title: sj-DK

city: Qingdao

first: Wei

last: Li

state: Shandong

address: No 7 Nanhai Road

institute: Institute of Oceanology, Chinese Academy of Sciences

description: small RNA sequencing

data_processing:
Raw data files: sj-BL.fq and sj-DK.fq are raw reads produeced by Solexa sequencing machine, fastq format.
Processed data files:  known_miRNAs_in_BL_and_DK_samples.txt and differentially_expressed_known_miRNAs.txt [linked as supplementary files on Series record]
Software = Beijing Genomics Institute (BGI) "tag2miRNA".
Remove low qulity reads strictly
Trim 3' adaptor sequence, Remove 5' adaptor contaminants
Plot data length distribution
Remove too small and polyA
Genome_build: model brown alga Ectocarpus siliculosus [EMBL: CABU01000001-CABU01013533, FN647682-FN649242]

organism: Saccharina japonica

source_name: blade of sporophyte

extract_protocol: Total RNA was extracted from blade of S. japonica using the improved method of Cetyl Trimethylammonium Bromide (CTAB), RNA integrity, quantity and size were detected by Agilent 2100 Bioanalyzer. Requirements for constructing library are as follows: content>200 ng/μl, total amount >10 μg, OD260/280 is 1.8-2.2, RIN≥8. Then, sRNAs were separated by size fractionation on denaturing polyacrylamide gels. Fragments of 18-30 nt were purified and ligated with 5’ and 3’ RNA adaptor and then amplified by reverse transcription PCR (RT-PCR). Thereafter the purified products were sequenced on a Solexa sequencer (Illumina) according to the manufacturer’s protocols.

tag: treatment

value: dark


title: siNSsiNS dex replicate 1

status: Public on Jun 12 2017

type: SRA

city: Los Angeles

first: Brian

middle: Hae Kang

last: Lee

state: CA

address: 1441 Eastlake Avenue, NOR 6316

department: Biochemistry and Molecular Medicine

country: USA

institute: University of Southern California

library_source: transcriptomic

data_processing:
NextSeq Control Software (NCS) v1.4 was used for base calling
After trimming the raw reads for quality and adapter sequence, the samples were mapped using TopHat 2.1.1 with default parameters against the GRCh38/hg38 human reference genome
Mapped reads were quantified to known UCSC genes using the GenomicAlignments R package
Gene expression levels were normalized with the upper quantile (UQ) method and lowly expressing genes were excluded such that genes with more than one count per million in at least 3 samples were analyzed
We implemented the remove unwanted variation (RUV) strategy to account for unknown nuisance technical effects between samples.
Differentially expressed genes were identified with edgeR using a 1.3-fold change in expression (log2 = 0.4) and false discovery rate adjusted p-value ≤ 0.05 as cutoffs
Genome_build: hg38
Supplementary_files_format_and_content: comma separated file (csv) containing CPM values with each gene represented in each row and the experimental conditions as columns

molecule: total RNA

organism: Homo sapiens

source_name: U2OS-GR⍺ cells

growth_protocol: Cells were grown in DMEM low glucose medium supplemented with 5% (vol/vol) FBS

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Scientific) and 3 biological replicates for each condition were performed on different days.
RNA samples were reverse transcribed using iScript cDNA synthesis kit (Bio-Rad) and quality of the cDNA was assessed using Agilent Technologies 2100 Bioanalyzer and RT-qPCR analysis was performed for selected GR target genes as quality control. Standard illumina protocols were used to construct the library for sequencing.

treatment_protocol: siRNA transfection was performed using Lipofractamine RNAimax (invitrogen) according to the manufacturer's protocol. 48 h after siRNA transfection the cells were either treated for 8 hours with 100 nM dex (Sigma) or an equivalent amount of ethanol as control.

tag: cell line

value: U2OS cell line stably transfected with GR{alpha}


title: sj-BL

country: China

description: small RNA sequencing

value: blue light irradiation


title: 6-D2-Th17_S6_L001_R1_001

city: London

first: Reuben

last: McGregor

address: Great Maze Pond

country: United Kingdom

institute: Kings College London

data_processing:
qiagen analysis pipeline for targeted RNAseq panels was used (http://www.qiagen.com/shop/genes-and-pathways/data-analysis-center-overview-page/?akamai-feo=off0
RNAseq was a targeted panel. Only targeted with primers at some 500 immunology genes.
adaptors trimmed, reads< 55bp droped, first 12bp dropped form every read (as they cointain molecular tags) and ampped using STAR RNA read mapper. Non mapped reads were dropped
bam files were then imported into PARTEk genomics suite for generation of RPKM values
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: tab-delimited text file (reubenmcg_RNASeq_results.gene.rpkm) includes RPKM values for each Sample

source_name: CD4+ T cell Peripheral Blood

extract_protocol:
FACS-sorted Th-like Tregs (2x105 per well) were activated with CD3/CD28 beads (ratio 1:4) for 72h. Cells were lysed in Trizol (Thermo Fisher Scientific) and RNA was isolated with Direct-Zol RNA MicroPrep w/Zymo-Spin columns (Cambridge Bioscience). RNA sequencing was performed using The Human Inflammation & Immunity Transcriptome RNA targeted panel (Qiagen). Samples were quantified with Agilent High Sensitivity DNA Kit (Agilent Technologies) and sequenced with Illumina MiSeq using MiSeq Reagent Kit v3 (150-cycle). 100ng of RNA was used to construct libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols provided but with kits procided by Qiagen

tag: donor

tag: t-helper like treg


title: 8-D2-Th1-17_S8_L001_R1_001


title: 4-D1-Th1-17_S4_L001_R1_001


title: 3-D1-Th1_S3_L001_R1_001


title: Stage 4 infected

city: New Delhi

first: Gopal

last: Joshi

state: Delhi

address: First Floor

department: Department of Botany

country: India

institute: Delhi University

description: small RNA profiling

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequencing data was filtered through a pipeline of UEA small RNA workbench 3.0 with default parameters (Stocks et al. 2012). The sequences without 3’ adaptor and those trimmed sequences not lying between the specified sequence lengths were discarded and sequences with the length specified by the user (16-35 nt) were extracted. Further, low complexity sequences (sequences containing less than 3 distinct nucleotides), invalid tags with ‘N’ nucleotides, degradation products and other non-small RNAs were discarded. The fragments of rRNA, tRNA, snRNA or snoRNA were removed after being mapped on plant t/rRNAs sequences from “Rfam” (except miRNA), Arabidopsis tRNAs from “The Genomic tRNA Database”, and plant t/rRNA sequences from “EMBL” release 95.
For identification of miRNAs and their precursors, the clean putative small RNA reads obtained after filtration through elimination pipeline were aligned to tomato reference genome dataset (Solanaceae Genomics Project Assembly SL2.40 obtained from NCBI) (The Tomato Genome Consortium) with no mismatch by using miRCat pipeline of UEA sRNA tool kit with set parameters (Stocks et al. 2012).
Genome_build: Solanaceae Genomics Project Assembly SL2.40
Supplementary_files_format_and_content: The .txt files report abundance measurements of small RNA reads

organism: Solanum lycopersicum

source_name: ROOT

growth_protocol: Disease development study was conducted using root knot nematode, M. incognita. RKN was propagated on susceptible Indian tomato cv. Pusa Ruby in infection house at Department of Botany, University of Delhi, India. Infection studies were conducted under controlled growth conditions at 22oC with 16 hour light and 8 hour dark photoperiod. For miRNA studies, tomato susceptible cv., Pusa Ruby and tomato resistant transgenic line that contains Mi-1 resistance gene were used.

extract_protocol:
Root tissue of equal weight of each disease development stage was processed for RNA isolation using TRI reagent (Sigma-Aldrich, St. Louis, MO, U.S.A.) as per manufacturer’s instructions. The integrity of RNA was checked on 1.2% agarose gel and quantification was done through optical density measurement using nanovue (GE Healthcare Bio-sciences, Uppsala, Sweden).
In total 11 small RNA libraries were prepared including five infected disease development stages and their corresponding uninfected tissue of same age and a library of five-week old uninfected root tissue of susceptible tomato cv. Small RNA libraries from root tissue of each stage were prepared independently using Illumina small RNA sample preparation kit (Illumina, San Diego, CA, U.S.A.) according to manufacturer’s instructions. Briefly, an equal amount of total RNA of each stage was used for sequential ligation of 3’and 5’adapter using T4 RNA ligase. Adapter ligated small RNA was reverse transcribed using SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA, U.S.A.) and 3’ adapter specific RT-primer. cDNA prepared was amplified and product of approximately 147 bp was eluted through 6% polyacrylamide gel. The quality and quantity of cDNA libraries prepared were determined through Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, U.S.A.). High-throughput sequencing of libraries was performed using Illumina Hiseq 2000 system at Institute of Genomics and Integrative Biology, Delhi, India, according to manufacturer’s instructions.

treatment_protocol: The second juvenile stage (J2) is the only parasitic stage that was used for infecting plants, therefore, egg masses were detached manually from infected roots and kept in deionised water at room temperature for hatching of eggs into J2s. After 2-3 days, J2s were separated from unhatched eggs by passing the suspension of J2s through three to four layered kim wipes. The five-week old plantlets of both susceptible cv. and resistant line were grown in sterile soil and inoculated with 1500 J2s. The control plantlets were also raised that have not been exposed to nematode. For tissue collection, in susceptible cv. for 30 days and resistant line for 7 days, plantlets were uprooted, roots were quickly washed under cold tap water, excised from the plant and snap chilled in liquid nitrogen. Tissue was kept in -80o C for subsequent storage. The root tissue of uninfected plantlets of the same age was also harvested as control samples. The additional one plant was harvested on each day to study the lifecycle of nematode inside the root and progression of the disease through acid fuchsin staining (Bybd et al. 1983). After uprooting, roots were washed and suspended in 1.5% sodium hypochlorite bleach for 4 mins and then washed to remove excess bleach. For staining, roots were boiled for a minute in 0.2% acid fuchsin stain prepared in lactophenol followed by clearing of roots. The whole plant root system was observed under the inverted microscope (Carl Zeiss, Gottingen, Germany) and number of nematodes at their different development stage were counted. Five disease development stages of susceptible response and two disease development stages of resistance response were selected for further study on the basis of the rate of nematode invasion, a number of knots/galls formed on infected root, transition of varied developmental stages of nematode and progression of disease in the host.

tag: cultivar

value: Pusa ruby

tag: tissue

value: root

tag: age

value: 5 week old + (18dpi+19dpi+20dpi)

tag: uninfected or infected

value: infected


title: 12-D3-Th1-17_S12_L001_R1_001


title: 2-D1-Th17_S2_L001_R1_001


title: 1-D1-Th2_S1_L001_R1_001


title: D87ALI31

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: Human Airway epithelial cells cultured in vitro obtained during late phase of differentiation (ALI31)

data_processing:
Mapping versus hg19 with lifescope v2.5.1 smallRNA pipeline.
Counting of smallRNAs with annotation from mirbase v18
Genome_build: hg19
Supplementary_files_format_and_content: 124_tableCount.txt contains raw read counts for each smallRNAs identified. Annotations files are mirbase release 18 and Ensembl ncRNA release 75.

