title: DMS-MaPseq on ex vivo native deproteinized E. coli total RNA (Replicate #2)

description: E. coli ex vivo (Replicate #2)


title: LLC cells wild type - replica 1

status: Public on May 05 2019

type: SRA

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence
Paired-end reads were mapped against the mouse reference genome (GRCm38.p4/mm10) using the STAR software to generate read alignments.
The annotation file Mus_musculus.GRCm38.84.gtf was obtained from the ftp.Ensembl.org server
Following transcript assembly, gene level counts were obtained using HTSeq
Genome_build: GRCm38.p4/mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: Wild type Lewis lung carcinoma cells

growth_protocol: LLC cells were inoculated subcutaneously into the back of syngeneic C57BL/6 mice. Tumors were collected after 5 days for further analysis.

extract_protocol:
Tumor tissue was lysed in TRIzol reagent (Life Technologies, Carlsbad, CA, US). Total RNA was extracted with the RNAeasy micro kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Truseq RNA Illumina protocols

tag: strain

tag: cells

value: Lewis lung carcinoma cells

tag: genotype

value: wild type

tag: tumor stage

value: 5 days following graft subcutaneously


title: LLC cells expressing chemerin - replica 2

source_name: Lewis lung carcinoma cells expressing bioactive chemerin

value: cells transfected  with pEFIN plasmids encoding full size murine chemerin (1-157)


title: LLC cells expressing chemerin - replica 1


title: DMS-MaPseq on untreated in vivo-purified Influenza A vmRNA

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description: Influenza untreated in vivo

data_processing:
Library strategy: DMS-MaPseq
All the relevant analysis steps, from reads alignment to data normalization and structure modeling, were performed using the RNA Framework (Incarnato et al., 2018). Briefly, sequencing reads were clipped from adapter sequences and terminal positions with Phred qualities <20 were trimmed. Alignment was performed using the rf-map tool and the Bowtie v2 algorithm (Langmead et al., 2012), with soft-clipping enabled (parameters: -b2 -cp -b5 5 -mp "--very-sensitive-local"). Before proceeding to DMS-MaPseq data analysis, sequencing of an untreated IAV sample was performed in order to annotate eventual mutations with respect to the reference strain. Positions with mutations exceeding a frequency of 50% were annotated. All the subsequent analysis steps were then performed using this updated reference. Per-base mutation count and coverage were calculated using the rf-count tool (parameters: -nm -r -m -mq 0 -na -md 3 -ni). A ratiometric score was then calculated as ri = (mi / Ci) where ri, mi, and Ci are respectively the raw reactivity, the mutation count and the coverage at position i. Reactivity normalization was performed as a 2-step process. First, each sample was normalized by 90% Winsorizing, in order to smooth the contribution of both over and under-reactive residues, using the rf-norm tool (parameters: -sm 4 -nm 2 -rb AC). Briefly, each reactivity value above the 95th percentile was set to the 95th percentile and each reactivity value below the 5th percentile was set to the 5th percentile, then the reactivity at each position of the transcript was divided by the value of the 95th percentile. Reactivity data from targeted DMS-MaPseq analysis of probe pairing regions was independently Winsorized and then used to replace original RAPiD-MaPseq data. Second, both the in vitro and the in vivo datasets were normalized to the respective denatured controls as Ri = min(Si/Di,1) where Ri, Si, and Di are respectively the normalized reactivity, the sample reactivity (either in vivo or in vitro), and the denatured control reactivity at position i. This normalization yielded reactivity values comprised between 0 (low single-strandedness probability) and 1 (high single-strandedness probability). Given the high correlation of all the datasets, biological replicates were combined using the rf-combine utility following normalization. Combined datasets were then used for all downstream analyses.
Genome_build: A/Puerto Rico/8/1934(H1N1) from NC_002016 to NC_002023
Supplementary_files_format_and_content: For each DMS-MaPseq sample (but the untreated controls) a Wiggle track file is provided, reporting the mutation frequency of A/C residues for each Influenza A vmRNA. For the untreated controls, a multi-Fasta file is provided with the sequence of Influenza A vmRNAs, annotated with the detected SNVs. Additional processed files are available at: http://www.incarnatolab.com/datasets/IAV_Simon_2019.php

organism: Influenza A virus

source_name: A/Puerto Rico/8/1934(H1N1)

growth_protocol: Confluent MDCK cells (Sigma Aldrich, #84121903-1VL) in a 10cm cell culture dish were infected with Influenza A virus (A/Puerto Rico/8/1934(H1N1)) at an MOI of 1 in DMEM, 0.14 % BSA and 1 µg/ml TPCK-Trypsin for 6h at 37 °C.

extract_protocol:
50 mg of total RNA were used for poly(A)-enrichment with Dynabeads Oligo(dT)25 (Thermo Fisher Scientific, #61002). The isolated poly(A) RNA was used as input for the viral mRNA capture using biotinylated DNA probes (1 probe for each segment with a length of 80 nt complementary to viral mRNA, for sequences refer to Table S1). 100 ml of Dynabeads MyOne Streptavidin T1 beads (ThermoFisher Scientific, #65601) were washed twice with 500 µl Wash Buffer 2 [100 mM NaOH; 50 mM NaCl], twice with 500 µl Wash Buffer 3 [100 mM NaCl], and resuspended in 200 ml 2X Binding & Wash Buffer 1 [10 mM Tris-HCl pH 7.5; 2 M NaCl; 1 mM EDTA]. 5 ml of an equimolar mix of all 8 probes (100 mM pool) in 200 ml water were denatured at 85 °C for 3 min, then immediately placed on ice and added to the washed beads. Probes were immobilized on beads for 20 min at 37 °C, with vigorous shaking. Beads were then washed twice with 500 µl 1x Binding & Wash Buffer 1 and resuspended in 100 µl RNA Binding Buffer [20 mM Tris-HCl pH 7.5; 1 M LiCl; 2 mM EDTA]. To the poly(A)-enriched RNA in 100 µl water, 100 µl RNA binding buffer were added and the sample was denatured at 70 °C for 5 min and immediately placed on ice. Washed beads, supplemented with 40 U of SUPERase In RNase Inhibitor, were then added to the poly(A) RNA and binding was allowed to occur at 37 °C for 2 h, with vigorous shaking. Samples were washed twice with 1 ml of Wash Buffer A (10 mM Tris-HCl pH 7.5; 150 mM LiCl; 1 mM EDTA; 0.1 % SDS] and once with 1 ml Wash Buffer B [10 mM Tris-HCl pH 7.5; 150 mM LiCl; 1 mM EDTA]. Beads were resuspended in 100 µl 95% formamide and 10 mM EDTA pH 8.0, and incubated at 90 °C for 10 min. Eluted RNA was separated from the beads and purified with 1 ml of TRIzol. To remove residual DNA probes, the eluate was treated with DNase I for 15 min at 37 °C and further purified on RNA Clean & Concentrator-5 columns.
RNA was fragmented in 64 mM Tris-HCl pH 8.3, 96 mM KCl, 3.9 mM MgCl2 for 8 min at 94 °C and subsequently purified on RNA Clean & Concentrator-5 columns. Reverse transcription (RT) was performed using the TGIRT-III enzyme (InGex, #TGIRT50) as described previously (Zubradt et al., 2016). Briefly, to the 5 µl of fragmented RNA, 1 µl 10 mM dNTPs and 0.5 µl 10 µM random hexamers were added, and the mixture was heated to 70 °C for 5 min and immediately placed on ice for 1 min. 2 µl of 5X RT Buffer [250 mM Tris-HCl pH 8.3; 375 mM KCl; 15 mM MgCl2], DTT to 5 mM, 10 U SUPERase In RNase Inhibitor, and 100 U TGIRT-III were added. Reverse transcription was then allowed to proceed at 25 °C for 5 min, followed by 1.5 h at 57 °C. To remove TGIRT-III from the RNA-DNA duplex, 1 µl of proteinase K was added to a final concentration of 0.1 µg/µl and the reaction incubated at 37 °C for 15 min., 1 µl of a 1:2 dilution of protease inhibitor cocktail (Sigma Aldrich, #P8340) was then added to inhibit proteinase K activity. The reaction volume was then adjusted to 25 µl by adding 3 µl of 5X RT Buffer and 10 µl water. Libraries were then prepared using the TruSeq RNA Library Prep Kit v2 (Illumina, #15025063), starting from second strand synthesis.

value: A/Puerto Rico/8/1934(H1N1)


title: DMS-MaPseq on in vivo Influenza A vmRNA mutated structural motifs

description: Influenza A mutated in vivo

extract_protocol:
Cells were collected by centrifugation and total RNA extracted with TRIzol Reagent (ThermoFisher Scientific, #15596018). After phase separation, the aqueous phase was added to 1 ml of 100% ethanol and the RNA purified on RNA Clean & Concentrator-5 columns (Zymo Research, #R1016).
RT reactions were performed using the TGIRT-III reverse transcriptase in 20 µl total reaction volume, using 50 µM of a specific primer (except for segment 5 for which an oligodT primer with an overhang was used). PCR was then performed on the resulting cDNA using specific primers amplifying a region of ~250-300 bp centered on the mutated domains. PCR products were pooled equimolarly and fragmented by sonication. Sonicated DNA was gel purified to remove residual full-length products and subjected to library preparation using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs, #E6240L) according to manufacturer’s instructions, but omitting size selection.

treatment_protocol: Cell pellets were resuspended in 1 ml of RNA probing buffer (RPB) [50 mM HEPES pH 7.9; 140 mM NaCl; 3 mM KCl] and pre-equilibrated at 30 °C for 5 min. 1.76 M DMS in ethanol was added to a final concentration of 100 mM. After gentle vortexing, probing was allowed to proceed at 30 °C for 3 min with moderate shaking. Reactions were quenched by addition of DTT to a final concentration of 0.7 M. Cells were collected at 2000 x g (4 °C) for 3 min and subsequently washed once with PBS/0.7 M DTT.


title: DMS-MaPseq on in vivo spliced segment 7/8 Influenza A vmRNAs (Replicate #2)

description: Influenza A spliced in vivo (Replicate #2)

growth_protocol: Confluent MDCK cells (Sigma Aldrich, #84121903-1VL) in a 10cm cell culture dish were infected with Influenza A virus (A/Puerto Rico/8/1934(H1N1)) at an MOI of 5 in DMEM, 0.14 % BSA and 1 µg/ml TPCK-Trypsin for 6h at 37 °C.

extract_protocol:
Cells were collected by centrifugation and total RNA extracted with TRIzol Reagent (ThermoFisher Scientific, #15596018). After phase separation, the aqueous phase was added to 1 ml of 100% ethanol and the RNA purified on RNA Clean & Concentrator-5 columns (Zymo Research, #R1016).
RT reactions were performed in 20 µl total reaction volume. An anchored oligo(dT) primer with overhang for subsequent PCR was used at a final concentration of 50 µM. The reaction was allowed to proceed at 57 °C for 2 h. Afterwards, RNA was degraded by adding 1 µl 5 M NaOH and heating to 95 °C for 3 min and subsequently purified on RNA Clean & Concentrator-5 columns. Short splice isoforms were then specifically amplified via PCR and gel purified. The short splice isoforms were mixed equimolarly and fragmented by sonication to yield fragments in the range of 100-300 bp. Sonicated DNA was gel purified to remove residual full-length products and subjected to library preparation using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs, #E6240L) according to manufacturer’s instructions, but omitting size selection.

treatment_protocol: Cell pellets were resuspended in 1 ml of RNA probing buffer (RPB) [50 mM HEPES pH 7.9; 140 mM NaCl; 3 mM KCl] and pre-equilibrated at 30 °C for 5 min. 1.76 M DMS in ethanol was added to a final concentration of 50 mM. After gentle vortexing, probing was allowed to proceed at 30 °C for 3 min with moderate shaking. Reactions were quenched by addition of DTT to a final concentration of 0.7 M. Cells were collected at 2000 x g (4 °C) for 3 min and subsequently washed once with PBS/0.7 M DTT.


title: DMS-MaPseq on in vivo spliced segment 7/8 Influenza A vmRNAs (Replicate #1)

description: Influenza A spliced in vivo (Replicate #1)


title: ameiotic1 (praI) maize anthers, male sterile, 1.5 mm rep 3.

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

country: USA

institute: Donald Danforth Plant Science Center

data_processing:
All reads from small RNA, PARE or RNA-seq libraries were trimmed to remove adapter sequences using a Perl script.
Genome_build: None
Supplementary_files_format_and_content: Flat file with tab separated reads and abundance counts

organism: Zea mays

source_name: maize anthers

extract_protocol:
Total RNA was isolated using Tri reagent (Molecular Research Center, Cincinnati, OH) or Plant RNA Reagent (Invitrogen, Carlsbad, CA).
Small RNA and RNA-seq libraries were constructed using TruSeq™ Small RNA Sample Prep Kit and TruSeq™ RNA Sample Prep Kit (Illumina, San Diego, CA). PARE libraries were constructed as previously described. All libraries were sequenced on an Illumina Hi-Seq 2000 instrument

tag: tissue

value: male sterile 15 mm

value: ameiotic1 (praI)


title: DMS-MaPseq on in vitro-transcibed and refolded Influenza A vmRNA (Replicate #2)

description: Influenza A in vitro (Replicate #2)

extract_protocol:
A T7 promoter was introduced 5’ to each segment via PCR using pDZ-PB2, PB1, PA, HA, NP, NA, M1/2, NS1/NEP plasmids as a template. Segments were then in vitro transcribed using T7-FlashScribe kit (CellScript, #C-ASF3507). Transcription products were verified by capillary electrophoresis on a Fragment Analyzer (Advanced Analytical). For in vitro refolding, segments were pooled equimolarly and 240 ng of the pool were used per replicate.
RNA was fragmented in 64 mM Tris-HCl pH 8.3, 96 mM KCl, 3.9 mM MgCl2 for 8 min at 94 °C and subsequently purified on RNA Clean & Concentrator-5 columns. Reverse transcription (RT) was performed using the TGIRT-III enzyme (InGex, #TGIRT50) as described previously (Zubradt et al., 2016). Briefly, to the 5 µl of fragmented RNA, 1 µl 10 mM dNTPs and 0.5 µl 10 µM random hexamers were added, and the mixture was heated to 70 °C for 5 min and immediately placed on ice for 1 min. 2 µl of 5X RT Buffer [250 mM Tris-HCl pH 8.3; 375 mM KCl; 15 mM MgCl2], DTT to 5 mM, 10 U SUPERase In RNase Inhibitor, and 100 U TGIRT-III were added. Reverse transcription was then allowed to proceed at 25 °C for 5 min, followed by 1.5 h at 57 °C. To remove TGIRT-III from the RNA-DNA duplex, 1 µl of proteinase K was added to a final concentration of 0.1 µg/µl and the reaction incubated at 37 °C for 15 min., 1 µl of a 1:2 dilution of protease inhibitor cocktail (Sigma Aldrich, #P8340) was then added to inhibit proteinase K activity. The reaction volume was then adjusted to 25 µl by adding 3 µl of 5X RT Buffer and 10 µl water. Libraries were then prepared using the TruSeq RNA Library Prep Kit v2 (Illumina, #15025063), starting from second strand synthesis.

