title: Blood_Platelets_Vumc-HD-102-TR1096


title: WT_normal_MCSF_LPS_rep3

status: Public on Aug 15 2017

type: SRA

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

country: USA

institute: Washington University in St.Louis

library_source: transcriptomic

data_processing:
Second mate was used for sample demultiplexing.
Individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All.
Gene expression was obtained via ht-seq and DESeq2 for differential expression.
Gene expression was obtained using in-house scripts bassed on MACS and HTSeq (https://github.com/ctlab/quant3p).
Genome_build: mm10
Supplementary_files_format_and_content: text file with read counts for genes

molecule: polyA RNA

organism: Mus musculus

source_name: Bone marrow-derived macrophages

growth_protocol: Trem2–/– mice were originally generated by Turnbull et al. (J. Immunol. 177, 3520-3524 (2006).)

extract_protocol:
mRNA was extracted from cell lysates using oligo-dT beads (Invitrogen).
For cDNA synthesis, we used custom oligo-dT primer with a barcode and adaptor-linker sequence (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15). After first-strand synthesis, samples were pooled together based on Actb qPCR values and RNA-DNA hybrids were degraded with consecutive acid-alkali treatment. Subsequently, a second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated with T4 ligase (NEB) followed by SPRI-beads (Agencourt AMPure XP, BeckmanCoulter) clean-up. The mixture was enriched by PCR for 12 cycles and SPRI-beads (Agencourt AMPure XP, BeckmanCoulter) purified to yield final strand-specific RNA-seq libraries.

treatment_protocol: Bone marrow-derived macrophages (BMDMs) from WT and Trem2–/– mice were cultured in either 0.5% or 10% LCCM overnight in complete RPMI. Some samples cells were stimulated with 10 ng/ml LPS for 4 hours.

tag: tissue

value: bone marrow

tag: cell type

value: macrophages

tag: strain

tag: genotype

value: WT

tag: mcsf

value: normal

tag: treatment

value: LPS


title: WT_normal_MCSF_no_LPS_rep3

value: Ctrl


title: Pum2 global knockout Rep1

city: New Haven

first: Haifan

last: Lin

state: Connecticut

address: 10 Amistad St.

department: Cell Biology

institute: Yale Univeristy

data_processing:
RNA-seq data are procssed via software tools including Tophat2 and Cufflinks. Differentially  expressed genes are identified by Cuffdiff program.
Genome_build: mm10
Supplementary_files_format_and_content: format: Cuffdiff output format of gene_expression.diff
Supplementary_files_format_and_content: content: differentially expressed genes among different comparisons

molecule: total RNA

source_name: brain

extract_protocol: Total RNA was extracted using RNeasy Plus Kit (QIAGEN Cat#74134) from half of a neonatal mouse brain. The libraries were constructed using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, Cat #: RS-122-2101) and the sequencing was performed on an Illumina HiSeq 2000 platform.

tag: genotype/variation


title: Blood_Platelets_Vumc-HD-106-TR1099

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

data_processing:
Single-end 100 bp reads were subjected to pre-aligment 5'-end quality trimming and sequence adapter clipping using Trimmomatic.
Cleaned-up reads were mapped to the hg19 reference genome using STAR (version 2.3.0), using splice aware alignments and allowing for 10 mismatches.
Intron-spanning read summarization was performed using a samtools-based filtering step and HTSeq (version 0.6.1) using union-mode, unstranded reads and minimal mapping quality of 35, all guided by the Ensembl gene annotation version 75.
Genome_build: hg19
Supplementary_files_format_and_content: Samples in the tab-delimited text file were processed according to the described protocol and data of all samples was merged in a comprehensive read count matrix.

organism: Homo sapiens

source_name: Thrombocytes

extract_protocol:
Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing the EDTA anti-coagulant. The cells and aggregates were removed by centrifugation at room temperature for 20 minutes at 120g, resulting in platelet-rich plasma. The platelets were isolated from the platelet-rich plasma by centrifugation at room temperature for 20 minutes at 360g. The platelet pellet was collected in 30 μl RNAlater (Life Technologies), incubated overnight at 4°C and frozen at -80°C for further use. Frozen platelets were thawed on ice and total RNA was isolated using the mirVana RNA isolation kit (Life Technologies) according to the manufacturers’ protocol. Complementary purification of small RNAs was included in the isolation procedure by addition of miRNA homogenate (Life Technologies). Total RNA was dissolved in 30 μl Elution Buffer (Life Technologies) and RNA quality and quantity was measured using Bioanalyzer 2100 with RNA 6000 Picochip (Agilent).
100-500 pg of platelet total RNA diluted in nuclease free H2O was subjected to cDNA synthesis and amplification using the SMARTer Ultra Low RNA Kit for Illumina Sequencing v3 (Clontech, cat. nr. 634853) according to the manufacturers’ protocol. Conversion and efficient amplification of cDNA was quality-controlled using the Bioanalyzer 2100 with DNA High Sensitivity chip (Agilent). Samples with detectable fragments in the 300-7500 bp region were selected for further processing and Covaris shearing by sonication (Covaris Inc). Sample preparation for Illumina sequencing was performed using the Truseq DNA Sample Preparation Kit (Illumina, cat nr. FC-121-2001) or Truseq Nano DNA Sample Preparation Kit (Illumina, cat nr. FC-121-4001). Sample quality and quantity was measured using the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High-quality samples with product sizes between 300-500 bp were pooled in equimolar concentrations (12-19 samples per Hiseq lane) and submitted for 100 bp Single Read sequencing on the Hiseq 2500 platform (Illumina).

tag: disease

value: Healthy Control


title: Pum1 global knockout Rep4


title: Pum1 global knockout Rep2


title: Blood_Platelets_AMC-HD-005-TR1143


title: Blood_Platelets_AMC-HD-004-TR1142


title: Blood_Platelets_AMC-HD-003-TR1141


title: Pum1 global knockout Rep3


title: WT_low_MCSF_no_LPS_rep4

value: low


title: WT_normal_MCSF_LPS_rep1


title: WT_low_MCSF_no_LPS_rep2


title: Nestin-Cre mediated Pum1; Pum2 double conditional knockout  Rep3

value: ndcko


title: WT_low_MCSF_no_LPS_rep1


title: Blood_Platelets_Vumc-HD-98-TR921


title: Blood_Platelets_AMC-HD-001-TR1139


title: Nestin-Cre mediated Pum1; Pum2 double conditional knockout  Rep2


title: Pum2 global knockout Rep2


title: Blood_Platelets_AMC-HD-002-TR1140


title: WT_low_MCSF_LPS_rep4


title: Nestin-Cre mediated Pum1; Pum2 double conditional knockout  Rep1


title: Blood_Platelets_Vumc-HD-91-TR897


title: Blood_Platelets_Vumc-HD-89-TR896


title: WT_low_MCSF_no_LPS_rep3


title: Pum1 global knockout Rep1


title: WT_normal_MCSF_LPS_rep2


title: Blood_Platelets_Vumc-HD-100-TR1095


title: WT_low_MCSF_LPS_rep1


title: WT_low_MCSF_LPS_rep2


title: WT_low_MCSF_LPS_rep3


title: T2KO_normal_MCSF_no_LPS_rep4


title: T2KO_normal_MCSF_no_LPS_rep3


title: T2KO_normal_MCSF_no_LPS_rep2


title: CD4+ Th1 Low IL-2 CTCF Rep 1

city: Birmingham

first: Amy

last: Weinmann

address: 1825 University Blvd

department: Department of Microbiology

institute: University of Alabama at Birmingham

library_source: genomic

data_processing:
Reads were aligned to the mm9 genome using Bowtie to generate BAM files
Bedgraph files were generated from BAM files using Bedtools
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph

molecule: genomic DNA

source_name: CD4+ Th1

growth_protocol: Primary CD4+ T cells were isolated from spleen and lymph nodes of C57BL/6 mice and stimulated with plate bound anti-CD3 and anti-CD28 in type 1 conditions (IL-12 and anti-IL4). On day 3, the cells were split and maintained in either high IL-2, low IL-2, or low IL-2 with αKG. The low IL-2 and low IL-2 with aKG replicate 1 for H3K27Ac and H3K27me3 were performed with 10 units/mL of IL-2. All other replicates were performed as described in Chisolm et. al.

extract_protocol:
ChIP-seq assays were performed as previously outlined (Reddy et al. Genome Research 2009, PMID: 19801529)
Library construction was performed as previously outlined (Reddy et al. Genome Research 2009, PMID: 19801529)

value: CD4+ Th1

tag: antibody

value: CTCF


title: Blood_Platelets_Vumc-HD-92-TR920


title: CD4+ Th1 Low IL-2 CTCF Rep 1 input


title: CD4+ Th1 Low IL-2 CTCF Rep 2


title: CD4+ Th1 Low IL-2 + aKG CTCF Rep 2


title: CD4+ Th1 High IL-2 CTCF Rep 2


title: T2KO_normal_MCSF_no_LPS_rep1


title: T2KO_normal_MCSF_LPS_rep4


title: Blood_Platelets_Vumc-HD-83-TR891


title: Blood_Platelets_Vumc-HD-84-TR892


title: Blood_Platelets_Vumc-HD-86-TR893


title: Blood_Platelets_Vumc-HD-87-TR894


title: CD4+ Th1 High IL-2 CTCF Rep 1 input


title: Blood_Platelets_Vumc-HD-88-TR895


title: Blood_Platelets_Vumc-HD-80-TR889


title: Blood_Platelets_Vumc-HD-74-TR888


title: CD4+ Th1 Low IL-2 + aKG CTCF Rep 1 input


title: CD4+ Th1 High IL-2 CTCF Rep 1


title: Blood_Platelets_Vumc-HD-73-TR887


title: T2KO_normal_MCSF_LPS_rep2


title: T2KO_normal_MCSF_LPS_rep3


title: CD4+ Th1 Low IL-2 + aKG CTCF Rep 1


title: Blood_Platelets_Vumc-HD-60-TR885


title: T2KO_low_MCSF_no_LPS_rep4


title: CD4+ Th1 Low IL-2 + aKG H3K27me3 Rep 2


title: Blood_Platelets_Vumc-HD-63-TR886


title: Blood_Platelets_Vumc-HD-56-TR884


title: T2KO_normal_MCSF_LPS_rep1


title: CD4+ Th1 Low IL-2 + aKG H3K27me3 and CTCF Rep 2 input


title: CD4+ Th1 Low IL-2 + aKG H3K27me3 Rep 1 input


title: CD4+ Th1 Low IL-2 + aKG H3K27me3 Rep 1


title: Blood_Platelets_Vumc-HD-156-TR935


title: T2KO_low_MCSF_no_LPS_rep2


title: T2KO_low_MCSF_no_LPS_rep3


title: T2KO_low_MCSF_no_LPS_rep1


title: CD4+ Th1 Low IL-2 H3K27me3 and CTCF Rep 2 input


title: CD4+ Th1 Low IL-2 H3K27me3 Rep 2


title: CD4+ Th1 Low IL-2 H3K27me3 Rep 1 input


title: CD4+ Th1 Low IL-2 H3K27me3 Rep 1


title: Blood_Platelets_Vumc-HD-155-TR934


title: T2KO_low_MCSF_LPS_rep4


title: Blood_Platelets_Vumc-HD-149-TR932


title: T2KO_low_MCSF_LPS_rep3


title: T2KO_low_MCSF_LPS_rep2


title: Blood_Platelets_Vumc-HD-145-TR930


title: CD4+ Th1 High IL-2 H3K27me3 Rep 2


title: Blood_Platelets_Vumc-HD-144-TR929


title: T2KO_low_MCSF_LPS_rep1


title: CD4+ Th1 High IL-2 H3K27me3 Rep 1


title: stalk_mRNA_Seq_3

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

data_processing:
Base call by bcl2fastq v. 2.17; adaptor and index sequences were trimmed
Fastq files were aligned using TopHat2
Gene-level quantification was presented as TPM and calculated by Partek Genomic Suite
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing RPKM values by gene

source_name: developing kidneys

extract_protocol:
Qiagen Rneasy micro kit (#74004)
Kapa stranded mRNA-Seq library (#KK8420)

value: CFW

tag: developing stage

tag: marker


title: Blood_Platelets_Vumc-HD-142-TR927


title: CD4+ Th1 Low IL-2 + aKG H3K27Ac Rep 2 input


title: CD4+ Th1 Low IL-2 + aKG H3K27Ac Rep 2


title: stalk_mRNA_Seq_2


title: stalk_mRNA_Seq_1


title: CD4+ Th1 Low IL-2 + aKG H3K27Ac Rep 1 input


title: Blood_Platelets_Vumc-HD-127-TR925


title: tip_mRNA_Seq_3


title: Blood_Platelets_Vumc-HD-151-TR933


title: CD4+ Th1 Low IL-2 + aKG H3K27Ac Rep 1


title: Blood_Platelets_Vumc-HD-108-TR924


title: tip_mRNA_Seq_2


title: CD4+ Th1 Low IL-2 H3K27Ac Rep 2 input


title: tip_mRNA_Seq_1


title: CD4+ Th1 Low IL-2 + aKG

data_processing:
Library strategy: HiC-Seq
Reads were first trimmed from the 3’ end of sequences to GATC (MboI restriction enzyme site). Trimmed reads were aligned to mm9 with Bowtie software with parameters --chunkmbs 128 --mm -m1 --best --strata -p4 -S.  A superRes of 52,000 kb was used.
The remainder of analysis was performed using Homer (Hypergeometric Optimization of Motif Enrichment)(Heinz et al., 2010).
Only unique reads and paired end tags with more than 1.5x fragment length on the same chromosome separating them were retained. Tag counts of all directories were normalized to the sample with lowest sequencing depth.
A map resolution of 26,000 kb was chosen to ensure that > 80% of loci had at least 1000 contacts.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

growth_protocol: Primary CD4+ T cells were isolated from spleen and lymph nodes of C57BL/6 mice and stimulated with plate bound anti-CD3 and anti-CD28 in type 1 conditions (IL-12 and anti-IL4). On day 3, the cells were split and maintained in either high IL-2, low IL-2, or low IL-2 with αKG.

