title: human smRNA-seq in HeLa cells rep2

first: Qi

last: Zheng

address: 1701 Rockland Road

institute: Nemours Children's Health

description:
smRNA (small RNA)
human_refGene_mRNA_invivo_HeLa_structScore.txt
human_refGene_mRNA_invivo_HeLa_struct_hotspot_anno.txt

data_processing:
Quality control of the reads. The quality scores for the raw read were carefully checked for their average values, minimum, maximum and standard deviations to make sure all library qualities were in good and comparable status. The correct labeling of 3'-adapters and multiplex indices were also checked to confirm the libraries.
Trimming of 3'-adapters. Reads were trimmed to remove 3'-adapters using Cutadapt (v1.0) program with ≤10% mismatches and ≥10 nt aligned bases. Reads ≤15 nt after trimming were discarded before all subsequent analysis. Untrimmed reads were kept separately from trimmed reads and processed independently in following steps.
Reducing to NR-tags. Both trimmed and untrimmed reads were reduced to NR-tags to save processing time and space requirements. However, the clone abundance of each NR-tag was retained and used in all subsequent abundance calculations in this study, therefore, we will call reads and NR-tags interchangeably hereafter.
Mapping to primate genomes. NR-tags (reads) were mapped to UCSC hg19, refMac2 and rheMac2 genomes using Bowtie (v.0.12.9) program for human, rhesus and cynomolgus, respectively. Note that cynomolgus only has a draft genome release and no corresponding gene model annotations, so we used the reference genome as well as genome annotation of rhesus for all cynomolgus analysis in this study. The mapping parameters for Bowtie program were carefully tuned to insure all alignments with ≤6% mismatches in the first 34 nt seeds and ≤8% mismatches in the whole reads will be reported, and up-to 100 random mapping hits were allowed. Note that for GMUCT reads up-to 10 random hits were allowed. Also note that for all libraries from cynomolgus, the mismatch criteria were 2% looser (8% for seed and 10% for entire read) for the mapping, because they were mapping to a slightly divergent genome instead their own. All mapping results were post-filtered to guarantee the mapping criteria listed above using in-house programs.
For reads with multiple hits on the genomes (multiply mapped), a max-diverge filter was also implemented, to select only those hits with a mismatch percentage no more than 4% to the best hit of each read. This filter is similar to UCSC BLAT and Bowtie “--best” mode. All mapping information, such as insert length, clone abundance, and number of locations on the genome were summarized and loaded into local MySQL databases for further queries.
Mapping across transcript splicing boundaries. To map across splicing boundaries, we first compiled our own GFF annotation files of transcript exons, including coding mRNAs (RefSeq-mRNA for human, Ensembl-mRNA for rhesus and cynomolgus), all non-coding RNAs (Rfam annotated structural RNAs for human and Ensembl-ncRNAs for rhesus and cynomolgus), and also lincRNAs for human. The unmapped reads from previous steps were collected and remapped to the genomes provided these GFF annotations using TopHap (v2.0.8) program. The parameters were tuned to meet the exact same criteria as for the Bowtie mapped reads. At last, the Tophat hits (spliced reads) were also selected for the max-diverge filter and summaries and stored into local MySQL database.
Genome_build: UCSC hg19 for human, UCSC rheMac2 for rhesus and cynomolgus libraries
Supplementary_files_format_and_content: The "*_expr.txt" files are tab-delimited text files containing the expression values of all primate mRNA transcripts in raw clone number (weighted), RPM and RPKM values.
Supplementary_files_format_and_content: The "*_structScore.txt" files are tab-delimited text files containing the calculated "structure score" of every nucleotide of all primate mRNA transcripts with sufficient dsRNA-seq and ssRNA-seq coverages, as well as other pertinent information such as their gene length, mRNA length, and (weighted) clone number of the dsRNA-seq and ssRNA-seq reads.
Supplementary_files_format_and_content: The "*_struct_hotspot_anno.txt" files are tab-delimited text files containing numerous information for all predicted "structure hotspots", defined as long regions with significantly high structure scores in three primates. They also contain many other pertinent information, such as the class, summit, average and max structure score of the hotspots, RPKM values from mRNA-seq, smRNA-seq and public GMUCT libraries for the entire mRNAs or just the structure hotspot regions. Information regarding whether they are bound by the DGCR8/Drosha microprocessor and whether are conserved between human and rhesus is also included.

source_name: HeLa cells

extract_protocol:
For all the in vitro dsRNA-seq and ssRNA-seq libraries, RNAs were treated with ssRNase (RNaseOne) and dsRNase (RNase V1), respectively; For mRNA-seq libraries poly A+ RNAs were isolated from total RNA using Dynabeads mRNA direct kit (Ambion, Austin, TX); For smRNA-seq libraries RNAs were prepared as previously described in F. Li et al., The Plant cell 24, 4346. Briefly, total RNA was run on a 15% TBE-Urea Gel and gel slices containing 15-35 nt RNAs were isolated and eluted from acrylimalyde by mixing with 0.3 M NaCl for 4 hours at RT.
The dsRNA-seq, ssRNA-seq, mRNA-seq and smRNA-seq libraries were constructed as previously described in F. Li et al., The Plant cell 24, 4346. The 3’ and 5’ adapters, Reverse Transcriptase Primer, 5’ PCR primer, and 3’ PCR Primers matching the TruSeq small RNA sequencing kit (Illumina, San Diego, CA) were synthesized and HPLC purified by IDT (Coralville, IA).

tag: library strategy

value: smRNA-seq

tag: enzyme treatment

tag: ngs platform

value: Illumina Hi-Seq2000 50 nt strand-specific


title: human invivo ssRNA-seq rep3

status: Public on May 01 2017

type: SRA

city: Wilmington

state: DE

country: USA

description:
ssRNA (single-stranded RNA)
RNA is treated with dsRNase (RNase V1) in vivo
human_refGene_mRNA_invivo_HEK293T_structScore.txt
human_refGene_mRNA_invivo_HEK293T_struct_hotspot_anno.txt

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: HEK293T cells

growth_protocol: For invivo HEK293T dsRNA-seq and ssRNA-seq libraries, HEK293T cells were seeded in 15-cm standard Corning tissue-culture treated culture dishes (Sigma, St Louis, MO), grown to 90% confluence (approximately 18 million cells) in DMEM media (Life Technologies, San Diego, CA) supplemented with L-glutamine, 4.5 g/L D-glucose, 10% fetal bovine serum (FBS (Atlanta Biologics, Atlanta, GA)) and Pen/Strep (Fisher Scientific, Waltham, MA).

treatment_protocol: For all the in vivo dsRNA-seq and ssRNA-seq libraries, a 37% formaldehyde solution (Sigma, St. Louis, MO) was added drop-wise with mixing directly to cell culture dishes containing 90% confluent cells to a final concentration of 1% and incubated at room temperature for 10 minutes to cross-link the RNAs with proteins. The cross-linking reaction was quenched with 1 M glycine (Sigma, St Louis, MO) at a final concentration of 125 mM for 5 minutes with mixing. Then, cells were washed twice with ice-cold PBS and collected.

value: ssRNA-seq

value: proteinase K then dsRNase in vivo

tag: cell line


title: human smRNA-seq in HeLa cells rep1


title: human smRNA-seq in HEK293T cells rep2

description:
smRNA (small RNA)
human_refGene_mRNA_invivo_HEK293T_structScore.txt
human_refGene_mRNA_invivo_HEK293T_struct_hotspot_anno.txt


title: human invivo ssRNA-seq rep1


title: human invivo ssRNA-seq rep2


title: human invivo dsRNA-seq rep1

description:
dsRNA (double-stranded RNA)
RNA is treated with ssRNase (RNaseOne) in vivo
human_refGene_mRNA_invivo_HEK293T_structScore.txt
human_refGene_mRNA_invivo_HEK293T_struct_hotspot_anno.txt

value: dsRNA-seq

value: proteinase K then ssRNase in vivo


title: human invivo dsRNA-seq rep3


title: human KRAS G12V mutant form overexpressed in HMEC cells [KRAS_G12V-2]

city: Salt Lake City

first: Mumtahena

last: Rahman

state: UT

address: 20 South 2030 East, Rm 420

department: Biomedical Informatics

institute: University of Utah

data_processing:
Quality checking with FASTQC
Alignment and quantification with R package Rsubread
FPKM normalization with edgeR and limma
TPM normalization from the FPKM values
log2 values of the TPM normalized gene counts
Genome_build: UCSC hg19
Supplementary_files_format_and_content: TPM-log2 normalized gene count processed file is a tab-delimited .txt file

growth_protocol: Human mammary epithelial cells, grown in Stemgent WIT-P culture medium at 3% CO2 and 37°C

extract_protocol:
Cells were scraped into RNA-Later and stored on ice until processing.  Then RNA was isolated from pelleted cells using a Qiagen Rneasy mini kit (with Rnase-free DNase set) and QIAshredders.
Illumina TruSeq stranded mRNA kit

treatment_protocol: Genes were introduced for over-expression by way of adenovirus.  Cells were infected with MOI 500 Adenovius for 30 hours.

tag: cell type

value: Human mammary epithelial (HMEC) cells

tag: genotype/variation

value: overexpressing human KRAS G12V mutant form


title: human invivo dsRNA-seq rep2


title: human mRNA-seq

description:
mRNA (polyA+ RNA)
RNA is polyA+ selected
human_refGene_mRNA_structScore.txt
human_refGene_expr.txt

source_name: brain tissue

value: mRNA-seq

tag: tissue

value: brain


title: seeds harvested at stage 8.3

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

country: France

institute: INRAE

data_processing:
Sequencing adaptors and low complexity reads were removed in an initial filtering step.
After quality control, reads were mapped to the ‘Williams 82’ soybean reference genome (assembly Glyma.Wm82.a1.0, annotation v2.0) using Bowtie2
Three lanes of a sequencing flowcell were clustered using the TruSeq PE Cluster kit v3-cBot-HS kit (Illumina)
Genome_build: Glyma.Wm82.a1.0

organism: Glycine max

source_name: seed

growth_protocol: Soybean plants (Glycine max L. cv. BRS284) were grown using standard planting and cultural techniques in the experimental farm of São Paulo State University in Botucatu (Brazil) in two consecutive years (2012/2013; 2013/2014).

extract_protocol:
Total RNA was extracted from while seeds using the NucleoSpin® RNA Plant kit (Macherey-Nagel)
cDNA libraries were generated using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA) to obtain single-end 100-bp long inserts

treatment_protocol: Seeds were freshly harvested and frozen inLN2 or subjected to fast drying by incubation at 40% RH at 30 ° C until they reached a moisture content of 10% (dry weight basis).

tag: genetic background

tag: developmental stage

value: stage 8.3

tag: treatment

value: fresh


title: seeds harvested at stage 9, replica 2

value: stage 9


title: seeds harvested at stage 8.2

value: stage 8.2


title: seeds harvested at stage 9, replica 1


title: seeds harvested at stage 7.2 and dried, replica 2

value: stage 7.2

value: dried


title: seeds harvested at stage 7.3

value: stage 7.3


title: human smRNA-seq in HEK293T cells rep1

value: smRNA-seq


title: seeds harvested at stage 7.1

value: stage 7.1


title: DR-ER-Hoxb8 cell SL0101-01 Rep1

city: Boston

first: Pui

last: Lee

state: MA

address: 60 Fenwood Rd.

institute: Brigham and Womens Hospital

description: sample 17

data_processing:
base calling by bustard
Alignment using BWA to mouse assembly 9 (UCSC 2009).
The processed data is separated by sample barcode and aligned using Tophat version 2.0.10 (Kim et. al. 2013) with default settings.
Transcripts are quantified using the Cufflinks suite version 2.2.1 (Trapnell et. al. 2012).
Data are processed through CuffNorm if 50% of the reads align and there are at least 100,000 aligned pairs per sample. This filtering is done to ensure the quality of the normalization step.
Genome_build: Mouse assembly 9 (UCSC 2009)
Supplementary_files_format_and_content: txt file with gene count from CuffNorm

organism: Mus musculus

source_name: Immortalized myeloid progenitor cell line

growth_protocol: For ER-Hoxb8 cells, cells were maintained in SCF-containing medium with b-estradiol until the time of differentiation.  Cells were differentiated for 3 days in SCF-containing medium without b-estradiol.

