title: WT_PA_2

first: Jing-Ke

last: Weng

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: PA treated biological replicate 2

data_processing:
Raw reads were mapped onto the Arabidopsis gene model (TAIR10_GFF3_genes.gff downloaded from ftp://ftp.arabidopsis.org/Maps/gbrowse_data/TAIR10/) using TOPHAT (version 1.4.1)
Number of reads mapped to each gene were then counted using htseq-count, a component of the HTSeq framework (version 0.5.3p3)
Differential Expression was evaluated using DESeq (version 1.8.3)
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel spread sheets concontaining cross-treatment comparisons based on normalized read counts

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis thaliana seeds were germinated on MS medium under continuous light at 22 °C untill 10 days old.

extract_protocol:
Total RNA extraction using RNeasy Plant Mini Kit (Qiagen)
Multiplex RNA library construction and Illumina sequencing were carried out at the Beijing Genome Institute (BGI). The total RNA samples are first treated with DNase I. Then the mRNA is enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library.
Approximately 20 million reads of 50 bp single-ended sequences were generated per sample using Illumina HiSeq2000.

treatment_protocol: 10-day-old Arabidopsis wildtype (Col) seedlings were mock treated, or exposed to 50μM ABA, PA, or DPA for 3 h in biological duplicates

tag: ecotype

value: Columbia

tag: exposed to

value: 50μM PA for 3h

value: whole seedlings


title: WT_DPA_2

status: Public on Aug 11 2016

type: SRA

city: Cambridge

state: MA

country: USA

description: DPA treated biological replicate 2

library_source: transcriptomic

molecule: total RNA

tag: age

value: 50μM DPA for 3h

tag: tissue


title: linc-p21_L25-7_KO-F_E14.5 Heart

first: Abbie

last: Groff

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology;

institute: Harvard University

description: Heart.tab

data_processing:
Casava 1.8.2 was used to call bases
Reads were aligned to mm10 using tophat2 (--no-coverage-search --max-multihits 10 -p 8)
Bams were quantified using cuffquant and a modified verson of the GENCODE M2 transcriptome (--no-update-check -p 8)
Differential analysis was performed using cuffdiff2 (-p 8)
Genome_build: mm10
Supplementary_files_format_and_content: Final measurements are reported in FPKMs.

molecule: polyA RNA

organism: Mus musculus

source_name: Heart

extract_protocol:
E14.5 organs were harvested and homogenized in TRIzol.
Standard illumina protocols were used to make libraries (TruSeq RNA Sample Preparation Kit v2)

tag: lncrna previous name

tag: background

tag: official strain name

tag: genotype

value: KO

tag: Sex

value: F

tag: litter

value: Heart


title: linc-p21_L24-2_WT-M_E14.5 Heart

description: Heart.tab

value: WT

value: M


title: linc-p21_L24-2_WT-M_E14.5 Liver

description: Liver.tab

source_name: Liver

value: Liver


title: linc-p21_L24-5_KO-M_E14.5 Liver

description: Liver.tab


title: WT_ABA_2

description: ABA treated biological replicate 2

value: 50μM ABA for 3h


title: WT_PA_1

description: PA treated biological replicate 1


title: WT_DPA_1

description: DPA treated biological replicate 1


title: WT_mock_2

description: mock treated biological replicate 2

value: none (mock control)


title: linc-p21_L24-5_KO-M_E14.5 Heart

description: Heart.tab


title: LO_8_M_1

city: London

first: Rafael

last: Di Marco Barros

address: 44 Lincolns Inn Fields

country: United Kingdom

institute: Francis Crick Institute

data_processing:
Base calling by Illumina CASAVA 2.0
Alignment and gene-level quantification using RSEM 1.2.11 with Bowtie2 2.1.0
The GTF file used was from UCSC knownGene table 17/06/2105
Genome_build: HG19
Supplementary_files_format_and_content: RSEM output file; The exprect_count value in the associated RSEM gene-level output files was used to determine differential gene expression

growth_protocol: Samples were lysed and RNA isolated directly ex vivo

extract_protocol:
RNA was prepared using the RNA-Micro-plus kit (Qiagen).
RNA libraries were generated using the KAPA Stranded RNA-seq Kit with RiboErase (HMR) (KAPA BIOSYSTEMS)

treatment_protocol: All paired samples were obtained by performing small intestinal IEL preps on 2-3 litters. Approximately 10-20,000 cells were isolated per sample

tag: strain

value: Post natal Day 14-17

value: small intestinal epithelium

tag: cell type

value: small intestinal intraepithelial lymphocytes (IEL)

tag: cell subtype


title: WT_ABA_1

description: ABA treated biological replicate 1


title: linc-p21_L23-8_KO-M_E14.5 Leg

description: Hindlimb.tab

source_name: Hindlimb

value: Leg


title: WT_mock_1

description: mock treated biological replicate 1


title: linc-p21_L22-6_KO-M_E14.5 Leg

description: Hindlimb.tab


title: HI_5_M_1


title: linc-p21_L23-3_WT-M_E14.5 Heart

description: Heart.tab


title: LO_5_M_1


title: linc-p21_L22-4_WT-M_E14.5 Leg

description: Hindlimb.tab


title: LO_2_M_1


title: HI_8_M_1


title: linc-p21_L25-2_WT-F_E14.5 Heart

description: Heart.tab


title: HI_3_M_1


title: HI_2_M_1


title: LO_3_M_1


title: linc-p21_L23-3_WT-M_E14.5 Liver

description: Liver.tab


title: vec_2

description: Vector DNA

library_source: genomic

data_processing:
Casava 1.8.2 was used to call bases
Reads containing barcodes with a perfect match to a designed barcode and originating from a read with GFP sequence were counted.
analysis scripts were run in R, and are provided in supplemental material for the paper
Supplementary_files_format_and_content: a tab-delimited processed file showing normalized counts for tags associated to lincp21 genomic sequence and all relevent annotation information

molecule: other

organism: synthetic construct

source_name: MPRA vector

extract_protocol:
C2C12 cells were harvested in TRIzol.
Libraries were generated from cDNA using indexed primers against the tag-containing GFP.

tag: tissue type

value: MPRA vector


title: linc-p21_L21-4_WT-M_E14.5 Leg

description: Hindlimb.tab


title: vec_3

description: Vector DNA


title: linc-p21_L22-5_KO-F_E14.5 Leg

description: Hindlimb.tab


title: vec_1

description: Vector DNA


title: 309 Lung 48

status: Public on Aug 10 2016

city: Fort Detrick

first: Matthew

last: Permenter

state: MD

address: 568 Doughten Dr

institute: US Army Center for Environmental Health Research

data_processing:
Adapter sequences were trimmed with Cutadapt software (version 2.6).  In addition, low complexity sequences, such as homopolymer sequences, were removed with the Prinseq tool (version 0.20.4). To reduce the time required for sequence mapping, the redundant sequences in the file were collapsed with the FASTX collapse script obtained from the FASTX toolkit (version 0.0.13).  The number of reads for each unique sequence were calculated and used in summarizing the mapping read count.  The unique read sequences were then mapped against the reference rat miRNA sequence database from miRBase (Release 19) under the perfect match condition.
Genome_build: miRBase (Release 19)
Supplementary_files_format_and_content: The proccessed data contains normalized counts.

organism: Rattus norvegicus

source_name: Lung

extract_protocol:
Frozen tissues (heart, lung, liver, and kidney) stored at -80 °C in cryovials were placed on dry ice, cut into aliquots with a sterile scalpel on a pre-chilled titanium block, and placed in new tubes pre-chilled on dry ice. While working on dry ice, whole tissues (~25 mg) from the lung, liver, and kidney were cut from each sample and placed in 700 mL of QIAzol Lysis Reagent. Samples were homogenized with a TissueLyzer LT (Qiagen, Valencia, CA) for 5 min at 25 Hz twice, allowed to sit at room temperature for 5 min, and then placed at -80 °C. We homogenized heart tissue with a 6750 Freezer Mill with three sample microvials (Spex SamplePrep, Metuchen, NJ). RNA was isolated using the miRNeasy 96 kit according to the manufacturer’s instructions. The quality and quantity of RNA samples were evaluated with a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) using the Agilent RNA 6000 Nano Reagents and a multi-well Nanodrop 8000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA).
Small RNA libraries were constructed using the TruSeq small RNA library preparation kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: We placed rats in the heat-stress arm of the experiment into a floor-standing incubator set at room temperature (22°C) 24 hours prior to initiation of heat stress experiments. Rats in the control arm were never introduced to the incubator environment and were kept at a normal housing temperature. Once Tc ≤ 37.3°C was measured the rats were returned to their original cages for the remainder of the experiment. Rats in the heat-stress arm were heated in the incubator at 37.0 ± 0.2°C until reaching a Tc of 41.8°C (Tc,Max). The remaining rats were placed in a new cage at the ambient housing temperature (22.0 ± 0.2°C) and euthanized at 24 hours or 48 hours. Time-matched controls were euthanized at times corresponding to Tc,Max, 24 hours, and 48 hours in the heat-stress arm.

tag: treatment

value: Heat

value: Lung


title: linc-p21_L23-8_KO-M_E14.5 heart

description: Heart.tab

value: heart


title: 308 Lung 48


title: 305 Lung 48


title: 307 Lung 48


title: 304 Lung 48


title: 315 Lung 48

value: Control


title: 314 Lung 48


title: 302 Lung 24


title: 318 Lung 48


title: 300 Lung 24


title: 317 Lung 48


title: 325 Lung 24


title: 323 Lung 24


title: 324 Lung 24


title: 282 Lung 03


title: 283 Lung 03


title: 290 Lung 24


title: 312 Lung 48


title: 285 Lung 03


title: 311 Lung 48


title: 280 Lung 03


title: 292 Lung 03


title: 301 Lung 24


title: linc-p21_L21-7_WT-F_E14.5 Leg

description: Hindlimb.tab


title: 299 Lung 24


title: 298 Lung 24


title: 297 Lung 24


title: 308 Liver 48


title: 322 Lung 24


title: 306 Lung 48


title: 284 Lung 03


title: 305 Liver 48


title: 293 Lung 03


title: 281 Lung 03


title: 294 Lung 03


title: 318 Liver 48


title: 289 Lung 03


title: 288 Lung 03


title: 302 Liver 24


title: 312 Liver 48


title: 301 Liver 24


title: 291 Lung 03


title: 307 Liver 48


title: 306 Liver 48


title: 304 Liver 48


title: 311 Liver 48


title: 300 Liver 24


title: 297 Liver 24


title: 290 Liver 24


title: 325 Liver 24


title: 321 Liver 24


title: 322 Liver 24


title: 298 Liver 24


title: 285 Liver 03


title: 299 Liver 24


title: 324 Liver 24


title: 323 Liver 24


title: 317 Liver 48


title: 284 Liver 03


title: 283 Liver 03


title: 315 Liver 48


title: 282 Liver 03


title: 314 Liver 48


title: 294 Liver 03


title: 280 Liver 03


title: 293 Liver 03


title: 292 Liver 03


title: 291 Liver 03


title: 281 Liver 03


title: 309 Kidney 48

source_name: Kidney

value: Kidney


title: 288 Liver 03


title: 305 Kidney 48


title: 306 Kidney 48


title: 318 Kidney 48


title: 312 Kidney 48


title: 302 Kidney 24


title: 301 Kidney 24


title: 313 Kidney 48


title: 300 Kidney 24


title: 311 Kidney 48


title: 297 Kidney 24


title: 323 Kidney 24


title: 299 Kidney 24


title: 298 Kidney 24


title: 321 Kidney 24


title: 289 Liver 03


title: 322 Kidney 24


title: 307 Kidney 48


title: 281 Kidney 03


title: 280 Kidney 03


title: 293 Kidney 03


title: 294 Kidney 03


title: 285 Kidney 03


title: 284 Kidney 03


title: 282 Kidney 03


title: 292 Kidney 03


title: 289 Kidney 03


title: 314 Kidney 48


title: 309 Heart 48


title: 291 Kidney 03


title: 308 Heart 48


title: 307 Heart 48


title: 304 Heart 48


title: 306 Heart 48


title: 305 Heart 48


title: 317 Heart 48


title: 315 Heart 48


title: 290 Kidney 24


title: 314 Heart 48


title: 318 Heart 48


title: 302 Heart 24


title: 311 Heart 48


title: 312 Heart 48


title: 300 Heart 24


title: 299 Heart 24


title: 301 Heart 24


title: 298 Heart 24


title: 297 Heart 24


title: 325 Heart 24


title: 321 Heart 24


title: 323 Heart 24


title: 322 Heart 24


title: 324 Heart 24


title: 290 Heart 24


title: 284 Heart 03


title: 285 Heart 03


title: 283 Heart 03


title: 281 Heart 03


title: 282 Heart 03


title: 280 Heart 03


title: 294 Heart 03


title: 293 Heart 03


title: 291 Heart 03


title: 289 Heart 03


title: sample2: DP

city: Taipei

first: Mai-Yi

last: Fan

address: No1, Sec. 1, Jen - Ai Rd.

