title: ZF4 cells with Edwardsiella tarda infection

city: Qingdao

first: Zejun

last: Zhou

address: 7 Nanhai Road

institute: Institute of Oceanology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCz10 whole genome using Tophat package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. Tophat allows multiple alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.Tophat build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The aligned read files were processed by Cufflinks, which uses the normalized RNA-seq fragement counts to measure the relative abundances of the tianscripts. The unit of measurement is Fragment Per Kilobase of exon per Million fragments mapped (FPKM).The reference zebrafish genome annotation file used in Cufflinks was downloaded from the NCBI database. Cufflink was used to de novo assemble the transcripiome at first; The second ,Cuffmerge was used to comerge all transcripts of samples to generate unique transcripts. The downloaded zebrafish genome file was passed to Cuffdiff along with the original alinment (SAM) files produced by Tophat. Cuffdiff re-estimates the abundance of the transcripts listed in the zebrafish genome file using aligments from the SAM file and concurrently test for different expression. Only the comparisons with q value less than 0.01 and status marked as OK in the Cuffdiff output were regarded as showing differential expression.
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text files include count and  RPKM values for each sample,

source_name: ZF4 cells_infected_Edwardsiella tarda

growth_protocol: ZF4 cells (American type culture collection, USA), a zebrafish cell line, were cultured at 24°C in 96-well cell culture plates (~105 cells/well) with DMEM/F-12 medium (GIBCO, Invitrogen, Carlsbad, USA) containing penicillin (60 μg/ml), streptomycin (100 μg/ml) and 10% fetal bovine serum (FBS).

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: ZF4 cells were infected with Edwardsiella tarda at 0 h.  At 12 h post-infection (hpi), total samples were subsequently stored at −80°C until RNA extraction for RNA-seq analysis.

value: embryo

tag: derivation

value: The ZF4 cell line was established from 1-day-old zebrafish embryos.

tag: morphology

value: fibroblast


title: ZF4 cells without Edwardsiella tarda infection

status: Public on Feb 14 2017

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Danio rerio

source_name: ZF4 cells_uninfected

tag: cell line

tag: tissue


title: x92_505_704B

city: Stockholm

first: Sophie

last: Petropoulos

address: liniskt Forskningscentrum  Novum

country: Sweden

institute: Karolinska Institutet

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR
Data was processed using in house pipeline rpkmforgene.py (Ramsköld D et al., 2009)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and counts for each sample

organism: Mus musculus

source_name: embryo

growth_protocol: The zona pellucida was removed using acid Tyrode’s solution and embryos were washed in M2. Dissociation was performed by incubating embryos in TrypLE (Life Technologies) for 3-6 minutes at 37°C followed by pipetting through fine pulled glass capillaries. Individual cells were picked, aligned in rows in M2 media under oil and imaged using a Zeiss Axiovert 200 inverted microscope equipped with a Hamamatsu C9100-13 EM-CCD camera, a Quorum spinning disk confocal scan head and Volocity aquisition software (Perkin Elmer, version 6.3.1) Cdx2-eGFP was quantified by taking single plain images of individual cells, focusing on the plain with maximum eGFP intensity. Average nuclear Cdx2-eGFP measurements were corrected for cytoplasmic background. The cut off between “Cdx2-eGFP low” and “Cdx2-eGFP high” was set at 500 fluorescent intensity units and was based on the clearly distinct Cdx2-eGFP low cell population at the 64-cell and >64-cell stages.

extract_protocol:
Cells were directly dispensed in lysis buffer and cDNA libraries were generated using Smart-seq2 as previously described (Picelli et al., 2013, 2014, Petropoulos et al., 2016).
Smart-seq2

tag: Stage

value: early 16 cell

tag: strain

tag: lineage

value: CO

tag: embryo derived from


title: x91_505_703B


title: x95_505_707B


title: x96_505_708B


title: x89_505_701B


title: x90_505_702B


title: x94_505_706B


title: x93_505_705B


title: 1.5N.c8

status: Public on Feb 15 2017

city: Singapore

first: Neil

last: Clarke

address: 16 College Avenue West

country: Singapore

institute: Yale-NUS College

data_processing:
Read mapping. Reads were mapped using Bowtie (v0.12.8) agaiinst de novo assembled transcripts (submitteed to Transcriptome Shotgun Assembly; GEEU00000000).
Transcript abundances. Tag counts were determined using RSEM (v1.2.0)
Differential expression. edgeR (v3.0.8 from BioConductor), with TMM normalization and a dispersion value of 0.1; all comparisons were to the control conditio (sample name 9.0N.c2)
Transcript selection and merging: any transcript with an edgeR estimated FDR value of 0.05 or better for at least one of the nine comparisons to control was retained.  Scaffolds that share the first two identification numbers assigned by Trinity (i.e, differing only in the third number in ID’s that are of the form <num>_c<num>_seq<num>) were deemed to belong to the same scaffold family.  Although some of these may be authentic variants,  others are likely to be sequencing or assembly artifacts; consequently, we treated scaffold families as individual transcripts, summing their RPKM values for purposes of gene expression analysis
processed data files format and content: tab-delimited text (RPKM values)

organism: Ettlia oleoabundans

source_name: cell culture, phototrophic conditions, 6 days

growth_protocol: cells were grown photoautotrophically in modified Bold Basal Medium plus vitamins B1 and B12, and varying concentrations of nitrate and NaCl concentations. Cells were grown under constant light (22-28 µmol. photons m-2s-1) at 25 degrees for 6 days. Initial cell densities were 1x10^6 cells/ml.

extract_protocol:
hot phenol followed by poly-A selection using Dynal oligo-T beads
Illumina protocol using mRNA-Seq kit

treatment_protocol: varying nitrate and NaCl as described under samples

tag: condition

value: 1.5mM nitrate


title: x86_711_506B

value: ICM


title: x85_711_505B


title: control_darkness_15min

city: Cambridge

first: Anna

middle: M

last: Puszynska

state: MA

address: 455 Main street

country: USA

institute: Whitehead Institute for Biomedical Research

description: Expression_timecoursexls, column E

data_processing:
Read alignment: Bowtie, v 0.12.7, -v 3 -m 1 --best –-un –-max
Gene expression quantification: the alignment output from Bowtie was analyzed in Matlab using custom code as described in Markson et al., 2013. To obtain gene expression values, we counted the number of coding-strand sequencing reads that had 5’ ends between the start and stop positions of the coding region of each gene (Markson et al., 2013).
Gene expression normalization: We performed RPKM normalization using a custom Matlab script.
Genome_build: Main chromosome: NC_007604.1; plasmid pANL (plasmid 1), NC_004073.2; plasmid pANS (plasmid 2), NC_004990.1
Supplementary_files_format_and_content: xls file with RPKM normalized gene expression values

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: cells

growth_protocol: Cell cultures were grown in tissue culture flasks under illumination with cool fluorescent light at 40 μE m-2 s-1 (μmoles photons m-2 s-1) in BG11 medium at 30 °C. Cells were initially inoculated in the presence of antibiotics (7.5 ug/mL kanamycin (“clock rescue” strain) or 2 ug/mL gentamycin and 7.5 ug/mL kanamycin (the rpaA- “clock rescue” strain)), and subsequently diluted with BG-11 only. The OD750 (optical density at 750 nm) was maintained at a constant level of 0.2.

extract_protocol:
Extraction was prepared as described previously by Vijayan et al 2009. Briefly, frozen cells were lysed in 65° C phenol/SDS by vortexing. Total RNA was extracted with phenol/chloroform followed by isopropanol precipitation. Then, total RNA was subjected to DNase I (Promega) treatment followed by phenol/chloroform extraction and ethanol precipitation. To assess integrity total RNA was analyzed on an agarose gel.
Ribosomal RNA was depleted from 6 μg of total RNA using the MICROBExpress Bacterial mRNA enrichment kit (ThermoFisher Scientific), following the protocol provided by the manufacturer. RNA-sequencing libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) from 400 ng of rRNA-depleted RNA. Samples were multiplexed and sequenced on an Illumina HiSeq 2000 platform by the Bauer Core Facility at the Harvard FAS Center for Systems Biology.

treatment_protocol: The “clock rescue ” cells were exposed to two light/dark cycles (12 hours of dark, followed by 12 h of light, followed by 12 h of dark), while the rpaA- “clock rescue” cells were exposed to one light/dark cycle for entrainment. Cells were harvested by filtering and freezing in liquid-nitrogen at following time points: dusk (ZT=12h); 5 min, 15 min, 30 min, 1 h, 2 h, 4 h, 8 h and 11 h 50 min after exposure to expected darkness; and 5 min, 15 min and 30 min after re-exposure to light at dawn, and stored in -80º C.

tag: genotype

value: "clock rescue"