source_name: Human Airway Epithelial Cells

growth_protocol: Human airway epithelial cells  (HAECs) isolated from nasal turbinates of one donor was cultured on collagen-coated permeable filters in liquid-liquid interface during proliferation stage. At confluency, HAECs  were cultured  in an air-liquid interface (ALi) until complete mucociliary differentiation, typically day 21 after Ali.

extract_protocol:
Total RNA extraction using Trizol reagent
0.5 µg of total RNA0 were ligated, reverse transcribed and amplified (11 cycles) with the reagents from the NEBNext Small RNA Library Prep Set for SOLiD. Amplified libraries were size-selected from 105 nt to 130 nt with the LabChip XT DNA 300 Assay Kit (Caliper Lifesciences). Libraries were then subjected to 4 additional PCR rounds with the primers from the 5500 W Conversion Primers Kit (Life Technologies), converted with the enzyme kit from the 5500 W Conversion Primers Kit (Life Technologies) and quantified with the Bioanalyzer High Sensitivity DNA Kit (Agilent).

treatment_protocol: Total RNAs were extracted from undifferentiated HAECs, 4 days after Ali (Ali4) and from fully-differentiated HAECs, 31 days after Ali (Ali31).

value: Human Airway Epithelial Cells

tag: differentiation status

value: fully-differentiated


title: D87ALI4

description: Human Airway epithelial cells cultured in vitro obtained during early phase of differentiation (ALI4)

value: undifferentiated


title: hsa-miR-449c-5p human nasal epithelial cells

description: transfection 48h 10 nM

data_processing:
Mapping versus hg19 with lifescope v2.5.1 whole transcriptome pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: 176_wt_tablecount.txt

source_name: human nasal epithelial cells

extract_protocol:
Qiazol miRNeasy mini kit
PolyA+ RNAs were selected from 2µg total RNA with Dynabeads mRNA purification kit (invitrogen). PolyA RNA were ligated, reverse transcribed and amplified (8 cycles) with the reagents from the NEBNext Small RNA Library Prep Set for SOLiD. Amplified libraries were subjected to 4 additional PCR rounds with the primers from the 5500 W Conversion Primers Kit (Life Technologies). Libraries were size-selected from 250 nt to 300 nt with the LabChip XT DNA 300 Assay Kit (Caliper Lifesciences). Libraries were converted with the enzyme kit from the 5500 W Conversion Primers Kit (Life Technologies) and quantified with the Bioanalyzer High Sensitivity DNA Kit (Agilent).

value: Cells from nasal turbinates

value: proliferating


title: hsa-isomiR-449c-5p human nasal epithelial cells

description: transfection 48h 10 nM


title: hsa-miR-449b-5p human nasal epithelial cells

description: transfection 48h 10 nM


title: hsa-miR-449a-5p human nasal epithelial cells

description: transfection 48h 10 nM


title: hsa-miR-34b-5p human nasal epithelial cells

description: transfection 48h 10 nM


title: hsa-miR-449c-5p Human Airway Epithelial Cells

data_processing:
Mapping versus hg19 with lifescope v2.5.1 smallRNA pipeline.
Counting of smallRNAs with annotation from mirbase v18,
Genome_build: hg19
Supplementary_files_format_and_content: 139_tableCount.txt contains raw read counts for each smallRNAs identified. Annotations files are mirbase release 18 and Ensembl ncRNA release 75.

extract_protocol:
Qiazol miRNeasy mini kit
1,5 µg of 3T3_MAX RNA and 0,01 ng of synthesized RNA were ligated, reverse transcribed and amplified (11 cycles) with the reagents from the NEBNext Small RNA Library Prep Set for SOLiD. Amplified libraries were size-selected from 105 nt to 130 nt with the LabChip XT DNA 300 Assay Kit (Caliper Lifesciences). Libraries were then subjected to 4 additional PCR rounds with the primers from the 5500 W Conversion Primers Kit (Life Technologies), converted with the enzyme kit from the 5500 W Conversion Primers Kit (Life Technologies) and quantified with the Bioanalyzer High Sensitivity DNA Kit (Agilent).


title: hsa-miR-34a-5p human nasal epithelial cells

description: transfection 48h 10 nM


title: 5-D2-Th2_S5_L001_R1_001


title: miRNeg human nasal epithelial cells

description: transfection 48h 10 nM


title: hsa-miR-449c-5p mix Human Airway Epithelial Cells

description: hsa-miR-449c-5p mix


title: hsa-isomiR-449c-5p Human Airway Epithelial Cells


title: hsa-miR-34b-5p mix Human Airway Epithelial Cells

description: hsa-miR-34b-5p mix


title: ERDR1MIGR1-1

city: Salt Lake City

first: Raymond

last: Soto

state: UT

address: 15 N Medical Drive East EEJMRB Rm.4208

department: Pathology

institute: University of Utah

data_processing:
Mm10 ensembl annotations (build 75) were downloaded and converted to genePred format.  Splice junction sequences were generated using USeq’s (v8.8.8) MakeTranscriptome application using a radius of 46.  These splice junction sequences were added to the mm10 chromosome sequences and run through novoindex (v2.8) to create the transcriptome index.
Reads were aligned to the transcriptome reference index described above using Novoalign (v2.08.01), allowing up to 50 alignments for each read.  USeq’s SamTranscriptomeParser application was used to select the best alignment for each read and convert the coordinates of reads aligning to splices back to genomic space.
Read counts for each gene were generated using USeq’s DefinedRegionDifferentialSeq application.  These counts were used in DESeq2 to measure the differential expression between each condition, controlling for sample preparation batch.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing EnsemblGeneId, Gene Name, Log2 Fold Change, Adjusted P-value, and DESeq2 normalized counts.

organism: Mus musculus

source_name: CD4+ T cells

extract_protocol:
Cells were collected in Trizol and total RNA was collected using Qiagen miRNeasy kit
ntact poly(A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit (RS-122-2101, RS-122-2102).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 10 nM and equal volumes were pooled in preparation for Illumina sequence analysis.

treatment_protocol: Purified CD4+ T cells were retrovirally infected with MSCV containing the MIGR1 vector with or without ERDR1, and sorted based on GFP positivity.

tag: strain

value: Spleen

tag: transfection

value: ERDR1 overexpressing MIGR1

value: 8 Weeks


title: ERDR1MIGR1-2


title: ERDR1MIGR1-3


title: ControlMIGR1-1

value: control MIGR1


title: ControlMIGR1-3


title: hsa-isomiR-34b-5p Human Airway Epithelial Cells


title: ControlMIGR1-2


title: hsa-miR-34b-5p Human Airway Epithelial Cells


title: Etaa1 MUTANT replicate #3

city: Melbourne

first: Ian

last: Parish

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Etaa1 DEx2/DEx2
Sample 6

data_processing:
Basecalls performed using CASAVA version 1.7
RNA-seq reads were aligned to the GRCm38.p5 genome assembly using TopHat version 2.1 which utilises Bowtie version 2.2.6
Abundance counts were computed using featureCounts version 1.4.6
Differential gene-expression analysis was performed using the R package edgeR version 3.16.5
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: abundance measurements are in tab-delimited text files

molecule: polyA RNA

source_name: Sorted CD8+ P14 TCR transgenic cells

growth_protocol: 5x10^4 CD45.1+ Etaa1+/+ or Etaa1 DEx2/DEx2 were injected i.v. into wild-type C57BL/6N mice that were subsequently infected with 2x10^5 pfu LCMV-Armstrong strain i.p.  At day 5 p.i., spleens were isolated and pooled according to P14 genotype (typically 3-8 spleens per P14 genotype), and then a splenocyte suspension was sorted by FACS to isolate CD45.1+ CD8+ T cells.

extract_protocol:
Cell pellets were snap frozen on dry ice, and total RNA was subsequently isolated using a Qiagen Rneasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: LCMV-specific P14 CD8+ T cell

tag: genotype

value: Etaa1 deltaEx2/DEx2

tag: background


title: Etaa1 WT replicate #4

description:
Etaa1 +/+
Sample 7

value: Etaa1 +/+


title: Etaa1 MUTANT replicate #2

description:
Etaa1 DEx2/DEx2
Sample 4


title: Etaa1 MUTANT replicate #4

description:
Etaa1 DEx2/DEx2
Sample 8


title: Etaa1 WT replicate #3

description:
Etaa1 +/+
Sample 5


title: Etaa1 WT replicate #2

description:
Etaa1 +/+
Sample 3


title: Etaa1 WT replicate #1

description:
Etaa1 +/+
Sample 1


title: PGE2 Rep 2

city: PHILADELPHIA

first: Arndt

last: Siekmann

state: Pennsylvania

address: 421 Curie Boulevard, 1114 Biomedical Research Building II/III

department: Perelman School of Medicine

institute: UNIVERSITY OF PENNSYLVANIA

data_processing:
Illumina Casava1.7 software used for basecalling.
STAR read mapping
RSEM
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files raw counts values for each Sample

source_name: Muscle stem cell

growth_protocol: CD45-Sca1-CD31-CD11b-alpha7Integrin+CD34+ stem cells were isolated by FACS from hindlimb muscles of 8-12wk old BL6 female mice

extract_protocol:
Qiagen RNAeasy Micro Kit
NuGEN Ovation v2 cDNA amplification, Illumina RNASeq v2 Library construction

treatment_protocol: 20% FBS/40% Low Glucose DMD/40% F-10

value: muscle

value: 24 hours with prostagland in E2


title: PGE2 Rep 1


title: PGE2 Rep 3


title: Etaa1 MUTANT replicate #1

description:
Etaa1 DEx2/DEx2
Sample 2


title: hsa-isomiR-34b-5p human nasal epithelial cells

description: transfection 48h 10 nM


title: Vehicle Rep 3

value: 24 hours with DMSO


title: Vehicle Rep 1


title: hsa-miR-34c-5p human nasal epithelial cells

description: transfection 48h 10 nM


title: H55316/IE2_striatal_RNA_L6.D708

city: Bellingham

first: Jeffrey

middle: Bryan

last: Carroll

state: WA

address: 188 E College Way, AIC 434/MS 9172

department: Psychology Department

institute: Western Washington University

data_processing:
Data were aligned to the mouse transcriptome using mRNA v7. Bowtie version 0.12.9.
Transcript reads were quantified using RSEM version 1.1.18.
Genome_build: mm9

source_name: Right Hemistriatum

growth_protocol: Mice were housed in a partially reversed light cycle, lights on from 12 am to 12 pm, with ad libitum access to food and water. Genotype and treatment were balanced across cages.

