title: ZWU19PlasmaB54A22

value: total cell-free biofluid RNA

value: postE (Postprandial Early, 1 Hour After Lunch)

tag: 3' adapter

value: 22 (TTGTATCGTATGCCGTCTTCTGCTTG)

tag: read count

tag: read depth


title: ZWU19SerumB61A1

status: Public on May 04 2018

type: SRA

city: New York

first: Thomas

last: Tuschl

state: NY

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

library_source: transcriptomic

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA sequencing data analysis platform (RSDAP) (Farazi T et. al, 2002, Methods 58:171-187), considering a size range of 16 to 45 nt and allowing up to two mismatches to the curated reference-transcriptome.
Genome_build: hg19
Supplementary_files_format_and_content: Each processed data file contains miRNA read counts and miRNA read frequencies for miRNA species found in a given sample.

molecule: total RNA

organism: Homo sapiens

source_name: Serum

extract_protocol:
Low speed centrifugation (2500 g x 15 minutes, room temperature) was performed, then transfer of supernatant, 2nd round of centrifugation (same parameters), then transfer of supernatant. A self-developed method and self-developed solutions were used for nucleic-acid extraction, nucleic-acid partitioning, and column purification (RNA isolation). Extracellular vesicles were not pre-purified. RNA isolation kit was a self developed protocol executed on epMotion 5075 liquid handling system. exRNA were quantified via use of two sets of spike-in calibrators added 1) prior to RNA isolation (set1), 2) at prior to cDNA library preparation (set2), to determine RNA quality and yield of miRNAs and other RNA molecules with 5P/3OH ends. Each set consists of ten individual 22-nt calibrators that do not map to the human genome. Relative to the material present in each sample cDNA library preparation, 1 attomole of each calibrator oligo was present unless stated otherwise. Calibrator sequences (labeled by set) are: >Set1_cali_01_rc TCCACGACGTCTCATGTATTTC, >Set1_cali_04_rc GGGTACCATACCGGTTGTCTTA, >Set1_cali_17_rc TCATGAGTCCGTACCTTGATTG, >Set1_cali_18_rc ATCATTTACGATTCGGAGCTGT, >Set1_cali_20_rc GATAGTTCGGGATCGCTGTAAC, >Set1_cali_24_rc TGCTACTCCGATCTTTAGCCTC, >Set1_cali_25_rc AGGGCCCTTTAGGCACTAATAG, >Set1_cali_27_rc GTAGCTGTCAGTACGTTCGTGC, >Set1_cali_43_rc TCTAGTTGCGTGATGGAGAGAA, >Set1_cali_44_rc AGCCGCATTTCGTAGTGATATT, >Set2_cali_07_rc GTCCCACTCCGTAGATCTGTTC, >Set2_cali_11_rc GATGTAACGAGTTGGAATGCAA, >Set2_cali_12_rc TAGCATATCGAGCCTGAGAACA, >Set2_cali_14_rc CATCGGTCGAACTTATGTGAAA, >Set2_cali_15_rc GAAGCACATTCGCACATCATAT, >Set2_cali_16_rc TCTTAACCCGGACCAGAAACTA, >Set2_cali_26_rc AGGTTCCGGATAAGTAAGAGCC, >Set2_cali_28_rc TAACTCCTTAAGCGAATCTCGC, >Set2_cali_31_rc AAAGTAGCATCCGAAATACGGA, >Set2_cali_35_rc TGATACGGATGTTATACGCAGC
Self developed protocol - 24 samples were multiplexed into one processing batch and their cDNA was sequenced using Illumina HiSeq flowcell.

tag: condition

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: individual

tag: time point

value: B13 (Day 43, 4 Hours After Lunch)

tag: nutrition state

value: postL (Postprandial Late, 4 Hours After Lunch)

tag: female hormonal cycle phase

value: L

tag: female hormonal cycle length

value: unknown

tag: replicate

value: no

tag: batch

value: 1 (TCACTTCGTATGCCGTCTTCTGCTTG)


title: ZWU19SerumB59A21

value: B10 (Day 29, 4 Hours After Lunch)

value: 21 (TTGACTCGTATGCCGTCTTCTGCTTG)


title: ZWU19PlasmaB57A24

source_name: Plasma

value: B11 (Day 43, Morning)

value: pre (Preprandial, Before Lunch)

value: B

value: 24 (TGCCATCGTATGCCGTCTTCTGCTTG)


title: ZWU19SerumB61A5

value: total cell-free biofluid RNA

value: 5 (TCCTATCGTATGCCGTCTTCTGCTTG)


title: ZWU19SerumB62A15

value: Healthy Subject

value: B4 (Day 1, 4 Hours After Lunch)

value: 15 (TGATGTCGTATGCCGTCTTCTGCTTG)


title: ZWU19PlasmaB55A5

value: Entire cardiovascular system

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

value: B12 (Day 43, 1 Hour After Lunch)

value: postE (Postprandial Early, 1 Hour After Lunch)


title: ZWU19PlasmaB54A12

value: B7 (Day 15, 4 Hours After Lunch)

value: postL (Postprandial Late, 4 Hours After Lunch)

value: F

value: no

value: 12 (TAATATCGTATGCCGTCTTCTGCTTG)


title: ZWU19SerumB59A11

value: B3 (Day 1, 1 Hour After Lunch)

value: 11 (TAACGTCGTATGCCGTCTTCTGCTTG)


title: WT Female 1265 Lung

type: RNA

city: Aberdeen Proving Ground

first: Heidi

last: Hoard-Fruchey

state: MD

address: 2900 Ricketts Point Rd

institute: USAMRICD

hyb_protocol: Labelled RNA was hybridized to Affymetrix GeneChip HT MG-430 PM oligonucleotide array plates within the GeneTitan system using standard manufacturer's protocols.

scan_protocol: An Affymetrix GeneTitan instrument was used as per manufacturer's instructions to stain, wash, and scan the array plates

data_processing: .CHP files were generated using Expression Console (Affymetrix, Inc.) with robust multiarray averaging (RMA); Raw data (CEL files) were imported into Partek Genomic suite v6.6 (Partek Incorporated, St. Louis, MO) and normalized using robust multiarray averaging (RMA)

label: Biotin

organism: Mus musculus

source_name: Lung, WT Female

label_protocol: 500 ng of total RNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer.  Following second-strand synthesis, in vitro transcription was performed with biotinylated nucleotides to generate cRNA.

growth_protocol: Mice were maintained on standard laboratory chow and water ad libitum with a 12-hour light-dark cycle. Ambient temperature was kept at 23 +/- 3 deg C and humidity was maintained at 50 +/- 20%.

extract_protocol: Frozen tissue was crypulverized under liquid nitrogen and homogenized in RLT buffer with 10 ul/mL  beta-mercaptoethanol. RNA was isolated using the Qiagen Rneasy kit according to manufacturer's instructions.

treatment_protocol: Mice were not treated for this experiment.

tag: tissue

value: Lung

tag: gender

value: Female

tag: genotype

value: WT

tag: strain

value: C57BL/6 background


title: WT Male 1953 Lung

source_name: Lung, WT Male

value: Male


title: ZWU19PlasmaB57A10

value: Healthy Subject

value: total cell-free biofluid RNA

value: B8 (Day 29, Morning)

value: pre (Preprandial, Before Lunch)

tag: 3' adapter

value: 10 (TTAAGTCGTATGCCGTCTTCTGCTTG)

tag: read count

tag: read depth


title: WT Female 1265 Kidney

source_name: Kidney, WT Female

value: Kidney


title: WT Female 1265 Brain

source_name: Brain, WT Female

value: Brain


title: WT Female 1264 Heart

source_name: Heart, WT Female

value: Heart


title: ZWU19SerumB62A19

tag: condition

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

value: B6 (Day 15, 1 Hour After Lunch)

value: postE (Postprandial Early, 1 Hour After Lunch)

value: L

value: unknown

value: no

value: 19 (TTATTTCGTATGCCGTCTTCTGCTTG)


title: WT Male 901 Brain

source_name: Brain, WT Male

value: Male

value: WT

value: C57BL/6 background


title: WT Female 1264 Liver

source_name: Liver, WT Female

value: Liver

value: Female


title: WT Female 1264 Lung

value: Lung


title: WT Male 1960 Lung


title: WT Female 1265 Liver


title: WT Female 1264 Kidney

value: Kidney


title: WT Male 1262 Lung


title: RNA-seq M4

city: Bryan

first: Irtisha

last: Singh

state: TX

address: 8447 Riverside Pkwy Medical Research and Education Building II

institute: Texas A&M Health Science Center

description: No processed data submitted to GEO. RNA-seq experiments were used for verification of IpA events focusing in the introns of the genes.

data_processing:
Low quality 3'-seq reads were trimmed by FASTQ Quality Trimmer: fastq_quality_filter Q33 -I input.fastq
Adaptors were trimmied by FASTX Clipper from FASTX-Toolkit (fastx_clipper).
Stretch of A's at the 3'end of reads were also trimmed. Reads with minimum length 21 were used for alignment.
3'-seq Reads were aligned using BWA aligner: bwa aln -t 24 -l 100000 -n 0.04 -q 0
RNA-seq Reads were aligned using STAR aligner
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited tpm values

source_name: Blood

extract_protocol:
Total RNA is isolated using Tri-reagent (Ambion) and DNase-treated (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Blood

tag: cell type

value: MemoryB cells CD19+ CD27+


title: RNA-seq M5

source_name: Tonsil

value: Tonsil


title: WT Female 1265 Heart

value: Heart


title: WT Female 1264 Brain

value: Brain


title: TOP-IBK-80_V04

city: Innsbruck

first: Johannes

last: Leierer

address: Anichstr. 35

department: Internal Medicine IV - Nephrology

country: Austria

institute: Medical University Innsbruck

hyb_protocol: For each sample 1.65 ug cRNA was fragmented and hybridized to an Agilent Human Whole Genome 44K oligoarray for 17 hours at 65oC.

scan_protocol: Arrays were washed and scanned at 5 um using an Axon Gene Pix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA), and signal intensity data was extracted using Agilent Feature Extraction software (v10.5.1).

data_processing: Data preprocessing consisted of (i) excluding low abundance features (intensity values < 1.5 above background signals), (ii) quantil-quantil data normalization, and (iii) summarization of identical sequence spots.

source_name: Kidney Biopsy

label_protocol: From each biopsy 200 ng of total RNA was used to generate Cyanine 3 (Cy3) labelled cRNA for hybridisation to Agilent oligonucleotide microarrays according to the Agilent One-Color Microarray protocol (Agilent Technologies, Santa Clara, CA, USA). Briefly, first and second strands of cDNA were generated containing a T7 RNA polymerase promoter using the Agilent Quick Amp Kit. A T7 RNA polymerase synthesized cRNA and incorporated Cy3-labelled CTP. Labelled cRNA was purified on Qiagen RNeasy columns and the final cRNA concentration and labeling efficiency were determined using a Nanodrop 1000 (Thermo Fisher Scientific, Wilmington, DE, USA).

extract_protocol: Total RNA was isolated using miRNeasy (Quiagen) following the manufacturers protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer, and only samples with a A260/280 ratio of >1.6 were used.