country: Taiwan

institute: National Taiwan University

data_processing:
RNA-seq reads were aligned to mm10 genome assembly using Tophat version 2.0.9 with parameters -p 12 --library-type fr-firststrand
Cufflinks verson 2.2.1 was then applied to assemble transcripts and quantify their abundance in terms of FPKM (fragments per kilobase of transcript per million fragments mapped)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: dermal fibroblasts

growth_protocol: All fibroblasts and DP cells were expanded and cultured in DMEM with 10% FBS

extract_protocol:
Totoal RNA was extracted using Qiagen RNeasy kit(Cat No./ID: 74104)  according to the manufacturer's protocol
Total 1~2 g RNA was purified by using poly-T oligo-attached magnetic beads.The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Paired-end 150 nucleotide reads from each mRNA library were obtained using NextSeq500 (Illumina Inc., CIC bioGUNE, Bilbao, Spain).

treatment_protocol: Fibroblasts were cultured with the indicated proteins (the concentration of each protein was 0.01 μg/ml) or E16.5 skin extract (2 μg/ml) for 3 days.

tag: background strain

value: hair follicle dermal papilla of adult skin

tag: passages


title: sample3: FBs

value: dermal fibroblast of adult skin


title: sample1: E14.5 FBs

value: dermal fibroblasts of embryonic skin


title: sample5: FBs cultured in Apoa1/ Lgals1/ Lum


title: sample4: FBs cultured in E16.5 skin extract


title: sample7: FBs cultured in Lgals1


title: sample8: FBs cultured in Apoa1


title: sample6: FBs cultured in Lum


title: polyA-KPDS.rep1

first: Giovanni

last: Marsico

address: Robinson Way

institute: CRUK Cambridge Institute

description: replicate 1

data_processing:
fastq files were trimmed for low quality tails and illumina adapters using trim_galore and aligned to the reference genome using tophat2
bam files from the alignment were cleaned (q > 30) using samtools
bedgraph coverage files were calculated using bedtools and scoring regions saved as bed files were identified using a customized procedure involving convolution-based filtering and linear model developed in R
Genome_build: hg19
Supplementary_files_format_and_content: aligned files; bedGraph files: ocverage file; bed files: scoring regions with the detected RNA G-quadruplexes.

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: HeLa cells were obtained from the European Collection of Animal Cell Cultures and grown in Dulbecco’s Modified Eagle Media (Sigma) supplemented with 10% fetal bovine serum (Sigma).

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) with gDNA eliminator and quantified with Qubit 2.0
Custom library construction was developed for Illumina sequencing (compatible with TruSeq adapters and 6nt index barcoding sequences)

tag: cell line

value: HeLa

tag: buffer

value: KPDS


title: polyA-KPDS.rep3

description: replicate 3


title: polyA-K.rep3

description: replicate 3

value: K


title: polyA-KPDS.rep2

description: replicate 2


title: polyA-K.rep2

description: replicate 2


title: polyA-KPDS.rep4

description: replicate 4


title: polyA-Li.rep1

description: replicate 1

value: Li


title: 288 Heart 03

value: Heart


title: polyA-Li.rep4

description: replicate 4


title: polyA-Li.rep3

description: replicate 3


title: SP1

city: Chicago

first: Zhong

last: Zheng

state: IL

address: 924 E57th ST, Room 402

department: Section of Rheumatology

institute: University of Chicago College of Medicine

data_processing:
1. FASTQ files were uploaded to Galaxy and processed with FASTQ groomer.
2. Output from step 1 was filtered with filter FASTQ with a minnium quality score of 30.0.
3. Output files from step 2 were converted to FASTA and all duplicate sequences were collapsed with "collapse".
4. Files from step 3 were uploaded to IMGT for the BCR analysis with High-V-Quest to determine IG sequence.
5. A home-made python script was used to generate BCR usage list from step 4 output. The BCR usage list was used to determine the BCRs enriched in each sample.
Supplementary_files_format_and_content: Excel files for the reads and percentage of BCR light chains in each sample

source_name: Splenic B cells

growth_protocol: Splenocytes or thymocytes were stained with surface antibodies and sorted with FACSAria. Because of the low number of cells recovered from these sorts, each sample was mixed with 10^6 Rag-/- splenocytes as carrier for RNA isolation.

extract_protocol:
Total RNA was isolated Zymo Quick RNA MicroPrep following manufacture's instructions.
Two rounds of amplification were used to generate the high throughput sequencing library, the first to amplify all Igk genes using primers Igk Forward: 5’-agacgtgtgctcttccgatcGAYATTGTGMTSACMCARWCTMCA, Ck Reverse: 5’- acacgacgctcttccgatctGGATACAGTTGGTGCAGCATC.  The first round was amplified for 10 cycles, after which, this product was used to prime a 2nd round PCR with primers to add the required adapters and barcodes for the Illumina platform. Universal Forward: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT and Index Reverse: 5’-CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC (where NNNNNN is a unique 6bp barcode for each sample).  This 2nd round PCR was amplified for 20 cycles.  PCR products were gel purified, mixed at equimolar ratios, and submitted to sequencing on the Illumina HiSeq (1x150bp).

tag: stain

value: Spleen

value: 3H9 Tg+

tag: cell population

value: CD19+B220+ cells


title: SP4

tag: tissue


title: SP3


title: SP2


title: 1.CCIC-G9a

city: TAIPEI

first: SHIH-TING

last: CHA

address: 6F., No.2, Syu-jhou Road,

data_processing:
Starting fromthe Illumina GA Pipeline v1.5, the range of base quality values is from 2 to 41
ChIP-seq reads were aligned to the hg19 genome assembly using
After filtering, the clean data was then mapped to the reference genome by SOAPaligner/SOAP2 (Version: 2.21t).
MACS (Model-based Analysis for ChIP -Seq, version: MACS-1.4.2) : The candidate peak region was extended to be long enough for modeling.  Dynamic Possion Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined  as a peak when p-value < le-05
Genome_build: hg19
Supplementary_files_format_and_content: wig

molecule: genomic DNA

growth_protocol: DMEM/F12, stem cell medium

extract_protocol:
Millipore EZ-ChIP #17-371 kit
(1)DNA-end repair,3'-dA overhang and ligation of methylated sequencing adaptor.(2)PCR amplification and size selection (usually 100-300bp,including adaptorsequence).(3)Qualified library forsequencing.  Which follow illumina instruction

treatment_protocol: T5088 CRC cells sorting by CD133 marker

tag: ID

value: colon cancer stem cells

tag: sorting marker


title: NS7

source_name: unswitched thymic B cells

value: Thymus

tag: genotype

value: CD19+B220+IgM+IgD+ cells


title: NS6


title: NS4


title: NS3


title: NS2


title: NS5


title: SP5


title: SW7

source_name: class-switched thymic B cells

value: CD19+B220+IgM-IgD- cells


title: polyA-K.rep4

description: replicate 4


title: NS1


title: polyA-Li.rep2

description: replicate 2


title: polyA-K.rep1

description: replicate 1


title: SW6


title: SW5


title: SW3


title: MUT-LSK2

city: Montreal

first: Xiang-Jiao

last: Yang

state: Quebec

address: 1160 Pine Ave W

department: Medicine

country: Canada

institute: McGill University

description: pair 2

data_processing:
Raw sequencing reads were mapped to the mouse reference genome NCBI37/mm9 via TopHat and differential expression between the wild-type and mutant was calculated by Cufflink.
Fold of change (FC) was calcuted based on normalized RPKM.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

source_name: Mutant LSK

extract_protocol:
LSK cells (~10,000) were sorted directly into a collecting tube containing 0.7 ml QIAZOL (Qiagen) and were kept on ice. Four embryos were used to pool sufficient wild-type or mutant LSK cell. The sorted cells were frozen immediately on dry ice and stored at -80°C. The total RNA was isolated by use of the miRNeasy Mini kit (QIAGEN). The yield was determined on a Nanodrop 2000 spectrophotometer (Thermo Scientific) and the integrity was assessed with an RNA Pico chip on an Agilent 2100 Bioanalyzer. Two independent pairs of wild-type and mutant RNA samples (each of which contained LSK cells pooled from four embryos) were used for oligo-dT primed RNA Seq on HiSeq2500 sequencers (Illumina).
Oligo-dT primed RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq was performed in two different companies, Otogenetics and Omega Bioservices. Two pairs of wild-type and Brpf1 mutant  samples were used for sequencing, with pair 1 sequenced loaded on two lanes and pair 2 loaded on 6 lanes of HiSeq2500 sequencers.

value: fetal liver

value: LSK

tag: developmental stage

value: E14.5 embryos


title: SW1


title: SW4


title: WT-LSK2

description: pair 2

source_name: Wild-type LSK

value: wildtype


title: MUT-LSK1

description: pair 1


title: Tumor RNA_1

city: Shanghai

first: Liu

last: Yanfang

address: 800 Xiangyin Road

department: Immunology

country: China

institute: Second Military Medical University

data_processing:
The exosome RNA sequence reads were pre-processed using FASTXToolkit (fastx_toolkit-0.0.13.2; http://hannonlab.cshl.edu/fastx_toolkit/commandline.html ), excluding low-quality reads (ambiguous N, quality < 10 nt, and length <18 nt) as well as adapter.
RNA sequencing reads that passed this quality control measure were then mapped to the mouse reference genome (GRCm38.p4) using TopHat (version:2.0.9).
Cufflinks v2.1.1 was used for the differential expression analysis: parameters of Cuffdiff were set to allow normalization of the number of fragments mapping to individual loci to improve the strength of differential expression analysis.
Cuffdiff labeled genes as significant or not significant based on whether the p-value of statistical test for differential expression was greater than the false discovery rate (FDR) after Benjamini-Hochberg correction for multiple testing. Genes with a q-value or FDR-adjusted p-value of < 0.05 and a fold change greater than 2 were considered statistically significant.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: Tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample.

source_name: Primary tumor

extract_protocol:
Total RNA was extracted and purified using miRNeasy Mini Kit (Cat # 217004, QIAGEN, GmbH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).
The 5' and 3' adaptors were ligated sequentially to the RNAs and amplified by RT-PCR. The amplification products were excised from 6% TBE urea gel (Invitrogen), and purified DNA fragments were clustered and sequenced by Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol:
We subcutaneously inoculated C57BL/6 mice with Lewis lung carcinoma (LLC). Three weeks later, tumor tissues were cut.
To purify tumor-derived exosomes, primary tumors were cut into small pieces and cultured in RPMI media without FBS for 12h. Then, the media was collected and centrifuged at 800g for 10 min, followed by a centrifugation step of 20,000g for 20 min to remove cellular debris. Next, the supernatant was filtered using a 0.2-μm filter (Pall Corporation). The collected media was then ultracentrifuged at 100,000g for 90 min at 4ºC. Then, the supernatant was discarded. Exosomes used for RNA and protein extraction were isolated using Exosome Precipitation Solution (ExoQuick-TC, System Biosciences) without ultracentrifugation.

tag: strain/background

tag: inoculated tumor

value: Lewis lung carcinoma (LLC)

value: Primary tumor


title: N2-sig-7RNAi-2

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

data_processing:
RNA-seq reads were quality-checked using FastQC version 0.5.2
FastQ Quality Trimmer version 1.0 was used to trim reads with less than optimal quality scores.
The DE analysis protocol outlined in Trapnell et. al. was used to perform the DE analysis
The quality filtered reads were mapped to C. elegans (ce10) reference genome using TopHat2 version 0.5.
Cufflinks version 2.1.1 was used to assemble transcripts and estimate their abundance. The transcript assembly outputs from Cufflinks were merged into a unified list of transcripts using Cuffmerge.
Cuffdiff version 2.0.2 was then used to quantify gene and transcript expression levels and test them for significant differences. Default parameters were utilized for all steps.
Genome_build: ce10
Supplementary_files_format_and_content: .txt files, cuffdiff differential expression output (gene-level, isoform-level, primary transcript)

organism: Caenorhabditis elegans

source_name: mixed stage early embryos

growth_protocol: Synchronized L1 worms were fed on OP50 bacteria for 72 hrs, then adult worms were treated with standard bleaching solution to collect embryos in utero

extract_protocol:
Total RNAs were purified using Trizol/chloroform extraction protocol.
1µg of total RNA was used as starting material, and a sequencing library was prepared using TruSeq Stranded Total RNA Sample Prep Kit after treatment with Ribo-Zero (Human/Mouse/Rat) for rDNA depletion.

