT
Supplementary_files_format_and_content: Alternative splicing events excel files between U2af1KO and WT

source_name: BMT LSK Cells

extract_protocol:
Bone marrow cells were harvested and lineage depleted by MACS mouse lineage depletion kit then sorted by flow cytometry.
Library prep was done according to protocol of NEB rRNA depletion kit and then NEBNext Ultra II RNA Library Prep Kit for Illumina

value: Bone Marrow


title: PA-GFP Foxp3IRES-RFP_785


title: ChIP-seq_∆CTCF_UT_CTCF_input


title: LSK_KO_2


title: PA-GFP Foxp3IRES-RFP_784


title: LSK_KO_1


title: PA-GFP Foxp3IRES-RFP_783


title: PA-GFP Foxp3IRES-RFP_782


title: LSK_WT_2

value: WT


title: LSK_WT_3


title: PA-GFP Foxp3IRES-RFP_781


title: LinNeg_KO_3

description:
DGE LinNeg BM U2af1KOvsWT.txt
LinNeg BM U2af1KOvsWT AS Events.xlsx

source_name: BM Lin- Cells


title: LinNeg_KO_2


title: PA-GFP Foxp3IRES-RFP_780


title: PA-GFP Foxp3IRES-RFP_779


title: PA-GFP Foxp3IRES-RFP_778


title: LinNeg_KO_1


title: LinNeg_WT_3


title: PA-GFP Foxp3IRES-RFP_776


title: LinNeg_WT_2


title: LinNeg_WT_1


title: PA-GFP Foxp3IRES-RFP_774


title: PA-GFP Foxp3IRES-RFP_770


title: PA-GFP Foxp3IRES-RFP_772


title: PA-GFP Foxp3IRES-RFP_771

value: Cycling


title: CT16_WT3

city: Philadelphia

first: Hoang

last: Nguyen

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania Perelman School of Medicine

data_processing:
#genome alignment single read: STAR --genomeDir ~/STAR_mm10_GENOME_DIR  --runThreadN 20 --readFilesIn $i --outFileNamePrefix ${i/.fastq.gz/}_ --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMstrandField intronMotif
#counting reads: featureCounts -t exon -g gene_id -a ~/mm10/mm10_genes.gtf -T 20
#DGE with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts read counts for all samples

extract_protocol:
2-4 independents hypothalamic nuclei punches were pooled together per biological replicate. Hypothalamus punches were homogenized manually by Pellet-Pestle (Kimble, 749515) for 1 minutes with 1mL QIAzol Lysis Reagent (Qiagen). Samples were then centrifuged at 4°C for 10min at 15,000 x g. In a new tube, 200uL chloroform was added to homogenate and mixed thoroughly before repeating the previous centrifugation. The aqueous chloroform phases were pipetted into new tubes, followed by addition of one volume of 70% EtOH to each sample. Total RNA was purified and collected from RNeasy Mini spin columns according to RNeasy Lipid Mini Kit (Qiagen, 74804).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: 8-12 weeks

value: control

tag: time point

tag: sample type

value: suprachiasmatic nuclei (SCN)


title: CT16_WT2


title: CT16_WT4


title: CT16_WT5


title: PA-GFP Foxp3IRES-RFP_769

tag: sequencing plate

tag: strain


title: CT16_KO4

value: REV-ERBS DKO


title: CT16_WT1


title: CT16_KO3


title: PA-GFP Foxp3IRES-RFP_768

tag: experiment

tag: cell annotation


title: PA-GFP Foxp3IRES-RFP_767


title: PA-GFP Foxp3IRES-RFP_766


title: LSK_WT_1


title: CT16_KO1


title: PA-GFP Foxp3IRES-RFP_777


title: CT16_KO2


title: PA-GFP Foxp3IRES-RFP_765


title: CT4_WT2


title: PA-GFP Foxp3IRES-RFP_764


title: CT4_WT3


title: PA-GFP Foxp3IRES-RFP_763


title: PA-GFP Foxp3IRES-RFP_775


title: CT4_WT1


title: CT4_KO3


title: PA-GFP Foxp3IRES-RFP_762


title: CT4_KO2


title: PA-GFP Foxp3IRES-RFP_761


title: PA-GFP Foxp3IRES-RFP_773


title: CT4_KO1


title: PA-GFP Foxp3IRES-RFP_760


title: PA-GFP Foxp3IRES-RFP_759


title: PA-GFP Foxp3IRES-RFP_758


title: PA-GFP Foxp3IRES-RFP_757


title: J-LatA2+PMA (P2771_N715-S511)

city: Scarborough

first: Guillaume

middle: J

last: Filion

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

institute: UTSC

data_processing:
In order to determine the levels of gene expression, we used the mapping-based model of Salmon version 1.5.1. The indexing step was run using the human transcriptome (Gencode release 38), to which the sequence of HIV miniconstruct was added manually. We used the human genome (GRCh38.p13 downloaded from Gencode) as a decoy sequence by concatenating the genome to the transcriptome, as explained in the Alevin tutorial from the Combine lab (https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/). The quantification step was run with default parameters and the addition of the -l A flag. Finally, for every gene we summed the read counts over all the possible transcripts corresponding to the given gene. Thus, the output is an expression matrix where the expression is quantified in unnormalized read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: exprMatrix.tsv.gz is a text file of tab-separated values, with the read number of every gene in every cell of the experiment. Cells are symbolized with the code "plate_index1-index2". For instance, reads from P2449_N716-S502 belong to the trancsriptome of the cell of plate 2449 indexed with N716 and S502.
Supplementary_files_format_and_content: sampleSheet.tsv is a text file of tab-separated values, with the treatment applied to every cell. Cells are symbolized in the same way as in exprMatrix.tsv.gz.

organism: Homo sapiens

source_name: J-Lat A2

growth_protocol: Jurkat and J-Lat A2 (Jordan et al., 2003, EMBO J. PMID: 12682019) cells were grown in RPMI 1640 (Thermo Fisher Scientific, MA, USA) supplemented with 10% FBS, 100 U/ml penicillin, 100 ug/ml streptomycin and 2 mM L-glutamine (10R medium).

extract_protocol:
Single cells were sorted by FACSAria II (Beckman Courter, CA, USA) to 96-well plates filled with lysis buffer (0.2% Triton X-100, 1 U/ul RNase inhibitors).
Reverse transcription was performed using SuperScript II (ThermoFisher Scientific) in the presence of 1 M betaine, 1 uM poly(T) primer with sequence 5'-T(30)VN-3', 1 uM template-switching oligonucleotide with sequence 5'-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3', where "rG" stands for a G with ribose instead of deoxyiribose, and "+" stands for a LNA bond (Locked Nucleic Acid). The thermo-cycling conditions were // 90 min 42C // 2 min 50C / 2 min 42C / x10 // 15 min 70C. cDNAs were amplified using the KAPA Hifi Hotstart ReadyMix (Kapa Biosystems) and IS PCR primer with sequence 5'-AAGCAGTGGTATCAACGCAGAGT-3' (IDT), with thermo-cycling conditions // 3 min 98C // 15 s 98C / 20 s 67C / 6 min 72C / x25 // 5 min 72C. Following purification with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitivity DNA Kit (Agilent Technologies). 140 pg of the amplified cDNA were fragmented using Nextera XT (Illumina) and amplified with Nextera XT indexes (Illumina). Products of each well of the 96-well plate were pooled and purified twice with Agencourt Ampure XP beads (Beckmann Coulter). Final libraries were quantified and checked for fragment size distribution using a Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).

treatment_protocol: Cells were seeded at 0.5 million cells per ml in T-75 flasks and treated for 24 hr with either 0.1% v/v DMSO, or 1 uM SAHA (suberoylanilide hydroxamic acid) or 1 ug/mL PMA (phorbol 12-myristate 13-acetate).  The cells (approximately 1 million) were then transferred to a tube and resuspended in 10R medium with 1 ug/ml DAPI.

value: J-Lat A2

value: PMA


title: PA-GFP Foxp3IRES-RFP_756

value: PA-GFP Foxp3IRES-RFP


title: PA-GFP Foxp3IRES-RFP_755


title: J-LatA2+PMA (P2771_N715-S508)


title: J-LatA2+SAHA (P2771_N715-S507)

value: SAHA


title: PA-GFP Foxp3IRES-RFP_754

value: Filtered cell


title: PA-GFP Foxp3IRES-RFP_753


title: PA-GFP Foxp3IRES-RFP_752


title: PA-GFP Foxp3IRES-RFP_751


title: PA-GFP Foxp3IRES-RFP_750


title: PA-GFP Foxp3IRES-RFP_749


title: Jurkat+SAHA (P2771_N715-S502)

source_name: Jurkat T cell

value: Jurkat T cell


title: J-LatA2+PMA (P2771_N714-S511)


title: J-LatA2+PMA (P2771_N714-S510)


title: PA-GFP Foxp3IRES-RFP_748


title: PA-GFP Foxp3IRES-RFP_747


title: J-LatA2+SAHA (P2771_N714-S507)


title: Jurkat+PMA (P2771_N715-S503)


title: J-LatA2+PMA (P2771_N714-S508)


title: J-LatA2+SAHA (P2771_N714-S506)


title: PA-GFP Foxp3IRES-RFP_746


title: J-LatA2+DMSO (P2771_N714-S505)

value: DMSO


title: J-LatA2+PMA (P2771_N715-S510)


title: PA-GFP Foxp3IRES-RFP_745


title: PA-GFP Foxp3IRES-RFP_744


title: Jurkat+SAHA (P2771_N714-S502)


title: J-LatA2+SAHA (P2771_N715-S506)


title: J-LatA2+PMA (P2771_N712-S511)


title: PA-GFP Foxp3IRES-RFP_743


title: PA-GFP Foxp3IRES-RFP_742


title: J-LatA2+PMA (P2771_N712-S510)


title: J-LatA2+DMSO (P2771_N715-S505)


title: PA-GFP Foxp3IRES-RFP_741


title: PA-GFP Foxp3IRES-RFP_740


title: J-LatA2+SAHA (P2771_N712-S507)


title: PA-GFP Foxp3IRES-RFP_739


title: J-LatA2+SAHA (P2771_N712-S506)


title: PA-GFP Foxp3IRES-RFP_738


title: Jurkat+PMA (P2771_N712-S503)


title: PA-GFP Foxp3IRES-RFP_735


title: PA-GFP Foxp3IRES-RFP_737


title: Jurkat+SAHA (P2771_N712-S502)