tag: time point

value: darkness 15 min


title: x82_711_502B


title: x83_711_503B


title: x78_705_506B


title: x77_705_505B


title: control_duskZT12

description: Expression_timecoursexls, column C

value: dusk ZT=12


title: x80_705_508B


title: x81_711_517B


title: x79_705_507B


title: x76_705_504B

value: TE


title: x70_712_506B


title: x69_712_505B


title: x72_712_508B


title: x75_705_503B


title: x66_712_502B


title: x62_706_506B


title: x67_712_503B


title: x88_711_508B


title: x59_706_503B


title: x60_706_504B


title: x8_710_508B


title: x6_710_506B


title: x58_706_502B


title: x56_506_708B


title: x55_506_707B


title: x54_506_706B


title: x52_506_704B


title: x53_506_705B


title: x50_506_702B


title: x51_506_703B


title: x48_505_708B


title: x47_505_707B


title: x5_710_505B


title: x46_505_706B


title: x44_505_704B


title: x43_505_703B


title: x45_505_705B


title: x42_505_702B


title: x41_505_701B


title: x40_517_708


title: x30_504_706B


title: x28_504_704B


title: x33_504_708B


title: x27_504_703B


title: x29_504_705B


title: x26_504_702B


title: x24_503_708B


title: x23_503_707B


title: x21_503_705B


title: x2_710_502B


title: x18_503_702B


title: x19_503_703B


title: x49_506_701B


title: x16_709_508B


title: x22_503_706B


title: x14_709_506B


title: x10_709_502B


title: x13_709_505B


title: L32_9

value: late 32 cell


title: x1_710_517B


title: x20_503_704B


title: x11_709_503B


title: L32_45


title: L32_48


title: L32_46


title: L32_47


title: L32_43


title: L32_41


title: L32_40


title: L32_39


title: L32_34


title: L32_38


title: L32_35


title: x17_503_701B


title: L32_21


title: L32_29


title: L32_31


title: L32_30


title: L32_26


title: L32_25


title: L32_32


title: L32_18


title: L32_20


title: L32_13


title: L32_19


title: L32_126


title: L32_127


title: L32_124


title: L32_122


title: L32_119


title: L32_114


title: L32_36


title: L32_117


title: L32_33


title: L32_113


title: L32_11


title: i98_503_702

value: late 16 cell


title: L32_17


title: i6_502_706


title: L32_128


title: i5_502_705


title: i4_502_704


title: i38_506_706


title: i95_502_708


title: i39_506_707


title: i34_506_702


title: L32_115


title: i9_503_701


title: i31_505_707


title: i32_505_708


title: i96_503_701


title: i40_506_708


title: i8_502_708


title: i30_505_706


title: i3_502_703


title: i81_517_702


title: i25_505_701


title: i35_506_703


title: i33_506_701


title: i19_504__703


title: i2_502_702


title: i20_504__704


title: L32_16


title: i29_505_705


title: i27_505_703


title: i28_505_704


title: i26_505_702


title: i7_502_707


title: i36_506_704


title: i10_503_702


title: i100_503_703


title: i24_504__708


title: i23_504__707


title: E64_99

value: 64 cell


title: E64_91


title: E64_97


title: i22_504__706


title: i21_504__705


title: i18_504__702


title: i17_504__701


title: E64_78


title: E64_77


title: i14_503_706


title: E64_69


title: i82_517_703


title: E64_67


title: E64_66


title: i13_503_705


title: i11_503_703


title: i12_503_704


title: E64_61


title: E64_62


title: i1_502_701


title: E64_59


title: E64_57


title: E64_89


title: E64_74


title: E64_51


title: E64_52


title: E64_73


title: E64_70


title: E64_58


title: E64_65


title: E64_6


title: E64_43


title: E64_60


title: E64_98


title: E64_53


title: E64_54


title: E64_5


title: E64_44


title: E64_26


title: E64_68


title: L32_116


title: E64_42


title: E64_2


title: E64_21


title: E64_25


title: E64_4


title: E64_155


title: E64_19


title: E64_154


title: E64_36


title: E64_38


title: E64_35


title: E64_140


title: E64_34


title: E64_14


title: E64_33


title: E64_27


title: E64_22


title: E64_153


title: E64_158


title: E64_1


title: E64_12


title: E64_11


title: E64_139


title: E64_138


title: E64_142


title: D97

value: early 32 cell


title: E64_20


title: D98


title: E64_137


title: E64_141


title: D93


title: D96


title: E64_102


title: D92


title: D90


title: D99


title: D95


title: D91


title: D94


title: D80


title: D89


title: D9_704_517B


title: D8_517_708B


title: D79


title: E64_101


title: D78


title: D7_517_707B


title: D77


title: D75


title: D74


title: D62


title: D76


title: D60


title: D63


title: D61


title: D58


title: D57


title: D3_517_703B


title: D5_517_705B


title: D23_504_707B


title: D21_504_705B


title: D26_707_502B


title: D4_517_704B


title: D18_504_702B


title: D20_504_704B


title: D14_704_506B


title: D17_504_701B


title: D22_504_706B


title: D13_704_505B


title: D103


title: D12_704_504B


title: D102


title: D101


title: T6.DNaseI

city: Milan

first: Marco

middle: J.

last: Morelli

address: via Adamello 16

department: Center for Genomic Science of IIT@SEMM

country: Italy

institute: Istituto Italiano di Tecnologia

library_source: genomic

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v ; fastq_masker -Q33 -q 20 -r -N -v
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Significant peaks call using the Model-based Analysis of ChIP-Seq (MACS) 2.0.9, pvalue cutoff 1e-5;
Genome_build: mm9
Supplementary_files_format_and_content: bed files with enriched regions

molecule: genomic DNA

source_name: Eμ-myc Arf-/- Trp53+/+ lymphomas

growth_protocol: Single cells suspension of tumor cells  were  obtained  by pressing the  lymphnodes through nylon cell strainers without further purification.

extract_protocol: Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers.

treatment_protocol: untreated

tag: cell type

value: B cells from lymph nodes


title: input.DNaseI(T6)


title: T6.3hrs.minusNutlin.shp53

description:
rRNA-depleted RNA (ribozero)
eRPKM.T6.3hrs.minusNutlin.shp53

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v ; fastq_masker -Q33 -q 20 -r -N -v
Read alignment with tophat 2.0.8: tophat -p 8 -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded R1.fastq R2.fastq
expression quantification with featureCounts 1.4.5 (options -T 2 -p -P) on mm9 standard gtf. Expression values, differently from regular RPKMs, were normalised to the total number of reads aligned on exons rather than library size.
Genome_build: mm9
Supplementary_files_format_and_content: text file with eRPKM

source_name: Eμ-myc Arf-/- Trp53+/+ lymphomas infected with pLEPG shp53.1224

extract_protocol:
Total RNA was purified using Trizol (Invitrogen), treated with Turbo DNase (Ambion) and purified with RNA Clean XP (Agencourt). 5 µg of purified RNA were then treated with Ribozero rRNA removal kit (Epicentre) and EtOH precipitated. RNA quality and removal of rRNA were checked with the Agilent 2100 Bioanalyzer (Agilent Technologies).
Libraries for RNA-Seq were then prepared with the TruSeq RNA Sample Prep Kits v2 (Illumina) following manufacturer instructions starting from the RNA fragmentation step.

treatment_protocol: 3hrs 5µM (-)-Nutlin


title: D100


title: D10_704_502B


title: T5.3hrs.minusNutlin.shp53

description:
rRNA-depleted RNA (ribozero)
eRPKM.T5.3hrs.minusNutlin.shp53


title: T6.3hrs.plusNutlin.shp53

description:
rRNA-depleted RNA (ribozero)
eRPKM.T6.3hrs.plusNutlin.shp53

treatment_protocol: 3hrs 5µM (+)-Nutlin


title: D19_504_703B


title: D1_517_701B


title: T5.3hrs.plusNutlin.shp53

description:
rRNA-depleted RNA (ribozero)
eRPKM.T5.3hrs.plusNutlin.shp53


title: T6.3hrs.doxorubicin.shp53

description:
rRNA-depleted RNA (ribozero)
eRPKM.T6.3hrs.doxorubicin.shp53

treatment_protocol: 3hrs 1µM doxorubicin


title: T5.3hrs.doxorubicin.shp53

description:
rRNA-depleted RNA (ribozero)
eRPKM.T5.3hrs.doxorubicin.shp53


title: D11_704_503B


title: T7.3hrs.plusNutlin.shp53

description:
rRNA-depleted RNA (ribozero)
eRPKM.T7.3hrs.plusNutlin.shp53


title: T7.3hrs.H2O.shp53

description:
rRNA-depleted RNA (ribozero)
eRPKM.T7.3hrs.H2O.shp53


title: D104


title: T7.3hrs.doxorubicin.shp53

description:
rRNA-depleted RNA (ribozero)
eRPKM.T7.3hrs.doxorubicin.shp53


title: T7.3hrs.minusNutlin.shp53

description:
rRNA-depleted RNA (ribozero)
eRPKM.T7.3hrs.minusNutlin.shp53


title: T6.3hrs.minusNutlin.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T6.3hrs.minusNutlin.rep2


title: T5.3hrs.H2O.shp53

description:
rRNA-depleted RNA (ribozero)
eRPKM.T5.3hrs.H2O.shp53


title: T7.3hrs.minusNutlin.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T7.3hrs.minusNutlin.rep1


title: T5.3hrs.minusNutlin.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T5.3hrs.minusNutlin.rep1


title: T6.3hrs.plusNutlin.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T6.3hrs.plusNutlin.rep2


title: T7.3hrs.plusNutlin.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T7.3hrs.plusNutlin.rep2


title: T7.3hrs.plusNutlin.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T7.3hrs.plusNutlin.rep1


title: T5.3hrs.plusNutlin.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T5.3hrs.plusNutlin.rep2


title: T6.3hrs.H2O.shp53

description:
rRNA-depleted RNA (ribozero)
eRPKM.T6.3hrs.H2O.shp53


title: T7.3hrs.doxorubicin.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T7.3hrs.doxorubicin.rep1


title: T5.3hrs.plusNutlin.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T5.3hrs.plusNutlin.rep1


title: T6.3hrs.doxorubicin.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T6.3hrs.doxorubicin.rep1


title: T5.3hrs.doxorubicin.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T5.3hrs.doxorubicin.rep1


title: E64_76


title: T7.3hrs.minusNutlin.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T7.3hrs.minusNutlin.rep2


title: T7.3hrs.doxorubicin.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T7.3hrs.doxorubicin.rep2


title: T6.3hrs.plusNutlin.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T6.3hrs.plusNutlin.rep1


title: T7.3hrs.H2O.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T7.3hrs.H2O.rep2


title: T5.3hrs.H2O.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T5.3hrs.H2O.rep1


title: T6.3hrs.H2O.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T6.3hrs.H2O.rep2


title: T6.3hrs.H2O.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T6.3hrs.H2O.rep1


title: T5.3hrs.H2O.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T5.3hrs.H2O.rep2


title: T6.3hrs.minusNutlin.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T6.3hrs.minusNutlin.rep1


title: T7.3hrs.H2O.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T7.3hrs.H2O.rep1


title: T4.2hrs.OHT.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T4.2hrs.OHT.rep2

source_name: Eμ-myc Trp53KI/∆ lymphomas

treatment_protocol: 2hrs 100nM OHT


title: T1.2hrs.OHT.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T1.2hrs.OHT.rep2


title: T3.2hrs.OHT.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T3.2hrs.OHT.rep2


title: T2.2hrs.OHT.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T2.2hrs.OHT.rep2


title: T6.3hrs.doxorubicin.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T6.3hrs.doxorubicin.rep2


title: T5.3hrs.doxorubicin.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T5.3hrs.doxorubicin.rep2


title: T1.2hrs.OHT.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T1.2hrs.OHT.rep1


title: T2.2hrs.OHT.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T2.2hrs.OHT.rep1


title: T4.2hrs.EtOH.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T4.2hrs.EtOH.rep2

treatment_protocol: 2hrs 1/1000 vol. EtOH


title: T2.2hrs.EtOH.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T2.2hrs.EtOH.rep2


title: T3.2hrs.EtOH.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T3.2hrs.EtOH.rep2


title: T4.2hrs.EtOH.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T4.2hrs.EtOH.rep1


title: T1.2hrs.EtOH.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T1.2hrs.EtOH.rep2


title: T2.2hrs.EtOH.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T2.2hrs.EtOH.rep1


title: T1.2hrs.EtOH.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T1.2hrs.EtOH.rep1


title: Input.T5

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using  p53 NCL-p53-CM5p (Novocastra laboratories) antibody.
Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers.


title: p53.T6.3hrs.minusNutlin

description: ChIP antibody: NCL-p53-CM5p (Novocastra laboratories)


title: Input.T7


title: p53.T5.3hrs.minusNutlin


title: p53.T7.3hrs.doxorubicin


title: p53.T6.3hrs.doxorubicin


title: T4.2hrs.OHT.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T4.2hrs.OHT.rep1


title: p53.T7.3hrs.plusNutlin


title: T3.2hrs.OHT.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T3.2hrs.OHT.rep1


title: p53.T6.3hrs.plusNutlin


title: p53.T5.3hrs.doxorubicin


title: p53.T5.3hrs.plusNutlin


title: p53.T6.3hrs.DMSO

treatment_protocol: 3hrs 0.5/1000 vol. DMSO


title: p53.T5.3hrs.DMSO


title: p53.T7.3hrs.DMSO


title: p53.T7.3hrs.H2O


title: p53.T6.3hrs.H2O


title: p53.T6.NT


title: T3.2hrs.EtOH.rep1

description:
rRNA-depleted RNA (ribozero)
eRPKM.T3.2hrs.EtOH.rep1


title: p53.T7.3hrs.minusNutlin


title: Input.T4


title: p53.T7.NT


title: Input.T3


title: p53.T5.NT


title: Input.T2


title: Input.T1


title: STH rep2

city: Changchun

first: Limin

last: Sun

state: Jilin

address: Xincheng Street 2888,Jingyue Distric

institute: Jilin Agricultural University

description: processed data file column header: B2

data_processing:
We applied the reads filtration to filter the reads with lower quality and short sequence under following criteria: read length > 50; over 30% base quality >13.
We applied the RNA-seq mapping using Mapsplice software to the Sheep genome for further study.
The differentially expressed genes were achieved by EB-Seq algorithms and annotated by NCBI Database and by blasting to Human protein sequence of the transcripts.
Gene Ontology (GO) terms were assigned to each differ-gene.
pathway analysis was used to find out the significant pathway of the differential genes according to KEGG database.
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: [.txt] tab-delimited text files include counta and RPKM values for each Sample

organism: Ovis aries

source_name: longissimus muscle

growth_protocol: Natural conditions

extract_protocol:
Total RNA was extracted from each sample using TRIzol Reagent (Life technologies, USA) according to the protocol from manufacturer. The concentration of each sample was measured by NanoDrop 2000 (Thermo Scientific, USA).
The sequencing library of each RNA sample was prepared by using Ion Total RNA-Seq Kit v2 according to the protocol provided by manufacturer (Life technologies, USA). Briefly, poly(A)-containing mRNA was purified from 5 ug total RNA with Dynabeads (Life technologies, USA). The mRNA was fragmented using RNaseIII and purified. The fragmented RNA was hybrized and ligated with Ion adaptor.