extract_protocol:
Hi-C protocol outlined in (Rao et al., 2014) was performed with the following alterations. Nuclei were resuspended in 0.5% SDS diluted in a final concentration of 1X NEB Buffer 2 in step 10. A smaller volume (21.6 uL) 10X NEB was added at step 12.
Hi-C protocol outlined in (Rao et al., 2014) was performed with the following alterations. Each sequencing library was incubated with USER enzyme for 15 minutes at 37 degrees C after step 56. Final libraries were submitted to paired-end on an Illumina HiSeq 2500. Read lengths of 100 bp (left read) and 90 bp (right read) were acquired.

tag: strand

value: aKG Low IL-2


title: Blood_Platelets_UMCU-Healthy Control-1-0212-TR818

description: UMCU-Healthy Control-1-0212-TR818


title: Blood_Platelets_Vumc-HD-103-TR923


title: Blood_Platelets_UMCU-Healthy Control-1-0211-TR826

description: UMCU-Healthy Control-1-0211-TR826


title: Blood_Platelets_Vumc-HD-101-TR922


title: CD4+ Th1 Low IL-2

value: Untreated Low IL-2


title: CD4+ Th1 Low IL-2 H3K27Ac Rep 1


title: seed collected 48 h into countinuous light (post-stratification), 48 h SL Replicate 3 [sRNA-seq]

city: Heidelberg

first: Quentin

last: Gouil

state: VIC

address: Studley Road

country: Australia

institute: Olivia Newton-John Cancer Research Institute

data_processing:
Sequenced reads were trimmed for adaptor sequence, and filtered for low-quality sequence, with Trim Galore v0.4.2. Sequences ranging between 18 to 24 bases in length were selected for mapping.
filered and trimmed reads were mapped and clustered onto A. thaliana TAIR10 genome with ShortStack v3.6
The reads counts on all 87,000 defined clusters were subjected to differential analysis with DESeq2 v1.10.1
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited files including cluster information, counts on all clusters, and the estimated sRNA abundance on differential sRNA loci

organism: Arabidopsis thaliana

growth_protocol: Seeds were sown on MS media, statified at 4 C for 2-d before being transferred to continious light at 22C.

extract_protocol:
RNA isolation was carried out using the Ambion Plant RNA isolation aid and RNAqeous RNA isolation kit.
sRNA-seq libraries were generated using the TruSeq small RNA kit (Illumina)

treatment_protocol:
Following 48 h of cold, dark stratification (4 °C), samples were transferred into light conditions (100 µE m -2 sec-1) at 22 °C and collected after 48h.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.

tag: ecotype

value: wild type

value: seedling

tag: time point

value: seed germinating in countinuous light 48 h SL


title: CD4+ Th1 Low IL-2 H3K27Ac Rep 2


title: Blood_Platelets_Vumc-HD-143-TR928


title: Blood_Platelets_UMCU-Healthy Control-1-0209-TR823

description: UMCU-Healthy Control-1-0209-TR823


title: CD4+ Th1 High IL-2 H3K27Ac Rep 2


title: seed collected 48 h into countinuous light (post-stratification), 48 h SL Replicate 2 [sRNA-seq]


title: CD4+ Th1 High IL-2

value: Untreated High IL-2


title: Pax9-Het-44-5

city: Salt Lake City

first: Shihai

last: Jia

state: ut

address: 20 South 2030 East, Room 320 BPRB

department: Department of Neurobiology

institute: University of Utah

description: E13.5 FPKM

data_processing:
Mouse ensembl annotations (build 74) were downloaded and converted to genePred format.  Splice junction sequences were generated using USeq’s (v8.8.8) MakeTranscriptome application using a radius of 46.  The splice junction sequences were added to the mouse chromosome sequences (mm10) and run through novoindex (v2.8) to create the transcriptome index.
Reads were aligned to the transcriptome index described above using Novoalign (v2.08.03), allowing up to 50 alignments for each read.  USeq’s SamTranscriptomeParser application was used to select the best alignment for each read and convert the coordinates of reads aligning to splices back to genomic space.
Read counts for each gene were generated using USeq’s DefinedRegionDifferentialSeq application.  These counts were used in DESeq2 to measure the differential expression between each condition.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: palate shelves

extract_protocol: E13.5 and E14 with or without treatment mouse embryo dissected and put on ice cold PBS, micro-dissect the palate shelves under microscope. Micro-dissected tissues were frozen at -80℃, total RNA was extracted by using RNeasy micro kit from Qiagen.cDNA was made by Illumina TruSeq RNA Sample Prep Kit v2 with oligo(dT) selection.

treatment_protocol: the pregnant Pax9+/- females were treated with WAY-262611 daily injection via tail vein from E10.5 to E14

value: Palate shelf

tag: age

value: embryonic day 13.5


title: Blood_Platelets_Vumc-HD-130-TR926


title: Blood_Platelets_UMCU-Healthy Control-1-0208-TR822

description: UMCU-Healthy Control-1-0208-TR822


title: Pax9-mt-44-9

description: E13.5 FPKM


title: Pax9-Het-56-2

description: E13.5 FPKM


title: Blood_Platelets_UMCU-Healthy Control-1-0206-TR815

description: UMCU-Healthy Control-1-0206-TR815


title: CD4+ Th1 High IL-2 H3K27Ac Rep 1


title: Blood_Platelets_UMCU-Healthy Control-1-0207-TR817

description: UMCU-Healthy Control-1-0207-TR817


title: Blood_Platelets_UMCU-Healthy Control-1-0205-TR811

description: UMCU-Healthy Control-1-0205-TR811


title: Blood_Platelets_UMCU-Healthy Control-1-0204-TR813

description: UMCU-Healthy Control-1-0204-TR813


title: Pax9-mt-44-1

description: E13.5 FPKM


title: seed collected 24 h into countinuous light (post-stratification), 24 h SL Replicate 3 [sRNA-seq]

treatment_protocol:
Following 48 h of cold, dark stratification (4 °C), samples were transferred into light conditions (100 µE m -2 sec-1) at 22 °C and collected after 24h.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.

value: germinating seed

value: seed germinating in countinuous light 24 h SL


title: seed collected 24 h into countinuous light (post-stratification), 24 h SL Replicate 2 [sRNA-seq]


title: seed collected 12 h into countinuous light (post-stratification), 12 h SL Replicate 3 [sRNA-seq]

treatment_protocol:
Following 48 h of cold, dark stratification (4 °C), samples were transferred into light conditions (100 µE m -2 sec-1) at 22 °C and collected after 12h.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.

value: seed germinating in countinuous light 12 h SL


title: seed collected 24 h into countinuous light (post-stratification), 24 h SL Replicate 1 [sRNA-seq]


title: seed collected 48 h into countinuous light (post-stratification), 48 h SL Replicate 1 [sRNA-seq]


title: Blood_Platelets_UMCU-Healthy Control-1-0203-TR814

description: UMCU-Healthy Control-1-0203-TR814

value: Healthy Control


title: Pax9-WT-56-6

description: E13.5 FPKM


title: CD4+ Th1 Low IL-2 H3K27Ac Rep 1 input


title: Blood_Platelets_UMCU-Healthy Control-1-0202-TR812

description: UMCU-Healthy Control-1-0202-TR812


title: Pax9-mt-56-1

description: E13.5 FPKM


title: seed collected 12 h into countinuous light (post-stratification), 12 h SL Replicate 2 [sRNA-seq]


title: Pax9-mt-56-3

description: E13.5 FPKM


title: seed collected 12 h into countinuous light (post-stratification), 12 h SL Replicate 1 [sRNA-seq]


title: Blood_Platelets_UMCU-Healthy Control-1-0201-TR821

description: UMCU-Healthy Control-1-0201-TR821


title: seed collected 6 h into countinuous light (post-stratification), 6 h SL Replicate 3 [sRNA-seq]

treatment_protocol:
Following 48 h of cold, dark stratification (4 °C), samples were transferred into light conditions (100 µE m -2 sec-1) at 22 °C and collected after 6h.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.

value: seed germinating in countinuous light 6 h SL


title: NP+ CD25low Rep 2

data_processing:
Library strategy: ATAC-Seq
Illumina Casava 1.8.4 software used for basecalling
Seqeunced reads were trimmed for adapter sequence, then mapped to mm9 using Bowtie2 v2.2.59 with parameters -p 4 -X 2000
Peaks were called using MACS2 v2.1.1.20160309 with parameters -f BAMPE -g mm -B -q 0.05 --call-summits --nomodel --nolambda --keep-dup all
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files containing peak locations and depth

source_name: CD8+ T cells

growth_protocol: Antigen specific CD8+ T cells were generated during the course of an influenza infection in mice. 7-9 days after the initial influenza infection, tetramer positive NP antigen specific or OTI specific CD8+ T cells were sorted into CD25high or CD25low populations as described in Chisolm et al.

extract_protocol: Libraries were amplified using Nextara primers with NEBNext High-Fidelity 2X PCR Master Mix, and reactions were purified with the PCR Purification Kit.

value: NP+ CD25low CD8+ T cells


title: CD4+ Th1 High IL-2 input

value: CD4+ Th1


title: seed collected 6 h into countinuous light (post-stratification), 6 h SL Replicate 2 [sRNA-seq]


title: Blood_Platelets_UMCU-Healthy Control-1-0200-TR816

description: UMCU-Healthy Control-1-0200-TR816


title: NP+ CD25high Rep 2

value: NP+ CD25high CD8+ T cells


title: Blood_Platelets_UMCU-Healthy Control-1-0199-TR825

description: UMCU-Healthy Control-1-0199-TR825


title: OTI+ CD25low

value: OTI+ CD25low CD8+ T cells


title: Pax9-WT-44-7

description: E13.5 FPKM


title: Blood_Platelets_UMCU-Healthy Control-1-0198-TR820

description: UMCU-Healthy Control-1-0198-TR820


title: NP+ CD25high Rep 1


title: NP+ CD25low Rep 1


title: Blood_Platelets_UMCU-Healthy Control-1-0197-TR824

description: UMCU-Healthy Control-1-0197-TR824


title: E14Tg2a +aKG Rep 3

data_processing:
All RNA-seq analyses were performed using the Penn State Galaxy publicly available server using the tuxedo suite analysis tools. Fastq files were aligned to the mm10 reference genome using TopHat (Galaxy Tool Version 0.9; Tool Version TopHat v2.0.14 for all studies except for the glutamine studies, Galaxy Tool Version 2.1.0 and Tool Version TopHat v2.1.0) were used with default parameters.
Cufflinks, Cuffmerge, Cuffquant, and Cuffnorm were performed to define FPKM values for genes. Cufflinks (Galaxy Tool Version 2.2.2.0; Tool Version Cufflinks v2.2.1.0) was performed using default parameters for all settings except bias and multi-read correction was performed.
Cuffmerge (Galaxy Tool Version 2.2.1.0) was performed using default parameters. Cuffquant (Galaxy Tool Version 2.2.1.0; Tool Version Cuffquant v2.2.1) was performed using default parameters for all settings except bias and multi-read correction was performed.
Cuffdiff (Galaxy Tool Version 2.2.1.3; Tool Version Cuffdiff v2.2.1) was performed using default parameters (using Cuffquant output files). Cuffnorm (Galaxy Tool Version 2.2.1.1; Tool Version Cuffnorm v2.2.1) was performed using default parameters with a Cuffdiff format output.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files showing FPKM values for each individual sample

growth_protocol:
Primary CD4+ or CD8+ T cells were isolated from spleen and lymph nodes of C57BL/6 mice and stimulated with plate bound anti-CD3 and anti-CD28 in type 1 conditions (IL-12 and anti-IL4). On day 3, the cells were split and maintained in either high IL-2, low IL-2, or low IL-2 with αKG.
For the experiments to define the role for glutamine, primary CD4+ T cells were isolated and stimulated with plate bound αCD3 and αCD28 in either IMDM media or RPMI without glutamine media in type 1 polarizing conditions. At day three, the cells were split into RPMI media either with or without glutamine and maintained in high IL-2, high IL-2 with αKG, low IL-2, or low IL-2 with αKG.
The ES cell line E14TG2a was either left untreated or treated with cell permeable αKG for two days in glutamine-free media.

