title: SIGNAL-seq ADT library of HeLa spheroid cells

description: ADT library from HeLa experiment generated using the SIGNAL-seq protocol, index 76 was used to generate the sublibrary.

data_processing:
Raw sequencing data were converted to fastq format using bcl2fastq (Illumina).
scRNA-seq reads were aligned and digital gene expression matrix generated with zUMIs-2.9.7e and  STAR-2.7.3a, (see https://github.com/TAPE-Lab/SIGNAL-seq) for more details on processing pipeline. implementation. Barcode maps are contained in the supplemental information.
ADT reads were assigned to individual cells using the Kallisto Kite workflow based on cell barcode, antibody barcode sequence, to generate UMI count data.
Assembly: GRCh38
Supplementary files format and content: ex0003_hela_rna_adata.h5ad is a .h5ad-formatted file containing Scanpy AnnData object of processed SIGNAL-seq RNA data, X matrix represents Log-normalised data. Metadata .obs sample_id slot encodes treatment.
Supplementary files format and content: ex0003_hela_adt_adata.h5ad is a .h5ad-formatted file containing Scanpy AnnData object of processed SIGNAL-seq ADT data, X matrix represents CLR transformed data. Metadata .obs slot sample_id encodes treatment.

source_name: Uterus

growth_protocol: HELA spheroids were grown in 96-well Eplasia plates for 48 hours in DMEM high-glucose with supplemented with 2 mM L-Glutamine and 10% FBS.

extract_protocol:
Spheroids were fixed in-situ using an adapted SPLiT-seq protocol (Rosenberg and Rocco et al., 2018) and dispersed by mechanical dissociation using a TissueGrinder. Single-cells were permeablilsed using an adapted SPLiT-seq protocol and frozen before processing with SIGNAL-seq.
scRNA-seq RNA and ADT libraries were generated using a modified combinatorial barcoding (Rosenberg and Rocco et al., 2018) SIGNAL-seq protocol producing two sequencing libraries (RNA and ADT) for each sublibrary.
SIGNAL-seq

treatment_protocol: Spheroids were serum starved for 4hrs and pre-treated with inhibitors 100nM Trametinib  and 500nM GDC0941 Pictilisib or vehicle (DMSO) for 10 minutes prior to growth factor treatment. Spheroids were then treated for 30 minutes with 100nM Human IGF1 and 100nM Human EGF or vehicle (water) before fixation in-situ.

value: Uterus

value: HeLa

value: Cervical carcinoma


title: Kidney, Fem_Def_K_2

status: Public on Feb 24 2024

type: SRA

city: Tampa

first: Alexander

last: Starushchenko

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

country: USA

institute: University of South Florida, College of medicine

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website 2 directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: reference genome was built using Hisat2 v2.0.5 a
Supplementary files format and content: tab-delimited text file with FPKM

molecule: total RNA

organism: Rattus norvegicus

source_name: Kidney

extract_protocol:
RNA was extracted using the Trizol reagent according to the manufacturer's protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification). The library was checked with Qubit and real-time PCR for quantification and a bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

tag: tissue

value: Kidney

tag: Sex

value: Female

tag: genotype

value: WT

tag: treatment

value: High NaCl and deficient in K


title: Kidney, Fem_Def_K_4


title: Ucp1-Stx4KO, Rep1

city: Bronx

first: Jeffrey

middle: E

last: Pessin

state: NY

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

data_processing:
Reads were aligned to mm10 reference genome using STAR software.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

organism: Mus musculus

source_name: brown adipose tissue

extract_protocol:
We use Trizol and Qiagen RNeasy Mini Kit, following the manufacturer's protocol to ensure high-quality RNA isolation.
mRNA is purified from total RNA using poly-T oligo-attached magnetic beads. NEB library method is used.

value: brown adipose tissue


title: SIGNAL-seq RNA library of CRC PDO and CAF co-cultures sublibrary 76

city: London

first: James

last: Opzoomer

address: 72 Huntley Street

department: Department of Oncology

country: United Kingdom

institute: University College London

description: RNA library from PDO experiment generated using the SIGNAL-seq protocol, index 76 was used to generate the sublibrary.

data_processing:
Raw sequencing data were converted to fastq format using bcl2fastq (Illumina).
scRNA-seq reads were aligned and digital gene expression matrix generated with zUMIs-2.9.7e and  STAR-2.7.3a, (see https://github.com/TAPE-Lab/SIGNAL-seq) for more details on processing pipeline. implementation. Barcode maps are contained in the supplemental information.
ADT reads were assigned to individual cells using the Kallisto Kite workflow based on cell barcode, antibody barcode sequence, to generate UMI count data.
Assembly: GRCh38
Supplementary files format and content: ex0015_pdo_rna_adata.h5ad is an .h5ad-formatted file containing Scanpy AnnData object of processed SIGNAL-seq RNA data, X matrix represents scaled and UMI-depth corrected Log-normalised data. The Log-normalised data is contained in the .raw slot. Metadata .obs slot sample_id encodes culture condition, cell_type encodes cell type label. Sublibrary index is encoded in .obs slot sublib_index.
Supplementary files format and content: ex0015_pdo_adt_adata.h5ad is an h5ad-formatted file containing Scanpy AnnData object of processed SIGNAL-seq ADT data, X matrix represents CLR transformed data. Metadata .obs slot sample_id encodes culture condition, cell_type encodes cell type label.  Sublibrary index is encoded in .obs slot sublib_index.

organism: Homo sapiens

source_name: Colorectal cancer

extract_protocol:
PDOs were extracted from matrigel with ice cold PBS. PDOs were then digested to a single-cell suspension with TrypLE Express Enzyme (Gibco #12604013) for 10 minutes at 37C on a heated orbital shaker at 300rpm. Cells were then re-suspended in 1 mL PBS + RNAse inhibitor cocktail (RI). Fixation and permeabilisation was then carried out with a modified SPLiT-seq protocol. Single-cell suspensions were fixed with on ice in 1% effective Formaldehyde for 10 minutes before the cells were permeabilized for a further 3 minutes with 0.2% effective Triton X-100. Fixation was then quenched with 50 mM of Tris-HCL (Invitrogen #15568025) before the cells were re-suspended in 300 μL of 0.5x PBS +RI +5% DMSO before freezing and storage at -80C until processing for SIGNAL-seq.
scRNA-seq RNA and ADT libraries were generated using a modified combinatorial barcoding (Rosenberg and Rocco et al., 2018) SIGNAL-seq protocol producing two sequencing libraries (RNA and ADT) for each sublibrary.
SIGNAL-seq

treatment_protocol: On Day 0 CRC PDOs were dissociated into single cells as described above, and expanded in 12-well plates in Growth Factor Reduced Matrigel with 1 mL per well of Advanced DMEM F/12, supplemented with 2 mML glutamine, 1 mM N-acetyl-l-cysteine, 10 mM HEPES, 1X HyClone Penicillin-Streptomycin Solution, 1X B-27 Supplement, 1X N-2 Supplement, 50 ng mL−1 EGF, 10 nM Gastrin I, 10 mM Nicotinamide, 500 nM A83-01 and 10 μM SB202190 at 5% CO2, 37◦C for 96 hours. On Day 1, CAFs were split into a new flask containing a low-serum media (DMEM supplemented with 2% FBS and 1X HyClone-Penicillin Streptomycin Solution). On Day 4, PDO culture media was changed to a reduced media; Advanced DMEM F/12 supplemented with 2 mM glutamine, 1 mM N-acetyl-L-cysteine, 10 mM HEPES, 1X B-27 Supplement, 1X N-2 Supplement, 10 mM Nicotinamide, 1X HyClone-Penicillin Streptomycin Solution and 25 ng mL−1 EGF). PDOs and CAFs were seeded on Day 5 in 96-well plates (Helena Biosciences #92696T) in 50 μL Growth Factor Reduced Matrigel with 300 μL of reduced media. PDOs were seeded at a density of approximately 1.5 x 103 organoids/well and CAFs at 3x 105 cells/well. PDOs and CAFs were either seeded in mono-culture alone, or in co-culture by mixing together in Matrigel on ice. Cultures were maintained for 72 hours at 5% CO2, 37◦C, with media changes every 24 hours. On Day 6 and 7, media was replaced with reduced media containing 15 nM SN-38 (Sigma #H0165) or DMSO (Merck #D2650), as a vehicle control. On Day 8, after 72-hours in culture and 48-hours of treatment, cultures were processed for SIGNAL-seq.

value: Colorectal cancer

tag: cell line

tag: cell type

value: CRC epithelial PDO and fibroblasts

tag: library type

value: RNA


title: SIGNAL-seq ADT library of CRC PDO and CAF co-cultures sublibrary 77

description: ADT library from PDO experiment generated using the SIGNAL-seq protocol, paired with index 77 RNA sublibrary.

library_source: other

molecule: other

value: ADT


title: Quercetin_2 [ncRNA-Seq]

city: Tai’an City

first: Yang

last: Jiang

state: Shandong Province

address: 61 Daizong Street

country: China

institute: Shandong Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion and CIRCExplorer2. All samples were generated unique circular RNAs.
Genome_build: Homo sapiens Ensembl relaese-90
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each isoforms

source_name: Human Umbilical Vein Endothelial Cells (HUVECs)

growth_protocol: The human umbilical vein endothelial cells were cultured in DMEM, supplemented with 10% of FBS, 0.6‰ of VEGF and 1% of a penicillin (100 U/mL)-streptomycin (100 μg/mL) mixture, in a humidified atmosphere with 5% CO2 and 95% room air at 37 ℃.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA removal kit (Illumina, San Diego, USA).Then the left RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the Truseq Stranded Total RNA HT Sample Prep Kit (Illumina, San Diego, USA).

treatment_protocol: The HUVECs were seeded into 96-well plates and treated for 24 h with quercetin. Then, the cells were washed with PBS and incubated with 125μg/mL ox-LDL for another 24 h.

tag: protocol

value: ox-LDL injured pretreated with quercetin


title: old, snRNAseq

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned against the mouse mm10 reference and converted to gene expression using Cell Ranger Software (version 7.0.1) with “--force-cells 10000”
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

extract_protocol:
In preparation for snRNA-seq, harvested mouse interscapular brown adipose tissues were minced in nuclear preparation buffer (10mM HEPES, 1.5mM MgCl2, 10mM KCl, 250mM Sucrose, 0.1% NP-40, 0.6U/μl Rnase inhibitor), and then homogenized in a Dounce homogenizer. The homogenate was passed through a 100μM filter and centrifuged at 750xg for 5min. The pellet was resuspended in 2% BSA/PBS, filtered again and sorted using a MoFloXDP Cell Sorter using the gating strategy previously described 29.
cDNA synthesis were performed using the Single Cell 3' v3.1 Dual Index Gene Expression Reagent kit (10x Genomics) following the manufacturer’s instructions

value: wild type

tag: age

value: 24 months


title: Quercetin_1 [ncRNA-Seq]

value: Human Umbilical Vein Endothelial Cells (HUVECs)


title: Ucp1-Stx4WT, Rep4


title: Ucp1-Stx4WT, Rep3


title: HCT116, shDOT1L

city: Seoul

first: Junyoung

last: Park

address: 84, Heukseok-ro

department: Department of Life Science

country: South Korea

institute: Chung-Ang University

data_processing:
*library strategy: PRO-seq
The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA Library Quantification kits for Illumina Sequencing platforms) and qualified using the TapeStation High Sensitivity D5000 ScreenTape
Paired-end sequencing reads were generated on the Illumina NovaSeq 6000 platform with indexed libraries
Before starting analysis, cutadapt v4.4 was used to remove adapter sequences and trim bases with poor base quality
The cleaned reads were aligned to the Homo sapiens (GRCh38) using HISAT v2.1.0
The reference genome sequence (hg38) and gene annotation data were downloaded from NCBI Genome assembly and NCBI RefSeq database respectively and aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9
Assembly: hg38
Supplementary files format and content: An indexed binary format BigWig generated from bam file by bamCoverage

source_name: colon

extract_protocol:
RNA was isolated after nuclear run-on reaction with biotin-11-CTP and biotin-11-UTP by biotin RNA enrichment process with magnetic streptavidin beads according to the PRO-seq protocol paper (Mahat et al., Nat Protoc, 2016)
The isolated RNA was ligated with 3' and 5' RNA adapter and reverse transcribed and amplified by PCR and library size (140-350bp) was selected by Pippin Prep

value: colon

value: Colorectal carcinoma

value: DOT1L knockdown


title: HCT116, shNC

description: shNC

value: Control


title: Quercetin_3 [ncRNA-Seq]


title: Kidney, Fem_High_K_1

value: Kidney

value: High NaCl and High K


title: SIGNAL-seq RNA library of CRC PDO and CAF co-cultures sublibrary 78

description: RNA library from PDO experiment generated using the SIGNAL-seq protocol, index 78 was used to generate the sublibrary.