extract_protocol:
Mice were perfused with saline to clear tissues of blood. Hemistriata were dissected and flash frozen on liquid nitrogen. Total RNA was extracted using the Lipid Tissue Mini Kit (Qiagen cat# 74804).
RNAseq was conducted at EA | Q2 Solutions with cDNA libraries prepared using the TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103).

treatment_protocol: Mice were treated weekly with 50 mg per kg body mass Htt ASO, control ASO, or 4 uL per g body mass saline. Treatment began at 2 months of age and continued until sacrifice at 10 months of age.

tag: mouse

tag: gender

value: Female

tag: age (days)

value: Saline


title: H55316/HT4_striatal_RNA_L3.D704

tag: treatment


title: H55316/HP2_striatal_RNA_L7.D710


title: H55316/HQ3_striatal_RNA_L8.D711


title: H55316/HO1_striatal_RNA_L3.D702


title: H55316/HN3_striatal_RNA_L4.D711


title: H55316/HI1_striatal_RNA_L6.D702

value: Control


title: H55316/HM3_striatal_RNA_L4.D710


title: 10-D3-Th17_S10_L001_R1_001


title: H55316/HA1_striatal_RNA_L6.D710


title: H55316/HD3_striatal_RNA_L5.D711

source_name: Left Hemistriatum


title: H55316/HE3_striatal_RNA_L6.D706


title: H55316/HI2_striatal_RNA_L7.D702


title: H55316/HA4_striatal_RNA_L6.D704


title: H55316/HC3_striatal_RNA_L5.D703


title: H55316/HA3_striatal_RNA_L6.D712


title: H55316/GW4_striatal_RNA_L4.D709


title: Vehicle Rep 2


title: H55316/GW2_striatal_RNA_L3.D701


title: H55316/GW1_striatal_RNA_L7.D705


title: H55316/GV4_striatal_RNA_L8.D707


title: H55316/IB2_striatal_RNA_L4.D708


title: H55316/GV2_striatal_RNA_L3.D703


title: H55316/GV3_striatal_RNA_L5.D701


title: H55316/GV1_striatal_RNA_L8.D703


title: H55316/GU2_striatal_RNA_L5.D709


title: H55316/GT3_striatal_RNA_L5.D707


title: H55316/HD4_striatal_RNA_L4.D712


title: H55316/GS4_striatal_RNA_L3.D705


title: H55316/GT2_striatal_RNA_L7.D701


title: H55316/GZ1_striatal_RNA_L4.D707


title: H55316/GT1_striatal_RNA_L5.D705


title: H55316/GS2_striatal_RNA_L3.D706


title: H55316/GS1_striatal_RNA_L7.D706


title: KO-4-lane1

city: Beijing

first: Hai

last: Qi

state: Beijing

address: Tsinghuayuan Street

department: School of Medicine

institute: Tsinghua University

description:
plxnb2_WT_KO_count.txt
plxnb2_WT_KO_fpkm.txt

data_processing:
Illumina Casava software used for basecalling and demultiplexing. Reads for the same sample from two lanes were merged.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to NCBI build37.2 whole genome using TopHat2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by Cufflinks and raw counts were summarized by htseq-count for DESeq2 input
Gene differential expression was analyzed by DESeq2 according to its mannual
Genome_build: NCBI build37.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and tab-delimited text files include raw reads counts for each Sample

source_name: Inguinal lymph node

growth_protocol: Plxnb2+/+ or Plxnb2-/- CFP-expressing MD4 B cells were co-transferred together with OT-II T cells into B6 recipients that were subsequently immunized with HEL-OVA subcutaneously. MD4 cells of the 7-AAD-CD19+IgD-GL7hiFashi GC phenotype were FACS-sorted from pooled draining lymph nodes on day 5

extract_protocol:
Cells were directly sorted into the lysis buffer and follow the modified the protocol initially developed for single-cell RNA-seq (Tang, 2011) to accommodate 10-400 sorted cells by doubling reaction volumes with extra buffers until the step for second strand DNA synthesis
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 7AAD-CD19+IgD-GL7hiFashi GC B cells

value: Plxnb2-/- MD4-CFP transgenic C57BL/6

tag: immunization

value: HEL-OVA s.c.


title: H55316/GR4_striatal_RNA_L8.D704


title: KO-3-lane1


title: KO-4-lane2


title: KO-2-lane2


title: KO-3-lane2


title: H55316/GY2_striatal_RNA_L7.D709


title: KO-1-lane2


title: KO-2-lane1


title: WT-4-lane1

value: Plxnb2+/+ MD4-CFP transgenic C57BL/6


title: KO-1-lane1


title: WT-2-lane1


title: WT-3-lane1


title: WT-2-lane2


title: H55316/GU4_striatal_RNA_L8.D708


title: WT-3-lane2


title: WT-4-lane2


title: WT-1-lane2


title: WT-1-lane1


title: Tmem.WT.LCMV_Arm.si354

city: Bethesda

first: Fred

middle: P.

last: Davis

state: MD

address: 9000 Rockville Pike

department: NIAMS

institute: NIH

data_processing:
abundance estimation, RNA-seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. To quantify transcript abundance we pseudo-aligned RNA-seq reads to ENSEMBL transcripts, using kallisto (v0.42.4, options: -b 50 --single -l 200 -s 30) (Bray et al., 2016)
alignment, RNA-seq: We aligned sequence reads from each RNA-seq library to the mouse genome (build mm10) using STAR (v2.4.2a, options: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout)(Dobin et al., 2013), guided by annotated transcript structures (cDNA sequences from ENSEMBL release 82 GRCm38) (Yates et al., 2016). We visualized these alignments by counting positional coverage across the genome (BEDTOOLS v2.15: genomeCoverageBed -split -bg ) (Quinlan and Hall, 2010), scaling to 10M total read depth, converting to bigWig (wigToBigWig) (Kent et al., 2010), and viewing in IGV (Thorvaldsdottir et al., 2013)
alignment, ChIP-seq: We aligned ChIP-seq reads to the mouse genome (build mm10) with Bowtie (v1.1.2, options -m 1) (Langmead et al., 2009), allowing only uniquely aligning reads. We visualized each ChIP-seq dataset by counting positional coverage across the genome (BEDTOOLS v2.24; options: genomeCoverageBed -split -bg ) (Quinlan and Hall, 2010), scaling to 10M total read depth, converting to bigWig (wigToBigWig) (Kent et al., 2010), and viewing in IGV (Thorvaldsdottir et al., 2013)
peaks, ChIP-seq: We then identified peaks using MACS (v 1.4.3; default p-value threshold of 1E-5) (Y. Zhang et al., 2008) and GEM (v2.6; options: --k_min 6 --k_max 15) (Guo et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig and MACS peak calls for ChIP-seq.  bigWig track for selected RNA-seq samples, combined transcript abundance table including all RNA-seq samples.

extract_protocol:
RNA Sequencing (RNA-seq) was performed and analyzed as described previously. Total RNA was prepared from approximately 1 million cells by using TRIzol or mirVana miRNA Isolation Kit (Thermo Fisher Scientific Inc.). 200 ng of total RNA was subsequently used to prepare RNA-seq library by using TruSeq SR RNA sample prep kit (FC-122-1001, Illumina) by following manufacturer’s protocol.
RNA-seq: 200 ng of total RNA was subsequently used to prepare RNA-seq library by using TruSeq SR RNA sample prep kit (FC-122-1001, Illumina) by following manufacturer’s protocol.
RNA-seq: The libraries were sequenced for 50 cycles (single read) with a HiSeq 2000 or HiSeq 2500 (Illumina)
ChIP-seq: Cells cultured as indicated were cross-linked for 10 minutes with 1% formaldehyde and harvested. Cells were lysed by sonication and immunoprecipitated with anti-T-bet (sc-21003, Santa Cruz Biotechnology), anti- STAT1 (sc-592, Santa Cruz Biotechnology), anti-STAT2 (ab124283, AbCam), anti-H3K4m1 (ab8895, AbCam) and anti-H3K27ac (ab4729, AbCam)
ChIP-seq: Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt-ended, then phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of NEBNext adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with NEBNext index primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen).
ChIP-Seq (size fractionation). The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.

treatment_protocol:
CD4+ T cells from spleens and lymph nodes of 6- to 8-week-old mice were purified by negative selection and magnetic separation (Miltenyi Biotec) followed by sorting of naïve CD4+CD62L+CD44-CD25- population using FACSAria III or FACSAria Fusion (BD).
RNA-seq in vitro culture protocol: All cells were cultured in RPMI medium with 10% (vol/vol) FCS, 2 mM glutamine, 100 IU/mL of penicillin, 0.1 mg/mL, of streptomycin and 20 mM HEPES buffer, pH 7.2-7.5 (all from Invitrogen), 1 mM sodium pyruvate, nonessential amino acids (gibco), and 2 μM β–mercaptoethanol (Sigma-Aldrich). Naïve CD4 T cells were activated by plate-bound anti- CD3 (10 μg/mL, Clone: 145-2C11) and anti-CD28 (10μg/mL, 37.51) in media for 6hr to 3 days either under neutral conditions or with IFN-γ (100 ng/mL, R&D Systems) or IFN-β (5000 U/mL, PBL interferon source)
ChIP-seq in vitro culture protocol: All cells were cultured in RPMI medium with 10% (vol/vol) FCS, 2 mM glutamine, 100 IU/mL of penicillin, 0.1 mg/mL, of streptomycin and 20 mM HEPES buffer, pH 7.2-7.5 (all from Invitrogen), 1 mM sodium pyruvate, nonessential amino acids (gibco), and 2 μM β–mercaptoethanol (Sigma-Aldrich). Naïve CD4 T cells were activated by plate-bound anti- CD3 (10 μg/mL, Clone: 145-2C11) and anti-CD28 (10μg/mL, 37.51) in media for 3 days either under neutral conditions (anti-IL-4 (10 μg/mL, 11B11) and anti-IFN-γ antibodies (10 μg/mL, XMG1.2)) or IFN-γ condition (IFN-γ (100 ng/mL, R&D Systems) and anti-IL-4 antibody (10 μg/mL)) or IFN-β condition (IFN-β (5000 U/mL, PBL interferon source), anti-IL-4 (10 μg/mL), and anti-IFN-γ antibodies (10 μg/mL))
Toxoplasma gondii infection protocol: We generated chimeric Rag2-/- mice, reconstituted with ~5 million WT (CD45.1) and ~5 million Tbx21-/- (CD45.2) naïve CD4+ T cells sorted from Age- and Sex- matched mice (Fig. 4A), and 5 days later i.p. infected them with approximately 20 cysts of the avirulent ME49 strain of T. gondii as described previously (Jankovic et al., 2007). Splenocytes and peritoneal exudate cells (PEC) were harvested at day 7 after the infection, and WT and Tbx21-/- CD4+ CD62Llo CD44hi NK1.1- GR-1- T cells were sorted based on congenic surface markers (CD45.1/CD45.2) by flow cytometer
LCMV infection protocol: WT and Tbx21-/- mice were infected either with 2 x 10^5 plaque-forming units (PFU) of LCMV Armstrong intraperitoneally or 2 x 10^6 PFU of LCMV Clone 13 intravenously. Eight and 7 days after inoculation, splenocytes were harvested and CD4+CD62Llo CD44hi memory T helper cell population was sorted by flow cytometer.