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit (Clontech)
RNA libraries were prepared for sequencing using standard Illumina protocols. CD8 replicates 1-3 (Eurofins); all other samples (Genewiz)

value: E14Tg2A Cell line

value: ES cell

value: aKG


title: AFX7

city: San Francisco

first: Kevin

last: Lai

state: CA

address: 2340 Sutter Street

department: Dermatology

institute: University of California, San Fransico

data_processing:
Quality was assessed using FastQC (v0.11.1)
Sequencing reads were aligned to the human genome (v19) using Tophat v2.0.14.
The aligned reads were quantified using htseq-count v0.6.0 using the RefSeq database as a reference.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample.

source_name: Human Skin

extract_protocol:
RNA was extracted using the Rneasy micro kit
RNA was reversed transcribed with the Nugen's Ovation RNA-Seq system kit and sequencing libraries were prepared using Nugen's Ovation ultralow kit.

value: Atypical Fibroxanthoma Tumor


title: seed collected 6 h into countinuous light (post-stratification), 6 h SL Replicate 1 [sRNA-seq]

value: wild type


title: E14Tg2a +aKG Rep 1


title: seed collected 1 h into countinuous light (post-stratification), 1 h SL Replicate 1 [sRNA-seq]

treatment_protocol:
Following 48 h of cold, dark stratification (4 °C), samples were transferred into light conditions (100 µE m -2 sec-1) at 22 °C and collected after 1h.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.

value: seed germinating in countinuous light 1 h SL


title: AFX6


title: seed collected 1 h into countinuous light (post-stratification), 1 h SL Replicate 2 [sRNA-seq]


title: OTI+ CD25high

value: OTI+ CD25high CD8+ T cells


title: seed following 48 h of stratification (S) Replicate 3 [sRNA-seq]

treatment_protocol:
Samples were collected 48 h into dark stratification started at 4 °C.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.

value: seed during stratification 48 h S


title: seed following 48 h of stratification (S) Replicate 2 [sRNA-seq]

value: germinating seed


title: AFX8


title: AFX3


title: seed following 48 h of stratification (S) Replicate 1 [sRNA-seq]


title: E14Tg2a +aKG Rep 2


title: seed following 12 h of stratification (S) Replicate 1 [sRNA-seq]

treatment_protocol:
Samples were collected 12 h into dark stratification started at 4 °C.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.

value: seed during stratification 12 h S


title: AFX5


title: seed following 12 h of stratification (S) Replicate 3 [sRNA-seq]


title: AFX4


title: AFX1


title: E14Tg2a UN Rep 2

value: Untreated


title: seed following 12 h of stratification (S) Replicate 2 [sRNA-seq]


title: Normal_Ker7

value: Normal Keratinocytes


title: Normal_Ker8


title: E14Tg2a UN Rep 3


title: E14Tg2a UN Rep 4


title: seed collected 1 h into countinuous light (post-stratification), 1 h SL Replicate 3 [sRNA-seq]


title: E14Tg2a +aKG Rep 4


title: seed following 1 h of stratification (S) Replicate 3 [sRNA-seq]

treatment_protocol:
Arabidopsis thaliana seeds were surface sterilised and plated on MS media. Samples were collected 1 h after dark stratification started at 4 °C.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.

value: seed during stratification 1 h S


title: Normal_Ker6


title: dry seed 0 h Replicate 2 [sRNA-seq]

source_name: dry seed 0 h

treatment_protocol:
Arabidopsis thaliana seeds were dried in the dark for 14 days and then snap frozen prior to plating.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.

value: seed

value: dry seed 0 h


title: E14Tg2a UN Rep 1


title: Normal_Ker5


title: CD4+ Th1 No Glut_D1 Glut_D3 High IL-2 Rep 2

description: CD4_Th1_GlutNoGlut_HighLowAKG_Cuffnorm.txt

value: CD4+ Th1

value: Untreated High IL-2


title: seed following 1 h of stratification (S) Replicate 2 [sRNA-seq]


title: CD4+ Th1 No Glut_D1 No Glut_D3 High IL-2 Rep 2


title: seed following 1 h of stratification (S) Replicate 1 [sRNA-seq]


title: CD4+ Th1 No Glut_D1 No Glut_D3 High IL-2 Rep 1


title: CD4+ Th1 No Glut Low IL-2 + aKG Rep 3

value: aKG Low IL-2


title: CD4+ Th1 No Glut Low IL-2 + aKG Rep 2


title: freshly harvested (H) seed Replicate 2 [sRNA-seq]

source_name: freshly harvested (H) seed

treatment_protocol:
Arabidopsis thaliana seeds were collected from mature plants and snap frozen upon collection.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.

value: seed freshly harvested H


title: AFX2


title: CD4+ Th1 No Glut_D1 Glut_D3 High IL-2 Rep 1


title: Normal_Ker4


title: Normal_Ker3


title: Normal_Ker2


title: seed collected 48 h into countinuous light (post-stratification), 48 h SL Replicate 3 [RNA-seq]

data_processing:
Sequenced reads were trimmed for adaptor sequence, and filtered for low-quality sequence, with Trim Galore v0.4.2
filered and trimmed reads were mapped onto A. thaliana TAIR10 genome with the Araport11 transcriptome annotation with HISAT2 v2.0.5. Gene counts were extracted with featureCounts v1.5.1 and analysed with DESeq2 v1.10.1
Araport11 transcripts were quantified with salmon v0.7.2, with a quasi-index built with k=31, 30 bootstraps and the VB optimizer. Transcript quantifications were then analysed for differential accumulation using Sleuth v0.28.1
Genome_build: TAIR10
Supplementary_files_format_and_content: gene_counts.txt.gz: tab-delimited text file including raw counts for genes
Supplementary_files_format_and_content: DE_gene_expr.txt.gz: tab-delimited text file with estimates of gene expression from DESeq2
Supplementary_files_format_and_content: isoform_expression.txt.gz: tab-delimited text file with estimated abundances of isoforms
Supplementary_files_format_and_content: isoform_test_results.txt.gz: tab-delimited text file with results of testing for differential exression of the isoforns (sleuth, LRT)

extract_protocol:
RNA isolation was carried out using the Ambion Plant RNA isolation aid and RNAqeous RNA isolation kit.
RNA-seq libraries were generated using the TruSeq Total RNA kit v2 according to manufacturer’s instructions (Illumina).
polyA selection, random fragmentation, unstranded library

treatment_protocol: Following 48 h of cold, dark stratification (4 °C), samples were transferred into light conditions (100 µE m -2 sec-1) at 22 °C and collected after 48h.

value: seedling

value: seed germinating in countinuous light 48 h SL


title: Normal_Ker1


title: freshly harvested (H) seed Replicate 3 [sRNA-seq]

value: wild type


title: CD4+ Th1 No Glut Low IL-2 Rep 3

value: Untreated Low IL-2


title: seed collected 48 h into countinuous light (post-stratification), 48 h SL Replicate 1 [RNA-seq]


title: CD4+ Th1 No Glut Low IL-2 + aKG Rep 1


title: CD4+ Th1 No Glut Low IL-2 Rep 1


title: dry seed 0 h Replicate 3 [sRNA-seq]


title: CD4+ Th1 No Glut High IL-2 + aKG Rep 3

value: aKG High IL-2


title: seed collected 24 h into countinuous light (post-stratification), 24 h SL Replicate 2 [RNA-seq]

treatment_protocol: Following 48 h of cold, dark stratification (4 °C), samples were transferred into light conditions (100 µE m -2 sec-1) at 22 °C and collected after 24h.

value: seed germinating in countinuous light 24 h SL


title: freshly harvested (H) seed Replicate 1 [sRNA-seq]


title: CD4+ Th1 No Glut High IL-2 + aKG Rep 1


title: seed collected 24 h into countinuous light (post-stratification), 24 h SL Replicate 1 [RNA-seq]

value: germinating seed


title: seed collected 24 h into countinuous light (post-stratification), 24 h SL Replicate 3 [RNA-seq]


title: dry seed 0 h Replicate 1 [sRNA-seq]


title: seed collected 6 h into countinuous light (post-stratification), 6 h SL Replicate 3 [RNA-seq]

treatment_protocol: Following 48 h of cold, dark stratification (4 °C), samples were transferred into light conditions (100 µE m -2 sec-1) at 22 °C and collected after 6h.

value: seed germinating in countinuous light 6 h SL


title: seed collected 12 h into countinuous light (post-stratification), 12 h SL Replicate 3 [RNA-seq]

treatment_protocol: Following 48 h of cold, dark stratification (4 °C), samples were transferred into light conditions (100 µE m -2 sec-1) at 22 °C and collected after 12h.

value: seed germinating in countinuous light 12 h SL


title: CD4+ Th1 Glut Low IL-2 + aKG Rep 3


title: CD4+ Th1 No Glut High IL-2 Rep 3


title: seed collected 12 h into countinuous light (post-stratification), 12 h SL Replicate 2 [RNA-seq]


title: seed collected 48 h into countinuous light (post-stratification), 48 h SL Replicate 2 [RNA-seq]


title: CD4+ Th1 No Glut Low IL-2 Rep 2


title: seed collected 12 h into countinuous light (post-stratification), 12 h SL Replicate 1 [RNA-seq]


title: CD4+ Th1 Glut Low IL-2 + aKG Rep 1


title: seed collected 1 h into countinuous light (post-stratification), 1 h SL Replicate 3 [RNA-seq]

treatment_protocol: Following 48 h of cold, dark stratification (4 °C), samples were transferred into light conditions (100 µE m -2 sec-1) at 22 °C and collected after 1h.

value: seed germinating in countinuous light 1 h SL


title: CD4+ Th1 Glut Low IL-2 + aKG Rep 2


title: CD4+ Th1 Glut Low IL-2 Rep 3


title: seed collected 6 h into countinuous light (post-stratification), 6 h SL Replicate 2 [RNA-seq]


title: seed collected 6 h into countinuous light (post-stratification), 6 h SL Replicate 1 [RNA-seq]


title: seed collected 1 h into countinuous light (post-stratification), 1 h SL Replicate 1 [RNA-seq]


title: CD4+ Th1 Glut Low IL-2 Rep 2


title: seed following 48 h of stratification (S) Replicate 3 [RNA-seq]

treatment_protocol: Samples were collected 48 h into dark stratification started at 4 °C.

value: seed during stratification 48 h S


title: CD4+ Th1 Glut High IL-2 + aKG Rep 3


title: CD4+ Th1 Glut Low IL-2 Rep 1


title: seed following 48 h of stratification (S) Replicate 2 [RNA-seq]


title: CD4+ Th1 No Glut High IL-2 Rep 2


title: CD4+ Th1 No Glut High IL-2 Rep 1


title: CD4+ Th1 Glut High IL-2 + aKG Rep 2


title: CD4+ Th1 No Glut High IL-2 + aKG Rep 2


title: CD4+ Th1 Glut High IL-2 + aKG Rep 1


title: seed following 12 h of stratification (S) Replicate 3 [RNA-seq]

treatment_protocol: Samples were collected 12 h into dark stratification started at 4 °C.