extract_protocol:
Bone marrow cells were isolated and stained with antibodies to lineage panel, c-kit, Sca-1, CD127, FcgRII/III, CD34, Ly6C, CD115, and CD135.  GMP (10,000 cells; kit+ Sca- CD127- FcgRII/III+, CD34-low, Ly6C-low, CD135-) were sorted directly into RLT buffer (Qiagen).  Total RNA was isolated by Qiagen RNAeasy Micro kit.  For ER-Hoxb8 cells, cells were pelleted and directly resuspended in RLT buffer for RNA isolation using Qiagen RNAeasy Micro Kit.
Illumina SmartSeq2 low-input RNA-seq

treatment_protocol: ER-Hoxb8 cells were differentiated in the presence of DMSO, rapamycin (100 nM) or SL0101-01 (10 nM).

value: DR-ER-Hoxb8 cells


title: DR-ER-Hoxb8 cell SL0101-01 Rep2

description: sample 18


title: DR-ER-Hoxb8 cell Rapamycin Rep1

description: sample 15


title: DR-ER-Hoxb8 cell Rapamycin Rep2

description: sample 16


title: DR-ER-Hoxb8 cell DMSO Rep2

description: sample 14


title: DR-ER-Hoxb8 cell DMSO Rep1

description: sample 13


title: Tsc2 KO Rep3

description: sample 12

source_name: Bone Marrow

value: Granulocyte-Monocyte Progenitors

tag: genotype

value: Raptor knockout


title: Tsc2 fl/fl Rep3

description: sample 9

value: Raptor fl/fl


title: Tsc2 fl/fl Rep2

description: sample 8


title: Tsc2 KO Rep1

description: sample 10


title: human ssRNA-seq

description:
ssRNA (single-stranded RNA)
RNA is treated with dsRNase (RNase V1) in vitro
human_refGene_mRNA_structScore.txt
human_refGene_mRNA_struct_hotspot_anno.txt

value: ssRNA-seq

value: dsRNase in vitro

value: Illumina Hi-Seq2000 50 nt strand-specific


title: seeds harvested at stage 8.1

value: stage 8.1


title: THP1 POLR2A 4C

city: Singapore

first: Melissa

middle: Jane

last: Fullwood

address: 14 Medical Drive, #12-01

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

library_source: genomic

data_processing:
Library strategy: 4C-seq
The viewpoint sequence was removed by Tagdust2
processed read was mapped by BOWTIE2 and over 80% of each library could be mapped to the hg19 genome.
The mapped 4C-seq data was analysed by r3CSeq
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited files with coordinates of interaction anchors with read counts and p-values and q-values.

molecule: genomic DNA

source_name: acute monocytic leukemia

growth_protocol: Thp-1, K562 and HL-60 were cultured in RPMI-1640 supplemented with 10% FBS at 37˚C, 5% CO2. SNU16 cells were cultured in RPMI media with 10% Fetal Bovine Serum (FBS) and 1% penicillin-streptomycin.

extract_protocol:
40 million cells were harvested and crosslinked with 1% formaldehyde for 10 min at room temperature with rotation. The crosslinking was quenched by glycine for 5 min at room temperature with rotation. Following SDS and Triton X-100 permeabilization, nuclei were digested with HindIII-HF (NEB, R3104L) overnight. Following proximity ligation, reverse cross-linking and DNA purification, the circular DNA was digested with DpnII (NEB, R0543S) 37 ˚C overnight, and circularized.
4C-seq was performed as previously described with some modifications (Splinter et. al. Methods 58 (2012) 221-230). The 4C-seq library was generated by performing nested inverse PCR using Phusion DNA polymerase (Thermo Scientific, F-531) with the primers listed in Table S3. The cycling condition of the 1st PCR was: 98˚C for 30s, 98˚C for 5s, 56˚C for 30s, 72˚C for 45s and repeat Step 2 to 4 for 15 times and the PCR end with a final extension at 72˚C for 60s. 10% of the 1st PCR product was used for 2nd PCR. The cycling condition for 2nd PCR was: 98˚C for 30s, 98˚C for 5s, 60˚C for 30s, 72˚C for 45s and repeat Step 2 to 4 for 14 or 16 times and the PCR end with a final extension at 72˚C for 60s.  The 4C-seq library was purified by 4-20% gradient TBE PAGE gel (ThermoFisher Scientific, EC6225BOX) and the smear band regions including expected size was excised. The library was recovered by incubating the shattered gel slice with 200uL TE buffer overnight at 37˚C and the DNA in supernatant was ethanol precipitated in presence of GlycoBlue (ThermoFisher Scientific AM9516). The multiplex 4C-seq library was pooled in equal molar ratio and sequenced on Mi-seq with 2X250bp or 1X150bp. The multiplex 4C-seq library consisted of 3 cell lines (HL60, THP1, K562) and 2 viewpoints (MYC, POLR2A) with 2 replicates per condition. 500,000-1,000,000 reads were produced for each library.

tag: view point


title: THP1 MYC 4C

value: MYC


title: K562 POLR2A 4C

source_name: chronic myelogenous leukemia


title: Tsc2 fl/fl Rep1

description: sample 7


title: human dsRNA-seq

description:
dsRNA (double-stranded RNA)
RNA is treated with ssRNase (RNaseOne) in vitro
human_refGene_mRNA_structScore.txt
human_refGene_mRNA_struct_hotspot_anno.txt

value: dsRNA-seq

value: ssRNase in vitro

value: brain


title: Raptor KO Rep3

description: sample 6


title: Raptor KO Rep2

description: sample 5


title: Raptor KO Rep1

description: sample 4


title: seeds harvested at stage 7.2 and dried, replica 1

value: stage 7.2


title: K562 MYC 4C


title: HL60 POLR2A 4C

source_name: acute promyelocytic leukemia


title: seeds harvested at stage 7.2, replica 2

value: fresh


title: seeds harvested at stage 7.2, replica 1


title: Raptor fl/fl Rep2

description: sample 2


title: Raptor fl/fl Rep3

description: sample 3


title: HL60 MYC 4C


title: Tsc2 KO Rep2

description: sample 11


title: YW_8pos

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

description:
Steady state untreated cells
RNAseq_pos_neg_all.xlsx

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7
alignment: hisat 0.1.5  with deafult parameters
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm9 -d <List of tag dir> -count exons -condenseGenes -strand + -norm 1e7
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

extract_protocol:
Enzymatic digestion and gradient seperation. Antibodies used throughout the research are: CD11b (clone M1/70), Ly6C (clone AL21), Ly6G (clone H129.19), f4/80 (clone BM8), CD64 (clone 90322), CD14 (clone Sa2-8), MerTK (polyclonal), MHCII (clone M5/114.15.2)
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
3' RNA-seq for digital gene expression quantitation

value: FACS sorted cells

value: Brown adipose tissue

tag: selection marker

value: CD11b+ Ly6C- f4/80+ cd64+ CD14+MerTK+MHCII+dTomato+


title: YW_8neg

value: CD11b+ Ly6C- f4/80+ cd64+ CD14+MerTK+MHCII+dTomato-


title: YW_7pos


title: input_shield_rep2

city: Oslo

first: Håvard

last: Aanes

address: Sognsvannsveien 20

department: Dept of microbiology

country: Norway

institute: Oslo University Hospital

description: RIP antibody: none

data_processing:
Base calling
The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end, and de-multiplexed (4 samples in each lane).
Reads were mapped to Zv10 using the STAR aligner (Dobin et al., 2013) with options --seedSearchStartLmax 15 --clip3pNbases 10 --clip5pNbases 10 --outFilterMultimapNmax 20 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNminOverLread 0.0 --outFilterMatchNmin 15 --outFilterScoreMinOverLread 0.0.
We performed peak calling and detection of differentially methylated genes using ExomePeak (Meng et al., 2013).
Genome_build: Zv10
Supplementary_files_format_and_content: Bed files with enriched regions from each developmental stage, and txt file with raw and normalized read counts for each gene using the input samples

organism: Danio rerio

source_name: Embryos

growth_protocol: Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14-10 hour light-dark cycle at a density of 5-10 fish/L. System water (SW) was prepared from particle and active charcoal filtrated tap water, deionized by reverse osmosis (RO) and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm, general hardness (GH) 4-5 and pH 7.5 by addition of 155g synthetic sea salt (Instant Ocean, Blacksburg, USA), 53g sodium carbonate and 15g calcium chloride (Sigma-Aldrich) per liter RO water. Adult fish were fed with Gemma Micro 300 (Skretting, Stavanger, Norway) dry feed twice a day and live artemia (Scanbur, Karlslunde, Denmark) once a day. Health monitoring was by daily inspection, use of sentinel fish sent for pathology (ZIRC, Eugene, Oregon) and water microbiology analysis (NMBU Vetbio, Oslo) every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks (Aquatic Habitats, Apopka, FL). Harvested embryos were kept in autoclaved SW at 28 °C, harvested by snap freezing (liquid nitrogen) and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act (2009), the EU Directive 2010/63.

extract_protocol:
We isolated total RNA from 4 stages (1-cell/20 minutes post fertilization, 2-, 4- and 6-hpf) in batches of 200 embryos using TRIzol (Invitrogen, cat.no. 15596-018). We added ERCC spike-in RNA (TermoFisher scientific, cat.no. 4456740) to the trizol. For each sequencing library two batches of total RNA (from 200 embryos) were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit (Ambion, #61006).
The m6A-RIP experiment was carried out as previously described (Ke et al., 2015) and the protocol can be found in supplementary file 1. Briefly, polyA+ enriched RNA was partially fragmented by alkaline hydrolysis, ethanol precipitated and SDS-PAGE size selected for 20-80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A (Life Technologies, # 10008D)-conjugated anti-m6A antibody (Synaptic systems, # 202003). After stringent washing, the bound RNA was eluted with 0.5mg/ml N6-methyladenosine sodium salt (Sigma-Aldrich, # M2780), ethanol precipitated, and resuspended with RNase-free water. The eluted RNA and input RNA were subjected to 3’pre-adenylated DNA liker ligation with T4 RNA ligase2, truncated KQ (NEB, #M0373L), at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine (BrdU)-CLIP protocol described in Weyn-Vanhentenryck et al. (2014), with improved RT primers indicated in Ke et al. (2015).

value: Shield stage embryos

tag: strain

value: AB wild type


title: YW_7neg


title: input_shield_rep1

description: RIP antibody: none


title: ip_shield_rep2

description: RIP antibody: Synaptic systems, # 202003


title: YW_6pos


title: YW_6neg


title: YW_5neg


title: YW_5pos


title: Triple_Ribo_WT_3_input_3a

description:
Steady state untreated cells
RNAseq_Ribo.xlsx

value: wildtype

tag: antibody

value: none, input


title: Triple_Ribo_WT_3_IP_3b

value: cells immunopercipitated by HA-tag antibody


title: Triple_Ribo_WT_1_input_1a


title: Triple_Ribo_WT_2_IP_2b


title: Triple_Ribo_WT_1_IP_1b


title: ip_shield_rep1


title: input_sphere_rep2

description: RIP antibody: none

value: sphere stage embryos


title: Triple_Ribo_Mecp2_4_input_7a

value: Mecp2 KO


title: Triple_Ribo_WT_2_input_2a


title: ip_sphere_rep1


title: ip_sphere_rep2


title: input_sphere_rep1

description: RIP antibody: none


title: input_64cell_rep2

description: RIP antibody: none

value: 64-cell embryos


title: Raptor fl/fl Rep1

description: sample 1

value: Granulocyte-Monocyte Progenitors

value: Raptor fl/fl


title: Triple_Ribo_Mecp2_3_IP_6b


title: Triple_Ribo_Mecp2_3_input_6a


title: Triple_Ribo_Mecp2_4_IP_7b


title: Triple_Ribo_Mecp2_2_input_5a


title: Triple_Ribo_Mecp2_1_input_4a


title: ip_64cell_rep2


title: input_64cell_rep1

description: RIP antibody: none


title: Triple_Ribo_Mecp2_1_IP_IgG_4c


title: Triple_Ribo_Mecp2_2_IP_5b


title: Triple_Ribo_Mecp2_1_IP_4b


title: CX3CR1_2

value: CD11b+ Ly6C- f4/80+ cd64+ CD14+MerTK+MHCII+


title: ip_64cell_rep1


title: input_1cell_rep2

description: RIP antibody: none

value: 1-cell embryos


title: CX3CR1_3


title: CX3CR1_1


title: ip_1cell_rep2


title: input_1cell_rep1

description: RIP antibody: none


title: ACSS2- Trained Rep 2

city: Philadelphia

first: Shelley

middle: L.