treatment_protocol: Two breeds of sheep

tag: breed

value: Small Tail Han (STH)

value: longissimus muscle


title: WT2

city: Wuhan

first: Xiaoming

state: Hubei

address: Lumo road, No. 1

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the TAIR10 Arabidopsis genome reference using TopHat software (Trapnell et al., 2009).
The number of sequencing reads generated from each sample was converted into fragments per kilobase of transcript per million fragments mapped (FPKM). Significantly differentially expressed transcripts between wild-type and transgenic lines were detected from 2 biological replicates using Cuffdiff with default Benjamini-Hochberg correction for multiple-testing, based on a False Discovery Rate (FDR) ≤ 0.05.
Genome_build: Arabidopsis thaliana Col-0 TAIR10
Supplementary_files_format_and_content: Excel files include RPKM values for each sample.

organism: Arabidopsis thaliana

source_name: whole plant

growth_protocol: Seeds of Arabidopsis thaliana (ecotype Columbia-0, Col-0) were surface-sterilized in 6% sodium hypochlorite for 5 min followed by three washed in sterile water, and then plated on 1/2 MS solid medium containing 0.7% agar. One-week-old seedlings were transferred from plates into pots filled with peat moss in a greenhouse under controlled environmental conditions, at 22 °C, 50-60% relative humidity and under 130 mol photons m-2 s-1 with a 16 h light and 8 h dark cycle.

extract_protocol:
The 4-week old wild-type and VaERF73 overexpressing Arabidopsis growing under normal condition were used to construct mRNA libraries. Total RNA was extracted from collected samples using Column Plant RNAOUT 2.0 kit (Tiandz, Beijing, China), following the instructions of the manufacturer. RNA concentration and quality were detected using Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: A transcription factor gene, VaERF73, isolated from Vitis amurensis, was transformed into Arabidopsis.

tag: genotype/variation

value: wild type

value: whole plant

tag: age

value: 4-week old


title: STH rep3

description: processed data file column header: B3


title: p53.T3.2hrs.OHT


title: WT1


title: A8-1

value: VaERF73 overexpressing Arabidopsis


title: p53.T4.2hrs.OHT


title: p53.T2.2hrs.OHT


title: STH rep1

description: processed data file column header: B1


title: p53.T5.3hrs.H2O


title: p53.T4.2hrs.EtOH


title: QHMM rep3

description: processed data file column header: A3

value: Qianhua Mutton Merino (QHMM)


title: QHMM rep2

description: processed data file column header: A2


title: p53.T1.2hrs.OHT


title: QHMM rep1

description: processed data file column header: A1


title: BS-seq HEK293 1

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

data_processing:
For BS-seq analysis, adapters were removed and the bisulfite-converted reads were mapped to the human reference genome (hg19/GRCh37) with Bismark using the option -non-directional allowing one non-cytosine mismatch (–n 1 –l 100). Methylation levels for all cytosines with more than 5X coverage were compiled with the Bismark methylation_extractor tool. Since the fraction of potential PCR duplicates for processed non-coding RNA fragments, which are shorter than read length, is unknown, methylation levels were called with and without removing duplicates.
Genome_build: hg19
Supplementary_files_format_and_content: bed file with genome-wide RNA methylation levels (available on the series record), bedfiles with miCLIP stop positions

organism: Homo sapiens

source_name: Embryonic kidney cells

extract_protocol:
For bisufite sequencing, total RNA was extracted using Trizol, and the polyA fraction isolated using oligodT dynabeads. Bisulfite conversion and desulfonation of RNAs was performed using the EZ RNA Methylation Kit (Zymo Research).
Libraries were prepared using Illumina TruSeq RNA prep kits


title: BS-seq HEK293 2

extract_protocol:
For bisufite sequencing, total RNA was extracted using Trizol, and the poly fraction isolated using oligodT dynabeads. Bisulfite conversion and desulfonation of RNAs was performed using the EZ RNA Methylation Kit (Zymo Research).
Libraries were prepared using Illumina TruSeq RNA prep kits


title: miCLIP_NSUN3_HEK293_rep3

data_processing:
For miCLIP analysis, miCLIP reads were mapped to the human reference genome (hg19/GRCh37) by using bowtie with parameters –m 1 –v 1 to select uniquely mapping reads allowing one mismatch.
Genome_build: hg19
Supplementary_files_format_and_content: bed file with genome-wide RNA methylation levels (available on the series record), bedfiles with miCLIP stop positions

extract_protocol:
For miCLIP, myc-tagged NSUN3 or NSun6 constructs were transfected into HEK293 cells which were harvested 24 hours post-transfection. Cells were then lysed in lysis buffer and treated with high concentration of DNase and low concentration of RNaseI to partially fragment RNAs. Lysates were incubated with proteinG dynabeads in the presence of anti-myc antibody to isolate NSUN-RNA complexes.  Libraries were then prepared following isolation of RNAs from the protein-RNA complexes.
Libraries were prepared using Illumina TruSeq RNA prep kits

tag: antibody

value: anti c-myc 9E10

tag: antibody manufacturer

value: Sigma; catalog number M4439


title: miCLIP_NSUN3_HEK293_rep2


title: WT_LPS_3

city: Indianapolis

first: Yunlong

last: Liu

state: IN

address: 410 West 10th Street, HS 5000

institute: IUPUI

data_processing:
Sequence reads were aligned with BFAST (v.0.7.0a) towards reference genome and junction library. Details refers to Breese and Liu, Bioinformatics, 2013, PMID: 23314324
Aligned reads were fitered with NGSUtils (Breese and Liu, Bioinformatics 2013, PMID: 23314324), only unique mapped reads with no more than 2 mismatchs were kept.
Read counts were calculated with NGSUtils.
Differential expression analysis was performed using edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes read counts, log2 fold change values, p-values and FDR for all samples.

source_name: bone marrow stromal cells

extract_protocol:
Trizol per manufacturer's (Invitrogen) protocol
RNA was fragmented with RNAaseIII, cDNA libraries constructed with SOLiD adaptors by reverse transcription

treatment_protocol: BMSCs were plated at 1×105 cells/well/ml for 24 h and further treated with LPS (200ng/ml) for another 24 h

tag: treatment

value: LPS treated

value: bone marrow stromal cells


title: p53.T3.2hrs.EtOH


title: A8-2


title: BS-seq skin wt 2

data_processing:
Adapters were removed and the bisulfite-converted reads were mapped to the human reference genome (hg19/GRCh37) with Bismark allowing one non-cytosine mismatch (–n 1 –l 100). Methylation levels for all cytosines with more than 3X coverage were compiled with the Bismark methylation_extractor tool. Since the fraction of potential PCR duplicates for processed non-coding RNA fragments, which are shorter than read length, is unknown, methylation levels were called after removing duplicates.
Genome_build: hg19/GRCh37 chrM
Supplementary_files_format_and_content: Processed data files contain methylation levels in bg format for chrM.

source_name: skin

extract_protocol:
For bisufite sequencing, mitochondrial enriched RNA was extracted using Trizol. Bisulfite conversion and desulfonation of RNAs was performed using the Epitect bisulfite Kit (Qiagen).
Libraries were prepared using Illumina TruSeq RNA prep kits

treatment_protocol: After mitochondrial extraction, RNA was extracted, and after Dnase treatment, RNA was used for bisulfite treatment and sequencing.

value: Dermal fibroblasts


title: WT_LPS_2


title: p53.T1.2hrs.EtOH


title: p53.T2.2hrs.EtOH


title: miCLIP_NSUN3_HEK293_rep1


title: BS-seq skin wt 1

data_processing:
Adapters were removed and the bisulfite-converted reads were mapped to the human reference genome (hg19/GRCh37) with Bismark allowing one non-cytosine mismatch (–n 1 –l 100). Methylation levels for all cytosines with more than 5X coverage were compiled with the Bismark methylation_extractor tool. Since the fraction of potential PCR duplicates for processed non-coding RNA fragments, which are shorter than read length, is unknown, methylation levels were called after removing duplicates.
Genome_build: hg19/GRCh37 chrM
Supplementary_files_format_and_content: Processed data files contain methylation levels in bg format for chrM.


title: WT_LPS_1


title: WT_CTR_2

value: untreated


title: Derm CD8+CD103+, biological replicate 7

first: Liv

last: Eidsmo

address: L8:02 Karolinska Univeristy Hospital

institute: Karolinska Insitutet

description: Derm CD8+CD103+, biological replicate 7

data_processing:
Basecalling softwares : HCS1.5.15.1+ RTA1.13.48 +OLB 1.9.4;  parameters are $OLB-1.9.4/bin/setupBclToQseq.py –b $BaseCalls -o $Bustard
Alignment: Bowtie alignment of gene reference, bowtie2-2.2.5, -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 16 -k 200; BWA alignment of genome reference, bwa-0.7.10, -o 1 -e 63 -i 90 -L -k 2 -l 31 -t 4 -q 10
Filtering: Remove reads with adapters; Remove reads with unknown bases more than 10%; Remove low quality reads (which are defined as reads having more than 50% bases with quality value <= 10).
Additional: Tophat alignment of genome reference (for AS, NovelTU, ExtendGene), TopHat v2.0.10, -p 16 --solexa1.3-quals  --segment-length 30 --segment-mismatches 2 -r 20 --mate-std-dev 20 --library-type  fr-unstranded
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include expected.count values for each and  all samples

source_name: Derm CD8+CD103+

extract_protocol:
CD8+T cells were sorted from peripheral blood, dermal or epidermal cell suspension from healthy donors according to their cellular markers expression by a MoFlo XDP sorter. Cells were sorted directly into Qiazol and stored at -80 degree before extraction using miRNeasy Mini Kit (Qiagen) according to manufacturer’s protocol.
library was constructed using SMART-Seq v4 Ultra Low Input RNA Kit (ClonTech)  according to manufacturer’s protocol.

treatment_protocol: Epidermis were separate from dermal tissue after dispase treatment overnight. The epidermal and dermal tissue were further digested by collagenase. The resulting cell suspension were stained and CD8+ T cells subset were sorted by FACS based on surface markers. PBMCs were prepared by Density Gradient Centrifugation.