value: seed during stratification 12 h S


title: CD4+ Th1 Glut High IL-2 Rep 3


title: CD4+ Th1 Glut High IL-2 Rep 2


title: seed following 12 h of stratification (S) Replicate 2 [RNA-seq]


title: seed following 12 h of stratification (S) Replicate 1 [RNA-seq]


title: seed following 48 h of stratification (S) Replicate 1 [RNA-seq]


title: seed following 1 h of stratification (S) Replicate 2 [RNA-seq]

treatment_protocol: Arabidopsis thaliana seeds were surface sterilised and plated on MS media. Samples were collected 1 h after dark stratification started at 4 °C.

value: seed during stratification 1 h S


title: CD4+ Th1 Glut High IL-2 Rep 1

value: CD4+ Th1


title: seed following 1 h of stratification (S) Replicate 1 [RNA-seq]


title: CD8+ Tc1 Low IL-2 + aKG Rep 4

source_name: CD8+ Tc1

value: CD8+ Tc1


title: CD8+ Tc1 Low IL-2 + aKG Rep 2

value: aKG Low IL-2


title: CD8+ Tc1 Low IL-2 + aKG Rep 3


title: Ribo_seq_mouse_liver_fasting_condition_rep2

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

country: China

institute: Zhejiang University

description: total RNA following rRNA removal

data_processing:
Library strategy: Ribo-seq
For m6A-seq, RNA-seq and Ribo-seq (rep1), the 3' adaptor AAAAAAAAAA and low quality bases were trimmed by Cutadapt. The trimmed reads were mapped to Mouse transcriptom (GRCm38.83) by Bowtie, using parameters: -a --best -m1 --strata. Two mismatches were permitted.
For replicate 2 of Ribo-seq, the 3' adaptor CTGTAGGCACCATCAAT were trimmed by Cutadapt. The first 6 nucleotide and the last 4 nucleotides were also clipped after adaptor removal. The trimmed reads were mapped to Mouse transcriptom (GRCm38.83) by Bowtie, using parameters: -a --best -m1 --strata. Two mismatches were permitted. The PCR duplicates were removed from the mapped reads using the methods in Lecanda et al., 2016 (PMID: 27450428)
Genome_build: GRCm38.83
Supplementary_files_format_and_content: For RNA-seq and m6A-seq, reads coverage files were generated. Each line reprents one mRNA. Coverage values were separated by Tabs. For Ribo-seq, each line reperents ribosome footprint reads at individual sites. Values were separated by commas

source_name: mouse liver

growth_protocol: MEF wild-type and knockdown cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
For cells Ribo-seq, MEF cells were washed using ice-cold PBS containing 100 µg ml-1 cycloheximide and then lysed in polysome lysis buffer ((10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 100 µg ml-1 cycloheximide and 2% Triton X-100).Cell debris were removed by centrifugation at14,000 rpm for 10 min at 4°C. For mouse liver samples, mice were sacrificed by decapitation, and their livers were quickly excised and chilled. Liver was immediately homogenized in 5 volumes of ice-cold polysome buffer containing CHX (100 μg/mL) or LTM (5 μM) using mortar and pestle. Homogenates were centrifuged at 4 °C and 12,000g for 10 min. To dissociate non-initiating ribosomes in QTI-seq, cell lysates or liver homogenates were incubated in a solution containing 16 mM HEPES buffer, pH 7.4, 10 mM creatine phosphate, 0.1 mM spermidine, 40 μg/mL creatine phosphokinase, 0.8 mM ATP, and 25 μM puromycin for 15 min. Puromycin-treated samples were then subjected to sucrose gradient sedimentation. For RNA-seq and m6A-seq, total RNA was first isolated using Trizol reagent followed by fragmentation using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2). 5 μg fragmented RNA was saved for RNA-seq as input control. For m6A-seq, 400 μg fragmented RNA was incubated with 10 μg anti-m6A antibody (Millipore ABE572) and 2.5 μg anti-m6A antibody (Synaptic Systems 200 203 ) in 1× IP buffer (10 mM Tris-HCl, pH 7.4, 150 mM NaCl, and 0.1% Igepal CA-630) for 2 hr at 4°C. The m6A-IP mixture was then incubated with Protein A/G beads for additional 2 hr at 4°C on a rotating wheel. After washing 3 times with IP buffer, bound RNA was eluted using 100 μl elution buffer twice (6.7 mM N6-Methyladenosine 5’-monophosphate sodium salt in 1× IP buffer), followed by ethanol precipitation.
Fragmented RNA were dephosphorylated for 1 hr at 37°C in 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions of the gel corresponding to 40-60 nt (for RNA-seq and m6A-seq ) or 25-35 nt (for Ribo-seq) were excised. The gel slices were disrupted by using centrifugation through the holes at the bottom of the tube. RNA fragments were dissolved by soaking overnight in 400 μl gel elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U/ml SUPERase_In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation.Purified RNA fragments were tailed followed by reverse transcription. Reverse transcription products were purified on a 10% polyacrylamide TBE-urea gel and circularized. Circular single-strand DNA was re-linearized and the expected 100-nt product bands were excised for purification followed by PCR amplification. PCR products were recovered and sent for deep sequencing.

treatment_protocol: For starvation treatment, MEF cells  were grown to 80% confluence on 10-cm petri dish and treated with HBSS puls 10% dialysed FBS for 2 h. For fasting treatment, mouse was fasting for 18 hr before sacrifice.

value: liver

tag: stress

value: fasting

tag: molecule

value: Ribo-associated RNA


title: Ribo_seq_mouse_liver_normal_condition_FTO_OE_rep2

description: total RNA following rRNA removal

tag: tissue

value: normal

value: FTO overexpression


title: Ribo_seq_mouse_liver_fasting_condition_FTO_OE_rep2

description: total RNA following rRNA removal


title: wrky14 gDNA

data_processing:
Reads were trimmed with trimgalore (v0.4.2) with options --phred33 --paired --nextera
mapped with bowtie2 (2.2.29) [Langmead 2012] with option -X 1500 onto the TAIR10 genome with the pROK2 T-DNA sequence as a supplementary chromosome [Baulcombe 1986, Ülker 2008]
Read pairs with one read mapping to the T-DNA and its mate mapping to the genome were extracted from the SAM output with awk ‘($3 == “pROK2_T-DNA_only” && $7 !=  “=”)’, to identify T-DNA insertion sites.
Genome_build: TAIR10 + pROK2 T-DNA
Supplementary_files_format_and_content: filtered alignments for read pairs mapping across the T-DNA – genome junction.

source_name: wrky14, seedlings

growth_protocol: Seeds were sown on MS media, statified at 4 C for 2-d before being transferred to long-day conditions  at 22°C.

extract_protocol:
QIAgen DNeasy extraction
Nextera DNA Library prep (Illumina)

value: seedlings

tag: developmental stage

value: two weeks old


title: Ribo_seq_mouse_liver_normal_condition_rep2

description: total RNA following rRNA removal

tag: strain


title: smb gDNA

source_name: smb, seedlings

tag: genotype

value: smb


title: vnd2 gDNA

source_name: vnd2, seedlings


title: dry seed 0 h Replicate 3 [RNA-seq]

treatment_protocol: Arabidopsis thaliana seeds were dried in the dark for 14 days and then snap frozen prior to plating.

value: wild type

value: seed

value: dry seed 0 h


title: obp1 gDNA

source_name: obp1, seedlings


title: dry seed 0 h Replicate 1 [RNA-seq]


title: Ribo_seq_mouse_liver_fasting_condition_FTO_OE

description: total RNA following rRNA removal


title: CD8+ Tc1 Low IL-2 Rep 4

tag: cell type

value: Untreated Low IL-2


title: CD8+ Tc1 Low IL-2 Rep 3

tag: treatment


title: Ribo_seq_mouse_liver_fasting_condition

description: total RNA following rRNA removal


title: dry seed 0 h Replicate 2 [RNA-seq]

tag: genotype/variation


title: Ribo_seq_mouse_liver_normal_condition_FTO_OE

description: total RNA following rRNA removal


title: freshly harvested (H) seed Replicate 3 [RNA-seq]

treatment_protocol: Arabidopsis thaliana seeds were collected from mature plants and snap frozen upon collection.

value: seed freshly harvested H


title: CD8+ Tc1 Low IL-2 + aKG Rep 1


title: CD8+ Tc1 Low IL-2 Rep 2


title: hat2 gDNA

source_name: hat2, seedlings


title: Ribo_seq_mouse_liver_normal_condition

description: total RNA following rRNA removal


title: CD8+ Tc1 Low IL-2 Rep 1


title: m6A_seq_mouse_liver_fasting_condition_rep2

data_processing:
Library strategy: m6A-seq
For m6A-seq, RNA-seq and Ribo-seq (rep1), the 3' adaptor AAAAAAAAAA and low quality bases were trimmed by Cutadapt. The trimmed reads were mapped to Mouse transcriptom (GRCm38.83) by Bowtie, using parameters: -a --best -m1 --strata. Two mismatches were permitted.
For replicate 2 of Ribo-seq, the 3' adaptor CTGTAGGCACCATCAAT were trimmed by Cutadapt. The first 6 nucleotide and the last 4 nucleotides were also clipped after adaptor removal. The trimmed reads were mapped to Mouse transcriptom (GRCm38.83) by Bowtie, using parameters: -a --best -m1 --strata. Two mismatches were permitted. The PCR duplicates were removed from the mapped reads using the methods in Lecanda et al., 2016 (PMID: 27450428)
Genome_build: GRCm38.83
Supplementary_files_format_and_content: For RNA-seq and m6A-seq, reads coverage files were generated. Each line reprents one mRNA. Coverage values were separated by Tabs. For Ribo-seq, each line reperents ribosome footprint reads at individual sites. Values were separated by commas

value: m6A-modified RNA

tag: chip antibody

value: Anti-N6-methyladenosine (m6A) Antibody


title: freshly harvested (H) seed Replicate 1 [RNA-seq]


title: athb25 gDNA

source_name: athb25, seedlings


title: CD8+ Tc1 High IL-2 Rep 4

value: CD8+ Tc1

value: Untreated High IL-2


title: athb15 gDNA

source_name: athb15, seedlings


title: seed collected 48 h into countinuous light (post-stratification), 48 h SL Replicate 3 [methylC-seq]

data_processing:
Sequenced reads were trimmed for adaptor sequence, and filtered for low-quality sequence, with Trim Galore v0.4.2
filered and trimmed reads were mapped with bismark v0.16.3 with default parameters
Deduplicated reads (deduplicate_bismark) were used to generate genome-wide cytosine reports (bismark_methylation_extractor, bismark2bedGraph, coverage2cytosine)
DMRs were identified using HOME (hten used to identify timeseries DMRs for three context CG, CHG and CHH using HOME-timeseries with default parameters. We further filtered out regions whose maximum absolute difference in methylation during the timecourse was lower than 20%.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited files including genome-wide cytosine report, and bed files of unfiltered DMRs in CG, CHG and CHH contexts.

extract_protocol:
gDNA was extracted from the seeds/seedlings using the Qiagen DNeasy Plant minikit and 600ng of purified gDNA was used for MethylC-seq library preparation after spiking in 0.5% lambda DNA (N6-methyladenine-free) (New England BioLabs).
MethylC-seq library preparation was carried out as described previously (Urich et al., 2015 - http://www.nature.com/nprot/journal/v10/n3/full/nprot.2014.114.html).

treatment_protocol:
Following 48 h of cold, dark stratification (4 °C), samples were transferred into light conditions (100 µE m -2 sec-1) at 22 °C and collected after 48h.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.