treatment_protocol: Renal wedge biopsies were stored in RNALater (Quiagen) immediately after removal

value: f

tag: age

tag: last donor creatinine

value: Kidney Biopsy


title: WT Male 1262 Liver

source_name: Liver, WT Male


title: TOP-IBK-75_I53


title: TOP-IBK-83_T03


title: RNA-seq M3


title: TOP-IBK-74_I18


title: WT Male 1262 Kidney

source_name: Kidney, WT Male


title: TOP-IBK-76_I57


title: RNA-seq M6


title: TOP-IBK-73_I10

value: m


title: RNA-seq NB5

value: NaiveB cells CD19+ CD27-


title: RNA-seq NB6


title: RNA-seq NB4


title: RNA-seq M2


title: RNA-seq NB2


title: RNA-seq NB3


title: WT Male 1262 Brain


title: RNA-seq GC3

value: Germinal center B cells CD19+ CD38+


title: RNA-seq CD5B4

value: B cells CD5+ CD19+


title: RNA-seq CD5B3


title: Es-1 KO Male 1259 Lung

source_name: Lung, Es-1 KO Male

value: Male

value: Es-1 KO


title: RNA-seq CD5B2


title: RNA-seq GC1


title: TOP-IBK-58_T25


title: RNA-seq GC2


title: RNA-seq GC4


title: TOP-IBK-55_T20


title: TOP-IBK-57_T23


title: RNA-seq NB1


title: Es-1 KO Male 1259 Liver

source_name: Liver, Es-1 KO Male

value: Liver

value: C57BL/6 background


title: WT Male 1262 Heart

source_name: Heart, WT Male

value: WT


title: TOP-IBK-52_T15


title: Es-1 KO Male 1259 Brain

source_name: Brain, Es-1 KO Male


title: TOP-IBK-56_T21


title: Es-1 KO Female 994 Lung

source_name: Lung, Es-1 KO Female

value: Lung

value: Female


title: Es-1 KO Male 1259 Heart

source_name: Heart, Es-1 KO Male


title: 3'-seq MM14

data_processing:
Library strategy: 3'-seq
Low quality 3'-seq reads were trimmed by FASTQ Quality Trimmer: fastq_quality_filter Q33 -I input.fastq
Adaptors were trimmied by FASTX Clipper from FASTX-Toolkit (fastx_clipper).
Stretch of A's at the 3'end of reads were also trimmed. Reads with minimum length 21 were used for alignment.
3'-seq Reads were aligned using BWA aligner: bwa aln -t 24 -l 100000 -n 0.04 -q 0
RNA-seq Reads were aligned using STAR aligner
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited tpm values

source_name: Bone marrow

extract_protocol:
Total RNA is isolated using Tri-reagent (Ambion) and DNase-treated (Ambion).
An oligo(dT) primer containing a VN-anker, a uridine, the sequence of the sequencing adapter and biotin (/5BiosG/CAGACGTGTGCTCTTCCGATCTTTTTTTTrUTTTTTTTTVN) is attached to streptavidin-coated magnetic beads (M280, Invitrogen). Total RNA is incubated for 5 min at 65°C, followed by incubation with the coated magnetic beads for 10 min at 45°C. First strand synthesis is carried out using Superscript III reverse transcriptase (Invitrogen) at 50°C. The enzyme is inactivated by incubation at 70°C for 15 min. Second strand synthesis is carried out using Second stand synthesis buffer (Invitrogen), dNTPs, DNA polymerase I (NEB), E. coli ligase (NEB) and RNase H (Invitrogen). To exchange the buffers and to remove enzymes from the previous step, we treat the samples with Pronase (Roche). We introduce a nick at the position of the uridine with RNAse HII (NEB). Then, nick translation is carried out with DNA polymerase I (NEB) and dNTPs for 8 min at 8°C. The reaction is stopped by the addition of EDTA. At the new position of the nick we create a blunt end using T7 exonuclease, mung bean nuclease (NEB) and Klenow enzyme (NEB). Previously annealed Illumina truseq sequencing adapters (Ad1: 5'- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT; Ad2: 5'- AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTAT) are then blunt- end ligated. The magnetic beads are suspended in 39 ul H2O. 5 ul of beads are used in a PCR reaction. 10-13 cycles of PCR are carried out with Phusion polymerase (NEB), a forward primer (5'-AATGATACGGCGACCACCGAGATC) and one of the Illumina truseq barcode reverse primers. For preparation of the library 6 PCR reactions are performed, run on 8% TBE gels (Invitrogen) and the smear between 160 bp and 220 bp is cut out, gel-extracted, ethanol-precipitated, analyzed by Bioanalyzer (Agilent) and sequenced on Illumina Hi-seq machines.

value: Bone marrow

value: Myeloma cells CD138+


title: TOP-IBK-51_T13


title: TOP-IBK-54_T18


title: Es-1 KO Male 1259 Kidney

source_name: Kidney, Es-1 KO Male

value: Kidney


title: 3'-seq MM15


title: 3'-seq MM13


title: 3'-seq MM12


title: 3'-seq MM11


title: Es-1 KO Female 994 Liver

source_name: Liver, Es-1 KO Female


title: 3'-seq MM9


title: TOP-IBK-49_T11


title: TOP-IBK-50_T12


title: 3'-seq MM7


title: 3'-seq MM10


title: Es-1 KO Female 994 Kidney

source_name: Kidney, Es-1 KO Female


title: Es-1 KO Female 994 Brain

source_name: Brain, Es-1 KO Female

value: Brain


title: 3'-seq MM5


title: 3'-seq MM4


title: 3'-seq MM6


title: TOP-IBK-47_T08


title: 3'-seq MM3


title: 3'-seq T2

value: Blood

value: T cells CD3+


title: 3'-seq MM1


title: 3'-seq T3


title: TOP-IBK-45_T04

value: m

value: Kidney Biopsy


title: TOP-IBK-43_V03


title: Es-1 KO Female 985 Kidney


title: TOP-IBK-44_V11

value: f


title: Es-1 KO Female 982 Kidney


title: TOP-IBK-46_T05


title: Es-1 KO Female 982 Liver


title: Es-1 KO Female 985 Liver


title: TOP-IBK-48_T09


title: 3'-seq PC2

value: Plasma cells CD138+


title: 3'-seq PC1


title: 3'-seq GC2

value: Tonsil

value: Germinal center B cells CD19+ CD38+


title: Es-1 KO Female 985 Brain

value: Es-1 KO


title: TOP-IBK-42_V02


title: 3'-seq M2

value: MemoryB cells CD19+ CD27+


title: 3'-seq MM2


title: TOP-IBK-41_V01


title: Es-1 KO Male 964 Liver

value: Liver

value: Male

value: C57BL/6 background


title: 3'-seq GC1


title: 3'-seq NB4

value: NaiveB cells CD19+ CD27-


title: Es-1 KO Male 964 Kidney


title: 3'-seq CD5+B6

value: B cells CD5+ CD19+


title: TOP-IBK-29_I59


title: Es-1 KO Female 982 Brain

value: Female


title: 3'-seq CD5+B5


title: Es-1 KO Male 964 Brain

value: Brain


title: TOP-IBK-28_I58


title: 3'-seq CD5+B4


title: 3'-seq CD5+B3


title: 3'-seq M1


title: TOP-IBK-27_I55


title: 3'-seq NB3


title: ZH_RiboTag_5c5_vs_7b4_CreER_noTAM_input_2

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
For example: the UMI GTACTGGT will appear in the following format: @NB501465:106:HFFKNBGX2:1:11101:5035:1075:AGGCTAAGTACTGGT:A6/A/E//EE////E:0
alignment: hisat 0.1.5  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8) located in fastq header.
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm9 -d <List of tag dir> -count exons -condenseGenes -strand + -raw
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: brain

extract_protocol:
microglia isolation: Mice were anesthetized with Pental (1:2 in PBS) and were perfused with PBS. Brains were dissected, crudely chopped and incubated for 20 min at 37°C in a 1 ml HBSS solution containing 2% BSA, 1 mg/ml Collagenase D (Sigma) and 50µg/ml DNase1 (Sigma). In the middle of incubation homogenates were pipetted for further dissociation. Next, the homogenates were filtered through a 150μm mesh, washed with cold FACS buffer (2% FCS, 1mM EDTA in PBS-/-) and centrifuged at 2200 RPM, at 4°C, for 5 min. For the enrichment of microglia, the cell pellet was re-suspended with 3ml of 40% percoll solution and centrifuged at 2200 RPM, no acceleration and breaks, at RT for 15 min. Next, the cell pellet was resuspended, passed through 80µm mesh, washed with 5ml FACS buffer and centrifuged at 1400 RPM at 4°C for 5 min, followed by antibody (Ab) labeling and flow cytometry analysis. For the protocol excluding the digest, brains were chopped and then filtered through a 150μm mesh. The subsequent steps were as above, but without the enzymatic digest.
immunoprecipitation: Samples were extracted from mice, flash-frozen in liquid nitrogen and stored at −80 °C until use. Samples were homogenized on ice in ice-cold homogenization buffer (50 mM Tris, pH 7.4, 100 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 1:100 protease inhibitor (Sigma), 200 units/ml RNasin (Promega) and 0.1 mg/ml cycloheximide (Sigma) in RNase free DDW) 10% w/v with a Dounce homogenizer (Sigma) until the suspension was homogeneous. To remove cell debris, 1 ml of the homogenate was transferred to an Eppendorf tube and was centrifuged at 10,000g and 4°C for 10 min. Supernatants were transferred to a fresh Eppendorf tube on ice, then 10μl was removed for 'input' analysis and 5μl (=125µg) of anti-HA antibody (H9658, Sigma) or 5μl (=1µg) of mouse monoclonal IgG1 antibody (Sigma, Cat# M5284) was added to the supernatant, followed by 4 h of incubation with slow rotation in a cold room at 4 °C. (Subsequent further calibration of the amounts of the antibodies showed that 5µg antibody of anti-HA antibody and mouse monoclonal IgG1 antibody (Merck, Cat# PP100) yielded similar results, including transcripts enriched in the IgG IP samples seen in cluster IV of Fig. 2B (data not shown)). Meanwhile, Dynabeads Protein G (Thermo Fisher Scientific), 100 μl per sample, were equilibrated to homogenization buffer by washing three times. At the end of 4 h of incubation with antibody, beads were added to each sample, followed by incubation overnight in cold room at 4 °C. After not more than 12 h, samples were washed three times with high-salt buffer (50 mM Tris, 300 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 1:200 protease inhibitor, 100 units/ml RNasin and 0.1 mg/ml cycloheximide in RNase free DDW), 5 min per wash in a cold room on a rotator. At the end of the washes, beads were magnetized and excess buffer was removed, 150µl Lysis Buffer was added to the beads and RNA was extracted with Dynabeads mRNA Direct purification kit (Thermo Fisher). RNA was eluted in 6μl H2O and taken for RNA sequencing. For Sort-IP samples (RiboTag IP after sorting), ~50-100*103 cells were sorted into cold PBS, centrifuged 400g for 5 min at 4°C. Supernatant was removed and the pellet was re-suspended in 1ml of lysis buffer, the rest of IP was continued as above.
5,000 microglia cells were sorted into 50μl of Lysis Buffer (Life Technologies) and stored at -80°C. mRNA was captured with Dynabeads oligo(dT) (Life Technologies) according to manufacturer’s guidelines. for library construction we used a derivation of MARS-seq as described (Jaitin et al., 2014)

treatment_protocol: Tamoxifen treatment: 5mg of tamoxifen (diluted in corn oil) were administered to mice by gavage 4 times every other day at the age of 4-6 weeks.   LPS treatment: LPS was injected intraperitonealy 2.5mg/kg, mice were sacrificed 3h post injection

