title: rheumatoid arthritis tissue 27


title: AF16 female control

status: Public on Jun 19 2017

type: SRA

city: Hong Kong

first: Runsheng

last: Li

address: To Yuen Building, 31 To Yuen Street, City University of Hong Kong

country: Hong Kong

institute: City University of Hong Kong

library_source: transcriptomic

data_processing:
Illumina MiSeq with v2 chemistry and software MCS v2.3.0.3 used for basecalling
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trimmomatic, then mapped to to C. briggsae genome (cb4) using CLC genomic workbench 8.0. The genome sequence and gene GFF annotation files were obtained from WormBase (WS250). The cutoff for C. nigoni reads are at least 85% similarity and 80% length while for C. birggsae reads, the cutoff are 90% similarity and 85% length. To de novo annotate putative TEs, RepeatMolder was run with the genome of C. nigoni (cn1, this study) and C. briggsae genome (cb4) as an input, respectively using default parameters. The consensus sequences of TEs produced were used as input to RepeatMasker to annotate all the possible TE loci over the two genomes. RMblast was used in the two annotation pipelines to align genome sequence against possible TEs. For the TE quantification, we mapped all reads from mRNAs against the consensus sequences of as described above using CLC genomic workbench 8.0, with a cutoff of at least 75% similarity and 75 % length.
The unique reads mapped to each genes were then counted with CLC genomic workbench 8.0. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with R package edgeR.
Genome_build: cb4
Supplementary_files_format_and_content: tab-delimited text files include unique reads mapped values for each sample

molecule: total RNA

organism: Caenorhabditis briggsae

source_name: whole worm

extract_protocol:
300 young adult females were picked for mRNA extraction for each sample for C. briggsae (AF16) and C. nigoni (JU1421).
RNA libraries were prepared for sequencing using Illumina’s TruSeq Stranded mRNA Library Preparation Kit based on the Kit’s manual

tag: strain

tag: Stage

value: young adult female

tag: genotype

value: wild type


title: rheumatoid arthritis tissue 40

city: Spring House

first: Alice

last: Walsh

state: PA

address: Welsh & McKean Roads

department: Immunology

country: USA

institute: Janssen R&D

data_processing:
Reads were trimmed for adaptors and sequence quality. The average number of clusters (post-trimming) per sample was 89 million.
Trimmed reads were aligned to human b37.3 reference genome using the STAR v2.4 aligner (Dobin et al., 2013).
Aligned reads were quantified using RSEM v1.2.14 algorithm (Li and Dewey, 2011) with UCSC transcriptome model (accessed on 03/17/2014) that included lincRNAs from Ensembl v75. This transcriptome model has a total of 34495 genes and 88933 isoforms
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited processed data matrix file contains feature counts for all samples and features

organism: Homo sapiens

source_name: synovial biopsy

extract_protocol:
Total RNA was extracted from RA synovial samples and the quality of all RNA samples was evaluated using an Agilent Bioanalyzer
Sequencing libraries were prepared using TruSeq Stranded Total RNA RiboZero protocol from Illumina. Libraries were pooled and sequenced with an Illumina HiSeq 2000 with paired-end 100 bp flow cells. Raw read quality was evaluated using FastQC.

tag: Sex

value: F

tag: age

tag: disease

value: Rheumatoid arthritis (early)

tag: acpa positivity

value: Positive


title: rheumatoid arthritis tissue 31

value: Negative


title: rheumatoid arthritis tissue 22

value: M


title: rheumatoid arthritis tissue 20


title: rheumatoid arthritis tissue 21


title: Input Control

city: Louisville

first: Kevin

middle: J

last: Sokoloski

state: KY

address: 505 S. Hancock St.

department: Microbiology and Immunology

institute: University of Louisville

description: Library generated from total RNA fragmented with RNAse T1

data_processing:
Libraries were demultiplex and trimmed to remove adaptors on the MiSeq interface to generate the raw sequence files.
All analyses of data sets were performed using the Galaxy web services found at Usegalaxy.org, where applicable the programs utilized are indicated by "_" and the version is noted by the (_) following immediately after. Deviations from the default settings are noted.
Library quality was assessed using "FastQC"
Fastq files were converted to Fasta via the "fastQ_to_fasta" tool.
The cDNA libraries were aligned to the SINV Toto1101 genome via "LastZ" (1.2.2) with the following parameters- Search Plus sense only, Require 22bp word with matches in 14 specific positions, allow 2 transitions per hit, Gap open penalty= 1000, Gap Extension. Penalty= 1000,
LastZ output files were converted from SAM format to BAM format using "SAM-to-BAM" (2.1.1) using the SINV Toto1101 Reference Genome.
Depth of coverage was determined using SAMTools to generate a pileup file for each library via "Generate Pileup" (1.2.2).
Base representation, identity, and coverage was determined via the filtering of the pileup data using "Filter Pileup" (1.0.2) to report coverage at each nucleotide.
Tabular data from the filtered pileup files was imported into Excel and analyzed via subtractive analysis to determine regions of significant enrichment for each cDNA library.
Genome_build: SINV Toto1101 Genomic Sequence
Supplementary_files_format_and_content: Single Processed Data File, in .xlsx format. This file contains summary information for the analysis, the depth of coverage at a nucleotide level of resolution for each cDNA library (on different tabs), and the subtractive analysis used to identify the sites of interaction is included on a separate tab.

source_name: 293HEK cells

growth_protocol: 293HEK cells were maintained in MEM supplemented with 10% FBS at 37 degrees Celsius in the presence of 5% CO2. Purified SINV particles were obtained from 293HEK cells and purified using a 27% sucrose cushion via ultracentrifugation.

extract_protocol:
Lysates were generated via the addition of RIPA buffer (50mM Tris [pH 7.6] / 150mM NaCl / 1.0% NP-40 / 0.5% Sodium Deoxycholate / 0.1% SDS). The lysates were clarified via centrifugation and immunoprecipitated with either nonspecific control sera, or anti-SINV Capsid polyclonal sera and Protein A agarose beads. Purified RNA:Protein complexes were treated with RNAse T1 for 15 minutes at room temperature, washed several times to remove contaminating sequences and then released from the resin via proteinase K digestion at 37 degrees Celsius for 30 minutes.
The libraries were generated using the NEBNext Small RNA Library Prep Set for Illumina, with the following Index / Sample pairs- (Input, Illumina 13 AGTCAA) (Nonspecific, Illumina 19 GTGAAA) (Cyto Capsid Set A, Illumina 20 GTGGCC) (Cyto Capsid Set B, Illumina 18 GTCCGC) (Capsid Virion, Illumina 15 ATGTCA)

treatment_protocol: Per library, a total of 2E7 293HEK tissue culture cells were infected with SINV Toto1101 at an MOI of 5 PFU/cell. Infection was allowed to proceed for 18 hours prior to UV crosslinking via 5700x100 ujoules per cm2. Purified viral particles, ~1E11 particles in total, were treated similarly.

tag: virus strain

value: SINV Toto1101

tag: antibody

value: Not immunoprecipitated

tag: rna treatment

value: RNAse T1


title: Nonspecific Control

description: Library generated from total RNA immunoprecipitated with nonspecific polyclonal sera, and fragmented with RNAse T1

value: Preimmune IgG


title: rheumatoid arthritis tissue 32


title: Capsid Cytoplasmic Set A

description: Library generated from total RNA immunoprecipitated with anti-SINV Capsid polyclonal sera, and fragmented with RNAse T1

value: anti-Capsid


title: Capsid Cytoplasmic Set B


title: Worms treated with daf-2 RNAi, rep 2

city: Jerusalem

first: Ehud

last: Cohen

address: Ein Karem

country: Israel

institute: The Hebrew University of Jerusalem

description: Processed data file: DESeq2_final.xls

data_processing:
The NextSeq basecalls files were converted to fastq files using the bcl2fastq (v2.15.0.4) program with default parameters.
Raw reads were quality-trimmed at both ends, using in-house Perl scripts, with a quality threshold of 32.
Cutadapt (version 1.7.1) was used to trim the SL1 and SL2 sequences from the 5' end, and the adapter sequence from the 3' end. Parameters were -O 1, --match-read-wildcards, and -m 15.
The remaining reads were filtered using the fastq_quality_filter program of the FASTX package (version 0.0.14), with parameters -q 20 -p 90.
Reads were mapped using TopHat2 (v2.0.13), with annotations from Ensembl release 82. Parameters were adjusted for short introns: -N 5 --read-gap-length 5 --read-edit-dist 10 --segment-length 20 --read-realign-edit-dist 4 -i 20 --microexon-search --min-segment-intron 20 --coverage-search --min-coverage-intron 20 --max-coverage-intron 10000 --library-type fr-firststrand.
Counting of raw reads was done with the Cufflinks package (v2.2.1), using the genome bias correction (-b parameter), multi-mapped reads assignment algorithm (-u parameter) and masking for genes of type rRNA, tRNA, miRNA, snRNA, snoRNA, piRNA and ncRNA (-M parameter). Additional parameters were --max-bundle-frags 10000000 and --library-type fr-firststrand.
Normalization and differential expression were done with the DESeq2 package (version 1.10.1), using a 2-factors design of the RNAi treatment and replicate number.
Genome_build: WBcel235
Supplementary_files_format_and_content: DESeq2_final.xls: An Excel file with the following columns: Ensembl_Gene_ID, Associated_Gene_Name (yellow); raw read counts for each sample (light green); normalized read counts for each sample (light blue); baseMean (purple); results from DESeq2 for each of the three comparisons, daf-2 RNAi vs. Empty vector, cav-1 RNAi vs. Empty vector, and cav-1 RNAi vs. daf-2 RNAi, each includes the log2FoldChange, lfcSE, stat, pvalue and padj (alternating green and yellow); “yes”/”no” columns for each comparison indicating significance (padj<0.1) (orange).

organism: Caenorhabditis elegans

source_name: whole worm lysate, daf-2 RNAi

growth_protocol: Eggs of CF512 worms were placed on plates seeded with the indicated RNAi bacteria and incubated at 25ºC for 48 hours (to achieve sterility).

extract_protocol:
The worms were grown from hatching until day one of adulthood, collected with M9 buffer and washed in RNase-free water. The worm pellet was resuspended in 2 volumes of QIAzol (QIAgen, Hilden, Germany; #79306) and frozen overnight. Chloroform was used to separate RNA from protein and other materials. The RNeasy Lipid Tissue Mini Kit (QIAgen; #74804) was used according to the manufacturer instructions to extract RNA.
Kapa stranded mRNA-Seq kit with mRNA capture Beads (kapabiosystems, KK8421, https://www.kapabiosystems.com/) was used. Briefly, 1ug was used for the library construction; library was eluted in 20ul of elution buffer. Libraries were adjusted to 10mM, then 10ul (50%) from each sample was collected and pooled in one tube.

treatment_protocol: The worms were treated with RNAi bacteria as described above.

tag: strain/background

tag: stage of development

value: Day 1 of adulthood

tag: RNAi treatment

tag: tissue

value: Whole body


title: Worms treated with daf-2 RNAi, rep 1

description: Processed data file: DESeq2_final.xls


title: rheumatoid arthritis tissue 19


title: Untreated worms, rep 2

description: Processed data file: DESeq2_final.xls

source_name: whole worm lysate, empty vector

value: Empty vector


title: Worms treated with cav-1 RNAi, rep 1

description: Processed data file: DESeq2_final.xls

source_name: whole worm lysate, cav-1 RNAi


title: Untreated worms, rep 1

description: Processed data file: DESeq2_final.xls


title: Worms treated with cav-1 RNAi, rep 2

description: Processed data file: DESeq2_final.xls


title: rheumatoid arthritis tissue 17


title: rheumatoid arthritis tissue 16


title: rheumatoid arthritis tissue 15


title: rheumatoid arthritis tissue 14


title: rheumatoid arthritis tissue 11


title: rheumatoid arthritis tissue 12


title: MCF7-LTED_1

city: St. Louis

first: John

middle: R.