tag: cell subset

value: Derm CD8+CD103+

tag: donor

value: Subject 7


title: Blood CD8+CLA+ TEM, biological replicate 7

source_name: Blood CD8+CLA+ TEM

value: Blood CD8+CLA- TEM


title: WT_CTR_1


title: NI_1_smallRNA-Seq

city: LONDON

first: Rodney

last: DeKoter

state: Ontario

address: 1151 Richmond street

department: Microbiology and Immunology

country: Canada

institute: University of Western Ontario

description: Trial 1

data_processing:
FASTQ files were trimmed to remove Illumina Small RNA adapters using TrimGalore! Galaxy version 0.4.0. Parameters: Overlap with adapter: 1, Error rate: 0.1. Discard reads smaller than 20 bp following trimming. Reads with a quality <20 were trimmed.
Reads from trimmed FASTQ files were collapsed and mapped to mm10 and mirbase V21 references using MirDeep2 Mapper V2.0.0. Parameters: Don't clip, collapse reads and map, map threshold: 5
Collapsed and mapped reads were quantified using MirDeep Quantifier V2.0.0. Settings: search in mouse, Upstream nucleotides: -2, downstream nucleotides: 5, allowed mismatches: 1
Samples reads were normalised and compared using DeSeq2 V.2.1.8.0. Primary factor: Treatment, Secondary Factor: Trial. Fit type parametric outlier filtering off. Independant filtering off.
miRNA transcripts were considered signficantly changes in expression if DeSeq2 reported a logFC>1 or <-1
Genome_build: mm10, mirBasev21
Supplementary_files_format_and_content: Tab-seperated xlsx files containing total reads per mature miRNA (counts) or normalised reads (reads per million)

source_name: BN cells, control

growth_protocol: iBN cells containing a PU.1-inducable system were grown as previously described (Ziliotto, Gruca et al. 2014). Cells were grown in Iscove's Modified Dulbecco's Media (IMDM) (Wisent) supplemented with 1ng/mL GM CSF (Peprotech), 10% fetal bovine serum (Wisent) , 100 U/mL penicillin–streptomycin + 2 mM L-glutamine, and 5 × 10−5 mol/L 2-mercaptoethanol. Cells were maintained as a suspension at 1^6 cells/10 ml media and maintained at 37°C with 5% C02.

extract_protocol:
Small RNAS were purified from iBN cells using the miRNeasy mini kit (Qiagen), and eluted in a final volume of 30µL RNase-free water
Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 and its integrity was assessed using a 2100 Bioanalyzer. Libraries were generated from 1000 ng of total RNA using the TruSeq® Small RNA Sample Prep Kit (Illumina), as per the manufacturer’s recommendations. cDNA construct purification has been performed on a Pippin Prep instrument. Final libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit. Average size fragment was determined using a LaChip GX (PerkinElmer) instrument. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 SR50.

treatment_protocol: Small RNAs were purified from un-induced cells and cells induced with 1000 ng/ml doxycycline for 72 hours.

value: BN cells (granulocyte-macrophage progenitor)


title: NI_2_smallRNA-Seq

description: Trial 2


title: Blood CD8+CLA+ TEM, biological replicate 6

value: Subject 6


title: Dox_3_smallRNA-Seq

description: Trial 3

source_name: BN cells, induced


title: HuR-CP1 (HuR cleavage product-1)+134

city: Charleston

first: Gary

last: Hardiman

state: SOUTH CAROLINA

address: 135 Cannon Street, Suite 303 MSC835

institute: MUSC

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using TopHat2
The resulting SAM files were sorted and inputted into Partek® Genomics Suite® to generate count data for gene-level differential expression analyses using the Partek built-in RNAseq workflow.
One-way Analysis of Variance (ANOVA) was performed on all sample comparisons using the Partek RNAseq pipeline. All factors were treated as fixed factors for control and treated samples. All data were treated as a balanced design where the number of samples in each group (control vs treatment) were equal.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values, fold change, etc.

source_name: HuR-CP1 (HuR cleavage product-1), UM-SCC 74B cells

growth_protocol: The oral cancer cell lines were maintained in DMEM with high glucose, 10% fetal bovine serum, penicillin-streptomycin-L-glutamine in a humidified 5% CO2 environment at 37°C.

extract_protocol:
HuR RNP IP was performed as previously described. Briefly, cell lysates were prepared from exponentially growing oral cancer cells that had been treated with IR or left untreated as a control. Equal amounts of protein were used (500-1000 μg). HuR monoclonal antibody 3A2 (Santa Cruz), GFP antibody (Clontech), or isotype control IgG (Sigma) were pre-coated onto Protein A/G Sepharose beads (PAS). Lysates were pre-absorbed with IgG (30 μg) and then removed by the addition of PAS beads. Individual pull-downs were performed at 4°C for 1–2 h to minimize the potential re-assortment of mRNAs. For RNA analysis, the beads were incubated with 1 ml of NT2 buffer containing 20 U of RNase-free DNase I (15 min, 30°C), washed twice with 1 ml of NT2 buffer, and further incubated in 1 ml of NT2 buffer containing 0.1% SDS and 0.5 mg/ml proteinase K (15 min, 55°C) to digest the proteins bound to the beads. RNA was extracted using phenol and chloroform and precipitated in the presence of glycogen.RNA was harvested using Trizol reagent. 100 ng of total RNA from RIP samples was used to prepare RNA-Seq libraries using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA), following the protocol described by the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The GFP plasmid vectors contained full-length HuR, HuR-D226A, HuR-CP1. The plasmid transfections were carried out using Lipofectamine 2000 (Invitrogen).

tag: cell line

value: University of Michigan Squamous Cell Carcinoma cell line 74B (UM-SCC 74B)

tag: transfection

value: GFP plasmid vector containing HuR-CP1

tag: rna ip

value: Protein A/G Sepharose beads (PAS) (Santa Cruz, Cat# sc-2003)


title: Derm CD8+CD103-, biological replicate 7

description: Derm CD8+CD103-, biological replicate 7

source_name: Derm CD8+CD103-

value: Derm CD8+CD103-


title: GFP control_131

source_name: GFP control, UM-SCC 74B cells

value: GFP empty vector

value: GFP antibody (Clontech, Cat# 632460, Lot# 1105002)


title: HuR-D226A (asp-aln mutant)_133

source_name: HuR-D226A (asp-aln mutant), UM-SCC 74B cells

value: GFP plasmid vector containing HuR-D226A

value: Isotype Control IgG (Santa Cruz, Cat# sc-2025)


title: HUR FL (full-length HuR)_132

source_name: HUR FL (full-length HuR), UM-SCC 74B cells

value: GFP plasmid vector containing full-length HuR

value: HuR monoclonal antibody 3A2 (Santa Cruz, Cat# sc-5261)


title: Blood CD8+CLA- TEM, biological replicate 7

source_name: Blood CD8+CLA- TEM


title: 24HAI

city: Pretoria

first: Daniel

last: Bellieny-Rabelo

state: Gauteng

address: Lynnwood Rd, Hatfield, Pretoria

department: Department of Biochemistry, Genetics and Microbiology

country: South Africa

institute: University of Pretoria

description: replicate nº1

data_processing:
The G. max genome (version 1.1) was used as reference.
The first 10bp low-quality regions of each read were filtered using Trimmomatic-0.30
Trimmed/filtered RNA-Seq reads were mapped to the reference genome Bowtie 2.1.0 and TopHat 2.0.9 [TopHat was executed using the “--b2-very-sensitive” parameters (-D 20 -R 3 -N 0 -L 20 -i S,1,0.50) ]
Genome_build: The soyebean genome (v1.1) was used to map the reads obtained from .
Supplementary_files_format_and_content: Plain-text tab-separated file containing all genes mapped using the sequenced reads. Scores represent FPKM values for each soybean gene in the five time-spans (dry, 3HAI, 6HAI, 12HAI, 24HAI).

organism: Glycine max

source_name: Embryonic axis 24 hours after imbibition

growth_protocol: Soybean seeds were sown in 15 cm Petri dishes containing 2g of cotton soaked with sterile distilled water (30 mL). Petri dishes were placed into a climate-controlled growth chamber at 28ºC with a 12/12 hours photo-period and 50-65% relative humidity.

extract_protocol:
For RNA extraction, embryonic axes were immediately placed in RNAlater (Qiagen) until RNA extraction. Total RNA was isolated using RNeasy plant mini kits (Qiagen).
RNA-Seq libraries were prepared using the TruSeq RNA Sample Preparation Kit v2 (Illumina, cat. RS-122-2001) and submitted to paired-end sequencing (2x100bp) using a HiSeq 2000 instrument

tag: cultivar

value: BRS 284

tag: tissue

value: embryonic axis

tag: time after imbibition

value: 24 hours


title: NI_2_ChIP-Seq

data_processing:
Illumina HiSeq2000 .bam files provided by the sequencing core were processed using rmdup (version 1.0.0) to remove duplicate reads
Files were converted to FASTQ format using Bam-to-FASTA/Q (version 1.0.0) and reads groomed to remove Illumina adapter sequences with TrimGalore!(Krueger 2015) in Galaxy Suite (Giardine, Riemer et al. 2005; Blankenberg, Von Kuster et al. 2010; Goecks, Nekrutenko et al. 2010).
Single-end reads aligned to reference MGSCv37 (MM9) using Bowtie (Langmead, Trapnell et al. 2009).
Bowtie reported only the best alignment for each fragment (--best) with a maximum number of 2 mismatches with an average quality score of at least 70. Peaks called in MACS 1.4.1 with an mfold of (10,30) (Zhang, Liu et al. 2008).
Peak-calling was conducted for two biological replicates for each condition, and replicate region files were used for determining differential peaks between the experimental conditions.
Genome_build: MM9
Supplementary_files_format_and_content: .bed files representing regions of enrichment, and .wig files represinging ChIP-signal were generated using using MACS1.4.1.

source_name: ChIP-seq for PU.1 on control, non-induced iBN cells

growth_protocol: iBN cells containing a PU.1-inducible system were grown as previously described (Ziliotto, Gruca et al. 2014). Cells were grown in Iscove's Modified Dulbecco's Media (IMDM) (Wisent) supplemented with 1ng/mL GM CSF (Peprotech), 10% fetal bovine serum (Wisent) , 100 U/mL penicillin–streptomycin + 2 mM L-glutamine, and 5 × 10−5 mol/L 2-mercaptoethanol. Cells were maintained as a suspension at 1^6 cells/10 ml media and maintained at 37°C with 5% C02.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes with rocking at room temperature, and cross-linking was terminated by addition of 125 mM glycine. Pellets were washed in cold PBS and snap frozen in liquid nitrogen. Cell pellets were lysed in buffer (50 mM Tris-HCl [pH 8.1], 10 mM EDTA, 1% SDS) containing Halt™ protease inhibitor mixture (Thermo Scientific). Chromatin fragmentation was conducted using 30 cycles of sonication on a Bioruptor (Diagenode). PU.1-chromatin complexes were immunoprecipitated overnight a 4°C with Rabbit polyclonal anti-mouse PU.1 (T-21) (Santa Cruz Biotechnology) or mouse control IgG (Abcam) conjugated to protein G dynabeads (Invitrogen, Burlington) on 300 ug of chromatin per sample. Bound beads were washed once in low salt wash buffer (0.1% SDS, 1% Triton-X-100, 2 mM EDTA, 20 mM Tris-HCl[pH 8.0], 150 mM NaCl), once with high salt wash buffer (0.1% SDS, 1% Triton-X-100, 2 mM EDTA, 20 mM Tris-HCL[pH 8.0], 500 mM NaCl), once with LiCl buffer (0.25 M LiCl, 1% NP-40, 1% Na-deoxycholate, 1mM EDTA, 10 mM Tris-HCl [pH 8.0]), and twice with Tris-EDTA buffer at pH 8.0. Immunocomplexes were eluted in elution buffer (1% SDS, 0.1 M NaHCO3) and the buffer adjusted to 200 mM NaCl. Cross-linking was reversed at 65°C overnight and DNA isolated using a Wizard SV Gel and PCR purification kit (Promega).
Libraries were generated robotically with 10 ng of fragmented DNA (100-300 bp) using the Kapa HTP Library Preparation Kit (Kapa Biosystems) as per the manufacturer’s recommendations except that adapters and PCR primers were diluted 100-fold, the size selection step was done after the PCR step and the number of PCR cycles increased by 6. Adapters and PCR primers were purchased from Integrated DNA Technologies whereas size selection has been performed on a Pippin Prep instrument (SAGE Biosciences Inc). Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (D-Mark). Average size fragment was determined using a LaChip GX (PerkinElmer) instrument. Libraries were sequenced on a single-end 100bp read length run on a HiSeq2000 (Illumina).