title: Ucp1-Stx4KO, Rep3


title: Ucp1-Stx4WT, Rep2


title: Ox_ldl_2 [ncRNA-Seq]

value: ox-LDL injured


title: Kidney, Fem_High_K_2

value: Female

value: WT


title: TUGI-2T.H3K27Ac

city: Salt Lake City

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

institute: University of Utah

library_source: genomic

data_processing:
BWA to align sequencing reads
MACS2 to identify ChIP-seq peaks and calculate Signal Per Million Reads (SPMR)
Assembly: hg19
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: gastric

extract_protocol:
Chromatin immunoprecipitation using antibodies to enrich DNA fragments, followed by tagmentation (Diagenode ChIPmentation Kit for Histones, C01011009)
Diagenode Auto ChIPmentation Kit for Histone (C01011009)

value: tumor

tag: disease

value: gastric cancer

tag: chip antibody

value: H3K27ac (Diagenode C15410174)


title: Ox_ldl_3 [ncRNA-Seq]


title: Ucp1-Stx4WT, Rep1

value: brown adipose tissue


title: TUGI-1T.H3K27Ac


title: Control_3 [ncRNA-Seq]

value: normal


title: TUGI-2N.H3K27Ac


title: Ox_ldl_1 [ncRNA-Seq]


title: Kidney, Fem_Def_K_1

value: High NaCl and deficient in K


title: Control_2 [ncRNA-Seq]


title: TUGI-1N.H3K27Ac


title: Spleen-derived tissue slice from wildtype mice 2

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

data_processing:
10x genomics V2.0.0 spaceranger count
10x genomics V2.0.0 spaceranger aggr
Assembly: mm10
Supplementary files format and content: h5 file of read counts, as provided by spaceranger
Library strategy: Spatial Transcriptomic

molecule: polyA RNA

source_name: spleen

extract_protocol:
8–12-week-old mice from either wildtype or STAT1 knockout strains were used for organ isolation. Mice were euthanized as per the institutional guidelines. The procedure was performed within an en-closed fume hood. Immediately after euthanasia, the thoracic cavity was opened and a 25G needle at-tached to a canula and syringe containing 7,5% formaldehyde was inserted into the ascending aorta within the left ventricle. The needle was secured in position via a hemostatic forcep. The right atrium was incised using a pair of fine scissors. Prior to perfusion, the abdominal cavity was opened to visu-alize the liver. Perfusion with 7,5% formaldehyde was performed at an average rate of 5ml/min, with a total of 20-25 ml of 7,5% formaldehyde used per animal. Successful perfusion was determined by general stiffness within tissues and pale appearance of the liver. Spleen was dissected carefully with minimal contact and utilizing the fascia associated with splenic capsule to gently isolate the tissue. The splenic tissue was cut (2mm) at either ends and the tissue was incubated in 12% Formalin for further fixation. Wherever possible, minimal pressure and handling of tissue was employed to avoid disrupt-ing the tissue architecture.   After fixation, tissue specimens were processed using a vacuum infiltration processor (Sakura Tissue-Tek VIP 6 AI) equipped with a graded series of alcohol solutions, xylene and molten paraffin. Subse-quently, formalin-fixed paraffin-embedded (FFPE) samples were embedded into paraffin blocks on an embedding workstation (Thermo Scientific HistoStar) before sectioning on a rotary microtome (Ther-mo Scientific HM 355S). Before starting, all surfaces and work areas were wiped with ethanol. After trimming excess paraffin, the FFPE blocks were placed in an ice bath and incubated for 15 minutes, before taking 5 µm tissue sections, which were placed on the respective capture area of the Visium Spatial slide for FFPE (10X Genomics). The Slide was then placed in a drying rack and incubated in an oven at 42°C for 3 hours before being placed in a desiccator overnight at room temperature. Subse-quent steps to obtain sequencing-ready libraries were performed following the manufacturer’s instructions.
Spatial transcriptomic libraries were generated using the Visium Spatial gene expression reagent kit (10x Genomics) according to the manufacturer’s protocol.
The sequencing-ready spatial transcriptomics libraries were sequenced by the Biomedical Sequencing Facility at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, using the Illumina Novaseq platform and the 75 bp paired-end configuration.

value: Wildtype


title: OE33 HiChIP

data_processing:
HiC-Pro (PMCID: PMC4665391) for sequencing reads alignment
hichipper (PMID: 29489746) for loop calling and signal profiling
Assembly: hg19
Supplementary files format and content: allValidPairs.txt, listing all aligned and valid contacts to call loops with
Library strategy: HiChIP

extract_protocol:
We followed the published HiChIP protocol (PMCID: PMC5501173) to extract H3K27ac-enriched DNA fragments that interact with each other
Illumina Tagment DNA Enzyme and Buffer Kit (20034197)

value: Esophageal adenocarcinoma cell line


title: Control_1 [ncRNA-Seq]

value: Human Umbilical Vein Endothelial Cells (HUVECs)


title: BICR31 HiChIP

value: Upper digestive squamous cancer cell line


title: Spleen-derived tissue slice from Stat1-ko mice 1

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences


title: BICR16 HiChIP


title: SIGNAL-seq RNA library of HeLa spheroid cells

description: RNA library from HeLa experiment generated using the SIGNAL-seq protocol, index 76 was used to generate the sublibrary.

value: Uterus

value: HeLa

value: Cervical carcinoma

value: RNA


title: Zbtb46 KD MCEC cells, rep1

city: Palo Alto

last: Thaiss

state: CA

address: 3181 Porter Dr.

department: Immunology and Pathology

institute: Arc Institute

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to GRCm38.101
Read counts were extracted
Assembly: mm10
Supplementary files format and content: Zbtb46RNA_SeqCounts.tsv

source_name: murine cardiac endothelial cells (MCEC)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.  Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: murine cardiac endothelial cells (MCEC)

value: Zbtb46 knockdown


title: Spleen-derived tissue slice from Stat1-ko mice 2


title: Zbtb46 KD MCEC cells, rep3


title: SC1_T2

city: Guangzhou

first: Jianfeng

last: Chen

address: No.651 East Dongfeng Road

institute: Sun Yat-sen University

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by STAR instruction
RSEM were used for counting
R were used for visualization
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

growth_protocol: Karpas-231 and SC1 are cultured in RPMI1640 medium supplemented with 20% fetal bovine serum, 1% penicillin-streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: Karpas-231  and SC1 were treated with DMSO, 0.5mm chidamide for 24h.

value: diffuse large B-cell lymphoma


title: Zbtb46 OE MCEC cells, rep3

value: Zbtb46 Overexpression


title: L-DOXR

city: Suwon

first: Inwoo

last: Hwang

address: 2066, SEOBU-RO, JANGAN-GU

department: School of Medicine

institute: Sungkyunkwan University

data_processing:
High-throughput paired-end sequencing was performed using a HiSeq X10 system (Illumina, Inc., USA). Quality control of raw sequencing data was performed using FastQC. Adapter and low-quality reads (<Q20) were removed using FASTX_Trimmer and BBMap, respectively. The trimmed reads were then mapped to the reference genome using TopHat. Gene expression levels were estimated using fragments per kb per million reads (FPKM) values and Cufflinks. The FPKM values were normalized based on the quantile normalization method using EdgeR within R.
Assembly: hg18
Supplementary files format and content: mRNA-seq.xlsx

growth_protocol: The MDA-MB-231 TNBC cell line was purchased from ATCC (Manassas, VA, USA) and cultured inRPMI-1640 medium (HyClone, Logan, UT, USA) supplemented with 10% fetal bovine serum(HyClone), 100 units per mL of penicillin (Life Technologies, Carlsbad, CA, USA), and 100 μg/mL ofstreptomycin (Life Technologies) and maintained at 37 ℃ with 5% CO2.

extract_protocol:
Total RNA from untreated and treated MDA-MB-231 cells was extracted using a RNeasy Mini Kit(Qiagen, Germantown, MD, USA).
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.
RNA sequencing was performed on the NextSeq 500 sequencingplatform (Illumina, San Diego, CA, USA).
For cluster generation, the library is loaded into a flow cell where fragments are captured on a lawn of surface-bound oligos complementary to the library adapters. Each fragment is then amplified into distinct, clonal clusters through bridge amplification. When cluster generation is complete, the templates are ready for sequencing.
Illumina SBS technology utilizes a proprietary reversible terminator-based method that detects single bases as they are incorporated into DNA template strands. As all 4 reversible, terminator-bound dNTPs are persent during each sequencing cycle, natural competition minimizes incorporation bias and greatly reduces raw error rates compared to other technologies. The result is highly accurate base-by-base sequencing that virtually eliminates sequence-context-specific errors, even within repetitive sequence regions and homopolymers.

treatment_protocol: A total of 1 ×10^5cells/10 μL was suspended in culture medium, and 1 μL of the solution was gently added to thechip using a pipette with a tip through the cell seeding hole. The next day, 250 μL ofculture medium and culture medium containing 1.5 μM DOX were added to two of the diagonalreservoirs, and 50 μL of culture medium was added to the rest of the diagonal reservoirs.

value: Doxorubicin resistant

value: Doxorubicin


title: SC1_C2


title: MDA-MB231 WT

value: WT

value: DMSO


title: AGS HiChIP

source_name: AGS

value: AGS

value: Gastric cancer cell line


title: K231_T2


title: Zbtb46 OE MCEC cells, rep2


title: SC1_C1


title: WT MCEC cells, rep3


title: K231_T1


title: Zbtb46 OE MCEC cells, rep1


title: K231_C2


title: Spleen-derived tissue slice from wildtype mice 1

value: Wildtype


title: WT MCEC cells, rep1


title: Zbtb46 KD MCEC cells, rep2


title: mESCs_ATAC_DTT

city: Boston

first: Qiangzong

last: Yin

state: MA

address: 3 Blackfan St, CLS building 440A

department: Medicine

institute: BIDMC/Harvard Medical School

data_processing:
Paired-end ATAC-seq reads were adapter-trimmed and aligned to the mm10 genome using Bowtie2 (Version 2.3.2) with the parameters: -t -q -N 1 -L 25 -X 2000 no-mixed no-discordant.
All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. MACS2 (Zhang et al. 2008) was used for peak calling with parameters: --nolambda --nomodel.
Reads with insert size larger than 150 bp were separated and used for nucleosome positioning analysis.
TSS enrichment analysis was done using Homer annotatePeaks (Heinz et al. 2010)
Assembly: mm10
Supplementary files format and content: bigWig

source_name: mESCs

extract_protocol:
About 1000 mESCs were on-ice lysed with Tagmentation buffer (10 mM TAPS-NaOH pH 8.5, 5 mM MgCl2, 10% DMF, 0.02% Digitonin) for 10 min.
mESCs were then resuspended in Tagmentation buffer (10 mM TAPS-NaOH pH 8.5, 5 mM MgCl2, 10% DMF, 0.02% Digitonin) and tagmentation was conducted by adding Tn5 transposase (Diagenode, C01070012) at 1:20 and incubated at 37C for 30min. Reaction was stopped by SDS and proteinase K and incubated at 55°C  overnight. SDS was quenched by tween-20 and library amplification was done with 1x NEBNext High-Fidelity PCR Master Mix containing 0.5 mM indexed primers using the following PCR conditions: 72°C for 5 min; 98°C for 3 min; and 14 cycles at 98°C for 15 s, 63°C for 30 s, and 72°C for 1 min.