value: microglia

value: CX3CR1CreER/WT RLP22HA/HA

value: brain

tag: isolation

value: immunoprecipitation

tag: selection marker

value: total extract

tag: tamoxifen treatment

value: Non treated


title: ZH_RiboTag_5c5_vs_7b4_CreER_wTAM_input_2

value: Tamoxifen treated


title: ZH_RiboTag_5c5_vs_7b4_CreER_wTAM_input_3


title: ZH_RiboTag_5c5_vs_7b4_CreER_noTAM_input_1


title: TOP-IBK-26_I54

value: m

value: Kidney Biopsy


title: Es-1 KO Male 962 Kidney

value: Kidney

value: Es-1 KO


title: TOP-IBK-24_I47


title: ZH_RiboTag_5c5_vs_7b4_Cre_input_2

value: CX3CR1Cre/WT RLP22HA/HA


title: ZH_RiboTag_5c5_vs_7b4_Cre_input_1


title: ZH_RiboTag_5c5_vs_7b4_CreER_noTAM_IgG_1

value: Isotype IgG


title: Es-1 KO Male 962 Liver

value: Liver

value: Male

value: C57BL/6 background


title: ZH_RiboTag_5c5_vs_7b4_CreER_noTAM_IgG_2


title: ZH_RiboTag_5c5_vs_7b4_CreER_wTAM_IgG_3


title: ZH_RiboTag_5c5_vs_7b4_Cre_input_3


title: TOP-IBK-25_I48


title: ZH_RiboTag_5c5_vs_7b4_CreER_wTAM_IgG_2


title: Es-1 KO Male 952 Liver


title: TOP-IBK-23_I46

value: f


title: Es-1 KO Male 962 Brain

value: Brain


title: TOP-IBK-22_I42


title: ZH_RiboTag_5c5_vs_7b4_CreER_wTAM_IgG_1

value: microglia

value: CX3CR1CreER/WT RLP22HA/HA


title: Es-1 KO Male 952 Lung

value: Lung


title: Es-1 KO Male 952 Kidney


title: TOP-IBK-20_I39


title: Es-1 KO Male 952 Heart

value: Heart


title: TOP-IBK-21_I40


title: ZH_RiboTag_5c5_vs_7b4_Cre_IgG_3

value: brain

value: immunoprecipitation

value: Non treated


title: ZH_RiboTag_5c5_vs_7b4_CreER_wTAM_input_1

value: total extract

value: Tamoxifen treated


title: Es-1 KO Female 982 Heart

source_name: Heart, Es-1 KO Female

value: Female

value: Es-1 KO


title: ZH_RiboTag_5c5_vs_7b4_Cre_IgG_2

value: CX3CR1Cre/WT RLP22HA/HA

value: Isotype IgG


title: TOP-IBK-19_I38

value: m

value: Kidney Biopsy


title: ZH_RiboTag_5c5_vs_7b4_Cre_IgG_1


title: ZH_RiboTag_5c5_vs_7b4_CreER_noTAM_IP_2

value: anti HA


title: 3'-seq MM8

value: Bone marrow

value: Myeloma cells CD138+


title: Es-1 KO Male 952 Brain

value: Brain

value: Male

value: C57BL/6 background


title: ZH_RiboTag_5c5_vs_7b4_CreER_wTAM_IP_2

value: microglia

value: CX3CR1CreER/WT RLP22HA/HA

value: brain


title: ZH_RiboTag_5c5_vs_7b4_CreER_noTAM_IP_1

value: immunoprecipitation

value: Non treated


title: ZH_RiboTag_5c5_vs_7b4_CreER_wTAM_IP_3

value: Tamoxifen treated


title: ZH_RiboTag_5c5_vs_7b4_Cre_IP_3


title: ZH_RiboTag_5c5_vs_7b4_CreER_wTAM_IP_1


title: TOP-IBK-17_I36

value: f


title: ZH_RiboTag_5c5_vs_7b4_Cre_IP_2

value: CX3CR1Cre/WT RLP22HA/HA


title: TOP-IBK-15_I31


title: ZH_Sorting_Methods_Sort_NO-Coll_4

value: cell sorting

value: GR1 negative, CD45 intermediate, CD11b positive


title: WT Female 936 Brain

source_name: Brain, WT Female

value: Female

value: WT


title: TOP-IBK-18_I37

source_name: Kidney Biopsy

value: m

value: Kidney Biopsy


title: WT Male 903 Liver

source_name: Liver, WT Male

value: Liver


title: TOP-IBK-14_I30


title: TOP-IBK-13_I29


title: TOP-IBK-16_I32


title: WT Male 903 Lung

source_name: Lung, WT Male

value: Lung

value: Male


title: WT Male 903 Kidney

source_name: Kidney, WT Male

value: Kidney

value: C57BL/6 background


title: WT Female 936 Liver

source_name: Liver, WT Female


title: WT Female 936 Kidney

source_name: Kidney, WT Female


title: ZH_Sorting_Methods_Sort_NO-Coll_2

value: microglia

value: CX3CR1CreER/WT RLP22HA/HA

value: brain


title: TOP-IBK-12_I27


title: ZH_Sorting_Methods_Sort_NO-Coll_1

value: Tamoxifen treated


title: ZH_Sorting_Methods_Sort_Coll_2


title: ZH_Sorting_Methods_Sort_Coll_3


title: ZH_Sorting_Methods_Sort_Coll_4


title: ZH_Sorting_Methods_Sort_Coll_1


title: ZH_RiboTag_5c5_vs_7b4_Cre_IP_1

value: immunoprecipitation

value: anti HA

value: Non treated


title: WT Male 903 Heart

source_name: Heart, WT Male

value: Heart


title: ZH_Sorting_Methods_IP_IgG_4

value: Isotype IgG


title: WT Male 903 Brain

source_name: Brain, WT Male

value: Brain

value: WT


title: TOP-IBK-11_I26

value: m

value: Kidney Biopsy


title: ZH_Sorting_Methods_IP_IgG_3


title: TOP-IBK-10_I23


title: WT Male 902 Kidney


title: ZH_Sorting_Methods_IP_IgG_1


title: WT Male 902 Brain


title: ZH_Sorting_Methods_IP_HA_2


title: ZH_Sorting_Methods_IP_HA_3


title: ZH_Sorting_Methods_IP_HA_1


title: ZH_IPvsSort_LPS_LPS_sortIP_Mg5_rep2

value: cell sorting followed by IP

value: GR1 negative, CD45 intermediate, CD11b positive, IP with anti HA

tag: treatment

value: LPS 2.5mg/kg


title: ZH_IPvsSort_LPS_LPS_sortIP_Mg7_rep4

tag: tissue


title: ZH_IPvsSort_LPS_LPS_sortIP_Mg6_rep3


title: ZH_IPvsSort_LPS_LPS_sortIP_Mg4_rep1


title: ZH_Sorting_Methods_IP_IgG_2


title: TOP-IBK-05_I07

tag: gender


title: WT Male 901 Liver

value: Liver

value: Male

tag: genotype

value: C57BL/6 background


title: ZH_IPvsSort_LPS_PBS_sortIP_Mg3_rep3

value: microglia

tag: strain

value: CX3CR1CreER/WT RLP22HA/HA

value: brain

value: PBS


title: TOP-IBK-09_I21


title: TOP-IBK-07_I17


title: WT Female 876 Lung

source_name: Lung, WT Female

value: Lung

value: Female


title: TOP-IBK-04_I06


title: WT Male 901 Kidney

value: Kidney


title: ZH_IPvsSort_LPS_PBS_sortIP_Mg2_rep2

value: Tamoxifen treated


title: TOP-IBK-02_I04


title: TOP-IBK-08_I20

value: f


title: ZH_IPvsSort_LPS_LPS_sort_Mg7_rep4

value: cell sorting

value: GR1 negative, CD45 intermediate, CD11b positive


title: ZH_Sorting_Methods_Sort_NO-Coll_3


title: ZH_IPvsSort_LPS_PBS_sortIP_Mg1_rep1

value: cell sorting followed by IP


title: WT Female 876 Liver

value: WT


title: ZH_IPvsSort_LPS_LPS_sort_Mg5_rep2

value: LPS 2.5mg/kg


title: ZH_IPvsSort_LPS_LPS_sort_Mg4_rep1


title: WT Female 876 Kidney


title: ZH_IPvsSort_LPS_LPS_sort_Mg6_rep3


title: TOP-IBK-01_I01

value: m

value: Kidney Biopsy


title: TOP-IBK-03_I05


title: lncRNA RNASeq

city: Hefei

first: Qiang

last: Liu

state: Anhui

address: 443 Huangshan Road

country: China

institute: University of Science and Technology of China

description: nucleoli RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated and analyzed using Cufflink.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt files include RPKM values for each Sample

source_name: N2a cells

growth_protocol: Standard protocol for N2a cell culture

extract_protocol:
Total RNA from nucleoli was extracted by Trizol, ribosomal RNA was removed and RNA-seq libraries were prepared using 1 ug of RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: neuroblastoma cells


title: WT Female 876 Brain

value: Brain

value: C57BL/6 background


title: WT Male 901 Heart

value: Heart

value: Male


title: ZH_IPvsSort_LPS_PBS_sort_Mg3_rep3

value: microglia

value: CX3CR1CreER/WT RLP22HA/HA

value: brain

value: PBS


title: ZH_IPvsSort_LPS_PBS_sort_Mg2_rep2

value: Tamoxifen treated


title: ZH_IPvsSort_LPS_PBS_sort_Mg1_rep1

value: cell sorting


title: Es-1 KO Female 781 Lung

source_name: Lung, Es-1 KO Female

value: Lung

value: Female

value: Es-1 KO


title: Es-1 KO Female 781 Liver

source_name: Liver, Es-1 KO Female

value: Liver


title: TOP-IBK-86_T34

value: m


title: TOP-IBK-85_T28

value: Kidney Biopsy


title: ZH_IPvsSort_LPS_LPS_IPctl5_rep2

value: immunoprecipitation

value: Isotype IgG

value: LPS 2.5mg/kg


title: ZH_IPvsSort_LPS_LPS_IPctl6_rep3


title: Es-1 KO Female 781 Heart

value: Heart

value: C57BL/6 background


title: ZH_IPvsSort_LPS_LPS_IPctl4_rep1

value: microglia


title: ZH_IPvsSort_LPS_LPS_IPctl7_rep4

value: CX3CR1CreER/WT RLP22HA/HA


title: PBMCs_Healthy Sibling A.II.5

city: Freiburg im Breisgau

first: Bodo

last: Grimbacher

address: Breisacher Str. 115

country: Germany

institute: Center for Chronic Immunodeficiency (CCI), Medical Center – University of Freiburg

hyb_protocol: Standard Illumina hybridization protocol Part #11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide)

scan_protocol: The Illumina iScan-Scanner was used according to Standard Illumina Scanning Protocol Part #11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide).

data_processing: Raw data was quantile normalized with R and using the Bioconductor package preprocessCore.

label: Biotin, Cy3-Streptavidin

source_name: PBMCs

label_protocol: The Illumina TotalPrep RNA Amplification Kit (life technologies) was used to generate single-stranded cRNA . Label: Biotin, Cy3-Streptavidin

growth_protocol: PBMCs isolated by Ficoll density gradient centrifugation were incubated in IMDM medium supplemented with 10% fetal calf serum and 1% Pen/strep at 37°C for 8 hours.