value: WT

tag: culture condition

value: LCMV infection protocol (Armstrong)


title: Tmem.WT.LCMV_Arm.si355


title: Tmem.WT.LCMV_Arm.si353


title: Tmem.TbetKO.LCMV_Arm.si358


title: Tmem.TbetKO.LCMV_Arm.si357


title: CD4.WT.nc.72hr.si35

value: RNA-seq in vitro culture protocol (neutral, 72hr)


title: Sm1

city: Riverside

first: Emma

last: Wilson

address: 900 University Ave

department: Biomedical Sciences

institute: University of California, Riverside

description: Barcode: TGACCA

data_processing:
base-calling, demultiplexing, and intial QC by Genomics Core Facility at UCR
Subsequent QC and adaptor trimming performed by FastQC and TrimGalore
Alignment to mouse genome GRCM38.84 using Tophat2
transcripts per gene count and TMM normalization using GenomicRanges package in R
Genome_build: GRCM38.84
Supplementary_files_format_and_content: tab delimited text file containing RPKM files for each sample

source_name: Spleen CD8+ CD103-

extract_protocol:
Brains and spleens were isolated and mononuclear cells extracted.  CD8+ T cells were isolated using mouse CD8+ T cell enrichment columns from R&D systems (Cat# MCD8C-1000).  CD103+ and CD103- subsets were sorted directly into lysis buffer (Buffer RLT) using a BD FACSAria.  Total RNA isolation was performed using the Qiagen RNeasy mini kit (Cat#74104).
rRNA was depleted using the Clontech Ribogone Mammalian kit (Cat # 634847) and libraries were generated with the Clontech SMARTer Stranded RNA-Seq kit (Cat# 634837) according to manufacturers protocol.

value: Spleen

tag: time

value: 5 weeks post infection


title: Sm3

description: Barcode: CTTGTA


title: Sm2

description: Barcode: ACTTGA


title: Sp3

description: Barcode: GGCTAC

source_name: Spleen CD8+ CD103+


title: CD4.WT.IFNg.72hr.si248

value: RNA-seq in vitro culture protocol (IFN-γ, 72hr)


title: CD4.WT.nc.6hr.si217

value: RNA-seq in vitro culture protocol (neutral, 6hr)


title: CD4.WT.nc.72hr.si247


title: Sp

description: Barcode: TGACCA


title: CD4.WT.IFNb.72hr.si5

value: RNA-seq in vitro culture protocol (IFN-β, 72hr)


title: CD4.WT.IFNb.72hr.si249


title: CD4.WT.nc.72hr.si251


title: Sp1

description: Barcode: TTAGGC


title: CD4.WT.IFNb.72hr.si253


title: Bm

description: Barcode: CGATGT

source_name: Brain CD8+ CD103-

value: Brain


title: CD4.WT.IFNg.72hr.si252

description: CD4.WT.IFNg.72hr.si252.star_scaled10M_nonRRNA.bw


title: wt3_wk24

city: New Haven

first: Dejian

last: Zhao

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale School of Medicine

data_processing:
reads were aligned with TopHat (v 2.0.13) to the mouse genome (GRCm38/mm10)
htseq (v0.6.1) was used to count reads for each gene (mode=union)
DESeq2 (v1.6.3) was then used to determine differentially expressed genes
DAVID 6.8 was used to identify gene enrichment in the KEGG pathway database, and the biological process and cellular component in gene ontology
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited gene expression values (htseq counts)

source_name: microglia dissected from mouse brain tissues

extract_protocol:
Total RNA was isolated from cells using miRNAeasy Kit (Qiagen) according to the manufacturer’s protocol. An additional DNaseI digestion step was performed to ensure that samples were not contaminated with genomic DNA. Reverse transcribed PCR (RT-PCR) was performed using a OneStep RT-PCR Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.
Libraries were prepared using an Illumina TrueSeq RNA prep kit.

value: microglia

tag: genotype/variation

value: wildtype

tag: Stage

value: week 24


title: Bm3

description: Barcode: TAGCTT

tag: tissue


title: Bp1

description: Barcode: TTAGGC

source_name: Brain CD8+ CD103+


title: Bp3

description: Barcode: GATCAG


title: wt2_wk24


title: Bm1

description: Barcode: CGATGT


title: Sp2

description: Barcode: CAGATC


title: wt1_wk24


title: Tmem.TbetKO.LCMV_Arm.si356


title: Sm

description: Barcode: ACAGTG


title: het2_wk24

value: Mecp2 knockout


title: wt3_wk5

value: week 5


title: het1_wk24


title: het3_wk24


title: wt2_wk5


title: het3_wk5


title: wt1_wk5


title: het1_wk5


title: het2_wk5


title: B3 Input EtOH rep2

first: Thomas

middle: Samuel

address: Hammersmith Hospital, Du Cane Rd

department: Bioinformatics

institute: MRC Clinical Sciences Centre

description: Input DNA from B3 cells after carrier ethanol treatment for 6h

library_source: genomic

data_processing:
Base-calling was performed using CASAVA version 1.7
Reads of 50 bases were aligned to the Mus musculus mm9 genome assembly using BWA version 0.7.2 with default parameters
Genome_build: mm9 build 37
Supplementary_files_format_and_content: Aligned reads were extended to predicted fragment length by ChIPQC package. bigWigs created using rtracklayer Bioconductor package normalised to total mapped reads.

molecule: genomic DNA

source_name: pre-B cell line B3

growth_protocol:
cell line reference: FerreirÃ³s-Vidal et al. 2013
Mouse pre-B cell line B3 was grown in IMDM, 10% FCS and  1% penicillin-streptomycin

extract_protocol: For RNAP2 ChIP, chromatin isolated from fixed nuclei was sonicated and incubated at 4ÂºC overnight with either Protein A Dynabeads (Invitrogen) coated with rabbit anti-RNAP2 antibody. Single-end high throughput sequencing libraries were prepared from 10ng of ChIP DNA using NEB Ultra DNA Library Prep kit for Illumina, and sequenced according to the manufacturer's protocols using Illumina Hi-seq2500. For MNase-seq, chromatin from fixed nuclei was digested with MNase and DNA was purified after digestion. Paired-end high throughput sequencing libraries were prepared from 50ng of digested DNA using NEB Ultra DNA Library Prep kit for Illumina, without size selection steps, and sequenced according to the manufacturer's protocols using Illumina Hi-seq2500.

treatment_protocol: B3 cells were transduced as described  (FerreirÃ³s-Vidal et al., 2013, Blood, 121(10):1769-82) with mouse stem cell virus (MSCV) vectors encoding full-length Ikaros with a haemagglutinin (HA) epitope at its N-terminal and estrogen receptor ligand binding domain (ERt2) at its C-terminal followed by an internal ribosomal entry site (IRES) and GFP (HA-Ikaros-ERt2-IRES-GFP). Ikaros translocation is induced by adding 0.5 Î¼M 4-hydroxytamoxifen (4-OHT).

tag: cell line

tag: chip antibody

value: Input DNA

tag: agent

value: ethanol


title: B3 Input 4-OHT rep1

description: Input DNA from B3 cells after 4-OHT treatment for 6h


title: DM1536

city: Dallas

first: Ronak

last: Lakhia

state: Texas

address: 5323 Harry Hines Blvd

department: Internal Medicine

institute: UTSW

data_processing:
Base calling using Illumina bcl2fastq 1.8.4
Sequenced reads were trimmed for adaptor sequence and low quality bases by fastq-mcf 1.1.2-806. parameters:  -l 35
Filtered reads were mapped to mouse genome (mm10) using Tophat 2.0.12, guided by igenome annotations. Parameters: --b2-sensitive --no-coverage-search --max-multihits 10 --library-type fr-firststrand. Then duplicates were marked but not removed.
Aligned reads were assemblied into transcripts by cufflinks. Transcripts of all samples in this experiment were merged to generated a comprehensive set of transcripts.
The resulting gtf file of assembled transcripts was used for read counting by featureCounts from subread software 1.4.6. parameters: --primary -O.
Read counts were used by edgeR 3.2.4 and cutdiff for normalization and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files for each comparison. edgeR results including log CPM values, log fold change, and test statistics.

source_name: Kidney

extract_protocol:
Kidneys were removed, flash frozen on dry ice, and RNA was harvested using Qiazol miRNeasy RNA extraction kit. Illumina TruSeq Stranded Total RNA LT Sample Prep Kit was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina.

value: KspCre; Pkd1 F/RC miR17~92 F/F

tag: age

value: Post-natal day 22


title: B3 Input EtOH rep1


title: B3 Input 4-OHT rep2


title: DM-1525


title: MNase-seq, rep1, EtOH

description: MNase-seq from B3 cells after carrier ethanol treatment for 6h

value: MNase digestion (Worthington)


title: MNase-seq, rep1, 4-OHT

description: MNase-seq from B3 cells after 4-OHT treatment for 6h


title: RNAP2 ChIP, rep4, 4-OHT

description: ChIP-Seq data from B3 cells after 4-OHT treatment for 6h using Rabbit anti-RNAP2 antibody

value: Rabbit anti-N-terminal RNAP2 (Santa cruz sc-899)


title: MNase-seq, rep2, EtOH


title: MNase-seq, rep3, 4-OHT


title: RNAP2 ChIP, rep3, 4-OHT


title: MNase-seq, rep3, EtOH


title: MNase-seq, rep2, 4-OHT


title: RNAP2 ChIP, rep3, EtOH

description: ChIP-Seq data from B3 cells after carrier ethanol treatment for 6h using Rabbit anti-RNAP2 antibody


title: RNAP2 ChIP, rep4, EtOH


title: RNAP2 ChIP, rep2, EtOH_P1


title: RNAP2 ChIP, rep1, EtOH_P1


title: SM-1483

value: KspCre; Pkd1 F/RC


title: SM-1529


title: 3HA-Sc-chip

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

data_processing:
Basecalls performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the BDGP6 genome assembly using Bowtie version 1.1.2 with -v 3 -m 1 parameters.
Peaks were called using MACS version 1.4.2 with the default parameters.
Genome_build: BDGP6
Supplementary_files_format_and_content: bigWig files were generated using makeUCSCfile script, which was contained in Homer package. Scores represent the abundance of reads which normalized to 1e7.
Supplementary_files_format_and_content: .xls files were generated using MACS.

organism: Drosophila melanogaster

source_name: adult intestine, 3HA-Sc ChIP

growth_protocol: Drosophila esg-gal4ts crossed with uas-3HA-sc or uas-3HA-esg lines at 18°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody according to ChIP-IT® High Sensitivity kit (Active Motif).
Libraries were prepared for sequencing using NEBNext Ultra DNA Library Preparation Kit for Illumina.