tag: range of embryonic cell stages

value: 1cell to 350 cell stage

tag: strain

tag: genotype/variation

value: sig-7 loss


title: Tumor RNA_2


title: ExoRNA_1

source_name: Tumor-derived exosomes

value: Tumor-derived exosomes


title: ExoRNA_2


title: 2.CCIC-H3K9me2

tag: cell type


title: N2-sig-7RNAi-1


title: N2-L4440-2

value: control


title: KW2309-Sig-7RNAi-1Ama-1-CHIP

data_processing:
bowtie 1.0.1 was run with the -m 2 option to map the Illumina reads to the genome version ws220
MACS2 was run on the bowtie output with the -bdg option to obtain degraph signal track files
MACS2 was run with the -broad peak call option and a significance cutoff of 0.01 to optain AMA-1 peak calls for each AMA-1 ChIP-seq replicate
Genes were called enriched for AMA-1 if a peak overlapped at least 250 bp (or 45% the length of the gene, whatever is smaller) with the body of the gene.
Genes needed to be called enriched for AMA-1 in both replicates of a condition to be called enriched for that condition.
Genome_build: ws220 (ce10)
Supplementary_files_format_and_content: bedgraph signal track files and txt file with genes that were called enriched for AMA-1 in L4440 and/or sig-7 RNAi.

growth_protocol: Synchronized L1s were grown on 15cm peptone rich plates seeded with NA22 bacteria for 72hrs, then adult worms were treated with standard bleaching solution to collect early embryos in utero

extract_protocol:
RNA Pol II-DNA complexes were isolated using AMA-1 antibody from prepared lysates.
DNA CHIP-seq library is prepared as described in Bowmen et al (doi:10.1186/1471-2164-14-466)

treatment_protocol: Collected embryos were fixed with 2% formaldehyde for 22min on rotator. Samples were sonicated using a Bioruptor sonicator at high setting for 40min (40sec on/ 20sec off).

tag: chip antibody

value: anti-AMA-1 (Novus Biological, Cat# 38520002)


title: N2-L4440-1


title: KW2309-Sig-7RNAi-1Ama-2-CHIP


title: KW2309-L4440-1Ama-2-CHIP


title: KW2309-Sig-7RNAi-1input


title: KW2309-Sig-7RNAi-2input


title: KW2309-L4440-1Ama-1-CHIP


title: KW2309-L4440-1input


title: KW2309-L4440-2input


title: SW2

value: 3H9 Tg+


title: 3.CCIC-shG9a-DNG9a


title: WT-LSK1

description: pair 1


title: bipolar-37

city: Jupiter

first: Ronald

middle: L

last: Davis

state: Florida

address: 130 Scripps Way

department: Neuroscience

institute: The Scripps Research Institute - Scripps Florida

data_processing:
Raw reads were processed by trimming out adapter sequences and low-quality base calls (PHRED < 30).
Reads were first aligned against a custom ribosomal DNA reference using BowTie2,23 and reads mapping to rRNA genes were purged.
The splice-aware aligner TopHat24 (v2.0.12) was used to map remaining reads against the reference human genome (GRCh38 from Ensemble 76). The HTSeq-count script in HTSeq25 (v0.6.0) was run in “union” mode to count all reads that mapped uniquely to annotated exons of each gene. TopHat and HTSeq parameters included a reverse setting for library strandedness; other parameters were set as default.
Genes located on alternative/unplaced scaffolds and the Y chromosome were removed, as well as certain categories of noncoding genes.
Duplicate gene symbols: for different Ensembl IDs sharing the same gene symbol, rows were collapsed by summing read counts if entries were on the same chromosome and strand; only the most recent Ensembl ID was retained otherwise.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file contains read counts/gene

source_name: dorsal striatum, bipolar

extract_protocol:
Frozen postmortem dorsal striatum samples were transferred to RNAlater-ICE (Ambion) and stored at -20C upon receipt. Total RNA was extracted from dissected caudate-putamen tissue by Trizol (Life Technologies), column-purified by the RNeasy Lipid Tissue Kit (Qiagen) and treated with the Turbo DNA-free Kit (Life Technologies). RNA samples were assayed on the BioAnalyzer (Agilent, Santa Clara, CA) to obtain RNA integrity number (RIN) values.
Ribosomal RNA (rRNA) was depleted from samples using the RiboMinus Eukaryote Kit v2 (Life Technologies). Strand-specific cDNA libraries were made using the Next Ultra Directional RNA Library Prep Kit (NEB) and sequenced on the Illumina HiSeq2000.

tag: age (years)

tag: Sex

value: female

tag: postmortem interval (hours)

tag: rin


title: bipolar-34


title: bipolar-30


title: bipolar-33


title: bipolar-40


title: bipolar-26


title: bipolar-24


title: bipolar-23

value: male


title: bipolar-25


title: bipolar-19


title: bipolar-20


title: total 8h WT rep1

city: Res Triangle Park

first: Guang

last: Hu

state: NORTH CAROLINA

address: 111 T. W. Alexander dr.

department: ESCBL

institute: NIH/NIEHS

description: total RNA

data_processing:
Sequenced reads were mapped to mm9 using STAR 2.3.0e with parameters --outFilterMultimapNmax 1 --outFilterMismatchNmax 3 --alignIntronMax 100000
Gene expressions were quantified by assigning aligned reads to Ensembl gene features using htseq-count
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads for Ensembl gene features

source_name: Cnot3 cKO ESCs

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time point

value: 8 hour


title: bipolar-10


title: total 4h WT rep2

description: total RNA

value: 4 hour


title: total 8h 4OH rep2

description: total RNA


title: total 4h WT rep1

description: total RNA


title: 3_cobB mutant

first: Yu

last: Sang

address: 280 S. Chongqing Rd

department: Microbiology and Immunology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Firstly, remove the low sequence to get the clean reads.
Then mapped to the gene sequence of Salmonella enterica serovar Typhimurium 14028S with bowtie2 software.
Count the gene reads number from each sample respectively, convert to RPM (ref: Mortazavi, A., et al., Nat   Methods, 2008)
Compare expression abundance difference of each gene in pat mutant and cobB mutant with WT strain.
Genome_build: NCBI Reference Sequence: NC_016856.1
Supplementary_files_format_and_content: txt files include processed file (remove joint, merge the same sequence), sequence arranged for two columns: SEQ and COUNT

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028

source_name: bacteria

growth_protocol: Salmonella enterica serovar Tyhimurium 14028S wild type, pat mutant (pat::cm), and cobB mutant (cobB::cm) were grown with overnight shaking (250 rpm) in 5 ml minimal E glucose (EG) medium (MgSO4 0.098 g/L, citric acid monohydrate 2.0 g/L, K2HPO4 •3H2O 13.1 g/L, NaNH4HPO4 2.29 g/L, pH 7.7, supplemented with 0.4% (w/v) glucose) at 37°C. For RNA isolation, overnight cultured bacteria was 1:100 diluted in fresh EG medium, grown to OD600 = 0.4, and then harvested by centrifugation.

extract_protocol:
RNA was isolated by using TRIzol (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: S. Typhimurium strain 14028S was used as parental strain in this study. λ-Red recombination system was employed to construct Δpat and ΔcobB.

tag: strain background

value: cobB mutant (cobB::cm)

tag: growth phase

value: log phase


title: bipolar-9


title: 2_pat mutant

value: pat mutant (pat::cm)


title: total 4h 4OH rep1

description: total RNA


title: bipolar-8


title: control-39

source_name: dorsal striatum, control


title: bipolar-5


title: 1_wild type

value: wild type


title: total 4h 4OH rep2

description: total RNA


title: total 0h WT rep1

description: total RNA

value: 0 hour


title: total 0h WT rep2

description: total RNA


title: control-38


title: bipolar-15


title: 4.CCIC-shGLP-DNG9a

tag: ID

value: colon cancer stem cells

tag: sorting marker


title: total 0h 4OH rep2

description: total RNA


title: control-28


title: control-32


title: total 8h WT rep2

description: total RNA


title: control-35


title: control-27


title: total 0h 4OH rep1

description: total RNA


title: bipolar-4


title: bipolar-16


title: total 8h 4OH rep1

description: total RNA


title: control-36


title: control-22


title: polysome WT rep2

description: polysome fraction RNA

source_name: E14Tg2a ESCs


title: control-18


title: control-17


title: polysome WT rep1

description: polysome fraction RNA


title: total Cnot3-KO rep2

description: total RNA


title: control-13


title: control-11


title: total WT rep1

description: total RNA


title: total WT rep2

description: total RNA


title: polysome Cnot3-KO rep2

description: polysome fraction RNA


title: control-12


title: control-3


title: GFP Input ChIP-Seq

city: Rochester

first: Jennifer Jane

last: Westendorf

state: MN

address: 200 First Street SW

institute: Mayo Clinic

description: GFP control adenovirus

data_processing:
bcl2fastq v1.8.4 is used for basecalling
Data was processed with Mayo chip-seq pipeline-- HiChIP (http://www.biomedcentral.com/1471-2105/15/280).
Paired_end reads are aligned to genome with BWA. Duplicated reads are filtered out with picard. Peak calling is performed with Sicer
Genome_build: mm10
Supplementary_files_format_and_content: This file contains a list of peaks, from left to right are: chr, start, end, peak ID, integer score for display, fold-change, -log10pvalue, -log10qvalue and peak summit position relative to peak start

source_name: Input DNA for GFP sample

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Libraries were prepared according to NuGene Ultralow library prep kit V2

value: Chondrocytes

value: wild-type

tag: transduction

value: GFP control adenovirus


title: polysome Cnot3-KO rep1

description: polysome fraction RNA


title: Cre RNA-Seq

description: Primary mouse chondrocytes, cultured ex vivo in micromass cultures, transduced with Cre-recombinase adenovirus

data_processing:
bcl2fastq v1.8.4 is used for basecalling
Paired-end reads are aligned by TopHat 2.0.6
Data was analyzed using Mayo Clinic's RNA-seq piepline : MAP-Rseq (http://www.biomedcentral.com/1471-2105/15/224)
Gene counts are generated using HTseq software
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Gene count values and rLogFC for each Sample

source_name: K27ac CHiP for hdac3-knockout Cre sample

extract_protocol:
Total RNA was isolated micromass cultures with TRIzol reagent (Invitrogen), followed by phenol/chloroform extraction
Libraries were prepared according to Illumina TruSeq v2 mRNA

value: Cre-recombinase adenovirus


title: control-2


title: control-6


title: Haloferax_volcanii_3_Ulm_TEX_plus

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

description:
dRNA-Seq
H. volcanii H26 is derived from H. volcanii DS2.

data_processing:
FastQ quality trimming using FastX (version 0.0.13) and a cut-off value of 20.
Fastq to fasta conversion using FastX FastX (version 0.0.13).
PolyA removal and size filtering by READemption 0.3.5.
Read alignment using READemption 0.3.5 and segemehl 0.2.0.
Coverage calculation using READemption 0.3.5.
Genome_build: ASM2568v1 (H. volcannii DS2)
Supplementary_files_format_and_content: wiggle

organism: Haloferax volcanii

source_name: Cell culture, Ulm, TEX+

growth_protocol: H26 was grown in complex medium under optimal conditions as described previously [PMID: 18493744]. In short, optimal conditions are a temperature of 42oC, a NaCl concentration of 2.2 M, and a good aeration. Cell growth was monitored spectroscopically (OD600) and via counting of the cell density using a Neubauer counting chamber. Cultures were inoculated with exponentially growing pre-cultures and grown to mid-exponential growth phase (4-5 x 10^8 cells ml-1), before they were harvested and used for the RNA-Seq analysis.