last: Edwards

state: MO

address: 660 S. Euclid Ave, Campus Box 8220

department: Center for Pharmacogenomics

institute: Washington University School of Medicine

data_processing:
Reads were mapped to the human genome (hg18) using TopHat (v1.4).
Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats according to RepeatMasker: snRNA, scRNA, srpRNA, tRNA, and RNA.
htseq-count 0.5.3p3 was used to obtain raw read counts based on Ensembl gene annotations (hg18 v54) using the union method.
Genes mapping to ribosomal and mitochondrial proteins were filtered. A floor of 10 counts per million (cpm) was applied to avoid artificially high fold changes resulting from one sample having a very small number of counts. This also effectively filters genes that were not expressed in either sample. Genes with an expression change less than two-fold are discarded. Differentially expressed genes (FDR=0.05) were identified using edgeR 2.6.12 with TMM normalization and tagwise dispersion. Ensembl gene annotations were mapped to RefSeq IDs and Gene Symbols using the corresponding UCSC Genome Browser tables.
Genome_build: hg18
Supplementary_files_format_and_content: 5-column tab-delimited (ENSG ID,  MCF7_PAR_1, MCF7_PAR_2, MCF7_LTED_1, MCF7_LTED_2), where each row represents a gene after the filtering above, CPM (counts per million) are provided for the expression values for sample MCF7_Par, MCF7_LTED, and replicates 1 and 2 respectively.  MCF7_Par data is from GSM1102650.

molecule: polyA RNA

source_name: Breast cancer cell line

growth_protocol: MCF7 LTED cells were maintained in RPMI 1640 without phenol red supplemented with 5% charcoal stripped fetal bovine serum, 10 mM HEPES, 4.5 g/L glucose, 2 mM L-glutamine, 1 mM sodium pyruvate, and 50 µg/ml gentamicin.

extract_protocol:
Total RNA (10 ug) was isolated , DNase treated, and twice oligo(dT) selected using the Dynabeads mRNA purification kit (Invitrogen).
RNA-seq libraries were constructed using the NEBNext Kit from New England Biolabs. MCF7-LTED_1 libraries were constructed with custom 4 bp barcodes and sequenced with an Illumina GAIIx (32 bp single-end reads). MCF7_LTED_2 libraries were constructed with standard Illumina indexed primers and sequenced using Illumina HiSeq 2000 (42 bp single-end reads).

tag: cell type

value: long-term estradiol deprived (LTED) MCF-7 cells


title: rheumatoid arthritis tissue 23


title: MCF7-LTED_2


title: rheumatoid arthritis tissue 9


title: rheumatoid arthritis tissue 7


title: rheumatoid arthritis tissue 5


title: rheumatoid arthritis tissue 10


title: rheumatoid arthritis tissue 4


title: rheumatoid arthritis tissue 8


title: rheumatoid arthritis tissue 18


title: rheumatoid arthritis tissue 6


title: rheumatoid arthritis tissue 1


title: rheumatoid arthritis tissue 2


title: undifferentiated arthritis tissue 4

value: Undifferentiated arthritis


title: undifferentiated arthritis tissue 5


title: arthralgia tissue 9

value: Arthralgia


title: rheumatoid arthritis tissue 3


title: undifferentiated arthritis tissue 2


title: undifferentiated arthritis tissue 1


title: arthralgia tissue 10


title: rheumatoid arthritis tissue 13


title: arthralgia tissue 8


title: undifferentiated arthritis tissue 3


title: arthralgia tissue 6


title: arthralgia tissue 5


title: arthralgia tissue 3


title: arthralgia tissue 1


title: arthralgia tissue 2


title: osteoarthritis tissue 19

value: Osteoarthritis


title: osteoarthritis tissue 18

value: F


title: osteoarthritis tissue 21


title: osteoarthritis tissue 17


title: osteoarthritis tissue 20


title: osteoarthritis tissue 15


title: osteoarthritis tissue 14


title: arthralgia tissue 7


title: osteoarthritis tissue 13


title: osteoarthritis tissue 9


title: osteoarthritis tissue 5


title: osteoarthritis tissue 8


title: osteoarthritis tissue 6


title: osteoarthritis tissue 7


title: osteoarthritis tissue 12


title: osteoarthritis tissue 3


title: arthralgia tissue 4


title: undifferentiated arthritis tissue 6


title: osteoarthritis tissue 2


title: osteoarthritis tissue 4


title: osteoarthritis tissue 1


title: healthy tissue 28

value: Normal


title: osteoarthritis tissue 22


title: healthy tissue 26


title: healthy tissue 22


title: osteoarthritis tissue 11


title: healthy tissue 21


title: healthy tissue 24


title: healthy tissue 23


title: osteoarthritis tissue 10


title: healthy tissue 18


title: healthy tissue 17


title: healthy tissue 16


title: osteoarthritis tissue 16


title: healthy tissue 15


title: rheumatoid arthritis tissue 60

value: Rheumatoid arthritis (established)


title: healthy tissue 27


title: healthy tissue 9


title: healthy tissue 12


title: healthy tissue 8


title: healthy tissue 14


title: healthy tissue 6


title: healthy tissue 11


title: healthy tissue 19


title: healthy tissue 5


title: healthy tissue 3


title: healthy tissue 4


title: healthy tissue 10


title: healthy tissue 7


title: healthy tissue 2


title: healthy tissue 1


title: healthy tissue 20


title: H_G14

city: Houston

first: Eduardo

last: Vilar

state: TX

address: 1515 Holcombe Blvd., Unit 1360

department: Clinical Cancer Prevention

institute: The University of Texas MD Anderson Cancer Center

data_processing:
mRNA sequences were aligned with Bowtie 1.1.2 on hg19 and quantified with RSEM 1.2.21 using default settings. RSEM expected counts were used for analysis
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited RSEM output with expected counts, TPM, FPKM values

source_name: colonic tubular adenoma from patient with Familial Adenomatous Polyposis (FAP)

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) and the RNeasy kit (Qiagen). RNA was quantified using Qubit (Life Technologies) and RNA quality was assessed with the Agilent 2100 Bioanalyzer to select samples with RNA integrity numbers (RIN) ≥8 for analysis.
Sample preparation, library construction, and sequencing was performed at the DNA Analysis Facility Core at MD Anderson

tag: subject status

value: patients with Familial Adenomatous Polyposis

value: tubular adenoma

tag: size


title: H_G3


title: healthy tissue 13

value: M


title: siPAPg

city: Bridgewater

first: Wencheng

state: NJ - New Jersey

institute: PTC Therapeutics

data_processing:
Data analysis for 3’READS or 3'READS+.  3’READS or 3'READS+ reads were mapped to the human genome (hg19) using bowtie2 (local mode). Uniquely mapped reads (with MAPQ score > 10) that had at least two additional 5’ Ts not aligned to genome (presumably derived from the poly(A) tail) were named pA site supporting (PASS) reads and were used to calculate pA isoform expression. pA isoforms expressed below 5% of all isoforms of a gene were discarded.  Significantly regulated APA events were identified by the Significance Analysis of Alternative Polyadenylation (SAAP) method [Li et al., 2015].
Genome_build: hg19
Supplementary_files_format_and_content: 3READS.pA.read.counts.txt, 3READS.pA.read.counts.siPAPag.txt, and 3READS+.batch2.pA.read.counts.siStarPAP.txt contain information of gene symbol, pA coordinates, read number of pAs in different 3'READS samples. "pA_type" is pA type based on location of a pA. "pAid" has information of chromosome, strand and coordinates (based on hg19).

source_name: PAPg knockdown

growth_protocol: Human embryonic kidney (HEK) 293 cells were obtained from American Type Culture Collection (ATCC). The cell culture conditions were performed as previously described (Li et al. 2012).

extract_protocol:
Total RNA was subjected to 1 round of poly(A) selection using the Poly(A)PuristTM MAG kit (Ambion), followed by fragmentation using the RNA fragmentation kit (Ambion).
Deep sequencing of mRNA was based on the 3’ region extraction and deep sequencing (3’READS) method (Hoque et al. 2013) or 3'READS+ method (Zheng et al., 2016). For 3'READS, poly(A)-containing RNA fragments were isolated using the MyOne streptavidin C1 beads (Invitrogen) coated with a 5’ biotinylated chimeric U5T45 oligo (Sigma) at room temperature for 1 hr in the binding buffer (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA), followed by washing with the washing buffer (10 mM Tris-HCl pH7.5, 1 mM NaCl, 1 mM EDTA, 10% Formamide). RNA bound to the beads was digested with RNase H (5U in 50 μl reaction volume) at 37 °C for 1 hr, which removed the poly(A) sequence and eluted RNA from the beads. Eluted RNA fragments were purified by Phenol:Chloroform extraction and Ethanol precipitation, followed by phosphorylation of the 5' end with T4 kinase (NEB). Phosphorylated RNA was then purified by the RNeasy kit (Qiagen) and was sequentially ligated to a 5’-adenylated 3’ adapter (5’-rApp/NNNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC) with the truncated T4 RNA ligase II (Bioo Scientific) and to a 5’ adapter (5’-GUUCAGAGUUCUACAGUCCGACGAUC) by T4 RNA ligase I (NEB). The resultant RNA was reverse-transcribed to cDNA with Superscript III (Invitrogen), followed by 12 cycles of PCR amplification with Phusion high fidelity polymerase (NEB). cDNA libraries were sequenced on an Illumina Hiseq 2000 sequencer.

treatment_protocol: The transfections of the siRNAs were performed as previously described (Li et al. 2012).

tag: cell line

tag: cell condition

value: knockdown

tag: library protocol


title: M_P60_Sal 3

city: Philadelphia

first: mark

last: alter

address: 125 S. 31st Street

department: Center for Neurobiology and Behvior

institute: University of Pennsylvania

description:
[[H6]]_tube48_P60_SAL_4.3.14_M-1
FGC0900_s_2_GAATTCGTGTACTGAC

data_processing:
Illumina Casava-1.8.2 software was used for basecalling.
RNA-Seq - Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to mouse genome mm9 and Refseq transcriptome and for transcript quantitation. Differential expression analysis was carried out using a custom script implementing EdgeR software.
Genome_build: mm9
Supplementary_files_format_and_content: Excel format file of transcript raw read counts of each sample

organism: Mus musculus

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols for the stranded polyA high-throughput kit.

tag: strain background

tag: Sex

value: male

tag: developmental stage

tag: treated with

value: Saline

value: microglia


title: M_P60_Sal 1

description:
[[F5]]_tube38_P60_SAL_3.27.14_M-2
FGC0900_s_2_ATTCAGAATAATCTTA


title: siStarPAP

source_name: StarPAP knockdown


title: F_P60_Sal 6

description:
[[B7]]_tube50_P60_SAL_4.3.14_M-3
FGC0900_s_2_CTGAAGCTATAGAGGC


title: H_G5


title: M_P60_LPS 6

description:
[[E9]]_tube69_P60_LPS_4.10.14_M-1
FGC0900_s_2_CGGCTATGAGGCGAAG

value: LPS


title: M_P60_LPS 5

description:
[[F8]]_tube62_P60_LPS_4.9.14_M-5
FGC0900_s_2_TAATGCGCTAATCTTA


title: M_P60_Sal 2

description:
[[B6]]_tube42_P60_SAL_3.31.14_M-1
FGC0900_s_2_GAATTCGTATAGAGGC


title: M_P60_LPS 3

description:
[[D8]]_tube60_P60_LPS_4.9.14_M-3
FGC0900_s_2_TAATGCGCGGCTCTGA


title: M_P14 7

description:
[[F4]]_tube30_P14_2.28.14_M-8
FGC0900_s_2_GAGATTCCTAATCTTA

value: none (untreated)