treatment_protocol: After eclosion, choosing 3- to 5-day-old flies to shift to 29°C for 3 days or 7 days.

value: 3HA-sc transgene

value: intestine

value: adult

value: 3 days at 29°C

value: anti-HA tag antibody - ChIP grade (Abcam, ab9110)


title: RNAP2 ChIP, rep2, 4-OHT_P1


title: DM1520


title: 3HA-Esg-input

source_name: adult intestine, 3HA-Esg input

value: 3HA-esg transgene

value: 7 days at 29°C


title: 3HA-Esg-chip

source_name: adult intestine, 3HA-Esg ChIP


title: Lung from mock-infected DBA/2J mouse 120hpi, rep4

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

country: Germany

institute: Helmholtz Centre for Infection Research

description:
DBA_120m_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

data_processing:
Small RNA-seq reads annotated using miRBase 19 and the CLC Genomics Workbench.
Differential expression was estimated using the R library edgeR.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: reads_miR.txt: Tab-delimited text file includes the raw counts per miRNA.
Supplementary_files_format_and_content: edgeR_miR.xls: Excel file includes the differentially expressed miRNAs (edgeR).

source_name: whole lung tissue, DBA/2J, mock treated, 120h

growth_protocol: Female mice were 12-13 weeks old.

extract_protocol:
miRNeasy kit (Qiagen).
TruSeq Small RNA Sequencing Kit (Illumina).

treatment_protocol: Mice were intranasally infected with 2000 focus forming units of mouse adapted A/Puerto Rico/8/34 (PR8, H1N1) influenza A virus (Blazejewska et al., Virology, 2011).

tag: strain/background

value: female

value: whole lung

value: mock treated (PBS)

tag: time post treatment [h]


title: RNAP2 ChIP, rep1, 4-OHT_P1


title: Lung from mock-infected DBA/2J mouse 120hpi, rep5

description:
DBA_120m_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: 3HA-Sc-input

source_name: adult intestine, 3HA-Sc input


title: Lung from mock-infected DBA/2J mouse 120hpi, rep3

description:
DBA_120m_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: SM-1484

tag: genotype


title: Lung from IAV-infected DBA/2J mouse 120hpi, rep4

description:
DBA_120_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, DBA/2J, influenza A virus infected, 120h

value: influenza A virus (PR8) infected


title: Lung from mock-infected DBA/2J mouse 120hpi, rep1

description:
DBA_120m_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected DBA/2J mouse 120hpi, rep3

description:
DBA_120_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from mock-infected DBA/2J mouse 120hpi, rep2

description:
DBA_120m_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected DBA/2J mouse 120hpi, rep2

description:
DBA_120_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected DBA/2J mouse 120hpi, rep5

description:
DBA_120_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from mock-infected DBA/2J mouse 48hpi, rep1

description:
DBA_48m_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, DBA/2J, mock treated, 48h


title: Lung from IAV-infected DBA/2J mouse 48hpi, rep5

description:
DBA_48_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, DBA/2J, influenza A virus infected, 48h


title: Lung from mock-infected DBA/2J mouse 48hpi, rep4

description:
DBA_48m_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected DBA/2J mouse 120hpi, rep1

description:
DBA_120_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from mock-infected DBA/2J mouse 48hpi, rep5

description:
DBA_48m_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from mock-infected DBA/2J mouse 48hpi, rep3

description:
DBA_48m_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected DBA/2J mouse 48hpi, rep4

description:
DBA_48_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from mock-infected DBA/2J mouse 48hpi, rep2

description:
DBA_48m_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected DBA/2J mouse 48hpi, rep3

description:
DBA_48_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected DBA/2J mouse 48hpi, rep2

description:
DBA_48_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected DBA/2J mouse 48hpi, rep1

description:
DBA_48_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from mock-infected DBA/2J mouse 24hpi, rep4

description:
DBA_24m_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, DBA/2J, mock treated, 24h


title: DeltaCspCE_16h_dualRNAseq2

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Reads were trimmed for a Phred quality of 20 using the FASTX toolkit version 0.0.13
Adapter trimming using Cutadapt version 1.3
Reads were mapped using the READemption pipeline (Förstner et al., 2014), segemehl, and the lack remapper to the SL1344 genome and associated plasmids (NCBI references: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1 )
Coverage plots (wig files) and read quantifications were produced by READemption
Genome_build: NCBI references: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1
Supplementary_files_format_and_content: text files are tab delimited including raw read counts; RIP-seq and RNA-seq contain fractional read counts for multimapping reads, while dual RNA-seq counts were generated solely from uniquely mapped reads.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: HeLa cell culture

growth_protocol: Salmonella was routine grown in LB (220 rpm, 37C), supplemented with appropriate antibiotics. For RIP-seq, cultures were supplemented with 0.2% L-Arabinose at an OD of 0.2. Cultures were grown to OD 2.0 before harvesting RNA. For dual RNA-seq, OD 2 cultures were used to infect HeLa cells at a multiplicity of infection of 5 and centrifuged for 10 minutes. After 30 minutes at 37C, gentamicin was added to the media to kill extracellular bacteria, and RNA was harvested at the listed time points.

extract_protocol:
For RIP-seq: When the culture reached an OD600 of 2, bacteria were re-suspended in 800 µl of ice-cold lysis buffer (Tris, pH 8.0, 20 mM, KCl 150 mM, MgCl2 1 mM, DTT 1 mM), and disrupted with 1 ml glass beads (BioSpec Products, 0.1 mm diameter) by shaking at 30 Hz for 10 min. The cleared lysate obtained after centrifugation (16000 rcf, 15 min, 4°C) was incubated with 0.5 µl/OD anti-Flag antibody (Sigma, F1804) at 4°C for 30 min followed by incubation with 64 µl pre-washed Protein-A sepharose (Sigma, P6649) for another 30 min. After 5 washes with ice-cold lysis buffer, the sepharose was subjected to Phenol:Chloroform:Isopropanol extraction to isolate RNA (PCI 25:24:1, pH 4.5; Roth, X985.3). For RNA-seq: Total RNA was extracted with hot phenol and chloroform followed by DNase I treatment. For dual RNA-seq: Total RNA from the infected and sorted cells was isolated using the mirVana kit (Ambion).
The samples were rRNA depleted (RNA-seq and dual RNA-seq), then poly(A)-tailed using poly(A) polymerase and the 5’triphosphate (and eukaryotic cap) structures were removed using tobacco acid pyrophosphatase (TAP). Afterwards, an RNA adapter was ligated to the 5’monophosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase (NEB). The resulting cDNA was PCR-amplified to about 20-30 ng/µL using a high fidelity DNA polymerase (barcode sequences for multiplexing were part of the 3’primers). The cDNA library was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis (Agilent Technologies).

tag: stategy

value: dual RNA-seq

value: deltaCE GFP


title: DeltaCspCE_16h_dualRNAseq1


title: Lung from mock-infected DBA/2J mouse 24hpi, rep3

description:
DBA_24m_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

tag: gender


title: Lung from mock-infected DBA/2J mouse 24hpi, rep1

description:
DBA_24m_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected DBA/2J mouse 24hpi, rep5

description:
DBA_24_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, DBA/2J, influenza A virus infected, 24h


title: Lung from mock-infected DBA/2J mouse 24hpi, rep5

description:
DBA_24m_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: WT_16h_dualRNAseq1

value: WT GFP


title: DeltaCspCE_4h_dualRNAseq2


title: Lung from mock-infected DBA/2J mouse 24hpi, rep2

description:
DBA_24m_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected DBA/2J mouse 24hpi, rep4

description:
DBA_24_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected DBA/2J mouse 24hpi, rep2

description:
DBA_24_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: DeltaCspCE_4h_dualRNAseq1


title: Lung from IAV-infected DBA/2J mouse 24hpi, rep1

description:
DBA_24_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected DBA/2J mouse 24hpi, rep3

description:
DBA_24_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: WT_4h_dualRNAseq2


title: WT_4h_dualRNAseq1


title: DeltaCspCE_0h_dualRNAseq1

source_name: OD 2


title: DeltaCspCE_0h_dualRNAseq2


title: Lung from mock-infected DBA/2J mouse 18hpi, rep1

description:
DBA_18m_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, DBA/2J, mock treated, 18h


title: WT_0h_dualRNAseq1


title: WT_0h_dualRNAseq2


title: Lung from mock-infected DBA/2J mouse 18hpi, rep2

description:
DBA_18m_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: H256

city: Copenhagen

first: Yu

last: Zhang

address: Grønnegårdsvej 7

country: Denmark

institute: University of Copenhagen

data_processing:
Illumina Casava1.8 software used for basecalling.
Clean reads were obtain by filtering reads with adaptor sequences and  low quality reads.
Clean reads that aligned to rRNA were removed.
After removing reads aligned to rRNA, we used SOAP2 to align clean reads to the hg19 UCSC RefSeq (RNA sequences, GRCh37) (para: -m 0 -x 1000 -s 40 -l 32 -v 5 -r 2 -p 4). Gene level expression was performed by transforming uniquely mapped transcript reads to TPM.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Healthy control neurons

growth_protocol: Dual SMAD protocol (Shi et al., Nature Protocol 2014) was employed to generate all the neurons in this study. Neurons were matured from iPSC-derived neural progenitor cells in mono layer cell culture dishes for 4 to 5 weeks.

extract_protocol:
RNeasy Plus Mini Kit (QIAGEN, Cat.no. 74134) was used for total RNA extraction.
After extracting the total RNA from samples, mRNA and non-coding RNAs are enriched by removing rRNA from the total RNA with kit. By using the fragmentation buffer, the mRNAs and non-coding RNAs are fragmented into short fragments(about 200-500nt), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates, and dTTP is substituted by dUTP during the synthesis of the second strand. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters, then the second strand is degraded using UNG(Uracil-N-Glycosylase) finally.

tag: cell type

value: iPSC-derived neurons


title: H242 ISO

source_name: Gene-corrected neurons


title: Lung from IAV-infected DBA/2J mouse 18hpi, rep4

description:
DBA_18_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, DBA/2J, influenza A virus infected, 18h

tag: treatment


title: H151 ISO


title: Lung from IAV-infected DBA/2J mouse 18hpi, rep2

description:
DBA_18_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: H242

source_name: FTD3 patient neurons


title: Lung from mock-infected DBA/2J mouse 12hpi, rep5

description:
DBA_12m_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, DBA/2J, mock treated, 12h


title: H151


title: H150


title: H150 ISO


title: Lung from mock-infected DBA/2J mouse 18hpi, rep5

description:
DBA_18m_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from mock-infected DBA/2J mouse 12hpi, rep3

description:
DBA_12m_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from mock-infected DBA/2J mouse 18hpi, rep4

description:
DBA_18m_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: SiChe-1 4H Hypoxia