treatment_protocol: Chromatin pellets were prepared from uninduced cells and cells induced with 1000 ng/ml doxycycline for 72 hours.

tag: chip antibody


title: Blood CD8+CLA- TEM, biological replicate 6


title: NI_input

source_name: sonicated chromatin from on control, non-induced iBN cells


title: Derm CD8+CD103-, biological replicate 6

description: Derm CD8+CD103-, biological replicate 6


title: 24HAI_rep

description: replicate nº2


title: 12HAI_rep

description: replicate nº2

source_name: Embryonic axis 12 hours after imbibition

value: 12 hours


title: Derm CD8+CD103+, biological replicate 6

description: Derm CD8+CD103+, biological replicate 6

value: Derm CD8+CD103+


title: WT_CTR_3

tag: strain

tag: genotype

value: wild type

value: untreated

value: bone marrow stromal cells


title: Input.T6

source_name: Eμ-myc Arf-/- Trp53+/+ lymphomas

tag: cell type

value: B cells from lymph nodes


title: Blood CD8+CLA- TEM, biological replicate 5

value: Blood CD8+CLA- TEM

value: Subject 5


title: Dox_2_ChIP-Seq

source_name: ChIP-seq for PU.1 on iBN cells induced for 72 hours with doxycyclin

value: BN cells (granulocyte-macrophage progenitor)

value: Rabbit polyclonal anti-mouse PU.1 (T-21) (Santa Cruz Biotechnology)


title: Blood CD8+CLA+ TEM, biological replicate 5


title: Dox_1_ChIP-Seq


title: NI_1_ChIP-Seq


title: Dox_1_smallRNA-Seq

description: Trial 1


title: Derm CD8+CD103+, biological replicate 5

description: Derm CD8+CD103+, biological replicate 5


title: DOX_input

source_name: sonicated chromatin from iBN cells induced for 72 hours with doxycyclin


title: 6HAI_rep

description: replicate nº2

source_name: Embryonic axis 6 hours after imbibition

value: 6 hours


title: Embryonic stem cell at passage 6 (P6 Clon6)

city: Madrid

first: Elisa

last: Varela

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

description: RNA-seq

data_processing:
RNA-seq processing:
Read files were quality-checked with FastQC.
Reads were aligned to the mouse genome (GRCm38/mm10) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Raw counts for genes were obtained with HTSeq v0.5.3p9, using the GRCm38/mm10 gene annotation.
Normalized counts and differential expression were obtained with DESeq2.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Normalized expression counts calculated with DESeq2.

molecule: polyA RNA

source_name: mouse blastocysts

growth_protocol: Cells were grown in DMEM with LIF

extract_protocol:
Rneasy Mini Kit (QUIAGEN)
1 µg of total RNA samples was used as provided by the user. Sample RNA Integrity Numbers were 10 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

value: Embryonic stem cells at passage 6

value: Cells were expanded in vitro


title: Dox_2_smallRNA-Seq

description: Trial 2


title: 3HAI_rep

description: replicate nº2

source_name: Embryonic axis 3 hours after imbibition

value: 3 hours


title: Derm CD8+CD103-, biological replicate 5

description: Derm CD8+CD103-, biological replicate 5

value: Derm CD8+CD103-


title: Embryonic stem cell at passage 6 (P6 Clon36)

description: RNA-seq


title: Blood CD8+CLA- TEM, biological replicate 4

value: Subject 4


title: Blood CD8+CLA+ TEM, biological replicate 4

source_name: Blood CD8+CLA+ TEM


title: 3HAI

description: replicate nº1

value: BRS 284

value: embryonic axis


title: dry_rep

description: replicate nº2

source_name: Dry embryonic axis

value: 0 hours


title: Embryonic stem cells at passage 16 (P16 Clon6)

description: RNA-seq

value: Embryonic stem cells at passage 16

value: wild type


title: dry

description: replicate nº1


title: Embryonic stem cell at passage 6 (P6 Clon20)

description: RNA-seq


title: Blood CD8+CLA- TEM, biological replicate 2

value: Subject 2


title: Blood CD8+CLA+ TEM, biological replicate 2


title: 12HAI

description: replicate nº1

value: 12 hours


title: Embryonic stem cells at passage 16 (P16 Clon36)

description: RNA-seq


title: Derm CD8+CD103+, biological replicate 2

description: Derm CD8+CD103+, biological replicate 2

source_name: Derm CD8+CD103+

value: Derm CD8+CD103+


title: Embryonic stem cells at passage 16 (P16 Clon20)

description: RNA-seq


title: Infected (Wild Type) - 4dpi - Rep2 [W4C]

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

address: Darwin 3

institute: CNB, CSIC

description:
Infected (Wild Type) - 4dpi - Rep2
W4C

data_processing:
Filtering: Strand-specific, single-end reads longer than 18 nt provided by BGI sequencing company were quality-checked with FASTQCjects/fastqc/). No additional filters were necessary.
Read alignment: Short reads were aligned against SARS-CoV genome, with BWA (Li and Durbin, 2009) allowing up to 1 mismatch and no gaps (bwa aln -n 1 -k 1 -o 0). Only unique hits were considered for posterior steps. SAM alignment files generated by BWA were compressed, sorted and indexed using “view”, “sort” and “index” functions of Samtools package (Li et al., 2009).
Ten peaks were selected by visual inspection of coverage reads for SARS-CoV genome with SeqMonk browser (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk) attending the high-abundance sequences above an uniformily distributed background. In all cases, the consensus mature svRNA sequence was determined by the summit of the peak that was between 18 to 22 nt in length.
Genome_build: SARS-CoV MA15
Supplementary_files_format_and_content: tab-delimited text file including sequence, genome coordinates and raw read count values for ten peaks manually selected.

source_name: Lung

growth_protocol: Specific-pathogen-free 8 week-old BALB/c OlaHsd female mice were purchased from Harlan. Mice were maintained for 8 additional weeks in the animal care facility at the National Center of Biotechnology (CNB-CSIC, Madrid).

extract_protocol:
Small RNAs were isolated (mirVana miRNA Isolation Kit, Ambion) from mouse lungs and analyzed using the Bioanalyzer 2100 expert_Eukaryote Total RNA to determine their integrity.
1 μg of the small RNA fraction was used for library construction (BGI Genomics, Hong-Kong).

treatment_protocol: 16-week-old mice were inoculated with rSARS-CoV wt or rSARS-CoV-ΔE in 50 μl of DMEM containing 2% fetal bovine serum (FBS, Biowhittaker). Mice were sacrificed at days 2 and 4 post infection and lung and serum samples were collected.

value: BALB/c OlaHsd


title: Derm CD8+CD103-, biological replicate 2

description: Derm CD8+CD103-, biological replicate 2

source_name: Derm CD8+CD103-


title: Embryonic stem cells at passage 6 (P6 Clon30)

description: RNA-seq


title: Infected (Wild Type) - 4dpi - Rep3 [W4D]

description:
Infected (Wild Type) - 4dpi - Rep3
W4D


title: Infected (Wild Type) - 4dpi - Rep1 [W4A]

description:
Infected (Wild Type) - 4dpi - Rep1
W4A


title: Infected (Wild Type) - 2dpi - Rep3 [W2E]

description:
Infected (Wild Type) - 2dpi - Rep3
W2E


title: Derm CD8+CD103+, biological replicate 4

description: Derm CD8+CD103+, biological replicate 4


title: Blood CD8+CLA+ TEM, biological replicate 1

value: Blood CD8+CLA- TEM

value: Subject 1


title: Infected (Wild Type) - 2dpi - Rep1 [W2B]

description:
Infected (Wild Type) - 2dpi - Rep1
W2B


title: Blood CD8+CLA- TEM, biological replicate 1


title: Derm CD8+CD103+, biological replicate 1

description: Derm CD8+CD103+, biological replicate 1


title: Derm CD8+CD103-, biological replicate 4

description: Derm CD8+CD103-, biological replicate 4


title: 6HAI

description: replicate nº1

value: 6 hours


title: Derm CD8+CD103-, biological replicate 1

description: Derm CD8+CD103-, biological replicate 1


title: Mock - 4dpi - Rep2 [M4B]

description:
Mock - 4dpi - Rep2
M4B


title: Embryonic stem cells at passage 16 (P16 Clon30)

description: RNA-seq


title: NI_3_smallRNA-Seq

description: Trial 3

source_name: BN cells, control

value: BN cells (granulocyte-macrophage progenitor)


title: T5.3hrs.minusNutlin.rep2

description:
rRNA-depleted RNA (ribozero)
eRPKM.T5.3hrs.minusNutlin.rep2

value: B cells from lymph nodes


title: Sample_WT3-IB

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

description:
Ibrutinib Treated
processed data file: IB-normalized-counts-per-million.txt

data_processing:
alignment: TopHat2 (version 2.0.12) was used to align reads to the mouse reference genome mm10. Samtools (version 0.1.19) was used to sort, convert between formats, and calculate mapping statistics.
QC: HTseq-qa was used to check for qualities of the FASTQ reads and aligned SAM/BAM files.
annotation: GENCODE annotation database (Version M2, GRCm38, Ensembl 73) was downloaded from the GENCODE project. Aligned reads were summarized at the gene level using HTseq-count. Annotation of genes was performed using Bioconductor packages biomaRt and org.Mm.eg.db.
differential expression analysis: Read count filtering, normalization, dispersion estimation, and identification of differential expression were carried out using Bioconductor package EdgeR. Genes that had very low expression were filtered out by keeping only genes that had a minimum of 0.5 count per million reads (CPM) in at least one sample. The Trimmed Mean of M-values (TMM) normalization was then implemented to compute the effective library size.
Genome_build: mm10
Supplementary_files_format_and_content: text file deliminated by tab, containing normalized count-per-million values.

source_name: tumor burdened spleens

extract_protocol:
B-cells were mechanicially disrupted from tumor burdened spleens and placed in culture for 24 hours (with or without ibrutinib).  RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background strain

value: spleen

tag: sample type

value: WT

value: IB

tag: primary cell type

value: B-cells from tumor burdened Em-TCL mice (C57b/6)


title: Sample_WT4-IB


title: Sample_WT3-DMSO

description:
DMSO Treated
processed data file: DMSO-normalized-counts-per-million.txt

value: DMSO


title: Sample_WT1-IIB


title: Sample_WT2-DMSO


title: Sample_WT4-DMSO


title: Mock - 4dpi - Rep1 [M4A]

description:
Mock - 4dpi - Rep1
M4A

tag: age


title: Sample_Hplus4_UntreatedDMSO

value: Hplus

tag: treatment

value: B-cells from tumor burdened Em-TCL;p53R172H/+ mice (C57b/6)


title: Sample_Hplus5_UntreatedDMSO


title: Mock - 2dpi - Rep1 [M2A]

description:
Mock - 2dpi - Rep1
M2A


title: Sample_Hplus3_UntreatedDMSO


title: Infected (deltaE) - 4dpi - Rep3 [E4E]

description:
Infected (deltaE) - 4dpi - Rep3
E4E


title: Infected (Wild Type) - 2dpi - Rep2 [W2C]

description:
Infected (Wild Type) - 2dpi - Rep2
W2C


title: Mock - 2dpi - Rep2 [M2B]

description:
Mock - 2dpi - Rep2
M2B


title: Infected (deltaE) - 4dpi - Rep2 [E4B]

description:
Infected (deltaE) - 4dpi - Rep2
E4B


title: Sample_Hplus2_UntreatedDMSO


title: Sample_Hplus5_IB


title: Sample_Hplus1_UntreatedDMSO


title: Sample_Hplus3_IB


title: Sample_Hplus4_IB


title: Infected (deltaE) - 4dpi - Rep1 [E4A]

description:
Infected (deltaE) - 4dpi - Rep1
E4A


title: Infected (deltaE) - 2dpi - Rep2 [E2C]

description:
Infected (deltaE) - 2dpi - Rep2
E2C


title: Infected (deltaE) - 2dpi - Rep1 [E2A]

description:
Infected (deltaE) - 2dpi - Rep1
E2A


title: Infected (deltaE) - 2dpi - Rep3 [E2D]

description:
Infected (deltaE) - 2dpi - Rep3
E2D


title: Sample_Hplus1_IB


title: MDA-MB-231-LB-4w_3

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

description: Treated cells

data_processing:
Base calling and de-multiplexing were processed using CASAVA v1.8
Sequencing reads were mapped to the GENCODE release 19 reference using STAR version 2.4.2a
Read counts were generated using the --quantMode GeneCounts option in STAR
The Bioconductor package DESeq2 was used to detect fold change differences in expression between conditions
Genome_build: hg19
Supplementary_files_format_and_content: read counts

source_name: Invasive breast carcinoma

growth_protocol: Cells were cultured at 37C in RPMI-1640 supplemented with 10mM HEPES, 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin-streptomycin (Full RPMI).