title: M_P14 10

description:
[[A5]]_tube33_P14_3.14.14_M-3
FGC0900_s_2_ATTCAGAATATAGCCT


title: F_P4 1

description:
[[A2]]_tube9_P4_2.21.14_M
FGC0900_s_2_TCCGGAGATATAGCCT


title: M_P4 4

description:
[[G2]]_tube15_P4_4.2.14_M
FGC0900_s_2_TCCGGAGACAGGACGT


title: F_P60_LPS 3

description:
[[A8]]_tube57_P60_LPS_4.8.14_M-5
FGC0900_s_2_TAATGCGCTATAGCCT


title: M_P4 3

description:
[[E2]]_tube13_P4_4.1.14_M
FGC0900_s_2_TCCGGAGAAGGCGAAG


title: M_P4 2

description:
[[C2]]_tube11_P4_3.7.14_M
FGC0900_s_2_TCCGGAGACCTATCCT


title: M_P14 6

description:
[[E4]]_tube29_P14_2.28.14_M-7
FGC0900_s_2_GAGATTCCAGGCGAAG


title: M_P14 9

description:
[[H4]]_tube32_P14_3.14.14_M-2
FGC0900_s_2_GAGATTCCGTACTGAC


title: siPAPa

source_name: PAPa knockdown


title: M_P14 8

description:
[[G4]]_tube31_P14_3.14.14_M-1
FGC0900_s_2_GAGATTCCCAGGACGT


title: M_P14 5

description:
[[D4]]_tube28_P14_2.28.14_M-6
FGC0900_s_2_GAGATTCCGGCTCTGA


title: siCtrl

source_name: knockdown control

value: knockdown control


title: M_P14 3

description:
[[C3]]_tube19_P14_2.24.14_M-3
FGC0900_s_2_CGCTCATTCCTATCCT


title: M_P14 4

description:
[[C4]]_tube27_P14_2.28.14_M-5
FGC0900_s_2_GAGATTCCCCTATCCT


title: M_P60_Sal 4

description:
[[A7]]_tube49_P60_SAL_4.3.14_M-2
FGC0900_s_2_CTGAAGCTTATAGCCT


title: F_E18 2

description:
[[C1]]_tube3_E18_1.27.14_M
FGC0900_s_2_ATTACTCGCCTATCCT


title: M_P14 1

description:
[[A3]]_tube17_P14_2.24.14_M-1
FGC0900_s_2_CGCTCATTTATAGCCT


title: M_P60_LPS 4

description:
[[E8]]_tube61_P60_LPS_4.9.14_M-4
FGC0900_s_2_TAATGCGCAGGCGAAG


title: M_E18 3

description:
[[G1]]_tube7_E18_4.11.14_M
FGC0900_s_2_ATTACTCGCAGGACGT


title: F_P60_Sal 7

description:
[[C7]]_tube51_P60_SAL_4.3.14_F-4
FGC0900_s_2_CTGAAGCTCCTATCCT

value: female


title: M_P14 2

description:
[[B3]]_tube18_P14_2.24.14_M-2
FGC0900_s_2_CGCTCATTATAGAGGC


title: M_E18 2

description:
[[E1]]_tube5_E18_3.15.14_M
FGC0900_s_2_ATTACTCGAGGCGAAG


title: M_P60_LPS 1

description:
[[H7]]_tube56_P60_LPS_4.8.14_M-4
FGC0900_s_2_CTGAAGCTGTACTGAC


title: F_P60_Sal 4

description:
[[E6]]_tube45_P60_SAL_3.31.14_F-4
FGC0900_s_2_GAATTCGTAGGCGAAG


title: F_P60_Sal 5

description:
[[F6]]_tube46_P60_SAL_3.31.14_F-5
FGC0900_s_2_GAATTCGTTAATCTTA


title: M_P60_Sal 5

description:
[[G6]]_tube47_P60_SAL_3.31.14_F-6
FGC0900_s_2_GAATTCGTCAGGACGT


title: F_P60_LPS 2

description:
[[F7]]_tube54_P60_LPS_4.8.14_F-2
FGC0900_s_2_CTGAAGCTTAATCTTA


title: F_P60_LPS 5

description:
[[H8]]_tube64_P60_LPS_4.10.14_F-1
FGC0900_s_2_TAATGCGCGTACTGAC


title: M_P60_LPS 7

description:
[[D9]]_tube68_P60_LPS_4.10.14_F-5
FGC0900_s_2_CGGCTATGGGCTCTGA


title: F_P60_LPS 6

description:
[[B9]]_tube66_P60_LPS_4.10.14_F-3
FGC0900_s_2_CGGCTATGATAGAGGC


title: F_P60_Sal 2

description:
[[C6]]_tube43_P60_SAL_3.31.14_F-2
FGC0900_s_2_GAATTCGTCCTATCCT


title: F_P60_Sal 1

description:
[[E5]]_tube37_P60_SAL_3.27.14_F-1
FGC0900_s_2_ATTCAGAAAGGCGAAG


title: F_P4 2

description:
[[D2]]_tube12_P4_3.7.14_F
FGC0900_s_2_TCCGGAGAGGCTCTGA


title: M_P60_LPS 2

description:
[[G7]]_tube55_P60_LPS_4.8.14_F-3
FGC0900_s_2_CTGAAGCTCAGGACGT


title: F_P4 4

description:
[[H2]]_tube16_P4_4.2.14_F
FGC0900_s_2_TCCGGAGAGTACTGAC


title: F_P60_Sal 3

description:
[[D6]]_tube44_P60_SAL_3.31.14_F-3
FGC0900_s_2_GAATTCGTGGCTCTGA


title: F_P4 3

description:
[[F2]]_tube14_P4_4.1.14_F
FGC0900_s_2_TCCGGAGATAATCTTA


title: F_P60_LPS 1

description:
[[E7]]_tube53_P60_LPS_4.8.14_F-1
FGC0900_s_2_CTGAAGCTAGGCGAAG


title: F_P14 10

description:
[[D5]]_tube36_P14_3.14.14_F-6
FGC0900_s_2_ATTCAGAAGGCTCTGA


title: F_P14 2

description:
[[E3]]_tube21_P14_2.24.14_F-5
FGC0900_s_2_CGCTCATTAGGCGAAG


title: F_P14 4

description:
[[G3]]_tube23_P14_2.28.14_F-1
FGC0900_s_2_CGCTCATTCAGGACGT


title: F_P14 7

description:
[[B4]]_tube26_P14_2.28.14_F-4
FGC0900_s_2_GAGATTCCATAGAGGC


title: F_P14 3

description:
[[F3]]_tube22_P14_2.24.14_F-6
FGC0900_s_2_CGCTCATTTAATCTTA


title: F_P14 1

description:
[[D3]]_tube20_P14_2.24.14_F-4
FGC0900_s_2_CGCTCATTGGCTCTGA


title: F_P14 5

description:
[[H3]]_tube24_P14_2.28.14_F-2
FGC0900_s_2_CGCTCATTGTACTGAC


title: F_P14 6

description:
[[A4]]_tube25_P14_2.28.14_F-3
FGC0900_s_2_GAGATTCCTATAGCCT


title: F_P14 9

description:
[[C5]]_tube35_P14_3.14.14_F-5
FGC0900_s_2_ATTCAGAACCTATCCT


title: F_E18 3

description:
[[F1]]_tube6_E18_3.15.14_F
FGC0900_s_2_ATTACTCGTAATCTTA


title: M_E18 4

description:
[[H1]]_tube8_E18_4.11.14_F
FGC0900_s_2_ATTACTCGGTACTGAC


title: M_E18 1

description:
[[D1]]_tube4_E18_1.27.14_F
FGC0900_s_2_ATTACTCGGGCTCTGA


title: M_P4 1

description:
[[B2]]_tube10_P4_2.21.14_F
FGC0900_s_2_TCCGGAGAATAGAGGC


title: F_P60_LPS 4

description:
[[B8]]_tube58_P60_LPS_4.9.14_F-1
FGC0900_s_2_TAATGCGCATAGAGGC


title: Cfms-d7-Sham_H8

city: South San Francisco

first: Ian

last: Driver

state: California

address: 486 Cabot Road

department: Bioinformatics

institute: Gordian Biotechnology

description:
Cells were collected from right lung lobes 7 days after sham surgery (opening of chest cavity)
rsem count and fpkm for all cells

data_processing:
De-multiplexed files were created using CASAVA 1.8
Each sample was filtered using Trimmatic (http://www.usadellab.org/cms/?page=trimmomatic) with the settings LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:70 and only paired matches were kept
Using the RSEM aligner and the Ensembl GRC m38 release 87 paired fastq files were aligned to the genome
The gene count matrix was then created by running the rsem command "rsem-generate-data-matrix" on all of the genes.results files for each cell
The fpkm mtrix was taken by combinding the fpkm counts from each cell and combining them into one matrix
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: The rsem_m38_Cfms-d7-Sham.gene.count.matrix file contains the raw counts output from rsem as a tab delimted file and the rsem_m38_Cfms-d7-Sham_gene_fpkm_matrix.txt contains the fpkm values for all individual cells as a tab delimited file

source_name: mouse lung immune cells

extract_protocol:
Single cells enriched by FACS were captured by C1 Single-cell Auto Prep System(Fluidigm).  polyA RNA from each single cell was reverse transcribed and cDNA amplified using SMARTer kit (SMARTer Ultra Low RNA Kit for the Fluidigm C1 System,Clontech#634936)
0.25 ng of amplified cDNA was used as input for the NexteraXT kit (Illumina #FC-131-1096) and indexed with dual indices (Illumina #FC-131-2001)

tag: genotype

value: CD45+, CSF1R-GFP+, F4/80+, Ly6G macrophages

tag: developmental time

value: 10 week adult


title: Cfms-d7-Sham_H5


title: F_E18 1

description:
[[B1]]_tube2_E18_1.25.14_F
FGC0900_s_2_ATTACTCGATAGAGGC


title: F_P14 8

description:
[[B5]]_tube34_P14_3.14.14_F-4
FGC0900_s_2_ATTCAGAAATAGAGGC


title: Cfms-d7-Sham_G3


title: Cfms-d7-Sham_G8


title: Cfms-d7-Sham_G1


title: Cfms-d7-Sham_F8


title: Cfms-d7-Sham_F2


title: Cfms-d7-Sham_F1


title: Cfms-d7-Sham_F10


title: Cfms-d7-Sham_E9


title: Cfms-d7-Sham_F11


title: Cfms-d7-Sham_E7


title: Cfms-d7-Sham_E5


title: Cfms-d7-Sham_E12


title: Cfms-d7-Sham_D8


title: Cfms-d7-Sham_D6


title: Cfms-d7-Sham_D4


title: Cfms-d7-Sham_D12


title: Cfms-d7-Sham_C6


title: Cfms-d7-Sham_D10


title: Cfms-d7-Sham_C8


title: Cfms-d7-Sham_C7


title: Cfms-d7-Sham_H4


title: tfcp2l1 rep2

city: New York

first: Max

last: Werth

state: NY

address: 1150 St. Nicholas Ave.

department: Medicine

institute: Columbia University

data_processing:
Base calling using RTA( (Illumina)
Read mapping using Tophat version 2.0.4 with 4 mismatches and 10 maximum multiple hits
Estimation of relative abundance of genes using cufflinks version 2.0.2
identification of differentially expressed genes using R limma
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimeted text files include FPKM values for each gene

organism: Rattus norvegicus

source_name: Metanephric Mesenchyme

extract_protocol:
10 mesenchymes were pulled to produce one replicate, total RNA was extracted using Qiagen RNAeasy Mini Kit according to manufacturer's instructions, quality and amount was analyzed on Bioanalyzer
Illumina TruSeq RNA prep kit

tag: transduction

value: Tfcp2l1 adenoviruses

value: Embryonic Day 13.5 (E13.5)


title: control rep3

value: GFP adenoviruses


title: tfcp2l1 rep1


title: tfcp2l1 rep3


title: Tfcp2l1_ChiPSeq

library_source: genomic

data_processing:
Basecalls using standard Illumina Pipeline
Alignment to the mm9 genome assembly using bowtie
Peak  calling using MACS2
Genome_build: mm9

molecule: genomic DNA

source_name: Kidney

extract_protocol:
Protein-DNA complexes were immunoprecipitated using Tfcp2l1 antibody (RnD AF5726) or Goat IgG as control
ChiP-Seq Library was prepared using Illumina ChiPSeq Library Preparation Kit according to manufacturer's instructions

value: kidney

value: Postnatal Day 1 (P1)

tag: chip antibody

value: Tfcp2l1 (RnD, AF5726)


title: Cfms-d7-Sham_B9


title: Cfms-d7-Sham_A6


title: Cfms-d7-Sham_A12


title: Cfms-d7-Sham_B7


title: Cfms-d7-Sham_B4


title: Cfms-d7-Sham_C11


title: control rep1


title: Cfms-d7-Sham_C4


title: IgG_ChiPSeq

value: Goat IgG (Jackson Immuno 005-000-003)


title: healthy tissue 25

value: F

tag: age

tag: disease

value: Normal

tag: acpa positivity


title: cfms_7dpnx_C94

description:
Cells were collected from right lung lobes 7 days after pneumonecomy surgery (opening of chest cavity and removal of the left lung lobe)
gene.count and gene.fpkm table for all cells

data_processing:
De-multiplexed files were created using CASAVA 1.8
Using Tophat2 version 2.1.0 each paired end file was aligned to the mm10 mouse genome
After alignment cufflinks version 2.2.1 was run on all accepted_hits.bam files from each cell to created the fpkm and abundances.cxb file for each cell
Cufflinks version 2.2.1 was used to normalize all samples using the cuffnorm command producing the gene fpkm and count matrix file for all cells
Genome_build: mm10
Supplementary_files_format_and_content: The "genes.count_table" file contains the counts output from cuffnorm as a tab delimted file and the "genes.fpkm_table" contains the cuffnorm output fpkm values for all individual cells as a tab delimited file

tag: cell type


title: Cfms-d7-Sham_A10


title: control rep2


title: cfms_7dpnx_C95


title: Bulk_RNA-Seq_HNSCC_41_TIL

city: La Jolla

first: Vijay

last: Pandurangan

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

description:
PolyAtail selected messenger RNA
01_RSS20_1_HN6_CD8_T

data_processing:
Bulk RNA-seq data was mapped against the human hg19 reference using TopHat43 (v1.4.1., --library-type fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site. Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id)
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements as a matrix table

source_name: Head & neck squamous cancer tumor

growth_protocol: CD8+ T cells were isolated from head and neck squamous cancer tumors and directly sorted by Flow cytometry into lysis buffer (Trizol LS). No particular cell growth procedure was required.