title: PA-GFP Foxp3IRES-RFP_734


title: J-LatA2+PMA (P2771_N711-S510)


title: J-LatA2+SAHA (P2771_N711-S508)


title: PA-GFP Foxp3IRES-RFP_732


title: PA-GFP Foxp3IRES-RFP_736


title: Jurkat+PMA (P2771_N714-S503)


title: J-LatA2+PMA (P2771_N711-S511)


title: PA-GFP Foxp3IRES-RFP_733


title: J-LatA2+SAHA (P2771_N711-S507)


title: PA-GFP Foxp3IRES-RFP_731


title: J-LatA2+SAHA (P2771_N711-S506)


title: PA-GFP Foxp3IRES-RFP_730


title: Jurkat+PMA (P2771_N711-S503)


title: PA-GFP Foxp3IRES-RFP_729


title: J-LatA2+DMSO (P2771_N711-S505)


title: PA-GFP Foxp3IRES-RFP_728


title: Jurkat+SAHA (P2771_N711-S502)


title: J-LatA2+PMA (P2771_N712-S508)


title: PA-GFP Foxp3IRES-RFP_727


title: J-LatA2+DMSO (P2771_N712-S505)


title: PA-GFP Foxp3IRES-RFP_726


title: J-LatA2+PMA (P2771_N710-S510)


title: J-LatA2+SAHA (P2771_N710-S508)


title: PA-GFP Foxp3IRES-RFP_723


title: PA-GFP Foxp3IRES-RFP_725


title: PA-GFP Foxp3IRES-RFP_722


title: PA-GFP Foxp3IRES-RFP_724

value: CD4+ Resting


title: J-LatA2+SAHA (P2771_N710-S507)


title: J-LatA2+DMSO (P2771_N710-S505)


title: Jurkat+PMA (P2771_N710-S503)


title: Jurkat+SAHA (P2771_N710-S502)


title: J-LatA2+PMA (P2771_N707-S511)


title: PA-GFP Foxp3IRES-RFP_721


title: PA-GFP Foxp3IRES-RFP_720


title: PA-GFP Foxp3IRES-RFP_718


title: PA-GFP Foxp3IRES-RFP_719


title: J-LatA2+PMA (P2771_N710-S511)


title: J-LatA2+PMA (P2771_N707-S510)


title: J-LatA2+SAHA (P2771_N707-S507)


title: PA-GFP Foxp3IRES-RFP_715


title: PA-GFP Foxp3IRES-RFP_713


title: J-LatA2+SAHA (P2771_N707-S506)


title: PA-GFP Foxp3IRES-RFP_714


title: Jurkat+PMA (P2771_N707-S503)


title: J-LatA2+SAHA (P2771_N710-S506)


title: PA-GFP Foxp3IRES-RFP_712

value: Tfr


title: J-LatA2+PMA (P2771_N706-S511)


title: PA-GFP Foxp3IRES-RFP_711


title: PA-GFP Foxp3IRES-RFP_709


title: J-LatA2+PMA (P2771_N706-S510)


title: PA-GFP Foxp3IRES-RFP_710


title: J-LatA2+SAHA (P2771_N706-S508)


title: J-LatA2+SAHA (P2771_N707-S508)


title: PA-GFP Foxp3IRES-RFP_708


title: J-LatA2+DMSO (P2771_N706-S506)


title: PA-GFP Foxp3IRES-RFP_717


title: PA-GFP Foxp3IRES-RFP_707


title: PA-GFP Foxp3IRES-RFP_706


title: PA-GFP Foxp3IRES-RFP_716


title: PA-GFP Foxp3IRES-RFP_705


title: Jurkat+PMA (P2771_N706-S505)


title: Jurkat+DMSO (P2771_N706-S502)


title: PA-GFP Foxp3IRES-RFP_704


title: PA-GFP Foxp3IRES-RFP_703


title: J-LatA2+DMSO (P2771_N707-S505)


title: J-LatA2+PMA (P2771_N705-S511)


title: PA-GFP Foxp3IRES-RFP_701


title: Jurkat+SAHA (P2771_N707-S502)


title: J-LatA2+PMA (P2771_N705-S510)


title: J-LatA2+SAHA (P2771_N705-S508)


title: PA-GFP Foxp3IRES-RFP_700


title: J-LatA2+SAHA (P2771_N706-S507)


title: Jurkat+PMA (P2771_N705-S505)


title: PA-GFP Foxp3IRES-RFP_699


title: PA-GFP Foxp3IRES-RFP_698


title: PA-GFP Foxp3IRES-RFP_697


title: PA-GFP Foxp3IRES-RFP_696


title: J-LatA2+SAHA (P2771_N705-S507)


title: Jurkat+SAHA (P2771_N705-S503)


title: Jurkat+SAHA (P2771_N706-S503)


title: Jurkat+DMSO (P2771_N705-S502)


title: PA-GFP Foxp3IRES-RFP_694


title: J-LatA2+PMA (P2771_N704-S511)


title: J-LatA2+PMA (P2771_N704-S510)


title: PA-GFP Foxp3IRES-RFP_693


title: PA-GFP Foxp3IRES-RFP_695


title: J-LatA2+SAHA (P2771_N704-S507)


title: PA-GFP Foxp3IRES-RFP_692


title: PA-GFP Foxp3IRES-RFP_702


title: PA-GFP Foxp3IRES-RFP_691


title: PA-GFP Foxp3IRES-RFP_690


title: J-LatA2+DMSO (P2771_N704-S506)


title: Jurkat+PMA (P2771_N704-S505)


title: J-LatA2+SAHA (P2771_N704-S508)


title: PA-GFP Foxp3IRES-RFP_688


title: J-LatA2+DMSO (P2771_N705-S506)


title: Jurkat+DMSO (P2771_N704-S502)


title: PA-GFP Foxp3IRES-RFP_689


title: Jurkat+SAHA (P2771_N704-S503)


title: J-LatA2+PMA (P2771_N703-S511)


title: PA-GFP Foxp3IRES-RFP_686


title: J-LatA2+PMA (P2771_N703-S510)


title: PA-GFP Foxp3IRES-RFP_683


title: J-LatA2+DMSO (P2771_N703-S506)


title: PA-GFP Foxp3IRES-RFP_684


title: J-LatA2+SAHA (P2771_N703-S508)


title: PA-GFP Foxp3IRES-RFP_682


title: Jurkat+PMA (P2771_N703-S505)


title: PA-GFP Foxp3IRES-RFP_681


title: PA-GFP Foxp3IRES-RFP_685


title: Jurkat+DMSO (P2771_N703-S502)


title: Jurkat+SAHA (P2771_N703-S503)


title: PA-GFP Foxp3IRES-RFP_678


title: J-LatA2+PMA (P2771_N702-S511)


title: J-LatA2+SAHA (P2771_N702-S508)


title: PA-GFP Foxp3IRES-RFP_677


title: J-LatA2+SAHA (P2771_N702-S507)


title: PA-GFP Foxp3IRES-RFP_687


title: J-LatA2+DMSO (P2771_N702-S506)


title: PA-GFP Foxp3IRES-RFP_676


title: J-LatA2+PMA (P2771_N702-S510)


title: PA-GFP Foxp3IRES-RFP_674


title: PA-GFP Foxp3IRES-RFP_673


title: PA-GFP Foxp3IRES-RFP_672


title: PA-GFP Foxp3IRES-RFP_675


title: Jurkat+SAHA (P2771_N702-S503)


title: Jurkat+PMA (P2771_N702-S505)


title: J-LatA2+SAHA (P2771_N703-S507)


title: Jurkat+DMSO (P2771_N702-S502)


title: PA-GFP Foxp3IRES-RFP_671


title: J-LatA2+PMA (P2771_N701-S511)


title: J-LatA2+SAHA (P2771_N701-S508)


title: PA-GFP Foxp3IRES-RFP_669


title: J-LatA2+PMA (P2771_N701-S510)


title: PA-GFP Foxp3IRES-RFP_679


title: PA-GFP Foxp3IRES-RFP_670


title: J-LatA2+SAHA (P2771_N701-S507)


title: PA-GFP Foxp3IRES-RFP_680


title: PA-GFP Foxp3IRES-RFP_667


title: PA-GFP Foxp3IRES-RFP_668


title: J-LatA2+DMSO (P2771_N701-S506)


title: Jurkat+PMA (P2771_N701-S505)


title: PA-GFP Foxp3IRES-RFP_665


title: Jurkat+SAHA (P2771_N701-S503)


title: Jurkat+DMSO (P2771_N701-S502)


title: PA-GFP Foxp3IRES-RFP_664


title: PA-GFP Foxp3IRES-RFP_662


title: J-LatA2+PMA (P2770_N715-S522)


title: J-LatA2+PMA (P2770_N715-S521)


title: PA-GFP Foxp3IRES-RFP_660


title: J-LatA2+SAHA (P2770_N715-S518)


title: J-LatA2+SAHA (P2770_N715-S517)


title: PA-GFP Foxp3IRES-RFP_663


title: PA-GFP Foxp3IRES-RFP_658


title: J-LatA2+PMA (P2770_N715-S520)


title: PA-GFP Foxp3IRES-RFP_661


title: J-LatA2+DMSO (P2770_N715-S516)


title: PA-GFP Foxp3IRES-RFP_656


title: Jurkat+PMA (P2770_N715-S515)


title: PA-GFP Foxp3IRES-RFP_659


title: J-LatA2+PMA (P2770_N714-S522)


title: Jurkat+SAHA (P2770_N715-S513)


title: J-LatA2+PMA (P2770_N714-S521)


title: PA-GFP Foxp3IRES-RFP_657


title: PA-GFP Foxp3IRES-RFP_653


title: PA-GFP Foxp3IRES-RFP_655


title: J-LatA2+PMA (P2770_N714-S520)


title: PA-GFP Foxp3IRES-RFP_652


title: PA-GFP Foxp3IRES-RFP_666


title: PA-GFP Foxp3IRES-RFP_651


title: PA-GFP Foxp3IRES-RFP_650


title: J-LatA2+SAHA (P2770_N714-S517)


title: J-LatA2+DMSO (P2770_N714-S516)


title: PA-GFP Foxp3IRES-RFP_649


title: Jurkat+PMA (P2770_N714-S515)


title: Jurkat+SAHA (P2770_N714-S513)


title: PA-GFP Foxp3IRES-RFP_648


title: PA-GFP Foxp3IRES-RFP_646


title: J-LatA2+PMA (P2770_N712-S522)


title: PA-GFP Foxp3IRES-RFP_647


title: J-LatA2+PMA (P2770_N712-S521)