extract_protocol:
Total RNA from HCC1806 and MDA-MB-231 cells was extracted using ZR-Duet DNA/RNA MiniPrep Plus (cat# D7003; Zymo Research, Irvine, CA)
RNA-seq libraries were generate using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina Inc., San Diego, CA).

treatment_protocol: Control cells were maintained in full RPMI + DMSO for 96 hours or 28 days, treated cells were maintained for 96 hours or 4 cycles of 5 days incubation in full RPMI + 10nM LBH589 followed by 2 days of incubation in full RPMI + DMSO.

tag: disease subtype

value: Triple-negative breast cancer

value: LBH589 (10nM) for 28 days


title: MDA-MB-231-LB-4w_2

description: Treated cells


title: CD103+CD49a+CD8 TRM, biological replicate 3

data_processing:
Basecalling softwares: HCS1.5.15.1+ RTA1.13.48 +OLB 1.9.4; parameters are $OLB-1.9.4/bin/setupBclToQseq.py –b $BaseCalls -o $Bustard
Alignment: Bowtie alignment of gene reference, bowtie2-2.2.5, -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 16 -k 200; BWA alignment of genome reference, bwa-0.7.10, -o 1 -e 63 -i 90 -L -k 2 -l 31 -t 4 -q 10
Filtering: Remove reads with adapters; Remove reads with unknown bases more than 10%; Remove low-quality reads (which are defined as reads having more than 50% bases with quality value <= 10).
Additional: TopHat alignment of genome reference (for AS, NovelTU, ExtendGene), TopHat v2.0.10, -p 16 --solexa1.3-quals --segment-length 30 --segment-mismatches 2 -r 20 --mate-std-dev 20 --library-type fr-unstranded
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files include expected.count values for each sample (*replicate#.txt) and all samples (all.gene.expected_count_ALL.txt). Gene ids in the processed data files (column 1) are the Gene IDs from the NCBI's Entrez Gene database (http://www.ncbi.nlm.nih.gov/gene/), and the "expected.count" values were obtained by the RSEM method.

source_name: CD103+CD49a+ CD8 TRM

extract_protocol:
Cells were sorted directly into Qiazol and stored at -80 degree before extraction using miRNeasy Mini Kit (Qiagen) according to manufacturer's protocol.
Library was constructed using SMART-Seq v4 Ultra Low Input RNA Kit (ClonTech) according to manufacturer's protocol.

treatment_protocol:
Epidermis were separate from dermal tissue after dispase treatment overnight. The epidermal tissue were further digested by collagenase. The resulting cell suspension were stained and sorted by FACS based on surface markers.
Epidermal T cells were sorted from epidermal cell suspension according to their cellular markers (live CD45+CD3+CD4-CD103+ CD49+/-) by a MoFlo XDP sorter.

tag: tissue origin

value: healthy skin

value: epidermal CD8+CD103+CD49a+ tissue resident memory T cells

tag: cell subset

tag: donor

value: Subject 3


title: CD103+CD49a-CD8 TRM, biological replicate 3

source_name: CD103+CD49a- CD8 TRM

value: epidermal CD8+CD103+CD49a- tissue resident memory T cells


title: MDA-MB-231-DMSO-4w_3

description: Untreated control

tag: cell line

value: DMSO for 28 days


title: MDA-MB-231-LB-4w_1

description: Treated cells


title: Huh7 CDCA8siRNA

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor, low-quality, and artifact sequence, then mapped to hg19 Tophat v.2.0.9 with parameters -p 4 --b2-very-sensitive
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using bam2rpkm v.0.06 from the University of Liverpool. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include genes, transcripts, and RPKM values for each sample.

source_name: Hepatocellular carcinoma cell line

extract_protocol:
Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: Huh7 Hepatocellular carcinoma cell line

tag: sirna

value: CDCA8 siRNA treated


title: p4 late spinous_rep1

city: New York

first: Amma

last: Asare

state: New York

address: 1230 York Ave

institute: Rockefeller University

description: Female and Male

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9, build 37) using the Bowtie program (Version 0.1.2.7). Unique reads mapped to a single genomic location (allowing two mismatches) were kept.
Transcript Assembly: Aligned reads were assembled into transcripts using Cufflinks (version 2.2.1)
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff gene expression files

source_name: Mouse back skins

growth_protocol: Keratinocytes were FACS-purifed from the back skins of indicated ages of mice

extract_protocol:
Cells were FACS sorted directly into trizol and RNA was extracted using the ZYMO Direct-Zol RNA miniprep kit (R2050) according to manufacturer instructions.
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit.

tag: tissue

value: skin

value: keratinocytes

tag: Sex

value: mixed

value: K14-H2BGFP (Tumbar et al., 2004) K10-H2BRFP

tag: strain background

tag: sorting markers

value: integrin α6, GFP, RFP


title: p4 early spinous_rep2

description: Female and Male

tag: genotype


title: p4 granular_rep2

description: Female and Male

tag: cell type


title: p4 late spinous_rep2

description: Female and Male


title: MDA-MB-231-LB-96hr_3

description: Treated cells

value: LBH589 (10nM) for 96hr


title: p4 granular_rep1

description: Female and Male


title: p4 early spinous_rep1

description: Female and Male


title: Huh1 CDCA8siRNA

value: Huh1 Hepatocellular carcinoma cell line


title: p4 basal_rep2

description: Female and Male


title: Huh7 Negative control siRNA

value: Negative control siRNA treated


title: MDA-MB-231-DMSO-4w_2

description: Untreated control

value: Triple-negative breast cancer


title: MDA-MB-231-LB-96hr_1

description: Treated cells


title: MDA-MB-231-DMSO-96hr_3

description: Untreated control

value: DMSO for 96hr


title: p4 basal_rep1

description: Female and Male


title: MDA-MB-231-DMSO-96hr_2

description: Untreated control


title: Huh1 Negative control siRNA


title: e16 early spinous_rep2

description: Female and Male embryos


title: e16 late spinous_rep1

description: Female and Male embryos


title: H1299_NSD2_sh3_H3K36me2+dox_Rep3

city: Majadahonda

first: Maria

last: Barrero

address: Crta. Majadahonda-Pozuelo KM 2.2

institute: ISCIII

data_processing:
RNA-seq processing:
Read files were quality-checked with FastQC.
Reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 2.2.1
Homo sapiens GRCh37/hg19 transcript annotations from the UCSC Genome Browser were used
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tables were generated with Cufflinks 2.2.1 and contain transcripts abundance measured in FPKM values
ChIP-seq processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie
peaks were called using SICER with the input as a control and the following settings: W200-G600-FDR0.01
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: SICER output of called peaks contains chrom, start, end, ChIP_island_read_count, CONTROL_island_read_count, p_value, fold_change, FDR_threshold

growth_protocol: Cells were maintained in RPMI-1640 medium supplemented with 10% FCS

extract_protocol:
For ChIP-seq assays were performed according to the Millipore protocol. Cells were fixed using 1% formaldehyde, harvested, resuspended in ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and sonicated using Bioruptor Pico (Diagenode) to generate fragments of 150 to 300 bp. Soluble chromatin was diluted 8 fold in ChIP RIPA buffer (10mMTris–HCl, pH 7.5, 140mMNaCl, 1mMEDTA, 0.5mMEGTA,1%Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate) and incubated with Dynabeads Protein A (Invitrogen) coupled to H3K36me2 antibody ab9049 from Abcam. After incubation, the immunocomplexes were washed sequentially with Low Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), High Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl Wash Buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.1) and TE. Immunocomplexes were eluted in ChIP elution buffer (1%SDS, 0.1M NaHCO3) and the crosslinking was reverted overnight at 65 ºC. Samples were treated with Proteinase K and RNase A and DNA was extracted using the QIAGEN PCR purification kit. Purified chromatin was used for library construction.
For ChIP-seq the amount of DNA used was 15ng from each sample. Samples were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEXTflex ChIP Sequencing kit" from Bioo Scientific (part # 5143). Adapter-ligated libraries were completed by limited-cycle PCR (13 cycles) and extracted with a double double-sided SPRI size selection. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: Cells were treated with 0.5 µg/ml doxycycline and/or 75 nM JQ1 and/or 10 nM PD0325901

tag: antibody

value: H3K36me2 (ab9049, abcam)

value: doxycycline

tag: shRNA


title: HCC1806-LB-4w_3

description: Treated cells

value: LBH589 (10nM) for 28 days


title: H1299_NSD2_sh3_H3K36me2+dox_Rep2


title: HCC1806-LB-4w_2

description: Treated cells


title: MDA-MB-231-DMSO-96hr_1

description: Untreated control


title: e16 basal_rep2

description: Female and Male embryos

value: integrin α6, GFP


title: Pooled Inputs_Rep2+3


title: e16 early spinous_rep1

description: Female and Male embryos


title: MDA-MB-231-DMSO-4w_1

description: Untreated control

value: DMSO for 28 days


title: HCC1806-DMSO-4w_3

description: Untreated control


title: MDA-MB-231-LB-96hr_2

description: Treated cells


title: e10 basal_rep2

description: Female and Male embryos

value: integrin α6, K14 H2B GFP


title: HCC1806-DMSO-4w_2

description: Untreated control


title: HCC1806-LB-4w_1

description: Treated cells


title: H1299_NSD2_sh3_H3K36me2+vehicle_Rep2

value: vehicle


title: e16 basal_rep1

description: Female and Male embryos

value: skin


title: Pooled Inputs_Rep1


title: H1299_NSD2_sh3_H3K36me2+dox_Rep1


title: H1299_NSD2_sh3_H3K36me2+vehicle_Rep1


title: HCC1806-LB-96hr_3

description: Treated cells


title: e10 basal_rep1

description: Female and Male embryos

value: keratinocytes


title: H1299_NSD2_sh3_dox+JQ1+PD0325901_Rep2

extract_protocol:
For RNA-seq Total RNA was extracted using the RNeasy kit (Qiagen)
For RNA-seq 1 µg of total RNA sample was used . PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

value: doxycycline, JQ1 and PD0325901


title: HCC1806-LB-96hr_2

description: Treated cells


title: H1299_NSD2_sh3_dox+JQ1+PD0325901_Rep1


title: HCC1806-LB-96hr_1

description: Treated cells


title: e16 late spinous_rep2

description: Female and Male embryos

value: mixed

value: K14-H2BGFP (Tumbar et al., 2004) K10-H2BRFP


title: H1299_NSD2_sh3_JQ1+PD0325901_Rep2


title: H1299_NSD2_sh3_JQ1+PD0325901_Rep1


title: H1299_NSD2_sh3_Dox+JQ1_Rep2

value: doxycycline and JQ1


title: HCC1806-DMSO-96hr_2

description: Untreated control

value: DMSO for 96 hours


title: H1299_NSD2_sh3_JQ1_Rep2


title: H1299_NSD2_sh3_dox+PD0325901_Rep2

value: doxycycline and PD0325901


title: H1299_NSD2_sh3_Dox+JQ1_Rep1


title: MDA-MB-231 cell line treated with LBH589 (10nM) for 28 days + DMSO for 14 days