extract_protocol:
Bulk RNA-seq was performed using Smartseq2 protocol as described in Seumois et al.2016, PMID: 27271570. Total RNA was purified using a miRNAeasy kit (Qiagen) and quantified as  described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: T cells were isolated from tumor (TILs) using a combination of mechanical and enzymatic dissociation. Briefly, tumor tissue was cut into small fragments and incubated at 37 °C for 15 minutes in an orbital shaker with 2 mL RPMI 1640 medium (Fisher Scientific) containing 20 units/mL Liberase DL (Roche) and 800 units/mL DNase I (Sigma-Aldrich). Dispersed cells were then passed through a 70 μm filter, centrifuged and re-suspended in MACS buffer (phosphate-buffered saline containing 2 mM EDTA and 0.5% bovine serum albumin) for flow sorting or flow cytometric analysis. For isolating and phenotyping CD8+ T cells from tumor or lung tissue, dispersed cells were first incubated with FcR block (Miltenyi Biotec), then stained with a mixture of fluorescently conjugated antibodies: anti-CD45-FITC (HI30; Biolegend), anti-CD4-PE (RPA-T4; BD Biosciences), anti-CD3-PE-Cy7 (SK7; Biolegend), anti-CD8a-PerCP-Cy5.5 (cSK1; BD Biosciences), anti-HLA-DR-APC (L243; BD Biosciences), anti-CD14-APC-H7 (MφP9; BD Biosciences), anti-CD19-PerCP-Cy5.5 (clone HIB19; Biolegend) and anti-CD20-PerCP-Cy5.5 (clone 2H7; Biolegend). Stained samples were analyzed using BD FACSAria™ (BD Biosciences) and FlowJo software (Treestar), and CD8+ T cells were sorted into ice-cold TRIzol LS reagent (Ambion).

value: CD8+ T cells

tag: cell subtype

value: CD45+, CD3+ CD8+, live singlets


title: Bulk_RNA-Seq_HNSCC_39_TIL

description:
PolyAtail selected messenger RNA
42_RSS20_47_HN92_CD8_T


title: Bulk_RNA-Seq_HNSCC_40_TIL

description:
PolyAtail selected messenger RNA
07_RSS20_7_HN12A_CD8_T


title: cfms_7dpnx_C93


title: cfms_7dpnx_C92


title: Bulk_RNA-Seq_HNSCC_38_TIL

description:
PolyAtail selected messenger RNA
15_RSS20_17_HN31_CD8_T


title: Bulk_RNA-Seq_HNSCC_36_TIL

description:
PolyAtail selected messenger RNA
06_RSS20_6_HN11_CD8_T


title: Bulk_RNA-Seq_HNSCC_37_TIL

description:
PolyAtail selected messenger RNA
31_RSS20_34_HN59_CD8_T


title: Bulk_RNA-Seq_HNSCC_34_TIL

description:
PolyAtail selected messenger RNA
09_RSS20_10_HN15_CD8_T


title: Bulk_RNA-Seq_HNSCC_35_TIL

description:
PolyAtail selected messenger RNA
22_RSS20_24_HN47_CD8_T


title: cfms_7dpnx_C87


title: Bulk_RNA-Seq_HNSCC_32_TIL

description:
PolyAtail selected messenger RNA
26_RSS20_29_HN61_CD8_T


title: Bulk_RNA-Seq_HNSCC_33_TIL

description:
PolyAtail selected messenger RNA
23_RSS20_25_HN53_CD8_T


title: Bulk_RNA-Seq_HNSCC_30_TIL

description:
PolyAtail selected messenger RNA
02_RSS20_2_HN7AB_CD8_T


title: Bulk_RNA-Seq_HNSCC_29_TIL

description:
PolyAtail selected messenger RNA
20_RSS20_22_HN41_CD8_T


title: Bulk_RNA-Seq_HNSCC_31_TIL

description:
PolyAtail selected messenger RNA
11_RSS20_13_HN20_CD8_T


title: Bulk_RNA-Seq_HNSCC_28_TIL

description:
PolyAtail selected messenger RNA
41_RSS20_45_HN84_CD8_T


title: cfms_7dpnx_C85


title: cfms_7dpnx_C86


title: cfms_7dpnx_C91


title: cfms_7dpnx_C75


title: cfms_7dpnx_C79


title: cfms_7dpnx_C77


title: cfms_7dpnx_C84


title: cfms_7dpnx_C76


title: cfms_7dpnx_C83


title: Bulk_RNA-Seq_HNSCC_27_TIL

description:
PolyAtail selected messenger RNA
36_RSS20_39_HN75_CD8_T


title: Bulk_RNA-Seq_HNSCC_25_TIL

description:
PolyAtail selected messenger RNA
21_RSS20_23_HN42_CD8_T


title: cfms_7dpnx_C73

description:
Cells were collected from right lung lobes 7 days after pneumonecomy surgery (opening of chest cavity and removal of the left lung lobe)
gene.count and gene.fpkm table for all cells


title: Bulk_RNA-Seq_HNSCC_24_TIL

description:
PolyAtail selected messenger RNA
10_RSS20_11_HN18_CD8_T


title: cfms_7dpnx_C89


title: cfms_7dpnx_C71


title: cfms_7dpnx_C69


title: cfms_7dpnx_C70


title: cfms_7dpnx_C68


title: cfms_7dpnx_C67


title: cfms_7dpnx_C66


title: Bulk_RNA-Seq_HNSCC_21_TIL

description:
PolyAtail selected messenger RNA
29_RSS20_32_HN64_CD8_T


title: Bulk_RNA-Seq_HNSCC_20_TIL

description:
PolyAtail selected messenger RNA
05_RSS20_5_HN10_CD8_T


title: Bulk_RNA-Seq_HNSCC_23_TIL

description:
PolyAtail selected messenger RNA
13_RSS20_15_HN24_CD8_T


title: Bulk_RNA-Seq_HNSCC_19_TIL

description:
PolyAtail selected messenger RNA
19_RSS20_21_HN40_CD8_T


title: cfms_7dpnx_C65


title: Bulk_RNA-Seq_HNSCC_26_TIL

description:
PolyAtail selected messenger RNA
39_RSS20_42_HN78_CD8_T


title: Bulk_RNA-Seq_HNSCC_18_TIL

description:
PolyAtail selected messenger RNA
28_RSS20_31_HN63_CD8_T


title: Bulk_RNA-Seq_HNSCC_17_TIL

description:
PolyAtail selected messenger RNA
18_RSS20_20_HN38_CD8_T


title: cfms_7dpnx_C64


title: cfms_7dpnx_C63


title: cfms_7dpnx_C62


title: cfms_7dpnx_C61


title: cfms_7dpnx_C6


title: Bulk_RNA-Seq_HNSCC_22_TIL

description:
PolyAtail selected messenger RNA
40_RSS20_44_HN81_CD8_T


title: Bulk_RNA-Seq_HNSCC_15_TIL

description:
PolyAtail selected messenger RNA
12_RSS20_14_HN23_CD8_T


title: cfms_7dpnx_C59


title: Bulk_RNA-Seq_HNSCC_12_TIL

description:
PolyAtail selected messenger RNA
04_RSS20_4_HN9_CD8_T


title: cfms_7dpnx_C58


title: cfms_7dpnx_C57


title: Bulk_RNA-Seq_HNSCC_13_TIL

description:
PolyAtail selected messenger RNA
37_RSS20_40_HN76_CD8_T


title: Bulk_RNA-Seq_HNSCC_11_TIL

description:
PolyAtail selected messenger RNA
34_RSS20_37_HN70_CD8_T


title: Bulk_RNA-Seq_HNSCC_10_TIL

description:
PolyAtail selected messenger RNA
03_RSS20_3_HN8_CD8_T


title: Bulk_RNA-Seq_HNSCC_09_TIL

description:
PolyAtail selected messenger RNA
30_RSS20_33_HN58_CD8_T


title: cfms_7dpnx_C55


title: cfms_7dpnx_C53


title: cfms_7dpnx_C54


title: Bulk_RNA-Seq_HNSCC_08_TIL

description:
PolyAtail selected messenger RNA
43_RSS20_48_HN34_CD8_T


title: cfms_7dpnx_C50

description:
Cells were collected from right lung lobes 7 days after pneumonecomy surgery (opening of chest cavity and removal of the left lung lobe)
gene.count and gene.fpkm table for all cells


title: Bulk_RNA-Seq_HNSCC_16_TIL

description:
PolyAtail selected messenger RNA
44_RSS20_51_HN44B_CD8_T


title: Bulk_RNA-Seq_HNSCC_05_TIL

description:
PolyAtail selected messenger RNA
08_RSS20_8_HN13_CD8_T


title: cfms_7dpnx_C48


title: Bulk_RNA-Seq_HNSCC_07_TIL

description:
PolyAtail selected messenger RNA
27_RSS20_30_HN62_CD8_T


title: Bulk_RNA-Seq_HNSCC_04_TIL

description:
PolyAtail selected messenger RNA
24_RSS20_26_HN54_CD8_T


title: Bulk_RNA-Seq_HNSCC_03_TIL

description:
PolyAtail selected messenger RNA
35_RSS20_38_HN74_CD8_T


title: Bulk_RNA-Seq_HNSCC_02_TIL

description:
PolyAtail selected messenger RNA
33_RSS20_36_HN68_CD8_T


title: Bulk_RNA-Seq_HNSCC_14_TIL

description:
PolyAtail selected messenger RNA
25_RSS20_28_HN60_CD8_T


title: Bulk_RNA-Seq_HNSCC_01_TIL

description:
PolyAtail selected messenger RNA
16_RSS20_18_HN36_CD8_T


title: cfms_7dpnx_C45


title: cfms_7dpnx_C42


title: cfms_7dpnx_C44


title: Bulk_RNA-Seq_NSCLC_17_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_39_99

source_name: Lung tumor (non-small cell lung cancer)

growth_protocol: CD8+ T cells were isolated from lung tumors or matched adjacent lung tissue and directly sorted by Flow cytometry into lysis buffer (Trizol LS). No particular cell growth procedure was required.