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

country: Italy

institute: Italian National Cancer Institute "Regina Elena"

data_processing:
Raw data was analyzed via RAP pipeline at CINECA, that  comprises of read mapping via Tophat and transcript-gene expression abundance estimation via Cufflinks. Differential expression was calculated via Cuffdiff.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Colorectal

extract_protocol:
HCT116 cell line was transfected with siChe-1 or siRNA negative control using Lipofectamine 3000 (Life Technologies), total RNA was extracted from cells using TRIzol reagent (Life Technologies) in accordance with the manufacturer's instructions.
Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies) and by Agilent 2100 Bioanalyzer (Agilent Technologies), respectively. RNA libraries for sequencing were generated according to the standard Illumina TruSeq RNA sample preparation protocol using 2ug total RNA as starting material. The resulting library was controlled qualitatively with the High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA, USA) and quantitatively with real-time analysis employing a SYBR Green qPCR protocol with specific primers complementary to adapter sequences. Therefore, only the adapter-ligated fragments that are appropriate for sequencing were quantified. Based on the qPCR quantification, libraries were normalized to 1 nM and denatured by using 0.1N NaOH. Cluster amplification of denatured templates was carried out according to manufacturer protocol (Illumina, Inc., San Diego, CA, USA). Sequencing was performed on a Genome Analyzer IIx (Illumina) in paired-end mode, sequencing from each side 51 bp.

tag: transfection


title: Lung from mock-infected DBA/2J mouse 12hpi, rep2

description:
DBA_12m_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from mock-infected DBA/2J mouse 18hpi, rep3

description:
DBA_18m_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: HBE_smartseq2

city: Guangzhou

first: Gong

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

institute: Jinan University

description: Illumina

data_processing:
Prefilter: the datasets created from ion torrent platform were filtered out the low-quality (Phred score<10) reads.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Mapping was performed using the hyper-accurate FANSe2 algorithm for quantitaion purpose.
Genome_build: hg19
Supplementary_files_format_and_content: .txt file includes log2 rpkm values

source_name: Human bronchial epithelial cells (HBE)

extract_protocol:
Total RNA of those cells were extracted using Trizol reagent.
10pg polyA+ mRNA was used as the input. mRNA was subjected to smart-seq2 method for illumina sequencing, and also in parallel subjected to low-input direct library construction of ion torrent sequencer.

value: HBE

tag: input amount

value: 10pg polyA+ mRNA

tag: library construction

value: smart-seq2 method


title: Lung from mock-infected DBA/2J mouse 12hpi, rep1

description:
DBA_12m_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: siControl

value: siControl


title: SiChe-1


title: Lung from IAV-infected DBA/2J mouse 12hpi, rep5

description:
DBA_12_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, DBA/2J, influenza A virus infected, 12h


title: siControl 4H Hypoxia


title: Lung from IAV-infected DBA/2J mouse 12hpi, rep4

description:
DBA_12_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected DBA/2J mouse 18hpi, rep3

description:
DBA_18_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected DBA/2J mouse 18hpi, rep1

description:
DBA_18_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: 12h_ca_rep4

city: Jena

first: Andreas

last: Dix

address: Beutenbergstraße 11a

institute: Hans-Knöll-Institut

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were trimmed to remove the adaptor sequence.
Reads were mapped to microRNA precursors (miRBase, version 20) using bowtie (version 0.12.9) with parameters -v 1 -a -p 1 –best –norc.
The reads which mapped to the locations of the mature microRNAs were counted (allowing deviation of 2 nt), multiple hits were counted proportionally to the number of hits.
Of the identical mature microRNAs, which could originate from multiple different precursors, the one with the maximum read count was kept.
Genome_build: human microRNA precursors, miRBase version 20
Supplementary_files_format_and_content: Format: Tab separated values; Content: counts of the human mature microRNAs for each sample

source_name: DCs from PBMCs_12h_ca

extract_protocol:
small RNA was extracted using TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA)
Total RNA was isolated using the miRNeasy Mini Kit (Qiagen, Hilden, Germany). RNA samples had a RNA integrity number (RIN) of 8.9±0.9 determined by Agilent Bioanalyzer. 500 ng total RNA, determined by Nanodrop 1000 (Thermo Scientific), was used to generate small RNA sequencing libraries by TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA).
According to TruSeq Small RNA Library Prep Kit from Illumina (Version 1500419)

value: PBMCs

value: monocyte-derived dendritic cells (DCs)

tag: stimulated with

value: C. albicans

tag: time point

value: after 12h of co-cultivation


title: 12h_lps_rep4

source_name: DCs from PBMCs_12h_lps

tag: tissue

value: LPS


title: 06h_ca_rep4

source_name: DCs from PBMCs_06h_ca

value: after 6h of co-cultivation


title: 06h_af_rep4

source_name: DCs from PBMCs_06h_af

value: A. fumigatus


title: 06h_lps_rep4

source_name: DCs from PBMCs_06h_lps


title: Lung from mock-infected DBA/2J mouse 12hpi, rep4

description:
DBA_12m_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

value: female

value: whole lung

value: mock treated (PBS)


title: 12h_lps_rep3


title: Lung from IAV-infected DBA/2J mouse 12hpi, rep2

description:
DBA_12_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

value: influenza A virus (PR8) infected


title: 12h_af_rep3

source_name: DCs from PBMCs_12h_af


title: 12h_ca_rep3


title: 06h_lps_rep3


title: 12h_control_rep3

source_name: DCs from PBMCs_12h_control

value: none (unstimulated control)


title: 12h_af_rep2


title: Lung from mock-infected DBA/2J mouse 6hpi, rep4

description:
DBA_6m_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, DBA/2J, mock treated, 6h


title: Lung from IAV-infected DBA/2J mouse 12hpi, rep1

description:
DBA_12_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: 06h_af_rep3


title: 06h_ca_rep3


title: 12h_af_rep4


title: Lung from mock-infected DBA/2J mouse 6hpi, rep3

description:
DBA_6m_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected DBA/2J mouse 12hpi, rep3

description:
DBA_12_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: WT_16h_dualRNAseq2

source_name: HeLa cell culture

value: dual RNA-seq

tag: genotype/variation

value: WT GFP


title: 12h_control_rep4


title: Lung from IAV-infected DBA/2J mouse 6hpi, rep5

description:
DBA_6_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, DBA/2J, influenza A virus infected, 6h


title: 06h_control_rep3

source_name: DCs from PBMCs_06h_control


title: 06h_af_rep2


title: 12h_control_rep2


title: Lung from mock-infected DBA/2J mouse 6hpi, rep1

description:
DBA_6m_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: 12h_af_rep1


title: 06h_lps_rep2


title: Lung from IAV-infected DBA/2J mouse 6hpi, rep2

description:
DBA_6_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: 12h_ca_rep1


title: 06h_ca_rep2


title: Lung from IAV-infected DBA/2J mouse 6hpi, rep4

description:
DBA_6_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: 12h_lps_rep1


title: 12h_control_rep1


title: 06h_control_rep2


title: Lung from IAV-infected DBA/2J mouse 6hpi, rep1

description:
DBA_6_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: 06h_ca_rep1


title: 06h_af_rep1


title: Lung from mock-infected DBA/2J mouse 6hpi, rep2

description:
DBA_6m_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from untreated DBA/2J mouse, rep4

description:
DBA_0_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, DBA/2J, untreated, 0h

value: untreated


title: 12h_lps_rep2


title: 06h_lps_rep1


title: 12h_ca_rep2


title: Lung from untreated DBA/2J mouse, rep3

description:
DBA_0_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from untreated DBA/2J mouse, rep1

description:
DBA_0_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from untreated DBA/2J mouse, rep2

description:
DBA_0_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from mock-infected C57BL/6J mouse 120hpi, rep3

description:
B6_120m_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, C57BL/6J, mock treated, 120h


title: 06h_control_rep1


title: Lung from mock-infected C57BL/6J mouse 120hpi, rep4

description:
B6_120m_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from mock-infected C57BL/6J mouse 120hpi, rep2

description:
B6_120m_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected C57BL/6J mouse 120hpi, rep5

description:
B6_120_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, C57BL/6J, influenza A virus infected, 120h


title: Lung from IAV-infected C57BL/6J mouse 120hpi, rep4

description:
B6_120_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected DBA/2J mouse 6hpi, rep3

description:
DBA_6_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected C57BL/6J mouse 120hpi, rep3

description:
B6_120_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from mock-infected C57BL/6J mouse 120hpi, rep1

description:
B6_120m_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: upf1-5 upf3-1

city: Seoul

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to TAIR 10 reference genome using tophat
Cufflinks package used for gene expression level
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Plant was growed at 23°C Long day condition on 1/2 MS plate

extract_protocol:
Total RNA was extracted using trizol reagent
mRNA libraries were prepared using TruSeq stranded mRNA sample preparation kit (illumina, San Diego, CA), according to manufacturer's instruction.

tag: time

value: ZT 16

tag: growth


title: Lung from IAV-infected C57BL/6J mouse 120hpi, rep1

description:
B6_120_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: upf1-5


title: Lung from IAV-infected C57BL/6J mouse 120hpi, rep2

description:
B6_120_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: upf3-1


title: Lung from mock-infected C57BL/6J mouse 48hpi, rep5

description:
B6_48m_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, C57BL/6J, mock treated, 48h


title: Gene_Expression_Kmt2b_cKO_11

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Reads were mapped to mouse genome mm10.
In ChIP-Seq reads were filtered leaving only high quality reads (MAPQ != (0, 2, 3, 4)).
In RNA-Seq reads were counted using FeaturesCount. In ChIP-Seq peaks were called using MACS2 with q-value < 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files and count files.

source_name: Hippocampal CA whole tissue

extract_protocol:
RNA was isolated using TRIZOL from whole tissue. Chromatin immunoprecipitation was performed from fixed neuronal nuclei sorted by FACS.
Libraries for ChIP-Seq were prepared using NEBNext Ultra DANN Library Preparation Kit for Illumina. Libraries for RNA-Seq were prepared using Illumina TruSeq RNA Sample Preparation v2 Kit.

tag: strain

value: Hippocampal CA whole tissue

tag: age

value: 4-6 month-old (adult)

tag: Sex

value: Male


title: Lung from mock-infected C57BL/6J mouse 48hpi, rep2

description:
B6_48m_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

tag: strain/background

tag: time post treatment [h]


title: Lung from mock-infected C57BL/6J mouse 48hpi, rep1

description:
B6_48m_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

tag: gender


title: Gene_Expression_Kmt2b_cKO_10


title: Lung from mock-infected C57BL/6J mouse 48hpi, rep3

description:
B6_48m_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Gene_Expression_Kmt2b_cKO_9

value: Female


title: Gene_Expression_Kmt2b_cKO_7


title: Gene_Expression_Kmt2b_cKO_8


title: Lung from IAV-infected C57BL/6J mouse 48hpi, rep4

description:
B6_48_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, C57BL/6J, influenza A virus infected, 48h


title: Gene_Expression_Kmt2b_cKO_6


title: Lung from IAV-infected C57BL/6J mouse 48hpi, rep3

description:
B6_48_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: BPDE-dG_tXR-seq_rep1

city: Athens

first: Wentao

last: Li

state: GA

address: 500 D. W Brooks Drive

department: Environmental Health Science

institute: University of Georgia

description:
translesion eXcision Repair-sequencing (tXR-seq)
Barcode: ACTGAT

data_processing:
Library strategy: tXR-seq
adaptor trimming
filtering reads based on length
random sampling
alignment
read filtering based on nucleotide composition
strand separation
gene coverage count
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: GM12878, BPDE-dG

growth_protocol: Human GM12878 cells were cultured in RPMI 1640 medium (no phenol red) with 15% fetal bovine serum and 2 mM glutamine at 37 °C in a 5% CO2 humidified chamber.