last: Berger

state: Pennsylvania

address: 3400 CIVIC CENTER BLVD

department: Cell and Developmental Biology

institute: University of Pennsylvania

description:
processed data file:
SOR.ACSS2_KD.mm10.bw
RNA-seq Adjusted Scores.txt

data_processing:
Demultiplexing: done using bcl2fastq (v02.14.01.07) on BaseSpace.
Alignment: data were aligned using STAR (RNA-STAR 2.3.0) on BaseSpace.
Quantitation: aligned tags were assigned to exons using HTSeq (v0.6.1) using parameters -f sam -r pos -s yes -t exon -i gene_id and the RefSeq gene/exon annotation. Tag counts per gene were then adjusted for library size using DESeq.
Track Creation: bigWigs were created for visualization of the RNA-seq data in the following way. First, BED files containing aligned tags were merged over replicates and coverage maps (bedGraphs) were made using BEDTools' genomeCoverageBed utility. Map scores were then normalized per million reads aligned. Finally, bigWigs were generated from subtracted maps using UCSC Genome Browser's bedGraphToBigWig utility.
Genome_build: mm10
Supplementary_files_format_and_content: BigWigs are RPM-adjusted coverage maps showing RNA-seq signal. The RNA-seq Adjusted Scores.txt file is a table showing quantitation of aligned tags over genes.

molecule: polyA RNA

source_name: ACSS2- Trained_hippocampus

growth_protocol: Male 10-12-week-old C57BL/6J mice were housed at 22–25 °C in a 12-h light/ dark cycle and provided food and water ad libitum.

extract_protocol:
The animals were sacrificed 30 minutes following training, and the dorsal hippocampus was dissected on ice. To generate libraries for RNA-seq, polyA+ RNA was extracted using the Dynabeads mRNA Direct kit (Ambion) according to the manufacturer's instructions.
RNA-seq libraries for were made using a ScriptSeq v2 RNA-seq Library Preparation Kit from Epicentre (now Illumina). The quantity and quality of the libraries were assessed by BioAnalyzer (Agilent) and qPCR (Kapa Biosystems). The multiplexed libraries were pooled and sequenced on the Illumina NextSeq 500 platform.

treatment_protocol: For the intracranial injection of knockdown or control vector, the animals were anesthetized with isoflurane gas (1-5% to maintain surgical plane) and placed in a sterile field within a stereotaxic device. A small hole (about 0.5 millimeters) was be drilled in the skull over the target area using a stereotax and a stereotactic drill. A micro-syringe filled with viral vector was inserted into the dorsal hippocampus and slowly removed following injection (AP, -2.0mm; DV, -1.4mm; ML, +/-1.5mm from Bregma; AAV2/9.U6.shACSS2.CMV.EGFP = ACSS2 knockdown vector; AAV2/9.CMV.EGFP.polyA = eGFP-control vector). All animals received a single dose of subcutaneous meloxicam (5 mg/kg) as analgesia (pain medicine) at induction and one dose per day for two days post-operatively as needed. Three weeks later, object location memory training was performed. Prior to training, each mouse was handled for 3 minutes a day for 3 days. During the training day, mice are placed in an arena (approx. 1 square foot) containing 3 different objects. The objects used were a glass bottle, a metal tower (5H x 2W x 2L inches), and a plastic cylinder. Mice were habituated to an empty arena with a black and white striped spatial cue on the wall, followed by object exposure in three 6 minute trials with and interval of 3 minutes.

tag: strain backgroud

value: ACSS2 Knockdown

tag: trained

value: Spatial Object Recognition Trained

value: hippocampus


title: ip_1cell_rep1


title: ACSS2- Trained Rep 1


title: WT Trained Rep 1

description:
processed data file:
SOR.eGFP.mm10.bw
RNA-seq Adjusted Scores.txt

source_name: WT Trained_hippocampus

value: WT


title: WT Trained Rep 2


title: Inhibitor Treated Replicate #1

data_processing:
Demultiplexing: done using bcl2fastq (v02.14.01.07) on BaseSpace.
Alignment: data were aligned using STAR (RNA-STAR 2.3.0) on BaseSpace.
Quantitation: aligned reads were mapped to genomic features using Cufflinks (v2.2.1) with the -G parameter to only quantitate known features. FPKMs were calculated using CuffDiff.
Genome_build: mm10
Supplementary_files_format_and_content: Only a single text table with CuffDiff-computed FPKM values for each gene is included.

source_name: differentiated CAD cells_ACSS2 inhibitor

growth_protocol: CAD cells (Cath.-a-differentiated; generously donated from the Holzbaur Lab at the University of Pennsylvania) were grown in DMEM:HAMS F12 (1:1), supplemented with 2mM Glutamine, 1% penicillin/streptomycin, and 10% Fetal Bovine Serum (FBS).

extract_protocol:
To generate libraries for RNA-seq, polyA+ RNA was was extracted using the Dynabeads mRNA Direct kit (Ambion) according to the manufacturer’s instructions.
RNA-seq libraries were made using a ScriptSeq v2 RNA-seq Library Preparation Kit from Epicentre (now Illumina). The quantity and quality of the libraries were assessed by BioAnalyzer (Agilent) and qPCR (Kapa Biosystems). The multiplexed libraries were pooled and sequenced on a single lane on the Illumina NextSeq 500 platform

treatment_protocol: Sub-confluent CAD cell cultures (50-60%) were transferred to serum-free media (DMEM:HAMS F12 (1:1) supplemented with 2mM Glutamine) and maintained in 15 cm2 culturing dishes for 5 days. Cells were treated for 24h with ACSS2i (1-(2,3-di(thiophen-2-yl)quinoxalin-6-yl)-3-(2-methoxyethyl)urea) at 20 µM, or DMSO for the no treatment control group.

value: CAD cells (Cath.-a-differentiated)

tag: treated with

value: ACSS2i 20 µM (1-(2,3-di(thiophen-2-yl)quinoxalin-6-yl)-3-(2-methoxyethyl)urea) for 24hrs

value: ACSS2 inhibitor treatment


title: Inhibitor Treated Replicate #2


title: Untreated Replicate #1

source_name: differentiated CAD cells_DMSO

value: DMSO for 24hrs

value: No treatment


title: H3.Hippocampus

data_processing:
Demultiplexing: done using bcl2fastq on BaseSpace.
Alignment: data were aligned with bowtie2 (v2.2.1), parameters -N 1 -k 1 to assembly mm9.
Peak Calling: peaks were called using MACS v2.1.0 with the FDR controlled at 1%. ACSS2 peaks were called using input as the control and H3K9ac peaks were called using H3 as the control.
Track Creation: bigWigs were created for visualization of the chIP data in the following way. First, coverage maps (bedGraphs) were made using BEDTools' genomeCoverageBed utility. Map scores were then normalized per million reads aligned and for ACSS2, normalized input tags at each position were subtracted while for H3K9ac, normalized H3 tags at each position were subtracted. Finally, bigWigs were generated from subtracted maps using UCSC Genome Browser's bedGraphToBigWig utility.
Genome_build: mm9
Supplementary_files_format_and_content: BED files are peak calls for ACSS2 and H3K9ac while bigWigs are track files of ACSS2-input and H3K9ac-H3.

source_name: hippocampus

extract_protocol:
For the in vivo ChIP, hippocampal tissue pooled from two animals was finely minced and cross-linked with formaldehyde (1% final concentration) for 15 minutes at room temperature, followed by glycine quenching for an additional 10 minutes at 4°C. To create a single cell suspension, samples were washed once with ice cold PBS and homogenized by passing through a 22G needle 10 times. Immunoprecipitation was performed using protein A Dynabeads (Life Technologies).
Sequencing libraries were prepared using NEBNext Ultra library preparation procedure, and then assessed for quality and quantity by BioAnalyzer (Agilent) and qPCR (Kapa Biosystems). Sequencing was performed on the Illumina NextSeq 500 platform.

treatment_protocol: Mice, housed five per cage, were habituated in our facility for at least 1 week before experimentation, and the order of testing was distributed across groups. All experiments were conducted in accordance with the guidelines of the Institutional Animal Care and Use Committee at the Perelman School of Medicine at the University of Pennsylania.

tag: gender

value: male

tag: chip antibody

tag: chip antibody vendor

value: Abcam ab1791

tag: antibody lot #


title: WT Untrained Rep 1

description:
processed data file:
HCC.eGFP.mm10.bw
RNA-seq Adjusted Scores.txt

source_name: WT Untrained_hippocampus

tag: genotype/variation

value: Home Cage Control


title: ACSS2- Untrained Rep 1

description:
processed data file:
HCC.ACSS2_KD.mm10.bw
RNA-seq Adjusted Scores.txt

source_name: ACSS2- Untrained_hippocampus

tag: tissue


title: WT Untrained Rep 2


title: adult_muscle_0

city: Baltimore

first: Yuji

last: Zhang

state: MD

address: 660 W. Redwood Street

institute: University of Maryland

data_processing:
The flow cells were sequenced as 50×2 paired-end reads on an Illumina HiSeq 2000 using TruSeq SBS Sequencing Kit version 3 and HCS version 2.0.12 data collection software.
Raw RNA-seq reads were aligned to the zebrafish genome assembly (Zv9) for each sample using the Ensembl annotation Zv9 (Danio_rerio.Zv9.79.gtf) by TopHat (Version 2.0.12) . Each transcriptome was assembled by Cufflinks (Version 2.2.1) .
FPKM (Fragments Per Kilobase of transcript per Million mapped reads) was calculated using a protocol from Cufflinks. Isoform_exp.diff was the result form Cuffdiff script, and isoforms.fpkm_table was the result from Cuffnorm script.
Genome_build: Zv9

source_name: zebrafish adult muscle

extract_protocol:
Tissues were homogenized using a mortar and pestle (Fisher Scientific), and total RNA was extracted using TRIzol (Sigma) according to the manufacturer’s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument (Agilent Technologies) in the Mayo DNA sequencing core facility.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adult

value: muscle

value: wild type

tag: age

value: adult fish


title: adult_muscle_2

tag: developmental stage


title: H3K9ac.Hippocampus

value: Abcam ab4441


title: adult_heart_2

source_name: zebrafish adult heart

value: heart

value: 6 months


title: ACSS2.Hippocampus

value: hippocampus

value: Thermo MA5-145810


title: Input.Hippocampus


title: adult_heart_0


title: ACSS2- Untrained Rep 2

value: ACSS2 Knockdown


title: 0h fear conditioning shACSS2

data_processing:
NextSeq sequencing data was demultiplexed using bcl2fastq2-v02.14.01.07.
Demultiplexed FASTQs were aligned by RNA-STAR 2.3.0.e using the genome index mm10 generated from iGenome UCSC mm10 FASTQ genome sequence.
The aligned reads were mapped to genomic features using cufflinks-2.2.1 (-G parameter to only quantitate known features), and iGenomes mm10 UCSC genomic transcript loci.
Genome_build: GRCm38 (mm10 UCSC)
Supplementary_files_format_and_content: bigWig

source_name: dorsal hippocampus, ACSS2-AAV knockdown, before memory retrieval

extract_protocol:
To generate libraries for RNA-seq, polyA+ RNA was extracted using the Dynabeads mRNA Direct kit (Ambion) according to the manufacturer's instructions.
RNA-seq libraries for scrambled control (referred to in text as WT), shACL, and shACSS2 were made using a ScriptSeq v2 RNA-seq Library Preparation Kit from Epicentre (now Illumina). The quantity and quality of the libraries were assessed by BioAnalyzer (Agilent) and qPCR (Kapa Biosystems). The multiplexed libraries were pooled and sequenced on a single lane on the Illumina NextSeq 500 platform (50bp, single-end reads).

treatment_protocol: CAD cells were infected with lentiviral hairpin constructs (TRC collection) designed against ACL (#TRCN0000055217) or ACSS2 (#TRCN0000076124, #TRCN0000076125) in medium containing 8 mg/mL polybrene and 10% FBS for 24 h. Cells then underwent selection in culture medium supplemented with 0.5 mg/mL puromycin for 5 days to obtain a stably infected population. To induce neuronal differentiation, sub-confluent CAD cell cultures (50-60%) were transferred to serum-free media (DMEM:HAMS F12 (1:1) supplemented with 2mM Glutamine) and maintained in 15 cm2 culturing dishes for 5 days.