treatment_protocol: T cells were isolated from tumor (TILs) or adjacent uninvolved lung (N-TILs) using a combination of mechanical and enzymatic dissociation. Briefly, tumor or lung tissue was cut into small fragments and incubated at 37 °C for 15 minutes in an orbital shaker with 2 mL RPMI 1640 medium (Fisher Scientific) containing 20 units/mL Liberase DL (Roche) and 800 units/mL DNase I (Sigma-Aldrich). Dispersed cells were then passed through a 70 μm filter, centrifuged and re-suspended in MACS buffer (phosphate-buffered saline containing 2 mM EDTA and 0.5% bovine serum albumin) for flow sorting or flow cytometric analysis. For isolating and phenotyping CD8+ T cells from tumor or lung tissue, dispersed cells were first incubated with FcR block (Miltenyi Biotec), then stained with a mixture of fluorescently conjugated antibodies: anti-CD45-FITC (HI30; Biolegend), anti-CD4-PE (RPA-T4; BD Biosciences), anti-CD3-PE-Cy7 (SK7; Biolegend), anti-CD8a-PerCP-Cy5.5 (cSK1; BD Biosciences), anti-HLA-DR-APC (L243; BD Biosciences), anti-CD14-APC-H7 (MφP9; BD Biosciences), anti-CD19-PerCP-Cy5.5 (clone HIB19; Biolegend) and anti-CD20-PerCP-Cy5.5 (clone 2H7; Biolegend). Stained samples were analyzed using BD FACSAria™ (BD Biosciences) and FlowJo software (Treestar), and CD8+ T cells were sorted into ice-cold TRIzol LS reagent (Ambion).


title: cfms_7dpnx_C41


title: cfms_7dpnx_C43


title: Bulk_RNA-Seq_NSCLC_16_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_40_201


title: cfms_7dpnx_C38


title: cfms_7dpnx_C37


title: Bulk_RNA-Seq_NSCLC_28_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_36_163


title: Bulk_RNA-Seq_NSCLC_19_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_38_238


title: Bulk_RNA-Seq_HNSCC_06_TIL

description:
PolyAtail selected messenger RNA
17_RSS20_19_HN37_CD8_T


title: cfms_7dpnx_C36


title: cfms_7dpnx_C46


title: Bulk_RNA-Seq_NSCLC_32_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_34_132


title: Bulk_RNA-Seq_NSCLC_07_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_28_242


title: cfms_7dpnx_C35


title: Bulk_RNA-Seq_NSCLC_27_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_27_219


title: Bulk_RNA-Seq_NSCLC_09_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_24_157


title: cfms_7dpnx_C34

description:
Cells were collected from right lung lobes 7 days after pneumonecomy surgery (opening of chest cavity and removal of the left lung lobe)
gene.count and gene.fpkm table for all cells


title: cfms_7dpnx_C32


title: cfms_7dpnx_C33


title: cfms_7dpnx_C31


title: cfms_7dpnx_C29


title: cfms_7dpnx_C39


title: Bulk_RNA-Seq_NSCLC_03_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_37_192


title: Bulk_RNA-Seq_NSCLC_13_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_16_103


title: Bulk_RNA-Seq_NSCLC_33_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_22_135


title: Bulk_RNA-Seq_NSCLC_26_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_23_153


title: cfms_7dpnx_C26


title: Bulk_RNA-Seq_NSCLC_24_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_15_74


title: cfms_7dpnx_C28


title: cfms_7dpnx_C30


title: cfms_7dpnx_C25


title: Bulk_RNA-Seq_NSCLC_18_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_08_119


title: Bulk_RNA-Seq_NSCLC_35_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_14_68


title: cfms_7dpnx_C27


title: Bulk_RNA-Seq_NSCLC_21_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_06_116


title: Bulk_RNA-Seq_NSCLC_20_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_02_71


title: cfms_7dpnx_C20


title: Bulk_RNA-Seq_NSCLC_25_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_49_228

source_name: Matched adjacent lung tissue


title: cfms_7dpnx_C24


title: cfms_7dpnx_C22


title: cfms_7dpnx_C18


title: cfms_7dpnx_C21


title: Bulk_RNA-Seq_NSCLC_15_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_01_50


title: cfms_7dpnx_C2


title: cfms_7dpnx_C19


title: Bulk_RNA-Seq_NSCLC_43_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_45_137


title: Bulk_RNA-Seq_NSCLC_11_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_46_96


title: Bulk_RNA-Seq_NSCLC_22_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_48_179


title: Bulk_RNA-Seq_NSCLC_30_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_05_91


title: cfms_7dpnx_C15


title: Bulk_RNA-Seq_NSCLC_04_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_04_81


title: cfms_7dpnx_C17

description:
Cells were collected from right lung lobes 7 days after pneumonecomy surgery (opening of chest cavity and removal of the left lung lobe)
gene.count and gene.fpkm table for all cells


title: Bulk_RNA-Seq_NSCLC_06_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_T_03_72


title: cfms_7dpnx_C12


title: cfms_7dpnx_C14


title: cfms_7dpnx_C16


title: Bulk_RNA-Seq_NSCLC_27_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_33_219


title: Bulk_RNA-Seq_NSCLC_17_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_43_99


title: cfms_7dpnx_C1


title: cfms_7dpnx_C13


title: Bulk_RNA-Seq_NSCLC_41_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_31_167


title: Bulk_RNA-Seq_NSCLC_42_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_32_210


title: Bulk_RNA-Seq_NSCLC_26_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_30_153


title: Bulk_RNA-Seq_NSCLC_33_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_29_135


title: cfms_7dpnx_C10


title: Bulk_RNA-Seq_NSCLC_40_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_12_150


title: Bulk_RNA-Seq_NSCLC_38_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_21_105


title: Bulk_RNA-Seq_NSCLC_37_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_19_88


title: Bulk_RNA-Seq_NSCLC_39_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_11_117


title: Bulk_RNA-Seq_NSCLC_35_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_18_68


title: Bulk_RNA-Seq_NSCLC_12_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_42_62


title: Bulk_RNA-Seq_NSCLC_30_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
CD8_NL_10_91


title: Bulk_RNA-Seq_NSCLC_02_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
48_RSS11B_48_Pt227Nrl_CD8


title: Bulk_RNA-Seq_NSCLC_10_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
46_RSS11B_46_Pt203Nrl_CD8


title: Bulk_RNA-Seq_NSCLC_01_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
44_RSS11B_44_Pt198Nrl_CD8


title: Bulk_RNA-Seq_NSCLC_03_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
42_RSS11B_42_Pt192Nrl_CD8


title: Bulk_RNA-Seq_NSCLC_16_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
45_RSS11B_45_Pt201Nrl_CD8


title: Bulk_RNA-Seq_NSCLC_14_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
43_RSS11B_43_Pt196Nrl_CD8


title: long term repopulating hematopoietic stem cells treated with YH250 3

city: Los Angeles

first: Kahn

last: Michael

address: NRT 4501, 1450 Biggy Street

department: Department of Biochemistry and Molecular Biology

institute: University of Southern California

data_processing:
Image analysis and base calling was carried out using RTA 1.13.48.0.  Final file formatting, demultiplexing and fastq generation were carried out using CASAVA v 1.8.2.
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25 nt were excluded from downstream analyses)
Trimmed reads were then mapped to the mouse genome mm10 using Tophat version 2.0.8 with default parameter settings
Gencode M3 annotation was used to quantify the aligned reads to genes/transcripts using Partek E/M method.
read counts per gene/transcript in all samples were normalized using Upper Quartile normalization and analyzed for differential expression using Partek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
Genome_build: mm10
Supplementary_files_format_and_content: .txt file with normalized gene counts

growth_protocol: C57BL mice were raised in animal facilities according to protocol.

extract_protocol:
Long term repopulating hematopoietic stem cells (LTR-HSC) cells were isolated by FACS. The collected LTR-HSC cells were Lin-Sca1+c-Kit+CD41-CD48-CD150+. Total RNA was prepared and cDNA generated using SMARTer Ultra Low Input RNA for Sequencing-v3 kit (Clontech).
The amplified cDNA was subsequently analyzed on Bioanalyzer Agilent, then sonicated to appropriate size (300-500 bp) using Covaris S2 sonicator. DNA fragments were made into libraries using the KAPA DNA Library Preparation Kits for Illumina sequencing platforms (Kapa Biosystems), using minimal number of PCR cycles to insure complexity.  Libraries were applied to an Illumina flow cell and sequenced on Illumina HiSeq 2000 to generate 50 bp single end reads with total reads per sample averaged around 31 millions.

treatment_protocol: Animals  were given either DMSO or YH250  (2mg/Kg, s.c) and 16 hrs later the bone marrow cells were isolated and FACS sorted for RNA extraction. .

value: bone marrow cells

tag: cell subpopulation

tag: cell surface marker


title: long term repopulating hematopoietic stem cells treated with YH250 1

value: Long term repopulating hematopoietic stem cells (LTR-HSC)


title: Bulk_RNA-Seq_NSCLC_28_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
39_RSS11B_39_Pt163Nrl_CD8


title: long term repopulating hematopoietic stem cells treated with YH250 2


title: cfms_7dpnx_C11

description:
Cells were collected from right lung lobes 7 days after pneumonecomy surgery (opening of chest cavity and removal of the left lung lobe)
gene.count and gene.fpkm table for all cells


title: long term repopulating hematopoietic stem cells control 3

value: DMSO


title: Bulk_RNA-Seq_NSCLC_29_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
37_RSS11B_37_Pt161Nrl_CD8


title: long term repopulating hematopoietic stem cells control 2


title: Bulk_RNA-Seq_NSCLC_19_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
50_RSS11B_50_Pt238Nrl_CD8


title: long term repopulating hematopoietic stem cells control 1


title: Bulk_RNA-Seq_NSCLC_08_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
31_RSS11B_31_Pt113Nrl_CD8


title: Bulk_RNA-Seq_NSCLC_34_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
36_RSS11B_36_Pt159Nrl_CD8


title: Bulk_RNA-Seq_NSCLC_36_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
34_RSS11B_34_Pt149Nrl_CD8


title: Bulk_RNA-Seq_NSCLC_02_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
23_RSS11B_23_Pt227Tum_CD8


title: Bulk_RNA-Seq_NSCLC_25_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
24_RSS11B_24_Pt228Tum_CD8


title: Bulk_RNA-Seq_NSCLC_05_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
27_RSS11B_27_Pt70Nrl_CD8


title: Bulk_RNA-Seq_NSCLC_34_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
10_RSS11B_10_Pt159Tum_CD8


title: Bulk_RNA-Seq_NSCLC_01_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
19_RSS11B_19_Pt198Tum_CD8


title: Bulk_RNA-Seq_NSCLC_29_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
11_RSS11B_11_Pt161Tum_CD8


title: Bulk_RNA-Seq_NSCLC_31_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
16_RSS11B_16_Pt186Tum_CD8


title: Bulk_RNA-Seq_NSCLC_14_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
18_RSS11B_18_Pt196Tum_CD8


title: Bulk_RNA-Seq_NSCLC_22_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
15_RSS11B_15_Pt179Tum_CD8


title: Bulk_RNA-Seq_NSCLC_23_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
09_RSS11B_9_Pt156Tum_CD8


title: Bulk_RNA-Seq_NSCLC_08_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
05_RSS11B_5_Pt113Tum_CD8


title: Bulk_RNA-Seq_NSCLC_36_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
08_RSS11B_8_Pt149Tum_CD8


title: Bulk_RNA-Seq_NSCLC_32_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
32_RSS11B_32_Pt132Nrl_CD8


title: MCF7_LTED.McrBC.slide2

data_processing:
Library strategy: Methyl-MAPS (Methylation Mapping Analysis by Paired-end Sequencing)
Tags for each sample and library (methylated and unmethylated compartment) were sequenced on two slides along with other samples. Tags were distinguished using custom barcodes (6 bp in length) on the F3 tags. Errors in the barcodes were recovered up to 2 bp (in colorspace). Tags were then trimmed to 25 bp.
ag mapping was performed using Corona Lite from the Applied Biosystems SOLiD System software analysis package. Paired tags were mapped individually in color space, allowing up to two mismatches in each 25-bp tag to hg18. Up to 10 hits per chromosome were recorded for each tag.
F3 and R3 tags were paired using the Corona Lite package. A mate pair was reported if a single uniquely placed pair could be made from the hits of each tag that met the contraints of order, orientation, and distance (0-15 kb). If no mate pair could be made, then mate-pair rescue was attempted in which each hit was used as an anchor and the region where an appropriate mate should be found was scanned while allowing a total of four mismatches across both tags. A rescued mate pair was reported if a single uniquely placed pair could be made.
Mapped reads from the same sample were pooled across slides. Fragment filtering, fragment count normalization and methylation level calculation was performed as in Edwards et al. 2010 Genome Research.
Genome_build: hg18
Supplementary_files_format_and_content: SOLiD .mates file; 4-column tab-delimited (chromosome, position, value, coverage)

extract_protocol:
Genomic DNA was isolated from 3 x 10^6 cells using the Quick-gDNA MiniPrep kit from Zymo Research (Irvine, CA) according to the manufacturers instructions. The quality of the isolated high molecular weight DNA was confirmed by agarose gel electrophoresis.
Methyl-MAPS libraries were prepared according to the protocol in Edwards et al Genome Research 2010. In brief, genomic DNA was split and unmethylated and methylated compartments were independently obtained by limit digestions of 10–15 ug of DNA with McrBC or five tetranucleotide methylation-sensitive restriction endonucleases (RE; HpaII, HhaI, AciI, BstUI, HpyCH4IV). Digested fragments were size selected by gel-electrophoresis for fragments >800 bp. Mate-pair SOLiD sequencing libraries were then prepared using custom 6 bp barcodes. As part of the Methyl-MAPS protocol, EcoP15I CAP linkers are ligated onto the ends of the fragments. The fragments are then circularized with biotinylated internal adapters, and digested with EcoP15I, which cleaves the DNA 25-27 bp away from its recognition site. Consequently, although we sequence 35 bp for both the F3 and R3 tags, only 25 bp comprise the genomic sequence tag. Each library was loaded on two sequencing slides.