extract_protocol: Total RNA from PBMCs (isolated by Ficoll density gradient centrifugation) was isolated with the RNeasy Mini Kit using QIAshredder and column DNA digestion (Qiagen)

tag: disease status

value: unaffected

value: female

tag: znf341 nonsense mutation status

value: wt/wt

value: PBMCs


title: ZH_IPvsSort_LPS_PBS_IPctl3_rep3

value: brain

value: Tamoxifen treated

value: PBS


title: TOP-IBK-72_T48

value: f


title: TOP-IBK-79_I68

value: m


title: TOP-IBK-71_T47

value: Kidney Biopsy


title: Es-1 KO Female 781 Kidney

source_name: Kidney, Es-1 KO Female

value: Kidney

value: Female

value: Es-1 KO


title: TOP-IBK-70_T46


title: ZH_IPvsSort_LPS_PBS_IPctl2_rep2

source_name: brain

value: immunoprecipitation

value: Isotype IgG


title: PBMCs_Patient A.II.1

value: affected

value: male

value: mut/mut


title: WT Female 1951 Lung

value: Lung

value: WT

value: C57BL/6 background


title: Es-1 KO Female 1898 Lung


title: TOP-IBK-78_I65


title: Es-1 KO Female 1897 Lung


title: Es-1 KO Male 1871 Lung

source_name: Lung, Es-1 KO Male

value: Male


title: TOP-IBK-66_T41


title: TOP-IBK-67_T42


title: Es-1 KO Female 781 Brain

source_name: Brain, Es-1 KO Female

value: Brain


title: ZH_IPvsSort_LPS_PBS_IPctl1_rep1

value: microglia

value: CX3CR1CreER/WT RLP22HA/HA

value: brain

value: Tamoxifen treated

value: PBS


title: ZH_IPvsSort_LPS_LPS_IP7_rep4

value: anti HA

value: LPS 2.5mg/kg


title: ZH_IPvsSort_LPS_LPS_IP6_rep3

value: immunoprecipitation


title: Es-1 KO Male 1870 Lung

value: Es-1 KO


title: ZH_IPvsSort_LPS_LPS_IP4_rep1


title: TOP-IBK-65_T36

source_name: Kidney Biopsy

value: m

value: Kidney Biopsy


title: TOP-IBK-62_T32


title: Es-1 KO Female 994 Heart

value: Female


title: TOP-IBK-59_T27

value: f


title: Es-1 KO Female 985 Heart

source_name: Heart, Es-1 KO Female

value: Heart


title: TOP-IBK-60_T30


title: Es-1 KO Male 962 Heart

source_name: Heart, Es-1 KO Male

value: C57BL/6 background


title: WT Female 876 Heart

source_name: Heart, WT Female

value: WT


title: ZH_IPvsSort_LPS_PBS_IP3_rep3


title: ZH_IPvsSort_LPS_PBS_IP1_rep1


title: ZH_IPvsSort_LPS_PBS_IP2_rep2


title: ZH_IPvsSort_LPS_LPS_IP5_rep2


title: WT Male 902 Heart

value: Male


title: TOP-IBK-39_I74


title: Es-1 KO Male 964 Heart


title: GABA (18 h)-WT BMDM (#2)

city: Daejeon

first: Jin Kyung

last: Kim

address: Jungku 6

country: South Korea

institute: Chungnam National University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality of the reads was checked using FastQC (v0.11.5) and trimming low-quality bases and adaptor sequences were performed using cutadapt (v1.11) and trim galore (v.0.4.4). High quality reads were aligned to the mouse reference (mm10) by STAR (v.2.5.2b).
Mapping data was imported into StrandNGS v2.9 (Strand Genomics, CA, USA) for gene counting and differential expression analysis based on DESeq algorithm.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized  reads counts by DESeq algorithm for each Sample

source_name: Bone marrow-dereived macrophages

growth_protocol: BMDMs were differentiated for 5–7 days in medium containing macrophage colony-stimulating factor. The culture medium consisted of Dulbecco's modiﬁed Eagle's medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1 mM sodium pyruvate, 50 U/mL penicillin, 50 μg/mL streptomycin, and 5×10 5 M 2-mercaptoethanol.

extract_protocol:
Total RNA was extracted using Trizol following manufacturer's instructions
RNA libraries were prepared for sequencing using NEXTflex® Rapid Directional qRNA-Seq™ Library Prep Kit (Bioo Scientific)

treatment_protocol: BMDMs from wild type mice were incubated with GABA (100 uM) for 6 h or 18 h

value: Bone marrow-dereived macrophages

value: female


title: GABA (6 h)-WT BMDM (#2)


title: TOP-IBK-40_I75


title: TOP-IBK-63_T33


title: WT Female 936 Heart


title: TOP-IBK-61_T31


title: SD-101 PLUS a-PD-1+a-CD4 n-4

city: berkeley

first: Cristiana

last: Guiducci

state: California

address: 2929 seventh street suite 100

department: Discovery

institute: Dynavax

hyb_protocol: Samples were hybridized using the Affymetrix GeneTitan Hybridization, Wash and  Stain Kit for 3’ IVT Array Plates • Heated hybridization cocktails at 95° for 5 minutes,   then 45° for 5 minutes centrifuge briefly to collect contents.   •Transfer 90μl of hybridization cocktail into appropriate well of the hybridization tray.  • Hybridize 16 hours at 45°• Hybridization, wash, stain and scan performed on the  Affymetrix GeneTitan Multi-Channel (MC) Instrument according to   manufacturer’s instructions.

data_processing:
R package affy was used to process the raw microarray data and rma method was used for background correction. Differential expression analysis was performed by using limma package and moderated t-test. Benjamini–Hochberg method was used to adjust the raw p-values for multiple testing.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: CD8+CD44+ T cells

label_protocol: Affymetrix protocol

growth_protocol: The CD8+CD44+ were purified from tumor bearing lung treated by intranasal administration with Saline as CTRL, SD-101 (TLR9 ligand), SD-101 plus a-PD-1, SD-101 plus a-PD-1 plus a-CD4 . Lung were bearing 4T-1 tumor cells

extract_protocol: Quiagen RNA extraction of purified CD8+CD44+ cells

tag: agent

value: Tumor bearing lung

value: CD44+CD8+ effector T cells


title: SD-101 PLUS a-PD-1+a-CD4 n-3

scan_protocol: Affymetrix GeneTitan Multi-Channel (MC) Instrument


title: TOP-IBK-38_I72


title: SD-101 PLUS a-PD-1+a-CD4 n-1


title: SD-101 PLUS a-PD-1+a-CD4 n-2


title: GABA (18 h)-WT BMDM (#1)


title: PBS-WT BMDM (#2)


title: TOP-IBK-36_I70


title: GABA (6 h)-WT BMDM (#1)


title: TOP-IBK-34_I67


title: SD-101 PLUS a-PD-1 n-2


title: TOP-IBK-37_I71


title: TOP-IBK-35_I69


title: PBS-WT BMDM (#1)


title: OA_10

city: La Jolla

first: Padma

last: Natarajan

state: CA

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

description:
normalized_counts.xlsx
raw_counts.xlsx

data_processing:
Raw data QC of the fastq files was performed with FastQC (v0.10.1). Raw data were aligned to the human genome (hg19) using the STAR aligner v(2.5.3a).
Aligned reads were quantified using HTSeq-count using UCSC RefSeq hg19 annotation (Release 57).
Raw counts were transformed into counts per million and normalized with TMM normalization.
Limma package (version 3.36.0) with its voom method,was used to assess differential expression and perform gene set testing.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file: OabyControl_allgenes.xlsx (results from differential gene expression analyses)

source_name: Knee articular cartilage

extract_protocol:
Cartilage was stored at -20ºC in Allprotect Tissue Reagent  immediately after harvest until RNA extraction. For RNA isolation, a minimum of 150 mg of cartilage (dry weight) was pulverized and homogenized in Qiazol Lysis Reagentat a concentration of 25mg tissue sample per 700µl Qiazol. To remove proteins and cellular debris, a initial phenol-chloroform extraction was performed. Briefly, samples were mixed with 0.2 volumes of chloroform, incubated for 5 minutes in ice, and centrifuged a t 14000 rpm for 15 minutes at 4ºC. The aqueous phase was collected, mixed with 1 volume of Qiazol and incubated for 30 minutes in ice. Then, samples were mixed with 1 volume of 100% ethanol, loaded into a mRNeasy Mini kit column and digested on-column with DNAse following manufacturer instructions. RNA was eluted in 15µl of RNase-free water.
mRNA libraries were prepared using the Encore Complete RNA-Seq DR Multiplex System 1-8 and 9-16 (NuGen) with 16 unique indexed adapters.

tag: Sex

value: F

tag: oa grade


title: TOP-IBK-33_I66


title: WT Male 902 Liver

source_name: Liver, WT Male

value: Liver


title: OA_08

description:
normalized_counts.xlsx
raw_counts.xlsx


title: SD-101 PLUS a-PD-1 n-3


title: SD-101 PLUS a-PD-1 n-5


title: SD-101 PLUS a-PD-1 n-1


title: TOP-IBK-31_I63


title: TOP-IBK-32_I64


title: OA_07

description:
normalized_counts.xlsx
raw_counts.xlsx


title: OA_04

description:
normalized_counts.xlsx
raw_counts.xlsx

value: M


title: SD-101 PLUS a-PD-1 n-4


title: OA_09

description:
normalized_counts.xlsx
raw_counts.xlsx


title: OA_05

description:
normalized_counts.xlsx
raw_counts.xlsx


title: DH44 neuron-7#

city: hangzhou

first: Rui

last: Huang

address: Yu-hang-tang road 866

institute: Zhejiang University

data_processing:
Raw reads were removed adapter contaminants (length < 37 bp) and low-quality bases (N > 10%) to get clean reads.
Index of reference genome was built using Drosophila melanogaster genome (r6.14). TopHat was used to align clean reads to the fly transcriptome.
Genome_build: Drosophila melanogaster genome (r6.14)
Supplementary_files_format_and_content: FPKM was used to quantify gene expression for each sample

organism: Drosophila melanogaster

source_name: DH44 producing neuron

growth_protocol: Flies containing containing cells labeled by mCD8GFP driven from DH44 GAL4 lines were cultured in normal food for 5d.

extract_protocol:
The cDNA were sequenced using a modified SMART-seq2 protocol.
The amplified cDNA were sonicated to ~250 bp fragments by the Covaris S2 system and then subjected to end-repair, dA-tail, adaptor ligation, and 12 cycles of PCR amplification using the library preparation kit (NEBNext Ultra II DNA Library Prep Kit, NEB).

treatment_protocol: After brain dissection, GFP labeled single cells were pooled in situ.

value: brain

value: DH44 neuron


title: OA_03

description:
normalized_counts.xlsx
raw_counts.xlsx


title: OA_06

description:
normalized_counts.xlsx
raw_counts.xlsx


title: SD-101 n-5


title: TOP-IBK-30_I61


title: OA_02

description:
normalized_counts.xlsx
raw_counts.xlsx


title: Saline-CTRL n-5

value: Saline-CTRL


title: DH44 neuron-4#


title: SD-101 n-2


title: DH44 neuron-3#


title: SD-101 n-6


title: SD-101 n-4


title: OA_01

description:
normalized_counts.xlsx
raw_counts.xlsx


title: normal_10

description:
normalized_counts.xlsx
raw_counts.xlsx


title: SD-101 n-3


title: SD-101 n-1


title: normal_08

description:
normalized_counts.xlsx
raw_counts.xlsx


title: TOP-IBK-64_T35

value: m

value: Kidney Biopsy


title: normal_09

description:
normalized_counts.xlsx
raw_counts.xlsx


title: normal_07

description:
normalized_counts.xlsx
raw_counts.xlsx


title: normal_05

description:
normalized_counts.xlsx
raw_counts.xlsx


title: Saline-CTRL n-4


title: wt rep1

city: Tel Aviv

first: Eilon

last: Shani

address: Ramat Aviv

institute: TAU

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using TopHat v2.0.6
Reads were attributed to genes using HTseq v0.62  (Anders, Pyl, and Huber 2015). Sample normalization was performed based on sample size. Differential expression was analyzed using DEseq2 (Love, Huber, and Anders 2014).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include Normalized counts for each Sample ...

organism: Arabidopsis thaliana

source_name: wt

growth_protocol: Plants were gorwn in 21 C for 6 weeks.

extract_protocol:
Qiagen RNeasy Plant Mini Kit (QIAGN 74,904)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MOCK- 0.02% siluwet-L-77. DEX- 10uM dexmetazon and 0.02% siluwet-L-77 were sparied. Samples were collected after 5 hours.

tag: background

value: Ler

value: Inflorescence meristem

value: wild-type


title: wt with DEX rep1

source_name: wt with DEX

value: DEX


title: wt rep2


title: wt with DEX rep2


title: normal_06

description:
normalized_counts.xlsx
raw_counts.xlsx


title: Saline-CTRL n-3

tag: cell type


title: Saline-CTRL n-1


title: Saline-CTRL n-2


title: 35s::STM-GR with MOCK rep3

source_name: 35s::STM-GR with MOCK

value: MOCK


title: normal_04

description:
normalized_counts.xlsx
raw_counts.xlsx

tag: age


title: OMC-2_Prex2a_shRNA2_2

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

hyb_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.5, May 2010).