extract_protocol:
Cultures were harvested by centrifugation and total RNA was isolated using the RNeasy kit according to the instruction of the manufacturer, including an extensive DNase treatment (Qiagen, Hilden, Germany). The intactness of the RNA was verified by analytical gel electrophoresis, the absence of DNA was verified by comparing PCR reactions with and without a prior cDNA step, and the concentration was determined using a NanoDrop 1000 photometer (Thermo Fisher Scientific).
For Hvolcani_1_Ulm_TEX_plus and Hvolcani_1_Ulm_TEX_minus: The enzymatic treatment with TEX and TAP (tobacco acid pyrophosphatase), RNA adaptor ligation with T4-RNA-ligase, and cDNA synthesis were performed as described [PMID: 20164839]. For the other 4 samples: RNA fractions were sent to vertis (vertis Biotechnologie AG, Martinsried, Germany) for cDNA preparation and high-throughput sequencing. Here, RNA fraction 1 was incubated with TEX to remove the RNA species which carry a 5' mono-phosphate, thus this RNA fraction is enriched in primary transcripts (fraction +TEX). For cDNA synthesis, both RNA fractions were poly(A)-tailed using poly(A) polymerase. This was followed by treatment with TAP to remove the 5' PPP structures. Afterwards, an RNA adapter was ligated to the 5'-monophosphate of the RNAs. First strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified to about 10-20 ng/μl using a high-fidelity DNA polymerase. PCR cycles performed and barcode sequences, which are part of the 3' sequencing adapter. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and were analyzed by capillary electrophoresis. For Illumina sequencing, the cDNAs were pooled in approximately equimolar amounts.

tag: strain/background

tag: tex

value: plus

tag: location generated

value: Ulm


title: ago3/TM6 small RNA-Seq

city: Singapore

first: Toshie

last: Kai

address: 1 Research Link, National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

description: whole testis was used for RNA -extraction

data_processing:
bad quality read removal -Fastq toolkit
Alignment to genome - Bowtie (v1)
Libarray Normalization - RLE method (DESeq2)
Obtaining normalized read data - DEseq2
Genome_build: Drosophila melanogaster rel 5.25
Supplementary_files_format_and_content: cluster and transposon mapping piRNAs

organism: Drosophila melanogaster

source_name: testis

extract_protocol:
RNA extraction from hand dissected testes
True-seq small RNA library construction

value: gonioblasts to mature sperms


title: aub (N11/HN2) mutants small RNA-Seq


title: aub/CyO  small RNA-Seq


title: control-21

value: female


title: Cre Input ChIP-Seq

source_name: Input DNA for Cre sample

tag: strain


title: y w  small RNA-Seq


title: ago3 (t2/t3) mutants  small RNA-Seq


title: Haloferax_volcanii_3_Ulm_TEX_minus

source_name: Cell culture, Ulm, TEX-

value: minus


title: Cre-K27ac ChIP-Seq

tag: genotype/variation


title: total Cnot3-KO rep1

description: total RNA


title: Haloferax_volcanii_2_Wue_TEX_plus

source_name: Cell culture, Wue, TEX+

value: Wurzburg


title: sa mutants small RNA-Seq

description: The apical tips were removed from testis to remove early mitotically dividing germline cells

tag: cell type

value: primary spermatocytes


title: can mutant small RNA-Seq


title: bgcn mutant small RNA-Seq

value: early mitotically dividing germline cells (gonioblasts)


title: Haloferax_volcanii_2_Wue_TEX_minus

source_name: Cell culture, Wue, TEX-


title: control-7


title: GFP RNA-Seq

description: GFP control adenovirus

source_name: K27ac CHiP for wild-type GFP sample


title: GFP-K27ac ChIP-Seq

description: GFP control adenovirus

tag: chip antibody


title: Haloferax_volcanii_1_Fra_TEX_minus

source_name: Cell culture, Fra, TEX-

value: Frankfurt


title: Haloferax_volcanii_1_Fra_TEX_plus

source_name: Cell culture, Fra, TEX+


title: wt Rep3

status: Public on Aug 09 2016

city: Houston

first: Rodney

middle: C

last: Samaco

state: TX

address: 1250 Moursund St.

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
Illumina HiSeq 2500 software used for basecalling
Raw reads were first groomed by removing 10bp from the 5'-ends with random base concentration, then mapped to Rattus norvegicus genome (Ensembl RGSC3.4) using TopHat using TopHat v1.4.1 (-r 400 –p 8).
Expression level for each gene was estimated using Python program HTSeq (Anders et al., Bioinformatics 2014). Specifically htseq-count function of HTSeq accumulated the number of aligned reads that falls under the exons of the gene (union of all the exons of the gene). This read counts obtained are analogous to the expression level of the gene.
Using the obtained read counts, differential gene analyses were carried out using the DESeq package in the R environment.
Genome_build: Ensembl RGSC3.4
Supplementary_files_format_and_content: Text files inclue read counts value for each gene; individual file for each sample.

source_name: wt

growth_protocol: Rats were maintained on a 12 h light:12 h dark cycle with standard rat chow (Pico Lab Rodent Diet, #5053, Purina USA) and water ad libitum. Animals were generated by mating female Sprague-Dawley rats lacking one copy of functional MeCP2 (Mecp2ZFN/+) with wild-type male Sprague-Dawley rats to obtain male rats completely lacking MeCP2 (Mecp2ZFN/y), and wild-type littermate male rats.

extract_protocol:
Rats were euthanized under anesthesia according to approved IACUC protocols. Hypothalami were rapidly dissected from brain tissue samples on ice and immediately snap frozen in liquid nitrogen. RNA extraction (N=4 biological replicates of each genotype, male Mecp2ZFN/y and male wild-type littermate rats, 6 weeks of life) was performed using TRizol reagent (ThermoFisher Scientific) and further purified with on-column DNase treatment using the RNeasy Mini Kit (Qiagen)  following the manufacturers’ instructions.
Ten µg of RNA was prepared for paired-end RNA-Sequencing using Illumina HiSeq 2500. The Baylor College of Medicine Genomic and RNA Profiling Core first conducted Sample Quality checks of the RNA using the NanoDrop ND-1000 spectrophotometer and Agilent Bioanalyzer 2100 using the Nano chip.  The Illumina EpiCentre Ribo-Zero rRNA Removal Kit was used to reduce the ribosomal RNA content.  The rRNA-reduced sample was then carried into the Illumina TruSeq RNA library preparation protocol.

treatment_protocol: Not applicable

value: Sprague-Dawley

tag: gender

value: male

tag: age

value: 6 weeks old

tag: tissue

value: Hypothalamus

tag: genotype


title: ko Rep3

source_name: ko

value: ZFN/y (Mecp2ZFN{delta}/y)


title: wt Rep2


title: wt Rep1


title: ko Rep1


title: ko Rep4


title: WT O/E_YAD

city: Toronto

first: Maria

last: Soloveychik

state: Ontario

address: 1 king's college circle

department: Molecular Genetics

institute: University of Toronto

description:
rRNA depleted using affinity beads
processed data file: Supplemental Table 6(JHD2 OE YAD).xls

data_processing:
FASTQ files were checked for sequencing quality using FastQC (Version 0.10.1 2011).
Sequences were aligned to the yeast genome (build 3.1) using TopHat (version 2.0.12), utilizing Bowtie2 aligner (version 2.1.0).
Files from TopHat were processed using Cufflinks (version 2.1.1) to yield transcript annotations and FPKM values (fragments per kilo base transcript per million reads).
Differential transcript abundance analysis was performed using Cuffdiff (version 2.1.1) with transcript identification guided by a .gtf file specifying the location of yeast transcripts compiled from SGD (Saccharomyces Genome Database).
K-means clustering was performed using Cluster 3.0 and visualized using Java TreeView (1.1.6r4).
Genome_build: NCBI 3.1
Supplementary_files_format_and_content: Cuffdiff output files

organism: Saccharomyces cerevisiae

source_name: vegatative cells

growth_protocol: Replicate cultures of MSY723 (WT) and MSY724 (jhd2∆) were serially outgrown to O.D.600 0.5.

extract_protocol:
RNA was prepared according to the Illumina TruSeq Stranded mRNA Library Prep Kit protocol following addition of 10uL of 1:100 dilution of ERCC92 Mix 1 (Ambion/Life) to each cell pellet as an external spike-in control. Total RNA was DNase treated, and purified with Qiagen RNeasy columns.
Ribosomal RNA was depleted using an Illumina Yeast RiboZero rRNA depletion kit (MRZY1306)
RNA fragmentation and priming with Illumina TruSeq Stranded mRNA library synthesis (CAT RS-122-2101). All protocols were performed according to manufacturer’s directions. Single read sequencing was completed on the Illumina HiSeq2500 platform with Version 4 reagents at the Donnelly Sequencing Centre. Single-end reads of 51 bp in length were acquired with a total of 240-250 million reads per lane.

treatment_protocol: Pellets of 1 O.D.600 were snap frozen in liquid nitrogen

value: wildtype

tag: mating type

value: Mat alpha

tag: growth media

value: YAD


title: WT empty vector_YAD


title: WT_RNA_SEQ_YAR

description:
rRNA depleted using affinity beads
processed data file: Supplemental Table 5(YAR RNA seq).xls, Supplemental Table 4(YAR vs YAD RNA seq).xls

value: Mat a

value: YAR


title: jhd2_RNA_SEQ_YAR


title: WT_RNA_SEQ_YGD

description:
rRNA depleted using affinity beads
processed data file: Supplemental Table 3(YGD RNA seq).xls

value: YGD


title: jhd2_RNA_SEQ_YGD


title: jhd2_RNA_SEQ_YAD

description:
rRNA depleted using affinity beads
processed data file: Supplemental Table 2(YAD RNA seq).xls


title: WT empty vector_YAR

description:
rRNA depleted using affinity beads
processed data file: Supplemental Table 7(JHD2 OE YAR).xls


title: jhd2_ChIP_SEQ_YAR_WCL

description: genomic DNA

data_processing:
Quality control was performed using FastQC (Babraham Bioinformatics) to assess read quality and GC% bias
Reads were aligned to the yeast genome (build 3.1) using bowtie2 (version 2.2.3) with standard parameters
File type conversion from .sam to .bam, read deduplication, sorting, and other formattting were performed with Samtools and Picard
Depth-of-coverage signal was obtained using GATK (Broad Institute) software, and peak calling was performed using MACS2 (Taoliu), with the broad reagion calling option turned off
Peaks were mapped to overlapping yeast genes using in-house perl scripts
Genome_build: NCBI 3.1
Supplementary_files_format_and_content: Tab-delimited files containing peak calls, and overlapping genes

growth_protocol: YAR cultures of MSY723 (WT) and MSY724 (jhd2∆) were serially outgrown to O.D.600 0.5.

extract_protocol:
Chromatin immunoprecipitation of H3K4me3 and H3 was performed using standard protocols
For ChIP-seq, sequencing libraries for IP and WCE were prepared at the Donnelly Sequencing Centre using standard methods. Single read sequencing was completed on the Illumina HiSeq2500 platform with Version 4 reagents. Single-end reads of 51 bp in length were acquired with ~14 million reads per sample, equivalent to 60-fold genome coverage.