tag: strain/background

value: dorsal hippocampus

tag: shRNA

tag: treatment

value: fear conditioning

tag: timepoint

value: 0h (before memory retrieval)


title: 1h fear conditioning EGFP

source_name: dorsal hippocampus, EGFP-AAV control, post memory retrieval

value: EGFP

value: 1h post memory retrieval


title: 1h fear conditioning shACSS2

source_name: dorsal hippocampus, ACSS2-AAV knockdown, post memory retrieval


title: adult_muscle_1

tag: genotype


title: embryonic_heart_1

source_name: zebrafish embryonic heart

value: embryo

value: 4 days


title: Untreated Replicate #2

tag: cell type

value: CAD cells (Cath.-a-differentiated)

value: DMSO for 24hrs

value: No treatment


title: embryonic_heart_2

value: wild type


title: Scramble control diff repeat 2

source_name: differentiated CAD neurons, scramble control

tag: cell line

value: CAD

tag: differentiation state

value: differentiated

value: scramble


title: 0h fear conditioning EGFP

source_name: dorsal hippocampus, EGFP-AAV control, before memory retrieval


title: Ndt80 untagged control 1

city: San Francisco

first: Isabel

last: Nocedal

state: CA

institute: UCSF

data_processing:
Quality analysis performed with FastQC
ChIP-seq reads were aligned to the S. stipitis genome assembly using bowtie2 and default parameters
Files were converted to sorted .bam files using Samtools
Peak separation distance was determined using the binding.characteristics function in the SPP package in R
Peaks and fold enrichment were calculated using MACS2, using peak separation distances calculated from SPP and --nomodel parameter
Genome_build: S. stipitis genome was downloaded from the Candida Gene Order Browser in December 2015.
Supplementary_files_format_and_content: bedGraph.wig files were generated from indexed, sorted .bam file using genomeCoverageBed tool in BedTools, followed by a .bed to .wig conversion script in Python.  FE.bdg.wig files were generated by MACS2 using the -SPMR parameter, and converted to .wig using the same Python script.  Peaks.xls files were generated for experiments with tagged proteins using untagged strains as a control in MACS2.

organism: Candida albicans

source_name: a/alpha cell

growth_protocol: Cells were grown overnight in YPD diluted back to OD = 0.02 in YPD and grown for 4-6 hours until log-phase.

extract_protocol:
Cells were lysed with glass bead vortexing, sonicated for 3 15-minute cycles, and immunoprecipitated at 4˚C overnight
Libraries were prepared using the NEBNext ChIP-Seq library prep kit for Illumina (New England Biolabs)

tag: media condition

value: YPD

value: human c-myc

tag: strain number


title: embryonic_heart_0

value: heart


title: Ndt80 untagged control 2

tag: chip antibody


title: Ndt80B-myc_2


title: Ndt80B-myc_1


title: ACSS2 knockdown diff repeat 2

source_name: differentiated CAD neurons, ACSS2 knockdown


title: ACSS2 knockdown undiff repeat 2

source_name: undifferentiated CAD cells, ACSS2 knockdown

value: undifferentiated


title: pTdh3-Ndt80B-myc_2


title: ACL knockdown undiff repeat 2

source_name: undifferentiated CAD cells, ACL knockdown

value: ACL


title: adult_heart_1

value: adult

value: 6 months


title: ACL knockdown diff repeat 2

source_name: differentiated CAD neurons, ACL knockdown


title: pTdh3-Ndt80B-myc_1


title: pTdh3-Ndt80A-myc_2


title: Δcre1 Cellulose 2

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

data_processing:
Illumina Casava1.8.2 software used for base-calling.
The Illumina HiSeq 2000 system was used to sequence the mutant transcriptome with approximately 104 million 100 bp paired-end reads. These sequences were firstly quality-filtered and mapped to the Trichoderma reesei 2.0 reference genome available the JGI Genome Portal (http://genome.jgi-psf.org/Trire2/Trire2.home.html) using the Bowtie aligner version 0.12.8 (Li, Durbin, 2009), allowing two mismatches and only unique alignments.
After alignment, Samtools version 0.1.18 (Li et al., 2009) was used to process the alignments files which were visualized using the Integrative Genomics Viewer (Thorvaldsdottir et al., 2012).
Bioconductor DESeq package version 1.10.1 (Anders, Huber, 2010) was employed to differential expression analysis, using two-fold change, i.e., log2 fold change ≥ 1 or ≤ -1 and adjusted p-value ≤ 0.05 as thresholds.
Genome_build: http://genome.jgi-psf.org/Trire2/Trire2.home.html
Supplementary_files_format_and_content: Processed data files are presented in tab delimited txt format. Normalized count data for each sample (*.counts.txt files), are expressed as follows: "Protein ID", "sample ID".
Supplementary_files_format_and_content: Gene expression is expressed as log2 Fold change between indicated samples and the respective p-value calculated by DESeq.

organism: Trichoderma reesei

source_name: mycelia

growth_protocol: The mutant strain was grown in MEX medium at 28°C for 7-10 days for complete sporulation. For gene expression assays, a spore suspension containing approximately 107 cells mL-1 was inoculated into 200 mL of Mandels-Andreotti medium (Schmollet al. 2009) containing 1% (w/v) of cellulose or 2% (w/v) of glucose as the carbon source.

extract_protocol:
Total RNA was extracted using the TRIzol kit (Invitrogen) according to manufacture's instructions.
RNA-seq libraries were prepared for sequencing using Illumina TruSeq RNA Sample Prep Kit.

value: QM9414 and <delta>cre1

value: mycelia


title: Δcre1 Glucose 1


title: Δcre1 Glucose 3


title: Δcre1 Glucose 2


title: ACSS2 knockdown undiff repeat 1


title: Scramble control undiff repeat 2

source_name: undifferentiated CAD cells, scramble control


title: pTdh3-Ndt80A-myc_1


title: Δcre1 Cellulose 1


title: ACL knockdown undiff repeat 1


title: ACSS2 knockdown diff repeat 1


title: Scramble control undiff repeat 1


title: Scramble control diff repeat 1


title: H3_ChIPseq_diff

description: Processed data file: none

data_processing:
NextSeq sequencing data was demultiplexed using bcl2fastq2-v02.14.01.07; the ACSS2 CS DIFF was produced by a separate demultiplexing using bcl2fastq2-v2.15.0.4.
All reads were aligned to the mm10 reference genome using bowtie2.2.1. One alignment was allowed per read and 1 mismatch was allowed in the seed region (-N1 -k1).
Reads were tabulated in fixed windows or to genes provided in the iGenome mm10 UCSC annotations using featureCounts from the subread1.4.6 software package.
ACSS2 ChIP-seq data was normalized to input controls, while all histone acetylation ChIP-seq data was H3-subtracted.
The sub tracks showing a delta in differentiation were created by subtracting Input- or H3-adjusted undifferentiated from differentiated tracks.
Genome_build: GRCm38 (mm10 UCSC)
Supplementary_files_format_and_content: bigWig

source_name: differentiated CAD neurons, H3 ChIP

extract_protocol:
ChIP was performed as previously described (Shah, P.P. et al. 2013), except that chromatin was sheared to an average size of <500 bp using the Covaris S220 Ultrasonicator. Equal aliquots of sonicated chromatin from undifferentiated and differentiated CAD neurons were used per immunoprecipitation reaction, and 10% of the amount was saved as input. Immunoprecipitation was performed using protein A Dynabeads (Life Technologies).
Sequencing libraries were prepared using NEBNext Ultra library preparation procedure, and then assessed for quality and quantity by BioAnalyzer (Agilent) and qPCR (Kapa Biosystems).

treatment_protocol: To induce neuronal differentiation, sub-confluent CAD cell cultures (50-60%) were transferred to serum-free media (DMEM:HAMS F12 (1:1) supplemented with 2mM Glutamine) and maintained in 15 cm2 culturing dishes for 5 days.

value: anti-H3 (Abcam ab1791, lot# GR10462-1)


title: Input_ChIPseq_diff

description: Processed data file: none

source_name: differentiated CAD neurons, input


title: H3K9ac_ChIPseq_diff

description:
Processed data file: K9ac_diff.unique.map_UCSC.bgr_norm.bw
Processed data file: K9ac_diff.unique.map_UCSC.bgr_norm.bgr_sub.bw

source_name: differentiated CAD neurons, H3K9ac ChIP

value: anti-H3K9ac (Abcam ab4441, lot# GR207546-1)


title: H4K5ac_ChIPseq_diff

description:
Processed data file: K5ac_diff.unique.map_UCSC.bgr_norm.bw
Processed data file: K5ac_diff.unique.map_UCSC.bgr_norm.bgr_sub.bw

source_name: differentiated CAD neurons, H4K5ac ChIP

value: anti-H4K5ac (Millipore 39-584, lot# NRG1726321)


title: H4K12ac_ChIPseq_diff

description:
Processed data file: K12ac_diff.unique.map_UCSC.bgr_norm.bw
Processed data file: K12ac_diff.unique.map_UCSC.bgr_norm.bgr_sub.bw

source_name: differentiated CAD neurons, H4K12ac ChIP

value: anti-H4K12ac (Abcam ab1761, lot# 94891)


title: ACSS2_CS_ChIPseq_diff

description:
Processed data file: AceCS1_CS_diff.unique.map_UCSC.bgr_norm.bw
Processed data file: AceCS1_CS_diff.unique.map_UCSC.bgr_norm.bgr_sub.bw

source_name: differentiated CAD neurons, ACSS2 ChIP

value: anti-ACSS2 (CS) (Cell Signaling 3658, lot# 1)


title: ACSS2_T_ChIPseq_diff

description:
Processed data file: AceCS1_T_diff.unique.map_UCSC.bgr_norm.bw
Processed data file: AceCS1_T_diff.unique.map_UCSC.bgr_norm.bgr_sub.bw

value: CAD


title: Δcre1 Cellulose 3


title: ACSS2_CS_ChIPseq_undiff

description:
Processed data file: AceCS1_CS_undiff.unique.map_UCSC.bgr_norm.bw
Processed data file: AceCS1_CS_diff.unique.map_UCSC.bgr_norm.bgr_sub.bw

source_name: undifferentiated CAD cells, ACSS2 ChIP


title: Input_ChIPseq_undiff

description: Processed data file: none

source_name: undifferentiated CAD cells, input


title: ACSS2_T_ChIPseq_undiff

description:
Processed data file: AceCS1_T_undiff.unique.map_UCSC.bgr_norm.bw
Processed data file: AceCS1_T_diff.unique.map_UCSC.bgr_norm.bgr_sub.bw


title: H4K12ac_ChIPseq_undiff

description:
Processed data file: K12ac_undiff.unique.map_UCSC.bgr_norm.bw
Processed data file: K12ac_diff.unique.map_UCSC.bgr_norm.bgr_sub.bw

source_name: undifferentiated CAD cells, H4K12ac ChIP


title: H4K5ac_ChIPseq_undiff

description:
Processed data file: K5ac_undiff.unique.map_UCSC.bgr_norm.bw
Processed data file: K5ac_diff.unique.map_UCSC.bgr_norm.bgr_sub.bw

source_name: undifferentiated CAD cells, H4K5ac ChIP


title: H3_ChIPseq_undiff

description: Processed data file: none

source_name: undifferentiated CAD cells, H3 ChIP


title: H3K9ac_ChIPseq_undiff

description:
Processed data file: K9ac_undiff.unique.map_UCSC.bgr_norm.bw
Processed data file: K9ac_diff.unique.map_UCSC.bgr_norm.bgr_sub.bw

source_name: undifferentiated CAD cells, H3K9ac ChIP


title: Ad-KLF15 rep3

city: Denver

first: Anthony

last: Gerber

state: CO

address: 1400 Jackson St

department: Medicine

institute: National Jewish Health

data_processing:
Basecalling, barcode demultiplexing and adapter trimming was performed by Ion Torrent Suite 4.0.2.
Sequence reads of at least 30 nt length were mapped to the UCSC release hg19 of the human genome using GSNAP version 2013-11-27 with SNP data version 137 and splice sites compatible with the Ensembl annotation, as well as detection of novel splice sites.
Reads mapping unambiguously to each gene in the Ensembl annotation (downloaded from the UCSC genome browser July 29, 2013) were quantified using the htseq-count program from the HTSeq package (version 0.6.0) in the “intersection-nonempty” mode.
Statistical comparisons of the gene expression between the cell genotypes were performed with the DESeq2 package version 1.4.5 for the R statistical software version 3.1.0.
Genome_build: hg19
Supplementary_files_format_and_content: read counts assigned to each gene and sample, as tab-separated text table

source_name: airway smooth muscle cells

growth_protocol: Primary human airway smooth muscle (HASM) cells were cultured in Ham's F-12 Medium with L-glutamine (Corning) supplemented with 10% Fetal Bovine Serum (FBS; Fisherbrand) and 1% penicillin/streptomycin (Corning) and maintained in 5% CO2 at 37 degrees C.