value: seedling

value: seed germinating in countinuous light 48 h SL


title: CD8+ Tc1 High IL-2 Rep 3


title: Col-0 gDNA

source_name: Col-0, seedlings

value: WT (Col-0)


title: lmi1 gDNA

source_name: lmi1, seedlings


title: m6A_seq_mouse_liver_normal_condition_rep2

value: liver

value: normal


title: CD8+ Tc1 High IL-2 Rep 2


title: wrky14 24 hSL replicate 2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and filtered for low-quality sequence, with Trim Galore v0.4.2
filered and trimmed reads were mapped onto A. thaliana TAIR10 genome with the Araport11 transcriptome annotation with HISAT2 v2.0.5. Gene counts were extracted with featureCounts v1.5.1 and analysed with DESeq2 v1.10.1
Araport11 transcripts were quantified with salmon v0.7.2, with a quasi-index built with k=31, 30 bootstraps and the VB optimizer. Transcript quantifications were then analysed for differential accumulation using Sleuth v0.28.1
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including raw counts for genes, output of featureCounts

source_name: germinating seed_wrky14 24 hSL

extract_protocol:
RNA isolation was carried out using the Sigma Spectrum RNA extraction kit, with on-column DNase treatment.
RNA-seq libraries were generated using the TruSeq Stranded mRNA kit according to manufacturer’s instructions (Illumina).
polyA selection, random fragmentation, stranded library

treatment_protocol:
Following 48 h of cold, dark stratification (4 °C), samples were transferred into light conditions (100 µE m -2 sec-1) at 22 °C and collected after 24h.
Seeds wer collected at 24 h in continuous light and snap frozen in liquid nitrogen

value: germinating seed


title: seed collected 48 h into countinuous light (post-stratification), 48 h SL Replicate 1 [methylC-seq]


title: CD8+ Tc1 High IL-2 Rep 1


title: wrky14 24 hSL replicate 1


title: CD4+ Th1 Low IL-2 + aKG Rep 3

source_name: CD4+ Th1

value: CD4+ Th1

value: aKG Low IL-2


title: freshly harvested (H) seed Replicate 2 [RNA-seq]

value: wild type


title: RNA_seq_mouse_liver_normal_condition_FTO_OE

data_processing:
For m6A-seq, RNA-seq and Ribo-seq (rep1), the 3' adaptor AAAAAAAAAA and low quality bases were trimmed by Cutadapt. The trimmed reads were mapped to Mouse transcriptom (GRCm38.83) by Bowtie, using parameters: -a --best -m1 --strata. Two mismatches were permitted.
For replicate 2 of Ribo-seq, the 3' adaptor CTGTAGGCACCATCAAT were trimmed by Cutadapt. The first 6 nucleotide and the last 4 nucleotides were also clipped after adaptor removal. The trimmed reads were mapped to Mouse transcriptom (GRCm38.83) by Bowtie, using parameters: -a --best -m1 --strata. Two mismatches were permitted. The PCR duplicates were removed from the mapped reads using the methods in Lecanda et al., 2016 (PMID: 27450428)
Genome_build: GRCm38.83
Supplementary_files_format_and_content: For RNA-seq and m6A-seq, reads coverage files were generated. Each line reprents one mRNA. Coverage values were separated by Tabs. For Ribo-seq, each line reperents ribosome footprint reads at individual sites. Values were separated by commas

value: FTO overexpression

value: total RNA


title: seed collected 24 h into countinuous light (post-stratification), 24 h SL Replicate 2 [methylC-seq]

treatment_protocol:
Following 48 h of cold, dark stratification (4 °C), samples were transferred into light conditions (100 µE m -2 sec-1) at 22 °C and collected after 24h.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.

value: seed germinating in countinuous light 24 h SL


title: seed collected 24 h into countinuous light (post-stratification), 24 h SL Replicate 3 [methylC-seq]


title: CD4+ Th1 Low IL-2 + aKG Rep 2


title: m6A_seq_mouse_liver_normal_condition_FTO_OE_rep2


title: smb 24 hSL replicate 2

source_name: germinating seed_smb 24 hSL

value: smb


title: RNA_seq_mouse_liver_normal_condition


title: seed collected 24 h into countinuous light (post-stratification), 24 h SL Replicate 1 [methylC-seq]


title: RNA_seq_mouse_liver_fasting_condition_FTO_OE

value: fasting


title: CD4+ Th1 Low IL-2 + aKG Rep 1


title: CD4+ Th1 Low IL-2 Rep 3

value: Untreated Low IL-2


title: seed collected 48 h into countinuous light (post-stratification), 48 h SL Replicate 2 [methylC-seq]


title: seed collected 6 h into countinuous light (post-stratification), 6 h SL Replicate 2 [methylC-seq]

treatment_protocol:
Following 48 h of cold, dark stratification (4 °C), samples were transferred into light conditions (100 µE m -2 sec-1) at 22 °C and collected after 6h.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.

value: seed germinating in countinuous light 6 h SL


title: seed collected 6 h into countinuous light (post-stratification), 6 h SL Replicate 3 [methylC-seq]


title: smb 24 hSL replicate 1


title: m6A_seq_mouse_liver_fasting_condition

value: m6A-modified RNA

value: Anti-N6-methyladenosine (m6A) Antibody


title: RNA_seq_mouse_liver_fasting_condition


title: CD4+ Th1 Low IL-2 Rep 1


title: seed following 1 h of stratification (S) Replicate 3 [RNA-seq]

value: seed during stratification 1 h S


title: seed collected 1 h into countinuous light (post-stratification), 1 h SL Replicate 2 [RNA-seq]

value: seed germinating in countinuous light 1 h SL


title: seed following 48 h of stratification (S) Replicate 3 [methylC-seq]

treatment_protocol:
Samples were collected 48 h into dark stratification started at 4 °C.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.

value: seed during stratification 48 h S


title: lmi1 24 hSL replicate 2

source_name: germinating seed_lmi1 24 hSL


title: m6A_seq_mouse_liver_fasting_condition_FTO_OE

value: liver


title: vnd2 24 hSL replicate 1

source_name: germinating seed_vnd2 24 hSL

value: germinating seed


title: CD4+ Th1 Low IL-2 Rep 2

value: CD4+ Th1


title: CD4+ Th1 High IL-2 Rep 3

value: Untreated High IL-2


title: m6A_seq_mouse_liver_normal_condition

value: normal


title: seed collected 6 h into countinuous light (post-stratification), 6 h SL Replicate 1 [methylC-seq]

value: wild type


title: seed following 48 h of stratification (S) Replicate 1 [methylC-seq]


title: CD4+ Th1 High IL-2 Rep 1


title: obp1 24 hSL replicate 2

source_name: germinating seed_obp1 24 hSL


title: CD4+ Th1 High IL-2 Rep 2


title: lmi1 24 hSL replicate 1


title: m6A_seq_shALKBH5_AA_starvation

source_name: mammalian cells

value: mouse embryonic fibroblast

value: starvation


title: Ribo_seq_shScram_AA_suff

description: total RNA following rRNA removal

value: Ribo-associated RNA

value: shScramble


title: hat2 24 hSL replicate 1

source_name: germinating seed_hat2 24 hSL


title: dry seed 0 h Replicate 3 [methylC-seq]

source_name: dry seed 0 h

treatment_protocol:
Arabidopsis thaliana seeds were dried in the dark for 14 days and then snap frozen prior to plating.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.

value: seed

value: dry seed 0 h


title: hat2 24 hSL replicate 2


title: dry seed 0 h Replicate 2 [methylC-seq]


title: obp1 24 hSL replicate 1


title: m6A_seq_shScram_AA_starvation

value: m6A-modified RNA


title: MII oocytes biologial replicate 1

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

description: MII oocytes 1

data_processing:
Trimming with Trimmomatics v0.33 with paarameters "ILLUMINACLIP:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:30”
High quality paired-end reads were aligned to mm9 genome with Tophat2 with “-p 8 -segment-length 25 -G gene annotation”
Calculating gene expression with Cufflinks v2.2.1 with parameter “-p 8 –G gene annotation”
Genome_build: mm9
Supplementary_files_format_and_content: gene expression table(format excel)

source_name: MII oocytes

extract_protocol:
cDNAs Preparation: Reverse transcription. 2.5μL of cell lysates were mixed with 0.5μL of 3′ SMART CDS primer II A (20 μM, 5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′, where “N” is any base and “V” is either “A”, “C” or “G”; invitrogen) and 1 μL of dNTP mix (10 mM), denatured at 72 °C for 3 min and immediately placed on ice afterwards. First-strand reaction mix, containing 0.50 μL SuperScript II reverse transcriptase (200 U/μL, Invitrogen), 0.25 μL RNase inhibitor (40 U/μL, Clontech), 2 μL Superscript II First-Strand Buffer (5×, Invitrogen), 0.5 μL DTT (100 mM, Invitrogen), 2 μL betaine (5 M, Sigma), 0.3 μL MgCl2 (200 mM, Sigma), 0.5 μL LNA-modified TSO (20 μM, Exiqon), were added to each sample. Reverse transcription reaction was carried out by incubating at 42 °C for 90 min. Finally, the reverse transcriptase was inactivated by incubation at 70 °C for 15 min.PCR preamplification： PCR master mix with the following composition: 12.5 μL KAPA HiFi HotStart ReadyMix (2×, KAPA Biosystems), 0.25 μL ISPCR primers (10 μM, 5′-AAGCAGTGGTATCAACGCAGAGT-3′, Invitrogen) and 2.25 μL nuclease-free water, was added to the first-strand cDNA synthesis product. The program used was as follows: 98 °C 3 min, then 16 cycles of (98 °C 15 s, 67 °C 20 s, 72 °C 6 min), with a final extension at 72 °C for 5 min. PCR was purified using a 1:1 ratio of AMPure XP beads (Beckman Coulter), with the final elution performed in 15 μL of EB solution (Qiagen). Library size distribution was checked on a High-Sensitivity DNA chip (Agilent Bioanalyzer). The reaction was considered successful if the average size was around 1.5-2.0 kb with negligible fraction of fragments below 300 bp. Quantification of cDNA was relied on the amount of product in the interval 300-9000 bp in the Agilent Bioanalyzer plot.
One nanograms of cDNA were then mixed with 74μL EB solution (Qiagen) in 0.65 ml microtube and sheared using Bioruptor (diagenode), with the setting of 30’’ON/90”OFF, Low power for 30 cycles. 10 μL of each DNA sample was used as input for library construction with Low input library prep kit (Clontech) following manufacturer's instructions. Purification was done with a 1:1 ratio of AMPure XP beads and samples were loaded on a High-Sensitivity DNA chip to check the quality of the library. Libraries of 16 samples were sequenced on two lanes of Illumina HiSeq 2500 with 100bp paired end reads.

tag: gender

value: female

value: Meiosis II oocytes (MII oocytes)

tag: passages


title: dry seed 0 h Replicate 1 [methylC-seq]


title: GV oocytes biologial replicate 2

description: GV oocytes 2

source_name: GV oocytes

value: Germinal-stage oocytes (GV oocytes)


title: athb25 24 hSL replicate 2

source_name: germinating seed_athb25 24 hSL


title: seed following 48 h of stratification (S) Replicate 2 [methylC-seq]

value: seed during stratification 48 h S


title: E. coli 402290_DMEM_0.5_BR2

city: Baltimore

first: Sean

last: Daugherty

state: Maryland

address: 801 W. Baltimore St.

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

data_processing:
Illumina reads were mapped to the EPEC genomes using Bowtie
The mapped reads were counted using HTSeq and normalized and then the differential expression of each gene for one sample compared to another was determined using DESeq v. 1.5.24, and statistical analyses were performed using R-2.15.2, and was represented as the log2 of the fold-change values.
Genome_build: E2348/69, HS, H10407, 102651, 102712, 401140, 402290
Supplementary_files_format_and_content: read count, FC, differential expression

organism: Escherichia coli 402290

source_name: Escherichia coli cells

growth_protocol: The E. coli strains were grown overnight in LB media and were inoculated 1:100 into 250 ml of fresh LB or DMEM with bile (LBB and DMEMB) or without and were incubated with shaking (225 rpm) at 37˚C to a final optical density (OD600) of approximately 0.5.