treatment_protocol: Cells were crosslinked at room temperature with formaldehyde and flash-frozen in liquid nitrogen


title: WT_ChIP_SEQ_YAR_WCL

description: genomic DNA


title: WT O/E_YAR


title: jhd2_ChIP_SEQ_YAR_H3

description:
ChIP DNA
Abcam ab1791 (pan-H3)


title: jhd2_ChIP_SEQ_YAR_H3K4me3

description:
ChIP DNA
Ab8580 (H3K4me3)


title: WT_RNA_SEQ_YAD


title: WT_ChIP_SEQ_YAR_H3

description:
ChIP DNA
Abcam ab1791 (pan-H3)


title: bam mutant small RNA-Seq


title: PcT

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

description:
RNA-seq
counts.txt

data_processing:
RNA-seq: alignment with Tophat2 (v. 2.0.10) to mm10 genome with known GRCm38 Ensembl transcripts
RNA-seq: gene assignment with Rsubread (featureCounts, args: annot.ext = gtf.file, isGTFAnnotationFile = TRUE, GTF.featureType="exon", GTF.attrType="gene_name", useMetaFeatures=TRUE, allowMultiOverlap=FALSE, isPairedEnd=TRUE, requireBothEndsMapped=TRUE, checkFragLength=FALSE)
ChIP-seq: adapter trimming with trimmomatic (v. 0.32, args: -phred33 ILLUMINACLIP:./adapters_GG/TruSeq_contaminant_list.fasta:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
ChIP-seq: alignment to mm10 genome with bwa aln (v. 0.7.5, args: -q 10), bwa sampe and stampy (v. 1.0.23, args: --bamkeepgoodreads)
ChIP-seq: remove PCR duplicates with Picard (v. 1.105) MarkDuplicates (args: REMOVE_DUPLICATES=true)
ChIP-seq: bedGraph generation on samtools merged bam files with MACS2 (v. 2.0.10, pileup)
ATAC-seq: adapter trimming with trimmomatic (v. 0.32, args: ILLUMINACLIP:adapters.fa:2:30:5 LEADING:3 CROP:89 MINLEN:20)
ATAC-seq: alignment with Bowtie2 (v. 2.2.3, args: --no-discordant --no-mixed -X 2000)
ATAC-seq: transposon positional insertion bias corrected in R as described in Buenrostro et al. Nature 2013
ATAC-seq: bedGraph generation on positional corrected read bed file with MACS2 (v. 2.0.10, pileup)
Genome_build: mm10 UCSC genome
Supplementary_files_format_and_content: RNA-seq: columns are sample ID and rows are genes with data represented as counts
Supplementary_files_format_and_content: ChIP-seq: bedGraph on merged Foxn1 ChIP and input bam files
Supplementary_files_format_and_content: ATAC-seq: bedGraph on transposon positional corrected reads

source_name: Cortical thymic epithelial cells

extract_protocol:
RNA-seq: TECs were stained using Abs against CD45 (30F11; eBioscience), EpCAM (G8.8; DSHB, University of Iowa), MHCII (M5/114.15.2; BioLegend), Ly51 (6C3; BioLegend), UEA-1 (Reactolab), Aire (5H12; eBioscience). Stained samples were sorted on a FACSAria II flow cytometer for cortical (CD45-EpCAM+MHCII+Ly51+UEA1-) and medullary (CD45-EpCAM+MHCII+Ly51-UEA1+) subpopulations and cell pelets were snap frozen in liquid nitrogen. RNA was isolated using RNeasy kit (Qiagen). ChIP-seq: TECs were enriched to 15-20% using magnetic beads (autoMACS Pro Separator, Miltenyi Biotech) and subjected to DNA crosslinking and chromatin fragmentation using truChIP Low Cell Chromatin Shearing Kit (Covaris). Chromatin was immunoprecipitated using M2 anti-FLAG antibody (F1804; Sigma) as described (Vokes et al., 2007). ATAC-seq: ~10,000 cTEC were sorted into ATAC lysis buffer and incubated with Tn5 as described in Buenrostro et al. Curr Protocol Mol Biol 2015.
RNA-seq: RNA was enriched for polyA RNA, reverse transcribed and sequenced using TruSeq library prep. ChIP-seq: Library prep was carried out using TruSeq kits. ATAC-seq: Library prep was carried out as described in Buenrostro et al. Curr Protocol Mol Biol 2015

value: Cortical thymic epithelial cells

value: Mice homozygous for beta5t-rtTA locus, homozygous for Foxn1fl/fl locus and heterozygous for tetO-Cre1Jaw/J(Jax006234) transgene.

tag: treatment

value: 72 hours post-doxycycline treatment


title: wt Rep4


title: NcT

description:
RNA-seq
counts.txt

value: Mice homozygous for beta5t-rtTA locus, homozygous for Foxn1fl/fl locus and lacking  the tetO-Cre1Jaw/J(Jax006234) transgene.


title: 96mT

description:
RNA-seq
counts.txt

source_name: Medullary thymic epithelial cells

value: Medullary thymic epithelial cells

value: Homozygous Foxn1 BAC transgenic mice on nude background


title: ko Rep2

value: Sprague-Dawley


title: WT_ChIP_SEQ_YAR_H3K4me3

description:
ChIP DNA
Ab8580 (H3K4me3)


title: 96cT

description:
RNA-seq
counts.txt


title: 42cT

description:
RNA-seq
counts.txt

value: Heterozygous Foxn1 BAC transgenic mice on nude background


title: 42mT

description:
RNA-seq
counts.txt


title: E3KO Rep 2

city: Worcester

first: Kasmir

last: Ramo

address: 273 Plantation Street, Biotech II, Suite 309

department: Molecular Medicine

institute: University of Massachusetts Medical School

data_processing:
Paired-end, 40-bp reads from each sample were aligned to the mouse genome (mm10) using TopHat and Bowtie.  Gene expression was quantified as fragments per kilobase of exon model per million mapped fragments (FPKM) using Cufflinks version 1.0.3.
Differential expression for E3KO MLEC compared to ECtrl MLEC or EfCtrl MLEC and ECtrl MLEC compared to EfCtrl MLEC was determined using the Cufflinks tool Cuffdiff. The criteria for differential expression were: genes with FPKMs ≥ 2 in at least one of the tested genotypes, whose absolute log2 fold-changes between genotypes were ≤ -0.5 or ≥ +0.5, and whose FDR-adjusted p-values for significance of differential expression were ≤ 0.05.
The processed data file is in the format of Cufflinks output.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data file is in Cufflinks format and was outputted as a tab-delimited text file that includes RPKM values.

source_name: Primary Mouse Lung Endothelial Cells

extract_protocol:
Extraction of total RNA from primary mouse lung endothelial cells was performed using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.  DNA was eliminated by on-column RNase-free DNase treatment.  RNA quality was verified (RNA integrity number >9) using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Messenger RNA was isolated, converted to cDNA, and amplified using the mRNA Purification Kit (Illumina, San-Diego, CA) according to the manufacturer’s instructions. An Illumina library was built and used to generate clusters on the Illumina flow cell according to the Illumina protocol and sequenced using a HiSeq 2000 (Illumina).

value: Adult (10-12 week old)

value: Cdh5-Cre+ Jnk1LoxP/LoxP Jnk2LoxP/LoxP Jnk3-/-

value: Primary Mouse Lung Endothelial Cells


title: E3KO Rep 3


title: ECtrl Rep 1

value: Cdh5-Cre+ Jnk1+/+ Jnk2+/+ Jnk3-/-


title: EfCtrl Rep 2

value: Cdh5-Cre- Jnk1LoxP/LoxP Jnk2LoxP/LoxP Jnk3-/-


title: EfCtrl Rep 3


title: EfCtrl Rep 1


title: GM12878 spiked with Sequins Mix B rep3

city: Darlinghurst

first: Simon

middle: Andrew

last: Hardwick

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Sequenced reads were trimmed to remove standard Illumina adapter sequences using CutAdapt with Trim Galore wrapper script.
Reads were mapped using TopHat2 to genome co-index comprising hg38 and our in silico chromosome.
Transcripts were assembled using StringTie, using reference annotations to calculate gene expression values (FPKMs).
Genome_build: hg38
Supplementary_files_format_and_content: GTF files for transcript assemblies, including quantitative expression values.

source_name: Blood

extract_protocol:
Total RNA was extracted from K562 and GM12878 cells using TRIzol (Invitrogen). DNAse treatment was performed with TURBO DNase (Life Technologies) followed by a cleanup with RNA Clean and Concentrator-25 Kit (Zymo Research).
K562 total RNA was spiked with RNA sequins Mix A prior to library preparation. GM12878 total RNA was spiked with RNA sequins Mix B prior to library preparation. The neat samples of RNA sequins were sequenced without addition of any natural RNA. RNA was ribo-depleted using Ribo-Zero™ Magnetic Kit (Human/Mouse/Rat) (Epicentre), and libraries were prepared using KAPA Stranded RNA-Seq Library Preparation Kit (KAPA Biosystems).

tag: cell line

tag: subject source

value: Female with normal 46XX karyotype

tag: biopsy source

value: Peripheral vein

value: Unknown


title: ECtrl Rep 2


title: GM12878 spiked with Sequins Mix B rep2


title: ECtrl Rep 3


title: GM12878 spiked with Sequins Mix B rep1


title: Wt2 in vivo

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

institute: Technische Universität Braunschweig

data_processing:
RNA-seq reads were mapped to the Salmonella enterica subsp. enterica serovar Typhimurium UK-1 (Genbank, CP002614.1) genome using the Stampy aligner with default settings.
Differential expression was estimated using the R library DESeq making use of the biological replicates for each condition
Genome_build: gi|332986951|gb|CP002614.1|
Supplementary_files_format_and_content: The processed files in TXT format include gene names and their recovered read counts for each sample

source_name: Wild-type

growth_protocol: LB medium at 37°C and 140 rpm until OD600=2.0.

extract_protocol:
Using Rneasy kit (Qiagen) plus Qiashredder columns.
The planktonic cultures were treated according to the ScriptSeq v2 protocol. The tumor samples were processed using a customized protocol (Dötsch et al., PloS ONE, 2012). Briefly, eukariotic RNA was depleted using MICROBEnrich Kit (both for tumor samples and control sampels), subsequently bacterial rRNA was depleted using MICROBExpress kit with the Pseudomonas module (Ambion) and fragmented by sonication using Covaris Adaptive Acoustics device (Covaris). Upon ligation of barcoded adapters, reverse transcription with SuperScript II kit (Invitrogen) followed. Amplification was done by PCR using Illumina platform compatible primers. Established cDNA library was normalized by double strand specific nuclease treatment (Evrogen) according DSN Normalization Sample Preparation Guide from Illumina.

value: wildtype

value: CT26 tumor infected with S. Typhimurium

tag: treatment protocol

value: Tumor development:5*10^5 CT26 cells were intradermally injected into the right flank of a BALB/c mouse. After the the tumors reached a size of approx. 150 mm³, the mice were infected i.v. with 5*10^6 Salmonella. RNA Extraction from CT26 tumors (Bielecki et al.. PLoS One 2011):Two days post-infection (p.i.) mice were necrotized and infected tumors prepared for stabilization of bacterial RNA in the following way:the tumors were removed and excised into 2–4 pieces, put onto nylon filters for cell culture (70 µm pore size) and suspended in 2 ml of RNAproctect Bacteria Reagent in 2 cm petri dishes. The single tumors  were spent through the membrane with a sterile spatula. The resulting mixture in the RNAprotect reagent was collected and centrifuged for 5 min at maximum speed 16,000 x g. The pellet was immediately frozen at −70°C for further RNA extraction.


title: Wt1 in vivo

organism: Salmonella enterica subsp. enterica serovar Typhimurium


title: SF100 II

source_name: ΔlpxR9 ΔpagL7 ΔpagP8

value: S. Typhimurium planktonic culture

value: Cells from 2 pooled cultures were harvested by addition of the same volume of RNA-protect buffer (Qiagen) and centrifugation. The RNA was stored at -70°C.


title: SF100 I


title: SF102 I

source_name: ΔlpxR9 ΔpagL7 ΔpagP8 ΔaroA


title: SF102 II in vivo


title: SF102 I in vivo


title: SF101 I

source_name: ΔaroA


title: Wt1


title: Wt2


title: CI224_M replicate 2

city: Hanover

first: Deborah

middle: A

last: Hogan

state: NH

institute: Dartmouth College

data_processing:
Reads were trimmed for adaptor sequences and mapped to the PAO1 whole genome with CLC Genomics Workbench platform (v8.5.1) using default parameters.
Mapped reads were quantile normalized to all reads using CLC Genomics Workbench.
Genome_build: PAO1 NC_002516
Supplementary_files_format_and_content: Processed data file is a data matrix that contains raw unique gene reads and quantile normalized reads.

organism: Pseudomonas aeruginosa

growth_protocol: P. aeruginosa strains were grown in liquid LB-Lennox for 8 h at 37˚C.

extract_protocol:
Samples were lyophilized and lysed (5 x 1 minute with 2 minutes on ice between rounds) using a mixture of 0.1 mm, 0.5 mm and 1 mm beads in a Biospec Mini-Beadbeater-16 (Biospec Products, Bartlesville, OK). Samples were then re-suspended in TRI-Reagent (Zymo Research Corporation, Irvine, CA). RNA was extracted using Direct-zol RNA MiniPrep kits (Zymo Research Corporation, Irvine, CA) according to the manufacturer’s instructions.
Directional RNAseq libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit with unique TruSeq indexes.