value: long-term estradiol deprived (LTED) MCF-7 cells

tag: genomic dna digested with

value: Methylation-dependent restriction enzyme McrBC

tag: genomic dna fraction

value: unmethylated


title: MCF7_LTED.RE.slide2

value: methylation-sensitive restriction endonucleases (RE)

value: methylated


title: Bulk_RNA-Seq_NSCLC_23_NTIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
35_RSS11B_35_Pt156Nrl_CD8


title: Bulk_RNA-Seq_NSCLC_11_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
03_RSS11B_3_Pt96Tum_CD8


title: Capsid Virion

description: Library generated from RNA extracted from purified viral particles, and immunoprecipitated with anti-SINV Capsid polyclonal sera, and fragmented with RNAse T1

organism: Sindbis virus

source_name: Purified Mature Sindbis virus Particles

tag: virus strain

value: SINV Toto1101

tag: antibody

value: anti-Capsid

tag: rna treatment

value: RNAse T1


title: Bulk_RNA-Seq_NSCLC_12_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
01_RSS11B_1_Pt62Tum_CD8


title: Bulk_RNA-Seq_NSCLC_05_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
02_RSS11B_2_Pt70Tum_CD8


title: MCF7_LTED.McrBC.slide1


title: Bulk_RNA-Seq_NSCLC_10_TIL

description:
PolyAtail selected messenger RNA
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
21_RSS11B_21_Pt203Tum_CD8


title: MCF7_LTED.RE.slide1


title: JSG3935_E

city: Columbus

last: Gunn

state: Ohio

address: 700 Children’s Drive

department: Center for Microbial Pathogenesis

institute: Abigail Wexner Research Institute at Nationwide Children’s Hospital

data_processing:
Each sample was aligned to the using version 0.7.5a of BWAMEM (http://bio-bwa.sourceforge.net/)
Transcript features were identified from the GFF file provided with the GCF_000009245.1 assembly from NCBI and raw coverage counts were calculated using HTSeq (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html)
The raw RNA-Seq gene expression data was normalized and post-alignment statistical analyses were performed using DESeq2 (http://genomebiology.com/2014/15/12/550) and custom analysis scripts written in R
Transcripts were considered significantly differentially expressed using a 10% false discovery rate (DESeq2 adjusted p value <= 0.1)
Genome_build: GCF_000009245.1 assembly of the Francisella tularensis subsp. holarctica LVS reference from NCBI
Supplementary_files_format_and_content: Excel spreadsheet containing normalized read counts for each sample (columns J - S) and differential expression data (columns H & I) for each feature

source_name: AR-13 resistant

growth_protocol: Wild type and AR-13 resistant mutant were grown in mTSB. The bacteria were collected at the mid-log phase and subjected to total RNA isolation

extract_protocol:
rRNA was removed from 2 µg of RNA with Ribo-ZeroTM rRNA removal kit for Gram-Negative bacteria (Epicentre Biotechnologies, WI)
libraries were constructed from first strand cDNA using ScriptSeqTM v2 RNA-Seq library preparation kit (Epicentre Biotechnologies, WI)

treatment_protocol: using the RNAeasy plus mini kit (Qiagen, Cat#74134)

tag: strain

value: subsp. holarctica strain LVS

tag: genotype/variation

value: AR-13 resistant


title: Ischemic_2

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Libraries were sequenced forcycles on an Illumina HiSeq 2000, respectively, according to the manufacturer’s instructions.
GRO-Seq results were trimmed to remove 3' A-stretches originating from the library preparation and poor quality reads were filtered out (minimum 97% of bp over quality cutoff 10).
Reads were aligned to the susScr3 genome using bowtie (v=2, m=3, k=1)
Genome_build: susScr3
Supplementary_files_format_and_content: Gene expression values (RPKM) and UCSC Bedgraphs are provided

organism: Sus scrofa

source_name: myocardium

extract_protocol:
To obtain single cell suspension, the heart tissue was minced with a scalpel and incubated in 2 ml DMEM containing 0.12 mg/ml collagenase (Sigma-Aldrich) for 15 min in +37 C. The supernatant was collected into stopping medium (DMEM with 0.01 M EDTA) and 1 ml DMEM with 0.12 mg/ml collagenase was added to the remaining tissue pieces. The samples were incubated 10 min in +37 C, supernatant collected and combined to the stopping medium and the procedure repeated four more times. The collected cell suspension was filtered through nylon mesh and centrifuged 8 min with 800 g.
Nuclei were extracted from tissues and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads and precipitated overnight. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified on a denaturing 10% polyacrylamide TBE-urea gel. The recovered cDNA was circularized, linearized, amplified for 15 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit.
GRO-Seq

treatment_protocol: Female farm pigs underwent cardiac catheterization under general anesthesia. Under fluoroscopic guidance a micro catheter was used to place an embolization coil into distal left anterior descending artery (LAD). The occlusion was confirmed by ST-elevation and angiography. After 24h the animals were sacrificed and myocardial samples extracted.

tag: animal number

value: pig 2

tag: sample type

value: nascent RNA


title: Ischemic_3

value: pig 3


title: Ischemic_1

value: pig 1


title: JSG3935_C

organism: Francisella tularensis subsp. holarctica LVS


title: JSG3935_A

source_name: wild type

value: wild type


title: BorderZone_3


title: JSG2086_E


title: JSG3935_B


title: JSG2086_D


title: JSG2086_C


title: JSG3935_D


title: Healthy_2


title: JSG2086_B


title: BorderZone_2


title: Healthy_3


title: Healthy_1


title: BorderZone_1


title: E ck_mRNA-seq

status: Public on Jun 18 2017

city: Anyang

first: Du

last: Xiongming

state: Henan

address: 38# Huanghe Avenue

country: China

institute: Institute of cotton research of CAAS

data_processing:
The raw image data was transformed by base-calling into sequence data and stored in fastq format. To control for the influence of error rate in the Solexa data results, quality pretreatment of the raw data was performed: the sliding window method was first used to remove low-quality fragments (quality threshold = 20, error rate = 1%, window size = 5 bp, and length threshold = 35 bp), followed by removal of partial (<35 bp) sequences containing “N” from the reads.
After filtering of low-quality and dirty raw reads, transcriptome de novo assembly was carried out using the paired-end assembly method as implemented in Trinity (http://trinityrnaseq.sourceforge.net/; trinityrnaseq_r2012-10-05) [123]. After removal of repeats from the spliced sequences, transcripts were obtained of the expected length and size.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
After removal of low-quality reads and adapter sequences from the Solexa sequencing reads, unique sequences of 17–35 nt were used for further analysis.
First, the unique sequences were queried against ribosomal and transfer RNAs from tRNAdb (http://trna.bioinf.uni-leipzig.de/DataOutput/Search), SILVArRNA (http://www.arb-silva.de/), and NONCODE v3.0 (http://www.noncode.org/NONCODERv3/; plant database only, single-nt mismatches allowed) databases to obtain matching rRNA, tRNA, snRNA, and snoRNA sequences.
Any small RNA sequences having exact matches to these sequences were removed from the analysis. The remaining unique small RNA sequences were then BLASTn-searched against the conserved plant miRNAs in the miRBase database (miRBase 19.0; www.mirbase.org/) to identify conserved miRNAs. Only perfectly matched sequences were considered to be conserved miRNAs.
miRNA expression abundance in each library was calculated as RPM (reads per million) according to the formula RPM = mapped reads × 106 / total reads. Calculation of P-values for comparing the miRNA expression between salt-treated samples and the control sample was based on previously established methods(Audic S et al.,1997)

organism: Gossypium hirsutum

source_name: United States

growth_protocol: The seeds were submerged in sterile water for 12 h at room temperature and then sown in sterile silica sand. After 3 days, germinated seedlings were transferred to hydroponic containers (600 × 350 × 120 mm) containing half-strength Hoagland’s solution (pH 6.0 )and grown in a phytotron (KR-III; Zhengzhou Henan Ke-rui Inc.). Growth conditions were 28/22°C day/night temperature, 60–80% relative humidity, and a 14h/10h light/dark cycle under 450 μmol m−2 s light intensity.

extract_protocol:
Samples were harvested directly into liquid nitrogen and stored at −80°C until used for RNA extraction.Total RNA was isolated from cotton leaf samples treated with either 200 mM NaCl or water (as a control) for 4 or 24 h using a modified CTAB method and purified using Qiagen RNeasy columns (Qiagen, Hilden, Germany to use with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Seedlings showing normal growth were randomly divided into two groups; one group was placed into tanks filled with a 200 mM solution of NaCl, and the remaining seedlings were transferred to tanks filled with plain water to serve as control. After exposure to the two solutions for 4, 24, 48, and 72 h, seedlings of control and treated Nan Dan Ba Di Da Hua and Earlistaple 7 were harvested directly into liquid nitrogen and stored at −80°C until used for RNA extraction.

tag: genotype

value: Earlistaple 7

tag: tissue

value: leaf

tag: culture condition

value: 1/2´ Hoagland’s solution


title: E 4h_small RNA-seq


title: N 24h_small RNA-seq

source_name: China

value: Nan Dan Ba Di Da Hua


title: E 4h_mRNA-seq


title: N ck_small RNA-seq


title: E 24h_small RNA-seq


title: N 4h_small RNA-seq


title: E 24h_mRNA-seq


title: N 24h_mRNA-seq


title: N ck_mRNA-seq


title: N 4h_mRNA-seq


title: Junb+/+CD4cre_RNA_2

status: Public on Jun 17 2017

city: Durham

first: Maria

last: Ciofani

state: NC

address: 207 Research Drive, 128 Jones Building

department: Integrative Immunobiology

institute: Duke University School of Medicine

data_processing:
Aligned to mouse genome using Tophat 2.0.13 with parameters “-a 10 -g 20 --no-novel-juncs -G”
Count reads in features from mm10 genome annotation using htseq-count 0.6.1 with options “-s no -m union”
Read counts were normalized and statistical analysis performed using edgeR ver 3.16, default settings
Genome_build: mm10
Supplementary_files_format_and_content: Matrices of raw and filtered / normalized read counts from edgeR in tab-delimited text format

source_name: Th17 cells

growth_protocol: Naïve CD4+ T cells were sort purified and cultured in Th17 cell polarizing conditions in vitro for 48 hours. Sorted cells were seeded into 12 well plates coated with anti-hamster IgG secondary antibody in IMDM supplemented with 10% FBS, penicillin (10U/ml), streptomycin (10μg/ml, glutamine (2mM), gentamicin (50μg/ml), and β-mercaptoethanol (55μM). For TCR stimulation, cultures were provided anti-CD3ε (0.25μg/ml) and anti-CD28 (1μg/ml). Cultures were also supplemented with anti-IL-4 (2μg/ml) and anti-IFNγ (2μg/ml), in addition to IL-6 (20ng/ml) and TGFβ1 (0.3ng/ml).