extract_protocol:
Cells were lysed in TRIzol Reagent (Life Technologies) and total RNA was purified using the PureLink RNA Mini Kit from Life Technologies. A second RNA purification step was performed using the RNA Clean & Concentrator-5 kit from Zymo Research.
A modified protocol was used with the KAPA Stranded mRNA-Seq Kit (KAPA Biosystems) to construct sequencing libraries from 100 ng of isolated total RNA. Libraries were sequenced as barcoded-pooled samples on a P1 Ion Proton chip/Ion Proton NGS platform (Life Technologies).

treatment_protocol: HASM cells in biological quadruplicate were transduced with adenoviral expression constructs obtained from Welgen for green fluorescent protein (Ad-GFP; control) or KLF15 (Ad-KLF15) at a Multiplicity of Infection (MOI) of 50 for ~17 hours in complete medium. Treatments were removed and cells were incubated for 4 additional hours in fresh complete medium prior to harvest.

value: primary human airway smooth muscle cells

tag: passage

value: transduced with KLF15-expressing adenovirus (Ad-KLF15)


title: Ad-KLF15 rep2


title: Ad-KLF15 rep4


title: Ad-GFP rep2

value: transduced with control adenovirus (Ad-GFP)


title: Ad-GFP rep4


title: Ad-KLF15 rep1


title: Ad-GFP rep3


title: Ad-GFP rep1


title: cynomolgus smRNA-seq

description:
smRNA (small RNA)
small RNA in 15-35 nt range
cynomolgus_ensGene_mRNA_structScore.txt

organism: Macaca fascicularis

source_name: brain tissue

tag: library strategy

value: smRNA-seq

tag: enzyme treatment

tag: ngs platform

value: Illumina GA2x with 58 nt strand-specific

value: brain


title: ACL knockdown diff repeat 1

source_name: differentiated CAD neurons, ACL knockdown

value: differentiated

value: ACL


title: EBC-CR3

city: Seoul

first: Seulki

last: Kim

address: 101, Daehak-ro

country: South Korea

institute: Seoul National University Cancer Research Institute

description: Barcode: ACGTCT

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Lung

growth_protocol: The EBC-1 cell line, which is an NSCLC cell line that harbors a MET amplification, was purchased from the JCRB Cell Bank (Osaka, Japan). Capmatinib-resistant EBC-1 cell lines (EBC-CR1, CR2 and CR3) were established via stepwise exposure to capmatinib at final concentrations of 1.5, 2.2, and 2.4 μmol/L, respectively. EBC-CR1, -CR2, and -CR3 cells were maintained in 1 μmol/L of capmatinib over 2 months. All cell lines were incubated in RPMI1640 medium (Gibco, Carlsbad, CA) with 10% FBS, 2 mmol/L L-glutamine (Gibco), and 1% penicillin/streptomycin (Gibco) in a 37˚C incubator.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Human lung squamous cancer cell line

tag: phenotype

value: capmatinib-resistant

tag: passages


title: EBC-CR2

description: Barcode: AGACCA


title: EBC-CR1

description: Barcode: GATTGT


title: CC-adult

city: Detroit

first: Tiffany

last: Cook

state: MI

address: 540 E. Canfield Avenue

department: Molecular Medicine and Genetics

institute: Wayne State University

data_processing:
Allignment-Genomic; Tophat version 2.0 aligned allowing up to 2 mismatches and 10 multiple mappings to genomic  targets
Alignment-Transcriptome; Bowtie version 1.0 aligned allowing up to 2 mismatches and 10 multiple mappings to annotated transcriptome
TMM normalized counts; Avadis (Strand Life Sciences, Bangladore, India) Version 1.6
Genome_build: dm3
Supplementary_files_format_and_content: TMM normalized transcript counts  - normalizaton across 4 sequenced samples

organism: Drosophila melanogaster

source_name: ConeCell-adult stage

growth_protocol: eye tissue dissected from 45-75 animals (larva (wandering late third instars), pupae (25% after puparium formation [25 hr at 25°C]) and adults (1-2 days post-eclosion))

extract_protocol:
RNeasy Micro kit (Qiagen, cat. 74004)
Ovation RNA Amplification System V2 (NuGEN, cat. 7102-08)

treatment_protocol: CC/PR cells FACS-sorted

tag: developmental stage

value: adult stage

value: retinal cone cells


title: EBC-1 parental

description: Barcode: ACCGTG

value: parental


title: CC-pupal

source_name: ConeCell-pupal stage

value: pupal stage


title: CC-larval

source_name: ConeCell-larval stage

value: larval stage


title: SCL28-OX_replicate2

first: Jeong-eun

last: Choe

address: 120 Neungdong-ro

institute: Konkuk University

data_processing:
Base-calling was performed using CASAVA (Version 1.8.2)
Reads were mapped using Tophat v2.0.13 based on the reference sequences
gtf file (annotation file) for each sample was produced using cufflink v2.2.0. Each file was merged by cuffmerge and quantification for each sample was performed using cuffquant.
Abundant calculation (FPKM) were perfomed using cuffdiff v2.2.0.
Genome_build: TAIR10
Supplementary_files_format_and_content: The excel file include matrix tables containing FPKM values for each sample and each sample group

organism: Arabidopsis thaliana

source_name: SCL28 overexpression

growth_protocol: Plant seedlings were grown on 1/2 MS agar plates under a constant light condition at 22 ℃ in a growth room

extract_protocol:
Total RNA samples were extracted from roots of 5 d-old seedlings using TRI REAGENT (Molecular Research Center, USA) according to the manufacturer’s instructions. The samples were cleaned up with RNeasy Plant Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions.
Libraries were prepared using Truseq Stranded mRNA Prep Kit

tag: ecotype

tag: genotype/variation

tag: age

value: 5 d-old

tag: tissue

value: root tip


title: Islet_Control_rp3

city: La Jolla

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

description: GFP lentivirus overexpression replicate 3

data_processing:
Reads were aligned to the mm9 by STAR with parameters: --outSAMstrandField intronMotif --outFilterMultimapNmax 1 --runThreadN 5.Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks.
Libraries that contained fewer than 1 million reads or for which more than 15% of fragments mapped to mitochondrial reads were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file

growth_protocol: Primary cells were cultured in 1640 RPMI medium supplemented with 10% FBS, 8.3mM glucose, and antibiotic at 37˚C and 5% CO2.

extract_protocol:
Total RNA was extracted by RNeasy Mini Kit.
Libraries were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit and the Illumina Nextera® XT DNA Sample Preparation Kit.

treatment_protocol: Islets were dissociated and reaggregated, transfected with lentivirus. Total RNA was prepared 72 hours post-transfection.

tag: cell type

value: primary islets

value: 4 weeks

tag: overexpression

value: GFP lentivirus


title: WT_replicate2

source_name: Wild type

value: Wild type


title: SCL28-OX_replicate1


title: Islet_Srf_rp1

description: Srf-GFP lentivirus overexpression replicate 1

value: Srf-GFP lentivirus


title: Islet_Srf_rp2

description: Srf-GFP lentivirus overexpression replicate 2


title: Islet_Control_rp2

description: GFP lentivirus overexpression replicate 2


title: Min6_siAtf_rp3

description: Atf3 siRNA replicate 3

data_processing:
Reads were aligned to the mm9 by STAR with parameters: --outSAMstrandField intronMotif --outFilterMultimapNmax 1 --runThreadN 5.Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
makeTagDirectory and makeUCSCfile in homer was used to generate bigWig file
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file

growth_protocol: Min6 cells were cultured in DMEM high glucose medium supplemented with 4% FBS and, antibiotic and 2-Mercaptoethanol, at 37˚C and 5% CO2

extract_protocol:
Total RNA was extracted by RNARNeasy Mini Kit
Libraries were prepared using the Illumina TrueSeq RNA Library Prep Kit V2

treatment_protocol: Min6 cells were transfected with 50nM siRNA using DharmaFECT 1 Transfection Reagent. Total RNA was prepared 72 hours post-transfection.

tag: strain

value: mouse insulinoma cells

tag: transfection

value: Atf3 siRNA


title: Islet_Srf_rp3

description: Srf-GFP lentivirus overexpression replicate 3


title: Islet_Control_rp1

description: GFP lentivirus overexpression replicate 1


title: Min6_siAtf_rp1

description: Atf3 siRNA replicate 1


title: Min6_siSrf_rp2

description: Srf siRNA replicate 2

value: Srf siRNA


title: Min6_siAtf_rp2

description: Atf3 siRNA replicate 2


title: Min6_siSrf_rp3

description: Srf siRNA replicate 3


title: PR

source_name: Retinal Photoreceptors-adult

value: adult

value: retinal photoreceptors


title: Min6_siSrf_rp1

description: Srf siRNA replicate 1


title: Min6_Control_rp3

description: scramble siRNA replicate 3

value: scramble siRNA


title: Min6_Control_rp2

description: scramble siRNA replicate 2


title: DGE_Di4_B

city: Hangzhou

first: Xiaojun

last: Liu

state: Zhejiang

address: No 16, Xuelin Street

department: College of Life and Environmental Sciences

country: China

institute: Hangzhou Normal University

description: female

data_processing:
Raw data (raw reads) in FASTQ format were processed using in-house Perl scripts. Clean data (clean reads) were obtained by removing reads containing adapter or poly(N) sequences and low-quality reads from the raw data.
the transcriptome was assembled using the Trinity program using an min_kmer_cov value of 2 and the default settings for the other parameters.
The annotation of the unigene sequences was conducted by comparing them to the sequences in the GenBank databases using the BLASTx computational tool.
The levels of gene expression were estimated based on the RNA-Seq by Expectation-Maximization (RSEM) for each sample.
Raw reads of the transcriptome have been deposited in the GenBank sequence read archive under accession code SRR1262364. The assembly data of the transcriptome have been deposited in the GenBank transcriptome shotgun assembly archive under accession code GBFE00000000.

organism: Locusta migratoria

source_name: fat body and ovary

growth_protocol: The locust models were established by rearing the insects in five surface net cages (25 ×25 × 25 cm) at densities of 200 to 300 insects per cage . The insects were reared using a 14:10 light/dark photo regime at 29°C ± 2°C, and were fed a diet of fresh greenhouse-grown wheat seedlings

extract_protocol:
The fat body and ovary were collected from different females in each group at the following post-treatment time points:  (1) the Sephadex group: 4 hours, 6 days; (2) the bacterial parasite group: 4 hours,6 days;(3) the dipteran parasite group: 4 hours,6 days.
The RNA was extracted using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions. Three micrograms of total RNA was used as the input material for sequencing. All of the samples had RIN values greater than 8.The sequencing library was generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, USA), according to the manufacturer’s recommendations. Four index codes were added to the sequence. The mRNA was purified from the total RNA using poly(T)-oligo-conjugated magnetic beads.  Fragmentation was performed by heating the RNA in fragmentation buffer (Illumina) containing divalent cations. First-strand complementary DNA (cDNA) was performed using random oligonucleotides and SuperScript II reverse transcriptase (Invitrogen). Second-strand cDNA synthesis and RNA degradation was performed using DNA Polymerase I and RNase H. The overhangs were converted to blunt ends through the exonuclease activity of the polymerase, and the double-stranded DNA fragments were purified. The 3' ends of the DNA fragments were adenylated, and Illumina PE adapter oligonucleotides were ligated to both termini of the adenylated fragments for hybridization. To select the adaptor-ligated cDNA fragments approximately 200 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter, Brea, CA, USA). The purified cDNA fragments were selectively enriched during 10 cycles of polymerase chain reaction (PCR) using the Illumina PCR Primer Cocktail. Products were purified again, and quantified by performing the High-sensitivity DNA Assay (Agilent Technologies, Santa Clara, CA, USA) using the Bioanalyzer 2100 system (Agilent). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina), according to the manufacturer’s instructions.