tag: sample type

value: Cystic fibrosis clinical isolate

tag: phenotype

value: Mucoid phenotype


title: FRD1 replicate 2

value: Clinical isolate


title: CI224_M replicate 1


title: E3KO Rep 1

tag: strain


title: SF101 II


title: FRD1 replicate 1


title: ssrB InSPI2

city: Liverpool

first: Jay

last: Hinton

address: Crown Street

department: Institute of Integrative Biology

institute: University of Liverpool

data_processing:
Reads were de-multiplexed and poly-A tails were removed.
Sequence reads were then mapped against the S. Typhimurium 4/74 reference genome using Segemehl with accuracy set to 100%.
To increase mapping quality, unmapped reads were sequentially truncated by one nucleotide from the end of the read and were mapped again. This process was iterated until a minimal read length of 20 nucleotides or until a read mapped into a single location on the chromosome.
Genome_build: RefSeq Genome Accession: PRJNA56087 ID: 56087. Salmonella enterica subsp. enterica serovar Typhimurium str. 4/74. Richardson EJ et al., "Genome sequences of Salmonella enterica serovar typhimurium, Choleraesuis, Dublin, and Gallinarum strains of well- defined virulence in food-producing animals.", J Bacteriol, 2011 Apr 8;193(12):3162-3.
Supplementary_files_format_and_content: Wig files (.wig) are provided showing uniquely mapped sequence reads. Ready to load into Jbrowse. The file consists of two columns showing nucleotide position on the chromosome and number of reads mapped at each location. "Plus" and "Minus" refer to the two strands of the Salmonella chromosome

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

source_name: Total RNA from bacteria

growth_protocol: Wild-type and mutant cells were grown overnight in 4 ml Lennox (L-) broth (10 g/l tryptone, 5 g/l yeast extract, 5 g/l NaCl) and diluted the next morning (1:1,000) in 250 ml flasks in 25 ml L-broth and grown at 37°C and 220 rpm. A New Brunswick Innova 3400 water bath was used to grow all agitated bacterial cultures prior to RNA isolation. Bacteria were grown to mid exponential growth phase (MEP; OD600 0.3), intermediate exponential growth phase (IEP; OD600 0.8), early stationary phase (ESP, OD600 2.0) and late stationary phase (LSP, OD600 2.0 + 6h) and RNA was isolated. For growth in phosphate carbon nitrogen (PCN) minimal medium, wild-type and mutant cells were grown over night in 4 ml L-broth and the next morning 1 ml culture was washed three times with, and then diluted 1:500 in 250 ml flasks in 25 ml of, SPI2-inducing PCN (pH5.8, 0.4 mM Pi). RNA was isolated at OD600 of 0.3.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and digested with DNase I.
cDNA libraries were constructed by Vertis Biotechnologie AG (Freising) using an in-house protocol. Total RNA (DNase I digested) was fragmented by ultrasound (4 pulses of 30s at 4°C). 3′ ends were subjected to poly(A)-tailing using poly(A) polymerase, pyrophosphate groups were removed from the 5′ terminus using tobacco acid pyrophosphatase (TAP), and an RNA adapter was ligated to the 5′ end of the RNA. First-strand synthesis was performed using an oligo(dT) adapter and M-MLV-RNaseH-reverse transcriptase, followed by PCR amplification of cDNA using high-fidelity DNA polymerase to ∼20–30 ng/μL. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis.

tag: growth conditions

value: Growth in PCN medium to OD600 0.3 (pH 5.8, 0.4 mM Pi)

value: ST4/74 delta-ssrB


title: ssrA/B InSPI2

value: ST4/74 delta-ssrA/B


title: ssrA InSPI2

value: ST4/74 delta-ssrA


title: ompR/envZ InSPI2

value: ST4/74 delta-ompR/envZ


title: SF102 II


title: phoP/Q InSPI2

value: ST4/74 delta-phoP/Q


title: phoB/R InSPI2

value: ST4/74 delta-phoB/R


title: slyA InSPI2

value: ST4/74 delta-slyA


title: hilD InSPI2

value: ST4/74 delta-hilD


title: NSUN3UV

city: Goettingen

first: Markus

middle: T.

last: Bohnsack

address: Humboldtallee 23

department: Institute for Molecular Biology

institute: Goettingen University

data_processing:
Sequencing reads for each experimental sample were demultiplexed using their 5' barcode sequences and barcodes were then clipped.
Reads of identical sequence that contained identical 5-nucleotide random barcodes were collapsed.
Reads were trimmed and quality controlled using flexbar and aligned to the human genome (Ensembl GRCh 37.75) by Bowtie2 (version 2.2.4).
Genome_build: Ensembl GRCh 37.75
Supplementary_files_format_and_content: We have determined the read distribution between the different RNA classes. The enrichment of mitochondrial sequences in the NSUN3 experiments, we analysed the distribution of reads within these and, as controls, we have used cytoplasmic tRNAs. Further analysis was done biochemically by "wet-lab" experiments. The corresponding data analysis files for the distribution of reads in mitochondrial RNAs and tRNAs have been collected and uploaded.

source_name: HEK293 cell culture

growth_protocol: Flp-In T-Rex HEK293 cells expressing His-FLAG-tagged NSUN3 or the His-FLAG tag only were grown at 37°C in 5% CO2 in high glucose DMEM supplemented with 10% foetal bovine serum, 2 mM L-glutamine.

extract_protocol:
Crosslinked RNA-protein complexes were purified under denaturing conditions and RNAs associated with His-FLAG-tagged proteins were trimmed (Bohnsack et al., 2012).
3' and 5' adapters were ligated and a cDNA library was prepared by reverse transcription and amplified by PCR (Bohnsack et al., 2012).

treatment_protocol: Expression of tagged proteins was induced by addition of tetracycline for 24 h before crosslinking/harvesting. For 5-AzaC CRAC cells were treated with 4 μM 5-azacytidine for 14 h prior to harvesting. For UV CRAC, cells were crosslinked as previously described (Sloan et al., 2015).

tag: antibody

value: anti-FLAG


title: rpoS LSP

value: Growth in Lennox broth to OD600 2.0 + 6hr

value: ST4/74 delta-rpoS


title: WT InSPI2 2

description: biological replicate

value: wild-type ST4/74


title: NSUN3Aza

data_processing:
Sequencing reads for each experimental sample were demultiplexed using their 5' barcode sequences and barcodes were then clipped.
Reads of identical sequence that contained identical 5-nucleotide random barcodes were collapsed.
Reads were trimmed and quality controlled using flexbar and aligned to the human genome (Ensembl GRCh 37.75) by Bowtie2 (version 2.2.4).
Genome_build: Ensembl GRCh 37.75
Supplementary_files_format_and_content: We have determined the read distribution between the different RNA classes. Due to the enrichment of mitochondrial sequences in the NSUN3 experiments, we analysed the distribution of reads within these and, as controls, we have used cytoplasmic tRNAs. Further analysis was done biochemically by "wet-lab" experiments. The corresponding data analysis files for the distribution of reads in mitochondrial RNAs and tRNAs have been collected and uploaded.


title: WT InSPI2 1

description: biological replicate


title: FlagUV

value: UV


title: S5_LV_36yo_Male_AGO2_bound_RNA

city: Iowa City

first: Ryan

last: Boudreau

state: IA

address: 500 Newton Rd

department: Internal Medicine

institute: University of Iowa

description: Isolated from upper band on autoradiogram, corresponding to Ago2-miRNA-target mRNA complexes.

data_processing:
Basecalls performed using CASAVA version 1.8  (ASCII offset = 33)
Adapter trimming (removed first 5 nts and trimmed remaining sequence based on alignment to 3' linker sequence, GTTACGCTCGCCGTAGAGG, allowing up to 2 mistmates)
Removed reads which align to mature human microRNAs annotated in miRBase (allowing up to 1 mismatch)
Aligned remaining trimmed reads to the human genome (hg19) using Bowtie (allowing up to 2 mismatches)
Peak-calling: 1) determine positional read coverage per sample using zero-truncated negative binomial model, 2) combine p-values across samples using Fisher's method, 3) calculate Bonferroni adjusted p-values.
Genome_build: hg19
Supplementary_files_format_and_content: BED file of significant Ago2 binding clusters (ie. peaks having Bonferroni corrected p-value < 0.05). Column 4 is formatted as: PeakID|Coordinates|P-value. Column 5 is the average peak height across the 6 samples.

source_name: left ventricle_male_AGO2_bound_RNA

extract_protocol:
Phenol-chloroform extraction of Ago2-bound RNAs recovered from human brain tissues by  crosslinked immunoprecipiation with anti-Ago2 antibody.
Ago2 HITS-CLIP performed as previously described by Chi et al Nature. 2009 Jul 23;460(7254):479-86 using an anti-Ago2 polyclonal antibody and some additional modifications, described in Boudreau et al  Neuron. 2014 Jan 22;81(2):294-305

tag: age (yrs)

tag: height (m)

tag: weight (kg)

tag: Sex

value: male

tag: ejectionfraction (%)

tag: enddiastolicdiameter

tag: pulmonarycapillarywedgepressure

tag: cardiacoutput

tag: cardiacindex

value: Left ventricle

tag: molecule subtype

value: Ago2-bound RNA


title: S6_LV_61yo_Male_AGO2_bound_RNA

tag: tissue


title: WT LSP 2

description: biological replicate


title: WT LSP 1

description: biological replicate


title: S1_LV_54yo_Male_AGO2_bound_RNA


title: fur ESP

value: Growth in Lennox broth to OD600 2.0

value: ST4/74 delta-fliZ


title: S3_LV_36yo_Male_AGO2_bound_RNA


title: S2_LV_25yo_Male_AGO2_bound_RNA


title: fliZ ESP

value: ST4/74 delta-barA/sirA


title: hfq ESP

value: ST4/74 delta-hfq


title: barA/sirA ESP

value: ST4/74 delta-fur


title: hilD ESP


title: E2-rep1

first: Mathieu

last: Lupien

address: 101 College street

department: Princess Margaret Cancer Centre

institute: University Health Network

data_processing:
Illumina bcl2fastq v1.8.4 to convert bcl files to fastq files
ChIP-seq reads were aligned to the Hg19 genome assembly using Bowtie v2.0.5
Peaks were called by MACS2.0
Genome_build: Hg19

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were grown in DMEM supplemented with 10% FBS and 1% P/S

extract_protocol:
Chromatin was sonicated by biorupter and immunoprecipitated with anti-ZNF143 antibody. DNA was extracted using MinElute PCR purification kit (Qiagen 28004).
Library construction was performed using New England Biolabs ChIP-seq library prep reagent set (E6200S)

treatment_protocol: MCF-7 cells were starved of estrogen for 48hrs, then stimulated with 10 μM 17β oestradiol (E2) or vehicle (EtOH) for 45 minutes prior to cross-linking

tag: cell line

tag: chip-antibody

value: ZNF143 (Novus Biologicals H00007702-M01)

tag: treatment

value: 10 uM 17-beta oestradiol (E2)


title: E2-rep2


title: Vehicle-rep2

value: vehicle


title: WT ESP 2

description: biological replicate

tag: strain


title: rpoE LSP

tag: growth conditions

value: ST4/74 delta-rpoE


title: WT ESP 1

description: biological replicate


title: siZNF143_E2_Rep2

description:
cuffdiff_E2.diff
cuffdiff_siZNF143.diff

data_processing:
Illumina bcl2fastq v1.8.4 to convert bcl files to fastq files
Sequenced reads were mapped to hg19 using TopHat2 with default parameters.
Cufflinks suite was used to assemble transcripts, estimate transcript abundance and test for differential expression. Differential expression was called using CuffDiff2 with the parameters: -u to correct for reads mapping to more than one location and -b to correct for fragment bias.
Genome_build: Hg19

extract_protocol:
RNA was harvested using Qiagen's Rneasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: MCF-7 cells were transfected with siZNF143 (Ambion siRNA ID: s15194) or a scrambled control siRNA and starved of oestrogen for 48hrs. They were stimulated with 10 nM 17-beta oestradiol for 3 hours prior to RNA extraction.

tag: transfection

value: 10 uM 17-beta oestradiol for 3 hours


title: hilE IEP

value: Growth in Lennox broth to OD600 0.8

value: ST4/74 delta-hilE


title: siZNF143_vehicle_Rep2

description:
cuffdiff_veh.diff
cuffdiff_siZNF143.diff


title: hilC IEP

value: ST4/74 delta-hilC


title: siZNF143_E2_Rep1

description:
cuffdiff_E2.diff
cuffdiff_siZNF143.diff


title: hilA IEP

value: ST4/74 delta-hilA


title: WT MEP

value: Growth in Lennox broth to OD600 0.3

value: wild-type ST4/74


title: S4_LV_29yo_Male_AGO2_bound_RNA

tag: age (yrs)

value: male

value: Left ventricle

value: Ago2-bound RNA


title: RISC-IP ΔmiR Ad2

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

description: RISC-enriched RNA

data_processing:
Sequence reads were trimmed and filtered for low quality sequences using the RawReadManipulator (unpublished)
RISC-IP reads were mapped using bwa-0.7.12. For RNA-Seq reads STAR 2.4.0 was used. STAR index was build using a hybrid gtf version of the human gencode 19 and EBV AJ507799.2
Read counts were created using FeatureCounts (subread v1.4.6) and the hybrid hg19_ebv gtf.
Genome_build: Human hg19 and EBV AJ507799.2
Supplementary_files_format_and_content: text file with Feature count ensemble gene or Feature count ensemble transcript

organism:
Homo sapiens
human gammaherpesvirus 4

source_name: Human primary B cells

growth_protocol: B-lymphocytes were prepared from adenoid biopsies, infected with EBV, incubated for 5 days with Cyclosporin A.