title: PA-GFP Foxp3IRES-RFP_645


title: PA-GFP Foxp3IRES-RFP_644


title: PA-GFP Foxp3IRES-RFP_654


title: J-LatA2+SAHA (P2770_N712-S518)


title: PA-GFP Foxp3IRES-RFP_643


title: PA-GFP Foxp3IRES-RFP_642


title: J-LatA2+SAHA (P2770_N712-S517)


title: Jurkat+PMA (P2770_N712-S515)


title: PA-GFP Foxp3IRES-RFP_641


title: J-LatA2+DMSO (P2770_N712-S516)


title: J-LatA2+SAHA (P2770_N714-S518)


title: Jurkat+SAHA (P2770_N712-S513)


title: J-LatA2+PMA (P2770_N711-S522)


title: PA-GFP Foxp3IRES-RFP_639


title: PA-GFP Foxp3IRES-RFP_638


title: PA-GFP Foxp3IRES-RFP_637


title: J-LatA2+SAHA (P2770_N711-S520)


title: PA-GFP Foxp3IRES-RFP_636


title: J-LatA2+PMA (P2770_N711-S521)


title: J-LatA2+SAHA (P2770_N711-S518)


title: PA-GFP Foxp3IRES-RFP_635


title: J-LatA2+SAHA (P2770_N711-S517)


title: J-LatA2+DMSO (P2770_N711-S516)


title: PA-GFP Foxp3IRES-RFP_634


title: PA-GFP Foxp3IRES-RFP_633


title: PA-GFP Foxp3IRES-RFP_632


title: Jurkat+PMA (P2770_N711-S515)


title: J-LatA2+PMA (P2770_N712-S520)


title: PA-GFP Foxp3IRES-RFP_631


title: Jurkat+SAHA (P2770_N711-S513)


title: PA-GFP Foxp3IRES-RFP_640


title: PA-GFP Foxp3IRES-RFP_630


title: J-LatA2+PMA (P2770_N710-S522)


title: J-LatA2+PMA (P2770_N710-S521)


title: PA-GFP Foxp3IRES-RFP_628


title: J-LatA2+SAHA (P2770_N710-S520)


title: PA-GFP Foxp3IRES-RFP_625


title: PA-GFP Foxp3IRES-RFP_626


title: PA-GFP Foxp3IRES-RFP_627


title: PA-GFP Foxp3IRES-RFP_624


title: J-LatA2+SAHA (P2770_N710-S518)


title: J-LatA2+DMSO (P2770_N710-S516)


title: PA-GFP Foxp3IRES-RFP_629


title: J-LatA2+SAHA (P2770_N710-S517)


title: PA-GFP Foxp3IRES-RFP_622


title: PA-GFP Foxp3IRES-RFP_623


title: Jurkat+SAHA (P2770_N710-S513)


title: Jurkat+PMA (P2770_N710-S515)


title: J-LatA2+PMA (P2770_N707-S522)


title: J-LatA2+PMA (P2770_N707-S521)


title: PA-GFP Foxp3IRES-RFP_619


title: PA-GFP Foxp3IRES-RFP_620


title: J-LatA2+SAHA (P2770_N707-S517)


title: J-LatA2+DMSO (P2770_N707-S516)


title: PA-GFP Foxp3IRES-RFP_618


title: J-LatA2+SAHA (P2770_N707-S518)


title: J-LatA2+SAHA (P2770_N707-S520)


title: PA-GFP Foxp3IRES-RFP_617


title: Jurkat+PMA (P2770_N707-S515)


title: PA-GFP Foxp3IRES-RFP_621


title: PA-GFP Foxp3IRES-RFP_616


title: Jurkat+SAHA (P2770_N707-S513)


title: J-LatA2+PMA (P2770_N706-S522)


title: PA-GFP Foxp3IRES-RFP_615


title: PA-GFP Foxp3IRES-RFP_614


title: J-LatA2+PMA (P2770_N706-S521)


title: PA-GFP Foxp3IRES-RFP_613


title: J-LatA2+SAHA (P2770_N706-S520)


title: J-LatA2+SAHA (P2770_N706-S518)


title: PA-GFP Foxp3IRES-RFP_611


title: PA-GFP Foxp3IRES-RFP_610


title: Jurkat+PMA (P2770_N706-S516)


title: J-LatA2+DMSO (P2770_N706-S517)


title: PA-GFP Foxp3IRES-RFP_609


title: Jurkat+SAHA (P2770_N706-S515)


title: J-LatA2+PMA (P2770_N705-S522)


title: PA-GFP Foxp3IRES-RFP_606


title: PA-GFP Foxp3IRES-RFP_605


title: J-LatA2+SAHA (P2770_N705-S520)


title: J-LatA2+PMA (P2770_N705-S521)


title: J-LatA2+SAHA (P2770_N705-S518)


title: PA-GFP Foxp3IRES-RFP_604


title: PA-GFP Foxp3IRES-RFP_603


title: PA-GFP Foxp3IRES-RFP_602


title: J-LatA2+DMSO (P2770_N705-S517)


title: Jurkat+PMA (P2770_N705-S516)


title: PA-GFP Foxp3IRES-RFP_601


title: Jurkat+SAHA (P2770_N705-S515)


title: PA-GFP Foxp3IRES-RFP_600


title: Jurkat+DMSO (P2770_N705-S513)


title: J-LatA2+PMA (P2770_N704-S522)


title: PA-GFP Foxp3IRES-RFP_612


title: PA-GFP Foxp3IRES-RFP_599


title: PA-GFP Foxp3IRES-RFP_598


title: J-LatA2+PMA (P2770_N704-S521)


title: PA-GFP Foxp3IRES-RFP_608


title: PA-GFP Foxp3IRES-RFP_597


title: Jurkat+DMSO (P2770_N706-S513)


title: PA-GFP Foxp3IRES-RFP_596


title: J-LatA2+SAHA (P2770_N704-S518)


title: J-LatA2+SAHA (P2770_N704-S520)


title: J-LatA2+DMSO (P2770_N704-S517)


title: PA-GFP Foxp3IRES-RFP_607


title: PA-GFP Foxp3IRES-RFP_595


title: Jurkat+PMA (P2770_N704-S516)


title: PA-GFP Foxp3IRES-RFP_593


title: PA-GFP Foxp3IRES-RFP_591


title: PA-GFP Foxp3IRES-RFP_592


title: Jurkat+DMSO (P2770_N704-S513)


title: J-LatA2+PMA (P2770_N703-S522)


title: PA-GFP Foxp3IRES-RFP_590


title: PA-GFP Foxp3IRES-RFP_589


title: J-LatA2+PMA (P2770_N703-S521)


title: PA-GFP Foxp3IRES-RFP_588


title: J-LatA2+SAHA (P2770_N703-S520)


title: J-LatA2+SAHA (P2770_N703-S518)


title: J-LatA2+DMSO (P2770_N703-S517)


title: Jurkat+PMA (P2770_N703-S516)


title: PA-GFP Foxp3IRES-RFP_587


title: PA-GFP Foxp3IRES-RFP_585


title: PA-GFP Foxp3IRES-RFP_584


title: Jurkat+SAHA (P2770_N703-S515)


title: Jurkat+DMSO (P2770_N703-S513)


title: PA-GFP Foxp3IRES-RFP_582


title: PA-GFP Foxp3IRES-RFP_583


title: PA-GFP Foxp3IRES-RFP_581


title: J-LatA2+PMA (P2770_N702-S521)


title: PA-GFP Foxp3IRES-RFP_594


title: J-LatA2+PMA (P2770_N702-S522)


title: J-LatA2+SAHA (P2770_N702-S520)


title: PA-GFP Foxp3IRES-RFP_580


title: PA-GFP Foxp3IRES-RFP_579


title: Jurkat+SAHA (P2770_N704-S515)


title: PA-GFP Foxp3IRES-RFP_578


title: Jurkat+SAHA (P2770_N702-S515)


title: Jurkat+PMA (P2770_N702-S516)


title: PA-GFP Foxp3IRES-RFP_577


title: Jurkat+DMSO (P2770_N702-S513)


title: PA-GFP Foxp3IRES-RFP_586


title: PA-GFP Foxp3IRES-RFP_575


title: J-LatA2+SAHA (P2770_N702-S518)


title: J-LatA2+PMA (P2770_N701-S522)


title: PA-GFP Foxp3IRES-RFP_574


title: PA-GFP Foxp3IRES-RFP_573


title: J-LatA2+SAHA (P2770_N701-S520)


title: PA-GFP Foxp3IRES-RFP_572


title: J-LatA2+SAHA (P2770_N701-S518)


title: J-LatA2+PMA (P2770_N701-S521)


title: PA-GFP Foxp3IRES-RFP_571


title: PA-GFP Foxp3IRES-RFP_570


title: Jurkat+PMA (P2770_N701-S516)


title: PA-GFP Foxp3IRES-RFP_569


title: Jurkat+SAHA (P2770_N701-S515)


title: PA-GFP Foxp3IRES-RFP_568


title: PA-GFP Foxp3IRES-RFP_567


title: Jurkat+DMSO (P2770_N701-S513)


title: PA-GFP Foxp3IRES-RFP_566


title: J-LatA2+DMSO (P2770_N702-S517)


title: J-LatA2+PMA (P2769_N715-S511)


title: PA-GFP Foxp3IRES-RFP_576


title: J-LatA2+PMA (P2769_N715-S508)


title: PA-GFP Foxp3IRES-RFP_565


title: J-LatA2+PMA (P2769_N715-S510)


title: PA-GFP Foxp3IRES-RFP_564


title: J-LatA2+SAHA (P2769_N715-S507)


title: PA-GFP Foxp3IRES-RFP_563


title: J-LatA2+DMSO (P2769_N715-S505)


title: PA-GFP Foxp3IRES-RFP_562


title: J-LatA2+SAHA (P2769_N715-S506)


title: PA-GFP Foxp3IRES-RFP_561


title: Jurkat+PMA (P2769_N715-S503)


title: Jurkat+SAHA (P2769_N715-S502)


title: J-LatA2+DMSO (P2770_N701-S517)


title: J-LatA2+PMA (P2769_N714-S511)


title: PA-GFP Foxp3IRES-RFP_559


title: PA-GFP Foxp3IRES-RFP_557


title: J-LatA2+PMA (P2769_N714-S510)


title: J-LatA2+PMA (P2769_N714-S508)


title: PA-GFP Foxp3IRES-RFP_556


title: PA-GFP Foxp3IRES-RFP_554


title: J-LatA2+SAHA (P2769_N714-S506)