treatment_protocol: RNA in 15.3 µl was heated to 95 °C for 2 min and immediately placed on ice for 1 min. 9 µl of 3.3X Folding Buffer [333 mM HEPES pH 7.9; 333 mM NaCl] were added and the sample incubated at 37 °C for 10 min before addition of 2.7 µl of 100 mM MgCl2 pre-warmed to 37 °C, and additional incubation at 37 °C for 20 min. For probing, 1.76 M DMS in 100% ethanol was added to 200 mM and probing allowed to occur at 30 °C for 2 min, with moderate shaking. Reactions were quenched by addition of DTT to 0.7 M and purified on RNA Clean & Concentrator-5 columns.


title: AP2-FG ChIP-seq experiment-1 INPUT

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

library_source: genomic

data_processing:
Reads were mapped on the P. berghei genome with allowing one mismatch within 60 bp sequence using Bowtie 2.0. Bedgraph files were ceated from the mapping data (IP).
The mapping data were analyzed with the MACS2 peak-calling algorithm using  approximately5.45 × 106  in the experiment-1 and 9.74 × 106 in the experiment-2, respectively.). Numbers of INPUT reads used for normalization were 138 × 107 in the experiment-1 and 1.62 × 107 in the experiment-2, respectively. Conditions for peak calling included an FDR < 0.01 in both experiments.
Genome_build: PlasmoDB, version 9.1
Supplementary_files_format_and_content: Mapping data, bedgraph; Peak-calling, text.

molecule: genomic DNA

organism: Plasmodium berghei ANKA

source_name: AP2-FG ChIP-seq experiment-1 INPUT

growth_protocol: Balb/c mice were infected with P. berghei expressing GFP-fused AP2-FG.

extract_protocol:
The infected whole blood was fixed immediately with formalin (1% in final concentration), and erythrocytes were depleted by lysis in 0.85% NH4Cl with changing the solution several times. ChIP was performed according to the protocol in “Standard protocols on Next Generation Sequencing” (edited by Ai Nikaido, Yodosha Co., Ltd., 2014). Briefly, chromatin was sheared by sonication using Bioruptor. Chromatin was IPed with anti-GFP polyclonal antibodies (Abcam) conjugated to Dynabeads Protein A (Life Technologies, Gaithersburg, MD).  Obtained DNA fragments were sequenced by the illumina NextSeq sequencer.
Single read - illumina NextSeq 500

treatment_protocol: Six mice were infected with AP2-FG::GFP parasites and treated with sulfadiazine in drinking water (10 mg/ml) for depletion of asexual blood stages.

tag: Stage

value: gametocyte

value: ANKA

value: GFP-fused AP2-FG expressing


title: DMS-MaPseq on denatured E. coli total RNA (Replicate #2)

description: E. coli denatured (Replicate #2)

organism: Escherichia coli

growth_protocol: LB medium, 37°C, 300 RPM

extract_protocol:
Cell pellets from exponential phase E. coli were resuspended in 1 ml of Resuspension Buffer [15 mM Tris-HCl pH 8.0; 450 mM Sucrose; 8 mM EDTA], and 18,500 U of Ready-Lyse Lysozyme (Epicentre, #R1810M) were added. After incubation at 22 °C for 5 min and on ice for 10 min, protoplasts were collected by centrifugation at 5000 x g (4 °C) for 5 min. Pellets were resuspended in 120 µl Protoplast Lysis Buffer [50 mM HEPES pH 8.0; 200 mM NaCl; 5 mM MgCl2; 1.5% SDS]. Samples were incubated for 5 min at 22 °C and for 5 min on ice, followed by addition of 30µl SDS precipitation buffer (50mM HEPES pH8, 1M KOAc, 5mM MgCl2). The precipitate was removed by centrifugation at 17000g (4 °C) for 5min and the supernatant was then extracted with TRIzol reagent, as per manufacturer instructions.
RNA was fragmented in 64 mM Tris-HCl pH 8.3, 96 mM KCl, 3.9 mM MgCl2 for 8 min at 94 °C and subsequently purified on RNA Clean & Concentrator-5 columns. Reverse transcription (RT) was performed using the TGIRT-III enzyme (InGex, #TGIRT50) as described previously (Zubradt et al., 2016). Briefly, to the 5 µl of fragmented RNA, 1 µl 10 mM dNTPs and 0.5 µl 10 µM random hexamers were added, and the mixture was heated to 70 °C for 5 min and immediately placed on ice for 1 min. 2 µl of 5X RT Buffer [250 mM Tris-HCl pH 8.3; 375 mM KCl; 15 mM MgCl2], DTT to 5 mM, 10 U SUPERase In RNase Inhibitor, and 100 U TGIRT-III were added. Reverse transcription was then allowed to proceed at 25 °C for 5 min, followed by 1.5 h at 57 °C. To remove TGIRT-III from the RNA-DNA duplex, 1 µl of proteinase K was added to a final concentration of 0.1 µg/µl and the reaction incubated at 37 °C for 15 min., 1 µl of a 1:2 dilution of protease inhibitor cocktail (Sigma Aldrich, #P8340) was then added to inhibit proteinase K activity. The reaction volume was then adjusted to 25 µl by adding 3 µl of 5X RT Buffer and 10 µl water. Libraries were then prepared using the TruSeq RNA Library Prep Kit v2 (Illumina, #15025063), starting from second strand synthesis.

treatment_protocol: RNA was heated to 95 °C for 1 min in a total volume of 90 µl with 55 mM HEPES pH 7.9, 4.4 mM EDTA, 55% formamide. 10 µl of 0.5 M DMS in ethanol were then added to obtain a probing concentration of 50 mM. Probing was allowed to proceed at 95 °C for 1 min. Reactions were quenched by adding 200 µl RNA Binding Buffer (from RNA Clean & Concentrator-5 columns) supplemented with DTT to a final concentration of 750 mM. Samples were then purified on RNA Clean & Concentrator-5 columns.


title: DMS-MaPseq on in vivo-purified Influenza A vmRNA (Replicate #1)

description: Influenza A in vivo (Replicate #1)

treatment_protocol: Cell pellets were resuspended in 1 ml of RNA probing buffer (RPB) [50 mM HEPES pH 7.9; 140 mM NaCl; 3 mM KCl] and pre-equilibrated at 30 °C for 5 min. 1.76 M DMS in ethanol was added to a final concentration of 200 mM. After gentle vortexing, probing was allowed to proceed at 30 °C for 3 min with moderate shaking. Reactions were quenched by addition of DTT to a final concentration of 0.7 M. Cells were collected at 2000 x g (4 °C) for 3 min and subsequently washed once with PBS/0.7 M DTT.


title: ZB24-KD3

city: Suzhou

first: Jun

last: Wang

state: Jiangsu

address: 199 Ren-Ai Rd, Suzhou University,, Suzhou Industrial Park,

country: China

institute: Soochow University

data_processing:
Raw reads are filtered to clean reads as follows: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads (we define the low quality base to be the base whose sequencing quality is no more than 5).
Clean reads are mapped to reference using HISAT/Bowtie2 tool.
Quantifications of gene expression were performed using RSEM.
Differential expressions between two groups with three independent replicates were compared via Deseq.
Genome_build: hg19

organism: Homo sapiens

source_name: Immortalized T cells

growth_protocol: All cells were cultured in RPMI-1640 medium (Hyclone) supplemented with 10% heat-inactivated fetal bovine serum (FBS, BI), 100 U/ml penicillin and 100 mg/ml streptomycin (Beyotime) at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Total cellular RNA was extracted with the Total RNA Kit II (OMEGA).
Library construction and sequencing was performed on a BGISEQ-500 by Beijing Genomics Institution (BGI) in Wuhan, China. Oligo (dT) magnetic beads are used to select mRNA with polyA tail, or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: Jurkat cells (1.0 x 105/well) were cultured in 48-well plate overnight. Then cells were incubated with medium containing lentiviral particles (multiplicity of infection (MOI) =10) and 5 mg/ml polybrene (Sigma-Aldrich), and were centrifuged for 99 mins at 500 g at 30 oC. Four to five days post-infection, GFP positive cells were purified via a FACS Aria cell sorter III (BD Biosciences) with purities typically greater than 95%. The analyzing & sorting gates were restricted to the living cells as determined by the forward and side scatter properties.

tag: cell types

value: Jurkat

tag: treatment

value: ZBTB24-knockdown virus


title: DMS-MaPseq on in vivo-purified Influenza A vmRNA (Replicate #2)

description: Influenza A in vivo (Replicate #2)


title: ZB24-KD1


title: DMS-MaPseq on in vitro-transcribed denatured Influenza A vmRNA (Replicate #2)

description: Influenza A denatured in vitro (Replicate #2)


title: TNFDEX 3

status: Public on May 06 2019

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

institute: VIB-UGent

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v1.0.0 with parameters -q -p 12 -n 0 -m 1 --best --strata
peak calling was performed using HOMER v4.6 using the 'factor' preset and with a minimum 4 fould enrichment over local background and input control
Genome_build: mm10
Supplementary_files_format_and_content: Peak files and bedgraph files were generated with the HOMER software. Bedgraph values were normalized to 1e7 tags

source_name: BWTG3 cell line

growth_protocol: cells were maintained and grown in Dulbecco’s modified Eagles medium (DMEM; house-made) containing 10% fetal calf serum (FCS), 1mM sodium pyruvate, 0.1mM non-essential amino acids and 2mM L-glutamine. Before performing experiments, cells were starved for 24h in optimem medium (Gibco, Invitrogen)

extract_protocol:
Immunoprecipitation (IP) was performed on 100μl lysates diluted 1:3 in incubation buffer.Immunoprecipitated material was collected the next day by centrifugation and washed once each with WBI, WBII, LiCl buffer, and twice with EDTA/HEPES buffer (0.5M EDTA and 1M HEPES) using spin columns with 0.35μM pore size filters (MoBiTec).The recovered DNA was purified by the PCR purification kit (Qiagen) according to the manufacturer’s protocol, eluting in 50μl of Qiagen Elution buffer
RNA libraries were prepared for sequencing using standard Illumina protocols (truseq)

treatment_protocol: Cells were then exposed to 1µM Dex (Sigma, D-2915) and/or 1000U/ml recombinant TNF (produced in E. coli and purified in our department) in optimem given 1h before Dex stimulation. Cells were stimulated for three hours in total

tag: cell type

value: mouse hepatoma derived cells

tag: chip antibody

value: rabbit anti-GR antibody; Santa Cruz Biotechnolgoy, sc-8992


title: DMS-MaPseq on in vitro-transcribed denatured Influenza A vmRNA (Replicate #1)

description: Influenza A denatured in vitro (Replicate #1)


title: ZB24-KD2


title: AP2-FG ChIP-seq experiment-2 INPUT

source_name: AP2-FG ChIP-seq experiment-2 INPUT


title: GFP3

value: Control virus


title: DMS-MaPseq on in vivo-purified denatured Influenza A vmRNA (Replicate #2)

description: Influenza A denatured in vivo (Replicate #2)


title: GFP2


title: DMS-MaPseq on in vivo Influenza A vmRNA probe pairing regions (Replicate #2)

description: Influenza A probe pairing regions in vivo (Replicate #2)

extract_protocol:
Cells were collected by centrifugation and total RNA extracted with TRIzol Reagent (ThermoFisher Scientific, #15596018). After phase separation, the aqueous phase was added to 1 ml of 100% ethanol and the RNA purified on RNA Clean & Concentrator-5 columns (Zymo Research, #R1016).
RT reactions were performed using the TGIRT-III reverse transcriptase in 20 µl total reaction volume. An anchored oligo(dT) primer with overhang for subsequent PCR was used at a final concentration of 50 µM. The reaction was allowed to proceed at 57 °C for 2 h. Afterwards, RNA was degraded by adding 1 µl 5 M NaOH and heating to 95 °C for 3 min and subsequently purified on RNA Clean & Concentrator-5 columns. Primers annealed directly before the respective probe pairing position and contained an overhang corresponding to the standard Illumina adapter . cDNA was PCR-amplified and the resulting amplicons were pooled equimolarly to 1 ng/µl. Indexed adapter sequences were further added by a second PCR enrichment step.


title: DMS-MaPseq on in vitro-transcribed and refolded Influenza A vmRNA (Replicate #1)

description: Influenza A in vitro (Replicate #1)


title: DMS-MaPseq on in vivo-purified denatured Influenza A vmRNA (Replicate #1)

description: Influenza A denatured in vivo (Replicate #1)


title: DMS-MaPseq on in vivo Influenza A vmRNA probe pairing regions (Replicate #1)

description: Influenza A probe pairing regions in vivo (Replicate #1)


title: hst34_Breakseq_rep2

status: Public on May 04 2019

city: Worcester

first: Jessica

middle: Lauren

last: Feldman

state: MA

address: 373 Plantation St

institute: UMass Medical School

description:
DNA
 MACspeaks_Breakseq_hst34vsWT.txt

data_processing:
FASTQ files from paired end libraries were collapsed by barcode and the Illumina adapter sequence was trimmed from the 3’ end.
Reads were aligned to the S. cerevisiae genome (SacCer3, SGD) using Bowtie2 with a maximum fragment length for valid paired-end alignments set to 500 bp.
Aligned reads were then filtered for quality and only uniquely mapped paired reads were used for future analyses
BAM files were uploaded to SeqMonk and normalized by scaling to 1 million reads.
MACS Peak Caller was used to identify new peaks in hst4∆ HST3-FRB biological replicates using the mean WT file as the input (p-value 1x10-5, 500 bp fragment size).
SacCer3
txt file of peaks called by MACS

organism: Saccharomyces cerevisiae

source_name: log phase S. cerevisiae

growth_protocol: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.1 to mid-log phase with an OD of 1

extract_protocol:
Cells were harvested and resuspended in 1 mL of 50 mM EDTA. Cells (50 μL) were combined with 50 μL of 1% low melting temperature agarose (Lonza).
Following in gel labeling and sonication, libraries were prepared as in (Hoffman et al., 2015). Paired-end sequencing was performed on an Illumina NextSeq 500 with a read length of 75 bp.

treatment_protocol: Rapamycin was added for 3 hours prior to harvest.