treatment_protocol: The second generation adult female insects were divided into four treatment groups. The female locusts on the first day of molting were collected and underwent the parasite treatments at 12:00 a.m. of the day. The treatment site for all of the various groups was sealed with petroleum jelly to prevent exogenous natural infection. The pronotum of the locusts in the first group was stabbed using an alcohol-sterilized needle to simulate the treatment in the other groups. The second group received a treatment that simulated parasitism. Their pronotum was injected with 100 µl of 50 mg/ml Sephadex G-50 (medium grade, Solarbio, Beijing, China) in 0.9% saline solution. We designated this experimental group as the “Co” in tables and figures. The third group was infected with the bacterial parasite, M. luteus (American Type Culture Collection, Manassas, VA, USA). The bacteria were cultured to the log phase, according to the manufacturer’s instructions, and the pronotum of each locust was injected with 10 μl of bacterial culture with an optical density of approximately 0.9 at 600 nm using a nanofil syringe. We designated this group as the “Bp” in tables and figures. The fourth group was parasitized with the larvae of the dipteran insect, B. lapidosa, a natural parasite of locusts. The tympanic membrane of the locusts was ruptured with an alcohol sterilized needle, and the fly larvae were placed in the wound. We designated the fourth group as the “Di” in tables and figures.

value: the mixture of the fat body and ovary

value: adult locust

tag: treament

value: parasitized with B. lapidosa

tag: post-treament time


title: DGE_Di4_A

description: female


title: DGE_Di6_A

description: female


title: DGE_Bp6_B

description: female

value: infected with M. luteus


title: DGE_Bp6_A

description: female


title: WT_replicate1

value: 5 d-old


title: DGE_Di6_B

description: female


title: DGE_Bp4_A

description: female


title: DGE_Co4_B

description: female

value: injected with Sephadex G-51


title: run2_HLA-DR+CD135+_cells

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: Single-cells human DCs from PBMC

data_processing:
After de-multiplexing, Cell barcode and RMT were extracted from Read 2 and stored in Read 1. Reads with a Phred<27 for any RMT base were removed from further analysis. Next, we removed contamination, by alignment against the e.coli genome and de-multiplexed the unmapped reads by pool barcode and cell barcode. Reads were aligned using Bowtie v 1.1.1 (parameters:“-m 1 -t --best --chunkmbs 64 –strata) to the Ensembl mouse mm10 + ERCC pseudo genome assembly. We used HTSeq-count (v 0.6.0) to quantify gene count levels based on the ensembl exon-model for mm10. Following UMI sequencing errors were filtered nad a gene expression matrix was generated. Please have a look at cell_barcodes.txt, pool_barcodes.txt, and pool_barcodes.txt..
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text file

extract_protocol:
Lin(CD3/14/16/19/20/34)-CD45+CD135+HLA-DR+CD123+CD33+ single cells were sorted into each well of 384-well plates filled with 2µl lysis buffer (Triton 0.2% (Sigma) in molecular biology grade H2O (Sigma), supplemented with 0.4 U/μl protein-based RNase inhibitor (Takara)), and barcoded (400 nM (IDT)) poly-T primers. Samples were pre-incubated (3 min at 80°C) and reverse transcriptase mix (10 mM DTT (Invitrogen), 4 mM dNTPs (NEB), 2.5 U/μl Superscript III RT enzyme (Invitrogen) in 50 mM Tris-HCl (pH 8.3; Sigma), 75 mM KCl (Sigma), 3 mM MgCl2 (Sigma), ERCC RNA Spike-In mix (Life Technologies) at 1:80*107 dilution per cell) was added to each well. mRNA was reverse-transcribed to cDNA (2 min at 42°C, 50 min at 50°C, 5 min at 85°C). Excess primers were digested (ExoI (NEB); 37°C for 30 min then 10 min at 80°C) followed by a 1.2 x SPRI (Beckman Coulter) cleanup. Samples were pooled and second strands synthesized (second strand synthesis kit (NEB); 2.5 h at 16°C) followed by a 1.4 x SPRI (Beckman Coulter) cleanup. Samples were linearly amplified by T7-promoter guided in vitro transcription (T7 High Yield RNA polymerase IVT kit (NEB); 37°C for 12h). DNA templates were digested (Turbo DNase I (Ambion); 15 min at 37°C) followed by a 1.2 x SPRI (Beckman Coulter) cleanup and the RNA was fragmented (Zn2+ RNA fragmentation solution (Ambion); 1.5 min at 70°C) followed by a 2 x SPRI (Beckman Coulter) cleanup. Barcoded ssDNA adapters (IDT) were ligated to the fragmented RNAs (9.5% DMSO (Sigma), 1 mM ATP, 20% PEG8000 and 1 U/μl T4 RNA ligase I (NEB) in 50 mM Tris HCl pH7.5 (Sigma), 10 mM MgCl2 and 1mM DTT; 22°C for 2 h) and a second RT reaction (Affinity Script RT buffer, 10 mM DTT, 4 mM dNTP, 2.5 U/μl Affinity Script RT enzyme (Agilent); 2 min at 42°C, 45 min at 50°C, 5 min at 85°C) was performed followed by a 1.5 x SPRI (Beckman Coulter) cleanup
Final libraries were generated by subsequent nested PCR reactions (0.5 μM of each Illumina primer (IDT; details of primers see (15)) and KAPA HiFi HotStart ready mix (Kapa Biosystems); 15 cycles according to manufacturer’s protocol) followed by a 0.7 x SPRI (Beckman Coulter) cleanup. Library quantity and quality was assessed using the Agilent 2200 tapestation system and libraries were subjected to next generation sequencing using an Illumina HiSeq1500 instrument (PE no index; read1: 61 reads (3 reads random nucleotides, 4 reads pool barcode, 53 reads sequence), read2: 13 reads (6 reads cell barcode, 6 reads unique molecular identifier))

value: DC

value: PBMC

tag: sorting

tag: batch

value: second run


title: DGE_Co6_A

description: female

value: injected with Sephadex G-52


title: DGE_Co4_A

description: female

value: injected with Sephadex G-50


title: run1_HLA-DR+CD135+_cells

description: Single-cells human DCs from PBMC

value: first run


title: Control root hairs 3

city: Cuernavaca

first: Damien

last: Formey

state: Morelos

address: Avenida de la Universidad

department: Center for Genomic Science

country: Mexico

institute: UNAM

data_processing:
Once sequenced, the 3' adaptor (TGGAATTCTCGGGTGCCAAGG) for sequencing was removed from the raw reads. Then, reads with the length less than 10 were excluded.
miRNAs were identified using the miRDeep-P pipeline. Precursors were identified with a window size of 250nt, no mismatch allowed and a number of hits in the genome lower than 40. Only the precursors with a mature miRNA between 18nt and 25nt wherein the mature miRNA lies within the top 5% of the most expressed sequences in a given library were selected
Genome_build: Phaseolus vulgaris v1.0
Supplementary_files_format_and_content: Tab-separated text File. Raw counts of sequencing reads

organism: Phaseolus vulgaris

source_name: Root hairs

extract_protocol:
Total RNA from these samples were isolated thanks to mirVana miRNA isolation kit (Ambion) according to manufacturer’s instructions
Small RNA libraries were generated using the Illumina TruSeq Small RNA Preparation Kit (Illunima, San Diego, CA, USA) according to the manufacturer's instructions. For degradome libraries, 5′ RNA oligonucleotide adaptors containing a MmeI site were ligated to RNAs, then reverse transcribed and amplified by PCR.

tag: genotype


title: Control root hairs 1


title: Control root hairs 2


title: NF-induced root hairs 3


title: Degradome NF-induced root hairs 3

data_processing:
Library strategy: Degradome-Seq
Once sequenced, the 3' adaptor (TGGAATTCTCGGGTGCCAAGG) for sequencing was removed from the raw reads. Then, reads with the length less than 10 were excluded.
miRNAs were identified using the miRDeep-P pipeline. Precursors were identified with a window size of 250nt, no mismatch allowed and a number of hits in the genome lower than 40. Only the precursors with a mature miRNA between 18nt and 25nt wherein the mature miRNA lies within the top 5% of the most expressed sequences in a given library were selected
Genome_build: Phaseolus vulgaris v1.0
Supplementary_files_format_and_content: Tab-separated text File. Raw counts of sequencing reads


title: Degradome Control root hairs 3


title: NF-induced root hairs 2


title: NF-induced root hairs 1


title: seed_degradome

city: Beijing

first: Zhixi

last: Tian

address: No.1 Building, No.1 West Beichen Road,Chaoyang District

data_processing:
remove adaptor using cutadapt V1.4.2, adaptor sequence see degradome_adaptor.fa
fastq to fasta using fastq_to_fasta
remove reads less than 4nt
CleaveLand4 to find miRNA target.
Genome_build: transcript reference: Glycine max V1.1
Supplementary_files_format_and_content: The format of processed data is the CleaveLand4 output in tabular format.

source_name: seed sample from 4 mixed tissues

growth_protocol: Soybean (Glycine max cv. Williams 82) plants were grown in the Experimental Station of the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, in Beijing.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen).
The degradome libraries were constructed as previously described (German et al. 2009).

tag: cultivar/line

value: cv. Williams 82

tag: tissue 1

value: the pods of one week

tag: tissue 2

value: the pods of two weeks

tag: tissue 3

value: the pods of three weeks

tag: tissue 4

value: developing seeds around 6 weeks.


title: flower_degradome

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

source_name: flower sample from 2 mixed tissues

value: flower bud from flower bud differentiation stage

value: flower bud from flowering stage


title: rootstem_degradome

source_name: root and stem sample from 2 mixed tissues

value: root from gemination stage

value: stem from gemination stage


title: Min6_Control_rp1

description: scramble siRNA replicate 1

value: mouse insulinoma cells

value: scramble siRNA


title: CD103009_140305_TARDIS_C3PC6ACXX.5.6096371

city: Bethesda

first: Jeffery

last: Miller

address: 10 Center Drive Room 9N311

department: NIDDK

institute: NIH

description: Galaxy502-[CD103009_SLC25A39KD_Cufflinks_on_data_57_and_data_500__transcript_expression].txt

data_processing:
The data were processed using RTA version 1.13.48 and CASAVA 1.8.2, The sequence reads were aligned to hg19 reference build using  Illumina’s Efficient Large-Scale Alignment of Nucleotide Databases (ELAND) mapping algorithm.
Bam files were converted to Fastq using SamtoFastq.
FASTQ files were loaded into the public main Galaxy server (https://usegalaxy.org/) processed with FASTQ Masker (Galaxy Version 1.0.0) and loaded into TopHat (Galaxy Version 2.1.0) was then used as a gapped-read mapper to align RNA-Seq reads against the hg19 genome with Bowtie to generate the FPKM value.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample generated using Galaxy

source_name: Donor 6

growth_protocol: Human adult CD34+ cells were cultured in 21 days three phase serum free media as described in previous publication PMID: 23798711.

extract_protocol:
Qiagen miRNAeasy Kit
GLOBINclear Kit (Life Technologies), RiboZero GOLD (Illumina, San Diego, CA) then paired-end sequenced.

treatment_protocol: Briefly, cells were transduced with Sigma shRNA Clone TRCN0000162889 targeting SLC25A39 gene Lentiviral particles on culture day 3.  After 24 hours, puromycin was added for 3 more days than transferred into phase 2 medium without puromycin for 7 more days as described in previouls publication PMID: 23798711.