value: mESCs

value: Tn5 transposase (Diagenode, C01070012)


title: mESCs_ATAC_untreated


title: mESCs_ATAC_DNaseDTT


title: mESCs_ATAC_Dnase


title: SC1_T1


title: PH KC rep3

status: Public on Feb 23 2024

city: Portland

first: Bin

last: Li

state: OR

address: 3181 SW Sam Jackson Pk Rd

department: Oregon Stem Cell Center

institute: Oregon Health and Science University

data_processing:
Base calling - using Illumina RTA version 1.13.48.
Conversion to FASTQ using CASAVA v1.8.2
We trimmed all reads to 44 bases and aligned to mm9 with Bowtie version 1.0.0 (Allowed up to 3 mismatches, but required unique best matches.)
Used R scripts to count tags that aligned to the exons of UCSC RefSeq gene models and calculate FPKM values.
Assembly: mm9

source_name: kupffer cell

extract_protocol:
RNA lysis buffer is TRIzol reagent
RNA libraries were prepared with standard Illumina protocols

tag: strain

value: liver

value: partial hepatectomy


title: PH HSC rep1

data_processing:
Base calling - using Illumina RTA version 1.13.48.
Conversion to FASTQ using CASAVA v1.8.2
We trimmed all reads to 44 bases and aligned to mm9 with Bowtie version 1.0.0 (Allowed up to 3 mismatches, but required unique best matches.)
Used R scripts to count tags that aligned to the exons of UCSC RefSeq gene models and calculate FPKM values.
Assembly: mm9
Supplementary files format and content: raw counts

source_name: hepatic stellate cell

value: hepatic stellate cell


title: PH KC rep1

value: kupffer cell


title: PH Thy1 rep2

source_name: Thy1 cell

value: Thy1 cell


title: PH HSC rep2


title: PH HSC rep3


title: PH Thy1 rep1


title: PH KC rep2


title: PH blood rep2

source_name: blood cell

value: blood cell


title: PH LSEC rep4

source_name: liver sinusoidal enthothelial cell

value: liver sinusoidal enthothelial cell


title: PH blood rep1


title: WT MCEC cells, rep2

value: murine cardiac endothelial cells (MCEC)


title: PH LSEC rep5


title: PH LSEC rep2


title: PH LSEC rep1


title: PH EC rep2

source_name: endothelial cell

value: endothelial cell


title: PH HC rep4

source_name: hepatocyte

value: hepatocyte


title: K231_C1

value: diffuse large B-cell lymphoma


title: PH EC rep1


title: PH HC rep3


title: PH EC rep3


title: PH HC rep2


title: PH NPD rep1

source_name: non progenitor ducts

value: non progenitor ducts


title: PH NPD rep2


title: Norm HSC rep2

value: normal


title: PH BEC rep1

source_name: biliary epithelial cell

value: biliary epithelial cell


title: Norm KC rep2


title: PH BEC rep2


title: Norm Thy1 rep2


title: Norm Thy1 rep1


title: PH cBEC rep2

source_name: clonal biliary epithelial cell

value: clonal biliary epithelial cell


title: PH cBEC rep1


title: Norm LSEC rep3


title: PH LSEC rep3


title: Norm blood rep2


title: Norm LSEC rep1


title: Norm EC rep2


title: Norm EC rep1


title: Norm NPD rep2


title: Norm NPD rep1


title: Norm HC rep4


title: Norm HC rep3


title: Norm HC rep2


title: Norm HC rep1


title: Norm BEC rep4


title: Norm BEC rep3


title: Norm BEC rep2


title: PH HC rep1


title: Norm cBEC rep4


title: Norm BEC rep1


title: Norm KC rep1


title: Norm cBEC rep3


title: Norm HSC rep1


title: Norm cBEC rep2


title: L. plantarum with pdxH

city: college station

first: Min

last: Feng

state: Texas

address: 200 Spence street

department: Chemical Engineering

institute: Texas A&M University

data_processing:
Adaptor sequences and low-quality reads were removed using Trimmomatic, the RNA-Seq reads were then mapped to the C. elegans genome using STAR 2.5.3a with default settings. Transcript abundance, measured as read counts per gene, was extracted using HTSeq. Differential gene expression analysis was performed using GFold
Assembly: c elegans ce11
Supplementary files format and content: text file includes raw counts

organism: Caenorhabditis elegans

source_name: whole worms

extract_protocol:
C. elegans at the same stage grown on L. plantarum together with trace amount (0.2 µl, 1.6x105 c.f.u.) of wild type BW25113 or pdxH mutant were collected from peptone-free NGM plates and washed three times with M9 buffer. Then 250 µl of TRIzol reagent (Invitrogen) was add to the worm pellet and worms were homogenized for 5 min. RNA was isolated by adding 50 µl of chloroform, followed by centrifugation to separate the aqueous phase. The aqueous phase was transferred to a new tube and mixed with isopropanol (125 µl) to precipitate RNA. The resulting RNA pellet was washed twice with 70% ethanol (250 µl). RNA pellets were air-dried and then re-suspended in RNase-free water. Any potential genomic DNA contamination was removed by DNaseI treatment using the TURBO DNA-free Kit (Invitrogen).
RNA libraries were prepared using TruSeq RNA library preparation kit following manufacture's protocol.

value: whole worms

value: Fed with L. plantarum with pdxH mutant


title: Tet-GFP, LBF (third instar larva brain fraction)

city: Piscataway

first: Ruth

last: Steward

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute of Microbiology

institute: Rutgers University

data_processing:
Tet-Chip sequencing data were pre-processed using the following steps: the raw sequencing data were first analysed with FastQC.
Low-complexity reads were removed with the AfterQC tool with default parameters and Trimmomatic with default parameters was used to remove adapter sequences. The resulting fastq data were again analysed with FastQC to ensure that no further processing was needed.
Pre-processed reads were then mapped against the Drosophila reference genome (BDGP6.28) with the bowtie2 algorithm 43 using the ensembl reference transcriptome (version 100).
Tet-binding peak regions were identified by applying the MACS2 peak-calling tool 32 to immunoprecipitated (IP) samples, using their input counterpart to estimate background noise (q-value < 0.05). It is worth noting that the “expected genome size” MACS2 parameter was set as the Drosophila genome length excluding ‘N’ bases (i.e. 142 573 024 bp), and summit positions were identified using the MACS2 “-call-summits” option. To avoid identifying extremely large peak regions, the peaks were resized to 100 bp on both sides of the identified summit.
bigWig files were generated using the deepTools2.0.
Assembly: dm6
Supplementary files format and content: bw and tab-delimited text annnotation files (except input).

organism: Drosophila melanogaster

source_name: LBF

growth_protocol: All flies were reared at 25oC and kept on standard medium.

extract_protocol:
The larval brain fraction (LBF), 300 frozen larval LBFs were thawed on ice and 1 ml of NU-1 buffer (5 mM HEPES-KOH pH 7.9, 5 mM MgCl2, 0.1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 350 mM sucrose, 1mM DTT). 1% formaldehyde was added to NU-1 buffer before use. Samples were homogenized immediately at room temperature using Dounce with a loose pestle 30 times without foaming for 15 minutes. Samples were filtered first through BD Falcon Cell Strainer 70 μm (Cat No.352350) followed by 50 μm Filcon (Cat No. 340603). Samples were quenched with freshly prepared 125 mM glycine incubated for 5 minutes at room temperature on a shaker and transferred to ice for 5 minutes. Samples were centrifuged at 4000 g at 4˚C for 5 minutes. The pellet was washed twice with 1 ml cold PBS and resuspended in 350 µl chilled sonication buffer (50mM HEPES-KOH pH 7.9, 140 mM NaCl, 1mM EDTA pH 8.0, 1% Triton X-100, 0.1% sodium deoxycholate, 1% SDS) and incubated for 20 minutes at 4˚C. Lysates were sonicated as described above and chromatin was stored at - 80˚C until immunoprecipitation.
ACCEL-NGS® 1S plus DNA library kit was used to prepare indexed libraries from IP and input DNA. Libraries were pooled respecting equimolarity. Sequencing was performed on Illumina MISeq sequencer in 150 bp paired-end reads.

treatment_protocol: No treatment applied.

value: LBF

value: LBF containing larval brain and imaginal discs

value: third instar larva

value: Tet-GFP

value: GFP-Trap Magnetic Agarose (Chromotek #gtma)


title: Norm cBEC rep1

value: liver


title: L. plantarum with wt E. coli

value: Fed with L. plantarum with wt E. coli


title: Norm blood rep1

value: blood cell


title: Norm LSEC rep2

value: liver sinusoidal enthothelial cell


title: L1777_25_2

city: 杭州市

first: Mingyue

last: Guo

state: 浙江省

address: 浙江大学紫金港校区

institute: 浙江大学

data_processing:
Briefly, nuclei were extracted and purified from samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads (Beckman, A63881) and library quality was assessed with Qubit (Thermo Fisher, Q32854). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform at Metware Biotechnology (Wuhan, China) and 150 bp paired-end reads were generated.
Assembly: Reference genome and gene model annotation files were downloaded from tomato genome website (https://solgenomics.net/) directly.
Supplementary files format and content: bigWig

organism: Solanum habrochaites

source_name: leaves

extract_protocol:
Samples were prepared using sucrose sedimentation as previously reported but with slight modifications.
Briefly, the young leaves of AC and LA1777 were collected under normal conditions or under cold stress for 6 h, respectively, and then ground to fine powder in liquid nitrogen. For each sample, 0.2 g of the frozen tissue powder was homogenized in prechilled 1 ml lysis buffer (15 mM Tris-HCl pH7.5, 20 mM NaCl, 80 mM KCl, 0.5 mM spermine, 5 mM 2-ME, 0.2% TritonX-100), and the nuclear fraction was purified as described47. The nuclei pellet was resuspended in 1 ml cold lysis buffer. For ATAC-seq and ATAC-qPCR, a nuclei aliquot (25 µl) was stained with DAPI (10 µl of 1 µg ml-1) and counted using a haemocytometer. Approximately 50000 nuclei were used for each ATAC-seq or ATAC-qPCR reaction.

value: leaves


title: L1777_25_1


title: L1777_4_1

value: cold


title: L1777_4_2


title: PBMCs from sample C9-9_Naive_CD8

city: Stanford

first: Aaron

middle: James

last: Wilk

state: California

address: 300 Pasteur Dr Bldg S131, Grant

institute: Stanford University

description: PBMCs from sample C9-9_Naive_CD8

data_processing:
Sequencing reads were aligned against V-, D-, J-, and C- human gene segment library database by MiXCR
Clonotypes were assembled from aligned reads by MiXCR
Assembly: Sequencing reads were aligned against V-, D-, J-, and C- human gene segment library database by MiXCR
Supplementary files format and content: .txt files containing counts of clonotypes in tabular form

source_name: PBMCs

growth_protocol: No growth or treatment performed

extract_protocol:
RNA was purified from each sorted sample using the RNAeasy Plus Micro kit (Qiagen)
Libraries were prepared for TCR sequencing as described by Rubelt, et al.. This was performed at the University of Cape Town. Briefly, purified RNA was reverse transcribed in a Rapid amplification of cDNA ends (RACE) reaction using SMARTScribe Reverse Transcriptase using previously designed oligos (isoC-5′-GTCAGATGTGTATAAGAGACAGnnnnnnnnnnCGATAGrGrGrG -3′-C3_Spacer and for the Poly A tail 5′-GTGTCACGTACAGAGTCATCtttttttttttttttttttttttttttttt -3′ VN) that captures polyadenylated transcripts and introduces a 10bp unique molecular identifier (UMI) at the 5’ end of the product. cDNA was purified with AmpureXP beads (Beckman Coulter) before whole transcriptome amplification using Advantage 2 Polymerase (Clontech) using oligos that introduce Illumina Nextera Multiplex Identifier (MID) P5 Adapter sequences. The libraries were then sent to Stanford University (Department of Microbiology and Immunology, Stanford University) in a blinded fashion, where TCRβ-specific amplification was achieved with Q5 Hot Start Master Mix (NEB) using constant region-specific oligos, simultaneously introducing P7 MID sequences. Final sequencing libraries were purified using SPRISelect beads (Beckman Coulter), quantified using the Agilent TapeStation and pooled for sequencing. Paired-end sequencing was performed on an Illumina NovaSeq SP with 2x250 cycles, performed by the Chan-Zuckerberg Biohub Initiative.

treatment_protocol: No growth or treatment performed

value: PBMCs


title: PBMCs from sample C9-9_Naive_CD4

description: PBMCs from sample C9-9_Naive_CD4


title: PBMCs from sample C9-8_Memory_CD8

description: PBMCs from sample C9-8_Memory_CD8


title: PBMCs from sample C9-9_Memory_CD8

description: PBMCs from sample C9-9_Memory_CD8


title: PBMCs from sample C9-8_Naive_CD8

description: PBMCs from sample C9-8_Naive_CD8


title: PBMCs from sample C9-9_Memory_CD4

description: PBMCs from sample C9-9_Memory_CD4


title: PBMCs from sample C9-8_Naive_CD4

description: PBMCs from sample C9-8_Naive_CD4


title: PBMCs from sample C9-8_Memory_CD4

description: PBMCs from sample C9-8_Memory_CD4


title: PBMCs from sample C9-7_Memory_CD4

description: PBMCs from sample C9-7_Memory_CD4


title: PBMCs from sample C9-7_Naive_CD4

description: PBMCs from sample C9-7_Naive_CD4


title: PBMCs from sample C9-6_Naive_CD4

description: PBMCs from sample C9-6_Naive_CD4


title: PBMCs from sample C9-6_Memory_CD8

description: PBMCs from sample C9-6_Memory_CD8


title: PBMCs from sample C9-7_Memory_CD8

description: PBMCs from sample C9-7_Memory_CD8


title: PBMCs from sample C9-5_Naive_CD8

description: PBMCs from sample C9-5_Naive_CD8


title: PBMCs from sample C9-6_Naive_CD8

description: PBMCs from sample C9-6_Naive_CD8


title: w1118 (wild-type), LBF (third instar larva brain fraction)

value: w1118 (wild type)