extract_protocol:
Samples were disolved in Trizol and Direct-Zol RNA kit (Zymo Research) were used for RNA extraction.
For RISC-IP, RNAs were polyA-tailed, ligated with an RNA adapter at 5’-phosphates to facilitate Illumina TruSeq sequencing, and  libraries were prepared with a oligo-dT primer.

treatment_protocol: EBV infection was performed with MOI of 0.1 GRU (Green Raji Unit).

tag: ebv strain

value: deltamiR maxiEBV

tag: cell type

value: EBV-infected primary B cells

tag: days post infection

tag: organism

value: mixed sample:human primary B cells and EBV


title: siCtl_E2_Rep2

description:
cuffdiff_E2.diff
cuffdiff_siCtl.diff

value: scrambled control siRNA


title: Vehicle-rep1

value: ZNF143 (Novus Biologicals H00007702-M01)


title: siZNF143_E2_Rep3

description:
cuffdiff_E2.diff
cuffdiff_siZNF143.diff


title: RISC-IP ΔmiR Ad1

description: RISC-enriched RNA


title: RISC-IP ΔmiR Ad5

description: RISC-enriched RNA


title: RISC-IP ΔmiR Ad6

description: RISC-enriched RNA


title: siCtl_E2_Rep1

description:
cuffdiff_E2.diff
cuffdiff_siCtl.diff


title: RISC-IP ΔmiR Ad4

description: RISC-enriched RNA


title: siZNF143_vehicle_Rep3

value: vehicle


title: siZNF143_vehicle_Rep1


title: RISC-IP ΔmiR Ad3

description: RISC-enriched RNA


title: WT IEP


title: RISC-IP wt/B95-8 Ad5

description: RISC-enriched RNA

value: wt/B95-8 maxiEBV


title: siCtl_vehicle_Rep3

description:
cuffdiff_veh.diff
cuffdiff_siCtl.diff


title: siCtl_vehicle_Rep2

description:
cuffdiff_veh.diff
cuffdiff_siCtl.diff


title: dam MEP

value: ST4/74 delta-dam


title: RISC-IP wt/B95-8 Ad4

description: RISC-enriched RNA


title: RISC-IP wt/B95-8 Ad6

description: RISC-enriched RNA


title: siCtl_E2_Rep3

description:
cuffdiff_E2.diff
cuffdiff_siCtl.diff

value: 10 uM 17-beta oestradiol for 3 hours


title: RISC-IP wt/B95-8 Ad2

description: RISC-enriched RNA


title: hilD IEP

value: Growth in Lennox broth to OD600 0.8

value: ST4/74 delta-hilD


title: RISC-IP wt/B95-8 Ad1

description: RISC-enriched RNA


title: RNA-Seq ΔmiR Ad4

extract_protocol:
Samples were disolved in Trizol and Direct-Zol RNA kit (Zymo Research) were used for RNA extraction.
For total RNA, rRNA were depleted and cDNA libraries were prepared using random primers.


title: RNA-Seq ΔmiR Ad5


title: RNA-Seq ΔmiR Ad2


title: RNA-Seq ΔmiR Ad1


title: RISC-IP wt/B95-8 Ad3

description: RISC-enriched RNA


title: RNA-Seq ΔmiR Ad3


title: siCtl_vehicle_Rep1

description:
cuffdiff_veh.diff
cuffdiff_siCtl.diff


title: RNA-Seq wt/B95-8 Ad5


title: RNA-Seq wt/B95-8 Ad4


title: RNA-Seq wt/B95-8 Ad1


title: RNA-Seq wt/B95-8 Ad2


title: Mock 36 hs replicate A

city: Ciudad Autonoma de Buenos Aires

first: Andrea

last: Gamarnik

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

description: processed data column: Mock36A

data_processing:
Base
Sequence reads were mapped to Homo sapiens UCSC hg19  genome using TopHat v2.1.1 with default parameters
Count tables for different feature levels were obtained from bam files using custom R v3.0.2 scripts.
Differential gene expression was estimated using edgeR package version 3.4.2 and resulting p-values were adjusted using false discovery rate (fdr) criterion.
The transcriptome was partitioned into subgenic joint features called bins and labeled as exon-bin, intron-bin or alternative-splicing (AS) bins. In addition AS-bins were further classified as exon skipping (ES), 5’ or 3’ alternative (5´alt, 3´alt), intron retention (IR) or multiple. Bins from monoexonic genes, with mean count values lower than 5 reads per condition and rd bin / rd gen lower than 0.05 were discarded.
COPIAR DE MyM
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Comprehensive spreadsheets with the results of the analysis of differential splicing detailed above

source_name: A549_Mock 36 hs

growth_protocol: Standard conditions for A549 infected cells

extract_protocol:
mRNA was purified using Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells where infected with Dengue virus 2 or Mock 1 h at 37°C (MOI 10)

tag: infected with

value: mock

tag: time point

value: 36 hours post infection


title: Mock 36 hs replicate B

description: processed data column: Mock36B


title: Mock 36 hs replicate C

description: processed data column: Mock36C


title: Mock 24 hs replicate A

description: processed data column: M24A

source_name: A549_Mock 24 hs

value: 24 hours post infection


title: Mock 24 hs replicate C

description: processed data column: M24C


title: Dengue virus 36 hs replicate B

description: processed data column: DV36B

source_name: A549_Dengue virus 36 hs

value: Dengue virus 2


title: Mock 24 hs replicate B

description: processed data column: M24B


title: Dengue virus 24 hs replicate C

description: processed data column: D24C

source_name: A549_Dengue virus 24 hs


title: Dengue virus 36 hs replicate A

description: processed data column: DV36A


title: light pulse rep 1

city: Buenos Aires

first: Marcelo

last: Yanovsky

state: Ciudad Autonoma de Buenos Aires

institute: Fundación Instituto Leloir. IIBBA- CONICET

data_processing:
Basecalling done with Bustard Illumina Pipelline
Sequence reads were mapped to Arabidopsis thaliana TAIR10 genome using TopHat v2.0.9 with default parameters, except of maximum intron length set in 5000
Count tables for different feature levels were obtained from bam files using custom R v3.1 scripts.
Genome_build: Arabidopsis thaliana TAIR10

source_name: pool of tissues

growth_protocol: Wild type seeds, Columbia ecotype, were sown onto Murashige and Skoog medium containing 0.8% agar, stratified for 4 days in the dark at 4ºC and then, transferred to 12 hour ligth / 12 hour dark cycles at 22°C (50 μmol.m−2.s−1).

extract_protocol:
RNA was extracted with RNeasy Plant Mini Kit (QIAGEN) following the manufacturer’s protocols. To estimate the concentration and quality of samples, NanoDrop 2000c (Thermo Scientific) and the Agilent 2100 Bioanalyzer (Agilent Technologies) with the Agilent RNA 6000 NanoKit were used, respectively
Libraries were prepared using 3 μg of total RNA and following the TruSeq RNA Sample Preparation Guide (Illumina), except for the enrichment step, where only 12 cycles of PCR were performed. Library validation included size and purity assessment with the Agilent 2100 Bioanalyzer and the Agilent DNA 1000 kit (Agilent Technologies).

treatment_protocol: After 9 days, in the middle of the night (ZT18), seedlings were irradiated with a two hours pulse light (treated group) or kept in darkness (control group) and harvested at the same time. Nine-day-old seedlings were treated with a two-hours pulse light in the middle of the night or kept in darkness. Both groups were harvested at the same time

tag: ecotype

value: Col

value: light pulse


title: light pulse rep 3


title: light pulse rep 2


title: RNA-Seq ΔmiR Ad6

value: deltamiR maxiEBV


title: dark control rep 3

value: dark control


title: Dengue virus 24 hs replicate B

description: processed data column: D24B


title: RNA-Seq wt/B95-8 Ad6

value: EBV-infected primary B cells

value: mixed sample:human primary B cells and EBV


title: S12_3

city: Chapel Hill

first: Peggy

last: Cotter

state: NC

address: 125 Mason Farm Rd, 6205 Marsico

institute: University of North Carolina

description: processed data files: WTvsS12, S12vsEKA

data_processing:
Base calling and initial data processing were performed using the Illumina CASAVA pipeline (v.1.8.2).
Reads were mapped to the Burkholderia thailandensis E264 reference genome using CLC Genomics Workbench v.7 using the default settings, except with calculation of RPKM for genes without transcripts.
RPKMs for each gene were compared pairwise between all three strains using CLC Genomics Workbench v.7.
Transcripts having significant differences in abundance between strains were identified using the empirical analysis of differential gene expression (DGE) test with an FDR-corrected cutoff of p<0.05 using CLC Genomics Workbench v.7.
Genome_build: Burkholderia thailandensis E264; http://www.ncbi.nlm.nih.gov/assembly/GCF_000012365.1
Supplementary_files_format_and_content: Excel sheets for pairwise comparisons between strains (each in triplicate). Transcripts with significant (p<0.05) differences in RPKM value are listed, along with the RPKM value for each replicate, average fold change, and p value.

organism: Burkholderia thailandensis

source_name: S12_bacterial cells

growth_protocol: Overnight cultures (in low-salt LB medium, 37°C) were washed in PBS and inoculated to OD600=0.02 in 2 ml M63 minimal medium. Bacteria were cultured at 37°C with aeration for 18 h.

extract_protocol:
Bacteria were pelleted and total RNA extracted using TRIzol reagent.
Libraries were prepared using Illumina RNA TruSeq Stranded reagents/protocol with rRNA depletion using bacterial RiboZero reagents/protocol.

tag: genotype/variation

tag: growth medium

value: M63 minimal medium


title: dark control rep 2


title: S12_2

description: processed data files: WTvsS12, S12vsEKA


title: RNA-Seq wt/B95-8 Ad3


title: dark control rep 1


title: Dengue virus 24 hs replicate A

description: processed data column: D24A


title: EKA_3

description: processed data files: WTvsEKA, S12vsEKA

source_name: EKA_bacterial cells

value: BtEKA


title: S12_1

description: processed data files: WTvsS12, S12vsEKA


title: EKA_2

description: processed data files: WTvsEKA, S12vsEKA


title: EKA_1

description: processed data files: WTvsEKA, S12vsEKA


title: C57BL/6 mice

description: ATAC-seq

source_name: Cortical thymic epithelial cells

value: Cortical thymic epithelial cells

tag: genotype

value: C57BL/6 mice


title: Input ChIP-seq

description: ChIP-seq

source_name: Thymic epithelial cells

value: Thymic epithelial cells

value: Homozygous Foxn1 BAC transgenic mice on nude background


title: WT_3

description: processed data files: WTvsEKA, WTvsS12

source_name: WT_bacterial cells

value: wild-type


title: WT_1

description: processed data files: WTvsEKA, WTvsS12


title: Foxn1 ChIP-seq

description: ChIP-seq


title: S2_H3R2Me2A

status: Public on Aug 08 2016

city: New York

first: Eric

last: Nestler

state: NY

address: 1425 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

data_processing:
CASAVA 1.8: /usr/local/bin/configureBuild.pl -id Aligned/C1_H3R2Me2A_BAM/Sample_C1_H3R2Me2A_Lib -ref /genomes/Mus_musculus/UCSC/mm9/Sequence/Chromosomes/ --targets sort bam
IGV Tools 2.3.57: igvtools count C1_H3R2Me2A.bam C1_H3R2Me2A.tdf mm9
pipeline on github: https://github.com/ny-shao/pipelines_for_ChIP-seq_analysis/tree/master/Differential_enrichment_detection/diffReps
Genome_build: mm9
Supplementary_files_format_and_content: tdf

source_name: nucleus accumbens

growth_protocol: For all experiments, 7 to 9-week-old C57BL/6J male mice (25-30 g; The Jackson Laboratory, Bar Harbor, ME, USA) were housed five per cage in a colony room set at constant temperature (23°C) on a 12 hr light/dark cycle (lights on from 0700 to 1900 hr) with ad libitum access to food and water.