extract_protocol:
Cells were lysed gently and small molecular weight DNA, consisting mostly of excised 26-27 mers was separated from chromosomal high molecular weight DNA by centrifugation
Briefly, the excised oligomers are immunopricipitated with anti-TFIIH (anti-XPB and anti-p62) antibodies because the excision product is released in a relatively stable complex with TFIIH, which also protects the excision product from degradation by non-specific nucleases. This is followed by extraction of the excised oligomers and ligation to adaptors and a second immunoprecipitation with either anti-CPD or anti-BPDE antibodies. Human DNA polymerases η and κ were used for primer extension in the presence of purified excised oligonucleotides containing either CPD or BPDE-dG damages, as polymerases η and κ can bypass CPD and BPDE-dG damage respectively in an error-free manner. This is followed by PCR amplification with index primers and NGS sequencing on HiSeq 2500 platform.

treatment_protocol: GM12878 cells were grown to about 80% confluence before UV irradiation or (±)-anti-BPDE (MRIGlobal) treatment. The UV (20 J/m2 at 254 nm) irradiation was performed as previously described(3), except 20 ml of GM12878 cells were irradiated in RPMI 1640 medium (no phenol red) in a 150 mm petri dish. BPDE stock solution (4 mM), which was freshly made by dissolving BPDE in DMSO, was added to the GM12878 cell suspension at a final concentration of 2 μM and cells were incubated for 1 h at 37 °C in a 5% CO2 humidified chamber.

value: Peripheral vein

tag: cell type

value: B-Lymphocyte

tag: cell line

value: BPDE-dG


title: BPDE-dG_tXR-seq_rep2

description:
translesion eXcision Repair-sequencing (tXR-seq)
Barcode: ATGAGC

tag: treatment


title: Gene_Expression_Kmt2b_cKO_4


title: CPD_tXR-seq_rep2

description:
translesion eXcision Repair-sequencing (tXR-seq)
Barcode: CAAAAG

value: CPD


title: Lung from IAV-infected C57BL/6J mouse 48hpi, rep2

description:
B6_48_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

value: female


title: Gene_Expression_Kmt2b_cKO_3


title: Lung from mock-infected C57BL/6J mouse 48hpi, rep4

description:
B6_48m_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

value: whole lung


title: Gene_Expression_Kmt2b_cKO_1


title: CPD_tXR-seq_rep1

description:
translesion eXcision Repair-sequencing (tXR-seq)
Barcode: ATTCCT


title: WT


title: Lung from IAV-infected C57BL/6J mouse 48hpi, rep1

description:
B6_48_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Gene_Expression_Kmt2b_cKO_2


title: Gene_Expression_Kmt2b_Control_8


title: Gene_Expression_Kmt2b_Control_7


title: hESneuron

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
Sequencing reads were mapped to the human genome (hg9) with TopHat v2.0.14 coupled with Bowtie v2.1.0. The mapped reads were subjected to Cufflinks v2.2.1 with the reference annotation (UCSC gene models) to calculate the FPKM values of each gene.
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] file contains gene ids and FPKM values

source_name: neurons derived from embryonic stem cells

extract_protocol:
Total RNA was purified with an RNeasy Mini Kit (QIAGEN), in which an on-column DNase treatment was included.
500 ng of purified RNA was then subjected to mRNA isolation and library preparation using a NEBNext Ultra RNA Directional Library Prep Kit for Illumina with the Poly (A) mRNA Magnetic Isolation Module (NEB) following manufacturer’s instructions.

value: neurons derived from ES cells


title: Day30

source_name: astrocytes treated with small molecules for 30 days

value: adult astrocytes

tag: agent

value: small molecules

value: 30 days


title: Gene_Expression_Kmt2b_Control_6


title: Lung from IAV-infected C57BL/6J mouse 48hpi, rep5

description:
B6_48_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

value: influenza A virus (PR8) infected


title: Gene_Expression_Kmt2b_Control_4


title: Lung from mock-infected C57BL/6J mouse 24hpi, rep3

description:
B6_24m_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, C57BL/6J, mock treated, 24h

value: mock treated (PBS)


title: Lung from mock-infected C57BL/6J mouse 24hpi, rep5

description:
B6_24m_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Gene_Expression_Kmt2b_Control_3


title: Gene_Expression_Kmt2b_Control_2


title: Day2

source_name: astrocytes treated with small molecules for 2 days

value: 2 days


title: Day0

source_name: astrocytes treated with small molecules for 0 days

value: 0 days


title: Gene_Expression_Kmt2b_Control_1

value: Hippocampal CA whole tissue

value: 4-6 month-old (adult)


title: Gene_Expression_Kmt2b_cKO_5

value: Female


title: Lung from mock-infected C57BL/6J mouse 24hpi, rep2

description:
B6_24m_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from mock-infected C57BL/6J mouse 24hpi, rep1

description:
B6_24m_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Input_Kmt2b_Control

source_name: Hippocampal CA neurons

value: Hippocampal CA neurons


title: Input_Kmt2b_cKO


title: H3K4me3_Kmt2b_cKO_5

value: Male

tag: chip antibody

value: H3K4me3 (Abcam ab8580)


title: RNAseq of LC26-RT tumor tissue

city: Chicago

first: Yingtao

last: Bi

state: IL

address: 750 North Lake shore drive

institute: Northwestern University

data_processing:
FastQC was applied on raw fastq files to examine the sequence quality
Tophat  was used for tag alignment
Counts for each gene were computed by means of HTSeq Python package using the annotation of the Ensembl genes and only reads that mapped to exons
Genome_build: hg19
Supplementary_files_format_and_content: Counts of sequenced reads for each gene

source_name: tumor tissue

growth_protocol: Transplantations of RG cells to the SVZ of 3rd ventrivle fo the brain of NOD-SCID mice

extract_protocol:
Total RNA isolation from tumor tissues was performed with the PureZOL RNA isolation reagnet, followed by DNAse treatment
Library making protocol guide for RiboZero selection was used followed by sequencing using Illumina HiSeq2500

tag: host strain

value: NOD-SCID

tag: transplanted with

value: Radial Glial (RG) cells

tag: cell source subject gender

tag: subject status

value: Aggressive medulloblastoma patient

tag: source subject age

value: 5 y/o

tag: tissue type

value: tumor tissue


title: RNAseq of LCAS-RT tumor tissue

value: Healthy child

value: 9 y/o


title: Lung from IAV-infected C57BL/6J mouse 24hpi, rep5

description:
B6_24_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, C57BL/6J, influenza A virus infected, 24h

value: female

tag: tissue

value: whole lung

value: influenza A virus (PR8) infected


title: H3K4me3_Kmt2b_cKO_4

tag: strain

tag: age


title: H3K4me3_Kmt2b_cKO_2

tag: Sex


title: H3K4me3_Kmt2b_cKO_3


title: Lung from mock-infected C57BL/6J mouse 24hpi, rep4

description:
B6_24m_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

tag: strain/background

value: mock treated (PBS)

tag: time post treatment [h]


title: RNAseq of LC25-RT tumor tissue

value: Germinoma patient


title: Lung from IAV-infected C57BL/6J mouse 24hpi, rep4

description:
B6_24_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

tag: gender


title: Gene_Expression_Kmt2b_Control_5

value: Hippocampal CA whole tissue

value: 4-6 month-old (adult)


title: H3K4me3_Kmt2b_Control_6

value: Hippocampal CA neurons


title: H3K4me3_Kmt2b_cKO_1

value: Female


title: Lung from IAV-infected C57BL/6J mouse 24hpi, rep3

description:
B6_24_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: H3K4me3_Kmt2b_Control_4

value: Male

value: H3K4me3 (Abcam ab8580)


title: H3K4me3_Kmt2b_Control_5


title: Lung from IAV-infected C57BL/6J mouse 24hpi, rep2

description:
B6_24_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: SHEEC

city: Luoyang

first: Jiachun

last: Sun

state: Henan

address: 24 Jinghua road, Jianxi district

institute: Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology

description: SHEE retained the phenotype of primary epithelial cells, such as single layer growth and anchor dependent cell aggregation without colony formation in soft agar or tumor formation after transplantation. From a biological perspective, SHEE was similar to the primary cell line and retained its proliferation ability and differentiation potential.

data_processing:
All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). All programs were performed with default setting (unless otherwise specified).
The unique mapped reads (85-90% of total reads) were subsequently assembled into transcripts guided by reference annotation (Gencode v20 and Refseq gene models) with Cufflinks v2.0.2 (Trapnell et al., 2012).  Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
For the analyses of lncRNAs, cufflinks was used to estimate the transcript level FPKM values with the Gencode v20 lincRNA annotation (Derrien et al., 2012), and human body map lincRNA annotations (Cabili et al., 2011).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: SHEEC cell lines

growth_protocol: SHEE and SHEEC were cultured in MEM medium (Gibco) supplemented with 100 ml/L fetal bovine serum (100 u/ml penicillin, 100 u/ml streptomycin) and incubated at 37oc in humidified atmosphere of 50 ml/L CO2. Cells were harvested when they grew into a full monolayer and kept at -70 until use.

extract_protocol:
Total RNA from each sample was extracted using TRK1001 (LC Sciences, Cat. TRK-1001, Total RNA Purification Kit) according to the manufacturer's procedure. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: SHEEC


title: Lung from IAV-infected C57BL/6J mouse 24hpi, rep1

description:
B6_24_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

tag: treatment


title: H3K4me3_Kmt2b_Control_2


title: H3K4me1_Kmt2b_cKO_5

value: H3K4me1 (Abcam ab8895)


title: H3K4me3_Kmt2b_Control_1


title: H3K4me1_Kmt2b_cKO_4


title: H3K4me3_Kmt2b_Control_3


title: H3K4me1_Kmt2b_cKO_3


title: Lung from mock-infected C57BL/6J mouse 18hpi, rep3

description:
B6_18m_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, C57BL/6J, mock treated, 18h


title: H3K4me1_Kmt2b_cKO_1


title: Lung from mock-infected C57BL/6J mouse 18hpi, rep4

description:
B6_18m_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: H3K4me1_Kmt2b_cKO_2


title: H3K4me1_Kmt2b_Control_4


title: H3K4me1_Kmt2b_Control_6


title: H3K4me1_Kmt2b_Control_5


title: Lung from mock-infected C57BL/6J mouse 18hpi, rep2

description:
B6_18m_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: H3K4me1_Kmt2b_Control_3


title: Gene_Expression_Kmt2a_cKO_6


title: SHEE

description: The SHEEC line was established through SHEE induced by 12-Otetradeanoy-lphorbol-13-acetate (TPA).This two cell lines is the most appropriate model of ESCC tumorigenesis.