title: PBMCs from sample C9-5_Naive_CD4

description: PBMCs from sample C9-5_Naive_CD4


title: PBMCs from sample C9-6_Memory_CD4

description: PBMCs from sample C9-6_Memory_CD4


title: PBMCs from sample C9-5_Memory_CD8

description: PBMCs from sample C9-5_Memory_CD8


title: PBMCs from sample C9-4_Naive_CD4

description: PBMCs from sample C9-4_Naive_CD4


title: PBMCs from sample C9-4_Memory_CD8

description: PBMCs from sample C9-4_Memory_CD8


title: PBMCs from sample C9-4_Naive_CD8

description: PBMCs from sample C9-4_Naive_CD8


title: PBMCs from sample C9-4_Memory_CD4

description: PBMCs from sample C9-4_Memory_CD4


title: PBMCs from sample C9-3_Naive_CD8

description: PBMCs from sample C9-3_Naive_CD8


title: PBMCs from sample C9-2_Naive_CD8

description: PBMCs from sample C9-2_Naive_CD8


title: PBMCs from sample C9-2_Memory_CD8

description: PBMCs from sample C9-2_Memory_CD8


title: PBMCs from sample C9-1_Naive_CD8

description: PBMCs from sample C9-1_Naive_CD8


title: PBMCs from sample C9-1_Memory_CD4

description: PBMCs from sample C9-1_Memory_CD4


title: PBMCs from sample C9-13_Naive_CD8

description: PBMCs from sample C9-13_Naive_CD8


title: PBMCs from sample C9-3_Memory_CD8

description: PBMCs from sample C9-3_Memory_CD8


title: PBMCs from sample C9-7_Naive_CD8

description: PBMCs from sample C9-7_Naive_CD8


title: PBMCs from sample C9-3_Naive_CD4

description: PBMCs from sample C9-3_Naive_CD4


title: PBMCs from sample C9-2_Naive_CD4

description: PBMCs from sample C9-2_Naive_CD4


title: PBMCs from sample C9-13_Memory_CD4

description: PBMCs from sample C9-13_Memory_CD4


title: PBMCs from sample C9-1_Memory_CD8

description: PBMCs from sample C9-1_Memory_CD8


title: PBMCs from sample C9-12_Naive_CD8

description: PBMCs from sample C9-12_Naive_CD8


title: PBMCs from sample C9-13_Naive_CD4

description: PBMCs from sample C9-13_Naive_CD4


title: PBMCs from sample C9-11_Naive_CD8

description: PBMCs from sample C9-11_Naive_CD8


title: PBMCs from sample C9-3_Memory_CD4

description: PBMCs from sample C9-3_Memory_CD4


title: PBMCs from sample C9-11_Naive_CD4

description: PBMCs from sample C9-11_Naive_CD4


title: PBMCs from sample C9-2_Memory_CD4

description: PBMCs from sample C9-2_Memory_CD4


title: PBMCs from sample C9-11_Memory_CD8

description: PBMCs from sample C9-11_Memory_CD8


title: PBMCs from sample C9-1_Naive_CD4

description: PBMCs from sample C9-1_Naive_CD4


title: PBMCs from sample C9-12_Memory_CD8

description: PBMCs from sample C9-12_Memory_CD8


title: PBMCs from sample C9-12_Memory_CD4

description: PBMCs from sample C9-12_Memory_CD4


title: PBMCs from sample C9-12_Naive_CD4

description: PBMCs from sample C9-12_Naive_CD4


title: PBMCs from sample C9-10_Naive_CD8

description: PBMCs from sample C9-10_Naive_CD8


title: PBMCs from sample C9-5_Memory_CD4

description: PBMCs from sample C9-5_Memory_CD4


title: PBMCs from sample C9-10_Memory_CD8

description: PBMCs from sample C9-10_Memory_CD8


title: PBMCs from sample C8-9_Naive_CD4

description: PBMCs from sample C8-9_Naive_CD4


title: PBMCs from sample C8-9_Naive_CD8

description: PBMCs from sample C8-9_Naive_CD8


title: PBMCs from sample C9-10_Naive_CD4

description: PBMCs from sample C9-10_Naive_CD4


title: PBMCs from sample C8-9_Memory_CD8

description: PBMCs from sample C8-9_Memory_CD8


title: PBMCs from sample C9-10_Memory_CD4

description: PBMCs from sample C9-10_Memory_CD4


title: PBMCs from sample C9-13_Memory_CD8

description: PBMCs from sample C9-13_Memory_CD8


title: PBMCs from sample C8-7_Memory_CD4

description: PBMCs from sample C8-7_Memory_CD4


title: PBMCs from sample C8-8_Memory_CD8

description: PBMCs from sample C8-8_Memory_CD8


title: PBMCs from sample C8-8_Naive_CD4

description: PBMCs from sample C8-8_Naive_CD4


title: PBMCs from sample C8-9_Memory_CD4

description: PBMCs from sample C8-9_Memory_CD4


title: PBMCs from sample C8-8_Naive_CD8

description: PBMCs from sample C8-8_Naive_CD8


title: PBMCs from sample C9-11_Memory_CD4

description: PBMCs from sample C9-11_Memory_CD4


title: PBMCs from sample C8-6_Naive_CD4

description: PBMCs from sample C8-6_Naive_CD4


title: PBMCs from sample C8-8_Memory_CD4

description: PBMCs from sample C8-8_Memory_CD4


title: PBMCs from sample C8-4_Naive_CD4

description: PBMCs from sample C8-4_Naive_CD4


title: PBMCs from sample C8-5_Naive_CD4

description: PBMCs from sample C8-5_Naive_CD4


title: PBMCs from sample C8-4_Memory_CD8

description: PBMCs from sample C8-4_Memory_CD8


title: PBMCs from sample C8-7_Naive_CD4

description: PBMCs from sample C8-7_Naive_CD4


title: PBMCs from sample C8-6_Memory_CD8

description: PBMCs from sample C8-6_Memory_CD8


title: PBMCs from sample C8-7_Naive_CD8

description: PBMCs from sample C8-7_Naive_CD8


title: PBMCs from sample C8-6_Naive_CD8

description: PBMCs from sample C8-6_Naive_CD8


title: PBMCs from sample C8-5_Naive_CD8

description: PBMCs from sample C8-5_Naive_CD8


title: PBMCs from sample C8-3_Naive_CD4

description: PBMCs from sample C8-3_Naive_CD4


title: PBMCs from sample C8-6_Memory_CD4

description: PBMCs from sample C8-6_Memory_CD4


title: PBMCs from sample C8-5_Memory_CD8

description: PBMCs from sample C8-5_Memory_CD8


title: PBMCs from sample C8-4_Naive_CD8

description: PBMCs from sample C8-4_Naive_CD8


title: PBMCs from sample C8-5_Memory_CD4

description: PBMCs from sample C8-5_Memory_CD4


title: PBMCs from sample C8-4_Memory_CD4

description: PBMCs from sample C8-4_Memory_CD4


title: PBMCs from sample C8-7_Memory_CD8

description: PBMCs from sample C8-7_Memory_CD8


title: PBMCs from sample C8-2_Memory_CD8

description: PBMCs from sample C8-2_Memory_CD8


title: PBMCs from sample C8-2_Memory_CD4

description: PBMCs from sample C8-2_Memory_CD4


title: PBMCs from sample C8-2_Naive_CD4

description: PBMCs from sample C8-2_Naive_CD4


title: PBMCs from sample C8-1_Naive_CD8

description: PBMCs from sample C8-1_Naive_CD8


title: PBMCs from sample C8-1_Memory_CD4

description: PBMCs from sample C8-1_Memory_CD4


title: PBMCs from sample C8-1_Memory_CD8

description: PBMCs from sample C8-1_Memory_CD8


title: PBMCs from sample C8-1_Naive_CD4

description: PBMCs from sample C8-1_Naive_CD4


title: PBMCs from sample C8-12_Naive_CD8

description: PBMCs from sample C8-12_Naive_CD8


title: PBMCs from sample C8-12_Memory_CD4

description: PBMCs from sample C8-12_Memory_CD4


title: PBMCs from sample C8-3_Naive_CD8

description: PBMCs from sample C8-3_Naive_CD8


title: PBMCs from sample C8-11_Naive_CD4

description: PBMCs from sample C8-11_Naive_CD4


title: PBMCs from sample C8-3_Memory_CD8

description: PBMCs from sample C8-3_Memory_CD8


title: PBMCs from sample C8-3_Memory_CD4

description: PBMCs from sample C8-3_Memory_CD4


title: PBMCs from sample C8-12_Naive_CD4

description: PBMCs from sample C8-12_Naive_CD4


title: PBMCs from sample C8-2_Naive_CD8

description: PBMCs from sample C8-2_Naive_CD8


title: PBMCs from sample C8-10_Naive_CD4

description: PBMCs from sample C8-10_Naive_CD4


title: PBMCs from sample C8-11_Naive_CD8

description: PBMCs from sample C8-11_Naive_CD8


title: PBMCs from sample C8-11_Memory_CD8

description: PBMCs from sample C8-11_Memory_CD8


title: PBMCs from sample C8-12_Memory_CD8

description: PBMCs from sample C8-12_Memory_CD8


title: PBMCs from sample C8-10_Memory_CD8

description: PBMCs from sample C8-10_Memory_CD8


title: PBMCs from sample C7-9_Naive_CD8

description: PBMCs from sample C7-9_Naive_CD8


title: PBMCs from sample C7-9_Naive_CD4

description: PBMCs from sample C7-9_Naive_CD4


title: PBMCs from sample C7-9_Memory_CD8

description: PBMCs from sample C7-9_Memory_CD8


title: PBMCs from sample C7-9_Memory_CD4

description: PBMCs from sample C7-9_Memory_CD4


title: PBMCs from sample C8-11_Memory_CD4

description: PBMCs from sample C8-11_Memory_CD4


title: PBMCs from sample C8-10_Naive_CD8

description: PBMCs from sample C8-10_Naive_CD8


title: PBMCs from sample C8-10_Memory_CD4

description: PBMCs from sample C8-10_Memory_CD4


title: PBMCs from sample C7-8_Naive_CD8

description: PBMCs from sample C7-8_Naive_CD8


title: PBMCs from sample C7-7_Naive_CD8

description: PBMCs from sample C7-7_Naive_CD8


title: PBMCs from sample C7-7_Memory_CD8

description: PBMCs from sample C7-7_Memory_CD8


title: PBMCs from sample C7-7_Memory_CD4

description: PBMCs from sample C7-7_Memory_CD4


title: PBMCs from sample C7-7_Naive_CD4

description: PBMCs from sample C7-7_Naive_CD4


title: PBMCs from sample C7-8_Naive_CD4

description: PBMCs from sample C7-8_Naive_CD4


title: PBMCs from sample C7-6_Naive_CD8

description: PBMCs from sample C7-6_Naive_CD8


title: PBMCs from sample C7-6_Naive_CD4

description: PBMCs from sample C7-6_Naive_CD4


title: PBMCs from sample C7-8_Memory_CD8

description: PBMCs from sample C7-8_Memory_CD8


title: PBMCs from sample C7-6_Memory_CD4

description: PBMCs from sample C7-6_Memory_CD4


title: PBMCs from sample C7-5_Naive_CD4

description: PBMCs from sample C7-5_Naive_CD4


title: PBMCs from sample C7-8_Memory_CD4

description: PBMCs from sample C7-8_Memory_CD4


title: PBMCs from sample C7-5_Memory_CD8

description: PBMCs from sample C7-5_Memory_CD8


title: PBMCs from sample C7-5_Naive_CD8

description: PBMCs from sample C7-5_Naive_CD8


title: PBMCs from sample C7-4_Naive_CD4

description: PBMCs from sample C7-4_Naive_CD4


title: PBMCs from sample C7-5_Memory_CD4

description: PBMCs from sample C7-5_Memory_CD4


title: PBMCs from sample C7-4_Naive_CD8

description: PBMCs from sample C7-4_Naive_CD8


title: PBMCs from sample C7-3_Naive_CD4

description: PBMCs from sample C7-3_Naive_CD4


title: PBMCs from sample C7-4_Memory_CD4

description: PBMCs from sample C7-4_Memory_CD4


title: PBMCs from sample C7-4_Memory_CD8

description: PBMCs from sample C7-4_Memory_CD8


title: PBMCs from sample C7-2_Memory_CD4

description: PBMCs from sample C7-2_Memory_CD4


title: PBMCs from sample C7-3_Memory_CD8

description: PBMCs from sample C7-3_Memory_CD8


title: PBMCs from sample C7-2_Naive_CD4

description: PBMCs from sample C7-2_Naive_CD4


title: PBMCs from sample C7-3_Memory_CD4

description: PBMCs from sample C7-3_Memory_CD4


title: PBMCs from sample C7-1_Naive_CD4

description: PBMCs from sample C7-1_Naive_CD4


title: PBMCs from sample C7-2_Memory_CD8

description: PBMCs from sample C7-2_Memory_CD8


title: PBMCs from sample C7-6_Memory_CD8

description: PBMCs from sample C7-6_Memory_CD8


title: PBMCs from sample C7-1_Memory_CD8

description: PBMCs from sample C7-1_Memory_CD8


title: PBMCs from sample C7-1_Naive_CD8

description: PBMCs from sample C7-1_Naive_CD8


title: PBMCs from sample C7-1_Memory_CD4

description: PBMCs from sample C7-1_Memory_CD4