scan_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.5, May 2010, Agilent C Scanner Settings).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. The data set from the scanned microarrays were analyzed with GeneSpring software 13.1 (Agilent). The parameter settings for importing the data into GeneSpring were as follows: Threshold, 1.0; Logbase, 2; Technology, Agilent.SingleColor.72363; Normalization, Shift to 75 percentile; Baseline Transformation, None.
Signal intensity after normalization by GeneSpring GX11.5 software (Agilent). [Threshold: 1.0, Logbase: 2, Normalization: Shift to 75 percentile, Baseline Transformation: None]

source_name: OMC-2, Prex2a shRNA type 2, sample 2

growth_protocol: JHUEM-14 were cultured in DMEM/ Ham F12 (Sigma) + 20% FBS (EQUITECH-BIO) + MEM NEAA (gibco). OMC-2 were cultured in Ham’s F-12 (Sigma) + 20% FBS.

extract_protocol: Total RNA was extracted using RNeasy Mini(QIAGEN).

treatment_protocol: We performed retroviral gene transduction for cells expressing short hairpin (sh) RNAs  and  lentiviral induction of  Prex2a.

tag: cell line

value: endometrium

tag: diagnosis

value: endometrioid adenocarcinoma


title: 35s::STM-GR with MOCK rep2


title: normal_02

description:
normalized_counts.xlsx
raw_counts.xlsx


title: normal_03

description:
normalized_counts.xlsx
raw_counts.xlsx


title: OMC-2_Prex2a_shRNA1_2

source_name: OMC-2, Prex2a shRNA type 1, sample 2

label_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.5, May 2010).


title: 35s::STM-GR with DEX rep2

source_name: 35s::STM-GR with DEX


title: 35s::STM-GR with DEX rep3


title: 35s::STM-GR with MOCK rep1


title: OMC-2_Prex2a_shRNA1_1

source_name: OMC-2, Prex2a shRNA type 1, sample 1


title: 35s::STM-GR with DEX rep1


title: normal_01

description:
normalized_counts.xlsx
raw_counts.xlsx


title: OMC-2_Prex2a_shRNA2_1

source_name: OMC-2, Prex2a shRNA type 2, sample 1


title: OMC-2_NC_shRNA_2

source_name: OMC-2, Negative Control shRNA, sample 2


title: OMC-2_Prex2a_induction_2

source_name: OMC-2, Prex2a induction, sample 2


title: OMC-2_Norm_2

source_name: OMC-2, unmodified, sample 2


title: ORR2

city: BeiJing

first: Xiong

last: Yao

address: No. 17, Tsinghua East Road, Haidian District

institute: China Agriculture University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts. In this step, clean data (clean reads) were obtained by removing  reads containing adapter, reads containing ploy-N and low quality reads from  raw data. At the same time, Q20, Q30 and GC content sequence of the clean  data were calculated. All the downstream analyses were based on the clean data  with high quality.
Reference genome and gene model annotation files were downloaded from  genome website directly (NC_014656.1). Both building index of reference genome and aligning  clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S.  L. Salzberg, 2012)
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And  then FPKM of each gene was calculated based on the length of the gene and  reads count mapped to this gene.
(For DESeq with biological replicates) Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using  the DESeq R package (1.18.0). DESeq provide statistical routines for  determining differential expression in digital gene expression data using a  model based on the negative binomial distribution. The resulting P-values were  adjusted using the Benjamini and Hochberg’s approach for controlling the false  discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were  assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was  implemented by the GOseq R package, in which gene length bias was corrected.  GO terms with corrected Pvalue less than 0.05 were considered significantly  enriched by differential expressed genes.
Genome_build: NC_014656.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Bifidobacterium longum subsp. longum BBMN68

source_name: B. longum BBMN68

growth_protocol: Bifidobacterium longum BBMN68 was cultured in de Man-Rogosa-Sharpe (MRS) medium supplemented with L-cysteine (0.05% w/v) anaerobically at 37℃ with or without 0.075% (w/v) oxgall for 24h

extract_protocol:
Total RNA isolation was carried out using TRIzol reagent (Invitrogen, Carlsbad, CA) as the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: medium

value: MRSc with 0.075 percent oxgall

tag: growth phase

value: late-stationary-phase,about 24h


title: BRR3

value: MRSc


title: pAP1>>miR STM/BP ap1-1 rep1

source_name: pAP1>>miR STM/BP ap1-1

tag: treatment

value: pAP1>>miR STM/BP ap1-1


title: pAP1>>miR STM/BP ap1-1 rep2

tag: tissue


title: ap1 rep3


title: ORR1


title: ap1 rep1


title: BRR2


title: ap1 rep2


title: BRR1


title: Orthologs_Replicate_3 DNA

status: Public on May 03 2018

city: Seattle

first: Jason

middle: C

last: Klein

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: Transfection of ortholog library into HepG2 cells

library_source: genomic

data_processing:
Library strategy: STARR-seq
Reads were merged with PEAR v 9.5 using default settings
Tiling expeirment reads were aligned to reference using BWA mem v7.13. Read counts for each construct were counted, and RNA to DNA ratios were calculated for each construct normalized to the read depth per library
Only perfect reads were extracted from the merged sequencing files and counted for each ortholog. Ratio of RNA reads over ratio of DNA reads was caluclated for each barcode, logged, and averaged across all barcodes over all three replicates
Genome_build: hg19

molecule: genomic DNA

source_name: Synthetic sequences (Agilent array)

growth_protocol: DMEM + 10% FBS + 1x Pen/Strep

extract_protocol:
Qiagen AllPrep
RT with SS3 followed by PCR with primers in manuscript

treatment_protocol: Lipofectamine 3000 Transfection


title: Orthologs_Replicate_3 RNA


title: Orthologs_Replicate_1 RNA


title: Orthologs_Replicate_2 RNA


title: Orthologs_Replicate_2 DNA


title: Tiling_Replicate_3 RNA

description: Transfection of tiling library into HepG2 cells


title: Tiling_Replicate_3 DNA


title: OMC-2_Norm_1

source_name: OMC-2, unmodified, sample 1


title: Tiling_Replicate_2 DNA


title: Tiling_Replicate_2 RNA


title: Tiling_Replicate_1 DNA


title: Tiling_Replicate_1 RNA


title: JHUEM14_Prex2a_shRNA2_1

source_name: JHUEM14, Prex2a shRNA type 2, sample 1

value: uterus


title: JHUEM14_Prex2a_shRNA1_1

source_name: JHUEM14, Prex2a shRNA type 1, sample 1


title: Orthologs_Replicate_1 DNA


title: JHUEM14_Prex2a_shRNA2_2

source_name: JHUEM14, Prex2a shRNA type 2, sample 2


title: JHUEM14_NCshRNA_1

source_name: JHUEM14, Negative Control shRNA, sample_1


title: JHUEM14_Prex2a_shRNA1_2

source_name: JHUEM14, Prex2a shRNA type 1, sample 2


title: spz84; Sperm_rep4; dye-swap tech rep2

type: genomic

city: Jouy en Josas Cedex

first: Helene

last: Kiefer

address: Domaine de Vilvert, Bat 230

country: France

institute: INRA

hyb_protocol: Microarrays were hybridized at 42°C for 17-18h in a NimbleGen hybridization system (transcriptomic platform POPS, IPS2, INRA, France) and washed using a wash buffer kit (Roche-NimbleGen) according to the manufacturer’s instructions. The hybridization lay-out incorporated technical dye-swaps for every sample.

scan_protocol: Fluorescent signals were scanned at 532 nm and 635 nm using an Innoscan 900 scanner (Innopsys) at a 3 μm resolution. Raw data files containing the Cy3 and Cy5 signal quantifications for each probe were generated using Nimblescan 2.6 software (Roche-NimbleGen).

data_processing:
Probes with signal enrichment in the MeDIP sample (“enriched probes”) were identified using the ChIPmix R package [Martin-Magniette ML, Mary-Huard T, Berard C, Robin S: ChIPmix: mixture model of regressions for two-color ChIP-chip analysis. Bioinformatics 2008, 24:i181-186] as follows. Hybridization data were normalized as described previously using an ANOVA model [Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, Buisine N, Gagnot S, Martienssen RA, Coupland G, Colot V: Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet 2007, 3:e86]. Data were averaged on the dye-swap to remove dye biases. For each probe, the local CpG percentage was then computed within a 400 bp genomic window centred on the probe position. Finally, ChIPmix was run on the normalized data, with three classes of probes analysed independently: low CpG class (CpGs<1%), intermediate CpG class (1%≤CpGs<4%) and high CpG class (CpGs≥4%).
Processed_data.txt values: 1: enriched probes (probes with signal enrichment in the MeDIP sample, as defined by ChIPmix); 0: not enriched probes

organism: Bos taurus

source_name: Input DNA from sperm sample #spz84

label_protocol: After purification with the QIAquick PCR purification kit (Qiagen), 1 μg amplified samples were labelled with Cy3 and Cy5 in two separate reactions using a dual-colour DNA labelling kit (Roche-NimbleGen). For each sample, 15 μg labelled MeDIP and 15 μg labelled input were then assembled in both combinations (Cy3-input with Cy5-MeDIP or Cy5-input with Cy3-MeDIP), dried and resuspended in hybridization reagents (hybridization kit, Roche-NimbleGen)

extract_protocol: DNA extraction from the liver samples, MeDIP and quality controls by PCR were performed as described in [Kiefer H: Genome-Wide Analysis of Methylation in Bovine Clones by Methylated DNA Immunoprecipitation (MeDIP). Methods Mol Biol 2015, 1222:267-280]. In order to prevent any technical biases, the products of 5 independent MeDIP experiments were pooled for each animal. 100 ng of this material, as well as 100 ng input DNA, were then subjected to moderate genome amplification (10 cycles; GenomePlex complete WGA kit, Sigma).

value: Sperm

source_name: MeDIP DNA from sperm sample #spz84


title: JHUEM14_NCshRNA_2

source_name: JHUEM14, Negative Control shRNA, sample_2


title: Warm WT2

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description:
1 μg
Warm TRPM2-KO-2_ Warm WT-2.anno.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other style.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw count and  RPKM values for each Sample

source_name: Brain

extract_protocol:
Total RNA extracted from embryonic cortex of TRPM2 KO and WT mice under warm stress during E14-16 was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cortex

tag: developmental stage


title: Warm Trpm2KO2

tag: genotype


title: Warm Trpm2KO1

description:
1 μg
Warm TRPM2-KO-1_ Warm WT-1.anno.txt

tag: strain


title: spz55; Sperm_rep2; dye-swap tech rep2

source_name: Input DNA from sperm sample #spz55

source_name: MeDIP DNA from sperm sample #spz55


title: 5055; Liver_rep4; dye-swap tech rep2

source_name: Input DNA from liver sample #5055

value: Liver

source_name: MeDIP DNA from liver sample #5055


title: spz34; Sperm_rep1; dye-swap tech rep2

source_name: Input DNA from sperm sample #spz34

source_name: MeDIP DNA from sperm sample #spz34


title: F029; Fibroblast_rep3; dye-swap tech rep2

source_name: Input DNA from fibroblast sample #F029

value: Fibroblast

source_name: MeDIP DNA from fibroblast sample #F029


title: F5538; Fibroblast_rep2; dye-swap tech rep2

source_name: Input DNA from fibroblast sample #F5538

source_name: MeDIP DNA from fibroblast sample #F5538


title: spz81; Sperm_rep3; dye-swap tech rep2

source_name: Input DNA from sperm sample #spz81

source_name: MeDIP DNA from sperm sample #spz81


title: 5538; Liver_rep2; dye-swap tech rep2

source_name: Input DNA from liver sample #5538

source_name: MeDIP DNA from liver sample #5538


title: F2251; Fibroblast_rep1; dye-swap tech rep2

source_name: Input DNA from fibroblast sample #F2251

source_name: MeDIP DNA from fibroblast sample #F2251


title: Warm WT1

source_name: Brain


title: spz84; Sperm_rep4; dye-swap tech rep1

source_name: MeDIP DNA from sperm sample #spz84

source_name: Input DNA from sperm sample #spz84


title: 029; Liver_rep1; dye-swap tech rep2

source_name: Input DNA from liver sample #029

source_name: MeDIP DNA from liver sample #029


title: Liver-HepKO-vs-WT-female-Cy5

city: Boston

first: Fasih

middle: Mubtasim

last: Ahsan

state: MA

address: 185 Cambridge Street, CPZN 6500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

hyb_protocol: Each labeled sample was hybridized against its gender-matched sample in fluor-reversed pairs of arrays to an Agilent-026655 4x44K v2 (Gene Name version) Mouse Whole Genome Microarray (GPL20889).