description: Treated cells + 2 weeks of drug holiday

data_processing:
Raw genomic sequence reads were mapped to the 1000 Genomes (b37) build of the human genome reference using BWA-MEM.
Alignments were further processed using GATK (version 2.8-1) for INDEL realignment and PicardTools for duplicate marking.
ATAC-Seq peaks were identified using the callpeaks function in the Model-based Analysis of ChIP-Seq 2 (MACS2) with a threshold set to -q=0.01.
BigWig files were generated using bedGraphToBigWig tool
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files containing pileup score generated using the MACS2

extract_protocol:
50,000 intact cells were lysed and the nuclei were collected by centrifugation at 500 x g for 10 min at 4°C. The pellet was then incubated with transposition reaction mix for 30 min at 37°C and then purified using the MinElute PCR Purification kit (Qiagen, Hilden, Germany).
The eluted transposed DNA was barcoded and amplified for 5 cycles, and then 5 µl of the product was used for a qPCR side-reaction to prevent amplification saturation.
The optimal amount of additional PCR cycles was determined based on the number of cycles that represented one-third of maximum fluorescence intensity in the qPCR reaction after 20 cycles. The final transposed DNA was amplified for a total of 9-11 cycles. The final amplified library was purified using MinElute PCR Purification kit and eluted in 20ul elution buffer. The ATAC libraries were sequenced on the Illumina HiSeq 2500 in Rapid Mode using 50 bp paired-end.

treatment_protocol: Control cells were maintained in full RPMI + DMSO for 28 days, treated cells were maintained for 4 cycles of 5 days incubation in full RPMI + 10nM LBH589 followed by 2 days of incubation in full RPMI + DMSO. Treated cells with drug holiday, were maintained in RPMI + DMSO for an additional period of 14 days.

value: Triple-negative breast cancer


title: H1299_NSD2_sh3_JQ1_Rep1


title: H1299_NSD2_sh3_dox+PD0325901_Rep1


title: MDA-MB-231 cell line treated with DMSO for 28 days

description: Untreated control


title: MDA-MB-231 cell line treated with LBH589 (10nM) for 28 days

description: Treated cells


title: H1299_NSD2_sh3_PD0325901_Rep1


title: HCC1806-DMSO-96hr_1

description: Untreated control


title: HCC1806 cell line treated with LBH589 (10nM) for 28 days

description: Treated cells


title: H1299_NSD2_sh3_PD0325901_Rep2


title: HCC1806 cell line treated with DMSO for 28 days

description: Untreated control


title: H1299_NSD2_sh3_dox_Rep2


title: H1299_NSD2_sh3_DMSO_Rep2

value: DMSO


title: HCC1806-DMSO-96hr_3

description: Untreated control


title: 1921 (UC)

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

data_processing:
Data processing was performed using partek Flow build version 4.0.15.0702
Bases were trimmed on quality score=20. Adaptors were also trimmed.
Filter BAM files with minimal mapping quality=20.
Alignment usign Bowtie2 version 2.1.0.
Quantification to transcriptome performed using Partek E/M algorithm.
Genome_build: hg18
Supplementary_files_format_and_content: raw expression values

source_name: UC, ileal mucosa

growth_protocol: Biopsies were taken from the terminal ileum of the unoperated groups. Biopsies from pouch patients were taken by a single endoscopist (I.D.) from the most affected part within the pouch or from the middle of the pouch if there was no evidence of pathology.

extract_protocol:
Total RNA was extracted from frozen biopsies using Trizol® (Invitrogen, Carlsbad, CA) according to a standard protocol. Sample quality was assessed by both a photospectrometer (Nano Drop Technologies®, Thermo Scientific, Wilmington, DE) and agarose gels (1%). The 260/280 ratios in all samples were >1.8 and the 260/230 ratios were >1.7
Massive parallel (next-generation) sequencing (NGS) was carried out according to Illumina’s Small RNA sample preparation protocol (TruSeq Small RNA Sample Prep Kits, Illumina, San Diego, CA) for generating small RNA libraries directly from total RNA and for sequencing. miRNA libraries were sequenced on the HiSeq 2500 (Illumina) following the manufacturer’s protocol.

treatment_protocol: The biopsies were snap frozen and kept at -80ºC until RNA extraction. Scoring of histopathologic slides according to the histology sub-score of the PDAI was performed by a single IBD-trained pathologist (EB). Briefly, active inflammatory characteristics were scored according to neutrophil infiltration (0-3) and area of ulceration (0-3). Infectious or mechanical etiologies for pouch inflammation were excluded using microbiological stool assessment and endoscopy, respectively.

tag: disease state

value: UC

value: ileal mucosa


title: H1299_NSD2_sh3_DMSO_Rep1


title: 1901 (UC)


title: 1911 (UC)


title: 1783 (UC)


title: H1299_shNT+dox_Rep2

value: doxycycline

value: shNT


title: H1299_NSD2_sh5+dox_Rep2


title: 1533 (UC)


title: H1299_NSD2_sh3_H3K36me2+vehicle_Rep3

value: H3K36me2 (ab9049, abcam)


title: H1299_shNT+dox_Rep1


title: 701 (UC)


title: 1171 (UC)


title: H1299_NSD2_sh3+dox_Rep2


title: 431 (UC)


title: 311 (UC)


title: 391 (UC)


title: HCC1806 cell line treated with LBH589 (10nM) for 28 days + DMSO for 14 days

description: Treated cells + 2 weeks of drug holiday


title: H1299_NSD2_sh3+dox_Rep1


title: CTRL1

city: Beijing

first: Weiqing

last: Wang

address: No.1 Shuai Fu Yuan Street

department: Department of Otolaryngology

institute: Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College

data_processing:
Illumina Casava1.8 software was used for basecalling.
Clean reads were obtained by removing sequences containing adapter, sequences containing N for more than 10% of all the bases and low quality sequences. Then paired-end clean reads were mapped to the human genome (hg19) with TopHat (v2.0.9).
The read counts of each transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as FPKM (Fragments per kilo-base of exon per million fragments mapped). FPKM  was calculated with Cuffdiff (v2.1.1)  according to the protocol of Trapnell, C. et al., Nature biotechnology, 2010.
The lncRNAs we identified in RNA-seq can be devided into two parts. One is known lncRNAs in GENCODE database that identified by previous researches, which start with their transcripts ID ENSTnnnn in "RNA-seq_processed_data.txt". The other is novel lncRNAs that have not been identified by any previous researches and newly identified by us, which start with their transcripts ID TCONS_nnnn in "RNA-seq_processed_data.txt". The nucleotide sequence of the known and novel lncRNAs (ENSTnnnn and TCONS_nnnn) are included in "RNA-seq_processed_data.txt" file.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Sphenoid sinus mucosa

extract_protocol:
Nasal polyp tissues and normal sinus mucosa were collected, snap frozen in liquid nitrogen then frozen in -80℃; RNA were extracted using TriZol, RNA quality confirmed with  Agilent Bioanalyzer 2100 (RIN>7)
A total amount of 3 μg RNA per sample was used as input material for library construction. Ribosomal RNA (rRNA) was removed by Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA) according to the manufacturer’s instructions. Subsequently, strand-specific sequencing libraries were generated with the dUTP method using the resulting RNA by NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations.

value: Sphenoid sinus mucosa

tag: diagnosis

value: Normal control


title: CTRL2


title: CTRL3


title: non-ECRSwNP3

source_name: Nasal polyp

value: Nasal polyp

value: Non-eosinophilic chronic rhinosinusitis with nasal polyps


title: 1861 (UC)


title: 2301 (IlealCD)

source_name: IlealCD, ileal mucosa

value: IlealCD


title: 1952 (IlealCD)


title: 2361 (IlealCD)


title: 1622 (IlealCD)


title: non-ECRSwNP2


title: 1402 (IlealCD)


title: ECRSwNP2

value: Eosinophilic chronic rhinosinusitis with nasal polyps


title: 1671 (IlealCD)


title: ECRSwNP3


title: H1299_NSD2_sh3_dox_Rep1

tag: treatment


title: H1299_NSD2_sh5+dox_Rep1


title: ECRSwNP1


title: 1394 (IlealCD)


title: 1091 (IlealCD)


title: 261 (IlealCD)


title: HCC1806-DMSO-4w_1

description: Untreated control

tag: disease subtype

value: DMSO for 28 days


title: hs_17y_Cortex_WhiteMatter

city: Bethesda

first: Mingan

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

description: Genome-scale hairpin bisulfite-seq

data_processing:
For hairpin-bisulfite sequencing data, each read was searched for adaptor and hairpin sequences with cross_match. Additional search on the 3’-end of sequence reads was conducted to eliminate any sub-string derived from hairpin sequence adaptor. After adaptor removal, sequence reads shorter than 10 bp were excluded from further analysis.
Following steps were taken to retrieve and map the original sequences onto reference genome: 1) the two arms for each read pair were globally aligned using Needleman-Wunsch algorithm; 2) the sequence reads with identity less than 90% between two arms were discarded; 3) after trimming the overhangs of the aligned sequences, original sequences were recovered according to the alignment information; 4) the recovered original sequences were mapped to human reference genome (hg19) using bowtie2 with parameters ( -N 1 -L 22), and only uniquely mapped reads were retained.
The methylation patterns for all cytosines were extracted based on the mapping result and the raw sequences.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include methylation level and methylation fidelity for each CpG dyads; tab-delimited text files include methylation level for cytosines in CHG and CHH context.

source_name: frontal cortex white matter

extract_protocol:
To extract genomic DNA from paraffin block for human cortex gray and white matter, xylene was first added to these blocks, vortexed for 1 minutes and gentle shaked at RT for 5-15min. The supernatant was discarded after centrifugation, the pellets were washed with absolute ethanol twice to remove xylene, dried them on bench. 1ml lysis solution was added  (50 mM Tris, 25 mM EDTA, 100 mM NaCl, 0.5% Tween-20/SDS, pH 8), inverted every 30 minutes until the pellets were completely lysed,  40 μl 20mg/ml proteinase K was added, Incubated overnight at 55 ºC.  After 1-hour 90 ºC incubation, 5ul RNase cocktail was added and incubated at 37 ºC for 30minutes. Phenol-cholorophorm method was used to extract the DNA from samples
Hairpin bisulfite-seq library construction:  10ug genomic DNA of each sample was spiked with 0.02% unmethylated Lambda DNA (Promega) and sonicated to 200bp fragments with Covaris. After purification with PureLink® PCR Purification Kit (Invitrogen), DNA fragments were subjected to MseI and MluCI digestion (NEB) for 1h at 37°C, after purification, the elute DNA was subjected to end repair with the end repair enzyme mix (T4 DNA polymerase, Klenow enzyme, T4 PNK; NEB), dA tailing using Klenow 3’-5’ exo- (NEB) with purification at each step. Ligation to Biotin-modified hairpin adapter (5’P - GGCCAGCTGCA AG/iBiodT/GAAGCAGCTGGCCT-3', IDT) were performed using T4 DNA ligase (NEB) at 16°C for 2h with molar ratio 1:1. Then hairpin adapter and Illumina TruSeq adapter (Illumina) was added and continued ligation overnight with the final ratio of DNA: hairpin adapter: Illumina TruSeq adapter =1:10:10.  After purification by Ampure XP beads (Agencourt), DNA fragments were pulled down by Dynabeads® MyOne™ Streptavidin C1 beads (Invitrogen). Dynabeads® MyOne™ Streptavidin C1 beads were boiled at 95°C for 15min, and then subjected to Bisulfite conversion using the EpiTect Bisulphite Kit (Qiagen). After desulfonation and purification, the single-stranded uracil-containing DNA was subjected to 16 cycles of PCR reaction with Illumina TruSeq PCR primers (IDT) and 2.5 U Pfu TurboCx Hotstart DNA polymerase (Agilent). After purification by Ampure XP beads, size selection of 400-700 bp fragments was conducted with 2% agarose Pippin Prep cassettes (sage science). Libraries were sequenced using Illumina HiSeq 2000 or MiSeq.