extract_protocol:
RNA was purified using the Trizol method.
Libraries were prepared from RNA using the Kapa stranded mRNA-Seq kit

tag: time point

tag: replicate

value: rep 2

value: C57Bl/6 (N5 backcross)


title: Junb+/+CD4cre_RNA_1

value: rep 1


title: JunB_Input_DNA_expt1

data_processing:
Raw sequence reads were aligned to the mm10 genome using Bowtie 2.2.5 with settings "-k 1"
JunB peaks were called using MACS2 (ver 2.1.0.20150731) with settings "-g mm -q 0.0005 -m 15 50 --bw=200"
JunD peaks were called using MACS2 (ver 2.1.0.20150731) with settings "-g mm -q 0.01 –m 5 50 --bw=200"
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 peak files

source_name: WT Th17 cells

extract_protocol:
Th17 cells were crosslinked and the resulting sonicate was subjected to immunoprecipitation using 10μg of anti-JunB or anti-JunD. Following reverse-crosslinking, ChIP and input samples were processed to obtain purified DNA.
Libraries were constructed from ChIP and Input DNA using the Kapa Hyper Prep Kit

tag: chip antibody


title: Junbfl/flCD4cre_RNA_2


title: JunB_ChIP_expt1


title: JunB_Input_DNA_expt2


title: E ck_small RNA-seq


title: JunD_ChIP_DNA_JunB_WT_1

source_name: Junb+/+CD4cre Th17 cells


title: JunD_ChIP_DNA_JunB_KO_2

source_name: Junbfl/flCD4cre Th17 cells


title: JunD_ChIP_DNA_JunB_KO_1


title: JunD_ChIP_DNA_JunB_WT_2


title: DsRed_4

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

description:
DsRed_25
Rat intracerebroventricularly injected with an adenovector with empty vector DsRed

data_processing:
Illumina HiSeq 2000 fluorescence images were transformed to BCL files with the Illumina BaseCaller software and samples were demultiplexed to FASTQ files with CASAVA (version 1.8.2).
Sequences were aligned to the genome reference sequence of Rattus norvegicus (RGSC assembly v5.0) using the STAR alignment software.
We used the Bioconductor package edgeR for differential expression analysis of reads counts arising from RNAseq between hippocampal samples from IGF-I and DsRed rats.
Genome_build: Rattus norvegicus (RGSC assembly v5.0)
processed data files format and content: matrixCPMlog2.txt: the Log2 counts per millons (CPM) as obtained by edgeR package
processed data files format and content: raw_read_counts_data.txt: the raw read counts data matrix after processing BAM files with HTSeq

source_name: Rat hippocampus

extract_protocol:
The brains from four rats per group (i.e., DsRed and IGF-I groups) were rapidly removed after euthanasia and their right hippocampus dissected for transcriptome analysis. Tissues were homogenized in TRIzol Reagent.
Library preparation for RNA-Seq was performed using the TruSeq  RNA Sample Preparation Kit (Illumina, Cat. N° RS-122-2002) starting from 500 ng of total RNA.
Accurate quantitation of cDNA libraries was performed using the QuantiFluor TM dsDNA System (Promega).

value: Sprague-Dawley rats

tag: Sex

value: female

tag: age


title: JSG2086_A


title: DsRed_2

description:
DsRed_12
Rat intracerebroventricularly injected with an adenovector with empty vector DsRed


title: DsRed_3

description:
DsRed_22
Rat intracerebroventricularly injected with an adenovector with empty vector DsRed


title: Junbfl/flCD4cre_RNA_1


title: JunD_Input_DNA_JunB_KO


title: DsRed_1

description:
DsRed_7
Rat intracerebroventricularly injected with an adenovector with empty vector DsRed


title: IGF1_1

description:
IGF1_16
Rat intracerebroventricularly injected with an adenovector expressing rat IGF-I


title: IGF1_2

description:
IGF1_24
Rat intracerebroventricularly injected with an adenovector expressing rat IGF-I


title: IGF1_3

description:
IGF1_27
Rat intracerebroventricularly injected with an adenovector expressing rat IGF-I


title: Sham, 72h, #2, whole kidney

city: Bethesda

first: Jae Wook

last: Lee

state: MD

address: 10 Center Drive, 6N314

institute: National Institutes of Health

data_processing:
Base-calling was performed using on-instrument real-time analysis (RTA) pipeline provided by Illumina HiSeq 2000.
Reads were inspected and nucleotides with phred33 score lower than 30 were trimmed with Trimmomatic 0.32 (http://www.usadellab.org/cms/?page=trimmomatic). For single-end reads, we used the following command: java -jar trimmomatic-0.32.jar SE -threads 8 -phred33 sample.fastq.gz sample_p.fastq TRAILING:30 MINLEN:35; For paired-end reads, we used the following command: java -jar trimmomatic-0.32.jar PE -threads 8 -phred33 sample_1.fastq.gz sample_2.fastq.gz sample1_p1.fastq. sample1_up1.fastq sample2_p2.fastq sample2_pup2.fastq TRAILING:30 MINLEN:35
FASTQ sequences that survived the trimming process were mapped to rat reference genome (ensembl Rnor6.0) with STAR 2.4.0.1 using the following command: STAR --genomeDir <genome directory> --readFilesIn sample_p1.fastq <sample_p2.fastq (for paired-end reads)> --runThread 8 --outFilterMismatchNmax 3 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchMax 3 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated
The raw mapping data was filtered for uniquely mapped reads using SAMtools.
HTSeq-count and R were used to count mapped reads and calculate RPKM/FPKMs.
Genome_build: Ensembl Rnor6.0
Supplementary_files_format_and_content: unilateral_nephrectomy_G_and_S1_RPKM.txt is a tab-delimited text file that contains a matrix of reads per kilobase exons per million mapped reads (RPKMs) for Ensembl Rnor6.0 genes. unilateral_nephrectomy_G_and_S1_htseqcount.txt is a tab-delimited text file that contains a matrix of read counts for Ensemble Rnor6.0 genes. unilateral_nephrectomy_wholekidney_FPKM.txt is a tab-delimited text file that contains a matrix of fragments per kilobase exons per million mapped reads (FPKMs) for Ensembl Rnor6.0 genes. unilateral_nephrectomy_wholekidney_htseqcount.txt is a tab-delimited text file that contains a matrix of fragment counts for Ensemble Rnor6.0 genes.

source_name: Rat kidney

growth_protocol: Male Sprague-Dawley rats were grown and maintained in the Animal Facility of the NHLBI. Normal rat chow was fed to the animals.

extract_protocol:
For glomeruli and S1 proximal tubule, RNAs were isolated using Quick-RNA kit (Zymo research) and eluted in 6 uL of RNAse-free water. For the whole kidney, total RNAs were isolated using RNeasy-mini (Qiagen).
RNAs isolated from glomeruli and S1 proximal tubule were made into cDNA libraries using NuGen Ovation RNA-seq V2. For RNAs from the whole kidney, Illumina TruSeq Stranded HT and LT were used to create strand-specific libraries.
Single-end sequencing was used for libraries created from microdissected glomeruli and S1 proximal tubule. Paired-end sequencing was used for libraries created from the whole kidney.

treatment_protocol: Rats received either right nephrectomy or sham surgery under general anesthesia. The right kidney was approached by right mid-abdominal incision. For sham surgery, right renal pedicle was dissected and the incision was closed. For right nephrectomy, the right renal artery, vein, and ureter were individually identified and ligated before excision of the right kidney.

value: rat kidney

tag: surgery

value: sham

value: Adult

tag: gender

value: male

value: Sprague-Dawley


title: IGF1_4

description:
IGF1_29
Rat intracerebroventricularly injected with an adenovector expressing rat IGF-I


title: Sham, 72h, #3, whole kidney


title: JunD_Input_DNA_JunB_WT


title: JunB_ChIP_expt2


title: Sham, 48h, #4, whole kidney


title: Sham, 72h, #1, whole kidney


title: Sham, 24h, #4, whole kidney


title: Sham, 24h, #2, whole kidney


title: Sham, 48h, #1, whole kidney


title: Nephrectomy, 72h, #4, whole kidney

value: Nephrectomy


title: Sham, 72h, #4, whole kidney


title: Sham, 24h, #1, whole kidney


title: Sham, 48h, #3, whole kidney


title: Nephrectomy, 72h, #1, whole kidney


title: Sham, 24h, #3, whole kidney


title: Nephrectomy, 48h, #4, whole kidney


title: Nephrectomy, 72h, #2, whole kidney


title: Nephrectomy, 48h, #3, whole kidney


title: Nephrectomy, 72h, #3, whole kidney


title: Nephrectomy, 48h, #2, whole kidney


title: Nephrectomy, 48h, #1, whole kidney


title: Sham, 48h, #2, whole kidney


title: Nephrectomy, 24h, #3, whole kidney


title: Nephrectomy, 24h, #4, whole kidney


title: Nephrectomy, 24h, #2, whole kidney


title: Sham, 72h, S1 proximal tubule, #3

source_name: Microdissected S1 proximal tubule

value: S1 proximal tubule


title: Sham, 72h, S1 proximal tubule, #1


title: Sham, 72h, glomerulus, #2

source_name: Microdissected glomeruli

value: glomeruli


title: Sham, 72h, S1 proximal tubule, #4


title: Sham, 72h, S1 proximal tubule, #2


title: Sham, 72h, glomerulus, #4


title: Sham, 72h, glomerulus, #3


title: Sham, 72h, glomerulus, #1


title: Sham, 48h, S1 proximal tubule, #3


title: Sham, 48h, glomerulus, #4


title: Sham, 48h, S1 proximal tubule, #1


title: Sham, 48h, glomerulus, #3


title: Sham, 48h, glomerulus, #2


title: Sham, 48h, S1 proximal tubule, #4


title: Sham, 24h, S1 proximal tubule, #4


title: Sham, 24h, glomerulus, #3


title: Sham, 48h, glomerulus, #1


title: Sham, 24h, glomerulus, #4


title: Sham, 24h, S1 proximal tubule, #3


title: Nephrectomy, 72h, S1 proximal tubule, #4


title: Sham, 24h, glomerulus, #2


title: Sham, 24h, S1 proximal tubule, #1


title: Sham, 24h, glomerulus, #1


title: Nephrectomy, 72h, glomerulus, #4


title: Nephrectomy, 24h, #1, whole kidney


title: Nephrectomy, 72h, S1 proximal tubule, #3


title: Nephrectomy, 72h, S1 proximal tubule, #2


title: Nephrectomy, 72h, glomerulus, #2


title: Sham, 48h, S1 proximal tubule, #2


title: Nephrectomy, 48h, S1 proximal tubule, #4


title: Nephrectomy, 72h, glomerulus, #1


title: Nephrectomy, 48h, glomerulus, #4


title: Nephrectomy, 48h, glomerulus, #3


title: Nephrectomy, 48h, S1 proximal tubule, #3


title: Nephrectomy, 72h, S1 proximal tubule, #1


title: Leaf BGM-infested 24hr biological rep 4

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

description:
B24-4
13455X28

data_processing:
Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCS v2.2.38 and RTA v1.18.61), a 125 cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4003), and the resulting reads were aligned to the Z. mays AGPv3 (Ensembl Release 31) reference genome with STAR 2.5.2b in two-pass alignment mode (alignments were independent of the existing reference annotation).
Read counts for genes (exonic features) in the AGPv3 (Ensembl Release 31) annotation were obtained using HTSeq 0.6.0 with --stranded reverse.
Genome_build: The AGPv3 genome sequence and annotation (Ensembl Release 31) were downloaded from the maize genome site at ensembl.org and used in the study.
Supplementary_files_format_and_content: Tab-delimited text file with counts of reads aligned per gene model as assessed with HTSeq (expression across all samples is included in the single processed data file).

organism: Zea mays

source_name: Leaf tissue

growth_protocol: The maize (Zea mays, B73 inbred) plants used for the experiments were germinated and grown in a greenhouse with an approximately 16h-light/8h-dark photoperiod at a temperature of about 25 degrees C. They were cultivated using SunGrow® Metro-Mix® 900 Grower Mix, watered as needed, and fertilized weekly with 200 ppm NutriCulture 16N-3P-16K.