source_name: SHEE cell lines

value: SHEE


title: Lung from IAV-infected C57BL/6J mouse 18hpi, rep5

description:
B6_18_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, C57BL/6J, influenza A virus infected, 18h


title: Lung from mock-infected C57BL/6J mouse 18hpi, rep1

description:
B6_18m_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: H3K4me1_Kmt2b_Control_2


title: H3K4me1_Kmt2b_Control_1


title: Gene_Expression_Kmt2a_cKO_3


title: Lung from IAV-infected C57BL/6J mouse 18hpi, rep4

description:
B6_18_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Gene_Expression_Kmt2a_cKO_4


title: Lung from mock-infected C57BL/6J mouse 18hpi, rep5

description:
B6_18m_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Gene_Expression_Kmt2a_cKO_2


title: Lung from IAV-infected C57BL/6J mouse 18hpi, rep3

description:
B6_18_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected C57BL/6J mouse 18hpi, rep2

description:
B6_18_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Gene_Expression_Kmt2a_cKO_1


title: Gene_Expression_Kmt2a_Control_4


title: Gene_Expression_Kmt2a_Control_5


title: Gene_Expression_Kmt2a_Control_1


title: Input_Kmt2a_cKO


title: Input_Kmt2a_Control


title: Gene_Expression_Kmt2a_Control_3


title: Lung from mock-infected C57BL/6J mouse 12hpi, rep5

description:
B6_12m_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, C57BL/6J, mock treated, 12h


title: Lung from IAV-infected C57BL/6J mouse 18hpi, rep1

description:
B6_18_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from mock-infected C57BL/6J mouse 12hpi, rep4

description:
B6_12m_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: H3K4me3_Kmt2a_cKO_1


title: H3K4me3_Kmt2a_cKO_3


title: Gene_Expression_Kmt2a_cKO_5


title: Lung from mock-infected C57BL/6J mouse 12hpi, rep2

description:
B6_12m_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: H3K4me3_Kmt2a_Control_4


title: H3K4me3_Kmt2a_Control_5


title: H3K4me3_Kmt2a_Control_2


title: H3K4me3_Kmt2a_Control_3


title: H3K4me3_Kmt2a_Control_1


title: Lung from mock-infected C57BL/6J mouse 12hpi, rep1

description:
B6_12m_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected C57BL/6J mouse 12hpi, rep5

description:
B6_12_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, C57BL/6J, influenza A virus infected, 12h


title: H3K4me1_Kmt2a_cKO_3


title: H3K4me1_Kmt2a_cKO_1


title: Lung from IAV-infected C57BL/6J mouse 12hpi, rep4

description:
B6_12_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected C57BL/6J mouse 12hpi, rep3

description:
B6_12_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: H3K4me1_Kmt2a_cKO_2


title: Gene_Expression_Kmt2a_Control_2

source_name: Hippocampal CA whole tissue


title: H3K4me1_Kmt2a_Control_4


title: H3K4me1_Kmt2a_Control_5


title: Lung from IAV-infected C57BL/6J mouse 12hpi, rep2

description:
B6_12_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: H3K4me1_Kmt2a_Control_2


title: Lung from mock-infected C57BL/6J mouse 12hpi, rep3

description:
B6_12m_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: H3K4me1_Kmt2a_Control_3


title: Lung from mock-infected C57BL/6J mouse 6hpi, rep4

description:
B6_6m_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, C57BL/6J, mock treated, 6h


title: Tmem.WT.LCMV_cl13.si360

first: Fred

address: 9000 Rockville Pike

institute: NIH

data_processing:
abundance estimation, RNA-seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. To quantify transcript abundance we pseudo-aligned RNA-seq reads to ENSEMBL transcripts, using kallisto (v0.42.4, options: -b 50 --single -l 200 -s 30) (Bray et al., 2016)
alignment, RNA-seq: We aligned sequence reads from each RNA-seq library to the mouse genome (build mm10) using STAR (v2.4.2a, options: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout)(Dobin et al., 2013), guided by annotated transcript structures (cDNA sequences from ENSEMBL release 82 GRCm38) (Yates et al., 2016). We visualized these alignments by counting positional coverage across the genome (BEDTOOLS v2.15: genomeCoverageBed -split -bg ) (Quinlan and Hall, 2010), scaling to 10M total read depth, converting to bigWig (wigToBigWig) (Kent et al., 2010), and viewing in IGV (Thorvaldsdottir et al., 2013)
alignment, ChIP-seq: We aligned ChIP-seq reads to the mouse genome (build mm10) with Bowtie (v1.1.2, options -m 1) (Langmead et al., 2009), allowing only uniquely aligning reads. We visualized each ChIP-seq dataset by counting positional coverage across the genome (BEDTOOLS v2.24; options: genomeCoverageBed -split -bg ) (Quinlan and Hall, 2010), scaling to 10M total read depth, converting to bigWig (wigToBigWig) (Kent et al., 2010), and viewing in IGV (Thorvaldsdottir et al., 2013)
peaks, ChIP-seq: We then identified peaks using MACS (v 1.4.3; default p-value threshold of 1E-5) (Y. Zhang et al., 2008) and GEM (v2.6; options: --k_min 6 --k_max 15) (Guo et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig and MACS peak calls for ChIP-seq.  bigWig track for selected RNA-seq samples, combined transcript abundance table including all RNA-seq samples.

source_name: CD4+ T cells

extract_protocol:
RNA Sequencing (RNA-seq) was performed and analyzed as described previously. Total RNA was prepared from approximately 1 million cells by using TRIzol or mirVana miRNA Isolation Kit (Thermo Fisher Scientific Inc.). 200 ng of total RNA was subsequently used to prepare RNA-seq library by using TruSeq SR RNA sample prep kit (FC-122-1001, Illumina) by following manufacturer’s protocol.
RNA-seq: 200 ng of total RNA was subsequently used to prepare RNA-seq library by using TruSeq SR RNA sample prep kit (FC-122-1001, Illumina) by following manufacturer’s protocol.
RNA-seq: The libraries were sequenced for 50 cycles (single read) with a HiSeq 2000 or HiSeq 2500 (Illumina)
ChIP-seq: Cells cultured as indicated were cross-linked for 10 minutes with 1% formaldehyde and harvested. Cells were lysed by sonication and immunoprecipitated with anti-T-bet (sc-21003, Santa Cruz Biotechnology), anti- STAT1 (sc-592, Santa Cruz Biotechnology), anti-STAT2 (ab124283, AbCam), anti-H3K4m1 (ab8895, AbCam) and anti-H3K27ac (ab4729, AbCam)
ChIP-seq: Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt-ended, then phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of NEBNext adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with NEBNext index primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen).
ChIP-Seq (size fractionation). The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.

tag: genotype

value: WT

tag: culture condition

value: LCMV infection protocol (Clone 13)


title: Tmem.WT.LCMV_cl13.si361


title: H3K4me3_Kmt2a_cKO_2

tag: chip antibody


title: H3K4me1_Kmt2a_Control_1


title: Lung from IAV-infected C57BL/6J mouse 12hpi, rep1

description:
B6_12_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from mock-infected C57BL/6J mouse 6hpi, rep3

description:
B6_6m_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Tmem.TbetKO.LCMV_cl13.si363


title: Tmem.TbetKO.LCMV_cl13.si364


title: Lung from mock-infected C57BL/6J mouse 6hpi, rep2

description:
B6_6m_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Tmem.TbetKO.LCMV_cl13.si362


title: Lung from mock-infected C57BL/6J mouse 6hpi, rep1

description:
B6_6m_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from IAV-infected C57BL/6J mouse 6hpi, rep5

description:
B6_6_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, C57BL/6J, influenza A virus infected, 6h


title: CD4.WT.nc.72hr.si145

value: RNA-seq in vitro culture protocol (neutral, 72hr)


title: CD4.WT.nc.6hr.si97

value: RNA-seq in vitro culture protocol (neutral, 6hr)


title: Lung from IAV-infected C57BL/6J mouse 6hpi, rep4

description:
B6_6_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

value: female

value: whole lung


title: CD4.WT.spleen.Toxo.si285

value: Toxoplasma gondii infection protocol (Spleen)


title: Lung from IAV-infected C57BL/6J mouse 6hpi, rep3

description:
B6_6_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

value: influenza A virus (PR8) infected


title: CD4.WT.PEC.Toxo.si287

value: Toxoplasma gondii infection protocol (PEC)


title: CD4.WT.PEC.Toxo.si283


title: CD4.WT.nc.6hr.si196


title: Lung from IAV-infected C57BL/6J mouse 6hpi, rep2

description:
B6_6_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: CD4.WT.nc.24hr.si208

value: RNA-seq in vitro culture protocol (neutral, 24hr)


title: CD4.WT.nc.6hr.si193


title: Tmem.WT.LCMV_cl13.si359


title: CD4.WT.nc.24hr.si205


title: CD4.WT.na.naive.si45

value: cell isolation protocol


title: Lung from untreated C57BL/6J mouse, rep5

description:
B6_0_5
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls

source_name: whole lung tissue, C57BL/6J, untreated, 0h

value: untreated


title: Lung from IAV-infected C57BL/6J mouse 6hpi, rep1

description:
B6_6_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: CD4.WT.na.naive.si277


title: CD4.WT.IFNg.6hr.si197

value: RNA-seq in vitro culture protocol (IFN-γ, 6hr)


title: Lung from untreated C57BL/6J mouse, rep4

description:
B6_0_4
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: CD4.WT.IFNg.72hr.si122

value: RNA-seq in vitro culture protocol (IFN-γ, 72hr)


title: Lung from untreated C57BL/6J mouse, rep2

description:
B6_0_2
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: CD4.WT.IFNg.24hr.si209

value: RNA-seq in vitro culture protocol (IFN-γ, 24hr)


title: Lung from untreated C57BL/6J mouse, rep1

description:
B6_0_1
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: Lung from untreated C57BL/6J mouse, rep3

description:
B6_0_3
Processed data file: reads_miR.txt
Processed data file: edgeR_miR.xls


title: CD4.WT.IFNg.24hr.si206


title: CD4.WT.IFNg.6hr.si194


title: CD4.WT.IFNb.72hr.si148

value: RNA-seq in vitro culture protocol (IFN-β, 72hr)


title: CD4.WT.spleen.Toxo.si281


title: CD4.WT.IFNb.6hr.si198

value: RNA-seq in vitro culture protocol (IFN-β, 6hr)