tag: time

value: Day 14 Culture

value: CD34+ Cells


title: CD103009_140305_TARDIS_C3PC6ACXX.8.6096371


title: CD103009_140305_TARDIS_C3PC6ACXX.4.6096371


title: CD103009_140305_TARDIS_C3PC6ACXX.6.6096371


title: DGE_Bp4_B

description: female

value: the mixture of the fat body and ovary

tag: age

value: adult locust

value: infected with M. luteus


title: CD93011_140305_TARDIS_C3PC6ACXX.8.6096370

description: Galaxy442-[CD93011_SLC25A39KD_Cufflinks_on_data_57_and_data_440__transcript_expression].txt

source_name: Donor 5


title: CD103009_140305_TARDIS_C3PC6ACXX.3.6096371


title: CD93011_140305_TARDIS_C3PC6ACXX.4.6096370


title: CD93011_140305_TARDIS_C3PC6ACXX.7.6096370


title: CD93011_140305_TARDIS_C3PC6ACXX.5.6096370


title: leaf_degradome

source_name: leaf samples from 4 mixed tissues

value: cotyledon from germination stage

value: new leaf from germination stage

value: old cotyledon from trefoil stage

value: new leaf from trefoil stage


title: CD40513_140305_TARDIS_C3PC6ACXX.5.6096351

description: Galaxy837-[CD40513_SLC25A39KD_Cufflinks_on_data_484_and_data_830__transcript_expression].txt

source_name: Donor 4


title: CD103009_140305_TARDIS_C3PC6ACXX.7.6096371


title: DGE_Co6_B

description: female

tag: tissue

value: injected with Sephadex G-53


title: CD40513_140305_TARDIS_C3PC6ACXX.7.6096351

tag: cell type


title: CD40513_140305_TARDIS_C3PC6ACXX.8.6096351


title: CD93011_140305_TARDIS_C3PC6ACXX.3.6096370


title: CD40513_140305_TARDIS_C3PC6ACXX.3.6096351


title: CD32913_140305_TARDIS_C3PC6ACXX.8.6096373

description: Galaxy358-[CD32913_SLC25A39KD_Cufflinks_on_data_57_and_data_356__transcript_expression].txt

source_name: Donor 3


title: CD32913_140305_TARDIS_C3PC6ACXX.5.6096373


title: CD32913_140305_TARDIS_C3PC6ACXX.4.6096373


title: CD40513_140305_TARDIS_C3PC6ACXX.6.6096351


title: CD32913_140305_TARDIS_C3PC6ACXX.3.6096373


title: CD31513_140305_TARDIS_C3PC6ACXX.7.6096356

description: Galaxy749-[CD31513_SLC25A39KD_Cufflinks_on_data_484_and_data_747__transcript_expression].txt

source_name: Donor 2


title: CD31513_140305_TARDIS_C3PC6ACXX.4.6096356


title: CD31513_140305_TARDIS_C3PC6ACXX.5.6096356


title: CD31513_140305_TARDIS_C3PC6ACXX.6.6096356


title: CD31513_140305_TARDIS_C3PC6ACXX.3.6096356


title: CD31513_140305_TARDIS_C3PC6ACXX.8.6096356


title: W420_140305_TARDIS_C3PC6ACXX.3.6096367

description: Galaxy684-[W420_SLC25A39KD_Cufflinks_on_data_484_and_data_682__transcript_expression].txt

source_name: Donor 1


title: CD93011_140305_TARDIS_C3PC6ACXX.6.6096370


title: W420_140305_TARDIS_C3PC6ACXX.7.6096367


title: W420_140305_TARDIS_C3PC6ACXX.5.6096367


title: W420_140305_TARDIS_C3PC6ACXX.6.6096367


title: W420_140305_TARDIS_C3PC6ACXX.8.6096367


title: Nst72hHL_bio_rep2_tech_rep4

city: Paris

first: Olivier

last: Vallon

address: 13 rue Pierre et Marie Curie

department: UMR CNRS 7141

institute: University of Paris, Institut de Biologie Physico-Chimique (IBPC)

data_processing:
Raw FASTQ files were generated by the sequencing platform using Illumina Casava 1.8 basecalling software.
Reads were adapter-trimmed using cutadapt 1.1 with options “-e 0.10 -O 20 -m 30” and quality-trimmed using prinseq-lite 0.15 with thresholds “-trim_left 12 -trim_qual_right 20 -trim_qual_left 20 -min_len 30 -min_qual_mean 28 -ns_max_p 20”.
Transcript abundance measurements and statistical analysis of differential expression were carried out following the protocol of Haas et al. (Nature Protocols 2013, 8:1494-1512) using tools from the Trinity package (release r20131110), RSEM 1.2.9, and the DESeq package. In this protocol RSEM estimates transcript- and gene-level abundances by mapping the RNA-Seq reads onto the predicted transcript sequences using Bowtie (version 1.0.0).
Based on the RSEM abundance measurements, DESeq performs the statistical analysis of differential gene or transcript expression between each pair of growth conditions taking into account variability among technical and biological replicates (all replicates pooled for a given condition). An analysis of deviance (ANODEV) comparing all four growth conditions simultaneously was also performed with DESeq. In all DESeq analyses the posterior mean estimate (PME) of the expected counts of RNA-Seq fragments per feature (“pme_expected_count”) computed by RSEM were used as abundance measures instead of the regular estimates (“expected_count”) because they are generally contained within the 95% confidence intervals. In addition, the following options were set for DESeq: “min_rowSum >= 10”, “method: pooled", “sharingMode: maximum", and “fitType: local". Genes and transcripts were considered as significantly regulated if the p-value adjusted for multiple testing (False Discovery Rate [FDR] calculated using the Benjamini-Hochberg [BH] method) was equal or lower than 5% (padj <= 5%).
Genome_build: Lobosphaera incisa SAG 2468 genome assembly
Supplementary_files_format_and_content: One Microsoft Excel spreadsheet with abundance measurements calculated using RSEM, and two Microsoft Excel spreadsheets with log2 fold changes and p-values computed using DESeq

organism: Lobosphaera incisa

source_name: 72h nitrogen starvation under high light (150 μmol photons.m-2.s-1); biological replicate 2, technical replicate 4

growth_protocol: Lobosphaera incisa SAG 2468 was cultivated in 350 mL modified BG-11 medium in 500 mL glass columns (3.8 cm internal diameter) placed in a temperature-regulated water bath at 25 oC. The cultures were aerated by bubbling a mixture of 2% CO2 in air. Before transfer to a nitrogen-depleted medium (mBG11-N), the cells of the logarithmically grown semi-continuous cultures grown under continuous illumination with the photon flux densities of 75 µmol photons m–2 s–1 were pelleted by centrifugation, and washed twice with sterile double-distilled water. At the onset of the nitrogen starvation experiments, the initial chlorophylls (a+b) concentration was adjusted to 15 µg ml–1. Illumination was provided by cool white fluorescent lamps external to the water bath at 75 and 150 µmol photons m–2 s–1 (referred to as normal light [NL], and high light [HL], respectively). The cultures used for RNA isolation were axenic.

extract_protocol:
Total RNA was isolated from samples collected at the specified time-points: time 0, 12h under HL, 72h under NL and 72h under HL. Lobosphaera incisa biomass of a total amount of approx. 15-20 mg (on the basis of DW measurements) was harvested by centrifugation in 2 ml safe-lock eppendorf tubes. The cell pellet was immediately frozen in liquid nitrogen. Cells were broken in the mixer mill MM 400 (Retsch, Germany) with the addition of 2 and 5 mm iron beads using 7-8 cycles of 45 sec with intermediate freezing in liquid nitrogen between the cycles. Broken cell powder was immediately used for RNA isolation with the SV Total RNA isolation System (Promega Corporation, USA) according to the user’s manual instructions. Total RNA concentration was measured by a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific Inc., USA) and calculated in the NanoDrop software, 3.0.0 (Coleman Technologies Inc., USA). The RNA integrity was estimated on the formaldehyde gel electrophoresis and on a 2100 Electrophoresis Bioanalyzer (Agilent technologies).
RNA libraries were prepared for sequencing using Illumina Truseq protocol (50-nt single-end reads and 100-nt paired-end reads, insert size ~150 bp). Sequencing was done on a on a HiSeq 1000 instrument. Library preparation and sequencing was performed by the transcriptomics platform of the Institut de Biologie de l'École Normale Supérieure, Paris, France.


title: Nst72hHL_bio_rep2_tech_rep3

source_name: 72h nitrogen starvation under high light (150 μmol photons.m-2.s-1); biological replicate 2, technical replicate 3


title: W420_140305_TARDIS_C3PC6ACXX.4.6096367


title: Nst72hHL_bio_rep2_tech_rep1

source_name: 72h nitrogen starvation under high light (150 μmol photons.m-2.s-1); biological replicate 2, technical replicate 1


title: Nst72hHL_bio_rep1_tech_rep3

source_name: 72h nitrogen starvation under high light (150 μmol photons.m-2.s-1); biological replicate 1, technical replicate 3


title: Nst72hHL_bio_rep1_tech_rep2

source_name: 72h nitrogen starvation under high light (150 μmol photons.m-2.s-1); biological replicate 1, technical replicate 2


title: CD32913_140305_TARDIS_C3PC6ACXX.7.6096373


title: Nst72hHL_bio_rep1_tech_rep4

source_name: 72h nitrogen starvation under high light (150 μmol photons.m-2.s-1); biological replicate 1, technical replicate 4


title: CD32913_140305_TARDIS_C3PC6ACXX.6.6096373


title: U266_10509

city: Boston

first: Irene

last: Ghobrial

address: 4 Blackfan Circle, 2nd Floor, Suite 240

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
We used Picard and topHat2 to process and align the reads with human reference genome (GRCh37).
RNA-SeQC was used to compute a series of quality control metrics
Reads were normalized by transcripts length and the total yield of each sequencing run via RNA-seq Gene Expression Workflow at the Broad.
Genes with low expression (RPKM < 1 across all samples) were filtered out.
Genome_build: GRCh37
Supplementary_files_format_and_content: RPKM files

source_name: U266 cell line

growth_protocol: Cells were grown in RPMI 10% FBS

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (QIAGEN).
NEBNext RNA library prep kit

treatment_protocol: Cells were treated by either CMLD010509-treated 50nM 6 hours or vehicle control (DMSO)

tag: cell line

value: Multiple Myeloma cell line

tag: condition

value: CMLD010509-treated 50nM 6 hours


title: Nst72hNL_bio_rep2_tech_rep4

source_name: 72h nitrogen starvation under normal light (75 μmol photons.m-2.s-1); biological replicate 2, technical replicate 4

tag: strain


title: Nst72hHL_bio_rep1_tech_rep1

source_name: 72h nitrogen starvation under high light (150 μmol photons.m-2.s-1); biological replicate 1, technical replicate 1


title: U266_WT

value: DMSO-treated


title: OPM2_10509

source_name: OPM2 cell line


title: MM1S_10509

source_name: MM1S cell line


title: Nst72hNL_bio_rep2_tech_rep3

source_name: 72h nitrogen starvation under normal light (75 μmol photons.m-2.s-1); biological replicate 2, technical replicate 3


title: OPM2_WT


title: Nst72hNL_bio_rep2_tech_rep2

source_name: 72h nitrogen starvation under normal light (75 μmol photons.m-2.s-1); biological replicate 2, technical replicate 2


title: CD40513_140305_TARDIS_C3PC6ACXX.4.6096351

source_name: Donor 4


title: MM1S_WT


title: NAMALWA_10509

source_name: NAMALWA cell line

value: NAMALWA

value: Burkitt Lymphoma cell line


title: Nst72hHL_bio_rep2_tech_rep2

source_name: 72h nitrogen starvation under high light (150 μmol photons.m-2.s-1); biological replicate 2, technical replicate 2


title: NCI-H929_10509

source_name: NCI-H929 cell line


title: NCI-H929_WT


title: NAMALWA_WT


title: Nst72hNL_bio_rep2_tech_rep1

source_name: 72h nitrogen starvation under normal light (75 μmol photons.m-2.s-1); biological replicate 2, technical replicate 1


title: Nst72hNL_bio_rep1_tech_rep4

source_name: 72h nitrogen starvation under normal light (75 μmol photons.m-2.s-1); biological replicate 1, technical replicate 4


title: Nst72hNL_bio_rep1_tech_rep3

source_name: 72h nitrogen starvation under normal light (75 μmol photons.m-2.s-1); biological replicate 1, technical replicate 3


title: Nst72hNL_bio_rep1_tech_rep2

source_name: 72h nitrogen starvation under normal light (75 μmol photons.m-2.s-1); biological replicate 1, technical replicate 2


title: pLKO_2

city: Shanghai

first: Chen-Ying

address: 1665 Kong Jiang Road

institute: Xinhua Hospital, Shanghai Jiao Tong University

data_processing:
Reads mapping by the STAR software
Differnetial expressed genes were analyzed by the Deseq2 software. P<0.05 was considered as statistically significant.
Genome_build: hg19
Supplementary_files_format_and_content: excel file generated by Deseq2. gene_id,baseMean, log2FoldChange,lfcSE,stat,pvalue,padj

source_name: DU145 control cells

growth_protocol: Grown in the DMEM+10% FBS

extract_protocol:
following the RNA protocol of RNAiso Plus (Takara)
A total amount of  0.2 μg RNA per sample was used as input material for the RNA  sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina®  (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis  was  subsequently  performed  using  DNA  Polymerase  I  and  RNase  H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of  DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100system.