extract_protocol:
Leaf tissue was ground to a fine powder in liquid nitrogen. Total RNA was prepared using the DirectZol RNA extraction kit (Zymo Research). Quality of the RNA extractions was assessed using a Bioanalyzer (Aligent).
The libraries were prepared at the University of Utah High Throughput Genomics facility using the Illumina TruSeq Stranded mRNA Library Preparation Kit with poly(A) selection.

treatment_protocol: The 4th leaves of 22-day-old maize plants were used for the experiment. Mite movement was restrained by barriers made of a non-toxic wax (TangleFoot). Mites were allowed to feed on both sides of a leaf section defined by TangleFoot barriers. The maize leaf sections were infested with healthy adult females, 400 mites per leaf section for 2hr-timepoints and 200 mites per leaf section for 24hr-timepoints. Wounding treatment was applied by rubbing 60 grit sand paper on both sides of the leaf. The control leaves received the TangleFoot barriers but none of the treatments. Mite infestation and wounding treatments were applied at 24hr and 2hr before sample collection. All samples were collected at the same time to limit the effects of the circadian cycle and any minor environmental differences on gene expression. Mite species used in the experiment were Tetranychus urticae, the two-spotted spider mite (TSSM), and Oligonychus pratensis, the Banks grass mite (BGM). Per treatment, a single plant (leaf) was used, and in total four biological replicates were collected per treatment.

tag: Stage

value: V4-22 days old

tag: leaf number

value: leaf number 4

tag: cultivar

tag: mite species (treatment)

value: Oligonychus pratensis, BGM


title: Nephrectomy, 48h, S1 proximal tubule, #1

tag: strain


title: Nephrectomy, 48h, S1 proximal tubule, #2


title: Nephrectomy, 48h, glomerulus, #2


title: Nephrectomy, 24h, S1 proximal tubule, #3


title: Nephrectomy, 24h, glomerulus, #4


title: Nephrectomy, 24h, S1 proximal tubule, #4


title: Sham, 24h, S1 proximal tubule, #2


title: Leaf BGM-infested 24hr biological rep 2

description:
B24-2
13455X11

value: leaf


title: Nephrectomy, 48h, glomerulus, #1


title: Nephrectomy, 24h, glomerulus, #3


title: Leaf BGM-infested 24hr biological rep 1

description:
B24-1
13455X3


title: Leaf BGM-infested 2hr biological rep 3

description:
B2-3
13455X16


title: Nephrectomy, 24h, glomerulus, #2


title: Leaf BGM-infested 2hr biological rep 4

description:
B2-4
13455X25


title: Nephrectomy, 24h, S1 proximal tubule, #2


title: Nephrectomy, 72h, glomerulus, #3


title: Leaf BGM-infested 2hr biological rep 2

description:
B2-2
13455X8


title: Nephrectomy, 24h, S1 proximal tubule, #1


title: Leaf BGM-infested 2hr biological rep 1

description:
B2-1
13455X1


title: Nephrectomy, 24h, glomerulus, #1


title: Leaf TSSM-infested 24hr biological rep 4

description:
T24-4
13455X22

value: Tetranychus urticae, TSSM


title: Leaf BGM-infested 24hr biological rep 3

description:
B24-3
13455X20


title: hepatocyte M 9d GFP(+)

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

data_processing:
All sequence reads were extracted in FASTQ format using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
Calculation of gene expression value and normalization were performed by RPKMforgenes (10th, Dec, 2012).
Genome_build: The sequence reads were mapped to hg19 reference genes, downloaded on 25th April 2014
Supplementary_files_format_and_content: The processed data file contains Genename, Refseq, RPKM, and Rawcount columns (from left to right), and the expression level was represented by RPKM.

source_name: Human iPS cell-derived hepatocyte-like cell

growth_protocol: The ALBUMIN-GFP reporter cell lines derived from a human iPS cell (hiPSC) line 201B6 were grown on feeder layers of mitomycin C-treated SNL 76/7 in media containing Primate ES medium (ReproCELL) supplemented with 500 U/ml penicillin/streptomycin and 4 ng/ml recombinant human basic fibroblast growth factor (bFGF) at 37 ºC in a humidified incubator with 5% CO2. The definitive endoderm cells were induced to differentiate into hepatoblast-like cells in Knockout-DMEM, 20% KSR, 1 mM L-glutamine, 1% nonessential amino acids, 0.1 mM 2-mercaptoethanol and 1% DMSO for 6-7 days. The hepatoblast-like cells were cultured to differentiate into hepatocyte-like cells in hepatocyte culture medium containing 20 ng/ml recombinant human hepatocyte growth factor (HGF) and 20 ng/ml recombinant human oncostatin M (OsM) for 7-8 days. For methoxamine treated group, cells were cultured with 1 µM methoxamine instead of HGF and OsM.

extract_protocol:
RNA was extracted with QIAGEN RNeasy mini kit, followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. RNA was quantified using a NanoDrop-1000 spectrophotometer.
We generated sequencing libraries using TruSeqStranded Total RNA with Ribo-Zero Gold from 100ng of total RNA.

treatment_protocol: The hiPSC-derived hepatoblast-like cells were differentiated into hepatocyte-like cells with either the combination of HGF and OsM or methoxamine. For hepatocyte-like cells, ALUBUMIN+ cells were isolated by flow cytometry.

tag: cell line

value: 201B6 derived ALUBUMIN reporter cell line 12C57


title: hepatoblast

source_name: Human iPS cell-derived hepatoblast-like cell


title: Leaf TSSM-infested 24hr biological rep 3

description:
T24-3
13455X19


title: iPSC

source_name: Human iPS cell


title: hepatocyte GFs 9d GFP(+)


title: Leaf TSSM-infested 24hr biological rep 1

description:
T24-1
13455X4


title: Leaf TSSM-infested 24hr biological rep 2

description:
T24-2
13455X14


title: Leaf TSSM-infested 2hr biological rep 3

description:
T2-3
13455X17


title: Leaf TSSM-infested 2hr biological rep 4

description:
T2-4
13455X27


title: Leaf wounded 24hr biological rep 4

description:
W24-4
13455X26


title: Leaf wounded 24hr biological rep 3

description:
W24-3
13455X21


title: Leaf TSSM-infested 2hr biological rep 2

description:
T2-2
13455X9


title: Leaf wounded 24hr biological rep 1

description:
W24-1
13455X6


title: Leaf TSSM-infested 2hr biological rep 1

description:
T2-1
13455X5


title: Leaf wounded 2hr biological rep 4

description:
W2-4
13455X24


title: Leaf wounded 2hr biological rep 2

description:
W2-2
13455X12


title: Leaf wounded 2hr biological rep 3

description:
W2-3
13455X15


title: H3K4me3

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

country: France

institute: CNRS

data_processing:
Data Analysis: After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8). After passing Solexa CHASTITY quality filter, the clean reads were aligned to Toxoplasma gondii reference genome (Tgo) using BOWTIE (V2.1.0). Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.0. Statistically significant ChIP-enriched regions (peaks) were identified by comparison of two samples, using a p-value threshold of 10-5. Then the peaks in each sample were annotated by the overlapped gene using the newest Toxoplasma gondii database. The EXCEL/BED format file containing the ChIP-enriched regions was generated for each sample.
Data visualization: The mapped 100 bp reads represent enriched DNA fragments by ChIP experiment. Any region of interest in the raw ChIP-seq signal profile can be directly visualized in genome browser. We use 10-bp resolution intervals (10-bp bins) to partition the stacked reads region, and count the number of reads in each bin.  All the 10 bp resolution ChIP-seq profiles of each sample are saved as UCSC wig format files, which can be visualized in Toxoplasma gondii Genome Browser (http://protists.ensembl.org/Toxoplasma_gondii/Info/ Index).
Genome_build: Toxoplasma gondii genome (ME49 strain) file "ToxoDB-13.0_TgondiiME49_Genome.fasta" to upload at ToxoDB website : http://toxodb.org/common/downloads/release-13.0/TgondiiME49/fasta/data/
Supplementary_files_format_and_content: Statistically significant ChIP-enriched regions (peaks) were identified by comparison of two samples, using a p-value threshold of 10-5. Then the peaks in each sample were annotated by the overlapped gene using the newest Toxoplasma gondii database. The EXCEL/BED format file containing the ChIP-enriched regions was generated for each sample. We use 10-bp resolution intervals (10-bp bins) to partition the stacked reads region, and count the number of reads in each bin.  All the 10 bp resolution ChIP-seq profiles of each sample are saved as UCSC wig format files, which can be visualized in Toxoplasma gondii Genome Browser (http://protists.ensembl.org/Toxoplasma_gondii/Info/ Index).

organism: Toxoplasma gondii

source_name: intracellular parasites

growth_protocol: Toxoplasma gondii type II strain Pruku80 was maintained by serial passage Human foreskin fibroblast (HFF) monolayer under tachyzoite conditions in DMEM (Life) supplemented with 10% (vol/vol) FBS (Life) and 25 mM Hepes buffer, pH 7.2.

extract_protocol:
Crosslinked chromatin was lysed in ice-cold lysis buffer (50mM HEPES KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5%NP-40, 0.125% triton X-100, protease inhibitor cocktail) and sheared in shearing buffer (1mM EDTA pH8.0, 0.5mM EGTA pH8.0, 10mM Tris pH8.0, protease inhibitor cocktail) by sonication using a Diagenode Biorupter. Samples were sonicated, for 16 cycles (30 seconds ON and 30 seconds OFF), to 200-500 base-pair average size. Immunoprecipitation was carried out using sheared chromatin, 5% BSA, protease inhibitor cocktail, 10% triton X-100, 10% deoxycholate, DiaMag Protein A-coated magnetic beads (Diagenode) and antibodies (H4K31ac, H4K31me1, pan acetyl H4, H4K20me3, H3K9me3, H3K4me3, H3K4me1, H3K14ac). A rabbit IgG antiserum was used as a control mock. After overnight incubation at 4°C on rotating wheel, chromatin-antibody complexes were washed and eluted from beads by using iDeal ChIP-seq kit for Histones (Diagenode) according to the manufacturer’s protocol. Samples were decrosslinked by heating for 4 hours at 65°C. DNA was purified by using IPure kit (Diagenode) and quantified by using Qubit Assays (Thermo Fisher Scientific) according to the manufacturer's protocol. For ChIP-seq, purified DNA was used to prepare libraries and then sequenced by Arraystar (USA, http://www.arraystar.com/ ).
ChIP-Sequencing library preparation was performed according to Illumina’s protocol Preparing Samples for ChIP Sequencing of DNA. Library Preparation: 10 ng DNA of each sample was converted to phosphorylated blunt-ended with T4 DNA polymerase, Klenow polymerase and T4 polymerase (NEB); An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments using the polymerase activity of Klenow (exo minus) polymerase (NEB); Illumina's genomic adapters were ligated to the A tailed DNA fragments; PCR amplification was performed to enrich ligated fragments using Phusion High Fidelity PCR Master Mix with HF Buffer (Finnzymes Oy). The enriched product of ~200-700 bp was cut out from gel and purified. Sequencing:  The library was denatured with 0.1M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell at 8pM concentration, amplified in situ using TruSeq Rapid SR cluster kit (#GD-402-4001, Illumina). Sequencing was carried out by running 100 cycles on Illumina HiSeq 4000 according to the manufacturer’s instructions.

treatment_protocol: HFF cells were grown to confluence and infected with Pru∆ku80 strain. Harvested intracellular parasites were crosslinked with formaldehyde (final concentration 1%) for 8 mins at room temperature and the crosslinking was stopped by addition of glycine (final concentration 0.125M) for 5 min at room temperature.

value: Type II (Pruku80)

value: H3K4me3 (Diagenode)

tag: dev. stage

value: tachyzoites


title: Leaf non-infested biological rep 4

description:
C4
13455X23


title: H3K14ac

value: H3K14ac (Diagenode)


title: H4K31me1

value: H4K31me1 - Home made antibody


title: H4K20me3

value: H4K20me3 (Diagenode)


title: Leaf non-infested biological rep 2

description:
C2
13455X13


title: Leaf non-infested biological rep 3

description:
C3
13455X18


title: H4K31ac

value: H4K31ac - Home made antibody


title: Leaf non-infested biological rep 1

description:
C1
13455X2


title: H3K9me3

value: H3K9me3 (Diagenode)