value: hst4-delta HST3-FRB

tag: protocol

value: Break-seq


title: hst34_Breakseq_rep1

description:
DNA
 MACspeaks_Breakseq_hst34vsWT.txt


title: WT_Breakseq_rep2

description:
DNA
 MACspeaks_Breakseq_hst34vsWT.txt

value: WT anchor away


title: GFP1


title: WT_Breakseq_rep1

description:
DNA
 MACspeaks_Breakseq_hst34vsWT.txt


title: WT_26h_4

type: RNA

hyb_protocol: 1.65  ug Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scannedon the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slide.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Whole blood was harvested from rats infected with AP2-FG(-) or wild-type parasites and cultured for 16 h. Mature schizonts were purified from the culture with Nicodenz  and inoculated into  Wistar rats. Whole blood was harvested from these ratsat 26 h after the innoculation.

extract_protocol: Total RNA was extracted using the RNAgents (Promega) according to the manufacturer’s protocols.

tag: genotype/variation

value: wild-type

value: blood

tag: agent

value: infected with P. berghei parasites


title: hst34_DRIPseq_RNH_rep2

description:
DNA
DRIPseq_readcounts_ORFs.xlsx
hst34_RNH_merge_DRIP.bg

data_processing:
FASTQ files from paired end libraries were collapsed by barcode and the Illumina adapter sequence was trimmed from the 3’ end.
Reads were aligned to the S. cerevisiae genome (SacCer3, SGD) using Bowtie2 with a maximum fragment length for valid paired-end alignments set to 500 bp.
Aligned reads were then filtered for quality and only uniquely mapped paired reads were used for future analyses.
Reads were scaled to 1M reads
To calculate DRIP-seq signals over genes, BEDtools was used to calculate normalized bp counts across the genome. Median read counts were then determined in 100 bp windows with a 50 bp step size. The median read counts were then summed over genes.
SacCer3
bigwig, abundance measurements

growth_protocol: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.1 to mid-log phase with an OD of 0.8.

extract_protocol:
Genomic DNA was extracted by spheroplasting and EtOH precipitation, excluding a RNase-A digestion. Purified DNA (50 μg) was digested by a cocktail of restriction enzymes (50 U HindIII, EcorI,  XbaI, SspI, BsrGI, NEB) in the presence or absence of 30 U of RNase-H (NEB) overnight at 37C. R-loops were enriched with the S9.6 antibody.
DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A-tailing was performed with Klenow fragment (3' to 5' exo minus) and dATP. Illumina adapters were ligated and PCR amplification was performed with Illumina compatible primers for 13 cycles and library fragments were purified using 1:1 ratio of ampur XP beads.  Paired-end sequencing was performed on an Illumina NextSeq 500 with a read length of 75 bp.

value: DRIP-seq


title: AP2-FG(-)_26h_4

value: AP2-FG KO


title: hst34_DRIPseq_rep2

description:
DNA
DRIPseq_readcounts_ORFs.xlsx
hst34_merge_DRIP.bg


title: AP2-FG(-)_26h_2


title: hst34_DRIPseq_RNH_rep1


title: WT_26h_2


title: hst34_DRIPseq_rep1


title: WT_26h_3


title: AP2-FG(-)_26h_1


title: WT_DRIPseq_RNH_rep1

description:
DNA
DRIPseq_readcounts_ORFs.xlsx
WT_RNH_merge_DRIP.bg


title: WT_26h_1


title: WT_DRIPseq_rep1

description:
DNA
DRIPseq_readcounts_ORFs.xlsx
WT_merge_DRIP.bg


title: hst34rrp6_RNAseq_rep1

description:
Total RNA
NormalizedRNAseq_pombe_length_HTseqcounts.xlsx
34rrp6_rna_merge_pos.bw
34rrp6_rna_merge_minus.bw

data_processing:
FASTQ files from paired end libraries were collapsed by barcode and the Illumina adapter sequence was trimmed from the 3’ end.
Reads were first aligned using Bowtie2 to a combined FASTA file of S. cerevisiae and S. pombe rRNA, tRNA, and RDN sequences to remove contaminating reads.
Reads were then aligned to a combined version of the S. cerevisiae genome (SacCer3, SGD) and the S. pombe genome (ASM294v.2, PomBase) with TopHat2, allowing up to two mismatches.
reads were separated by their respective genomes with SAMtools, and only uniquely mapped reads were used for further analyses
For visualization in USCS genome browser, libraries were normalized by scaling the uniquely mapped S. pombe reads to 100,000 reads.
To compare RNA expression between samples, HTseq 0.9.1 was used to count the number of reads that aligned to each annotated gene.
Normalized S. cerevisiae read counts were generated by using a linear regression model to scale the S. pombe read counts relative to WT biological replicate 1 to determine scaling factors for S. cerevisiae read counts
SacCer3, ASM294v.2
bigwig, abundance measurments

growth_protocol: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.05 to mid-log phase with an OD of 0.6-0.8.

extract_protocol:
Total RNA was purified by hot-phenol extraction and ethanol precipitation and rRNA was depleted
Libraries were then prepared as in (Zhang et al., 2012), and paired-end sequencing was performed on an Illumina NextSeq 500 with a read length of 75 bp.

treatment_protocol: Rapamycin was added for 3 hours prior to harvest. S. pombe cells were added in a 1:6 ratio at time of harvest for library spike-in

value: hst4-delta HST3-FRB RRP6-FRB

value: RNA-seq


title: WT_26h_5


title: AP2-FG(-)_26h_3


title: hst34rrp6_RNAseq_rep2


title: WT_DRIPseq_rep2


title: CRC-cancer-1 [C1]

city: Minhang district of Shanghai

first: yani

last: Kang

address: Dongchuan Road 800

institute: Shanghai Jiaotong University

hyb_protocol: The hybridized samples were transferred to the sample preparation station for purification, the unhybridized probes were washed off, and the remaining samples were coupled to the sample cartridge of nCounter.

scan_protocol: The sample cartridge was placed on the data analyzer for data collection. Different fluorescent barcodes on the sample clip were classified and counted to obtain the molecular number of each target gene.

data_processing:
The raw counts were normalized via the nCounter positive and housekeeping spike-in and then analyzed by using nSolver 4.0 software.
NanoString nCounter data were calculated using a 2-tailed t test and were considered significant when P < 0.05.

label: color-coded digital barcodes

source_name: Colon Cancer tissue

label_protocol: A NanoString nCounter system (NanoString Technologies, Seattle, Washington, USA) using two probes with a total length of 70-100 nt to hybridize targeted genes were performed directly on 100 ng of total RNA without amplification. The reporter probe carried fluorescent molecular barcodes with the length of 35-50 nt. The capture probe contained a 35-50 nt sequence and was used for the immobilization of the hybrid complex for data collection. Each probe contained sequences complementary to a particular target mRNA.

extract_protocol: After collection, samples were quickly put in liquid nitrogen, and preserved in a low temperature environment. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate the total RNA of samples following the manufacturer’s protocol. Total RNA quantity was determined with a Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA) and the quality was assessed by running 1% agarose gel electrophoresis, stained with 4S Red Plus Nucleic Acid Stain (Sango, Shanghai, China).

tag: subject status

value: colorectal cancer patient

value: Rectum

tag: tissue type

value: colorectal cancer tissue


title: CRC-normal-1 [N1]

source_name: matched normal tissue

value: matched normal tissue


title: rrp6_RNAseq_rep2

description:
Total RNA
NormalizedRNAseq_pombe_length_HTseqcounts.xlsx
rrp6_rna_merge_pos.bw
rrp6_rna_merge_minus.bw


title: DMS-MaPseq on in vitro refolded E. coli total RNA

description: E. coli in vitro


title: hst34_RNAseq_rep1

description:
Total RNA
NormalizedRNAseq_pombe_length_HTseqcounts.xlsx
hst34_rna_merge_pos.bw
hst34_rna_merge_minus.bw


title: WT_RNAseq_rep1

description:
Total RNA
NormalizedRNAseq_pombe_length_HTseqcounts.xlsx
WT_rna_merge_pos.bw
WT_rna_merge_minus.bw


title: WT NET-seq rep3

description:
Nascent RNA
WT_NETseq_3_pos.bw
WT_NETseq_3_minus.bw
WT_NETseq_merge_pos.bw
WT_NETseq_merge_minus.bw

data_processing:
The adapter sequence was (ATCTCGTATGCCGTCTTCTGCTTG) removed and the random hexamer sequence was removed from the 5’ end. The 3’ ends of the reads were then trimmed for quality using FASTQ Quality Timmer by sliding window (Blankenberg et al., 2010) with a window size of 10 and a step size of 5. The reads were trimmed until the aggregate score was ≥ 21.
Reads were first aligned using Bowtie2 to a combined FASTA file of S. cerevisiae and S. pombe rRNA, tRNA, and RDN sequences to remove contaminating reads.
Reads were then aligned to a combined version of the S. cerevisiae genome (SacCer3, SGD) and the S. pombe genome (ASM294v.2, PomBase) with TopHat2, allowing up to three mismatches.
reads were separated by their respective genomes with SAMtools, and only uniquely mapped reads were used for further analyses
libraries were normalized by scaling the uniquely mapped S. pombe reads to 100,000 reads. This scaling factor was then used to scale the uniquely mapped S. cerevisiae reads. the pombe-scaled WT S. cerevisiae read counts were then scaled to 1 M reads, and this additional scaling factor was included to scale the sample reads
Only the 5’ end of the sequencing read, which corresponds to the 3’ end of the nascent RNA was recorded and used for downstream analyses.
SacCer3, ASM294v.2
bigwig

extract_protocol:
Cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004).
RNA Pol II IP, RNA purification, and library construction was carried out as described previously (Churchman and Weissman, 2011; Mayer et al., 2015). 3’ end sequencing was performed on an Illumina NextSeq 500 with a read length of 75 bp.

treatment_protocol: Rapamycin was added for 3 hours prior to harvest. S. pombe cells containnig a flag-tagged Rpb3 were added in a 1:10 ratio at time of harvest for library spike-in

value: Native elongating transcript sequencing (NET-seq)


title: hst34 NET-seq rep3

description:
Nascent RNA
hst34_NETseq_3_pos.bw
hst34_NETseq_3_minus.bw
hst34_NETseq_merge_pos.bw
hst34_NETseq_merge_minus.bw


title: hst34 NET-seq rep1

description:
Nascent RNA
hst34_NETseq_1_pos.bw
hst34_NETseq_1_minus.bw
hst34_NETseq_merge_pos.bw
hst34_NETseq_merge_minus.bw


title: WT NET-seq rep4

description:
Nascent RNA
WT_NETseq_4_pos.bw
WT_NETseq_4_minus.bw
WT_NETseq_merge_pos.bw
WT_NETseq_merge_minus.bw


title: WT NET-seq rep2

description:
Nascent RNA
WT_NETseq_2_pos.bw
WT_NETseq_2_minus.bw
WT_NETseq_merge_pos.bw
WT_NETseq_merge_minus.bw


title: Breast cancer cell line, WT, 8905 WT H3K27me3 ChIP-Seq

city: Montreal

first: Harvey

middle: Wilmore

last: Smith

state: Quebec

address: Life Sciences Complex, Room 602, 1160 Pine Avenue West

department: Goodman Cancer Research Centre

country: Canada

institute: McGill University

data_processing:
Data was assayed for quality through the use of FASTQC and processed using trimmomatic
D. melanogaster and mouse sequences were aligned to the BDGP6 and mm10 reference genomes, respectively, through the use of BWA
D. melanogaster sequence data were used to normalize mouse sequence data to remove background noise from random reads as previously described (PMID: 27875550, Egan et al.).
PCR bias and other artifacts were removed through the use of SAMtools and PICARDtools using default parameters
Broad peaks were called through the use of MACS2 and HOMER with default parameters
Genome_build: Mus musculus: mm10, D. melanogaster: BDGP6
Supplementary_files_format_and_content: bedgraph files were generated using MACS2 with default parameters

source_name: Breast cancer cell line

growth_protocol: Breast cancer cell lines were established from the MMTV-NIC (ErbB2-IRES-Cre) model (PMID: 18273058, Ursini-Siegel et al.) and routinely cultured in DMEM supplemented with 5% FBS, EGF (5 ng/ml), Hydrocortisone (1 μg/ml), Insulin (5 μg/ml) and Bovine Pituitary Extract (BPE) (35μg/ml)). Cells were grown in a humidified, 5% CO2, 37°C incubator.

extract_protocol:
NIC cells in 15 cm plates were fixed with a 1% final concentration of formaldehyde for 5 min at room temperature and then lysed and sonicated. Three plates of cells were pooled for each sample (approximately 3x107 cells). Equal amounts of chromatin from 2 individual cell lines of each genotype were diluted in 2.5X ChIP dilution buffer (EDTA 2 mM, NaCl 100 mM, Tris 20 mM, Triton 0.5%) + 100 μL of PBS+0.5% BSA and 750 ng of D. melanogaster chromatin and 0.4 µg of a D. melanogaster H2Av-specific antibody (Active Motif) were added to each sample. 5 μg of anti-H3K27me3 antibody immobilized overnight at 4ºC on 20 μl of Magna ChIP Protein A+G magnetic beads (Millipore) were added to each sample and immunoprecipitation was performed overnight at 4ºC. Beads were washed 3 times for 3 min at 4ºC with 1 mL LiCl buffer (Tris 100mM, LiCl 500 mM, Na-deoxycholate 1%) then once with 1 mL TE buffer. DNA was eluted with 150 μL of elution buffer (0.1M NaHCO3, 0.1% SDS) overnight at 65ºC. Chromatin immunoprecipitated DNA was purified using a QIAquick PCR purification kit (Qiagen) and eluted in 35 μL of elution buffer.
Libraries were constructed with the Illumina TruSeq ChIP Library Preparation Kit using Illumina's standard protocols.

value: FVB/N

tag: cell line

value: Breast cancer cell line

value: MMTV-NIC/c-Src WT/WT

tag: passages

value: mammary gland

value: Anti-H3K27me3 (C36B11), Cell Signaling, Cat. #9733 + Anti-Drosophila H2Av, Active Motif, Cat. #39715


title: hst34 NET-seq rep2

description:
Nascent RNA
hst34_NETseq_2_pos.bw
hst34_NETseq_2_minus.bw
hst34_NETseq_merge_pos.bw
hst34_NETseq_merge_minus.bw

value: hst4-delta HST3-FRB


title: WT_DRIPseq_RNH_rep2

value: WT anchor away


title: P4-3-RNA-FF

city: Edinburgh

first: Carlos

last: Martinez-Perez

address: Western General Hospital, Crewe Road South

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: The University of Edinburgh

description:
Patient 4 late on-treatment biopsy sequenced using Ion TotalRNAseq technology from fresh frozen.
Sample 9

data_processing:
For RNASeq samples the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) was used and sequencing was performed on an Illumina HiSeq 2500 using a 2x50bp configuration with an average of 136 million read pairs per sample.
Probes were mapped to Ensembl gene annotations using BioMart.
Data were log2 transformed and quantile normalised using R/Bioconductor software and packages.
Genome_build: Human genome version GRCh38.77
Supplementary_files_format_and_content: The processed data files contain expression data for each sample mapped to Ensemble gene IDS.