title: J-LatA2+DMSO (P2769_N714-S505)


title: Jurkat+PMA (P2769_N714-S503)


title: PA-GFP Foxp3IRES-RFP_553


title: PA-GFP Foxp3IRES-RFP_552


title: Jurkat+SAHA (P2769_N714-S502)


title: PA-GFP Foxp3IRES-RFP_551


title: J-LatA2+PMA (P2769_N712-S511)


title: PA-GFP Foxp3IRES-RFP_549


title: PA-GFP Foxp3IRES-RFP_560


title: J-LatA2+SAHA (P2769_N712-S507)


title: PA-GFP Foxp3IRES-RFP_547


title: J-LatA2+SAHA (P2769_N712-S506)


title: PA-GFP Foxp3IRES-RFP_548


title: PA-GFP Foxp3IRES-RFP_546


title: PA-GFP Foxp3IRES-RFP_558


title: PA-GFP Foxp3IRES-RFP_545


title: PA-GFP Foxp3IRES-RFP_544


title: J-LatA2+DMSO (P2769_N712-S505)


title: J-LatA2+PMA (P2769_N711-S511)


title: PA-GFP Foxp3IRES-RFP_555


title: Jurkat+SAHA (P2769_N712-S502)


title: PA-GFP Foxp3IRES-RFP_543


title: J-LatA2+PMA (P2769_N711-S510)


title: PA-GFP Foxp3IRES-RFP_541


title: J-LatA2+SAHA (P2769_N711-S508)


title: J-LatA2+SAHA (P2769_N711-S507)


title: PA-GFP Foxp3IRES-RFP_540


title: J-LatA2+PMA (P2769_N712-S510)


title: J-LatA2+SAHA (P2769_N711-S506)


title: J-LatA2+PMA (P2769_N712-S508)


title: PA-GFP Foxp3IRES-RFP_539


title: J-LatA2+DMSO (P2769_N711-S505)


title: PA-GFP Foxp3IRES-RFP_537


title: Jurkat+PMA (P2769_N711-S503)


title: PA-GFP Foxp3IRES-RFP_535


title: Jurkat+PMA (P2769_N712-S503)


title: Jurkat+SAHA (P2769_N711-S502)


title: PA-GFP Foxp3IRES-RFP_534


title: J-LatA2+PMA (P2769_N710-S511)


title: J-LatA2+SAHA (P2769_N714-S507)


title: PA-GFP Foxp3IRES-RFP_550


title: J-LatA2+PMA (P2769_N710-S510)


title: PA-GFP Foxp3IRES-RFP_536


title: PA-GFP Foxp3IRES-RFP_533


title: PA-GFP Foxp3IRES-RFP_542


title: J-LatA2+SAHA (P2769_N710-S507)


title: PA-GFP Foxp3IRES-RFP_531


title: PA-GFP Foxp3IRES-RFP_530


title: J-LatA2+DMSO (P2769_N710-S505)


title: J-LatA2+SAHA (P2769_N710-S506)


title: PA-GFP Foxp3IRES-RFP_529


title: PA-GFP Foxp3IRES-RFP_538


title: J-LatA2+SAHA (P2769_N710-S508)


title: Jurkat+PMA (P2769_N710-S503)


title: Jurkat+SAHA (P2769_N710-S502)


title: PA-GFP Foxp3IRES-RFP_528


title: PA-GFP Foxp3IRES-RFP_527


title: J-LatA2+PMA (P2769_N707-S511)


title: J-LatA2+PMA (P2769_N707-S510)


title: PA-GFP Foxp3IRES-RFP_526


title: PA-GFP Foxp3IRES-RFP_525


title: PA-GFP Foxp3IRES-RFP_532


title: J-LatA2+SAHA (P2769_N707-S508)


title: PA-GFP Foxp3IRES-RFP_522


title: PA-GFP Foxp3IRES-RFP_524


title: J-LatA2+SAHA (P2769_N707-S507)


title: PA-GFP Foxp3IRES-RFP_523


title: PA-GFP Foxp3IRES-RFP_520


title: Jurkat+PMA (P2769_N707-S503)


title: PA-GFP Foxp3IRES-RFP_521


title: J-LatA2+PMA (P2769_N706-S511)


title: Jurkat+SAHA (P2769_N707-S502)


title: PA-GFP Foxp3IRES-RFP_519


title: PA-GFP Foxp3IRES-RFP_518


title: J-LatA2+PMA (P2769_N706-S510)


title: PA-GFP Foxp3IRES-RFP_517


title: PA-GFP Foxp3IRES-RFP_516


title: J-LatA2+SAHA (P2769_N706-S508)


title: PA-GFP Foxp3IRES-RFP_515


title: J-LatA2+DMSO (P2769_N706-S506)


title: J-LatA2+SAHA (P2769_N707-S506)


title: PA-GFP Foxp3IRES-RFP_514


title: Jurkat+PMA (P2769_N706-S505)


title: PA-GFP Foxp3IRES-RFP_513


title: J-LatA2+DMSO (P2769_N707-S505)


title: Jurkat+SAHA (P2769_N706-S503)


title: PA-GFP Foxp3IRES-RFP_511


title: Jurkat+DMSO (P2769_N706-S502)


title: PA-GFP Foxp3IRES-RFP_512


title: J-LatA2+PMA (P2769_N705-S511)


title: PA-GFP Foxp3IRES-RFP_510


title: J-LatA2+SAHA (P2769_N705-S508)


title: PA-GFP Foxp3IRES-RFP_509


title: J-LatA2+SAHA (P2769_N705-S507)


title: J-LatA2+SAHA (P2769_N706-S507)


title: PA-GFP Foxp3IRES-RFP_507


title: J-LatA2+PMA (P2769_N705-S510)


title: J-LatA2+DMSO (P2769_N705-S506)


title: PA-GFP Foxp3IRES-RFP_506


title: PA-GFP Foxp3IRES-RFP_505


title: PA-GFP Foxp3IRES-RFP_504


title: Jurkat+SAHA (P2769_N705-S503)


title: Jurkat+DMSO (P2769_N705-S502)


title: Jurkat+PMA (P2769_N705-S505)


title: PA-GFP Foxp3IRES-RFP_503


title: J-LatA2+PMA (P2769_N704-S510)


title: J-LatA2+PMA (P2769_N704-S511)


title: PA-GFP Foxp3IRES-RFP_502


title: PA-GFP Foxp3IRES-RFP_501


title: PA-GFP Foxp3IRES-RFP_508


title: J-LatA2+SAHA (P2769_N704-S507)


title: J-LatA2+DMSO (P2769_N704-S506)


title: PA-GFP Foxp3IRES-RFP_499


title: PA-GFP Foxp3IRES-RFP_500


title: J-LatA2+SAHA (P2769_N704-S508)


title: PA-GFP Foxp3IRES-RFP_498


title: Jurkat+PMA (P2769_N704-S505)


title: Jurkat+SAHA (P2769_N704-S503)


title: PA-GFP Foxp3IRES-RFP_496


title: PA-GFP Foxp3IRES-RFP_495


title: J-LatA2+PMA (P2769_N703-S511)


title: Jurkat+DMSO (P2769_N704-S502)


title: J-LatA2+PMA (P2769_N703-S510)


title: PA-GFP Foxp3IRES-RFP_493


title: J-LatA2+SAHA (P2769_N703-S508)


title: PA-GFP Foxp3IRES-RFP_492


title: J-LatA2+SAHA (P2769_N703-S507)


title: PA-GFP Foxp3IRES-RFP_491


title: Jurkat+PMA (P2769_N703-S505)


title: PA-GFP Foxp3IRES-RFP_489


title: J-LatA2+DMSO (P2769_N703-S506)


title: PA-GFP Foxp3IRES-RFP_494


title: PA-GFP Foxp3IRES-RFP_490


title: PA-GFP Foxp3IRES-RFP_488


title: PA-GFP Foxp3IRES-RFP_487


title: PA-GFP Foxp3IRES-RFP_486


title: PA-GFP Foxp3IRES-RFP_497


title: PA-GFP Foxp3IRES-RFP_485


title: J-LatA2+SAHA (P2769_N702-S508)


title: J-LatA2+PMA (P2769_N702-S510)


title: PA-GFP Foxp3IRES-RFP_484


title: J-LatA2+PMA (P2769_N702-S511)


title: PA-GFP Foxp3IRES-RFP_482


title: Jurkat+PMA (P2769_N702-S505)


title: PA-GFP Foxp3IRES-RFP_483


title: J-LatA2+SAHA (P2769_N702-S507)


title: J-LatA2+DMSO (P2769_N702-S506)


title: PA-GFP Foxp3IRES-RFP_481


title: PA-GFP Foxp3IRES-RFP_480


title: PA-GFP Foxp3IRES-RFP_479


title: Jurkat+DMSO (P2769_N702-S502)


title: Jurkat+SAHA (P2769_N703-S503)


title: PA-GFP Foxp3IRES-RFP_478


title: PA-GFP Foxp3IRES-RFP_477


title: J-LatA2+PMA (P2769_N701-S510)


title: J-LatA2+SAHA (P2769_N701-S508)


title: PA-GFP Foxp3IRES-RFP_476


title: J-LatA2+SAHA (P2769_N701-S507)


title: PA-GFP Foxp3IRES-RFP_475


title: Jurkat+DMSO (P2769_N703-S502)


title: PA-GFP Foxp3IRES-RFP_474


title: J-LatA2+DMSO (P2769_N701-S506)


title: Jurkat+PMA (P2769_N701-S505)


title: Jurkat+SAHA (P2769_N701-S503)


title: J-LatA2+SAHA (P2458_N715-S522)


title: PA-GFP Foxp3IRES-RFP_472


title: PA-GFP Foxp3IRES-RFP_470


title: PA-GFP Foxp3IRES-RFP_471


title: Jurkat+SAHA (P2769_N702-S503)


title: PA-GFP Foxp3IRES-RFP_469


title: J-LatA2+SAHA (P2458_N715-S521)


title: J-LatA2+SAHA (P2458_N715-S518)


title: PA-GFP Foxp3IRES-RFP_467


title: Jurkat+DMSO (P2769_N701-S502)


title: PA-GFP Foxp3IRES-RFP_473


title: PA-GFP Foxp3IRES-RFP_468


title: J-LatA2+SAHA (P2458_N715-S517)


title: J-LatA2+DMSO (P2458_N715-S516)


title: J-LatA2+PMA (P2769_N701-S511)


title: J-LatA2+SAHA (P2458_N715-S520)