title: PBMCs from sample C7-12_Naive_CD8

description: PBMCs from sample C7-12_Naive_CD8


title: PBMCs from sample C7-12_Memory_CD8

description: PBMCs from sample C7-12_Memory_CD8


title: PBMCs from sample C7-12_Naive_CD4

description: PBMCs from sample C7-12_Naive_CD4


title: PBMCs from sample C7-12_Memory_CD4

description: PBMCs from sample C7-12_Memory_CD4


title: PBMCs from sample C7-11_Naive_CD8

description: PBMCs from sample C7-11_Naive_CD8


title: PBMCs from sample C7-3_Naive_CD8

description: PBMCs from sample C7-3_Naive_CD8


title: PBMCs from sample C7-11_Memory_CD8

description: PBMCs from sample C7-11_Memory_CD8


title: PBMCs from sample C7-10_Naive_CD8

description: PBMCs from sample C7-10_Naive_CD8


title: PBMCs from sample C7-10_Naive_CD4

description: PBMCs from sample C7-10_Naive_CD4


title: PBMCs from sample C7-10_Memory_CD8

description: PBMCs from sample C7-10_Memory_CD8


title: PBMCs from sample C7-11_Memory_CD4

description: PBMCs from sample C7-11_Memory_CD4


title: PBMCs from sample C6-9_Memory_CD8

description: PBMCs from sample C6-9_Memory_CD8


title: PBMCs from sample C7-2_Naive_CD8

description: PBMCs from sample C7-2_Naive_CD8


title: PBMCs from sample C7-11_Naive_CD4

description: PBMCs from sample C7-11_Naive_CD4


title: PBMCs from sample C6-9_Memory_CD4

description: PBMCs from sample C6-9_Memory_CD4


title: PBMCs from sample C7-10_Memory_CD4

description: PBMCs from sample C7-10_Memory_CD4


title: PBMCs from sample C6-8_Naive_CD4

description: PBMCs from sample C6-8_Naive_CD4


title: PBMCs from sample C6-8_Naive_CD8

description: PBMCs from sample C6-8_Naive_CD8


title: PBMCs from sample C6-9_Naive_CD8

description: PBMCs from sample C6-9_Naive_CD8


title: PBMCs from sample C6-9_Naive_CD4

description: PBMCs from sample C6-9_Naive_CD4


title: PBMCs from sample C6-8_Memory_CD4

description: PBMCs from sample C6-8_Memory_CD4


title: PBMCs from sample C6-8_Memory_CD8

description: PBMCs from sample C6-8_Memory_CD8


title: PBMCs from sample C6-7_Naive_CD8

description: PBMCs from sample C6-7_Naive_CD8


title: PBMCs from sample C6-6_Memory_CD8

description: PBMCs from sample C6-6_Memory_CD8


title: PBMCs from sample C6-7_Naive_CD4

description: PBMCs from sample C6-7_Naive_CD4


title: PBMCs from sample C6-7_Memory_CD4

description: PBMCs from sample C6-7_Memory_CD4


title: PBMCs from sample C6-7_Memory_CD8

description: PBMCs from sample C6-7_Memory_CD8


title: PBMCs from sample C6-6_Naive_CD8

description: PBMCs from sample C6-6_Naive_CD8


title: PBMCs from sample C6-5_Memory_CD8

description: PBMCs from sample C6-5_Memory_CD8


title: PBMCs from sample C6-3_Naive_CD8

description: PBMCs from sample C6-3_Naive_CD8


title: PBMCs from sample C6-6_Memory_CD4

description: PBMCs from sample C6-6_Memory_CD4


title: PBMCs from sample C6-6_Naive_CD4

description: PBMCs from sample C6-6_Naive_CD4


title: PBMCs from sample C6-3_Memory_CD8

description: PBMCs from sample C6-3_Memory_CD8


title: PBMCs from sample C6-5_Naive_CD4

description: PBMCs from sample C6-5_Naive_CD4


title: PBMCs from sample C6-2_Memory_CD4

description: PBMCs from sample C6-2_Memory_CD4


title: PBMCs from sample C6-4_Memory_CD8

description: PBMCs from sample C6-4_Memory_CD8


title: PBMCs from sample C6-4_Naive_CD4

description: PBMCs from sample C6-4_Naive_CD4


title: PBMCs from sample C6-4_Naive_CD8

description: PBMCs from sample C6-4_Naive_CD8


title: PBMCs from sample C6-4_Memory_CD4

description: PBMCs from sample C6-4_Memory_CD4


title: PBMCs from sample C6-3_Memory_CD4

description: PBMCs from sample C6-3_Memory_CD4


title: PBMCs from sample C6-3_Naive_CD4

description: PBMCs from sample C6-3_Naive_CD4


title: PBMCs from sample C6-2_Naive_CD8

description: PBMCs from sample C6-2_Naive_CD8


title: PBMCs from sample C6-10_Memory_CD8

description: PBMCs from sample C6-10_Memory_CD8


title: PBMCs from sample C6-10_Memory_CD4

description: PBMCs from sample C6-10_Memory_CD4


title: PBMCs from sample C5-8_Naive_CD4

description: PBMCs from sample C5-8_Naive_CD4


title: PBMCs from sample C5-9_Memory_CD4

description: PBMCs from sample C5-9_Memory_CD4


title: PBMCs from sample C6-2_Naive_CD4

description: PBMCs from sample C6-2_Naive_CD4


title: PBMCs from sample C6-2_Memory_CD8

description: PBMCs from sample C6-2_Memory_CD8


title: PBMCs from sample C6-1_Naive_CD4

description: PBMCs from sample C6-1_Naive_CD4


title: PBMCs from sample C6-1_Naive_CD8

description: PBMCs from sample C6-1_Naive_CD8


title: PBMCs from sample C6-1_Memory_CD4

description: PBMCs from sample C6-1_Memory_CD4


title: PBMCs from sample C6-1_Memory_CD8

description: PBMCs from sample C6-1_Memory_CD8


title: PBMCs from sample C5-7_Naive_CD8

description: PBMCs from sample C5-7_Naive_CD8


title: PBMCs from sample C6-10_Naive_CD4

description: PBMCs from sample C6-10_Naive_CD4


title: PBMCs from sample C6-5_Naive_CD8

description: PBMCs from sample C6-5_Naive_CD8


title: PBMCs from sample C5-6_Naive_CD8

description: PBMCs from sample C5-6_Naive_CD8


title: PBMCs from sample C5-9_Naive_CD8

description: PBMCs from sample C5-9_Naive_CD8


title: PBMCs from sample C6-5_Memory_CD4

description: PBMCs from sample C6-5_Memory_CD4


title: PBMCs from sample C6-11_Naive_CD8

description: PBMCs from sample C6-11_Naive_CD8


title: PBMCs from sample C6-11_Naive_CD4

description: PBMCs from sample C6-11_Naive_CD4


title: PBMCs from sample C5-6_Memory_CD4

description: PBMCs from sample C5-6_Memory_CD4


title: PBMCs from sample C6-11_Memory_CD8

description: PBMCs from sample C6-11_Memory_CD8


title: PBMCs from sample C6-11_Memory_CD4

description: PBMCs from sample C6-11_Memory_CD4


title: PBMCs from sample C5-9_Naive_CD4

description: PBMCs from sample C5-9_Naive_CD4


title: PBMCs from sample C5-5_Naive_CD4

description: PBMCs from sample C5-5_Naive_CD4


title: PBMCs from sample C5-9_Memory_CD8

description: PBMCs from sample C5-9_Memory_CD8


title: PBMCs from sample C5-4_Naive_CD8

description: PBMCs from sample C5-4_Naive_CD8


title: PBMCs from sample C5-4_Memory_CD4

description: PBMCs from sample C5-4_Memory_CD4


title: PBMCs from sample C5-8_Memory_CD8

description: PBMCs from sample C5-8_Memory_CD8


title: PBMCs from sample C5-8_Memory_CD4

description: PBMCs from sample C5-8_Memory_CD4


title: PBMCs from sample C6-10_Naive_CD8

description: PBMCs from sample C6-10_Naive_CD8


title: PBMCs from sample C5-8_Naive_CD8

description: PBMCs from sample C5-8_Naive_CD8


title: PBMCs from sample C5-3_Naive_CD4

description: PBMCs from sample C5-3_Naive_CD4


title: PBMCs from sample C5-7_Memory_CD4

description: PBMCs from sample C5-7_Memory_CD4


title: PBMCs from sample C5-6_Memory_CD8

description: PBMCs from sample C5-6_Memory_CD8


title: PBMCs from sample C5-3_Memory_CD4

description: PBMCs from sample C5-3_Memory_CD4


title: PBMCs from sample C5-3_Memory_CD8

description: PBMCs from sample C5-3_Memory_CD8


title: PBMCs from sample C5-6_Naive_CD4

description: PBMCs from sample C5-6_Naive_CD4


title: PBMCs from sample C5-7_Memory_CD8

description: PBMCs from sample C5-7_Memory_CD8


title: PBMCs from sample C5-2_Naive_CD8

description: PBMCs from sample C5-2_Naive_CD8


title: PBMCs from sample C5-2_Naive_CD4

description: PBMCs from sample C5-2_Naive_CD4


title: PBMCs from sample C5-5_Memory_CD8

description: PBMCs from sample C5-5_Memory_CD8


title: PBMCs from sample C5-5_Naive_CD8

description: PBMCs from sample C5-5_Naive_CD8


title: PBMCs from sample C5-5_Memory_CD4

description: PBMCs from sample C5-5_Memory_CD4


title: PBMCs from sample C5-4_Memory_CD8

description: PBMCs from sample C5-4_Memory_CD8


title: PBMCs from sample C5-4_Naive_CD4

description: PBMCs from sample C5-4_Naive_CD4


title: PBMCs from sample C5-1_Naive_CD4

description: PBMCs from sample C5-1_Naive_CD4


title: PBMCs from sample C5-3_Naive_CD8

description: PBMCs from sample C5-3_Naive_CD8


title: PBMCs from sample C5-1_Memory_CD8

description: PBMCs from sample C5-1_Memory_CD8


title: PBMCs from sample C5-2_Memory_CD8

description: PBMCs from sample C5-2_Memory_CD8


title: PBMCs from sample C5-13_Memory_CD8

description: PBMCs from sample C5-13_Memory_CD8


title: PBMCs from sample C5-12_Naive_CD8

description: PBMCs from sample C5-12_Naive_CD8


title: PBMCs from sample C5-12_Memory_CD8

description: PBMCs from sample C5-12_Memory_CD8


title: PBMCs from sample C5-1_Memory_CD4

description: PBMCs from sample C5-1_Memory_CD4


title: PBMCs from sample C5-13_Naive_CD8

description: PBMCs from sample C5-13_Naive_CD8


title: PBMCs from sample C5-10_Naive_CD8

description: PBMCs from sample C5-10_Naive_CD8


title: PBMCs from sample C5-11_Naive_CD8

description: PBMCs from sample C5-11_Naive_CD8


title: PBMCs from sample C5-12_Memory_CD4

description: PBMCs from sample C5-12_Memory_CD4


title: PBMCs from sample C4-9_Naive_CD8

description: PBMCs from sample C4-9_Naive_CD8


title: PBMCs from sample C4-9_Naive_CD4

description: PBMCs from sample C4-9_Naive_CD4


title: PBMCs from sample C5-11_Memory_CD4

description: PBMCs from sample C5-11_Memory_CD4


title: PBMCs from sample C5-1_Naive_CD8

description: PBMCs from sample C5-1_Naive_CD8


title: PBMCs from sample C5-10_Naive_CD4

description: PBMCs from sample C5-10_Naive_CD4


title: PBMCs from sample C5-11_Naive_CD4

description: PBMCs from sample C5-11_Naive_CD4


title: PBMCs from sample C5-13_Naive_CD4

description: PBMCs from sample C5-13_Naive_CD4


title: PBMCs from sample C4-8_Memory_CD8

description: PBMCs from sample C4-8_Memory_CD8


title: PBMCs from sample C5-12_Naive_CD4

description: PBMCs from sample C5-12_Naive_CD4


title: PBMCs from sample C5-2_Memory_CD4

description: PBMCs from sample C5-2_Memory_CD4


title: PBMCs from sample C4-8_Memory_CD4

description: PBMCs from sample C4-8_Memory_CD4


title: PBMCs from sample C5-10_Memory_CD8

description: PBMCs from sample C5-10_Memory_CD8


title: PBMCs from sample C4-6_Naive_CD8

description: PBMCs from sample C4-6_Naive_CD8


title: PBMCs from sample C4-9_Memory_CD8

description: PBMCs from sample C4-9_Memory_CD8


title: PBMCs from sample C5-10_Memory_CD4

description: PBMCs from sample C5-10_Memory_CD4


title: PBMCs from sample C4-6_Naive_CD4

description: PBMCs from sample C4-6_Naive_CD4


title: PBMCs from sample C4-8_Naive_CD8

description: PBMCs from sample C4-8_Naive_CD8


title: PBMCs from sample C4-6_Memory_CD8

description: PBMCs from sample C4-6_Memory_CD8


title: PBMCs from sample C4-8_Naive_CD4

description: PBMCs from sample C4-8_Naive_CD4


title: PBMCs from sample C4-9_Memory_CD4

description: PBMCs from sample C4-9_Memory_CD4


title: PBMCs from sample C5-13_Memory_CD4