extract_protocol:
RNA was isolated from pelleted cells using the Ribopure Bacteria kit (Ambion) and contaminating DNA was removed using the Ribopure Dnase I and also the Turbo DNA-free kit (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth media

value: DMEM


title: athb25 24 hSL replicate 1

value: germinating seed


title: athb15 24 hSL replicate 2

source_name: germinating seed_athb15 24 hSL


title: RNA_seq_normal_condition

value: total RNA


title: m6A_seq_shScram_AA_suff

value: Anti-N6-methyladenosine (m6A) Antibody


title: GV oocytes biologial replicate 1

description: GV oocytes 1


title: m6A_seq_mouse_liver_normal_condition_FTO_OE

source_name: mouse liver

value: liver

value: normal

value: FTO overexpression


title: E. coli 402290_LB_0.5_BR2

value: LB


title: FGSCs biologial replicate 1

description: FGSCs 1

source_name: FGSCs

value: Female germline stem cells (FGSCs)


title: RNA_seq_AA_starvation

value: mouse embryonic fibroblast

value: starvation


title: Col-0 (wt) 24 hSL replicate 2

source_name: germinating seed_Col-0 (wt) 24 hSL


title: m6A_seq_AA_starvation


title: FGSCs biologial replicate 2

description: FGSCs 2


title: athb15 24 hSL replicate 1


title: E12.5 PGCs biologial replicate 3

description: E12.5 PGCs  3

source_name: PGCs

value: embryonic 12.5 day (E12.5)

value: primordial germ cells (PGCs)


title: E. coli 402290_DMEM_0.5_BR1


title: E. coli 401140_DMEMB_0.5_BR1

description: 401140_DMEMB_vs_LBB.txt,401140_DMEMB_vs_DMEM.txt

organism: Escherichia coli 401140

value: DMEMB


title: MII oocytes biologial replicate 2

description: MII oocytes 2

value: female

value: Meiosis II oocytes (MII oocytes)


title: J2E-KLF3-ER 4sU-RNA-seq rep3

city: Woolloongabba

first: Melissa

middle: D

last: Ilsley

state: Queensland

address: 36 Kent street

institute: Mater Research

description:
4sU-labelled RNA
J2EvsKLF3_RNA-seq.csv.gz

data_processing:
Annotated_KLF3_peak_list.csv.gz
Base calling was performed with Torrent Suite v4.0.1
TMAP (v3.0.1) with the following options: mapall, -v, -Y, -u, -o 2, stage1, map4 was used to map reads to the reference genome (mm9; ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm9/Mus_musculus_UCSC_mm9.tar.gz)
Fragments mapping to the same position on the same strand were taken to be PCR duplicates and were subsequently discarded, retaining only unique alignments with the highest MAPQ score.
ChIP-seq peaks were called with MACS (v1.4.2) using uniquely mapped ChIP and input sequence alignments.
Significant peaks identified by MACS2
Each peak summit was subsequently annotated with the genomic context, overlapping peaks and closest TSS
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited annotated MACS2 peaks file
Annotated_KLF1_peak_list.csv.gz
Base calling was performed with Torrent Suite v4.0.1
TMAP (v3.0.1) with the following options: mapall, -v, -Y, -u, -o 2, stage1, map4 was used to map reads to the reference genome (mm9; ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm9/Mus_musculus_UCSC_mm9.tar.gz)
Fragments mapping to the same position on the same strand were taken to be PCR duplicates and were subsequently discarded, retaining only unique alignments with the highest MAPQ score.
ChIP-seq peaks were called with MACS (v1.4.2) using uniquely mapped ChIP and input sequence alignments.
Significant peaks identified by MACS2
Each peak summit was subsequently annotated with the genomic context, overlapping peaks and closest TSS
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited annotated MACS2 peaks file
J2EvsKLF3_RNA-seq.csv.gz
Base calling was performed with Torrent Suite v4.0.1
Tophat2 (v2.0.10) was used to perform spliced alignment to the reference transcriptome and genome (mm9; ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm9/Mus_musculus_UCSC_mm9.tar.gz) using default options with the following additional parameters: -N 4, --read-gap-length 4, --read-edit-dist 4, --read-realign-edit-dist 0, -a 5, -i 50, -g 6, --coverage-search, --microexon-search, --library-type fr-firststrand.
Unaligned sequences were subsequently remapped using TMAP (v3.0.1) with the following options: mapall, -v, -Y, -u, -o 2, stage1, map4.
Successful alignments were merged back into the Tophat2 SAM file.
Alignments of less than 30 nt were discarded.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was calculated and differential expression testing between replicate groups was performed with Cuffdiff2 using default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited FPKM values and differential gene expression analysis

source_name: J2E-KLF3-ER (clone E)

growth_protocol: Erythroid cell lines were passaged (1:5) every 2-3 days in DMEM supplemented with 10% FBS, 1% Glutamine & 1% Penicillin-Streptomycin in a standard tissue culture incubator at 37 °C with 5% CO7

extract_protocol:
Total RNA was extracted using TRIzol® Reagent (Life Technologies, #15596026) according to the manufacturer’s instructions with manually dissociated cells washed in 1 ml DPBS (Gibco™, #14190-136). Extracted RNA was subsequently treated with DNase I (New England Biolabs, #M0303L) to remove residual gDNA contamination. Isolation of 4sU-RNA was performed essentially as previously described (Rabani et al. Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol 2011) with minor modifications. Purified RNA was biotinylated with EZ-Link Biotin-HPDP (Pierce; #21341) and isolated using µMacs Streptavidin Kit (Miltenyi; #130-074-101). 4sU-enriched RNA was then purified with RNeasy MinElute Spin Columns (Qiagen; #74204).
Purified 4sU-labelled RNA was used with the Ion Total RNA-Seq Kit v2 (Life Technologies; #4479789) to prepare libraries for sequencing on the Ion Proton™ System.

treatment_protocol: Cells were induced through the addition of (Z)-4-Hydroxytamoxifen at a final concentration of 200 nM and newly transcribed RNA labeled with 500 μM 4sU for 30 minutes.

value: J2E cells with tamoxifen-inducible KLF3-ER fusion protein

tag: transgene

value: induced with tamoxifen


title: J2E-KLF3-ER 4sU-RNA-seq rep2

source_name: J2E-KLF3-ER (clone C)

growth_protocol: Erythroid cell lines were passaged (1:5) every 2-3 days in DMEM supplemented with 10% FBS, 1% Glutamine & 1% Penicillin-Streptomycin in a standard tissue culture incubator at 37 °C with 5% CO6


title: E12.5 PGCs biologial replicate 1

description: E12.5 PGCs  1


title: E. coli 402290_LB_0.5_BR1


title: E. coli 401140_LBB_0.5_BR2

description: 401140_DMEMB_vs_LBB.txt,401140_LBB_vs_LB.txt

value: LBB


title: m6A_seq_shALKBH5_AA_suff

value: m6A-modified RNA


title: m6A_seq_normal_condition

value: Anti-N6-methyladenosine (m6A) Antibody


title: E. coli 401140_DMEMB_0.5_BR2


title: E12.5 PGCs biologial replicate 2

description: E12.5 PGCs  2


title: Ribo_seq_shALKBH5_AA_suff

description: total RNA following rRNA removal

value: Ribo-associated RNA


title: J2E 4sU-RNA-seq rep3

source_name: J2E erythroid cell line

growth_protocol: Erythroid cell lines were passaged (1:5) every 2-3 days in DMEM supplemented with 10% FBS, 1% Glutamine & 1% Penicillin-Streptomycin in a standard tissue culture incubator at 37 °C with 5% CO4

value: wildtype immortalised fetal liver erythroid cell line

value: treated with ethanol (vehicle)


title: E. coli 401140_LBB_0.5_BR1


title: E. coli 401140_DMEM_0.5_BR2

description: 401140_DMEM_vs_LB.txt,401140_DMEMB_vs_DMEM.txt

value: DMEM


title: 15EC

city: Philadelphia

first: Rebecca

middle: A

last: Simmons

state: PA

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

data_processing:
RNA-Seq data was aligned with STAR 2.5.0c
fastq files for each lane were merged with samtools
featureCounts extracted counts from bam files
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated variable, counts and EdgeR normalized counts

source_name: EC of female embryos from diet-induced obese dam

growth_protocol: 20 week old female C57Bl/6 that had been fed either a control of high-fat diet (60% kcal from fat) from 4 weeks age-20 weeks age were naturally mated with control C57Bl/6 mice.  Vaginal plugs were checked to time mating.  6.5 days post-coitus mice were euthanized and gravid uteri were removed.  Embyros were dissected out from uterus and deciduoma and ectoplacental cone was separated from epiblast using microinjection pipettes under disecting microscope.  Each ectoplacental cone was placed in a separate 0.5 mL tube with 50 uL Acturus PicoPure RNA extraction buffer and heated to 42 degrees C for 30 minutes then snap frozen and stored in -80 degrees C freezer.

extract_protocol:
RNA was extracted using Acturus Picopure RNA extraction kit with minor modifications.  Second elutions of RNA from each embryo were used to sex embryos. RNA quality was assessed using Agilent BioAnalyzer Pico kit.  Only samples in which RNA integrity was ensured (RIN>7) were used for further processing.
Libraries were prepared according to ClonTech's instructions accompanying the Low-Input Strand-Specific Total RNA-Seq for Illumina RNA-Seq (Cat.# 634861). Briefly, rRNA depletion was performed using ClonTech RiboGone Mammalian kit.  First RNA is fragmented and converted to single-stranded (ss) cDNA that contains sequences complementary to the SMARTer Stranded Oligo.  The purified first-strand cDNA is amplified into RNA-seq libraries using SeqAmp DNA Polymerase, the Universal Forward PCR Primer, and the Reverse PCR Primers from the Illumina Indexing Primer Set.  Library quality was assessed using the Agilent 2100 Bioanalyzer and the High Sensitivity DNA Chip from Agilent’s High Sensitivity DNA Kit (Cat. No. 5067-4626). Individual and pooled library concentrations was assessed using KAPA Library Quantification Kit-Illumina® Platforms.

tag: embryo sex

value: FEMALE

tag: diet

value: HFD

value: Ectoplacental cone (EC)


title: 18EC


title: 16EC


title: J2E 4sU-RNA-seq rep2

growth_protocol: Erythroid cell lines were passaged (1:5) every 2-3 days in DMEM supplemented with 10% FBS, 1% Glutamine & 1% Penicillin-Streptomycin in a standard tissue culture incubator at 37 °C with 5% CO3

value: treated with tamoxifen


title: E. coli 401140_LB_0.5_BR2

description: 401140_DMEM_vs_LB.txt,401140_LBB_vs_LB.txt

value: LB


title: 17EC


title: J2E 4sU-RNA-seq rep1

source_name: J2E erythroid cell line (Klinken et al. 1998)

growth_protocol: Erythroid cell lines were passaged (1:5) every 2-3 days in DMEM supplemented with 10% FBS, 1% Glutamine & 1% Penicillin-Streptomycin in a standard tissue culture incubator at 37 °C with 5% CO2


title: Col-0 (wt) 24 hSL replicate 1

value: germinating seed


title: KLF1 Input DNA

source_name: K1-ER (clone A and C)

growth_protocol: Erythroid cell lines were passaged (1:5) every 2-3 days in DMEM supplemented with 10% FBS, 1% Glutamine & 1% Penicillin-Streptomycin in a standard tissue culture incubator at 37 °C with 5% CO5

extract_protocol:
ChIP was performed as described (Hodge et al. A global role for EKLF in definitive and primitive erythropoiesis. Blood 2006). Cell lines were induced with 4-OHT (or ethanol control) and incubated for 3 hours before fixation with 0.4% formaldehyde. Chromatin was fragmented to approximately 200-400bp by sonication (Diagenode Bioruptor® for 15 minutes cycling between 30 seconds ‘ON’ and 30 seconds ‘OFF’), pre-cleared and immunoprecipitated with protein G sepharose beads (GE Healthcare).
Sequencing libraries were generated from 3 pooled replicates using the Ion Xpress™ Plus gDNA Fragment Library Preparation Kit following the Ion ChIP-Seq Library Preparation protocol.

treatment_protocol: Cells were induced through the addition of (Z)-4-Hydroxytamoxifen at a final concentration of 200 nM for 3 h.

value: KLF1 null erythroblasts with tamoxifen-inducible transgene


title: E. coli 401140_LB_0.5_BR1


title: 13EC

source_name: EC of female embryos from control dam

value: CONTROL


title: KLF1 ChIP-seq

value: KLF1 Antibody

tag: chip antibody reference

value: Perkins, A. C., Sharpe, A. H. & Orkin, S. H. Lethal beta-thalassaemia in mice lacking the erythroid CACCC-transcription factor EKLF. Nature 375, 318–322 (1995).


title: Sample_stage 3-repeat 3

city: WuHan

first: jin

middle: zhi

last: zhang

address: College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China

institute: Huazhong Agricultural University

data_processing:
The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
To get the clean reads, removing the dirty raw reads is needed before data analysis.    Filter steps:    Remove reads with adaptors;  Remove reads in which unknown bases are more than 10%;   Remove low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) .
Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads).
read-mapped to citrus genome (http://citrus.hzau.edu.cn/orange/index.php)
Supplementary_files_format_and_content: RPKM represent the expression of genes.

organism: Citrus x limon

source_name: stage 3: one week after rehabilitation of irrigation

growth_protocol: All plants were grown in the experiment fields of the Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agriculture Sciences. We used 1- to 2-year-old lemon trees (Femminello) propagated by bud-grafting to trifoliate orange rootstocks.

extract_protocol:
Total RNA was isolated from bud (three biological replicates per genotype) using the Plant RNAiso Plus according to the manufacturer’s instructions (Takara, Kusatsu, Japan). Genomic DNA was removed from total RNA by DNase treatment (Promega, Madison, WI, USA). All RNA samples were quantified and examined for protein contamination and reagent contamination by a Nanodrop ND 1000 spectrophotometer (NanoDrop, Wilmington, DE, USA).
Total RNA were sent to Beijing Genomics Institute (Shenzhen, China) where the libraries were produced and sequenced using Illumina’s Genome Analyzer (Solexa). The sequencing and data analysis was carried out essentially as in previous studies (Mortazavi et al. 2008). In this study, probability ≥ 0.8 and the absolute value of log2Ratio ≥ 1 were used as the threshold to judge the significance of gene expression difference (Tarazona et al. 2011).