title: PA-GFP Foxp3IRES-RFP_464


title: PA-GFP Foxp3IRES-RFP_465


title: J-LatA2+DMSO (P2458_N715-S513)


title: J-LatA2+SAHA (P2458_N714-S522)


title: J-LatA2+SAHA (P2458_N714-S521)


title: PA-GFP Foxp3IRES-RFP_462


title: PA-GFP Foxp3IRES-RFP_463


title: PA-GFP Foxp3IRES-RFP_461


title: J-LatA2+SAHA (P2458_N714-S520)


title: J-LatA2+DMSO (P2458_N715-S515)


title: PA-GFP Foxp3IRES-RFP_460


title: J-LatA2+SAHA (P2458_N714-S518)


title: PA-GFP Foxp3IRES-RFP_459


title: J-LatA2+DMSO (P2458_N714-S516)


title: PA-GFP Foxp3IRES-RFP_458


title: J-LatA2+SAHA (P2458_N714-S517)


title: PA-GFP Foxp3IRES-RFP_457


title: J-LatA2+DMSO (P2458_N714-S515)


title: PA-GFP Foxp3IRES-RFP_456


title: J-LatA2+DMSO (P2458_N714-S513)


title: PA-GFP Foxp3IRES-RFP_455


title: J-LatA2+SAHA (P2458_N712-S522)


title: PA-GFP Foxp3IRES-RFP_453


title: PA-GFP Foxp3IRES-RFP_454


title: PA-GFP Foxp3IRES-RFP_452


title: J-LatA2+SAHA (P2458_N712-S521)


title: J-LatA2+SAHA (P2458_N712-S517)


title: J-LatA2+SAHA (P2458_N712-S520)


title: J-LatA2+SAHA (P2458_N712-S518)


title: PA-GFP Foxp3IRES-RFP_451


title: PA-GFP Foxp3IRES-RFP_450


title: PA-GFP Foxp3IRES-RFP_449


title: J-LatA2+DMSO (P2458_N712-S515)


title: PA-GFP Foxp3IRES-RFP_447


title: J-LatA2+DMSO (P2458_N712-S513)


title: J-LatA2+SAHA (P2458_N711-S521)


title: PA-GFP Foxp3IRES-RFP_446


title: J-LatA2+DMSO (P2458_N712-S516)


title: J-LatA2+SAHA (P2458_N711-S522)


title: J-LatA2+SAHA (P2458_N711-S520)


title: J-LatA2+SAHA (P2458_N711-S518)


title: J-LatA2+DMSO (P2458_N711-S516)


title: J-LatA2+SAHA (P2458_N711-S517)


title: PA-GFP Foxp3IRES-RFP_443


title: PA-GFP Foxp3IRES-RFP_442


title: PA-GFP Foxp3IRES-RFP_441


title: J-LatA2+DMSO (P2458_N711-S515)


title: PA-GFP Foxp3IRES-RFP_440


title: PA-GFP Foxp3IRES-RFP_438


title: PA-GFP Foxp3IRES-RFP_448


title: J-LatA2+DMSO (P2458_N711-S513)


title: J-LatA2+SAHA (P2458_N710-S522)


title: J-LatA2+SAHA (P2458_N710-S521)


title: PA-GFP Foxp3IRES-RFP_437


title: PA-GFP Foxp3IRES-RFP_445


title: J-LatA2+SAHA (P2458_N710-S520)


title: J-LatA2+SAHA (P2458_N710-S518)


title: J-LatA2+SAHA (P2458_N710-S517)


title: PA-GFP Foxp3IRES-RFP_444


title: PA-GFP Foxp3IRES-RFP_436


title: PA-GFP Foxp3IRES-RFP_435


title: PA-GFP Foxp3IRES-RFP_434


title: PA-GFP Foxp3IRES-RFP_432


title: PA-GFP Foxp3IRES-RFP_433


title: J-LatA2+DMSO (P2458_N710-S513)


title: J-LatA2+DMSO (P2458_N710-S516)


title: PA-GFP Foxp3IRES-RFP_431


title: J-LatA2+DMSO (P2458_N710-S515)


title: J-LatA2+SAHA (P2458_N707-S520)


title: PA-GFP Foxp3IRES-RFP_439


title: J-LatA2+SAHA (P2458_N707-S522)


title: J-LatA2+SAHA (P2458_N707-S518)


title: J-LatA2+SAHA (P2458_N707-S521)


title: PA-GFP Foxp3IRES-RFP_428


title: PA-GFP Foxp3IRES-RFP_427


title: J-LatA2+SAHA (P2458_N707-S517)


title: PA-GFP Foxp3IRES-RFP_426


title: PA-GFP Foxp3IRES-RFP_425


title: PA-GFP Foxp3IRES-RFP_423


title: PA-GFP Foxp3IRES-RFP_424


title: PA-GFP Foxp3IRES-RFP_422


title: J-LatA2+SAHA (P2458_N706-S521)


title: J-LatA2+DMSO (P2458_N707-S516)


title: PA-GFP Foxp3IRES-RFP_430


title: PA-GFP Foxp3IRES-RFP_420


title: PA-GFP Foxp3IRES-RFP_429


title: PA-GFP Foxp3IRES-RFP_421


title: J-LatA2+DMSO (P2458_N707-S513)


title: J-LatA2+SAHA (P2458_N706-S518)


title: J-LatA2+SAHA (P2458_N706-S520)


title: J-LatA2+SAHA (P2458_N706-S517)


title: PA-GFP Foxp3IRES-RFP_417


title: J-LatA2+DMSO (P2458_N706-S516)


title: J-LatA2+SAHA (P2458_N706-S522)


title: Jurkat+DMSO (P2458_N706-S513)


title: J-LatA2+DMSO (P2458_N706-S515)


title: PA-GFP Foxp3IRES-RFP_419


title: PA-GFP Foxp3IRES-RFP_415


title: PA-GFP Foxp3IRES-RFP_418


title: PA-GFP Foxp3IRES-RFP_416


title: PA-GFP Foxp3IRES-RFP_413


title: J-LatA2+SAHA (P2458_N705-S521)


title: J-LatA2+DMSO (P2458_N707-S515)


title: J-LatA2+SAHA (P2458_N705-S520)


title: PA-GFP Foxp3IRES-RFP_412


title: J-LatA2+SAHA (P2458_N705-S518)


title: PA-GFP Foxp3IRES-RFP_411


title: J-LatA2+SAHA (P2458_N705-S517)


title: J-LatA2+DMSO (P2458_N705-S516)


title: PA-GFP Foxp3IRES-RFP_409


title: PA-GFP Foxp3IRES-RFP_408


title: Jurkat+DMSO (P2458_N705-S513)


title: PA-GFP Foxp3IRES-RFP_410


title: PA-GFP Foxp3IRES-RFP_414


title: J-LatA2+SAHA (P2458_N704-S522)


title: PA-GFP Foxp3IRES-RFP_405


title: PA-GFP Foxp3IRES-RFP_407


title: PA-GFP Foxp3IRES-RFP_404


title: PA-GFP Foxp3IRES-RFP_403


title: J-LatA2+DMSO (P2458_N705-S515)


title: J-LatA2+SAHA (P2458_N704-S521)


title: J-LatA2+SAHA (P2458_N704-S518)


title: J-LatA2+SAHA (P2458_N704-S520)


title: PA-GFP Foxp3IRES-RFP_406


title: J-LatA2+SAHA (P2458_N705-S522)


title: J-LatA2+DMSO (P2458_N704-S516)


title: PA-GFP Foxp3IRES-RFP_402


title: PA-GFP Foxp3IRES-RFP_401


title: J-LatA2+DMSO (P2458_N704-S515)


title: PA-GFP Foxp3IRES-RFP_399


title: Jurkat+DMSO (P2458_N704-S513)


title: J-LatA2+SAHA (P2458_N703-S522)


title: PA-GFP Foxp3IRES-RFP_398


title: J-LatA2+SAHA (P2458_N703-S521)


title: PA-GFP Foxp3IRES-RFP_397


title: J-LatA2+SAHA (P2458_N703-S520)


title: J-LatA2+SAHA (P2458_N704-S517)


title: J-LatA2+SAHA (P2458_N703-S517)


title: PA-GFP Foxp3IRES-RFP_395


title: PA-GFP Foxp3IRES-RFP_396


title: PA-GFP Foxp3IRES-RFP_391


title: PA-GFP Foxp3IRES-RFP_392


title: PA-GFP Foxp3IRES-RFP_394


title: J-LatA2+DMSO (P2458_N703-S516)


title: J-LatA2+SAHA (P2458_N703-S518)


title: J-LatA2+SAHA (P2458_N702-S522)


title: PA-GFP Foxp3IRES-RFP_390


title: PA-GFP Foxp3IRES-RFP_400


title: PA-GFP Foxp3IRES-RFP_393


title: J-LatA2+DMSO (P2458_N703-S515)


title: PA-GFP Foxp3IRES-RFP_389


title: Jurkat+DMSO (P2458_N703-S513)


title: J-LatA2+SAHA (P2458_N702-S520)


title: J-LatA2+SAHA (P2458_N702-S517)


title: J-LatA2+SAHA (P2458_N702-S521)


title: PA-GFP Foxp3IRES-RFP_386


title: PA-GFP Foxp3IRES-RFP_387


title: J-LatA2+DMSO (P2458_N702-S516)


title: PA-GFP Foxp3IRES-RFP_466


title: PA-GFP Foxp3IRES-RFP_385


title: J-LatA2+DMSO (P2458_N702-S515)


title: PA-GFP Foxp3IRES-RFP_384


title: PA-GFP Foxp3IRES-RFP_383


title: J-LatA2+SAHA (P2458_N701-S522)


title: J-LatA2+SAHA (P2458_N702-S518)


title: PA-GFP Foxp3IRES-RFP_388


title: PA-GFP Foxp3IRES-RFP_382


title: J-LatA2+SAHA (P2458_N701-S520)


title: J-LatA2+SAHA (P2458_N701-S518)


title: PA-GFP Foxp3IRES-RFP_381


title: PA-GFP Foxp3IRES-RFP_380


title: PA-GFP Foxp3IRES-RFP_377


title: PA-GFP Foxp3IRES-RFP_376


title: J-LatA2+SAHA (P2458_N701-S517)


title: J-LatA2+DMSO (P2458_N701-S516)


title: J-LatA2+SAHA (P2449_N729-S511)


title: PA-GFP Foxp3IRES-RFP_375


title: PA-GFP Foxp3IRES-RFP_374


title: J-LatA2+SAHA (P2449_N729-S510)