source_name: breast cancer

extract_protocol:
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) was used
All samples were processed and libraries constructed following the manufacturer's.

value: breast cancer

tag: time point

value: late on-treatment biopsy


title: P4-1-RNA-FF

description:
Patient 4 pre-treatment biopsy sequenced using Ion TotalRNAseq technology from fresh frozen.
Sample 7

value: pre-treatment biopsy


title: WT NET-seq rep1

description:
Nascent RNA
WT_NETseq_1_pos.bw
WT_NETseq_1_minus.bw
WT_NETseq_merge_pos.bw
WT_NETseq_merge_minus.bw


title: P3-3-RNA-FF

description:
Patient 3 late on-treatment biopsy sequenced using Ion TotalRNAseq technology from fresh frozen.
Sample 6


title: P4-2-RNA-FF

description:
Patient 4 early on-treatment biopsy sequenced using Ion TotalRNAseq technology from fresh frozen.
Sample 8

value: early on-treatment biopsy


title: P3-1-RNA-FF

description:
Patient 3 pre-treatment biopsy sequenced using Ion TotalRNAseq technology from fresh frozen.
Sample 4


title: P2-1-RNA-FF

description:
Patient 2 pre-treatment biopsy sequenced using Ion TotalRNAseq technology from fresh frozen.
Sample 1


title: P3-2-RNA-FF

description:
Patient 3 early on-treatment biopsy sequenced using Ion TotalRNAseq technology from fresh frozen.
Sample 5


title: P2-3-RNA-FF

description:
Patient 2 late on-treatment biopsy sequenced using Ion TotalRNAseq technology from fresh frozen.
Sample 3


title: P2-2-RNA-FF

description:
Patient 2 early on-treatment biopsy sequenced using Ion TotalRNAseq technology from fresh frozen.
Sample 2


title: UbxDegrad_control_RNA_R3

city: Heidelberg

first: Katrin

last: Domsch

address: INF 230

department: COS - Developmental Biology

country: Germany

institute: Heidelberg University

data_processing:
RNA reads were first analysed with FastQC and aligned with TopHat2111 using BDGP6.86
The count table were generated using HTSeq
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files

organism: Drosophila melanogaster

source_name: mesoderm stage 14-17

extract_protocol:
tissue specific nuclei were extracted vis the INTACT method (Steiner et al., 2012)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mesoderm

value: twi-INTACT; UAS-Nslmb,GFP-Ubx


title: UbxDegrad_experiment_RNA_R1

value: twi-INTACT, Mef2>Nslmb,GFP-Ubx


title: UbxDegrad_experiment_RNA_R2


title: UbxDegrad_experiment_RNA_R3


title: rrp6_RNAseq_rep1

description:
Total RNA
NormalizedRNAseq_pombe_length_HTseqcounts.xlsx
rrp6_rna_merge_pos.bw
rrp6_rna_merge_minus.bw

value: RNA-seq


title: hst34_RNAseq_rep2

description:
Total RNA
NormalizedRNAseq_pombe_length_HTseqcounts.xlsx
hst34_rna_merge_pos.bw
hst34_rna_merge_minus.bw


title: UbxDegrad_control_RNA_R2


title: UbxDegrad_control_RNA_R1


title: WT_RNAseq_rep2

description:
Total RNA
NormalizedRNAseq_pombe_length_HTseqcounts.xlsx
WT_rna_merge_pos.bw
WT_rna_merge_minus.bw


title: neRNA_R2

source_name: neuronal stage 10-13

value: neuronal

value: elav>INTACT


title: neRNA_R1


title: meRNA_R1

source_name: mesoderm stage 10-13

value: twi-INTACT


title: meRNA_R2


title: mlRNA_R1


title: mlRNA_R2


title: nlRNA_R1

source_name: neuronal stage 14-17


title: CY3+E_15°C

city: Düsseldorf

first: Heidrun

middle: Sigrid

last: Windisch

state: NRW

address: Universitätsstrasse 1

department: Cell Biology and Zoology

institute: Heinrich-Heine-University

data_processing:
Raw sequencing data were clipped and trimmed using Trimmomatic (Bolger, Lohse, & Usadel, 2014) to remove bias of sequencing adapters and low quality regions at the beginning and end of sequences.
Reads were mapped to the Daphnia magna genome assembly version 2.4 (NCBI BioProject accession No. PRJNA298946), containing 26.646 translations (open access since April 2016). Mapping was conducted using RSEM v.1.2.31 (Li & Dewey, 2011) connected to bowtie2 (Langdon, 2015) to generate FPKM outputs for transcript analysis.
MeV software v. 4.8.1 (Howe, Sinha, Schlauch, & Quackenbush, 2011) connected to edgeR (Robinson, McCarthy, & Smyth, 2010) was used for the analysis and clustering of differential gene expression. One-Way ANOVA was used on the basis of normalized FPKM values generated with RSEM (Li & Dewey, 2011) to identify differently expressed genes among all treatments.
The available annotation from the Daphnia magna genome was enriched through assignments from the artNOG (EggNOG 4.0) database. COG categories as well as functional descriptions were added to the existing annotation.
Genome_build: NCBI BioProject accession No. PRJNA298946
Supplementary_files_format_and_content: txt files were generated using RSEM. FPKM values were used for the analysis of DGE in MeV

organism: Daphnia magna

source_name: pool of 3 whole specimen

growth_protocol: Daphnia magna clone P132.85 originating from the pond Driehoek in Heusden (The Netherlands; N51°44'01", E5°08'17") were cultured at 15°C in aged, aerated and sterile-filtered (45 µm) tap water under dim light conditions. The animals were kept at a maximum density of 15 individuals per L under non-limiting food conditions by feeding them 2 mg carbon per L of Acutodesmus obliquus (formerly: Scenedesmus obliquus) during pre-culture every second day by transferring them into fresh glasses with food.

extract_protocol:
In total, 5 treatment groups were prepared for sequencing with 3 replicates each. Replicate sample pools consisted of 5 specimens to ensure appropriate amounts for RNA extraction and comparability. Total RNA was extracted using the NucleoSpin RNA extraction kit (Machery und Nagel, Düren/Germany) according to the manufacturer´s instructions. In addition, traces of remaining genomic DNA were removed using the Turbo DNA-free Kit (Invitrogen, Karlsruhe/Germany) in line with the manufacturer´s manual. The quality of the isolated RNA was monitored using capillary electrophoresis on a Bioanalyzer (Agilent Technologies, Santa Clara/USA). Only samples with OD280/OD260≤ 2.0,  OD280/OD230 ≤ 2.0 and RIN ≤ 8.0 were used for sequencing.
Clean-up of mRNA, cDNA library construction as well as sequencing was conducted at the University of Cologne’s Cologne Centre for Genomics (CCG)

treatment_protocol: Juvenile D. magna for experiments originated from mothers that carried the third clutch of parthenogenetic offspring. Neonates (within 8 h after release from the mothers’ brood pouch) were randomly distributed to jars containing 600 ml tap water, the respective food and if scheduled, supplements. In total we analysed 5 treatments with RNAseq: GA, GA+ EPA, CY, Cy + EPA, and CRY. All D. magna individuals were raised until they deposited the first clutch of eggs into their brood pouch (reaching maturity) before sampling. Daphnia were rinsed twice with deionized water before blotting them dry with lint-free tissue. Whole animal samples were shock-frozen in liquid nitrogen and stored at -80°C thereafter until further experimentation.

tag: strain

tag: developmental stage

value: mothers reproducing parthenogenetically, carrying the first clutch of eggs

value: CY +EPA

tag: temperature


title: GA1_15°C

value: GA


title: CY3_15°C

value: CY


title: GA3_15°C


title: GA3+E_15°C

value: GA +EPA


title: CY2+E_15°C


title: GA2+E_15°C


title: CY2_15°C


title: GA1+E_15°C


title: 250.3.T4H

city: Santiago

first: Rodrigo

last: De la Iglesia

address: Portugal 49

country: Chile

institute: Pontificia Universidad Católica de Chile

description:
250.3.T4H
HDB-29

data_processing:
Raw image data were converted into sequence data by base-calling, defined as raw reads.
Pandaseq was used to assemble the paired-end sequences with default values.
All sequences were searched for homologies against the KEGG database and against the most recent O. tauri genome annotation using the DIAMOND protein aligner.
The DEseq2 routine was applied for comparisons between treatments
Genes with absolute Log2FC values over 0.3 and p-adjusted values below 0.1 were selected for further analysis.
Genome_build: Ostreococcus tauri reference genome was used for sequence alignment (Blanc-Mathieu et al., 2014).
Supplementary_files_format_and_content: Excel file with log2fold change of gene expresion and the associated statistical values.
Supplementary_files_format_and_content: counts

organism: Ostreococcus tauri

source_name: Liquid cultures

growth_protocol: O. tauri RCC745 cultures were grown until the exponential phase (15 x106 cells/mL) in T175 aerated flasks under a 12:12 light-dark cycle (20 µmol photons cm-2 s), in artificial seawater media supplemented with Keller nutrients (0.88 mM nitrate, 22 µM phosphate, and f/2 vitamins)

extract_protocol:
Total RNA was extracted from frozen cell pellets using the TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA concentrations were determined by absorption at 260 nm, and purity was evaluated by the 260/280 nm absorption ratio. Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer.
RNAseq libraries were constructed using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) by the NGS Service FASTERIS (Switzerland).
Libraries were multiplexed in one channel of 1 x 50 bp run on a MiSeq run for titration and quality control. Finally, the libraries were sequenced using an Illumina HiSeq 2000 sequencer.

treatment_protocol: Cultures were incubated with a final Cu concentration of 0.4 µM or 2 µM, for 1, 4 and 12 h after the addition of copper

value: 250 uM Copper treatment

value: 4 H incubation


title: ameiotic1 (489) maize anthers, male sterile, 1.0 mm rep 1.

extract_protocol:
Total RNA was isolated using Tri reagent (Molecular Research Center, Cincinnati, OH) or Plant RNA Reagent (Invitrogen, Carlsbad, CA).
Small RNA and RNA-seq libraries were constructed using TruSeq™ Small RNA Sample Prep Kit and TruSeq™ RNA Sample Prep Kit (Illumina, San Diego, CA). PARE libraries were constructed as previously described. All libraries were sequenced on an Illumina Hi-Seq 2000 instrument

tag: tissue

value: male sterile 10 mm

tag: genotype

value: ameiotic1 (489)


title: CY1+E_15°C


title: GA2_15°C


title: 250.3.T12H

description:
250.3.T12H
HDB-30

value: 12 H incubation


title: CRY1_15°C

value: CRY


title: CRY3_15°C


title: 25.3.T4H

description:
25.3.T4H
HDB-26

value: 25 uM Copper treatment


title: CRY2_15°C


title: nlRNA_R2


title: 250.3.T1H

description:
250.3.T1H
HDB-28

value: 1 H Incubation


title: 25.3.T12H

description:
25.3.T12H
HDB-27


title: 25.3.T1H

description:
25.3.T1H
HDB-25


title: 250.2.T12H

description:
250.2.T12H
HDB-20


title: 250.2.T4H

description:
250.2.T4H
HDB-19


title: Control.3.T12H

description:
C3.T12H
HDB-24

value: Control


title: Control.3.T4H

description:
C3.T4H
HDB-23


title: CY1_15°C


title: 250.2.T1H

description:
250.2.T1H
HDB-18


title: 25.2.T4H

description:
25.2.T4H
HDB-16


title: 25.2.T12H

description:
25.2.T12H
HDB-17


title: 25.2.T1H

description:
25.2.T1H
HDB-15


title: 250.1.T1H

description:
250.1.T1H
HDB-8


title: Control.1.T12H

description:
C1.T12H
HDB-4


title: 25.1.T12H

description:
25.1.T12H
HDB-7


title: 25.1.T4H

description:
25.1.T4H
HDB-6


title: Control.2.T12H

description:
C2.T12H
HDB-14


title: Control.2.T0

description:
C2.T0
HDB-11

value: Time 0


title: Control.1.T1H

description:
C1.T1H
HDB-2


title: Control.3.T1H

description:
C3.T1H
HDB-22


title: 250.1.T12H

description:
250.1.T12H
HDB-10


title: Control.1.T0

description:
C1.T0
HDB-1


title: 25.1.T1H

description:
25.1.T1H
HDB-5


title: Control.1.T4H

description:
C1.T4H
HDB-3


title: Control.3.T0

description:
C3.T0
HDB-21


title: Lymphocyte-ETV078_T2_TEM_H3

city: Memphis

first: Jeremy

middle: Chase

last: Crawford

state: TN

address: MS 221, 262 Danny Thomas Place

department: Department of Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

scan_protocol: The chips were then loaded using the IFC Controller HX (Fluidigm) and transferred to the Biomark HD real-time PCR reader to analyze using the GE Fast 96x96 PCR+Melt v2 protocol.

data_processing: Ct values were recovered from the BioMark HD. Single-cell qPCR data Ct values are non-normalized.  The value 999 is reported by the Fluidigm software and we consider these zero values.

source_name: Tumor infiltrating lymphocyte

label_protocol: The remaining components of the RT reaction were added to each well, including 0.15 μL 10X SuperScript Enzyme Mix (Thermo Fisher), 0.12 μL T4 Gene 32 Protein (NEB), and nuclease free water (Teknova). Thermal cycling conditions for the reverse transcription of single-cell mRNA into cDNA was 25°C for 5 min, 50°C for 30 min, 55°C for 25 min, 60°C for 5 min, 70°C for 10 min, and then hold at 4°C. After reverse transcription, the cDNA was amplified using 1.5 μL of a pool of the designed primers (STA mix; Fluidigm), 7.5 μL TaqMan PreAmp Master Mix (Thermo Fisher), and 0.075 μL 0.5M EDTA (Thermo Fisher). The thermal cycling conditions were 95°C for 10 min, 20 cycles of 96° for 5 sec and 60°C for 4 min, and then hold at 4°C. Amplified cDNA was then treated with Exonuclease I (NEB) to remove any unincorporated primers by adding 6 μL of 4 U/μL Exonuclease I (20 U/μL Exonuclease I diluted with water and 10X Exonuclease I Reaction buffer). Thermal cycling conditions were 37°C for 30 min, 80°C for 15 min, and then hold at 4°C. The cDNA was then diluted 5-fold for loading onto the chip. The sample mix to be loaded onto the chip included 2.5 μL 2X Sso Fast EvaGreen Supermix with low ROX (Bio-Rad), 0.25 μL 20S DNA Binding Dye Sample Loading Reagent (Fluidigm), and 2.25 μL of the prepared cDNA. The assay mix loaded onto the chip included 2.5 μL 2X Assay Loading Reagent (Fluidigm), 1X DNA Suspension Buffer (Teknova), and 100 μM of each forward and reverse primer mix (Fluidigm).