description: PBMCs from sample C5-13_Memory_CD4


title: PBMCs from sample C4-7_Naive_CD4

description: PBMCs from sample C4-7_Naive_CD4


title: PBMCs from sample C4-5_Memory_CD4

description: PBMCs from sample C4-5_Memory_CD4


title: PBMCs from sample C4-4_Naive_CD8

description: PBMCs from sample C4-4_Naive_CD8


title: PBMCs from sample C4-7_Naive_CD8

description: PBMCs from sample C4-7_Naive_CD8


title: PBMCs from sample C4-4_Memory_CD4

description: PBMCs from sample C4-4_Memory_CD4


title: PBMCs from sample C4-7_Memory_CD8

description: PBMCs from sample C4-7_Memory_CD8


title: PBMCs from sample C4-3_Naive_CD8

description: PBMCs from sample C4-3_Naive_CD8


title: PBMCs from sample C4-7_Memory_CD4

description: PBMCs from sample C4-7_Memory_CD4


title: PBMCs from sample C4-3_Memory_CD4

description: PBMCs from sample C4-3_Memory_CD4


title: PBMCs from sample C5-11_Memory_CD8

description: PBMCs from sample C5-11_Memory_CD8


title: PBMCs from sample C4-5_Naive_CD8

description: PBMCs from sample C4-5_Naive_CD8


title: PBMCs from sample C4-6_Memory_CD4

description: PBMCs from sample C4-6_Memory_CD4


title: PBMCs from sample C4-3_Naive_CD4

description: PBMCs from sample C4-3_Naive_CD4


title: PBMCs from sample C4-5_Memory_CD8

description: PBMCs from sample C4-5_Memory_CD8


title: PBMCs from sample C4-2_Memory_CD8

description: PBMCs from sample C4-2_Memory_CD8


title: PBMCs from sample C4-5_Naive_CD4

description: PBMCs from sample C4-5_Naive_CD4


title: PBMCs from sample C4-2_Memory_CD4

description: PBMCs from sample C4-2_Memory_CD4


title: PBMCs from sample C4-1_Memory_CD4

description: PBMCs from sample C4-1_Memory_CD4


title: PBMCs from sample C4-4_Naive_CD4

description: PBMCs from sample C4-4_Naive_CD4


title: PBMCs from sample C4-4_Memory_CD8

description: PBMCs from sample C4-4_Memory_CD8


title: PBMCs from sample C4-12_Naive_CD8

description: PBMCs from sample C4-12_Naive_CD8


title: PBMCs from sample C4-2_Naive_CD8

description: PBMCs from sample C4-2_Naive_CD8


title: PBMCs from sample C4-3_Memory_CD8

description: PBMCs from sample C4-3_Memory_CD8


title: PBMCs from sample C4-12_Memory_CD8

description: PBMCs from sample C4-12_Memory_CD8


title: PBMCs from sample C4-1_Memory_CD8

description: PBMCs from sample C4-1_Memory_CD8


title: PBMCs from sample C4-11_Naive_CD4

description: PBMCs from sample C4-11_Naive_CD4


title: PBMCs from sample C4-1_Naive_CD8

description: PBMCs from sample C4-1_Naive_CD8


title: PBMCs from sample C4-12_Memory_CD4

description: PBMCs from sample C4-12_Memory_CD4


title: PBMCs from sample C4-13_Naive_CD8

description: PBMCs from sample C4-13_Naive_CD8


title: PBMCs from sample C4-11_Naive_CD8

description: PBMCs from sample C4-11_Naive_CD8


title: PBMCs from sample C4-11_Memory_CD8

description: PBMCs from sample C4-11_Memory_CD8


title: PBMCs from sample C4-10_Naive_CD4

description: PBMCs from sample C4-10_Naive_CD4


title: PBMCs from sample C3-9_Naive_CD4

description: PBMCs from sample C3-9_Naive_CD4


title: PBMCs from sample C4-1_Naive_CD4

description: PBMCs from sample C4-1_Naive_CD4


title: PBMCs from sample C4-13_Memory_CD8

description: PBMCs from sample C4-13_Memory_CD8


title: PBMCs from sample C4-13_Memory_CD4

description: PBMCs from sample C4-13_Memory_CD4


title: PBMCs from sample C4-13_Naive_CD4

description: PBMCs from sample C4-13_Naive_CD4


title: PBMCs from sample C4-12_Naive_CD4

description: PBMCs from sample C4-12_Naive_CD4


title: PBMCs from sample C4-2_Naive_CD4

description: PBMCs from sample C4-2_Naive_CD4


title: PBMCs from sample C4-11_Memory_CD4

description: PBMCs from sample C4-11_Memory_CD4


title: PBMCs from sample C4-10_Naive_CD8

description: PBMCs from sample C4-10_Naive_CD8


title: PBMCs from sample C4-10_Memory_CD8

description: PBMCs from sample C4-10_Memory_CD8


title: PBMCs from sample C3-9_Memory_CD4

description: PBMCs from sample C3-9_Memory_CD4


title: PBMCs from sample C3-9_Naive_CD8

description: PBMCs from sample C3-9_Naive_CD8


title: PBMCs from sample C4-10_Memory_CD4

description: PBMCs from sample C4-10_Memory_CD4


title: PBMCs from sample C3-8_Naive_CD4

description: PBMCs from sample C3-8_Naive_CD4


title: PBMCs from sample C3-6_Naive_CD4

description: PBMCs from sample C3-6_Naive_CD4


title: PBMCs from sample C3-8_Memory_CD4

description: PBMCs from sample C3-8_Memory_CD4


title: PBMCs from sample C3-8_Memory_CD8

description: PBMCs from sample C3-8_Memory_CD8


title: PBMCs from sample C3-7_Memory_CD4

description: PBMCs from sample C3-7_Memory_CD4


title: PBMCs from sample C3-7_Naive_CD4

description: PBMCs from sample C3-7_Naive_CD4


title: PBMCs from sample C3-6_Naive_CD8

description: PBMCs from sample C3-6_Naive_CD8


title: PBMCs from sample C3-6_Memory_CD8

description: PBMCs from sample C3-6_Memory_CD8


title: PBMCs from sample C3-6_Memory_CD4

description: PBMCs from sample C3-6_Memory_CD4


title: PBMCs from sample C3-5_Naive_CD8

description: PBMCs from sample C3-5_Naive_CD8


title: PBMCs from sample C3-4_Memory_CD8

description: PBMCs from sample C3-4_Memory_CD8


title: PBMCs from sample C3-5_Naive_CD4

description: PBMCs from sample C3-5_Naive_CD4


title: PBMCs from sample C3-4_Memory_CD4

description: PBMCs from sample C3-4_Memory_CD4


title: PBMCs from sample C3-4_Naive_CD4

description: PBMCs from sample C3-4_Naive_CD4


title: PBMCs from sample C3-3_Naive_CD8

description: PBMCs from sample C3-3_Naive_CD8


title: PBMCs from sample C3-5_Memory_CD8

description: PBMCs from sample C3-5_Memory_CD8


title: PBMCs from sample C3-3_Naive_CD4

description: PBMCs from sample C3-3_Naive_CD4


title: PBMCs from sample C3-9_Memory_CD8

description: PBMCs from sample C3-9_Memory_CD8


title: PBMCs from sample C3-5_Memory_CD4

description: PBMCs from sample C3-5_Memory_CD4


title: PBMCs from sample C3-8_Naive_CD8

description: PBMCs from sample C3-8_Naive_CD8


title: PBMCs from sample C3-2_Memory_CD4

description: PBMCs from sample C3-2_Memory_CD4


title: PBMCs from sample C3-4_Naive_CD8

description: PBMCs from sample C3-4_Naive_CD8


title: PBMCs from sample C3-1_Naive_CD4

description: PBMCs from sample C3-1_Naive_CD4


title: PBMCs from sample C3-1_Memory_CD4

description: PBMCs from sample C3-1_Memory_CD4


title: PBMCs from sample C3-3_Memory_CD4

description: PBMCs from sample C3-3_Memory_CD4


title: PBMCs from sample C3-13_Naive_CD8

description: PBMCs from sample C3-13_Naive_CD8


title: PBMCs from sample C3-3_Memory_CD8

description: PBMCs from sample C3-3_Memory_CD8


title: PBMCs from sample C3-13_Naive_CD4

description: PBMCs from sample C3-13_Naive_CD4


title: PBMCs from sample C3-2_Naive_CD8

description: PBMCs from sample C3-2_Naive_CD8


title: PBMCs from sample C3-2_Naive_CD4

description: PBMCs from sample C3-2_Naive_CD4


title: PBMCs from sample C3-1_Memory_CD8

description: PBMCs from sample C3-1_Memory_CD8


title: PBMCs from sample C3-7_Memory_CD8

description: PBMCs from sample C3-7_Memory_CD8


title: PBMCs from sample C3-2_Memory_CD8

description: PBMCs from sample C3-2_Memory_CD8


title: PBMCs from sample C3-12_Naive_CD8

description: PBMCs from sample C3-12_Naive_CD8


title: PBMCs from sample C3-7_Naive_CD8

description: PBMCs from sample C3-7_Naive_CD8


title: PBMCs from sample C3-13_Memory_CD4

description: PBMCs from sample C3-13_Memory_CD4


title: PBMCs from sample C3-13_Memory_CD8

description: PBMCs from sample C3-13_Memory_CD8


title: PBMCs from sample C3-11_Naive_CD4

description: PBMCs from sample C3-11_Naive_CD4


title: PBMCs from sample C3-12_Naive_CD4

description: PBMCs from sample C3-12_Naive_CD4


title: PBMCs from sample C3-11_Naive_CD8

description: PBMCs from sample C3-11_Naive_CD8


title: PBMCs from sample C3-10_Memory_CD8

description: PBMCs from sample C3-10_Memory_CD8


title: PBMCs from sample C3-12_Memory_CD4

description: PBMCs from sample C3-12_Memory_CD4


title: PBMCs from sample C3-10_Naive_CD8

description: PBMCs from sample C3-10_Naive_CD8


title: PBMCs from sample C3-11_Memory_CD8

description: PBMCs from sample C3-11_Memory_CD8


title: PBMCs from sample C2-9_Naive_CD4

description: PBMCs from sample C2-9_Naive_CD4


title: PBMCs from sample C3-1_Naive_CD8

description: PBMCs from sample C3-1_Naive_CD8


title: PBMCs from sample C2-9_Memory_CD8

description: PBMCs from sample C2-9_Memory_CD8


title: PBMCs from sample C3-10_Memory_CD4

description: PBMCs from sample C3-10_Memory_CD4


title: PBMCs from sample C3-11_Memory_CD4

description: PBMCs from sample C3-11_Memory_CD4


title: PBMCs from sample C2-8_Naive_CD4

description: PBMCs from sample C2-8_Naive_CD4


title: PBMCs from sample C2-8_Memory_CD4

description: PBMCs from sample C2-8_Memory_CD4


title: PBMCs from sample C2-8_Naive_CD8

description: PBMCs from sample C2-8_Naive_CD8


title: PBMCs from sample C2-9_Memory_CD4

description: PBMCs from sample C2-9_Memory_CD4


title: PBMCs from sample C2-7_Naive_CD4

description: PBMCs from sample C2-7_Naive_CD4


title: PBMCs from sample C2-7_Memory_CD8

description: PBMCs from sample C2-7_Memory_CD8


title: PBMCs from sample C2-7_Naive_CD8

description: PBMCs from sample C2-7_Naive_CD8


title: PBMCs from sample C2-9_Naive_CD8

description: PBMCs from sample C2-9_Naive_CD8


title: PBMCs from sample C2-8_Memory_CD8

description: PBMCs from sample C2-8_Memory_CD8


title: PBMCs from sample C2-6_Memory_CD4

description: PBMCs from sample C2-6_Memory_CD4


title: PBMCs from sample C3-12_Memory_CD8

description: PBMCs from sample C3-12_Memory_CD8


title: PBMCs from sample C2-7_Memory_CD4

description: PBMCs from sample C2-7_Memory_CD4


title: PBMCs from sample C2-5_Memory_CD8

description: PBMCs from sample C2-5_Memory_CD8


title: PBMCs from sample C2-6_Memory_CD8

description: PBMCs from sample C2-6_Memory_CD8


title: PBMCs from sample C2-6_Naive_CD8

description: PBMCs from sample C2-6_Naive_CD8


title: PBMCs from sample C2-5_Memory_CD4

description: PBMCs from sample C2-5_Memory_CD4


title: PBMCs from sample C2-5_Naive_CD8

description: PBMCs from sample C2-5_Naive_CD8


title: PBMCs from sample C2-3_Naive_CD8

description: PBMCs from sample C2-3_Naive_CD8


title: PBMCs from sample C2-4_Naive_CD4

description: PBMCs from sample C2-4_Naive_CD4


title: PBMCs from sample C3-10_Naive_CD4

description: PBMCs from sample C3-10_Naive_CD4


title: PBMCs from sample C2-5_Naive_CD4

description: PBMCs from sample C2-5_Naive_CD4


title: PBMCs from sample C2-4_Memory_CD4

description: PBMCs from sample C2-4_Memory_CD4


title: PBMCs from sample C2-3_Naive_CD4

description: PBMCs from sample C2-3_Naive_CD4


title: PBMCs from sample C2-3_Memory_CD8

description: PBMCs from sample C2-3_Memory_CD8


title: PBMCs from sample C2-4_Memory_CD8