value: brain

tag: tissue region

value: frontal cortex white matter

tag: age

value: 17 year


title: 351 (IlealCD)


title: 2092 (CP-P)

source_name: CP-P, ileal mucosa

value: CP-P


title: 2042 (CP-P)


title: 1752 (CP-P)


title: 1312 (CP-P)


title: hs_Fetal_Cortex_WhiteMatter

description: Genome-scale hairpin bisulfite-seq

value: fetal (22 week of gestation)


title: hs_Fetal_Cortex_GrayMatter

description: Genome-scale hairpin bisulfite-seq

source_name: frontal cortex gray matter

value: frontal cortex gray matter


title: 1683 (CP-P)

value: ileal mucosa


title: 1032 (CP-P)


title: non-ECRSwNP1


title: NorcadiaCP_mcherry_R2877H_Ess6_RH-R2877--H__9

city: Palo Alto

first: Robert

middle: Peter

address: 3165 Porter Drive

department: Biochemistry

institute: Stanford University

description:
CRISPRi competitive growth PCR of gRNA locus
processed data file: Table_S6.xlsx

data_processing:
Library strategy: REDI
Sequence analysis of DNA library composition. Paired-end Illumina DNA sequencing was used to examine the composition of DNA libraries produced during this study. Amplification of the molecular probe library with DirMP-fwd and DirMP-rev primers produced amplicons of 276 bp in length. These amplicons were paired-end sequenced (2 x 250 cycles) to cover the entire length of the molecular probe sequences in both directions. To mitigate the confounding effect of sequencing-derived errors, analyses were restricted to sequences located between the molecular probe common amplification sites (TAGACGTAAGCCTGGTCTCA and ATCGGGAATCGAGTCTACCT) where the forward and reverse reads were in perfect agreement. In addition, the same sequencing run was used to analyze and compare the array- and yeast-derived libraries. The calculated sequencing error rates for this run (based on PhiX control DNA that was included in the sample) were 1.78% and 2.63% for read1 and read2, respectively. Based on these rates, sequencing artifacts are predicted to contribute ~0.01% of the observed errors (.0178 x 0.0263 x 0.25). Notably, an 8 nt random barcode was included in the design and synthesis of the molecular probes. These sequences become clonal after transformation into yeast and are no longer useful for improving quantification of target DNA (as they were originally intended). As the sequences of these barcodes are not known beforehand, they were excluded from the library composition analysis. Sequencing analysis of the molecular probe libraries revealed that 61.8% of the array-synthesized library and 3.6% of the library produced by REDI, did not match any of the probes that were targeted for selection (Figure 2B). We refer to these DNA sequences as ‘contaminating DNA’. These sequences were analyzed for similarity to a designed probe using bowtie2 (version 2.2.8) and samtools (version 1.2), and for hybrids (i.e. sequences where the first Homer is identical or similar to one probe, and where the second Homer is identical or similar to a different probe). For the library produced by REDI, we excluded sequencing reads that were associated with 66 clones that were selected (i.e. cherry-picked) but later determined to have a ‘petite’ phenotype (reduced growth due to spontaneous loss of mitochondrial DNA). We attempted to remove these clones by replica plating the entire collection onto growth medium that only supports respiration prior to creating the probe library. We still observed low levels of sequencing reads from these clones in the library. As they do not represent true contaminating DNA, they were excluded from the analysis presented in Figure 2.
Analysis of competitive growth assay data. Counts were generated by enumerating all sequences with perfect matches in both Read 1 and Read 2 of paired-end MiSeq data (i.e. requiring that the first 60 nucleotides of Read 1 containing the barcode and gRNA target complementarity were also present without mismatch in Read 2 (reverse complement)). These sequences were then mapped to the gRNAs that we had designed. Given the nature of our experimental design, we expect many strains to exhibit growth defects upon addition of ATc, and, consequently, produce a major change in the distribution of the resulting pool composition. This phenomenon created a unique challenge to the data normalization that is required when comparing across separate experiments. Widely used normalization methods, such as quantile normalization that assumes an unchanged shape of the distributions, or z-score normalization that assumes common mean (or median) across samples, cannot be applied.  To address this challenge, we developed a novel normalization strategy that relies on the identification of a set of “neutral” guides. Based on the experimental design, we make the following two assumptions: 1) many of the guides are damaging, i.e. lead to reduced fitness of the cells, and hence a reduced proportion of the guides in the pool; 2) a smaller but significant portion of the guides are neutral, i.e. they do not change the fitness of the cells, but their relative proportion will slightly increase in the pool due to the decreased fitness of the other strains. Based on these two assumptions, the following three steps were taken to define neutral guides:   A) We normalize all samples by the relative values of their respective total sequencing read counts. B)We clustered the log-transformed data using Euclidean distance measure and complete linkage algorithm, and chose a distance cutoff value of 11 to obtain the major clusters. C)We calculated the average log counts of all guides in each cluster and selected the cluster with the highest average counts as the neutral cluster. Guides in the neutral cluster had slightly increased counts in the ATc samples when compared to the non-ATc samples, consistent with the expected behavior of neutral guides.
Sequence analysis of diploid recombinants. Paired-end Illumina sequencing was used to identify the exogenous DNA physically linked to each barcode in the diploid recombinants. For each plate of recombinants, total genomic DNA was purified from ~150-200 million cells using the YeaStar Genomic DNA Kit (Zymo Research) and following the manufacturer’s directions. The genomic region of interest was PCR amplified from 1µl of purified genomic DNA template [98°C for 2 min, (98°C for 10 sec, 60°C for 20 sec, 72°C for 30 sec) x 30 cycles, 72°C for 7 min], producing a 429 bp amplicon (molecular probe library) or a 941 bp amplicon (CRISPRi library). Typically, 240 cycles were used to sequence the exogenous DNA in the forward direction, and 60 sequencing cycles were used to sequence the barcode in the reverse direction. Briefly, sequencing reads were binned according to short (i.e. six nucleotide) indexing barcodes included in both the forward and reverse sequencing primers (index pairs were unique to each plate of diploid recombinants), and, then, by the 26 bp barcode (unique to each barcoder strain and, thus, colony position in the arrayed plate of recombinants). From each set of binned reads, the exogenous DNA sequence between the common priming regions was identified and compared to the designed molecular probe or guide RNA libraries. Sequences matching a designed sequence perfectly were of interest and were prioritized for selection. We further refined this list by de-prioritizing clones where the perfect match sequence was supported by fewer than 50 reads. In some cases, we also filtered diploid recombinants having multiple different sequences that perfectly matched multiple different designed sequences (likely indicating robotic picking of a ‘mixed colony’). Extending this last filter to accommodate partially matching sequences will mitigate contamination from mixed colonies (Figure S3) and will improve library quality.
Sequence analysis of probes missing or poorly represented from the molecular probe library. We identified 49 molecular probes that were absent or poorly represented in the molecular probe library following parsing in yeast. These probes were identified by fewer than 50 sequencing reads in the DNA library composition analyses. To explore explanations for the poor representation of these probes, we selected the 49 colonies representing these probes, collectively amplified the exogenous DNA (i.e. the amplified array-synthesized oligonucleotides that integrated into the target locus of the recipient strain), and sequenced those amplicons using MiSeq (Illumina). Sequences matching those found in the composition analyses of the original library were identified and are presented in different colors in Figure S3A. An examination of diploid recombinant sequences associated with the 49 indexing barcode pair/barcode combinations of the poorly represented clones are given in Figure S3B. Sequences represented by fewer than five reads were excluded from these analyses.
Molecular probe prepara

organism: Saccharomyces cerevisiae

source_name: Yeast Genomic DNA

extract_protocol:
Total genomic DNA was purified from ~150-200 million cells using the YeaStar Genomic DNA Kit (Zymo Research) and following the manufacturer’s directions.
The genomic region of interest was PCR amplified from 1µl of purified genomic DNA template [98°C for 2 min, (98°C for 10 sec, 60°C for 20 sec, 72°C for 30 sec) x 30 cycles, 72°C for 7 min], producing a 429 bp amplicon (molecular probe library) or a 941 bp amplicon (CRISPRi library).

tag: sample number

tag: miseq run

tag: sample type


title: 542 (CP-P)

tag: tissue


title: NorcadiaCP_mcherry_R2877H_Ess6_RH-R2877--H__8


title: 752 (CP-P)


title: NorcadiaCP_mcherry_R2877H_Ess6_RH-R2877--H__2


title: NorcadiaCP_mcherry_R2877H_Ess6_RH-R2877--H__6


title: NorcadiaCP_mcherry_R2877H_Ess6_RH-R2877--H__5


title: 282 (CP-P)


title: NorcadiaCP_mcherry_R2877H_Ess6_RH-R2877--H__12


title: hs_17y_Cortex_GrayMatter

description: Genome-scale hairpin bisulfite-seq


title: 2242 (NP-P)

source_name: NP-P, ileal mucosa

value: NP-P


title: 112 (CP-P)


title: NorcadiaCP_mcherry_R2877H_Ess6_RH-R2877--H__11


title: Justin-Becky-7_YPD_+_ATC

value: Justin-Becky


title: 1842 (NP-P)


title: Justin-Becky-4_YPEG


title: 802 (CP-P)


title: 1422 (NP-P)


title: 1253 (NP-P)


title: Cas9_Sec14_RH-YPEG_ATC_3


title: Justin-Becky-1_YPEG_+_ATC


title: 482 (CP-P)


title: Cas9_Sec14_RH-YPEG_ATC_2


title: 822 (NP-P)


title: 582 (NP-P)


title: Cas9_Sec14_RH-YPEG_ATC_1


title: Cas9_Sec14_RH-YPEG_5


title: 522 (NP-P)


title: 722 (NP-P)


title: 442 (NP-P)


title: Cas9_Sec14_RH-YPEG_6


title: 202 (NP-P)


title: Cas9_Sec14_RH-YPEG_4


title: 2141 (NC)

source_name: NC, ileal mucosa

value: NC


title: 2232 (NP-P)


title: Cas9_Sec14_RH-YPD_ATC_8


title: Justin-Becky-10_YPD


title: Cas9_Sec14_RH-YPD_ATC_7


title: Cas9_Sec14_RH-YPD_12


title: 2101 (NC)


title: Cas9_Sec14_RH-YPD_11


title: 1412 (NP-P)


title: 1932 (NC)


title: 1931 (NC)


title: Cas9_Sec14_RH-YPD_10


title: 1801 (NC)


title: DirMPCA-Mp3322_Sec14_RH-MP__4

description:
Molecular probe library analysis
processed data file: Table_S3.xlsx


title: 1882 (NC)


title: 1713 (NC)


title: Cas9_Sec14_RH-YPD_ATC_9


title: 1661 (NC)


title: NorcadiaCP_mcherry_R2877H_Ess6_RH-R2877--H__3


title: 1232 (CLDP)

source_name: CLDP, ileal mucosa

value: CLDP


title: 1061 (NC)


title: DirMPCA-Mp3322_Sec14_RH-CA__1

description:
Molecular probe library analysis
processed data file: Table_S2.xlsx

source_name: PCR of Custom Array Oligos