extract_protocol: After successful sorting, the plates were incubated at 65°C for 90 seconds, and chilled on ice for 5 minutes for RNA denaturation.

treatment_protocol: Cells were stained with a variety of antibodies and tetramers prior to single-cell sorting into 386-well plates.

tag: tumor type

value: Pediatric leukemia

value: Tumor infiltrating lymphocyte

tag: platewell id

tag: patient id

tag: tetname

tag: tetramer

tag: cell subtype

value: Tem

tag: tet type

value: TetPos


title: Lymphocyte-ETV078_T2_TEM_H5

tag: cell type


title: Lymphocyte-ETV078_T2_TEM_H6


title: Lymphocyte-ETV078_T2_TEM_H1


title: Lymphocyte-ETV078_T2_TEM_H4


title: Lymphocyte-ETV078_T2_TEM_H2


title: Lymphocyte-ETV078_T2_TEM_G4


title: Lymphocyte-ETV078_T2_TEM_G6


title: Lymphocyte-ETV078_T2_TEM_G5


title: Lymphocyte-ETV078_T2_TEM_G2


title: Lymphocyte-ETV078_T2_TEM_G3


title: Control.2.T4H

description:
C2.T4H
HDB-13

tag: agent


title: Control.2.T1H

description:
C2.T1H
HDB-12


title: 250.1.T4H

description:
250.1.T4H
HDB-9


title: Lymphocyte-ETV078_T2_TEM_G1


title: Lymphocyte-ETV078_T2_TEM_F5


title: Lymphocyte-ETV078_T2_TEM_E2


title: Lymphocyte-ETV078_T2_TEM_E4


title: Lymphocyte-ETV078_T2_TEM_E3


title: Lymphocyte-ETV078_T2_TEM_F1


title: Lymphocyte-ETV078_T2_TEM_E1


title: Lymphocyte-ETV078_T2_TEM_E5


title: Lymphocyte-ETV078_T2_TEM_D3


title: Lymphocyte-ETV078_T2_TEM_D6


title: Lymphocyte-ETV078_T2_TEM_E6


title: Lymphocyte-ETV078_T2_TEM_D5


title: Lymphocyte-ETV078_T2_TEM_D4


title: Lymphocyte-ETV078_T2_TEM_D2


title: Lymphocyte-ETV078_T2_TEM_C3


title: Lymphocyte-ETV078_T2_TEM_C5


title: Lymphocyte-ETV078_T2_TEM_C1


title: Lymphocyte-ETV078_T2_TEM_C4


title: Lymphocyte-ETV078_T2_TEM_C6


title: Lymphocyte-ETV078_T2_TEM_F6


title: Lymphocyte-ETV078_T2_TEM_C2


title: Lymphocyte-ETV078_T2_TEM_B1


title: Lymphocyte-ETV078_T2_TEM_B5


title: Lymphocyte-ETV078_T2_TEM_B4


title: Lymphocyte-ETV078_T2_TEM_B2


title: Lymphocyte-ETV078_T2_TEM_B3


title: Lymphocyte-ETV078_T2_TEM_A6


title: Lymphocyte-ETV078_T2_TEM_B6


title: Lymphocyte-ETV078_T2_TEM_A4


title: Lymphocyte-ETV078_T2_TEM_A1


title: Lymphocyte-ETV078_T2_TEM_A2


title: Lymphocyte-ETV078_T2_TEM_A3


title: Lymphocyte-ETV078_T2_TEM_D1


title: Lymphocyte-ETV078_T2_CCR7HI_H9


title: Lymphocyte-ETV078_T2_CCR7HI_H8


title: Lymphocyte-ETV078_T2_CCR7HI_H7


title: Lymphocyte-ETV078_T2_CCR7HI_H12


title: Lymphocyte-ETV078_T2_CCR7HI_H10


title: Lymphocyte-ETV078_T2_CCR7HI_H11


title: Lymphocyte-ETV078_T2_CCR7HI_G12


title: Lymphocyte-ETV078_T2_CCR7HI_G7


title: Lymphocyte-ETV078_T2_TEM_A5


title: Lymphocyte-ETV078_T2_CCR7HI_G8


title: Lymphocyte-ETV078_T2_CCR7HI_G9


title: Lymphocyte-ETV078_T2_CCR7HI_G10


title: Lymphocyte-ETV078_T2_CCR7HI_G11


title: Lymphocyte-ETV078_T2_CCR7HI_F12


title: Lymphocyte-ETV078_T2_CCR7HI_F11


title: Lymphocyte-ETV078_T2_CCR7HI_E7


title: Lymphocyte-ETV078_T2_CCR7HI_E8


title: Lymphocyte-ETV078_T2_CCR7HI_F7


title: Lymphocyte-ETV078_T2_CCR7HI_F8


title: Lymphocyte-ETV078_T2_CCR7HI_E11


title: Lymphocyte-ETV078_T2_CCR7HI_F10


title: Lymphocyte-ETV078_T2_CCR7HI_F9


title: Lymphocyte-ETV078_T2_CCR7HI_E9


title: Lymphocyte-ETV078_T2_CCR7HI_E12


title: Lymphocyte-ETV078_T2_CCR7HI_E10


title: Lymphocyte-ETV078_T2_CCR7HI_D9


title: Lymphocyte-ETV078_T2_CCR7HI_D7


title: Lymphocyte-ETV078_T2_CCR7HI_D8


title: Lymphocyte-ETV078_T2_CCR7HI_D12


title: Lymphocyte-ETV078_T2_CCR7HI_D10


title: Lymphocyte-ETV078_T2_CCR7HI_D11


title: Lymphocyte-ETV078_T2_CCR7HI_C8


title: Lymphocyte-ETV078_T2_CCR7HI_C9


title: Lymphocyte-ETV078_T2_CCR7HI_C7


title: Lymphocyte-ETV078_T2_CCR7HI_C10


title: Lymphocyte-ETV078_T2_CCR7HI_C12


title: Lymphocyte-ETV078_T2_CCR7HI_B9


title: Lymphocyte-ETV078_T2_CCR7HI_B7


title: Lymphocyte-ETV078_T2_CCR7HI_C11


title: Lymphocyte-ETV078_T2_CCR7HI_A10


title: Lymphocyte-ETV078_T2_CCR7HI_B11


title: Lymphocyte-ETV078_T2_CCR7HI_B10


title: Lymphocyte-ETV078_T2_CCR7HI_A11


title: Lymphocyte-ETV078_T2_CCR7HI_A7


title: Lymphocyte-ETV078_T2_CCR7HI_A8


title: Lymphocyte-ETV078_T1NEG_TEM_H4

value: TetNeg


title: Lymphocyte-ETV078_T1NEG_TEM_H5


title: Lymphocyte-ETV078_T1NEG_TEM_H6


title: Lymphocyte-ETV078_T2_CCR7HI_A9


title: Lymphocyte-ETV078_T2_CCR7HI_B12


title: Lymphocyte-ETV078_T1NEG_TEM_H2


title: Lymphocyte-ETV078_T2_CCR7HI_A12


title: Lymphocyte-ETV078_T2_CCR7HI_B8


title: Lymphocyte-ETV078_T1NEG_TEM_G6


title: Lymphocyte-ETV078_T1NEG_TEM_G5


title: Lymphocyte-ETV078_T1NEG_TEM_G4


title: Lymphocyte-ETV078_T1NEG_TEM_G2


title: Lymphocyte-ETV078_T1NEG_TEM_G3


title: Lymphocyte-ETV078_T1NEG_TEM_G1


title: Lymphocyte-ETV078_T1NEG_TEM_H3


title: Lymphocyte-ETV078_T1NEG_TEM_F4


title: Lymphocyte-ETV078_T1NEG_TEM_H1


title: Lymphocyte-ETV078_T1NEG_TEM_F3


title: Lymphocyte-ETV078_T1NEG_TEM_F6


title: Lymphocyte-ETV078_T1NEG_TEM_E4


title: Lymphocyte-ETV078_T1NEG_TEM_E5


title: Lymphocyte-ETV078_T1NEG_TEM_F1


title: Lymphocyte-ETV078_T1NEG_TEM_E3


title: Lymphocyte-ETV078_T1NEG_TEM_C6


title: Lymphocyte-ETV078_T1NEG_TEM_D1


title: Lymphocyte-ETV078_T1NEG_TEM_E2


title: Lymphocyte-ETV078_T1NEG_TEM_D2


title: Lymphocyte-ETV078_T1NEG_TEM_D4


title: Lymphocyte-ETV078_T1NEG_TEM_D3


title: Lymphocyte-ETV078_T1NEG_TEM_D5


title: Lymphocyte-ETV078_T1NEG_TEM_E6


title: Lymphocyte-ETV078_T1NEG_TEM_D6


title: Lymphocyte-ETV078_T1NEG_TEM_C4


title: Lymphocyte-ETV078_T1NEG_TEM_C1


title: Lymphocyte-ETV078_T1NEG_TEM_C2


title: Lymphocyte-ETV078_T1NEG_TEM_B6


title: Lymphocyte-ETV078_T1NEG_TEM_F2


title: Lymphocyte-ETV078_T1NEG_TEM_B4


title: Lymphocyte-ETV078_T1NEG_TEM_B3


title: Lymphocyte-ETV078_T1NEG_TEM_A6


title: Lymphocyte-ETV078_T1NEG_TEM_A5


title: Lymphocyte-ETV078_T1NEG_TEM_E1


title: Lymphocyte-ETV078_T1NEG_TEM_B1


title: Lymphocyte-ETV078_T1NEG_TEM_A4


title: Lymphocyte-ETV078_T1NEG_TEM_A3


title: Lymphocyte-ETV078_T1NEG_TEM_C3


title: Lymphocyte-ETV078_T1NEG_TEM_A1


title: Lymphocyte-ETV078_T1NEG_TEM_B5


title: Lymphocyte-ETV078_T1NEG_CCR7HI_H8


title: Lymphocyte-ETV078_T1NEG_CCR7HI_H12


title: Lymphocyte-ETV078_T1NEG_CCR7HI_H7


title: Lymphocyte-ETV078_T1NEG_CCR7HI_H10


title: Lymphocyte-ETV078_T1NEG_CCR7HI_H11


title: Lymphocyte-ETV078_T1NEG_CCR7HI_G8


title: Lymphocyte-ETV078_T1NEG_CCR7HI_G9


title: Lymphocyte-ETV078_T1NEG_CCR7HI_G12


title: Lymphocyte-ETV078_T1NEG_TEM_B2


title: Lymphocyte-ETV078_T1NEG_CCR7HI_G7


title: Lymphocyte-ETV078_T1NEG_CCR7HI_F8


title: Lymphocyte-ETV078_T1NEG_CCR7HI_F9


title: Lymphocyte-ETV078_T1NEG_CCR7HI_G10


title: Lymphocyte-ETV078_T1NEG_CCR7HI_F12


title: Lymphocyte-ETV078_T1NEG_TEM_A2


title: Lymphocyte-ETV078_T1NEG_CCR7HI_F11


title: Lymphocyte-ETV078_T1NEG_CCR7HI_F10


title: Lymphocyte-ETV078_T1NEG_CCR7HI_H9


title: Lymphocyte-ETV078_T1NEG_CCR7HI_E7


title: Lymphocyte-ETV078_T1NEG_CCR7HI_E11


title: Lymphocyte-ETV078_T1NEG_CCR7HI_E10


title: Lymphocyte-ETV078_T1NEG_CCR7HI_G11


title: Lymphocyte-ETV078_T1NEG_CCR7HI_D12


title: Lymphocyte-ETV078_T1NEG_CCR7HI_D7


title: Lymphocyte-ETV078_T1NEG_CCR7HI_E8


title: Lymphocyte-ETV078_T1NEG_CCR7HI_F7


title: Lymphocyte-ETV078_T1NEG_CCR7HI_D9


title: Lymphocyte-ETV078_T1NEG_CCR7HI_D8


title: Lymphocyte-ETV078_T1NEG_CCR7HI_D10


title: Lymphocyte-ETV078_T1NEG_CCR7HI_D11


title: Lymphocyte-ETV078_T1NEG_CCR7HI_C8


title: Lymphocyte-ETV078_T1NEG_CCR7HI_C9


title: Lymphocyte-ETV078_T1NEG_CCR7HI_C7


title: Lymphocyte-ETV078_T1NEG_CCR7HI_E9


title: Lymphocyte-ETV078_T1NEG_CCR7HI_C12


title: Lymphocyte-ETV078_T1NEG_CCR7HI_C11


title: Lymphocyte-ETV078_T1NEG_CCR7HI_C10


title: Lymphocyte-ETV078_T1NEG_CCR7HI_B8


title: Lymphocyte-ETV078_T1NEG_CCR7HI_A9


title: Lymphocyte-ETV078_T1NEG_CCR7HI_B10


title: Lymphocyte-ETV078_T1NEG_CCR7HI_B12


title: Lymphocyte-ETV078_T1NEG_CCR7HI_B11


title: Lymphocyte-ETV078_T1NEG_CCR7HI_A10


title: Lymphocyte-ETV078_T1NEG_CCR7HI_A11


title: Lymphocyte-ETV078_T1NEG_CCR7HI_A12


title: Lymphocyte-ETV078_T1_TEM_H6


title: Lymphocyte-ETV078_T1_TEM_H5


title: Lymphocyte-ETV078_T1_TEM_H2


title: Lymphocyte-ETV078_T1_TEM_H3


title: Lymphocyte-ETV078_T1_TEM_H1


title: Lymphocyte-ETV078_T1_TEM_G2


title: Lymphocyte-ETV078_T1_TEM_G1


title: Lymphocyte-ETV078_T1_TEM_G3


title: Lymphocyte-ETV078_T1NEG_CCR7HI_A8


title: Lymphocyte-ETV078_T1_TEM_F4


title: Lymphocyte-ETV078_T1_TEM_G5


title: Lymphocyte-ETV078_T1_TEM_G6


title: Lymphocyte-ETV078_T1NEG_CCR7HI_A7


title: Lymphocyte-ETV078_T1_TEM_F3


title: Lymphocyte-ETV078_T1_TEM_F5


title: Lymphocyte-ETV078_T1_TEM_F1


title: Lymphocyte-ETV078_T1_TEM_F2


title: Lymphocyte-ETV078_T1_TEM_E6


title: Lymphocyte-ETV078_T1_TEM_E5


title: Lymphocyte-ETV078_T1_TEM_E4


title: Lymphocyte-ETV078_T1_TEM_D5


title: Lymphocyte-ETV078_T1_TEM_E3


title: Lymphocyte-ETV078_T1_TEM_E2


title: Lymphocyte-ETV078_T1_TEM_D3


title: Lymphocyte-ETV078_T1_TEM_F6


title: Lymphocyte-ETV078_T1_TEM_D4


title: Lymphocyte-ETV078_T1_TEM_D1


title: Lymphocyte-ETV078_T1_TEM_C6


title: Lymphocyte-ETV078_T1_TEM_C5


title: Lymphocyte-ETV078_T1_TEM_C3


title: Lymphocyte-ETV078_T1_TEM_C4


title: Lymphocyte-ETV078_T1_TEM_C1


title: Lymphocyte-ETV078_T1_TEM_B3