description: PBMCs from sample C2-4_Memory_CD8


title: PBMCs from sample C2-3_Memory_CD4

description: PBMCs from sample C2-3_Memory_CD4


title: PBMCs from sample C2-2_Naive_CD4

description: PBMCs from sample C2-2_Naive_CD4


title: PBMCs from sample C2-2_Naive_CD8

description: PBMCs from sample C2-2_Naive_CD8


title: PBMCs from sample C2-6_Naive_CD4

description: PBMCs from sample C2-6_Naive_CD4


title: PBMCs from sample C2-4_Naive_CD8

description: PBMCs from sample C2-4_Naive_CD8


title: PBMCs from sample C2-1_Naive_CD4

description: PBMCs from sample C2-1_Naive_CD4


title: PBMCs from sample C2-2_Memory_CD4

description: PBMCs from sample C2-2_Memory_CD4


title: PBMCs from sample C2-12_Naive_CD8

description: PBMCs from sample C2-12_Naive_CD8


title: PBMCs from sample C2-1_Memory_CD4

description: PBMCs from sample C2-1_Memory_CD4


title: PBMCs from sample C2-10_Naive_CD8

description: PBMCs from sample C2-10_Naive_CD8


title: PBMCs from sample C2-12_Naive_CD4

description: PBMCs from sample C2-12_Naive_CD4


title: PBMCs from sample C2-1_Naive_CD8

description: PBMCs from sample C2-1_Naive_CD8


title: PBMCs from sample C2-12_Memory_CD8

description: PBMCs from sample C2-12_Memory_CD8


title: PBMCs from sample C2-12_Memory_CD4

description: PBMCs from sample C2-12_Memory_CD4


title: PBMCs from sample C2-10_Naive_CD4

description: PBMCs from sample C2-10_Naive_CD4


title: PBMCs from sample C2-10_Memory_CD8

description: PBMCs from sample C2-10_Memory_CD8


title: PBMCs from sample C1-12_Naive_CD8

description: PBMCs from sample C1-12_Naive_CD8


title: PBMCs from sample C1-12_Naive_CD4

description: PBMCs from sample C1-12_Naive_CD4


title: PBMCs from sample C2-10_Memory_CD4

description: PBMCs from sample C2-10_Memory_CD4


title: PBMCs from sample C1-12_Memory_CD4

description: PBMCs from sample C1-12_Memory_CD4


title: PBMCs from sample C1-11_Naive_CD8

description: PBMCs from sample C1-11_Naive_CD8


title: PBMCs from sample C1-11_Memory_CD8

description: PBMCs from sample C1-11_Memory_CD8


title: PBMCs from sample C1-9_Naive_CD4

description: PBMCs from sample C1-9_Naive_CD4


title: PBMCs from sample C1-11_Naive_CD4

description: PBMCs from sample C1-11_Naive_CD4


title: PBMCs from sample C1-11_Memory_CD4

description: PBMCs from sample C1-11_Memory_CD4


title: PBMCs from sample C1-9_Naive_CD8

description: PBMCs from sample C1-9_Naive_CD8


title: PBMCs from sample C1-8_Naive_CD4

description: PBMCs from sample C1-8_Naive_CD4


title: PBMCs from sample C1-9_Memory_CD8

description: PBMCs from sample C1-9_Memory_CD8


title: PBMCs from sample C2-2_Memory_CD8

description: PBMCs from sample C2-2_Memory_CD8


title: PBMCs from sample C1-9_Memory_CD4

description: PBMCs from sample C1-9_Memory_CD4


title: PBMCs from sample C1-8_Naive_CD8

description: PBMCs from sample C1-8_Naive_CD8


title: PBMCs from sample C1-8_Memory_CD4

description: PBMCs from sample C1-8_Memory_CD4


title: PBMCs from sample C1-7_Naive_CD8

description: PBMCs from sample C1-7_Naive_CD8


title: PBMCs from sample C2-1_Memory_CD8

description: PBMCs from sample C2-1_Memory_CD8


title: hMeRIP, Tetnull, LBF, rep1

data_processing:
The processed reads were mapped to the reference genome Drosophila melanogaster BDGP6 (dm6) from Ensembl by using Hisat2 (version 2.1.0) for RNA seq and hMeRIP seq.
To analyze gene expression, HTSeq framework, version 0.5.3p9, was used to count the aligned reads in genes.  Mode “union” and mapping quality cut-off 20 were used for our analysis. Count-table was normalized so that all samples have the same level of total mapped reads.
DEseq2 was used to identify differentially expressed genes. Cufflinks v2.2.1 was applied to calculate the rpkm values 48,49.  A gene was considered as significantly changed when fold change >=2 or <= -2 and adjusted p value < 0.05.
“SplitNCigarReads” funciton in GATK v3.3-0 were used to split reads that contain Ns in their cigar string (e.g., spanning splicing events in hMeRIP-seq data). “rmdup” function of samtools v1.3.1 were used to remove a duplicate mapping of reads.
Then the same peak calling procedure as ChIP seq data analysis was performed to call peaks of hMeRIP-seq data. The peaks of hMeRIP-seq were selected using P-value < 10e-5.
Assembly: dm6
Supplementary files format and content: bw and tab-delimited text files for hMeRIP peak annotation (except input).

source_name: LBF (third instar larva brain fraction)

extract_protocol:
0-12h embryos were collected, immediately frozen on dry ice, and stored at -80oC until RNA purification. The larval brain fraction (LBF), was dissected, immediately frozen on dry ice and stored at -80oC until RNA isolation. The RNA immunoprecipitation was performed essentially as described in Dominissi et al. Briefly, total RNA was isolated using RNeasy Maxi Kit (Qiagen). For each sample 1 mg of total RNA (1 μg/μl) was divided into batches of 45µg and incubated at 94°C in fragmentation buffer (100 mM Tris-HCl pH7.0, 100 mM ZnCl2) for 40 seconds. Fragmented RNA batches were pooled, and ethanol precipitated at -80˚C overnight. RNA samples were washed with 75% ethanol and resuspended in RNase-free water. Fragmentation efficiency was checked on a Bioanalyzer RNA chip (Agilent). RNA fragments were denatured by heating at 70°C for 5 minutes, then chilled on ice for 5 minutes. For immunoprecipitation, RNA samples were incubated overnight at 4°C with 12.5 µg of anti-5-hmC antibody (Diagenode rat monoclonal MAb-633HMC) or without antibody as negative control in IP buffer (750 mM NaCl, 50 mM Tris-HCl pH7.4, 0.5% IGEPAL CA-630, RNasin 400 U/ml and RVC 2 mM). 60 μl of equilibrated Dynabeads Protein G (Life Technologies) were added to the samples and incubated at 4°C for 2.5 hours.  The magnetic stand beads were washed with 1 ml IP buffer for 5 minutes three times. To elute immunoprecipitated RNA, 1 ml TriPure Reagent (Roche) was added, mixed thoroughly and centrifuged at room temperature for 5 minutes. Aqueous phase was recovered, and equal amount of chloroform was added, vortexed and aqueous phase was collected after centrifugation and ethanol precipitated at -80˚C overnight. RNA was resuspended in nuclease free water and used for library preparation. All buffers contained cOmplete EDTA-free protease inhibitor cocktail (Roche).
Library preparation was done with the TruSeq ChIP Sample Prep Kit (Illumina) after reverse transcription of pulled-down RNA and synthesis of a second strand (NEB) by Next mRNA second strand synthesis module (NEB)). Briefly, 5 to 10 ng dsDNA was subjected to 5’ and 3’ protruding end repair. Then, non-templated adenines were added to the 3’ ends of the blunted DNA fragments. This last step allows ligation of Illumina multiplex adapters. The DNA fragments were then size selected in order to remove all unligated adapters and to sequence 200-300-bp fragments. 18 cycles of PCR were carried out to amplify the library. DNA was quantified by fluorometry with the Qubit 2.0 and DNA integrity was assessed with a 2100 bioanalyzer (Agilent). 6 pM of DNA library spiked with .5% PhiX viral DNA was clustered on cBot (Illumina) and then sequenced on a HiScanSQ module (Illumina).

value: LBF (third instar larva brain fraction)

tag: development stage

value: Tetnull

tag: rip antibody

value: Rat anti-5hmrC antibody (Diagenode #C15220001-100)


title: PBMCs from sample C1-7_Memory_CD8

description: PBMCs from sample C1-7_Memory_CD8


title: Input, WT, LBF, rep2


title: PBMCs from sample C1-8_Memory_CD8

description: PBMCs from sample C1-8_Memory_CD8


title: Input, WT, Tetnull, rep2


title: PBMCs from sample C1-6_Naive_CD8

description: PBMCs from sample C1-6_Naive_CD8


title: Input, WT, LBF, rep1


title: Input, WT, Tetnull, rep1


title: PBMCs from sample C1-6_Naive_CD4

description: PBMCs from sample C1-6_Naive_CD4


title: hMeRIP, Tetnull, LBF, rep2


title: PBMCs from sample C1-12_Memory_CD8

description: PBMCs from sample C1-12_Memory_CD8


title: PBMCs from sample C1-7_Naive_CD4

description: PBMCs from sample C1-7_Naive_CD4


title: PBMCs from sample C1-7_Memory_CD4

description: PBMCs from sample C1-7_Memory_CD4


title: Input, WT, 0-12h Embryo

source_name: Embryo

value: Embryo

value: whole embryo

value: 0-12h embryo


title: hMeRIP, WT, LBF, rep2

value: LBF containing larval brain and imaginal discs

value: third instar larva


title: hMeRIP, WT, LBF, rep1


title: PBMCs from sample C1-5_Memory_CD4

description: PBMCs from sample C1-5_Memory_CD4


title: MM029 DMSO Rep 2

city: Illkirch-Graffenstaden

first: Frédéric

last: Coin

address: 1 Rue Laurent Fries

country: France

institute: IGBMC

data_processing:
P2683: Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422. P2988: Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq None. P3057: Image analysis and base calling were performed using RTA 2.7.7 and bclconvert 3.8.4.
Assembly: hg38
Supplementary files format and content: xlsx files containing RPKM values for each sample, and log2(FC) and adjPvals of drug-treated samples vs DMSO controls.

extract_protocol:
P2683
The RNAs of all the samples have been extracted using the Macherey-Nagel NucleoSpin RNA Plus Kit (Ref. 740984.250) and stored at -80*
P2683 : Total RNA-Seq libraries were generated from 700 ng of total RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 8 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.  P2988 : RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and IDT for Illumina - TruSeq RNA UD Indexes (Illumina, San Diego, USA), according to manufacturer's instructions with minor modifications. Following polyA selection, mRNAs were fragmented at 94oC for 8 minutes. DNA library were amplified using 12 cycles of PCR. Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).  P3057 : Total RNA-Seq libraries were generated from 500 ng of total RNA. Before cDNA synthesis, cytoplasmic and mitochondrial ribosomal RNA (rRNA) were removed using a biotin-streptavidin magnetic bead-based procedure with the riboPOOL kit targeting h/m/r ribosomal rRNA (siTOOLs Biotech, Planegg/Martinsried, DE) according to manufacturer's instructions. Ribodepleted RNAs were purified using Agencourt RNAClean XP (Beckman-Coulter, Villepinte, France) and eluted in 8,5 µl ELB buffer (Illumina, San Diego, USA). Purified RNAs were then processed using Illumina TruSeq Stranded Total RNA Library Prep Gold and IDT for Illumina - TruSeq RNA UD Indexes, omitting the ribodepletion step and starting directly from the fragmentation step. RNAs were fragmented at 94oC for 8 minutes. DNA library were amplified using 13 cycles of PCR. Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter) and the final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).