title: PA-GFP Foxp3IRES-RFP_373


title: J-LatA2+SAHA (P2449_N729-S508)


title: J-LatA2+SAHA (P2449_N729-S507)


title: PA-GFP Foxp3IRES-RFP_372


title: PA-GFP Foxp3IRES-RFP_371


title: Jurkat+DMSO (P2458_N702-S513)


title: J-LatA2+SAHA (P2449_N729-S506)


title: J-LatA2+DMSO (P2449_N729-S505)


title: J-LatA2+SAHA (P2458_N701-S521)


title: PA-GFP Foxp3IRES-RFP_379


title: PA-GFP Foxp3IRES-RFP_369


title: Jurkat+DMSO (P2458_N701-S513)


title: J-LatA2+DMSO (P2458_N701-S515)


title: J-LatA2+SAHA (P2449_N728-S511)


title: PA-GFP Foxp3IRES-RFP_367


title: PA-GFP Foxp3IRES-RFP_368


title: J-LatA2+DMSO (P2449_N729-S502)


title: PA-GFP Foxp3IRES-RFP_364


title: PA-GFP Foxp3IRES-RFP_378


title: PA-GFP Foxp3IRES-RFP_363


title: PA-GFP Foxp3IRES-RFP_366


title: J-LatA2+DMSO (P2449_N729-S503)


title: PA-GFP Foxp3IRES-RFP_365


title: J-LatA2+SAHA (P2449_N728-S508)


title: J-LatA2+DMSO (P2449_N728-S505)


title: J-LatA2+SAHA (P2449_N728-S506)


title: PA-GFP Foxp3IRES-RFP_362


title: J-LatA2+SAHA (P2449_N728-S510)


title: PA-GFP Foxp3IRES-RFP_361


title: J-LatA2+DMSO (P2449_N728-S503)


title: PA-GFP Foxp3IRES-RFP_360


title: J-LatA2+DMSO (P2449_N728-S502)


title: PA-GFP Foxp3IRES-RFP_370


title: J-LatA2+SAHA (P2449_N727-S511)


title: PA-GFP Foxp3IRES-RFP_358


title: PA-GFP Foxp3IRES-RFP_357


title: J-LatA2+SAHA (P2449_N727-S508)


title: PA-GFP Foxp3IRES-RFP_356


title: J-LatA2+SAHA (P2449_N727-S507)


title: J-LatA2+SAHA (P2449_N727-S506)


title: J-LatA2+SAHA (P2449_N728-S507)


title: PA-GFP Foxp3IRES-RFP_355


title: J-LatA2+DMSO (P2449_N727-S505)


title: PA-GFP Foxp3IRES-RFP_354


title: J-LatA2+DMSO (P2449_N727-S503)


title: PA-GFP Foxp3IRES-RFP_352


title: PA-GFP Foxp3IRES-RFP_353


title: PA-GFP Foxp3IRES-RFP_351


title: J-LatA2+SAHA (P2449_N726-S511)


title: PA-GFP Foxp3IRES-RFP_350


title: PA-GFP Foxp3IRES-RFP_349


title: J-LatA2+SAHA (P2449_N726-S510)


title: J-LatA2+DMSO (P2449_N727-S502)


title: J-LatA2+SAHA (P2449_N726-S508)


title: J-LatA2+SAHA (P2449_N726-S507)


title: J-LatA2+SAHA (P2449_N726-S506)


title: PA-GFP Foxp3IRES-RFP_347


title: PA-GFP Foxp3IRES-RFP_359


title: J-LatA2+DMSO (P2449_N726-S505)


title: PA-GFP Foxp3IRES-RFP_345


title: J-LatA2+SAHA (P2449_N727-S510)


title: J-LatA2+DMSO (P2449_N726-S503)


title: PA-GFP Foxp3IRES-RFP_346


title: PA-GFP Foxp3IRES-RFP_344


title: J-LatA2+DMSO (P2449_N726-S502)


title: PA-GFP Foxp3IRES-RFP_343


title: PA-GFP Foxp3IRES-RFP_341


title: PA-GFP Foxp3IRES-RFP_340


title: PA-GFP Foxp3IRES-RFP_339


title: J-LatA2+SAHA (P2449_N724-S511)


title: J-LatA2+SAHA (P2449_N724-S510)


title: J-LatA2+SAHA (P2449_N724-S508)


title: PA-GFP Foxp3IRES-RFP_342


title: PA-GFP Foxp3IRES-RFP_338


title: PA-GFP Foxp3IRES-RFP_348


title: J-LatA2+SAHA (P2449_N724-S507)


title: J-LatA2+DMSO (P2449_N724-S505)


title: PA-GFP Foxp3IRES-RFP_337


title: J-LatA2+SAHA (P2449_N724-S506)


title: J-LatA2+DMSO (P2449_N724-S502)


title: J-LatA2+SAHA (P2449_N723-S511)


title: PA-GFP Foxp3IRES-RFP_334


title: J-LatA2+DMSO (P2449_N724-S503)


title: PA-GFP Foxp3IRES-RFP_335


title: J-LatA2+SAHA (P2449_N723-S508)


title: J-LatA2+SAHA (P2449_N723-S507)


title: J-LatA2+SAHA (P2449_N723-S510)


title: PA-GFP Foxp3IRES-RFP_333


title: PA-GFP Foxp3IRES-RFP_332


title: PA-GFP Foxp3IRES-RFP_331


title: PA-GFP Foxp3IRES-RFP_330


title: J-LatA2+DMSO (P2449_N723-S505)


title: J-LatA2+SAHA (P2449_N723-S506)


title: PA-GFP Foxp3IRES-RFP_329


title: J-LatA2+DMSO (P2449_N723-S503)


title: PA-GFP Foxp3IRES-RFP_328


title: PA-GFP Foxp3IRES-RFP_326


title: PA-GFP Foxp3IRES-RFP_336


title: PA-GFP Foxp3IRES-RFP_327


title: J-LatA2+SAHA (P2449_N722-S510)


title: J-LatA2+DMSO (P2449_N723-S502)


title: J-LatA2+SAHA (P2449_N722-S511)


title: J-LatA2+SAHA (P2449_N722-S508)


title: J-LatA2+SAHA (P2449_N722-S506)


title: PA-GFP Foxp3IRES-RFP_320


title: PA-GFP Foxp3IRES-RFP_323


title: J-LatA2+DMSO (P2449_N722-S505)


title: PA-GFP Foxp3IRES-RFP_325


title: PA-GFP Foxp3IRES-RFP_324


title: PA-GFP Foxp3IRES-RFP_322


title: J-LatA2+SAHA (P2449_N721-S511)


title: PA-GFP Foxp3IRES-RFP_317


title: J-LatA2+SAHA (P2449_N721-S508)


title: Jurkat+DMSO (P2449_N722-S502)


title: PA-GFP Foxp3IRES-RFP_315


title: PA-GFP Foxp3IRES-RFP_318


title: J-LatA2+SAHA (P2449_N721-S510)


title: PA-GFP Foxp3IRES-RFP_319


title: J-LatA2+SAHA (P2449_N721-S506)


title: PA-GFP Foxp3IRES-RFP_314


title: J-LatA2+SAHA (P2449_N722-S507)


title: J-LatA2+DMSO (P2449_N721-S505)


title: J-LatA2+DMSO (P2449_N721-S503)


title: PA-GFP Foxp3IRES-RFP_311


title: Jurkat+DMSO (P2449_N721-S502)


title: J-LatA2+SAHA (P2449_N720-S511)


title: J-LatA2+DMSO (P2449_N722-S503)


title: PA-GFP Foxp3IRES-RFP_313


title: PA-GFP Foxp3IRES-RFP_321


title: PA-GFP Foxp3IRES-RFP_312


title: PA-GFP Foxp3IRES-RFP_310


title: PA-GFP Foxp3IRES-RFP_308


title: PA-GFP Foxp3IRES-RFP_309


title: PA-GFP Foxp3IRES-RFP_307


title: J-LatA2+SAHA (P2449_N720-S510)


title: J-LatA2+SAHA (P2449_N720-S507)


title: PA-GFP Foxp3IRES-RFP_316


title: J-LatA2+DMSO (P2449_N720-S505)


title: J-LatA2+SAHA (P2449_N720-S508)


title: PA-GFP Foxp3IRES-RFP_306


title: J-LatA2+SAHA (P2449_N720-S506)


title: PA-GFP Foxp3IRES-RFP_305


title: J-LatA2+DMSO (P2449_N720-S503)


title: PA-GFP Foxp3IRES-RFP_304


title: J-LatA2+SAHA (P2449_N721-S507)


title: PA-GFP Foxp3IRES-RFP_303


title: J-LatA2+SAHA (P2449_N719-S511)


title: PA-GFP Foxp3IRES-RFP_302


title: Jurkat+DMSO (P2449_N720-S502)


title: J-LatA2+SAHA (P2449_N719-S510)


title: PA-GFP Foxp3IRES-RFP_301


title: PA-GFP Foxp3IRES-RFP_300


title: J-LatA2+SAHA (P2449_N719-S508)


title: J-LatA2+DMSO (P2449_N719-S505)


title: PA-GFP Foxp3IRES-RFP_299


title: J-LatA2+SAHA (P2449_N719-S507)


title: PA-GFP Foxp3IRES-RFP_297


title: PA-GFP Foxp3IRES-RFP_298


title: J-LatA2+SAHA (P2449_N719-S506)


title: PA-GFP Foxp3IRES-RFP_296


title: PA-GFP Foxp3IRES-RFP_295


title: J-LatA2+SAHA (P2449_N718-S511)


title: J-LatA2+DMSO (P2449_N719-S503)


title: PA-GFP Foxp3IRES-RFP_293


title: PA-GFP Foxp3IRES-RFP_294


title: Jurkat+DMSO (P2449_N719-S502)


title: J-LatA2+SAHA (P2449_N718-S510)


title: J-LatA2+SAHA (P2449_N718-S508)


title: J-LatA2+SAHA (P2449_N718-S507)


title: J-LatA2+DMSO (P2449_N718-S505)


title: PA-GFP Foxp3IRES-RFP_291


title: PA-GFP Foxp3IRES-RFP_292


title: PA-GFP Foxp3IRES-RFP_289


title: PA-GFP Foxp3IRES-RFP_290


title: J-LatA2+SAHA (P2449_N718-S506)


title: PA-GFP Foxp3IRES-RFP_288


title: Jurkat+DMSO (P2449_N718-S502)