title: Lymphocyte-ETV078_T1_TEM_C2


title: Lymphocyte-ETV078_T1_TEM_B6


title: Lymphocyte-ETV078_T1_TEM_B5


title: Lymphocyte-ETV078_T1_TEM_B4


title: Lymphocyte-ETV078_T1_TEM_B2


title: Lymphocyte-ETV078_T1_TEM_E1


title: Lymphocyte-ETV078_T1_TEM_B1


title: Lymphocyte-ETV078_T1_TEM_A5


title: Lymphocyte-ETV078_T1_TEM_A6


title: Lymphocyte-ETV078_T1_TEM_A2


title: Lymphocyte-ETV078_T1_TEM_A3


title: Lymphocyte-ETV078_T1_CCR7HI_H8


title: Lymphocyte-ETV078_T1_CCR7HI_H9


title: Lymphocyte-ETV078_T1_TEM_A1


title: Lymphocyte-ETV078_T1_TEM_D2


title: Lymphocyte-ETV078_T1_CCR7HI_G11


title: Lymphocyte-ETV078_T1_CCR7HI_G9


title: Lymphocyte-ETV078_T1_CCR7HI_H12


title: Lymphocyte-ETV078_T1_CCR7HI_H7


title: Lymphocyte-ETV078_T1_CCR7HI_G7


title: Lymphocyte-ETV078_T1_CCR7HI_H11


title: Lymphocyte-ETV078_T1_CCR7HI_G12


title: Lymphocyte-ETV078_T1_CCR7HI_G8


title: Lymphocyte-ETV078_T1_CCR7HI_G10


title: Lymphocyte-ETV078_T1_TEM_A4


title: Lymphocyte-ETV078_T1_CCR7HI_F9


title: Lymphocyte-ETV078_T1_CCR7HI_F7


title: Lymphocyte-ETV078_T1_CCR7HI_F11


title: Lymphocyte-ETV078_T1_CCR7HI_E7


title: Lymphocyte-ETV078_T1_CCR7HI_F10


title: Lymphocyte-ETV078_T1_CCR7HI_F12


title: Lymphocyte-ETV078_T1_CCR7HI_E9


title: Lymphocyte-ETV078_T1_CCR7HI_E12


title: Lymphocyte-ETV078_T1_CCR7HI_E8


title: Lymphocyte-ETV078_T1_CCR7HI_E11


title: Lymphocyte-ETV078_T1_CCR7HI_E10


title: Lymphocyte-ETV078_T1_CCR7HI_H10


title: Lymphocyte-ETV078_T1_CCR7HI_C9


title: Lymphocyte-ETV078_T1_CCR7HI_D12


title: Lymphocyte-ETV078_T1_CCR7HI_D10


title: Lymphocyte-ETV078_T1_CCR7HI_D8


title: Lymphocyte-ETV078_T1_CCR7HI_D7


title: Lymphocyte-ETV078_T1_CCR7HI_F8


title: Lymphocyte-ETV078_T1_CCR7HI_C7


title: Lymphocyte-ETV078_T1_CCR7HI_C8


title: Lymphocyte-ETV078_T1_CCR7HI_B10


title: Lymphocyte-ETV078_T1_CCR7HI_B7


title: Lymphocyte-ETV078_T1_CCR7HI_B8


title: Lymphocyte-ETV078_T1_CCR7HI_C11


title: Lymphocyte-ETV078_T1_CCR7HI_B11


title: Lymphocyte-ETV078_T1_CCR7HI_B9


title: Lymphocyte-ETV078_T1_CCR7HI_D9


title: Lymphocyte-ETV078_T1_CCR7HI_A9


title: Lymphocyte-ETV078_T1_CCR7HI_A12


title: Lymphocyte-ETV078_T1_CCR7HI_A7


title: Lymphocyte-ETV078_T1_CCR7HI_A10


title: Lymphocyte-ETV078_T1_CCR7HI_A11


title: Lymphocyte-ETV078_T1_CCR7HI_A8


title: Lymphocyte-ETV001_T2_TEM_H5


title: Lymphocyte-ETV001_T2_TEM_H6


title: Lymphocyte-ETV001_T2_TEM_H3


title: Lymphocyte-ETV001_T2_TEM_H4


title: Lymphocyte-ETV078_T1_CCR7HI_C10


title: Lymphocyte-ETV078_T1_CCR7HI_C12


title: Lymphocyte-ETV001_T2_TEM_H2


title: Lymphocyte-ETV001_T2_TEM_G6


title: Lymphocyte-ETV001_T2_TEM_H1


title: Lymphocyte-ETV001_T2_TEM_G3


title: Lymphocyte-ETV001_T2_TEM_G4


title: Lymphocyte-ETV001_T2_TEM_G5


title: Lymphocyte-ETV001_T2_TEM_G1


title: Lymphocyte-ETV001_T2_TEM_F5


title: Lymphocyte-ETV001_T2_TEM_F4


title: Lymphocyte-ETV001_T2_TEM_F6


title: Lymphocyte-ETV001_T2_TEM_F2


title: Lymphocyte-ETV001_T2_TEM_F1


title: Lymphocyte-ETV001_T2_TEM_E4


title: Lymphocyte-ETV001_T2_TEM_E5


title: Lymphocyte-ETV001_T2_TEM_E6


title: Lymphocyte-ETV001_T2_TEM_E3


title: Lymphocyte-ETV001_T2_TEM_D5


title: Lymphocyte-ETV001_T2_TEM_F3


title: Lymphocyte-ETV001_T2_TEM_D6


title: Lymphocyte-ETV001_T2_TEM_D4


title: Lymphocyte-ETV001_T2_TEM_D3


title: Lymphocyte-ETV001_T2_TEM_D1


title: Lymphocyte-ETV001_T2_TEM_D2


title: Lymphocyte-ETV001_T2_TEM_E2


title: Lymphocyte-ETV001_T2_TEM_E1


title: Lymphocyte-ETV001_T2_TEM_C2


title: Lymphocyte-ETV001_T2_TEM_C3


title: Lymphocyte-ETV001_T2_TEM_C5


title: Lymphocyte-ETV001_T2_TEM_B5


title: Lymphocyte-ETV001_T2_TEM_C6


title: Lymphocyte-ETV001_T2_TEM_G2


title: Lymphocyte-ETV001_T2_TEM_B2


title: Lymphocyte-ETV001_T2_TEM_B4


title: Lymphocyte-ETV001_T2_TEM_C4


title: Lymphocyte-ETV001_T2_TEM_A3


title: Lymphocyte-ETV001_T2_TEM_A4


title: Lymphocyte-ETV001_T2_TEM_A5


title: Lymphocyte-ETV001_T2_TEM_A6


title: Lymphocyte-ETV001_T2_TEM_A1


title: Lymphocyte-ETV001_T2_CCR7HI_H8


title: Lymphocyte-ETV001_T2_CCR7HI_H9


title: Lymphocyte-ETV001_T2_TEM_B6


title: Lymphocyte-ETV001_T2_CCR7HI_H7


title: Lymphocyte-ETV001_T2_CCR7HI_H12


title: Lymphocyte-ETV001_T2_CCR7HI_H10


title: Lymphocyte-ETV001_T2_CCR7HI_G9


title: Lymphocyte-ETV001_T2_CCR7HI_G7


title: Lymphocyte-ETV001_T2_CCR7HI_G12


title: Lymphocyte-ETV001_T2_CCR7HI_H11


title: Lymphocyte-ETV001_T2_CCR7HI_G11


title: Lymphocyte-ETV001_T2_TEM_B3


title: Lymphocyte-ETV001_T2_CCR7HI_F8


title: Lymphocyte-ETV001_T2_CCR7HI_F12


title: Lymphocyte-ETV001_T2_CCR7HI_G10


title: Lymphocyte-ETV001_T2_TEM_A2


title: Lymphocyte-ETV001_T2_CCR7HI_E7


title: Lymphocyte-ETV001_T2_CCR7HI_F7


title: Lymphocyte-ETV001_T2_CCR7HI_F11


title: Lymphocyte-ETV001_T2_CCR7HI_E9


title: Lymphocyte-ETV001_T2_CCR7HI_F10


title: Lymphocyte-ETV001_T2_CCR7HI_E12


title: Lymphocyte-ETV001_T2_TEM_B1


title: Lymphocyte-ETV001_T2_CCR7HI_E11


title: Lymphocyte-ETV001_T2_CCR7HI_G8


title: Lymphocyte-ETV001_T2_CCR7HI_D9


title: Lymphocyte-ETV001_T2_CCR7HI_D7


title: Lymphocyte-ETV001_T2_CCR7HI_D8


title: Lymphocyte-ETV001_T2_CCR7HI_D11


title: Lymphocyte-ETV001_T2_CCR7HI_E8


title: Lymphocyte-ETV001_T2_CCR7HI_D10


title: Lymphocyte-ETV001_T2_CCR7HI_C11


title: Lymphocyte-ETV001_T2_CCR7HI_C9


title: Lymphocyte-ETV001_T2_CCR7HI_C8


title: Lymphocyte-ETV001_T2_CCR7HI_C12


title: Lymphocyte-ETV001_T2_CCR7HI_C7


title: Lymphocyte-ETV001_T2_CCR7HI_B7


title: Lymphocyte-ETV001_T2_CCR7HI_C10


title: Lymphocyte-ETV001_T2_CCR7HI_B9


title: Lymphocyte-ETV001_T2_CCR7HI_B8


title: Lymphocyte-ETV001_T2_CCR7HI_A11


title: Lymphocyte-ETV001_T2_CCR7HI_A8


title: Lymphocyte-ETV001_T2_CCR7HI_B12


title: Lymphocyte-ETV001_T2_CCR7HI_A7


title: Lymphocyte-ETV001_T1NEG_TEM_H5


title: Lymphocyte-ETV001_T2_CCR7HI_A12


title: Lymphocyte-ETV001_T2_CCR7HI_B10


title: Lymphocyte-ETV001_T2_CCR7HI_A9


title: Lymphocyte-ETV001_T2_CCR7HI_A10


title: Lymphocyte-ETV001_T1NEG_TEM_H6


title: Lymphocyte-ETV001_T2_CCR7HI_B11


title: Lymphocyte-ETV001_T1NEG_TEM_H4


title: Lymphocyte-ETV001_T1NEG_TEM_H3


title: Lymphocyte-ETV001_T1NEG_TEM_H1


title: Lymphocyte-ETV001_T1NEG_TEM_H2


title: Lymphocyte-ETV001_T1NEG_TEM_G5


title: Lymphocyte-ETV001_T1NEG_TEM_G6


title: Lymphocyte-ETV001_T1NEG_TEM_G2


title: Lymphocyte-ETV001_T1NEG_TEM_F6


title: Lymphocyte-ETV001_T1NEG_TEM_G1


title: Lymphocyte-ETV001_T1NEG_TEM_G3


title: Lymphocyte-ETV001_T1NEG_TEM_F4


title: Lymphocyte-ETV001_T1NEG_TEM_F3


title: Lymphocyte-ETV001_T1NEG_TEM_F5


title: Lymphocyte-ETV001_T1NEG_TEM_F1


title: Lymphocyte-ETV001_T2_CCR7HI_E10


title: Lymphocyte-ETV001_T1NEG_TEM_E5


title: Lymphocyte-ETV001_T1NEG_TEM_E6


title: Lymphocyte-ETV001_T1NEG_TEM_E3


title: Lymphocyte-ETV001_T1NEG_TEM_E2


title: Lymphocyte-ETV001_T1NEG_TEM_C5


title: Lymphocyte-ETV001_T1NEG_TEM_C6


title: Lymphocyte-ETV001_T1NEG_TEM_E4


title: Lymphocyte-ETV001_T1NEG_TEM_D3


title: Lymphocyte-ETV001_T1NEG_TEM_D2


title: Lymphocyte-ETV001_T1NEG_TEM_F2


title: Lymphocyte-ETV001_T1NEG_TEM_D1


title: Lymphocyte-ETV001_T1NEG_TEM_D5


title: Lymphocyte-ETV001_T1NEG_TEM_D6


title: Lymphocyte-ETV001_T1NEG_TEM_D4


title: Lymphocyte-ETV001_T1NEG_TEM_E1


title: Lymphocyte-ETV001_T1NEG_TEM_G4


title: Lymphocyte-ETV001_T1NEG_TEM_C4


title: Lymphocyte-ETV001_T1NEG_TEM_C2


title: Lymphocyte-ETV001_T1NEG_TEM_C3


title: Lymphocyte-ETV001_T1NEG_TEM_B6


title: Lymphocyte-ETV001_T1NEG_TEM_C1


title: Lymphocyte-ETV001_T1NEG_TEM_B5


title: Lymphocyte-ETV001_T1NEG_TEM_B4


title: Lymphocyte-ETV001_T1NEG_TEM_B3


title: Lymphocyte-ETV001_T1NEG_TEM_B1


title: Lymphocyte-ETV001_T1NEG_TEM_B2


title: Lymphocyte-ETV001_T1NEG_TEM_A6


title: Lymphocyte-ETV001_T1NEG_TEM_A5


title: Lymphocyte-ETV001_T1NEG_TEM_A2


title: Lymphocyte-ETV001_T1NEG_TEM_A3


title: Lymphocyte-ETV001_T1NEG_CCR7HI_H12


title: Lymphocyte-ETV001_T1NEG_CCR7HI_H9


title: Lymphocyte-ETV001_T1NEG_CCR7HI_H8


title: Lymphocyte-ETV001_T1NEG_CCR7HI_H7


title: Lymphocyte-ETV001_T1NEG_TEM_A4


title: Lymphocyte-ETV001_T1NEG_CCR7HI_H11


title: Lymphocyte-ETV001_T1NEG_CCR7HI_F9


title: Lymphocyte-ETV001_T1NEG_CCR7HI_G11


title: Lymphocyte-ETV001_T1NEG_CCR7HI_G9


title: Lymphocyte-ETV001_T1NEG_CCR7HI_G10


title: Lymphocyte-ETV001_T1NEG_CCR7HI_G8


title: Lymphocyte-ETV001_T1NEG_CCR7HI_H10


title: Lymphocyte-ETV001_T1NEG_CCR7HI_F8


title: Lymphocyte-ETV001_T1NEG_CCR7HI_G12


title: Lymphocyte-ETV001_T1NEG_CCR7HI_F12


title: Lymphocyte-ETV001_T1NEG_CCR7HI_F11


title: Lymphocyte-ETV001_T1NEG_CCR7HI_E9


title: Lymphocyte-ETV001_T1NEG_CCR7HI_E7


title: Lymphocyte-ETV001_T1NEG_CCR7HI_E8


title: Lymphocyte-ETV001_T1NEG_CCR7HI_F10


title: Lymphocyte-ETV001_T1NEG_TEM_A1


title: Lymphocyte-ETV001_T1NEG_CCR7HI_G7


title: Lymphocyte-ETV001_T1NEG_CCR7HI_E11


title: Lymphocyte-ETV001_T1NEG_CCR7HI_E10


title: Lymphocyte-ETV001_T1NEG_CCR7HI_D9


title: Lymphocyte-ETV001_T1NEG_CCR7HI_D12


title: Lymphocyte-ETV001_T1NEG_CCR7HI_D8


title: Lymphocyte-ETV001_T1NEG_CCR7HI_D10


title: Lymphocyte-ETV001_T1NEG_CCR7HI_C9


title: Lymphocyte-ETV001_T1NEG_CCR7HI_D7


title: Lymphocyte-ETV001_T1NEG_CCR7HI_C8


title: Lymphocyte-ETV001_T1NEG_CCR7HI_F7