treatment_protocol: The trees ranged in height from 1 to 1.5 m and were grown. Before the water deficit treatment, trees were kept in greenhouse with a minimum temperature of 23°C and watered every 2 d to saturation. At beginning of water deficit, trees were fully watered and soil moisture was measured 4 h later by Theta probe type ML2x (Delta-T Devices Ltd; Cambridge England), the soil water naturally evaporated until reaching the set level. Then the soil moisture was maintained by accurately watering according to the daily loss of water. Leaf water potential was measured with a pressure chamber (PMS Instrument Co., Corvallis, Oregon, USA). After two weeks, trees were fully watered. In this study, the soil moisture was measured three times per pot and leaf water potential was detected once per plant with the values indicated as the means ± SE of three plants.

value: The terminal bud and the five following buds (the major node position for flower formation) from spring flushes

tag: cultivar

value: Femminello


title: 12EC


title: KLF3 input DNA

value: J2E cells with tamoxifen-inducible KLF3-ER fusion protein

value: induced with tamoxifen


title: 11EC


title: KLF3 ChIP-seq

value: Mouse monoclonal Estrogen receptor Ab-10 (clone TE111.5D11)

value: ThermoScientific cat. #MS-315-P


title: Sample_stage 3-repeat 2

department: College of Horticulture and Forestry Science


title: Sample_stage 3-repeat 1


title: J2E-KLF3-ER 4sU-RNA-seq rep1

source_name: J2E-KLF3-ER (clone A)


title: Sample_stage 2-repeat 3

source_name: stage 2: one week after the beginning of water deficit


title: 10EC


title: 9EC


title: E. coli 401140_DMEM_0.5_BR1

value: DMEM


title: 8EC

source_name: EC of male embryos from diet-induced obese dam

value: MALE


title: 5'-UTR Spliced Leader PCR Library

city: Aurora

first: Jianbin

last: Wang

state: CO

address: 12801 East 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado Denver

data_processing:
RNA sequencing reads were mapped to the reference genomes using Tophat2 (Kim et al. 2013) and the expression level (RPKM) for transcripts were derived using Cufflinks (Trapnell et al. 2012).
To define the 5’ ends of mRNAs, we constructed Teloprime (Lexogen) libraries that enrich for the mRNA 5’ cap and spliced leader enriched libraries. Two independent approaches were used for the spliced leader enriched libraries.  In the first, we isolated polyadenylated RNA, chemically fragmented the RNA, and generated first strand cDNA using a random primer adaptor (TGACTGGAGTTCAGACGNNNNNN). Second strand cDNA was synthesized using a spliced leader adaptor (CTCTTTCCCTACACGACGCTCTTCCGATCTNNNNATGGTTTAATTACCCAAGTTTGAGTGAG) and the cDNA amplified with sequences corresponding to the adaptors and containing the Illumina adaptors.  In the second method, ribosomal RNA was removed from total RNA using Ribo-Zero (Human/Mouse/Rat, Epicentre MRZH116) and first strand cDNA synthesized with a random primer adaptor (TGACTGGAGTTCAGACGNNNNNN).  Second strand cDNA was synthesized using a spliced leader adaptor (CTCTTTCCCTACACGACGCTCTTCCGATCTNNNNATGGTTTAATTACCCAAGTTTGAGTGAG) and the cDNA amplified with adaptors containing the Illumina adaptors with short extension times.  cDNA with Illumina adaptors in the size range of 250-350 bp were gel purified and used for sequencing on an Ilumina Hi-Seq 4000.
To obtain sequences of the 5’ ends of non-trans-spliced mRNAs, we used a Lexogen custom adaptation of the TeloPrime Full-Length cDNA Amplification Kit, a 5‘ mRNA Seq TeloPrime Add-on Kit (Lexogen). Following synthesis of full-length cDNA, third strand cDNA was synthesized using a random primer adaptor.  The cDNA was then amplified using an Illumina adaptor to the 5’ teloprime primer and to the random primer.  cDNA products in the size range of 250-350 bp were gel purified and used for sequencing on an Ilumina Hi-Seq 4000.
Genome_build: Ascaris suum (Davis Lab, 2017) germline genome
Supplementary_files_format_and_content: tab-delimited BED format like text files include RPKM values and splicing type(SL/TeloPrime) for each Sample

organism: Ascaris suum

source_name: Mixed sample

growth_protocol: Adult Ascaris were collected from freshly isolated pig intestines. Male and female Ascaris were dissected and different regions of the germline tissues were collected. These samples were frozen in liquid nitrogen, and stored at -80C.

extract_protocol:
RNA were extracted directly with Trizol (Invitrogen). Frozen tissues were first ground with a mortar and pestle in liquid nitrogen and then extracted with Trizol.
The transcriptome libraries were prepared from ribosome depleted total RNA (Ribo-Zero™ rRNA Removal Kits, Human/Mouse/Rat, Epicentre MRZH116) using a TotalScript RNA-seq kit (Epicentre, TSRNA1296).

value: North American wildtype

value: Mixed sample


title: 14EC

value: FEMALE

value: HFD

value: Ectoplacental cone (EC)


title: 5'-UTR TeloPrime PCR Library


title: Female diplotene

source_name: Female diplotene

value: Female germline

value: Diplotene


title: Sample_stage 2-repeat 1


title: Female oocyte

source_name: Female oocyte

value: Oocyte


title: 7EC


title: Sample_stage 2-repeat 2


title: Sample_stage 1-repeat 3

source_name: stage 1: one week before water deficit


title: Female late pacheytene

source_name: Female late pacheytene

value: Late pacheytene


title: Sample_stage 1-repeat 2

value: The terminal bud and the five following buds (the major node position for flower formation) from spring flushes


title: auxin_control_seedlings

city: Seattle

first: Christine

last: Queitsch

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

data_processing:
Basecalls performed using eland
Reads were trimmed to 36bp.
Reads were aligned as single-end to A. thaliana reference TAIR10 with TopHat v.1.4.1 with default parameters
Genome_build: TAIR10
Supplementary_files_format_and_content: fpkm_tracking with cufflinks output

source_name: 7 day old Col-0 seedlings

growth_protocol: Seedlings were planted on 1XMS, 0.8% agar and stratified for 2-4 days before being placed in an incubator with LD (16hr light, 22°C; 8hr dark, 20°C) conditions for 7 days.

extract_protocol:
Total RNA of aerial parts 7 days old, long-day grown seedlings of Col-0 was extracted with QIAGEN RNeasy kit. Two RiboMinus treatments (Invitrogen) were performed.
libraries were prepared using the TruSeq kit v2

tag: age

value: 7 day old

value: whole seedling

value: sprayed with dH2O


title: 5EC


title: 6EC


title: auxin_seedlings

tag: tissue

value: sprayed with 750ul 1uM IAA


title: BRZdark-grown_seedlings

value: grown in 24hr darkness on media containing 5uM brassinazole


title: Female early pachytene

source_name: Female early pachytene

tag: developmental stage

value: Early pachytene


title: 4EC

source_name: EC of male embryos from control dam

tag: strain

value: MALE

value: CONTROL


title: Sample_stage 1-repeat 1

value: Femminello


title: 3EC


title: Male spermatids

source_name: Male spermatids

value: North American wildtype

value: Male germline

value: Spermatids


title: Female mitotic region

source_name: Female mitotic region

value: Female germline

value: Mitotic region


title: SHMT late blastoderm rep3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1.8.2.
Reads were aligned by Bowtie2 v2.1.0 to the UCSC reference genome (dm3).
Counting the reads to each gene to the UCSC gtf gene annotation file (dm3) was done via HTSeq python scripts (0.5.4p3).
Genome_build: dm3
Supplementary_files_format_and_content: abundance measurements

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: Adult flies were kept on apple juice plates with yeast for egg laying

extract_protocol:
Embryos were dechorionated with hypochloride, frozen in liquid nitrogen. RNA was extracted with Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: SHMT[X238] germline clones

tag: Stage

value: 1.5–2.5h late blastoderm

value: whole embryo


title: Male seminal vesicle

source_name: Male seminal vesicle

value: Seminal vesicle


title: 2EC

tag: cell type

value: Ectoplacental cone (EC)


title: SHMT late blastoderm rep2


title: SHMT late blastoderm rep1


title: Adult male 3, oxidized

city: Plymouth, Devon

first: vengamanaidu

last: modepalli

address: The Laboratory,Citadel Hill

department: Cell and Molecular

country: United Kingdom

institute: Marine Biological Association of the UK

description: Barcode: CAACTA

data_processing:
A minimum of 13 -15 million 50bp sequencing reads were collected from each sample.
The data were pre-processed to remove the adapters using cutadapt
pre-processed reads were analysed using miRDeep2 software (https://www.mdc-berlin.de/8551903/en/)

organism: Nematostella vectensis

source_name: whole animal

extract_protocol:
Total RNA was extracted using Trizol (Life technologies, USA) as instructed in manual, the small (18-30 nt long) RNA were purified on a denaturing 15% acrylamide gel, from 20 μg total RNA per sample. RNAs were eluted from the acrylamide bands overnight in 0.3 M NaCl, then ethanol/glycogen-precipitated. Half of each sample was oxidized (5X borate buffer, ph=8.6; 5 μL freshly prepared 50mM sodium periodate) for 30 minutes at 25 degrees C, then precipitated with sodium acetate, ethanol and glycogen; the other half was not treated.
Small RNA libraries were constructed as described in Phillip Zamore Lab Illumina TruSeq Small RNA Cloning Protocol April, 2014 (http://www.umassmed.edu/zamore/resources/protocols/). Each library was indexed in order to multiplex 30 samples per sequencing run on the Illumina.

treatment_protocol: Half of each sample was treated with periodate (oxidized).

value: whole animal

value: Adult male

tag: treatment

value: RNA Periodate


title: Adult male 2, untreated

description: Barcode: CAAAAG

value: untreated


title: vnd2 24 hSL replicate 2

source_name: germinating seed_vnd2 24 hSL

growth_protocol: Seeds were sown on MS media, statified at 4 C for 2-d before being transferred to continious light at 22C.

value: germinating seed


title: Male post-meiotic region

source_name: Male post-meiotic region

value: Post-meiotic region


title: SHMT preblastoderm rep3

value: 0–1h preblastoderm


title: 1EC

value: MALE

value: CONTROL


title: Male spermatogenesis

source_name: Male spermatogenesis

value: North American wildtype

value: Male germline

value: Spermatogenesis


title: SHMT preblastoderm rep2

value: SHMT[X238] germline clones


title: Adult male 2, oxidized

description: Barcode: ACTGAT


title: E. coli E2348_DMEMB_0.5_BR1

description: E2348_69_DMEMB_vs_LBB.txt,E2348_69_DMEMB_vs_DMEM.txt

organism: Escherichia coli O127:H6 str. E2348/69

source_name: Escherichia coli cells

value: DMEMB


title: Male mitotic region

source_name: Male mitotic region

value: Mitotic region


title: Adult male 1, untreated

description: Barcode: GGTAGC


title: SHMT preblastoderm rep1

value: whole embryo


title: Adult male 1, oxidized

description: Barcode: GAGTGG


title: E. coli E2348_DMEMB_0.5_BR2


title: Adult female 3, untreated

description: Barcode: ATTCCT

value: Adult female


title: wild type lateblastoderm rep3

value: wild type (OregonR)