title: PA-GFP Foxp3IRES-RFP_287


title: J-LatA2+SAHA (P2449_N716-S511)


title: PA-GFP Foxp3IRES-RFP_286


title: J-LatA2+SAHA (P2449_N716-S510)


title: J-LatA2+SAHA (P2449_N716-S508)


title: PA-GFP Foxp3IRES-RFP_285


title: PA-GFP Foxp3IRES-RFP_284


title: PA-GFP Foxp3IRES-RFP_283


title: J-LatA2+SAHA (P2449_N716-S507)


title: PA-GFP Foxp3IRES-RFP_282


title: J-LatA2+SAHA (P2449_N716-S506)


title: J-LatA2+DMSO (P2449_N716-S503)


title: PA-GFP Foxp3IRES-RFP_280


title: PA-GFP Foxp3IRES-RFP_279


title: PA-GFP Foxp3IRES-RFP_281


title: J-LatA2+DMSO (P2449_N718-S503)


title: Jurkat+DMSO (P2449_N716-S502)


title: PA-GFP Foxp3IRES-RFP_278


title: L4-19

city: Cheonan-si

first: Jae-A

last: Han

address: 25 Bongjeong-ro Dongnam-gu

country: South Korea

institute: Soonchunhyang University

data_processing:
The libraries were sequenced on an Illumina HiSeq 2500 to generate 101 base reads. Image decomposition and quality value calulation were performed using the modules of the Illumina pipeline.
Raw sequences were pre-processed and analyzed with miRDeep2. Adapters were trimmed using cutadapt program.
Trimmed fastq files were submitted as the raw data.
The reads were normalized by Trimmed mean of M value (TMM) normalization using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample, and RPM values for each sample

source_name: Human sample19 - Fibrosis stage 4

extract_protocol:
miRNA was extracted from human serum exosomes
RNA libraries were prepared for sequencing using the SMARTer smRNA-Seq Kit from Illumina

tag: fibrosis state

value: Liver Fibrosis Stage 4

value: serum


title: L4-11

source_name: Human sample11 - Fibrosis stage 4

tag: tissue


title: PA-GFP Foxp3IRES-RFP_275


title: L3-13

source_name: Human sample13 - Fibrosis stage 3

value: Liver Fibrosis Stage 3


title: L3-16

source_name: Human sample16 - Fibrosis stage 3


title: PA-GFP Foxp3IRES-RFP_273


title: PA-GFP Foxp3IRES-RFP_272


title: L3-15

source_name: Human sample15 - Fibrosis stage 3


title: PA-GFP Foxp3IRES-RFP_277

source_name: Germinal Centers


title: PA-GFP Foxp3IRES-RFP_276

value: Cycling


title: L2-12

source_name: Human sample12 - Fibrosis stage 2

value: Liver Fibrosis Stage 2


title: L3-21

source_name: Human sample21 - Fibrosis stage 3


title: L2-10

source_name: Human sample10 - Fibrosis stage 2


title: PA-GFP Foxp3IRES-RFP_274


title: L2-9

source_name: Human sample9 - Fibrosis stage 2


title: PA-GFP Foxp3IRES-RFP_271


title: L2-8

source_name: Human sample8 - Fibrosis stage 2


title: PA-GFP Foxp3IRES-RFP_268


title: PA-GFP Foxp3IRES-RFP_267


title: PA-GFP Foxp3IRES-RFP_270


title: PA-GFP Foxp3IRES-RFP_269


title: PA-GFP Foxp3IRES-RFP_266


title: J-LatA2+DMSO (P2449_N716-S505)


title: L4-20

source_name: Human sample20 - Fibrosis stage 4


title: L1-5

source_name: Human sample5 - Fibrosis stage 0,1

value: Liver Fibrosis Stage 0 or 1


title: PA-GFP Foxp3IRES-RFP_265


title: L1-4

source_name: Human sample4 - Fibrosis stage 0,1


title: PA-GFP Foxp3IRES-RFP_264


title: L3-14

source_name: Human sample14 - Fibrosis stage 3


title: PA-GFP Foxp3IRES-RFP_263


title: L1-2

source_name: Human sample2 - Fibrosis stage 0,1


title: PA-GFP Foxp3IRES-RFP_261


title: PA-GFP Foxp3IRES-RFP_262


title: ucMSC - Pol2 - Old - Batch1

city: Houston

first: Weiwei

last: Dang

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

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

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


title: PA-GFP Foxp3IRES-RFP_259


title: L1-1

source_name: Human sample1 - Fibrosis stage 0,1


title: PA-GFP Foxp3IRES-RFP_260


title: ucMSC - Pol2 - Young - Batch1

value: umbilical cord-derived mesenchymal stem cells (PCS-500-010, lot #63216950)


title: PA-GFP Foxp3IRES-RFP_257


title: Flow_0.5_3

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

data_processing:
adapter trimming using trimgalore v0.4.1
astqc v0.10.1 for quality score assessment
star version v2.5.2b for alignment
ht-seq-gene v0.5.3 to consoldiate reads to features
Genome_build: hg37
Supplementary_files_format_and_content: Raw count table at the gene level for all 22 samples

source_name: Renal Proximal Tubule Epithelial Cells/TERT-immortalized 1

growth_protocol: Human immortalized hRPTECs (RPTEC/TERT1, ATCC CRL-4031) and were cultured and maintained in hTERT Immortalized RPTEC Growth Kit (ATCC ACS-4007), supplemented with Geneticin (Gibco, 10131035), in phenol red free DMEM/F-12 medium (Gibco, 11039021) according to the vendor's instructions.

extract_protocol:
Total RNA was obtained from cells grown in independent device channels after exposure to flow for 24 hours using the ReliaPrep™ RNA Miniprep Systems (Z6011, Promega) following the manufacturer's instruction.
RNA libraries were prepared for sequencing using poly(A) selection and sequencing using standard Illumina protocols

treatment_protocol: Treatment of cells placed under flow rates treatments of static, 0.1dyn/cm2, 0.25 dyn/cm2, and a physiological level of 0.5 dyn/cm2

tag: treatment group

value: Fluid shear stress - 0.5

value: proximal tubule epithelial cells

tag: replicate


title: Static_0.5_4

value: Static - 0.5


title: Flow_0.5_2


title: PA-GFP Foxp3IRES-RFP_254

value: PA-GFP Foxp3IRES-RFP


title: L2-7

source_name: Human sample7 - Fibrosis stage 2


title: PA-GFP Foxp3IRES-RFP_255


title: PA-GFP Foxp3IRES-RFP_253

value: Filtered cell


title: Static_0.5_3


title: Static_0.5_2


title: Static_0.5_1


title: PA-GFP Foxp3IRES-RFP_256


title: PA-GFP Foxp3IRES-RFP_252


title: PA-GFP Foxp3IRES-RFP_250


title: Flow_0.25_4

value: Fluid shear stress - 0.25


title: L1-3

source_name: Human sample3 - Fibrosis stage 0,1


title: PA-GFP Foxp3IRES-RFP_251


title: Flow_0.5_1


title: Flow_0.25_3


title: Flow_0.5_4


title: PA-GFP Foxp3IRES-RFP_249


title: PA-GFP Foxp3IRES-RFP_258


title: PA-GFP Foxp3IRES-RFP_247


title: Flow_0.25_1


title: Flow_0.25_2


title: PA-GFP Foxp3IRES-RFP_248


title: Static_0.25_3

value: Static - 0.25


title: PA-GFP Foxp3IRES-RFP_245


title: Static_0.25_2


title: PA-GFP Foxp3IRES-RFP_244


title: Flow_0.1_4

value: Fluid shear stress - 0.1


title: Static_0.25_1


title: Flow_0.1_3


title: PA-GFP Foxp3IRES-RFP_242

value: CD4+ Resting


title: PA-GFP Foxp3IRES-RFP_241


title: Flow_0.1_1


title: PA-GFP Foxp3IRES-RFP_240


title: Static_0.1_2

value: Static - 0.1


title: PA-GFP Foxp3IRES-RFP_238


title: PA-GFP Foxp3IRES-RFP_243


title: PA-GFP Foxp3IRES-RFP_239


title: Static_0.1_1


title: PA-GFP Foxp3IRES-RFP_237


title: PA-GFP Foxp3IRES-RFP_236


title: PA-GFP Foxp3IRES-RFP_246

value: Tfr


title: PA-GFP Foxp3IRES-RFP_235


title: PA-GFP Foxp3IRES-RFP_234


title: PA-GFP Foxp3IRES-RFP_233


title: Flow_0.1_2


title: Static_0.1_3


title: PA-GFP Foxp3IRES-RFP_232


title: PA-GFP Foxp3IRES-RFP_231


title: PA-GFP Foxp3IRES-RFP_230


title: PA-GFP Foxp3IRES-RFP_229


title: ucMSC-RNA-seq-Young-rep3

description: rRNA-depleted RNA

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low quality reads using Trim Galore version 0.4.4 with default parameters.
Reads were aligned to the hg19/mm10  genome assembly using using HISAT2 version 2.1.0 with default parameters.
Transcript-level read count, and subsequent FPKM and TPM measurements, were performed using salmon version 1.0.0
Genome_build: hg19 for human and mm10 for mouse
Supplementary_files_format_and_content: read counts file generated by salmon

extract_protocol:
Total RNA was extracted from PD12 and PD32 hMSCs using the RNEasy Mini Kit (Qiagen 74104) following the manufacturer’s protocol, including the optional DNase treatment. 100ng of total RNA was depleted of rRNA (NEB, E6310) following the manufacturer’s protocol;NSCs were isolated by FACS using the surface markers prominin-1 (CD133) and the EGF receptor, and GFAP-GFP fluorescence. For sorting, cells were stained with 1:300 EGF-Alexa 647 (Molecular probes, E-35351), and 1:400 Prominin-1-biotin (eBioscience, 13-1331-80). Dead cells were excluded using propidium iodide and cells were sorted on a BD FACS Aria into PBS. aNSCs and qNSCs can be distinguished by the surface expression of EGFR. Using this scheme, aNSC are prominin-1+; GFP+; EGFR+ and qNSC are prominin-1+; GFP+; EGFR-. We performed this experiment in biological triplicate, generating each RNA-seq library from a single animal, using ~400 cells per library.
hMSC rRNA-depleted RNA was used as the template for a stranded RNA-seq library using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760) following the manufacturer’s protocol. mNSC RNA-seq libraries were generated by GENEWIZ LLC. using the SMART-Seq v4 Ultra Low Input RNA Kit for cDNA synthesis and the Nextera XT DNA Library Preparation Kit.