title: Lymphocyte-ETV001_T1NEG_CCR7HI_C7


title: Lymphocyte-ETV001_T1NEG_CCR7HI_C12


title: Lymphocyte-ETV001_T1NEG_CCR7HI_B8


title: Lymphocyte-ETV001_T1NEG_CCR7HI_B7


title: Lymphocyte-ETV001_T1NEG_CCR7HI_C10


title: Lymphocyte-ETV001_T1NEG_CCR7HI_B9


title: Lymphocyte-ETV001_T1NEG_CCR7HI_C11


title: Lymphocyte-ETV001_T1NEG_CCR7HI_A9


title: Lymphocyte-ETV001_T1NEG_CCR7HI_B11


title: Lymphocyte-ETV001_T1NEG_CCR7HI_A8


title: Lymphocyte-ETV001_T1NEG_CCR7HI_E12


title: Lymphocyte-ETV001_T1NEG_CCR7HI_A10


title: Lymphocyte-ETV001_T1NEG_CCR7HI_A11


title: Lymphocyte-ETV001_T1_TEM_H4


title: Lymphocyte-ETV001_T1NEG_CCR7HI_D11


title: Lymphocyte-ETV001_T1NEG_CCR7HI_B12


title: Lymphocyte-ETV001_T1_TEM_H5


title: Lymphocyte-ETV001_T1_TEM_G4


title: Lymphocyte-ETV001_T1_TEM_G6


title: Lymphocyte-ETV001_T1_TEM_G5


title: Lymphocyte-ETV001_T1_TEM_G3


title: Lymphocyte-ETV001_T1NEG_CCR7HI_A7


title: Lymphocyte-ETV001_T1_TEM_F5


title: Lymphocyte-ETV001_T1_TEM_F3


title: Lymphocyte-ETV001_T1NEG_CCR7HI_A12


title: Lymphocyte-ETV001_T1_TEM_G1


title: Lymphocyte-ETV001_T1_TEM_F6


title: Lymphocyte-ETV001_T1_TEM_F2


title: Lymphocyte-ETV001_T1_TEM_F4


title: Lymphocyte-ETV001_T1_TEM_F1


title: Lymphocyte-ETV001_T1_TEM_E6


title: Lymphocyte-ETV001_T1_TEM_E2


title: Lymphocyte-ETV001_T1_TEM_H6


title: Lymphocyte-ETV001_T1_TEM_E3


title: Lymphocyte-ETV001_T1_TEM_E4


title: Lymphocyte-ETV001_T1_TEM_E1


title: Lymphocyte-ETV001_T1_TEM_H3


title: Lymphocyte-ETV001_T1_TEM_H1


title: Lymphocyte-ETV001_T1_TEM_D6


title: Lymphocyte-ETV001_T1_TEM_D5


title: Lymphocyte-ETV001_T1_TEM_D4


title: Lymphocyte-ETV001_T1_TEM_E5


title: Lymphocyte-ETV001_T1_TEM_D3


title: Lymphocyte-ETV001_T1_TEM_D2


title: Lymphocyte-ETV001_T1_TEM_G2


title: Lymphocyte-ETV001_T1_TEM_C6


title: Lymphocyte-ETV001_T1_TEM_C5


title: Lymphocyte-ETV001_T1_TEM_D1


title: Lymphocyte-ETV001_T1_TEM_C3


title: Lymphocyte-ETV001_T1_TEM_C2


title: Lymphocyte-ETV001_T1_TEM_C4


title: Lymphocyte-ETV001_T1_TEM_B6


title: Lymphocyte-ETV001_T1_TEM_B2


title: Lymphocyte-ETV001_T1_TEM_B5


title: Lymphocyte-ETV001_T1_TEM_B4


title: Lymphocyte-ETV001_T1_TEM_B3


title: Lymphocyte-ETV001_T1_TEM_A6


title: Lymphocyte-ETV001_T1_TEM_A5


title: Lymphocyte-ETV001_T1_TEM_A4


title: Lymphocyte-ETV001_T1_TEM_A3


title: Lymphocyte-ETV001_T1_TEM_A2


title: Lymphocyte-ETV001_T1_CCR7HI_H9


title: Lymphocyte-ETV001_T1_CCR7HI_H8


title: Lymphocyte-ETV001_T1_CCR7HI_H7


title: Lymphocyte-ETV001_T1_TEM_A1


title: Lymphocyte-ETV001_T1_CCR7HI_H11


title: Lymphocyte-ETV001_T1_CCR7HI_H10


title: Lymphocyte-ETV001_T1_TEM_C1


title: Lymphocyte-ETV001_T1_CCR7HI_G8


title: Lymphocyte-ETV001_T1_CCR7HI_G10


title: Lymphocyte-ETV001_T1_CCR7HI_G7


title: Lymphocyte-ETV001_T1_TEM_B1


title: Lymphocyte-ETV001_T1_CCR7HI_G12


title: Lymphocyte-ETV001_T1_CCR7HI_F8


title: Lymphocyte-ETV001_T1_CCR7HI_F11


title: Lymphocyte-ETV001_T1_CCR7HI_G11


title: Lymphocyte-ETV001_T1_CCR7HI_F7


title: Lymphocyte-ETV001_T1_CCR7HI_F12


title: Lymphocyte-ETV001_T1_CCR7HI_F10


title: Lymphocyte-ETV001_T1_CCR7HI_E11


title: Lymphocyte-ETV001_T1_CCR7HI_E12


title: Lymphocyte-ETV001_T1_CCR7HI_E10


title: Lymphocyte-ETV001_T1_CCR7HI_E7


title: Lymphocyte-ETV001_T1_CCR7HI_H12


title: Lymphocyte-ETV001_T1_CCR7HI_D8


title: Lymphocyte-ETV001_T1_CCR7HI_C9


title: Lymphocyte-ETV001_T1_CCR7HI_D7


title: Lymphocyte-ETV001_T1_CCR7HI_D10


title: Lymphocyte-ETV001_T1_CCR7HI_D11


title: Lymphocyte-ETV001_T1_CCR7HI_C8


title: Lymphocyte-ETV001_T1_CCR7HI_C12


title: Lymphocyte-ETV001_T1_CCR7HI_C7


title: Lymphocyte-ETV001_T1_CCR7HI_C11


title: Lymphocyte-ETV001_T1_CCR7HI_B9


title: Lymphocyte-ETV001_T1_CCR7HI_C10


title: Lymphocyte-ETV001_T1_CCR7HI_B12


title: Lymphocyte-ETV001_T1_CCR7HI_E8


title: Lymphocyte-ETV001_T1_CCR7HI_B7


title: Lymphocyte-ETV001_T1_CCR7HI_B11


title: Lymphocyte-ETV001_T1_CCR7HI_B8


title: Lymphocyte-ETV001_T1_CCR7HI_B10


title: Lymphocyte-ETV001_T1_CCR7HI_A12


title: Lymphocyte-ETV001_T1_CCR7HI_A7


title: Lymphocyte-ETV001_T1_CCR7HI_D12


title: Lymphocyte-ETV001_T1_CCR7HI_A10


title: Lymphocyte-ETV001_T1_CCR7HI_A11


title: Lymphocyte-ETV001_T1_CCR7HI_A9


title: Lymphocyte-ERG009_T2_TEM_H1


title: Lymphocyte-ERG009_T2_TEM_H4


title: Lymphocyte-ERG009_T2_TEM_H5


title: Lymphocyte-ERG009_T2_TEM_H2


title: Lymphocyte-ERG009_T2_TEM_H6


title: Lymphocyte-ERG009_T2_TEM_G3


title: Lymphocyte-ERG009_T2_TEM_G6


title: Lymphocyte-ERG009_T2_TEM_G5


title: Lymphocyte-ERG009_T2_TEM_G1


title: Lymphocyte-ERG009_T2_TEM_F6


title: Lymphocyte-ERG009_T2_TEM_G2


title: Lymphocyte-ERG009_T2_TEM_F5


title: Lymphocyte-ERG009_T2_TEM_F4


title: Lymphocyte-ERG009_T2_TEM_G4


title: Lymphocyte-ERG009_T2_TEM_F3


title: Lymphocyte-ERG009_T2_TEM_F2


title: Lymphocyte-ERG009_T2_TEM_F1


title: Lymphocyte-ERG009_T2_TEM_H3


title: Lymphocyte-ERG009_T2_TEM_E5


title: Lymphocyte-ERG009_T2_TEM_E4


title: Lymphocyte-ERG009_T2_TEM_E1


title: Lymphocyte-ERG009_T2_TEM_E2


title: Lymphocyte-ERG009_T2_TEM_E3


title: Lymphocyte-ERG009_T2_TEM_D6


title: Lymphocyte-ERG009_T2_TEM_E6


title: Lymphocyte-ETV001_T1_CCR7HI_A8


title: Lymphocyte-ERG009_T2_TEM_C6


title: Lymphocyte-ERG009_T2_TEM_D3


title: Lymphocyte-ERG009_T2_TEM_C4


title: Lymphocyte-ERG009_T2_TEM_C5


title: Lymphocyte-ERG009_T2_TEM_D1


title: Lymphocyte-ERG009_T2_TEM_C1


title: Lymphocyte-ERG009_T2_TEM_B1


title: Lymphocyte-ERG009_T2_TEM_B5


title: Lymphocyte-ERG009_T2_TEM_C2


title: Lymphocyte-ERG009_T2_TEM_B2


title: Lymphocyte-ERG009_T2_TEM_B4


title: Lymphocyte-ERG009_T2_TEM_A5


title: Lymphocyte-ERG009_T2_TEM_A6


title: Lymphocyte-ERG009_T2_TEM_D5


title: Lymphocyte-ERG009_T2_TEM_B3


title: Lymphocyte-ERG009_T2_TEM_A3


title: Lymphocyte-ERG009_T2_TEM_A4


title: Lymphocyte-ERG009_T2_TEM_D2


title: Lymphocyte-ERG009_T2_TEM_A1


title: Lymphocyte-ERG009_T2_CCR7HI_H7


title: Lymphocyte-ERG009_T2_TEM_A2


title: Lymphocyte-ERG009_T2_CCR7HI_H12


title: Lymphocyte-ERG009_T2_CCR7HI_H8


title: Lymphocyte-ERG009_T2_TEM_C3


title: Lymphocyte-ERG009_T2_CCR7HI_G7


title: Lymphocyte-ERG009_T2_CCR7HI_H11


title: Lymphocyte-ERG009_T2_CCR7HI_H10


title: Lymphocyte-ERG009_T2_TEM_B6


title: Lymphocyte-ERG009_T2_CCR7HI_G9


title: Lymphocyte-ERG009_T2_CCR7HI_G11


title: Lymphocyte-ERG009_T2_CCR7HI_H9


title: Lymphocyte-ERG009_T2_CCR7HI_G12


title: Lymphocyte-ETV001_T1_TEM_H2


title: Lymphocyte-ERG009_T2_CCR7HI_D8


title: Lymphocyte-ERG009_T2_CCR7HI_F9


title: Lymphocyte-ERG009_T2_CCR7HI_F11


title: Lymphocyte-ERG009_T2_CCR7HI_G8


title: Lymphocyte-ERG009_T2_CCR7HI_E10


title: Lymphocyte-ERG009_T2_CCR7HI_D10


title: Lymphocyte-ERG009_T2_CCR7HI_F10


title: Lymphocyte-ERG009_T2_CCR7HI_F7


title: Lymphocyte-ERG009_T2_CCR7HI_C9


title: Lymphocyte-ERG009_T2_CCR7HI_D11


title: Lymphocyte-ERG009_T2_CCR7HI_D12


title: Lymphocyte-ERG009_T2_CCR7HI_D9


title: Lymphocyte-ERG009_T2_CCR7HI_E8


title: Lymphocyte-ERG009_T2_CCR7HI_E9


title: Lymphocyte-ERG009_T2_CCR7HI_F12


title: Lymphocyte-ERG009_T2_CCR7HI_G10


title: Lymphocyte-ERG009_T2_CCR7HI_C11


title: Lymphocyte-ERG009_T2_CCR7HI_C10


title: Lymphocyte-ERG009_T2_CCR7HI_E7


title: Lymphocyte-ERG009_T2_CCR7HI_B12


title: Lymphocyte-ERG009_T2_CCR7HI_C8


title: Lymphocyte-ERG009_T2_CCR7HI_B7


title: Lymphocyte-ERG009_T2_CCR7HI_B9


title: Lymphocyte-ERG009_T2_CCR7HI_C7


title: Lymphocyte-ERG009_T2_CCR7HI_A11


title: Lymphocyte-ERG009_T2_CCR7HI_A8


title: Lymphocyte-ERG009_T2_CCR7HI_B10


title: Lymphocyte-ERG009_T2_CCR7HI_A7


title: Lymphocyte-ERG009_T2_CCR7HI_A12


title: Lymphocyte-ERG009_T2_CCR7HI_A10


title: Lymphocyte-ERG009_T2_CCR7HI_C12


title: Lymphocyte-ERG009_T1NEG_TEM_H4


title: Lymphocyte-ERG009_T1NEG_TEM_G5


title: Lymphocyte-ERG009_T1NEG_TEM_G2


title: Lymphocyte-ERG009_T1NEG_TEM_G6


title: Lymphocyte-ERG009_T1NEG_TEM_H1


title: Lymphocyte-ERG009_T1NEG_TEM_G4


title: Lymphocyte-ERG009_T1NEG_TEM_H3


title: Lymphocyte-ERG009_T1NEG_TEM_G3


title: Lymphocyte-ERG009_T1NEG_TEM_H5


title: Lymphocyte-ERG009_T1NEG_TEM_F4


title: Lymphocyte-ERG009_T1NEG_TEM_G1


title: Lymphocyte-ERG009_T1NEG_TEM_F3


title: Lymphocyte-ERG009_T1NEG_TEM_F2


title: Lymphocyte-ERG009_T2_CCR7HI_B8


title: Lymphocyte-ERG009_T1NEG_TEM_F5


title: Lymphocyte-ERG009_T1NEG_TEM_F6


title: Lymphocyte-ERG009_T2_CCR7HI_F8


title: Lymphocyte-ERG009_T1NEG_TEM_D3


title: Lymphocyte-ERG009_T1NEG_TEM_D5


title: Lymphocyte-ERG009_T1NEG_TEM_E2


title: Lymphocyte-ERG009_T1NEG_TEM_E4


title: Lymphocyte-ERG009_T1NEG_TEM_E5


title: Lymphocyte-ERG009_T2_CCR7HI_E11


title: Lymphocyte-ERG009_T1NEG_TEM_F1


title: Lymphocyte-ERG009_T1NEG_TEM_E3


title: Lymphocyte-ERG009_T1NEG_TEM_E1


title: Lymphocyte-ERG009_T1NEG_TEM_H6


title: Lymphocyte-ERG009_T1NEG_TEM_E6


title: Lymphocyte-ERG009_T1NEG_TEM_C6


title: Lymphocyte-ERG009_T1NEG_TEM_D1


title: Lymphocyte-ERG009_T1NEG_TEM_D2


title: Lymphocyte-ERG009_T1NEG_TEM_C2


title: Lymphocyte-ERG009_T1NEG_TEM_C3


title: Lymphocyte-ERG009_T1NEG_TEM_C5


title: Lymphocyte-ERG009_T2_TEM_D4


title: Lymphocyte-ERG009_T1NEG_TEM_B3


title: Lymphocyte-ERG009_T1NEG_TEM_B6