value: prostate cancer cells

tag: genotype/variation

value: control (pLKO)


title: shTAZ_2

source_name: DU145 TAZ knockdown cells

value: TAZ knockdown


title: pLKO_1


title: Nst72hNL_bio_rep1_tech_rep1

source_name: 72h nitrogen starvation under normal light (75 μmol photons.m-2.s-1); biological replicate 1, technical replicate 1


title: Nst12hHL_bio_rep2_tech_rep2

source_name: 12h nitrogen starvation under high light (150 μmol photons.m-2.s-1); biological replicate 2, technical replicate 2


title: Nst12hHL_bio_rep2_tech_rep1

source_name: 12h nitrogen starvation under high light (150 μmol photons.m-2.s-1); biological replicate 2, technical replicate 1


title: Nst12hHL_bio_rep1_tech_rep4

source_name: 12h nitrogen starvation under high light (150 μmol photons.m-2.s-1); biological replicate 1, technical replicate 4


title: Nst12hHL_bio_rep1_tech_rep3

source_name: 12h nitrogen starvation under high light (150 μmol photons.m-2.s-1); biological replicate 1, technical replicate 3


title: Nst12hHL_bio_rep1_tech_rep2

source_name: 12h nitrogen starvation under high light (150 μmol photons.m-2.s-1); biological replicate 1, technical replicate 2


title: Control_bio_rep2_tech_rep3

source_name: logarithmic growth under normal light (75 μmol photons.m-2.s-1); biological replicate 2, technical replicate 3


title: drop_singlecell_RNA-seq

city: Bei Jing

first: huang

last: jiaying

address: Yiheyuan Road

department: School of life science

institute: Peking University

data_processing:
Tophat (version 2.0.14) was used to map the Arabidopsis thaliana genome
Cufflinks (version 2.2.1) was used to normalize and verify expression level (FPKM: Fragments Per Kilobase of exon model per Million mapped fragments) of the two samples
Genome_build: Arabidopsis thaliana genome of TAIR10 version
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for two samples

source_name: semi-in-vivo of mutative pollen tubes

growth_protocol: pollen tubes were growed on the solid pollen germination medium (SPGM), which10% sucrose, 0.01% boric acid, 5 mM CaCl2, 5 mM KCl, 1 mM MgSO4 and pH=7.5.

extract_protocol:
Pollen tubes cut from two independent stigmas were pooled and directly placed into cell lysis buffer [0.45 μL 10×PCR buffer II, 0.27 μL 25 mM MgCl2, 0.225 μL 10% NP40, 0.225 μL 0.1 M DTT, 0.045 μL SUPERase-In (20 U/μL, Ambion), 0.045 μL RNase inhibitor (40 U/μL, Ambion), 0.125 μL 0.5 μM V1-T24 Primer, 0.09 μL 2.5 mM dNTP Mix, add H2O to 4.45 μL] and lysed by vortexing. The lysed solution was used to generate the cDNA libraries.
The cDNA libraries follow the Smart-seq2 protocol.

treatment_protocol: About 500-600 double mutant pollen grains were hand-picked under a stereoscopic microscope and pollinated on a single stigma (emasculated for 36 hours) and cut together with the style. When the SIV PTs grew about 300-400 μm outside of the style, they were cut from the end of the style with tiny scissors (VANNAS, 8.5 cm, STR) under a stereo microscope.

tag: pollen tube

value: tissue

tag: developmental stage

value: 300-400 um outside of the style

value: drop1- drop2-


title: Control_bio_rep2_tech_rep4

source_name: logarithmic growth under normal light (75 μmol photons.m-2.s-1); biological replicate 2, technical replicate 4


title: Control_bio_rep2_tech_rep2

source_name: logarithmic growth under normal light (75 μmol photons.m-2.s-1); biological replicate 2, technical replicate 2


title: Control_bio_rep1_tech_rep1

source_name: logarithmic growth under normal light (75 μmol photons.m-2.s-1); biological replicate 1, technical replicate 1


title: Control_bio_rep2_tech_rep1

source_name: logarithmic growth under normal light (75 μmol photons.m-2.s-1); biological replicate 2, technical replicate 1


title: Control_bio_rep1_tech_rep2

source_name: logarithmic growth under normal light (75 μmol photons.m-2.s-1); biological replicate 1, technical replicate 2


title: Control_bio_rep1_tech_rep4

source_name: logarithmic growth under normal light (75 μmol photons.m-2.s-1); biological replicate 1, technical replicate 4


title: WT_singlecell_RNA-seq

source_name: semi-in-vivo of wild type pollen tubes

value: wild type


title: shTAZ_1


title: PJ01ΔmexT

city: Besançon

first: Catherine

last: Llanes

state: Doubs

address: 19 rue Ambroise Paré

department: UFR Sciences médicales et pharmaceutiques

institute: Université de Bourgonge Franche-Comté

data_processing:
Reads were mapped on 5892 annotated coding sequences (CDS) of PA14 using CLC Genomic Workbench 7.5 software
Transcripts abundance and differential expression results between the 3 replicates of PA14, PJ01 and PJ01ΔmexT were performed using Cuflinks and Cuffdiff algorithms
A significant difference between gene expression was considered when the q-value was less than 0.05 and when the expression ratio was between 0.3 and 3.0 folding.
Genome_build: UCBPP-PA14 accession number: NC_008463.1
Supplementary_files_format_and_content: The processed data is integrated in one only .xls file (Transcriptome CmrA + PA numbers.xls). This file contains 4 spreadsheets named: Summarized results (green tag), PA14vsPJ01, PA14vsPJ01dT and PJ01vsPJ01dT. For each gene, its homolog in the reference strain PAO1 is indicated in the column PA number. The "summarized results" sheet contains genes whose expression was found to be statistically different between the comparisons (Threshold ≥3 and ≤-3), these are the resullts presented in the Table S3 of our current manuscript. The remaining sheets (PA14vsPJ01, PA14vsPJ01dT and PJ01vsPJ01dT) contain all genes whose expression was found to be statistically different between the comparisons without any threshold.

organism: Pseudomonas aeruginosa

source_name: In vitro strains

growth_protocol: Bacterial strains were grown on Mueller-Hinton broth with adjusted concentrations of Ca2+ and Mg2+ under aeration (250rpm) at 37°C.

extract_protocol:
When reached OD600=1, cells were harvested in RNA protect bacteria reagent  (Qiagen) and disrupted with 2.8 mm  and 0.25 mm ceramic beads in a TissueLyzer II (Qiagen) acording to manufacturer's recommendations. Total RNA was extracted using the RneasyPlus 96 kit (Qiagen), Depletion of rRNA from total RNA samples was performed with the Ribo-zero rRNA Removal reagents (Epicentre).
Libraries were constructed using the TruSeq Stranded mRNA HT Sample Prep kit (Illumina). The libraries were quantified with the Picogreen fluorescent dye and yielded around 200 to 800 ng.

tag: description

value: PJ01 strain deleted from its mexT gene

tag: phenotype

value: WT


title: Nst12hHL_bio_rep2_tech_rep4

source_name: 12h nitrogen starvation under high light (150 μmol photons.m-2.s-1); biological replicate 2, technical replicate 4


title: Nst12hHL_bio_rep2_tech_rep3

source_name: 12h nitrogen starvation under high light (150 μmol photons.m-2.s-1); biological replicate 2, technical replicate 3


title: Ndt80 untagged control SRaff 2

first: Isabel

institute: UCSF

data_processing:
Quality analysis performed with FastQC
ChIP-seq reads were aligned to the K.lactis genome assembly using bowtie2 and default parameters
Files were converted to sorted .bam files using Samtools
Peak separation distance was determined using the binding.characteristics function in the SPP package in R
Peaks and fold enrichment were calculated using MACS2, using peak separation distances calculated from SPP and --nomodel parameter
Genome_build: K. lactis genome was downloaded from the Yeast Gene Order Browser in December 2015
Supplementary_files_format_and_content: bedGraph.wig files were generated from indexed, sorted .bam file using genomeCoverageBed tool in BedTools, followed by a .bed to .wig conversion script in Python.  FE.bdg.wig files were generated by MACS2 using the -SPMR parameter, and converted to .wig using the same Python script.  Peaks.xls files were generated for experiments with tagged proteins using untagged strains as a control in MACS2.

organism: Kluyveromyces lactis

source_name: a/alpha cell

growth_protocol: Cells were grown overnight in Sraffinose, diluted back to OD = 0.02 in Sraffinose and grown for 16 hours, then galactose (1.7% total) was added and cells were grown for 5 hours.

extract_protocol:
Cells were lysed with glass bead vortexing, sonicated for 3 15-minute cycles, and immunoprecipitated at 4˚C overnight
Libraries were prepared using the NEBNext ChIP-Seq library prep kit for Illumina (New England Biolabs)

tag: media condition

value: Sraffinose + 1.7% galactose

tag: chip antibody

value: human c-myc

tag: strain number


title: PJ01

value: Spontaneus cmrA+ strain derived from PA14


title: KO_SPO_3

data_processing:
Quality analysis performed with FastQC
Reads were aligned to the P. pastoris genome assembly using TopHat
Transcripts assembled using Cufflinks
Transcripts merged using Cuffmerge
Differential expression calculated using CuffDiff
Genome_build: P. pastoris genome was downloaded from NCBI in December 2015, genome annotated using Yeast Gene Annotation Pipeline in December 2015.
Supplementary_files_format_and_content: .gtf files were generated by Cufflinks from reads aligned to the genome using TopHat

organism: Komagataella pastoris

source_name: diploid cell

growth_protocol: Cells were grown overnight in YPD diluted back to OD = 0.1 in YPD or sporulation media and grown for 4-6 hours (for YPD) or 30  hours (for spo media).

extract_protocol:
mRNA isolated using Qiagen Oligotex mRNA mini kit
Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs)

treatment_protocol: Total RNA isolated using Ambion RiboPure kit

value: 0.5% sodium acetate, 1% potassium chloride, 1% glucose, 2% agar plates

tag: genotype

value: Ndt80 del

tag: cell cycle

value: meiotic


title: KO_SPO_2


title: PA14

value: Pseudomonas aeruginosa reference strain UCBPP-PA14


title: Ndt80 untagged control SRaff 1


title: Nst12hHL_bio_rep1_tech_rep1

source_name: 12h nitrogen starvation under high light (150 μmol photons.m-2.s-1); biological replicate 1, technical replicate 1


title: Ndt80 untagged control 2

data_processing:
Quality analysis performed with FastQC
ChIP-seq reads were aligned to the S. stipitis genome assembly using bowtie2 and default parameters
Files were converted to sorted .bam files using Samtools
Peak separation distance was determined using the binding.characteristics function in the SPP package in R
Peaks and fold enrichment were calculated using MACS2, using peak separation distances calculated from SPP and --nomodel parameter
Genome_build: S. stipitis genome was downloaded from the Candida Gene Order Browser in December 2015.
Supplementary_files_format_and_content: bedGraph.wig files were generated from indexed, sorted .bam file using genomeCoverageBed tool in BedTools, followed by a .bed to .wig conversion script in Python.  FE.bdg.wig files were generated by MACS2 using the -SPMR parameter, and converted to .wig using the same Python script.  Peaks.xls files were generated for experiments with tagged proteins using untagged strains as a control in MACS2.

organism: Scheffersomyces stipitis

source_name: prototrophic cell

growth_protocol: Cells were grown overnight in YPD diluted back to OD = 0.02 in YPD and grown for 4-6 hours until log-phase.

value: YPD


title: WT_SPO_3

value: wildtype


title: pGal1-Ndt80-myc_2


title: WT_SPO_2


title: Control_bio_rep1_tech_rep3

source_name: logarithmic growth under normal light (75 μmol photons.m-2.s-1); biological replicate 1, technical replicate 3


title: WT_YPD_3

value: mitotic


title: pTef1-Ndt80B-myc_2


title: Ndt80 untagged control 1


title: pGal1-Ndt80-myc_1


title: WT_YPD_2