value: Undifferentiated melanoma

value: WT

value: DMSO 8h


title: PBMCs from sample C1-6_Memory_CD8

description: PBMCs from sample C1-6_Memory_CD8


title: PBMCs from sample C1-6_Memory_CD4

description: PBMCs from sample C1-6_Memory_CD4


title: PBMCs from sample C1-4_Naive_CD4

description: PBMCs from sample C1-4_Naive_CD4


title: PBMCs from sample C1-5_Memory_CD8

description: PBMCs from sample C1-5_Memory_CD8


title: hMeRIP, WT, 0-12h Embryo


title: PBMCs from sample C1-4_Memory_CD8

description: PBMCs from sample C1-4_Memory_CD8


title: PBMCs from sample C1-5_Naive_CD4

description: PBMCs from sample C1-5_Naive_CD4


title: MM029 Ecub Rep 2

value: Ecubectedin 10xIC50, 8h


title: PBMCs from sample C1-4_Naive_CD8

description: PBMCs from sample C1-4_Naive_CD8


title: PBMCs from sample C1-5_Naive_CD8

description: PBMCs from sample C1-5_Naive_CD8


title: MM029 DMSO Rep 1


title: MM029 Lurbi Rep 2

value: Lurbinectedin 10xIC50, 8h


title: PBMCs from sample C1-3_Naive_CD8

description: PBMCs from sample C1-3_Naive_CD8


title: MM074 Ecub Rep 2

value: Differentiated melanoma


title: MM029 Ecub Rep 1


title: PBMCs from sample C1-3_Memory_CD8

description: PBMCs from sample C1-3_Memory_CD8


title: MM029 Comp Rep 1

value: CompIA 10xIC50, 8h


title: MM074 DMSO Rep 2


title: MM029 Lurbi Rep 1


title: PBMCs from sample C1-4_Memory_CD4

description: PBMCs from sample C1-4_Memory_CD4

value: PBMCs


title: MM074 Comp Rep 2


title: MM074 Lurbi Rep 2


title: PBMCs from sample C1-3_Naive_CD4

description: PBMCs from sample C1-3_Naive_CD4


title: PBMCs from sample C1-2_Naive_CD4

description: PBMCs from sample C1-2_Naive_CD4


title: PBMCs from sample C1-3_Memory_CD4

description: PBMCs from sample C1-3_Memory_CD4


title: PBMCs from sample C1-2_Naive_CD8

description: PBMCs from sample C1-2_Naive_CD8


title: MM029 Comp Rep 2


title: MM074 Ecub Rep 1


title: PBMCs from sample C1-2_Memory_CD8

description: PBMCs from sample C1-2_Memory_CD8


title: MM074 Comp Rep 1


title: PBMCs from sample C1-1_Memory_CD4

description: PBMCs from sample C1-1_Memory_CD4


title: PBMCs from sample C1-1_Naive_CD4

description: PBMCs from sample C1-1_Naive_CD4


title: PBMCs from sample C1-2_Memory_CD4

description: PBMCs from sample C1-2_Memory_CD4


title: MM074 DMSO Rep 1


title: MM074 Lurbi Rep 1


title: PBMCs from sample C1-10_Memory_CD8

description: PBMCs from sample C1-10_Memory_CD8


title: SOLINA,4do,sig2-2,Stroma,Rep1

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM

data_processing:
Reads were adapter trimmed using Trim-galore v0.4.1
Mapping was performed using Bowtie2 v2.2.8.9 with normal paired reads and no errors were allowed
Read counts on defined genomic regions were determined using bedtools v.2.25.0
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: Genome coverage per nucleotide is included for all the datasets in txt format

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Seeds were stratified in darkness at 4ºC for 48 hours, and for fourteen days-old plants, they grown on soil at 22ºC under white LED light (100 umol m-2 s-1) in 16h/8h day/night Cycle. For four days-old plants they were grown on 0.5X MS plates under continuous light (100 umol m-2 s-1).

extract_protocol:
Fifty 4-5 days-old seedlings were harvested, crosslinked with 4 % formaldehyde for 4 hours, and homogenized in chloroplast enrichment buffer (0.33 M Sorbitol, 30 mM HEPES-KOH (pH 7.5), 0.001% beta-mercaptoethanol) using a pestle. The homogenate was filtered through two layers of miracloth, and centrifuged at 1500 g for 5 minutes at 4ºC. The pelleted chloroplasts were resuspended in 1 ml of chloroplast enrichment buffer.
Sequencing libraries were prepared as reported (Bowman, et al. 2013, BMC Genomics, 14:466).

value: Seedling

value: Chloroplast

value: wild type


title: SOLINA,4do,sig2-2,Membrane,Rep4


title: SOLINA,4do,sig2-2,Stroma,Rep4


title: SOLINA,4do,sig2-2,Stroma,Rep3


title: PBMCs from sample C1-1_Memory_CD8

description: PBMCs from sample C1-1_Memory_CD8


title: SOLINA,4do,sig2-2,Stroma,Rep2


title: SOLINA,4do,sig2-2,Membrane,Rep3


title: PBMCs from sample C1-10_Naive_CD8

description: PBMCs from sample C1-10_Naive_CD8


title: PBMCs from sample C1-10_Naive_CD4

description: PBMCs from sample C1-10_Naive_CD4


title: PBMCs from sample C1-10_Memory_CD4

description: PBMCs from sample C1-10_Memory_CD4


title: SOLINA,4do,Col0,Stroma,Rep3


title: PBMCs from sample B9-9_Memory_CD4

description: PBMCs from sample B9-9_Memory_CD4


title: PBMCs from sample C1-1_Naive_CD8

description: PBMCs from sample C1-1_Naive_CD8


title: SOLINA,4do,Col0,Stroma,Rep1


title: PBMCs from sample B9-9_Naive_CD8

description: PBMCs from sample B9-9_Naive_CD8


title: PBMCs from sample B9-9_Memory_CD8

description: PBMCs from sample B9-9_Memory_CD8


title: SOLINA,4do,Col0,Stroma,Rep4


title: PBMCs from sample B9-9_Naive_CD4

description: PBMCs from sample B9-9_Naive_CD4


title: SOLINA,4do,Col0,Membrane,Rep4


title: PBMCs from sample B9-8_Naive_CD4

description: PBMCs from sample B9-8_Naive_CD4


title: SOLINA,4do,Col0,Stroma,Rep2


title: PBMCs from sample B9-8_Naive_CD8

description: PBMCs from sample B9-8_Naive_CD8


title: SOLINA,4do,Col0,Membrane,Rep3


title: SOLINA,4do,Col0,Membrane,Rep1


title: SOLINA,4do,Col0,Membrane,Rep2


title: PBMCs from sample B9-7_Naive_CD4

description: PBMCs from sample B9-7_Naive_CD4


title: SOLINA,4do,chlm,Stroma,Rep2

value: chlm


title: PBMCs from sample B9-8_Memory_CD8

description: PBMCs from sample B9-8_Memory_CD8


title: SOLINA,4do,chlm,Stroma,Rep1


title: SOLINA,4do,sig2-2,Membrane,Rep1


title: SOLINA,4do,sig2-2,Membrane,Rep2


title: PBMCs from sample B9-6_Naive_CD8

description: PBMCs from sample B9-6_Naive_CD8


title: SOLINA,4do,chlm,Stroma,Rep3


title: PBMCs from sample B9-8_Memory_CD4

description: PBMCs from sample B9-8_Memory_CD4


title: SOLINA,4do,chlm,Membrane,Rep4


title: SOLINA,4do,chlm,Membrane,Rep3


title: PBMCs from sample B9-7_Memory_CD4

description: PBMCs from sample B9-7_Memory_CD4


title: SOLINA,4do,chlm,Membrane,Rep1


title: PBMCs from sample B9-6_Memory_CD8

description: PBMCs from sample B9-6_Memory_CD8


title: PBMCs from sample B9-5_Naive_CD8

description: PBMCs from sample B9-5_Naive_CD8


title: PBMCs from sample B9-6_Naive_CD4

description: PBMCs from sample B9-6_Naive_CD4


title: PBMCs from sample B9-7_Memory_CD8

description: PBMCs from sample B9-7_Memory_CD8


title: SOLINA,4do,chlm,Membrane,Rep2


title: PBMCs from sample B9-6_Memory_CD4

description: PBMCs from sample B9-6_Memory_CD4


title: PBMCs from sample B9-7_Naive_CD8

description: PBMCs from sample B9-7_Naive_CD8


title: SOLINA,4do,chl27,Stroma,Rep3


title: PBMCs from sample B9-5_Naive_CD4

description: PBMCs from sample B9-5_Naive_CD4


title: SOLINA,4do,chl27,Stroma,Rep2


title: PBMCs from sample B9-5_Memory_CD8

description: PBMCs from sample B9-5_Memory_CD8


title: SOLINA,4do,chl27,Membrane,Rep4


title: SOLINA,4do,chl27,Stroma,Rep1


title: SOLINA,4do,chlm,Stroma,Rep4


title: PBMCs from sample B9-4_Naive_CD8

description: PBMCs from sample B9-4_Naive_CD8


title: SOLINA,4do,chl27,Membrane,Rep3


title: PBMCs from sample B9-4_Naive_CD4

description: PBMCs from sample B9-4_Naive_CD4


title: SOLINA,4do,chl27,Membrane,Rep2


title: PBMCs from sample B9-4_Memory_CD8

description: PBMCs from sample B9-4_Memory_CD8


title: SOLINA,4do,chl27,Membrane,Rep1


title: PBMCs from sample B9-3_Naive_CD4

description: PBMCs from sample B9-3_Naive_CD4


title: PBMCs from sample B9-4_Memory_CD4

description: PBMCs from sample B9-4_Memory_CD4


title: PBMCs from sample B9-3_Naive_CD8

description: PBMCs from sample B9-3_Naive_CD8


title: IPOD,4do,pTAC3,IPOD,Rep3


title: SOLINA,4do,chl27,Stroma,Rep4


title: PBMCs from sample B9-3_Memory_CD8

description: PBMCs from sample B9-3_Memory_CD8


title: IPOD,4do,pTAC3,input,Rep3


title: PBMCs from sample B9-3_Memory_CD4

description: PBMCs from sample B9-3_Memory_CD4


title: PBMCs from sample B9-5_Memory_CD4

description: PBMCs from sample B9-5_Memory_CD4


title: IPOD,4do,pTAC3,input,Rep2


title: IPOD,4do,pTAC3,input,Rep1


title: PBMCs from sample B9-2_Memory_CD8

description: PBMCs from sample B9-2_Memory_CD8


title: PBMCs from sample B9-2_Naive_CD4

description: PBMCs from sample B9-2_Naive_CD4


title: IPOD,4do,Col0,IPOD,Rep2


title: IPOD,4do,Col0,IPOD,Rep3


title: PBMCs from sample B9-1_Naive_CD8

description: PBMCs from sample B9-1_Naive_CD8


title: PBMCs from sample B9-2_Memory_CD4

description: PBMCs from sample B9-2_Memory_CD4


title: IPOD,4do,Col0,IPOD,Rep1


title: IPOD,4do,Col0,input,Rep3


title: IPOD,4do,Col0,input,Rep2


title: PBMCs from sample B9-1_Memory_CD8

description: PBMCs from sample B9-1_Memory_CD8


title: PBMCs from sample B9-1_Naive_CD4

description: PBMCs from sample B9-1_Naive_CD4


title: IPOD,4do,pTAC3,IPOD,Rep2


title: PBMCs from sample B9-1_Memory_CD4

description: PBMCs from sample B9-1_Memory_CD4


title: PBMCs from sample B9-12_Naive_CD4

description: PBMCs from sample B9-12_Naive_CD4


title: PBMCs from sample B9-12_Naive_CD8

description: PBMCs from sample B9-12_Naive_CD8


title: PBMCs from sample B9-12_Memory_CD8

description: PBMCs from sample B9-12_Memory_CD8


title: IPOD,4do,pTAC3,IPOD,Rep1


title: PBMCs from sample B9-12_Memory_CD4

description: PBMCs from sample B9-12_Memory_CD4


title: PBMCs from sample B9-11_Naive_CD8

description: PBMCs from sample B9-11_Naive_CD8


title: PBMCs from sample B9-2_Naive_CD8

description: PBMCs from sample B9-2_Naive_CD8


title: ChIP,4do,sig2-2,input,Rep3


title: ChIP,4do,sig2-2,ChIP,Rep1


title: ChIP,4do,sig2-2,ChIP,Rep2


title: ChIP,4do,sig2-2,input,Rep2


title: PBMCs from sample B9-11_Naive_CD4

description: PBMCs from sample B9-11_Naive_CD4


title: ChIP,4do,sig2-2,input,Rep1


title: PBMCs from sample B9-11_Memory_CD8

description: PBMCs from sample B9-11_Memory_CD8


title: PBMCs from sample B9-11_Memory_CD4

description: PBMCs from sample B9-11_Memory_CD4


title: ChIP,4do,Col0,ChIP,Rep3


title: PBMCs from sample B9-10_Naive_CD8

description: PBMCs from sample B9-10_Naive_CD8


title: ChIP,4do,Col0,ChIP,Rep1


title: IPOD,4do,Col0,input,Rep1


title: ChIP,4do,Col0,input,Rep3


title: PBMCs from sample B9-10_Naive_CD4

description: PBMCs from sample B9-10_Naive_CD4


title: ChIP,4do,Col0,input,Rep1


title: ChIP,4do,sig22-,ChIP,Rep3


title: ChIP,4do,Col0,input,Rep2


title: PBMCs from sample B9-10_Memory_CD8

description: PBMCs from sample B9-10_Memory_CD8


title: ChIP,4do,chlm,ChIP,Rep3


title: PBMCs from sample B9-10_Memory_CD4

description: PBMCs from sample B9-10_Memory_CD4


title: ChIP,4do,chlm,ChIP,Rep2


title: PBMCs from sample B8-9_Memory_CD8

description: PBMCs from sample B8-9_Memory_CD8


title: ChIP,4do,chlm,ChIP,Rep1


title: PBMCs from sample B8-9_Memory_CD4

description: PBMCs from sample B8-9_Memory_CD4


title: PBMCs from sample B8-8_Naive_CD8

description: PBMCs from sample B8-8_Naive_CD8


title: ChIP,4do,chlm,input,Rep3


title: ChIP,4do,chlm,input,Rep2


title: ChIP,4do,chlm,input,Rep1