title: Lymphocyte-ERG009_T1NEG_TEM_C1


title: Lymphocyte-ERG009_T1NEG_TEM_A6


title: Lymphocyte-ERG009_T1NEG_TEM_B5


title: Lymphocyte-ERG009_T1NEG_TEM_B2


title: Lymphocyte-ERG009_T1NEG_TEM_B1


title: Lymphocyte-ERG009_T1NEG_TEM_B4


title: Lymphocyte-ERG009_T1NEG_TEM_A4


title: Lymphocyte-ERG009_T1NEG_TEM_A5


title: Lymphocyte-ERG009_T1NEG_CCR7HI_F8


title: Lymphocyte-ERG009_T1NEG_CCR7HI_F9


title: Lymphocyte-ERG009_T1NEG_CCR7HI_H10


title: Lymphocyte-ERG009_T1NEG_CCR7HI_H8


title: Lymphocyte-ERG009_T1NEG_CCR7HI_H12


title: Lymphocyte-ERG009_T1NEG_CCR7HI_G8


title: Lymphocyte-ERG009_T1NEG_CCR7HI_H7


title: Lymphocyte-ERG009_T1NEG_CCR7HI_G12


title: Lymphocyte-ERG009_T1NEG_CCR7HI_G10


title: Lymphocyte-ERG009_T1NEG_CCR7HI_G11


title: Lymphocyte-ERG009_T1NEG_CCR7HI_H9


title: Lymphocyte-ERG009_T1NEG_CCR7HI_H11


title: Lymphocyte-ERG009_T1NEG_CCR7HI_G7


title: Lymphocyte-ERG009_T1NEG_CCR7HI_F10


title: Lymphocyte-ERG009_T1NEG_TEM_A2


title: Lymphocyte-ERG009_T1NEG_CCR7HI_E8


title: Lymphocyte-ERG009_T1NEG_CCR7HI_E7


title: Lymphocyte-ERG009_T1NEG_CCR7HI_E11


title: Lymphocyte-ERG009_T1NEG_TEM_C4


title: Lymphocyte-ERG009_T1NEG_CCR7HI_E10


title: Lymphocyte-ERG009_T1NEG_CCR7HI_F7


title: Lymphocyte-ERG009_T1NEG_CCR7HI_D9


title: Lymphocyte-ERG009_T1NEG_CCR7HI_D8


title: Lymphocyte-ERG009_T1NEG_CCR7HI_G9


title: Lymphocyte-ERG009_T1NEG_CCR7HI_F11


title: Lymphocyte-ERG009_T1NEG_CCR7HI_F12


title: Lymphocyte-ERG009_T1NEG_TEM_A3


title: Lymphocyte-ERG009_T1NEG_CCR7HI_E9


title: Lymphocyte-ERG009_T1NEG_CCR7HI_E12


title: Lymphocyte-ERG009_T1NEG_CCR7HI_D12


title: Lymphocyte-ERG009_T1NEG_CCR7HI_D7


title: Lymphocyte-ERG009_T1NEG_TEM_A1


title: Lymphocyte-ERG009_T1NEG_CCR7HI_C8


title: Lymphocyte-ERG009_T1NEG_CCR7HI_C9


title: Lymphocyte-ERG009_T1NEG_CCR7HI_D11


title: Lymphocyte-ERG009_T1NEG_CCR7HI_C10


title: Lymphocyte-ERG009_T1NEG_CCR7HI_C11


title: Lymphocyte-ERG009_T1NEG_CCR7HI_B8


title: Lymphocyte-ERG009_T1NEG_CCR7HI_D10


title: Lymphocyte-ERG009_T1NEG_CCR7HI_B7


title: Lymphocyte-ERG009_T1NEG_CCR7HI_B12


title: Lymphocyte-ERG009_T1NEG_CCR7HI_B9


title: Lymphocyte-ERG009_T1NEG_CCR7HI_A8


title: Lymphocyte-ERG009_T1NEG_CCR7HI_A9


title: Lymphocyte-ERG009_T1NEG_CCR7HI_A12


title: Lymphocyte-ERG009_T1NEG_CCR7HI_A7


title: Lymphocyte-ERG009_T1NEG_CCR7HI_A11


title: Lymphocyte-ERG009_T1NEG_CCR7HI_C7


title: Lymphocyte-ERG009_T1_TEM_H6


title: Lymphocyte-ERG009_T1_TEM_H3


title: Lymphocyte-ERG009_T1_TEM_H4


title: Lymphocyte-ERG009_T1_TEM_H5


title: Lymphocyte-ERG009_T1NEG_CCR7HI_B10


title: Lymphocyte-ERG009_T1_TEM_H1


title: Lymphocyte-ERG009_T1NEG_CCR7HI_A10


title: Lymphocyte-ERG009_T1_TEM_G4


title: Lymphocyte-ERG009_T1NEG_CCR7HI_B11


title: Lymphocyte-ERG009_T1_TEM_G3


title: Lymphocyte-ERG009_T1_TEM_F4


title: Lymphocyte-ERG009_T1_TEM_G2


title: Lymphocyte-ERG009_T1_TEM_G1


title: Lymphocyte-ERG009_T1_TEM_F5


title: Lymphocyte-ERG009_T1_TEM_F2


title: Lymphocyte-ERG009_T1_TEM_E4


title: Lymphocyte-ERG009_T1_TEM_G5


title: Lymphocyte-ERG009_T1_TEM_F1


title: Lymphocyte-ERG009_T1_TEM_D3


title: Lymphocyte-ERG009_T1_TEM_E3


title: Lymphocyte-ERG009_T1_TEM_D4


title: Lymphocyte-ERG009_T1_TEM_F3


title: Lymphocyte-ERG009_T1_TEM_D5


title: Lymphocyte-ERG009_T1_TEM_F6


title: Lymphocyte-ERG009_T1_TEM_H2


title: Lymphocyte-ERG009_T1_TEM_C6


title: Lymphocyte-ERG009_T1_TEM_D1


title: Lymphocyte-ERG009_T1_TEM_D2


title: Lymphocyte-ERG009_T1_TEM_E5


title: Lymphocyte-ERG009_T1_TEM_C2


title: Lymphocyte-ERG009_T1_TEM_C3


title: Lymphocyte-ERG009_T1_TEM_B6


title: Lymphocyte-ERG009_T1_TEM_B5


title: Lymphocyte-ERG009_T1_TEM_C1


title: Lymphocyte-ERG009_T1_TEM_C4


title: Lymphocyte-ERG009_T1_TEM_E2


title: Ni4-3

city: Piscataway

first: Joachim

last: Messing

state: NJ

address: 190 Frelinghuysen Rd

institute: Waksman Institute of Microbiology, Rutgers University

data_processing:
For library construction, DNA/RNA is extracted from a sample. After performing quality  control(QC), qualified samples proceed to library construction.
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.
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.
Sequencing data is converted into raw data for the analysis
Genome_build: B73v4 genome
Supplementary_files_format_and_content: the text files include counts of raw reads and the normalized FPKM values

source_name: developing endosperm

extract_protocol:
Total RNA was extracted from developing endosperms and other tissues using TRIzol reagent (Invitrogen) and purified with the RNeasy Mini Kit and DNase 1 digestion (Qiagen).
Truseq mRNA kit was used for the sequencing library 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.

tag: genotype/variation

value: nacRNAi siblings (Ni4)

tag: inbred

value: Endosperm

value: 20 day after pollination


title: Lymphocyte-ERG009_T1_TEM_E1


title: Ni4-2

tag: time point


title: Lymphocyte-ERG009_T1_TEM_B4


title: Lymphocyte-ERG009_T1_TEM_B2


title: Lymphocyte-ERG009_T1_TEM_D6


title: B73-3

value: wildtype


title: B73-2


title: Ni4-1


title: Lymphocyte-ERG009_T1_TEM_A6


title: Lymphocyte-ERG009_T1_TEM_B1


title: Lymphocyte-ERG009_T1_TEM_A5


title: Lymphocyte-ERG009_T1_TEM_A2


title: Lymphocyte-ERG009_T1_TEM_A1


title: Lymphocyte-ERG009_T1_TEM_B3


title: Lymphocyte-ERG009_T1_CCR7HI_H9


title: Lymphocyte-ERG009_T1_CCR7HI_H8


title: Lymphocyte-ERG009_T1_CCR7HI_H12


title: Lymphocyte-ERG009_T1_CCR7HI_H7


title: B73-1


title: Lymphocyte-ERG009_T1_CCR7HI_H11


title: Lymphocyte-ERG009_T1_TEM_A3


title: Lymphocyte-ERG009_T1_TEM_A4


title: Lymphocyte-ERG009_T1_CCR7HI_G7


title: Lymphocyte-ERG009_T1_CCR7HI_G12


title: Pax5+/- IR leukemic bone marrow B cells, biological replicate 10

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description: Gene expression data from leukemic Pax5+/- IR bone marrow cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The RMA function provided by the package oligo from R/Bioconductor was applied to the raw expression data.

label: biotin

source_name: Leukemic Pax5+/- IR

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Ambion)

growth_protocol: Animals were housed in SPF facility after 2 Gy irradiation

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Not applicable

tag: disease state

value: leukemic

value: Bone marrow

value: B cells

tag: treatment

value: three weeks of 2Gy irradiation


title: Pax5+/- IR leukemic bone marrow B cells, biological replicate 6


title: Pax5+/- IR leukemic bone marrow B cells, biological replicate 8


title: Pax5+/- IR leukemic bone marrow B cells, biological replicate 9


title: Lymphocyte-ERG009_T1_CCR7HI_G10


title: Pax5+/- IR leukemic bone marrow B cells, biological replicate 4


title: Pax5+/- IR leukemic bone marrow B cells, biological replicate 7


title: Pax5+/- IR leukemic bone marrow B cells, biological replicate 3


title: Pax5+/- IR preleukemic bone marrow pro/pre-B cells, biological replicate 7

description: Gene expression data from preleukemic Pax5+/- IR pro/pre-B cells

source_name: Preleukemic Pax5+/- IR

value: preleukemic

value: pro/pre-B cells


title: Pax5+/- IR leukemic bone marrow B cells, biological replicate 1


title: Pax5+/- IR leukemic bone marrow B cells, biological replicate 2


title: Pax5+/- IR preleukemic bone marrow pro/pre-B cells, biological replicate 5


title: Lymphocyte-ERG009_T1_CCR7HI_F9


title: Lymphocyte-ERG009_T1_CCR7HI_H10


title: Lymphocyte-ERG009_T1_CCR7HI_G9


title: Pax5+/- IR preleukemic bone marrow pro/pre-B cells, biological replicate 3


title: Lymphocyte-ERG009_T1_CCR7HI_G8


title: Pax5+/- IR preleukemic bone marrow pro/pre-B cells, biological replicate 4


title: Pax5+/- IR leukemic bone marrow B cells, biological replicate 5


title: Pax5+/- IR preleukemic bone marrow pro/pre-B cells, biological replicate 2


title: Pax5+/- IR preleukemic bone marrow pro/pre-B cells, biological replicate 6


title: WT-IR preleukemic bone marrow pro/pre-B cells, biological replicate 3

description: Gene expression data from preleukemic WT-IR pro/pre-B cells

source_name: Preleukemic WT-IR

value: WT


title: Pax5+/- IR preleukemic bone marrow pro/pre-B cells, biological replicate 1


title: Lymphocyte-ERG009_T1_CCR7HI_F11


title: Lymphocyte-ERG009_T1_CCR7HI_F12


title: WT-IR preleukemic bone marrow pro/pre-B cells, biological replicate 2


title: Lymphocyte-ERG009_T1_CCR7HI_F8


title: Lymphocyte-ERG009_T1_CCR7HI_F10


title: Lymphocyte-ERG009_T1_CCR7HI_F7


title: Lymphocyte-ERG009_T1_CCR7HI_E9


title: Lymphocyte-ERG009_T1_CCR7HI_E8


title: Lymphocyte-ERG009_T1_CCR7HI_E7


title: Lymphocyte-ERG009_T1_CCR7HI_E10


title: Lymphocyte-ERG009_T1_CCR7HI_E11


title: Lymphocyte-ERG009_T1_CCR7HI_E12


title: Lymphocyte-ERG009_T1_CCR7HI_D9


title: Lymphocyte-ERG009_T1_CCR7HI_D8


title: Lymphocyte-ERG009_T1_CCR7HI_D7


title: WT-IR leukemic bone marrow B cells, biological replicate 4

description: Gene expression data from leukemic WT-IR bone marrow cells

source_name: Leukemic WT-IR


title: WT-IR preleukemic bone marrow pro/pre-B cells, biological replicate 1


title: Lymphocyte-ERG009_T1_CCR7HI_D11


title: Lymphocyte-ERG009_T1_CCR7HI_D12