extract_protocol:
3 fully independent biological replicates for saline and for cocaine treatment were obtained for H3R2me2a. For each ChIP-seq replicate, bilateral 14-gauge NAc punches were pooled from 10 mice. Tissue was lightly fixed to cross-link DNA with associated proteins, and the material was further sheared (Bioruptor to obtain mostly 100-300 bps fragments) and immunoprecipitated using sheep anti-rabbit magnetic beads (Invitrogen) conjugated to an antibody that specifically recognizes H3R2me2a (Millipore 04-808) and which we validated extensively.
Immunoprecipitated DNA were prepared for ChIP-seq using an Illumina kit according to the manufacturer’s instructions. Each sample underwent end repair followed by addition of an A base to the 3′ end. Proprietary adapters were then ligated to the ends, followed by size selection on a 2% agarose gel. The range of excision was 200–300 bp. After DNA clean up, samples were amplified with 21 cycles of PCR. Amplification and size selection were confirmed with a BioAnalyzer. The resulting libraries were sequenced on an Illumina HiSeq 2500 with 100 bp read length.

treatment_protocol: Animals were randomly assigned to experimental groups to which experimenters were blinded. For repeated cocaine treatment, animals received daily intraperitoneal (IP) injections for seven consecutive days of cocaine (Sigma-Aldrich, St. Louis, MO, USA) at 20 mg/kg body weight ('repeated cocaine'). Mice were used 24 hr after the final injection. Control mice for all groups received daily saline injections for seven days.

tag: tissue

value: brain

tag: brain region

value: nucleus accumbens

tag: gender

value: male

value: Saline

tag: antibody manufacturer & catalog number

value: Millipore 04-808


title: S3_H3R2Me2A

tag: strain

tag: treatment


title: C3_H3R2Me2A

value: Cocaine


title: C1_H3R2Me2A


title: S1_H3R2Me2A


title: C2_H3R2Me2A


title: Dengue virus 36 hs replicate C

description: processed data column: DV36C

tag: cell line

value: Dengue virus 2

value: 36 hours post infection


title: Kupffer ID3+/- 3

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

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

data_processing:
alignment using rnaStar
quantification using HTSeq v0.5.4
normalization and differential expression analysis using DESeq v1.18.0 in  R v3.1.2
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated text file

source_name: Kupffer cells, ID3 +/-

extract_protocol:
Tissues were included in cold PBS and mechanically disrupted under a 100um filter
SMART-seq V4 (Clonetech) ultra low input RNA kit was used for library preparation. 10 ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR.

value: Kupffer cell

value: liver

value: het


title: yol pro e10.25_2

description: mouse EMPs from yolksac at day E10.25

data_processing:
After de-multiplexing and adapter removal, we aligned reads using Bowtie v 1.1.1 (parameters: -q -p 6 -a -m 100 --minins 0 --maxins 5000 --fr --sam --chunkmbs 200) to the Ensembl cDNA reference. We used BitSeq (v 1.12.0) to quantify transcript levels.
Raw read counts were loaded into R and all transcripts that were detected with at least 50 reads in at least four samples (n = 37,521), were processed with DESeq2's variance stabilizing transformation to output normalized read counts, which we subsequently further adjusted by accounting for batch effect with ComBat.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated text file

source_name: yolksac EMP, E10.25

extract_protocol:
SMART-Seq2
SMART-Seq2

value: EMP

value: yolksac

tag: tissue group

value: Yolksac

tag: time


title: Kupffer ID3-/- 2

source_name: Kupffer cells, ID3 -/-

tag: cell type

value: ko


title: Kupffer ID3-/- 3


title: yol pro e9_1

description: mouse EMPs from yolksac at day E9

source_name: yolksac EMP, E9


title: yol pre e9.5_1

description: mouse pMacs from yolksac at day E9.5

source_name: yolksac pMac, E9.5

value: pMac


title: yol mac e10.5_3

description: mouse Macs from yolksac at day E10.5

source_name: yolksac Mac, E10.5

value: Mac


title: yol pre e10.25_1

description: mouse pMacs from yolksac at day E10.25

source_name: yolksac pMac, E10.25


title: Kupffer ID3+/- 2


title: yol pre e9.5_2

description: mouse pMacs from yolksac at day E9.5


title: yol mac e10.5_2

description: mouse Macs from yolksac at day E10.5


title: yol mac e10.25_4

description: mouse Macs from yolksac at day E10.25

source_name: yolksac Mac, E10.25


title: yol pro e10.25_1

description: mouse EMPs from yolksac at day E10.25


title: yol mac e10.25_2

description: mouse Macs from yolksac at day E10.25


title: ski mac p8_2

description: mouse Macs from skin at day P8

source_name: skin Mac, P8

value: skin

value: Caudal / skin


title: ski mac p2_3

description: mouse Macs from skin at day P2

source_name: skin Mac, P2


title: yol mac e10.25_1

description: mouse Macs from yolksac at day E10.25


title: yol mac e10.25_3

description: mouse Macs from yolksac at day E10.25


title: ski mac p21_1

description: mouse Macs from skin at day P21

source_name: skin Mac, P21


title: yol mac e10.5_1

description: mouse Macs from yolksac at day E10.5


title: ski mac p2_1

description: mouse Macs from skin at day P2


title: yol pro e9_2

description: mouse EMPs from yolksac at day E9


title: Kupffer ID3+/- 1


title: ski mac e14.5_2

description: mouse Macs from skin at day E14.5

source_name: skin Mac, E14.5


title: ski mac e18.5_1

description: mouse Macs from skin at day E18.5

source_name: skin Mac, E18.5


title: lun mac p21_2

description: mouse Macs from lung at day P21

source_name: lung Mac, P21

value: lung

value: Lung


title: lun mac p8_2

description: mouse Macs from lung at day P8

source_name: lung Mac, P8


title: lun mac p2_2

description: mouse Macs from lung at day P2

source_name: lung Mac, P2


title: lun mac e18.5_1

description: mouse Macs from lung at day E18.5

source_name: lung Mac, E18.5


title: lun mac e18.5_2

description: mouse Macs from lung at day E18.5


title: lun mac e14.5_2

description: mouse Macs from lung at day E14.5

source_name: lung Mac, E14.5


title: lun mac e14.5_1

description: mouse Macs from lung at day E14.5


title: liv pro e10.25_3

description: mouse EMPs from liver at day E10.25

source_name: liver EMP, E10.25

value: Liver


title: liv mac p8_2

description: mouse Macs from liver at day P8

source_name: liver Mac, P8


title: ski mac p21_2

description: mouse Macs from skin at day P21


title: liv pre e10.25_1

description: mouse pMacs from liver at day E10.25

source_name: liver pMac, E10.25


title: ski mac p8_1

description: mouse Macs from skin at day P8


title: liv mac p8_1

description: mouse Macs from liver at day P8


title: liv mac p2_1

description: mouse Macs from liver at day P2

source_name: liver Mac, P2


title: liv mac p2_2

description: mouse Macs from liver at day P2


title: WT_2

description: processed data files: WTvsEKA, WTvsS12

source_name: WT_bacterial cells

value: wild-type

value: M63 minimal medium


title: ski mac e18.5_2

description: mouse Macs from skin at day E18.5


title: liv mac e14.5_2

description: mouse Macs from liver at day E14.5

source_name: liver Mac, E14.5


title: liv mac e18.5_1

description: mouse Macs from liver at day E18.5

source_name: liver Mac, E18.5


title: ski mac e14.5_1

description: mouse Macs from skin at day E14.5


title: liv mac e12.5_1

description: mouse Macs from liver at day E12.5

source_name: liver Mac, E12.5


title: liv mac e12.5_2

description: mouse Macs from liver at day E12.5


title: lun mac p2_1

description: mouse Macs from lung at day P2


title: liv mac e10.5_2

description: mouse Macs from liver at day E10.5

source_name: liver Mac, E10.5


title: liv pro e10.25_2

description: mouse EMPs from liver at day E10.25


title: liv mac e10.5_1

description: mouse Macs from liver at day E10.5


title: liv mac e10.25_2

description: mouse Macs from liver at day E10.25

source_name: liver Mac, E10.25


title: liv mac e10.25_1

description: mouse Macs from liver at day E10.25


title: lim mac e12.5_2

description: mouse Macs from limbs at day E12.5

source_name: limbs Mac, E12.5

value: limbs


title: lim mac e12.5_1

description: mouse Macs from limbs at day E12.5


title: lim mac e10.5_2

description: mouse Macs from limbs at day E10.5

source_name: limbs Mac, E10.5


title: liv mac p21_2

description: mouse Macs from liver at day P21

source_name: liver Mac, P21


title: lim pre e10.25_1

description: mouse pMacs from limbs at day E10.25

source_name: limbs pMac, E10.25


title: lim mac e10.25_1

description: mouse Macs from limbs at day E10.25

source_name: limbs Mac, E10.25


title: kid mac p8_2

description: mouse Macs from kidney at day P8

source_name: kidney Mac, P8

value: kidney

value: Kidney


title: lim mac e10.25_2

description: mouse Macs from limbs at day E10.25


title: lim mac e10.5_1

description: mouse Macs from limbs at day E10.5


title: kid mac p8_1

description: mouse Macs from kidney at day P8


title: liv mac e18.5_2

description: mouse Macs from liver at day E18.5

value: liver


title: kid mac p2_1

description: mouse Macs from kidney at day P2

source_name: kidney Mac, P2


title: kid mac p21_2

description: mouse Macs from kidney at day P21

source_name: kidney Mac, P21


title: liv mac p21_1

description: mouse Macs from liver at day P21


title: kid mac e18.5_1

description: mouse Macs from kidney at day E18.5

source_name: kidney Mac, E18.5


title: kid mac p2_2

description: mouse Macs from kidney at day P2


title: ski mac p2_2

description: mouse Macs from skin at day P2

source_name: skin Mac, P2


title: cau pre e9.5_3

description: mouse pMacs from caudal at day E9.5

source_name: caudal pMac, E9.5

value: caudal


title: kid mac e14.5_2

description: mouse Macs from kidney at day E14.5

source_name: kidney Mac, E14.5


title: kid mac p21_1

description: mouse Macs from kidney at day P21


title: kid mac e14.5_1

description: mouse Macs from kidney at day E14.5


title: bra pre e9.5_4

description: mouse pMacs from brain at day E9.5

source_name: brain pMac, E9.5

value: brain

value: Head / brain


title: cau pre e9.5_1

description: mouse pMacs from caudal at day E9.5


title: bra pre e9.5_3

description: mouse pMacs from brain at day E9.5


title: bra pre e9.5_1

description: mouse pMacs from brain at day E9.5


title: bra pre e9.5_2

description: mouse pMacs from brain at day E9.5


title: bra pre e10.25_1

description: mouse pMacs from brain at day E10.25

source_name: brain pMac, E10.25


title: bra mac p8_3

description: mouse Macs from brain at day P8

source_name: brain Mac, P8


title: bra mac p21_1

description: mouse Macs from brain at day P21

source_name: brain Mac, P21


title: bra mac p21_2

description: mouse Macs from brain at day P21


title: bra mac p8_2

description: mouse Macs from brain at day P8


title: bra mac p2_1

description: mouse Macs from brain at day P2

source_name: brain Mac, P2


title: bra mac p2_2

description: mouse Macs from brain at day P2


title: kid mac e18.5_2

description: mouse Macs from kidney at day E18.5


title: bra mac e12.5_2

description: mouse Macs from brain at day E12.5

source_name: brain Mac, E12.5


title: bra mac e14.5_1

description: mouse Macs from brain at day E14.5

source_name: brain Mac, E14.5


title: bra mac e18.5_1

description: mouse Macs from brain at day E18.5

source_name: brain Mac, E18.5


title: bra mac e14.5_2

description: mouse Macs from brain at day E14.5


title: bra mac e12.5_1

description: mouse Macs from brain at day E12.5


title: bra mac e10.25_3

description: mouse Macs from brain at day E10.25

source_name: brain Mac, E10.25


title: bra mac e10.25_1

description: mouse Macs from brain at day E10.25


title: cau pre e9.5_2

description: mouse pMacs from caudal at day E9.5


title: bra mac e10.25_2

description: mouse Macs from brain at day E10.25


title: bra mac e10.5_1

description: mouse Macs from brain at day E10.5

source_name: brain Mac, E10.5