value: 1.5–2.5h late blastoderm


title: E. coli E2348_LBB_0.5_BR2

description: E2348_69_DMEMB_vs_LBB.txt,E2348_69_LBB_vs_LB.txt

value: LBB


title: Adult female 3, oxidized

description: Barcode: ATGAGC

value: whole animal

value: RNA Periodate


title: Adult male 3, untreated

description: Barcode: CACCGG

value: Adult male

value: untreated


title: wild type late blastoderm rep2


title: E. coli E2348_DMEM_0.5_BR2

description: E2348_69_DMEM_vs_LB.txt,E2348_69_DMEMB_vs_DMEM.txt

value: DMEM


title: E. coli E2348_LBB_0.5_BR1


title: Adult female 2, untreated

description: Barcode: GTGGCC


title: 5'-UTR TeloPrime PCR Library

data_processing:
RNA sequencing reads were mapped to the reference genomes using Tophat2 (Kim et al. 2013) and the expression level (RPKM) for transcripts were derived using Cufflinks (Trapnell et al. 2012).
To define the 5’ ends of mRNAs, we constructed Teloprime (Lexogen) libraries that enrich for the mRNA 5’ cap and spliced leader enriched libraries. Two independent approaches were used for the spliced leader enriched libraries.  In the first, we isolated polyadenylated RNA, chemically fragmented the RNA, and generated first strand cDNA using a random primer adaptor (TGACTGGAGTTCAGACGNNNNNN). Second strand cDNA was synthesized using a spliced leader adaptor (CTCTTTCCCTACACGACGCTCTTCCGATCTNNNNATGGTTTAATTACCCAAGTTTGAGTGAG) and the cDNA amplified with sequences corresponding to the adaptors and containing the Illumina adaptors.  In the second method, ribosomal RNA was removed from total RNA using Ribo-Zero (Human/Mouse/Rat, Epicentre MRZH116) and first strand cDNA synthesized with a random primer adaptor (TGACTGGAGTTCAGACGNNNNNN).  Second strand cDNA was synthesized using a spliced leader adaptor (CTCTTTCCCTACACGACGCTCTTCCGATCTNNNNATGGTTTAATTACCCAAGTTTGAGTGAG) and the cDNA amplified with adaptors containing the Illumina adaptors with short extension times.  cDNA with Illumina adaptors in the size range of 250-350 bp were gel purified and used for sequencing on an Ilumina Hi-Seq 4000.
To obtain sequences of the 5’ ends of non-trans-spliced mRNAs, we used a Lexogen custom adaptation of the TeloPrime Full-Length cDNA Amplification Kit, a 5‘ mRNA Seq TeloPrime Add-on Kit (Lexogen). Following synthesis of full-length cDNA, third strand cDNA was synthesized using a random primer adaptor.  The cDNA was then amplified using an Illumina adaptor to the 5’ teloprime primer and to the random primer.  cDNA products in the size range of 250-350 bp were gel purified and used for sequencing on an Ilumina Hi-Seq 4000.
Genome_build: Parascaris univalens (Davis Lab, 2017) germline genome
Supplementary_files_format_and_content: tab-delimited BED format like text files include RPKM values and splicing type(SL/TeloPrime) for each Sample

organism: Parascaris univalens

source_name: Mixed sample

growth_protocol: Adult Parascaris were collected from freshly isolated horse intestine. Male and female Ascaris were dissected and different regions of the germline and somatic tissues were collected. These samples were frozen in liquid nitrogen, and stored at -80C. Embryos were collected and stored at 4C.

extract_protocol:
RNA from early embryos were extracted directly with Trizol (Invitrogen). Frozen tissues were first ground with a mortar and pestle in liquid nitrogen and then extracted with Trizol.
The transcriptome libraries were prepared from ribosome depleted total RNA (Ribo-Zero™ rRNA Removal Kits, Human/Mouse/Rat, Epicentre MRZH116) using a TotalScript RNA-seq kit (Epicentre, TSRNA1296).

value: Mixed sample


title: E. coli E2348_DMEM_0.5_BR1


title: wild type preblastoderm rep3

value: 0–1h preblastoderm


title: E. coli E2348_LB_0.5_BR2

description: E2348_69_DMEM_vs_LB.txt,E2348_69_LBB_vs_LB.txt

value: LB


title: 5'-UTR Spliced Leader PCR Library

value: North American wildtype


title: Extracellular Vesicles from 3-6mm bovine ovarian follicles

city: Pirassununga

first: Juliano

middle: C

last: da Silveira

state: Sao Paulo

address: Duque de Caxias 225

department: Veterinary Medicine

country: Brazil

institute: University of Sao Paulo

description:
Bos taurus indicus
Single sample

data_processing:
Quality Control of sequencing data. Program: FASTQC v.0.11.5.
Alignment processing against the Bos taurus UMD3.1 assembly. Program: Tophat v2.0.9, the default parameters were used.
Abundance measurement. Program: Cufflinks v.2.2.0, the default parameters were used.
Gene annotation. Database: DAVID v. 6.7.
Genome_build: Bos_taurus_UMD_3.1
Supplementary_files_format_and_content: Gene_fpkm.xlsx (Excel spreadsheet) is the default output from Cufflinks program, which contains: FPKM estimated expression values, genomic coordinates, number of base pairs in the transcripts, absolute depth of read coverage across the object, and gene annotation.

organism: Bos indicus

source_name: Extracellular vesicles from ovarian follicular fluid

extract_protocol:
Trizol LS
TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA).
The libraries' average sizes were estimated using the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA), and quantified using quantitative PCR with the KAPA Library Quantification kit (KAPA Biosystems, Foster City, CA, USA). Four lanes of a sequencing flowcell, using the TruSeq PE Cluster kit v3-cBot-HS kit (Illumina, San Diego, CA, USA), were clustered and sequenced using HiScanSQ equipment (Illumina, San Diego, CA, USA) with a TruSeq SBS Kit v3-HS (200 cycles).

treatment_protocol: No treatment was applied.

value: ovarian follicle 3-6mm


title: wild type late blastoderm rep1


title: Adult female 2, oxidized

description: Barcode: CGTACG


title: Parascaris testis

source_name: Parascaris testis

value: Male germline

value: Testis


title: wild type preblastoderm rep1

value: whole embryo


title: Adult female 1, untreated

description: Barcode: GTTTCG

value: Adult female


title: Parascaris intestine

source_name: Parascaris intestine

value: Male somatic

value: Intestine


title: ΔgaaC strain grows on medium with GA for 2h_replicate2

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

institute: Centre of fungal biodiversity

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed for low-quality sequence, then mapped to Aspergillus niger NRRL3  whole genome using Bowtie2 (Langmead B et al., Genome Biology, 2009) and BWA software (Li H & Durbin R, Bioinformatics, 2009).
“Fragments per kilobase of exon model per million mapped reads” (FPKM) was calculated using RSEM tool (Li B & Dewey CN, BMC bioinformatics, 2011).
Genome_build: Aspergillus niger NRRL3 (http://genome.jgi.doe.gov/Aspni_NRRL3_1)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Aspergillus niger

source_name: Mycelium sample

growth_protocol: Freshly harvested spores were inoculated with a final concentration of 10E06 spores/ml in 100 ml complete medium (pH 5.8) with 2% (w/v) D-fructose (Sigma-Aldrich) and were pre-grown for 16h. Mycelium was harvested by filtration through sterile myracloth, washed twice with minimal medium (MM) with no carbon source (pH 6) and 2.5 g of pre-grown mycelia were transferred to 50 ml MM (pH 6) with 25 mM GA and incubated for 2h. All incubations were performed in rotary shaker at 30°C and 250 rpm.

extract_protocol:
The mycelium of SDP20.6 (ΔgaaC) was ground in Tissue Lyser II (Qiagen) and RNA was extracted using TRIzol reagent (Invitrogen) and purified with NucleoSpin RNA Clean-up kit (Macherey-Nagel) with rDNase treatment. RNA quantity of the samples was checked with a NanoDrop-1000 spectrophotometer and the quality by RNA gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: sampling time

value: 2 hour


title: Adult female 1, oxidized

description: Barcode: ATGTCA

value: whole animal


title: E. coli 102712_DMEMB_0.5_BR2

description: 102712_DMEMB_vs_LBB.txt,102712_DMEMB_vs_DMEM.txt

organism: Escherichia coli 102712

value: DMEMB


title: Primary polyps 3, oxidized

description: Barcode: TAGCTT

value: Primary polyps

value: RNA Periodate


title: Primary polyps 3, untreated

description: Barcode: CCGTCC

value: untreated


title: E. coli HS_DMEMB_0.5_BR2

description: HS_DMEMB_vs_LBB.txt,HS_DMEMB_vs_DMEM.txt

organism: Escherichia coli HS

value: HS


title: P5

city: Zhenjiang

first: Xiangfeng

last: Zheng

state: Jiangsu

address: 301, Xuefu Road

department: Food school

institute: Jiangsu university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase Million was the value of expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced.TPM means transcripts per million,using the formula of R1*1000*1000000/(L1*Rtoatl),R1: The count value of the gene;L1: The length of the gene;Rtotal: the sum value of all the corrected count value .
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and TPM for each Sample ...

organism: Penicillium citrinum

source_name: Fungus cultured in CYA medium at pH 5

growth_protocol: Penicillium citrinum was cultured in CYA medium at pH 3 or pH 5， at 25℃ in dark for 2 weeks.

extract_protocol:
The medium was removed,Penicillium citrinum was collected and ground to powder, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The sample of P3 was the control, cultured at pH 3, and P5 was Penicillium citrinum cultured at pH 5.

value: Penicillium citrinum cultured in CYA medium at pH 5

tag: incubation time

value: 2 weeks

tag: incubation conditions

value: 25℃ in dark


title: Primary polyps 2, untreated

description: Barcode: GATCAG


title: P3

source_name: Fungus cultured in CYA medium at pH 3

value: Penicillium citrinum cultured in CYA medium at pH 3


title: Parascaris carcass

source_name: Parascaris carcass

value: North American wildtype

value: Carcass


title: E. coli HS_DMEMB_0.5_BR1

tag: growth media


title: E. coli 102712_DMEMB_0.5_BR1


title: E. coli 102712_LBB_0.5_BR2

description: 102712_DMEMB_vs_LBB.txt,102712_LBB_vs_LB.txt

value: LBB


title: wild type preblastoderm rep2

value: wild type (OregonR)

value: 0–1h preblastoderm

value: whole embryo


title: Primary polyps 2, oxidized

description: Barcode: GGCTAC


title: E. coli 102712_LBB_0.5_BR1


title: rods RNA-seq rep3

city: Guangzhou

first: chunjie

last: zhu

state: Guangdong

address: 100 xianlie road, yuexiu district

institute: Guangdong Institute of Microbiology

data_processing:
raw sequence data were filtered to remove those containing adapter and reads with more than 10% unknown nucleotides, and reads with more than 40% of low quality base (Qvalue <20)
clean data were align to Lysinibacillus varians genome  and reference genomes using Samtools 0.1.18.0 and tophat 2.0.1
RPKM of each gene was calculated using cufflink 2.0.0
Genome_build: CP006837
Supplementary_files_format_and_content: excel files include RPKM values for each Sample

organism: Lysinibacillus varians

source_name: rod cell rep3

growth_protocol: The isolates were inoculated into Luria–Bertani (LB) medium containing yeast extract 5 g l-1 , tryptone 10 g l-1 and NaCl 5 g l-1 (5%, v/v) and incubated on a rotary shaker with 160 rev min-1 at 30 ˚С.

extract_protocol:
the cultures were fixed with 2 vols RNA protect bacteria (Qiagen) and harvested. RNA was isolated from triplicate bacterial pellets with an RNeasy mini kit (Qiagen, USA). Extraction was performed according to manufacturer’s instruction.
Libraries were prepared according to Illumina's instructions

treatment_protocol: 5 h and 10 h culture of the strain were collected and used for RNA extraction

value: rod

tag: growth time

value: 10 hrs


title: E. coli E2348_LB_0.5_BR1

growth_protocol: The E. coli strains were grown overnight in LB media and were inoculated 1:100 into 250 ml of fresh LB or DMEM with bile (LBB and DMEMB) or without and were incubated with shaking (225 rpm) at 37˚C to a final optical density (OD600) of approximately 0.5.

value: LB


title: E. coli HS_LBB_0.5_BR2


title: E. coli HS_LBB_0.5_BR1


title: rods RNA-seq rep2

source_name: rod cell rep2


title: Primary polyps 1, oxidized

description: Barcode: ACAGTG

value: whole animal

value: Primary polyps


title: E. coli 102712_DMEM_0.5_BR2

description: 102712_DMEM_vs_LB.txt,102712_DMEMB_vs_DMEM.txt

value: DMEM


title: E. coli HS_DMEM_0.5_BR2

value: HS


title: Parascaris ovary

source_name: Parascaris ovary

value: Female germline

value: Ovary


title: rods RNA-seq rep1

source_name: rod cell rep1


title: ΔgaaC strain grows on medium with GA for 2h_replicate1

value: 2 hour


title: E. coli 102712_DMEM_0.5_BR1


title: Parascaris embryo

source_name: Parascaris embryo

value: Male somatic

value: Embryo


title: Late planula 3, untreated

description: Barcode: GTCCGC

source_name: whole animal

value: Late planula

value: untreated


title: E. coli HS_DMEM_0.5_BR1