scan_protocol: The arrays were scanned using the Agilent DNA Microarray Scanner, and data was extracted using the Agilent Feature Extraction (version 9.5.1.1) software using the standard Agilent protocol except without Lowess normalization.

data_processing: The fluor-reversed pairs were combined into Experiments in Rosetta Resolver 7.1 to produce the male and female signature gene ratios.

source_name: Perfused liver hepatocytes from HepKO Albumin-Cre Pnpt1 fl/fl C57BL/6J mouse, 4.29 weeks.

label_protocol: Labeled cRNA was generated using 200ng of total RNA from each sample and the Agilent Low RNA Input Linear Amplification labeling kit (Agilent).

growth_protocol: Hepatocytes were isolated from perfused livers of two PNPASE (Pnpt1) liver specific knockout C57BL/6J mice (HepKO; 1 male aged 12.9 weeks, 1 female aged 4.29 weeks, two independent experiments) and two age-, litter-, and sex-matched wildtype control mice (WT)

extract_protocol: Mice were euthanized at the weeks stated in the growth protocol; livers perfused for 5 minutes with perfusion buffer and collagenase. Livers were then homogenized between two glass slides, washed in 1x DMEM media three times at 1000rpm for 5 minutes each, cell pellets resuspended in 1x DPBS without magnesium and calcium, and 2x10^6 cells in each sample were used for total RNA isolation using TriZol Reagent (Invitrogen) and the Qiagen RNeasy Mini Kit (Qiagen).

treatment_protocol: HepKO mice were generated using an Albumin-Cre/wt x Pnpt1 neo-fl/neo-fl breeding scheme to generate liver specific knockouts and validated using conventional PCR genotyping.

tag: background strain

value: liver

tag: gender

value: Female

tag: age (weeks)

value: Albumin-Cre/wt Pnpt1 fl/fl

tag: body weight (g)

tag: liver weight (g)

tag: total rna concentration (ug/ul)

source_name: Perfused liver hepatocytes from wildtype C57BL/6J mouse, 4.29 weeks.

value: wildtype Pnpt1 fl/fl


title: spz81; Sperm_rep3; dye-swap tech rep1


title: Liver-HepKO-vs-WT-male-Cy3

source_name: Perfused liver hepatocytes from wildtype C57BL/6J mouse, 12.29 weeks.

value: Male

source_name: Perfused liver hepatocytes from HepKO Albumin-Cre Pnpt1 fl/fl C57BL/6J mouse, 12.9 weeks.


title: Liver-HepKO-vs-WT-female-Cy3


title: spz55; Sperm_rep2; dye-swap tech rep1

source_name: MeDIP DNA from sperm sample #spz55

source_name: Input DNA from sperm sample #spz55


title: spz34; Sperm_rep1; dye-swap tech rep1

source_name: MeDIP DNA from sperm sample #spz34

source_name: Input DNA from sperm sample #spz34


title: 5055; Liver_rep4; dye-swap tech rep1

source_name: MeDIP DNA from liver sample #5055

source_name: Input DNA from liver sample #5055


title: F5538; Fibroblast_rep2; dye-swap tech rep1

source_name: MeDIP DNA from fibroblast sample #F5538

source_name: Input DNA from fibroblast sample #F5538


title: F029; Fibroblast_rep3; dye-swap tech rep1

source_name: MeDIP DNA from fibroblast sample #F029

source_name: Input DNA from fibroblast sample #F029


title: 414; Liver_rep3; dye-swap tech rep2

source_name: Input DNA from liver sample #414

source_name: MeDIP DNA from liver sample #414


title: 414; Liver_rep3; dye-swap tech rep1


title: 029; Liver_rep1; dye-swap tech rep1

source_name: MeDIP DNA from liver sample #029

source_name: Input DNA from liver sample #029


title: T6 FFPE mRNA-seq (100ng)

city: Rehovot

first: Noa

last: Bossel Ben-Moshe

address: Hertzl Street

institute: Weizmann

data_processing:
Fragments were mapped to the human genome (hg19) using TopHat version V2.0.5
Only uniquely mapped fragments to the genome were considered and exonic and intronic signals were calculated using HTSeq
The signals of the same sample from all lanes were summed
The number of fragments obtained for each gene in each sample was normalized to the total number of fragments obtained from this sample
The minimum expression level threshold was set to 5 (log2 scale) to reduce noise (based on data distribution).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized number of reads (log2 scale) for each sample

source_name: breast cancer tumor sample

extract_protocol:
FFPE tumor samples were sectioned to 5 micron slices and deparafinized at 90°C for 5 min. Total RNA was extracted using nucleic acid isolation kit (AllPrep® Qiagen) according to the protocol instructions, with the following modifications: DNAse treatment was at 37° for 20 minutes and the column was incubated for 1 min before each washing step with buffer RPE. Samples were eluted in 30 μL purified water. RNA from FF tumor samples was extracted using Trizol. RNA concentrations were determined by Qubit™ fluorometer (Thermofisher scientific) and the RNA quality was determined by measuring the RNA integrity number (RIN) using Agilent TapeStation.
Total RNA from FFPE and FF samples was processed using two protocols: 1. Truseq RNA Sample preparation kit v2 (illumina) (cat# RS-122-2002) for mRNA-seq libraries. Briefly, polyA fraction (mRNA) was purified from 500ng or 100ng of total RNA following by fragmentation and generation of double stranded cDNA. Then, end repair, A base addition, adapter ligation and PCR amplification steps were performed. 2. Truseq Stranded total RNA with Ribo-Zero Gold. Library Protocol: TruSeq® Stranded Total RNA (Illumina) (Cat # RS-122-2301, RS-122-2302) for ribosomal-depletion libraries. Briefly, After rRNA depletion from 500ng total RNA with rRNA  Ribo-Zero Gold removal mix, cDNA was performed followed by second strand synthesis with dUTP instead of dTTP. Then, A base addition, adapter ligation, UDG treatment and PCR amplification steps were performed

value: breast cancer tumor sample

value: FFPE

tag: protocol

value: mRNA-seq

tag: starting material (ng)

tag: patient

tag: archival time

value: more than 10 years


title: T5 FFPE mRNA-seq (100ng)


title: T6 FFPE mRNA-seq (500ng)


title: T4 FFPE mRNA-seq (500ng)


title: T4 FFPE mRNA-seq (100ng)


title: T3 FFPE RiboZero (500ng)

value: RiboZero

value: 4-5 years


title: 5538; Liver_rep2; dye-swap tech rep1

source_name: MeDIP DNA from liver sample #5538

source_name: Input DNA from liver sample #5538


title: T3 FFPE mRNA-seq (500ng)


title: F2251; Fibroblast_rep1; dye-swap tech rep1

source_name: MeDIP DNA from fibroblast sample #F2251

source_name: Input DNA from fibroblast sample #F2251


title: healthy control N14

city: Shanghai

first: Shi

last: Jianbo

state: Shanghai

address: 639, ZhiZaoJu Road, Shanghai

department: Department of Oral & Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital

institute: Shanghai Jiao Tong University School of Medicine

description: serum miRNA expression of OSCC patients from age, gender, smoking and drinking matched normal control people. The clinical characteristics of OCSS patients contain pathological grade, lymph node metastasis, TNM stage and survival status.

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: Hybridization signals were scanned and analyzed by Genepix 4000B microarray scanner. The scanned images were imported into the GenePix Pro 6.0 software (Axon Instruments) for grid alignment and data extraction. Replicated miRNAs were averaged, and the miRNAs with intensities in all samples were chosen to calculate the median normalization factor. The expressed miRNA data were normalized using the median normalization and chosen for the differentially expressed miRNA screening.

data_processing:
The scanned images were imported into the GenePix Pro 6.0 software (Axon Instruments) for grid alignment and data extraction.Replicated miRNAs were averaged, and the miRNAs with intensities in all samples were chosen to calculate the median normalization factor. The expressed miRNA data were normalized using the median normalization and chosen for the differentially expressed miRNA screening.
[Filtering criteria] We only analyzed the detected human related microRNAs. We excluded the probes of which signal intensity was less than 30.0 in all samples.

source_name: healthy control serum

label_protocol: After RNA isolation from the samples, the miRCURYTM Hy3TM/Hy5TM Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: TRIzolTM LS reagent (Invitrogen Life Technologies) was used according to the manufacturer instructions for isolating total RNA.

tag: disease state

value: healthy control

tag: age

tag: Sex

value: female

tag: somking

value: no

tag: drinking

tag: lymph node metastasis

tag: pathological grade

tag: tnm stage

tag: status after 5 years

value: serum


title: T5 FFPE mRNA-seq (500ng)

tag: tissue


title: HY3,biological rep1

city: anyang

first: Man

last: Wu

state: henan

address: huanghe street

institute: CAAS

description:
Gene expression data from Backcross inbred lines (BILs)
HY3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Affymetrix GeneChip Operating System v1.4 (GCOS; Affymetrix), the relative mean signal, detection calls, signal-log ratios and change calls were independently calculated using four different algorithms for each probe set. Fold changes in expression (e.g., >2-fold), the Microarray Suite (MAS) 5.0 probe set detection p values, and/or p values (e.g., Bonferroni-corrected P-value threshold <0.05) from standard statistical tests (e.g., independent t test, Welch’s t test, Wilcoxon’s rank sum test, ANOVA, etc.) were used to identify genes with significant changes in expression.

label: biotin

organism: Gossypium hirsutum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: The 6 BILs with a designation of NMGA and their two parents were planted in five environments in three locations: Anyang, Henan province in 2006, 2007 and 2008; Wangjing, Anhui province in 2007; and Aksu, Xinjiang Uyghur Autonomous Region in 2007. The three locations represent the major cotton production regions with three different cultivation systems in China-Yellow River valley (Henan province), Yangtze River valley (Anhui province) and Northwest (Xinjiang Uygur Autonomous Region).

extract_protocol: Total RNA was extracted using the Sigma Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO, USA) with an on-column DNaseI digestion according to the manufacturer’s instructions.

treatment_protocol: Tissue samples for total RNA isolation were prepared from 1 g of cotton fiber harvested from ovules of each genotype at 10 DPA.

tag: line

tag: phenotype

value: high-yielding

tag: developmental stage

value: 10 DPA

value: Fibers


title: T3 FF mRNA-seq (100ng)

value: FF

tag: protocol


title: InVitro_24hr_MSTO-211H_afuresertib

first: Akinobu

last: Ota

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

description: Gene expression after 24hr in afuresertib-treated MSTO-211H cells

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2519F-026652) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 039494_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MSTO-211H, 24hr,  afuresertib, 10 μmol/L