treatment_protocol: human MSC were cultured to PD12 and PD32. Activated and quiescent NSCs (aNSC and qNSC, respectively) were freshly isolated from the subventricular zone of adult (~7 month) and aged (19-21 month) hGFAP-GFP transgenic mice according to established methods (Leeman, D. S. et al. Lysosome activation clears aggregates and enhances quiescent neural stem cell activation during aging. Science (80-. ). 359, 1277–1283 (2018)).

tag: cell passage/age


title: ucMSC-RNA-seq-Old-rep3

description: rRNA-depleted RNA

tag: treatment


title: PA-GFP Foxp3IRES-RFP_227


title: PA-GFP Foxp3IRES-RFP_228


title: TNL-3

city: Shanghai

first: Wangsheng

last: Wang

state: Please Select

address: 845 Lingshan Rd.

country: China

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava software used for base calling.
After removing the adaptor sequences and low-quality reads, the clean reads were aligned to human genome (GRCh38, NCBI) using Hisat2 with default options
High-throughput sequencing (HTseq)  was used to get gene counts and reads per kilo base per million mapped reads (RPKM) were used to determine gene expression levels
Differential expression analysis was performed using the DESeq2 algorithm
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: amnion

extract_protocol:
Total RNA was extracted from cultured primary amnion fibroblasts prepared from the TNL amnion  using Trizol reagent (Life Technologies Inc., Grand Island, NY)
RNA-sequence libraries were constructed using a TruSeq RNA sample preparation kit (Illumina Inc.) following the manufacturer’s protocol.

value: primary amnion fibroblasts

value: amnion

tag: patient diagnosis

value: TNL


title: ucMSC-RNA-seq-Young-rep2

description: rRNA-depleted RNA


title: Old-CMS-seq-IP-rep1

description: CMS-seq IP data replicate1 of old MSC

data_processing:
Library strategy: CMS-seq
Raw reads were trimmed to remove sequencing adaptors and low quality reads using Trim Galore version 0.4.4 with default parameters.
CMS-seq (5hmC) data were mapped using Bismark version 0.22.3.
Peaks was called by MACS2 version 2.1.0 callpeak function using input as control, q-value < 0.01.
Signaltracks were generated using macs2 bdgcmp function with -m ppois parameter.
Genome_build: hg19
Supplementary_files_format_and_content: normalized signal tracks in bigwig format

extract_protocol:
Genomic DNA was extracted from approximately 1 million hMSCs using the DNeasy Blood and Tissue kit (Qiagen #69504) and was sonicated to ~300bp with a Covaris focused ultrasonicator. Sonicated genomic DNA was ligated to methylated NEBNext Illumina adaptors using the NEBNext Ultra II DNA Library Prep (NEB, #E7645). Following bisulfite conversion with the EZ DNA methylation-lightning kit (Zymo Research, #D5030), samples were incubated with an anti-CMS antibody (from PMID:  PMC3124347) bound to protein A/G Dynabeads (Thermo Fisher #10003D and #10001D). ChIP'ed DNA underwent phenol/chloroform/isoamyl acid cleanup and precipitation.
Libraries were amplified for 10 PCR cycles with KAPA HiFi Uracil+ polymerase (KAPA Biosystems, #KK2801).

value: umbilical cord-derived mesenchymal stem cells (PCS-500-010, lot #63216951)

tag: age

tag: antibody

value: anti-CMS antibody described in PMID:21552279


title: Old-MSC-WGBS

description: Whole Gonome Bisulfite Seqencing data of old human MSC

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low quality reads using Trim Galore version 0.4.4 with default parameters.
WGBS Reads were aligned to the hg19 genome assembly using Bismark version 0.22.3.
Duplicated reads were removed using Bismark deduplicate_bismark function.
Then, DNA methylation information were extracted using bismark_methylation_extractor function.
Statistical analysis of DNA methylation and annotation were performed using methylKit R package version 1.16.1
Only mCpG sites with > 10 read coverage were included in the analysis. Sites with extremely high read coverage (Top 0.1%) were excluded.
Genome_build: hg19
Supplementary_files_format_and_content: Genome-wide CpG methylation coverage file generated by Bismark

extract_protocol:
Genomic DNA was extracted from approximately 1 million hMSCs using the DNeasy Blood and Tissue kit (Qiagen #69504) and was sonicated to ~300bp with a Covaris focused ultrasonicator
Sonicated genomic DNA was ligated to methylated NEBNext Illumina adaptors using the NEBNext Ultra II DNA Library Prep (NEB, #E7645). Following bisulfite conversion with the EZ DNA methylation-lightning kit (Zymo Research, #D5030), libraries were amplified for 4 cycles using KAPA HiFi Uracil+ polymerase (KAPA Biosystems, #KK2801)

value: umbilical cord-derived mesenchymal stem cells (PCS-500-010, lot #63216950)


title: Old-CMS-seq-IP-rep2

description: CMS-seq IP data replicate2 of old MSC

value: umbilical cord-derived mesenchymal stem cells (PCS-500-010, lot #63216952)


title: Young-CMS-seq-IP-rep1

description: CMS-seq IP data replicate1 of young MSC

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


title: Young-MSC-WGBS

description: Whole Gonome Bisulfite Seqencing data of young human MSC


title: Young-CMS-seq-IP-rep2

description: CMS-seq IP data replicate2 of young MSC


title: CMS-seq-INPUT

description: CMS-seq INPUT control for both replicate1 and replicate 2

value: N/A (input sample)


title: TNL-2


title: PA-GFP Foxp3IRES-RFP_224

source_name: Germinal Centers

value: PA-GFP Foxp3IRES-RFP


title: PA-GFP Foxp3IRES-RFP_226


title: TNL-1


title: PA-GFP Foxp3IRES-RFP_223


title: TL-3

value: TL


title: TL-2


title: PA-GFP Foxp3IRES-RFP_222


title: PA-GFP Foxp3IRES-RFP_221


title: ucMSC-RNA-seq-Old-rep2

description: rRNA-depleted RNA


title: TL-1


title: PA-GFP Foxp3IRES-RFP_220


title: PA-GFP Foxp3IRES-RFP_218


title: control-3

data_processing:
Illumina Casava software used for base calling.
After removing the adaptor sequences and low-quality reads, the clean reads were aligned to human genome (GRCh38, NCBI) using Hisat2 with default options.
High-throughput sequencing (HTseq) was used to get gene counts, and reads per kilo base per million mapped reads (RPKM) were used to determine gene expression levels.
Differential expression analysis was performed using the DESeq2 algorithm.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: amnion fibroblasts

extract_protocol:
Total RNA was extracted from cultured primary amnion fibroblasts prepared from the TNL amnion using Trizol reagent (Life Technologies Inc., Grand Island, NY).
RNA-sequence libraries were constructed using a TruSeq RNA sample preparation kit (Illumina Inc.) following the manufacturer’s protocol.

value: amnion fibroblasts

value: untreated


title: PA-GFP Foxp3IRES-RFP_217

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: cortisol-1

value: cortisol treatment for 24 hours


title: PA-GFP Foxp3IRES-RFP_216


title: PA-GFP Foxp3IRES-RFP_225


title: PA-GFP Foxp3IRES-RFP_215


title: PA-GFP Foxp3IRES-RFP_211


title: ucMSC-TL-Seq-NegativeControl

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low quality reads using Trim Galore version 0.4.4 with default parameters.
TL-seq reads were aligned to the hg19 genome assembly using using STAR version 2.7 with default parameters.
Mapped reads on forward and reverse stands were separated by samtools view function. Reads from read2 were filtered due to the nature of the sequencing technology.
Cryptic TSSes (cTSSes) were identified in 10bp bins across the genome by comparing sample data to the negative control. Read count assessment was performed using the csaw package version 1.20 and the count data was normalized using the TMM method in edgeR version 3.28.
Signal tracks were generated with deeptools bamCompare version 3.2.0 with parameters: --operation subtract --binSize 10 --minMappingQuality 30
Genome_build: hg19
Supplementary_files_format_and_content: normalized signal tracks in bigwig format

molecule: polyA RNA

extract_protocol:
DECAP-seq was performed as described in ref. 18 with some modifications. The starting material was poly-A+ RNA was isolated from 100mg of total RNA using the Dynabeads mRNA Purification Kit (Life Technologies, 61006). 5’ phosphate groups were removed using CIP (NEB, M0290) rather than AP, and Cap-Clip acid pyrophosphatase (CellScript, C-CC15011H) was used in place of RppH to de-cap the mRNAs.
Size selection of products was performed after 5’ adapter ligation, rather than after 1st strand synthesis to select against cDNAs generated solely from binding of the RT primer to the 5’ adapter. A negative control library was generated by omitting the de-capping step
TL-seq signal tracks were generated by bamCompare

treatment_protocol: Cells were cultured to PD12 and PD32

tag: group

value: Negative control


title: PA-GFP Foxp3IRES-RFP_212


title: PA-GFP Foxp3IRES-RFP_210


title: ucMSC-TL-Seq-Young

value: Young


title: PA-GFP Foxp3IRES-RFP_213


title: ucMSC-RNA-seq-Old

description: rRNA-depleted RNA


title: ucMSC-TL-Seq-Old

value: Old


title: PA-GFP Foxp3IRES-RFP_214

value: Filtered cell


title: ucMSC-RNA-seq-Young

description: rRNA-depleted RNA


title: ucMSC - TBP - Young - Batch1

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

tag: chip antibody

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


title: ucMSC - input DNA - Young - Batch2


title: PA-GFP Foxp3IRES-RFP_209

tag: sequencing plate


title: PA-GFP Foxp3IRES-RFP_207

tag: strain

value: CD4+ Resting


title: PA-GFP Foxp3IRES-RFP_208

tag: experiment


title: ucMSC - input DNA - Young - Batch1


title: cortisol-2


title: cortisol-3


title: PA-GFP Foxp3IRES-RFP_219

tag: cell annotation


title: PA-GFP Foxp3IRES-RFP_205


title: PA-GFP Foxp3IRES-RFP_206


title: PA-GFP Foxp3IRES-RFP_204


title: PA-GFP Foxp3IRES-RFP_203


title: control-2


title: ucMSC - H3K4me3- Young - Batch1


title: ucMSC - H3K9me3- Young - Batch2


title: control-1


title: ucMSC - H3K36me3 - Young - Batch1


title: PA-GFP Foxp3IRES-RFP_202


title: ucMSC - H3K27me3 - Young - Batch2