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using  NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations.  RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The MPM cell lines were incubated in a RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cells were then treated with the indicated concentration of afuresertib for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell line

value: human MPM cell line, biphasic

tag: gender

value: 62 years

tag: agent

value: afuresertib


title: LY1,biological rep1

description:
Gene expression data from Backcross inbred lines (BILs)
LY1

organism: Gossypium barbadense

value: low-yielding


title: HYP,biological rep1

description: HYP

value: SG747 (parental)


title: InVitro_24hr_MSTO-211H_none

description: Gene expression after 24hr in untreated MSTO-211Hcells

source_name: MSTO-211H, 24hr, no treatment

value: control


title: LY3,biological rep1

description:
Gene expression data from Backcross inbred lines (BILs)
LY3


title: LYP,biological rep1

description: LYP

value: Giza75 (parental)


title: LY2,biological rep1

description:
Gene expression data from Backcross inbred lines (BILs)
LY2


title: InVitro_24hr_ACC-MESO-4_none

description: Gene expression after 24hr in untreated ACC-MESO-4 cells

source_name: ACC-MESO-4, 24hr, no treatment

value: human MPM cell line, epithelioid

value: male

value: 59 years


title: InVitro_24hr_ACC-MESO-4_afuresertib

description: Gene expression after 24hr in afuresertib-treated ACC-MESO-4 cells

source_name: ACC-MESO-4, 24hr, afuresertib, 10 μmol/L


title: HY2,biological rep1

description:
Gene expression data from Backcross inbred lines (BILs)
HY2


title: HY1,biological rep1

description:
Gene expression data from Backcross inbred lines (BILs)
HY1


title: Liver-HepKO-vs-WT-male-Cy5

source_name: Perfused liver hepatocytes from HepKO Albumin-Cre Pnpt1 fl/fl C57BL/6J mouse, 12.29 weeks.

tag: background strain

value: liver

value: Male

tag: age (weeks)

tag: genotype

value: Albumin-Cre/wt Pnpt1 fl/fl

tag: body weight (g)

tag: liver weight (g)

tag: total rna concentration (ug/ul)

source_name: Perfused liver hepatocytes from wildtype C57BL/6J mouse, 12.9 weeks.

value: wildtype Pnpt1 fl/fl


title: T3 FF mRNA-seq (500ng)

value: breast cancer tumor sample

value: mRNA-seq

tag: starting material (ng)

tag: patient

tag: archival time

value: 4-5 years


title: T3 FF RiboZero (500ng)

tag: tissue

value: FF

value: RiboZero


title: T3 FFPE mRNA-seq (100ng)

value: FFPE


title: healthy control N15

tag: disease state

value: healthy control

tag: age

tag: Sex

tag: somking

value: yes

tag: drinking

value: no

tag: lymph node metastasis

tag: pathological grade

tag: tnm stage

tag: status after 5 years

value: serum


title: healthy control N13

value: female


title: healthy control N12


title: healthy control N11


title: T2 FFPE mRNA-seq (100ng)

tag: protocol


title: healthy control N10

value: male


title: T2 FF mRNA-seq (100ng)


title: T2 FF mRNA-seq (500ng)


title: healthy control N9


title: T1 FF RiboZero (500ng)


title: T2 FF RiboZero (500ng)


title: healthy control N8


title: healthy control N7


title: T1 FFPE mRNA-seq (100ng)


title: T1 FFPE RiboZero (500ng)


title: healthy control N5


title: T1 FFPE mRNA-seq (500ng)


title: T1 FF mRNA-seq (100ng)


title: T1 FF mRNA-seq (500ng)


title: RNA-seq_Mt-87-18-UT

city: Kyoto

first: Akira

last: Niwa

address: 53, Shogoin-Kawahara-cho, Sakyo-ku

department: Department of Clinical Application

institute: CiRA, Kyoto University

description: Bulk RNA-Seq data

data_processing:
All sequence reads were extracted in FASTQ format.  mRNA profiles were calculated with a Cufflinks (ver 2.2.1) software and expressed as FPKM (fragments per kilobase of exon model per million mapped fragments)
Data sets which filtered by the criterion requiring FPKM >0 in at least one sample were first performed variance-stabilizing transformation and interquartile range filtering.
Upper-quartile (UQ) normalization followed by RUV normalization regarding each three line of treated and untreated samples as a replicated group (RUVs), modeling k = 1 factors of unwanted variation was performed to remove unwanted variations*(ref.).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw FPKM values for each Sample

molecule: polyA RNA

source_name: Disease iPSC-derived monocytic cell lines

growth_protocol: Monocytic cell lines establishment protocol: Monocytic cell lines were established from ESC/iPSC-derived monocytes

extract_protocol:
Total RNA was extracted using the RNeasy kit, and the quality was tested with a Bioanalyzer.
RNA-seq libraries were prepared using a SureSelect Strand Specific RNA Library Preparation kit (Agilent). Sequencing was performed on an Illumina HiSeq1500 using a HiSeq Rapid SBS kit v2 (Illumina) in a 50-base single-end mode.

treatment_protocol: When mentioned, IFN-γ+TNF-α were added to culture

tag: cell type

value: iPSC-derived monocytic cell line

tag: genotype

value: MT

tag: infg + tnfa treatment

value: No


title: RNA-seq_Mt-87-18-IplusT

description: Bulk RNA-Seq data

value: Yes


title: healthy control N4


title: healthy control N3


title: RNA-seq_Kh-1-WT-UT

description: Bulk RNA-Seq data

source_name: Normal ESC-derived monocytic cell lines

value: ESC-derived monocytic cell line

value: WT


title: RNA-seq_Kh-1-WT-IplusT

description: Bulk RNA-Seq data


title: RNA-seq_Kh-1-KI-UT

description: Bulk RNA-Seq data

source_name: Disease ESC-derived monocytic cell lines

value: MT(Introduced)


title: healthy control N1


title: Differentiated Myogenic Progenitors Control 2B (4 days)

city: Rotterdam

last: Pijnappel

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

description:
genes-fpkm.tsv
transcripts-fpkm.tsv

data_processing:
RNA-seq data were aligned using Hisat2 (version 2.1.0) to hg38 from UCSC. The alignments were converted to BAM format using Samtools (version 1.3.1). Then, StringTie was used according to Pertea et al. 2016 to quantify transcript expression levels according to the reference transcripts. For KEGG analysis, StringTie was used with the -e option to quantify gene expression levels according to the reference transcripts.
Table counts were also produced using the -B option for Ballgown (version 2.10.0) under R (version 3.4.1). Genes whose mean FPKM levels across all samples is less than 1 were removed. Then, only genes which have an FPKM of at least 5 in at least one sample was kept.
Genome_build: hg38
Supplementary_files_format_and_content: Table of genes/transcripts by samples of FPKM values, as calculated using StringTie

source_name: Myogenic Progenitors

growth_protocol: Myogenic progenitor cells were expanded for ~15 days and harvested either in proliferation conditions or after 4 days of differentiation as described previously (van der Wal et al., 2017b)

extract_protocol:
RNA was extracted using the RNeasy minikit with DNAse treatment (Qiagen, Germantown, MD).
Sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, California, USA) according to the manufacturer’s instructions.
Libraries were sequenced on a HiSeq2500 sequencer (Illumina, San Diego, California, USA) in rapid-run mode according to the manufacturer’s instructions. Reads 50 base-pairs in length were generated.

value: iPSC derived myogenic progenitors differentiated for 4 days into myotubes

tag: passage


title: Differentiated Myogenic Progenitors Control 2A (4 days)

description:
genes-fpkm.tsv
transcripts-fpkm.tsv


title: RNA-seq_Kh-1-KI-IplusT

description: Bulk RNA-Seq data


title: Differentiated Myogenic Progenitors Control 1B (4 days)

description:
genes-fpkm.tsv
transcripts-fpkm.tsv


title: healthy control N6


title: Differentiated Myogenic Progenitors Control 1A (4 days)

description:
genes-fpkm.tsv
transcripts-fpkm.tsv


title: RNA-seq_Ct-87-18-Ut

description: Bulk RNA-Seq data

source_name: Corrected iPSC-derived monocytic cell lines

value: WT(Corrected)


title: Proliferated Myogenic Progenitors Control 2B

description:
genes-fpkm.tsv
transcripts-fpkm.tsv

value: iPSC derived myogenic progenitors in proliferation phase


title: healthy control N2


title: RNA-seq_Ct-87-18-IplusT

description: Bulk RNA-Seq data


title: designed_library

first: Paul

middle: J

last: Sample

state: Washington

address: West Stevens Way NE

department: Electrical Engineering

data_processing:
After sequencing, RNA from each polysome fraction was identified by fraction-specific barcodes
cutadapt --length 59 --minimum-length 59 -o r1.fastq -p r2.fastq
Combine r1.fastq sequences (UTRs) and r2.fastq (UMIs) into a single CSV for Bartender
bartender_single_com -f input_csv -o output_file.csv  -c 2 -d 2 -z -1
Calculate relative reads within fractions and then, using these values, calculate relative reads per fraction for a given UTR. Calculate mean ribosome load (MRL) by multiplying each fraction’s relative reads by the number of ribosomes associated with each fraction and then sum the values.
Supplementary_files_format_and_content: CSV files contain 5' UTR sequences, read counts per fraction, relative counts, and MRL ('rl').

source_name: eGFP 100,000 member designed 5' UTR library

growth_protocol: HEK293T cells were cultured on ECM-coated plates in Dubelco's DMEM media supplemented with FBS (5%), penicillin (.05%), and streptomycin (.05%)

extract_protocol:
Salt solution (10x): 100 mM NaCl, 100 mM MgCl2,100 mM Tris-HCl pH 7.5, and RNase-free water (Zuccotti P, Modelska A 2016). Wash buffer: 100 µg/ml cycloheximide in RNase-free DPBS (10 ml per plate). Lysis buffer: 1x salt solution, 1% of 20% Triton X-100, 1 mM DTT, 0.2 U/µl SUPERase-In (Thermo Fisher Scientific), 100 µg/ml cycloheximide. Wash buffer and lysis buffer were chilled throughout the protocol. After 12 hours of growth at 37 °C, cells were placed on ice and media was aspirated. Translating ribosomes were halted by adding 5 ml of wash buffer and were then placed at 37 °C for 5 minutes followed by aspiration on ice. Washed by adding 5 ml wash buffer and aspirating thoroughly. Added 300 µl of ice-cold lysis buffer, scraped cells, broke up cell clumps by pipetting ~5 times, and then placed suspended cells into a pre-chilled microcentrifuge tube. Let sit for 10 minutes on ice and then triturated by passing through a 25-G needle 10 times [1]. Spun at 16,000 x g for 5 minutes to pellet cell debris and nuclei. Saved supernatant and added 1.5 µl of 1 U/µl DNase I (final concentration of 0.005 U/µl) and placed on ice for 30 minutes. Either stored at -80 °C or proceeded directly to polysome profiling.
For both the eGFP and mCherry library, randomized 50-mer oligos were Gibson assembled to serve as 5' UTRs for each CDS. To create the designed library, oligos were made via oligo synthesis array (CustomArray Inc.) and cloned into the eGFP vector.For all libraries, 25 nucleotides of defined sequence preceed the inserted 5' UTRs.

treatment_protocol: HEK293T cells were plated on 10cm cell culture dishes 24 hours before transfection (1 - 2 million per plate). At 60% to 80% confluency, cells were transfected with 14.5 µg of library mRNA using Lipofectamine MessengerMAX (Thermo Fisher Scientific) following the manufacturer’s protocol. Washed plates with 10 ml 1x DBPS and 10 ml media (DMEM with 10% FBS and 1% Penicillin-Streptomycin) after one hour of incubation. Cells were lysed 12 hours after transfection.


title: Proliferated Myogenic Progenitors Control 2A

description:
genes-fpkm.tsv
transcripts-fpkm.tsv


title: Proliferated Myogenic Progenitors Control 1B

description:
genes-fpkm.tsv
transcripts-fpkm.tsv


title: Proliferated Myogenic Progenitors Control 1A

description:
genes-fpkm.tsv
transcripts-fpkm.tsv


title: mcherry_unmod_2

source_name: mCherry 200,000 member 5' UTR library


title: mcherry_unmod_1


title: egfp_m1pseudo_2

source_name: eGFP 300,000 member 5' UTR library


title: egfp_m1pseudo_1


title: egfp_pseudo_2


title: egfp_pseudo_1


title: egfp_unmod_2


title: egfp_unmod_1


title: CD8+Cho

city: Houston

first: xingzhe

last: ma

address: 6565 fannin street

department: cancer center

institute: houston methodist hospital

hyb_protocol: GeneChip Hybridization.

scan_protocol: Affymetrix GeneChip Command Console (AGCC).

data_processing:
Affymetrix GeneChip Command Console (AGCC) Software.
The 'GSE111033_array_cd8_cd8_cho.txt' file includes raw signals, ratios, and array annotation.

source_name: CD8 T cells treated with cholesterol

label_protocol: WT Sense Target Labeling.

growth_protocol: T cell culture.

extract_protocol: Trizol RNA extraction.

treatment_protocol: CD8 under Tc1 cytokine condition and CD8 under Tc1 cytokine condition with cholesterol treatment.

value: CD8 T cells

tag: treatment

value: Cholesterol


title: CD8

source_name: CD8 T cells


title: Tc1-2

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Affymetrix GeneChip Command Console (AGCC) Software

growth_protocol: T cell culture

extract_protocol: Trizol RNA extration

treatment_protocol: Tc1 under Tc1 cytokine condition and Tc9 under Tc9 cytokine condition


title: Tc9-2


title: Tc1-1


title: Tc9-1


title: Gy30

city: Suzhou

first: Li

last: Zhong

state: Jiang Su

address: No.199 Renai Road,Industrial Park,

institute: Suzhou University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: Transcriptome assembly   The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default.
Supplementary_files_format_and_content: read counts and FPKM values for each Sample

organism: Pelophylax nigromaculatus

source_name: skin

extract_protocol:
Skin were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin

tag: radiation

value: wild type


title: Control

tag: tissue


title: Sample_56517

status: Public on May 02 2018

city: Ann Arbor

first: Richard

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

data_processing:
FastQC was used to identify features of the raw data that may indicate quality problems
GSNAP, in its SNP-tolerant mode, was used to align the reads to the human reference genome
StingTie was used to assemble transcripts
GATK's ASEReadCounter was used to calculate allele-specific read depth at heterozygous SNPs that were identified from paired genotyping data
Genome_build: hg19

source_name: Primary Monocytes

growth_protocol: Primary monocytes were isolated from thawed peripheral blood mononuclear cells via negative selection using the Pan Monocyte Isolation Kit, following the manufacturer’s instructions (Miltenyi Biotec Inc., San Diego California)

extract_protocol:
Total RNA was isolated from primary monocytes using the Direct-zol RNA Isolation Kit (Zymo Research, Irvine California), and then DNase treated using the TURBO DNA-free kit (Invitrogen, Carlsbad California).
RNA integrity and concentration was verified using the Agilent Bioanalyzer (RIN> 8) (Agilent Technologies, Santa Clara California). A minimum of 500ng RNA was processed per sample. RNA was ribo-depleted using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (New England Biolabs, Ipswich Massechusetts), and sequencing libraries were prepared for every RNA sample. Sequence-specific magnetic bead capture was performed on RNA libraries according to the manufacturer’s instructions, using the custom-designed probes (SeqCap EZ Choice XL Library System, Roche Nimblegen, Inc, Madison Wisconsin). Samples were multiplexed, four samples per capture reaction. All post-capture cDNA libraries were sequenced in one lane.

value: Primary Monocytes

tag: Stage

value: Mature

tag: stimulation

value: Unstimulated


title: Sample_55345


title: Sample_55344


title: Sample_55339


title: Sample_56518


title: Sample_55341


title: Sample_55346


title: Sample_55336


title: Sample_55337


title: Sample_56519


title: Sample_55347


title: Sample_55338


title: HSF 6.1 Treated

city: Rochester

first: Michael

middle: K

last: Asiedu

state: MN

address: 200 Fisrt ST SW

department: Surgery

institute: Mayo Foundation for Medical Education and Research

description:
Gene expression data from patient derived fibroblast cell lines
HSF 6.1 HSF 6.1 Treated

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 and performed by the Mayo Clinic Genomic Core

data_processing: The data were analyzed with using Partek Genomic Suite Ver. 6.6 (Partek Inc, St. Louis, MO) Partek Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Patient-derived iPS differentiated cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was purified with the RNeasy Mini-kit (Qiagen, CA).

value: epithelial cells

tag: cell line

value: HSF 6.1


title: NKX 6.1 Control

description:
Gene expression data from patient derived fibroblast cell lines
NKX 6.1 NKX 6.1 Control

value: NKX 6.1


title: MB231 Treated

description:
Gene expression data from patient derived fibroblast cell lines
MB231 MB231 Treated

source_name: commercial cell lines

value: Cancer cell lines


title: HSF 6.1 Control

description:
Gene expression data from patient derived fibroblast cell lines
HSF 6.1 HSF 6.1 Control


title: MB231 Control

description:
Gene expression data from patient derived fibroblast cell lines
MB231 MB231 Control


title: MB157 Control

description:
Gene expression data from patient derived fibroblast cell lines
MB157 MB157 Control


title: ENDO 6.1 Control

description:
Gene expression data from patient derived fibroblast cell lines
ENDO 6.1 ENDO 6.1 Control

value: ENDO 6.1


title: PANC1 Control

description:
Gene expression data from patient derived fibroblast cell lines
PANC1 PANC1 Control


title: HEPG2 Treated

description:
Gene expression data from patient derived fibroblast cell lines
HEPG2 HEPG2 Treated


title: PANC1 Treated

description:
Gene expression data from patient derived fibroblast cell lines
PANC1 PANC1 Treated


title: NKX 6.1 Treated

description:
Gene expression data from patient derived fibroblast cell lines
NKX 6.1 NKX 6.1 Treated


title: SNU Treated

description:
Gene expression data from patient derived fibroblast cell lines
SNU SNU Treated

value: SNU


title: HEPG2 Control

description:
Gene expression data from patient derived fibroblast cell lines
HEPG2 HEPG2 Control


title: SNU Control

description:
Gene expression data from patient derived fibroblast cell lines
SNU SNU Control


title: Array Tn5::BPSL0117_3

city: Greifswald

first: Christian

last: Kohler

address: Ferdinand Sauerbruch Strasse 1

department: Friedrich Loeffler Institue of Medical Microbiology

institute: University Medicine Greifswald

description: This sample is of Tn5::BPSL0117 mutant of Burkholderia pseudomallei E8 and the third of three Tn5::BPSL0117 mutant biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Microarray hybridizations were performed at 65°C in a MAUI hybridization station (BioMicro Systems, USA) for 17hrs.

scan_protocol: The slides were washed, dried in a centrifuge at 500rpm for 2mins, and scanned on an Axon Genepix 4000B scanner (Molecular Devices, USA) at a resolution of 5 microns

data_processing: The raw data (.pair file) was subjected to Robust Multi-array Average (RMA) procedure as implemented in Roche NimbleGen (USA) and normalized using the quantile normalization method developed from Bolstad et al. (2005) (Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003). A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 19 (2): 185–93.

organism: Burkholderia pseudomallei

source_name: transposon mutant Tn5::BPSL0117

label_protocol: 1.5 µg of obtained cDNA were used for the labeling procedure using the ULSTM arrayCGH Labeling Kit (Leica Microsystem) according to the manufacturer´s instructions.

growth_protocol: B. pseudomallei was cultivated in 60 ml M9 minimal broth containing 0.4% glucose as a carbon source at 37 °C and 140 rpm.

extract_protocol: 50 ml of cell suspension were harvested and centrifuged at 2°C at 10,000 g for 5 min. The cell pellets were quickly resuspended in 1 ml of Trizol Reagent (Invitrogen). After the RNA extraction procedure according to manufacturer's instructions, the integrity of the RNA was assessed by agarose gel electrophoresis and tested for the absence of DNA contamination by PCR.

treatment_protocol: 100 µg total RNA per sample were treated with DNA-freeTM Kit from Ambion (USA) according to the manufacturer's instructions to obtain DNA-free RNA. After precipitation of the RNA with ethanol and resuspension in nuclease free water, 10 µg per sample were subjected to ribosomal RNA depletion using the MICROBExpressTM kit from Ambion (USA) according to the manufacturer's instructions. Afterwards, 2 µg of purified mRNA were used for cDNA synthesis utilizing Superscript II Reverse Transcriptase (Life Technologies).

value: transposon mutant Tn5::BPSL0117

tag: strain

tag: phenotype

value: avirulent


title: HCT15 Treated

description:
Gene expression data from patient derived fibroblast cell lines
HCT15 HCT15 Treated


title: HCT15 Control

description:
Gene expression data from patient derived fibroblast cell lines
HCT15 HCT15 Control


title: T2 FFPE RiboZero (500ng)

source_name: breast cancer tumor sample

value: breast cancer tumor sample

value: FFPE

value: RiboZero

tag: starting material (ng)

tag: patient

tag: archival time

value: 4-5 years


title: MB157 Treated

description:
Gene expression data from patient derived fibroblast cell lines
MB157 MB157 Treated


title: Array Tn5::BPSL0117_2

description: This sample is of Tn5::BPSL0117 mutant of Burkholderia pseudomallei E8 and the second of three Tn5::BPSL0117 mutant biological replicates used in this experiment, each from separate cultures.


title: HCT116 Control

description:
Gene expression data from patient derived fibroblast cell lines
HCT116 HCT116 Control


title: H2170 Control

description:
Gene expression data from patient derived fibroblast cell lines
H2170 H2170 Control


title: HCT116 Treated

description:
Gene expression data from patient derived fibroblast cell lines
HCT116 HCT116 Treated


title: H520 Control

description:
Gene expression data from patient derived fibroblast cell lines
H520 H520 Control


title: Array Tn5::BPSL0117_1

description: This sample is of Tn5::BPSL0117 mutant of Burkholderia pseudomallei E8 and the first of three Tn5::BPSL0117 mutant biological replicates used in this experiment, each from separate cultures.


title: Array wild type_3

description: This sample is of wild-type Burkholderia pseudomallei E8 and the third of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: wild type E8

value: wild type E8

value: virulent


title: Control-HSF14,Sensitive 1431005408_165

description:
Gene expression data from patient derived fibroblast cell lines
Technical replicates 1

source_name: Patient-derived Fibroblast cell line

value: Fibroblast cell line


title: H2170 Treated

description:
Gene expression data from patient derived fibroblast cell lines
H2170 H2170 Treated


title: Treated-HSF14,Sensitive 1431005411_168

description:
Gene expression data from patient derived fibroblast cell lines
Technical replicates 2


title: Treated-HSF8,Resistant 1431005398_123


title: Treated-HSF7,Resistant 1431005395_120


title: Control-HSF8,Resistant 1431005396_121


title: Control-HSF14,Sensitive 1431005409_166


title: Array wild type_1

description: This sample is of wild-type Burkholderia pseudomallei E8 and the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Treated-HSF8,Resistant 1431005399_124


title: Array wild type_2

description: This sample is of wild-type Burkholderia pseudomallei E8 and the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Control-HSF8,Resistant 1431005397_122


title: Control-HSF7,Resistant 1431005393_118


title: Treated-HSF15,Sensitive 1431005391_96


title: H520 Treated

description:
Gene expression data from patient derived fibroblast cell lines
H520 H520 Treated


title: Treated-HSF14,Sensitive 1431005410_167


title: Treated-HSF7,Resistant 1431005394_119


title: Treated-HSF15,Sensitive 1431005390_95


title: Control-HSF7,Resistant 1431005392_117


title: Control-HSF15,Sensitive 1431005389_94