title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS50 mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS50_B


title: u1chx

status: Public on Feb 01 2019

type: SRA

city: Amsterdam

first: Kat

last: Moore

address: Plesmanlaan 125

country: Netherlands

institute: Sanquin Research

description:
Ribosome footprint
a1
merged_u_chx_F.wig5.wig.gz
merged_u_chx_R.wig5.wig.gz

library_source: transcriptomic

data_processing:
Library strategy: Ribosome profiling
For peak calling ribosome footprint samples,the entire (very long) pipeline and all scripts can be found at: htts://git.lumc.nl/i.f.a.c.fokkema/ribosome-profiling.
For production of ribosome footprint read counts found in ribofoot_raw_reads_by_feature_plus_total_rnaseq.csv.gz, reads were adapter trimmed and aligned genome using STAR. Counts by feature type were produced usign HTSeq count with the corresponding feature type of 5'UTR, CDS, or 3'UTR. RNAseq read counts produced directly by STAR were subsequently added.
Ribfootprinting STAR parameters were –outFilterMultimapNmax 20 --outFilterMismatchNmax 1 --outSAMmultNmax 1 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts Also includes a UCSC refseq gtf file accessed on 11-9-15 passed to STAR with –sjdbGTFfile.
For RNAseq, alignment to genome via STAR, with parameters: --outFilterMultimapNmax 20 --outFilterMismatchNmax 1 --outSAMmultNmax 1 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM. Also includes a UCSC refseq gtf file accessed on 11-9-15 passed to STAR with –sjdbGTFfile.
For RNAseq, differential expression with edgeR
Genome_build: mm10/GRCm38.5
Supplementary_files_format_and_content: Wiggle files were produced either using STAR or using the custom script available at https://git.lumc.nl/i.f.a.c.fokkema/ribosome-profiling.
Merged wiggles of ribosome footprinting replicates are presented to compensate for lower depth. Individual RNAseq wiggle files are available per replicate.
Harringtonine peak files are a combination of both tunicamycin and cyclohexamide, presented separately for forward and reverse strands.
Read count tables in ribofoot_raw_reads_by_feature_plus_total_rnaseq.csv.gz include ribofootprinting reads reported separately for the 5', CDS, and 3'UTR and total RNAseq reads (across the entire transcript).

molecule: total RNA

organism: Mus musculus

source_name: Erythroblasts

growth_protocol: Murine erythroblasts, isolated from p53-/- mouse fetal livers, were cultured in Stempro supplemented with L-glutamine and Pen/Strep (Thermo Fisher), 0.5 U/ml erythropoietin (Epo, Jansen-Cilag), 1% stem cell factor (supernatant) and 1 nM dexamethasone (Sigma).

extract_protocol:
Rneasy plus kit
Nebnext small RNA library prep set (for ribofootprint molecules) or Truseq (for RNAseq molecules)

treatment_protocol: Where applicable: tunicamycin 2.5ug.ml for 1.5h, cyclohexamide 100ug/ml for 5 min prior to harvest or 2ug/ml harringtonine prior to harvest.

tag: strain

value: FVB/n x C57BL/6

tag: genotype

tag: tissue

value: fetal liver

tag: cell type

value: Erythroblasts

tag: translation stalled by

value: cyclohexamide

tag: stress induced by

value: untreated


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS50 mice (rep. A, sequencing batch 3)

city: Aurora

first: Laura

last: Saba

state: CO

address: 12850 E. Montview Blvd

department: Skaggs School of Pharmacy and Pharmaceutical Sciences

country: USA

institute: University of Colorado Anschutz Medical Campus

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS50_A

data_processing:
samples were aligned/quantified using MiR-MaGiC
Fastx toolkit  was used to clip adapters and filter reads for quality (>95% Q20 bases)
miRDeep2 was used to identify putative novel miRNAs
RUVr was used for batch correction and correcting for unwanted variation
CPMM or NBMM was used for normalization (HeritSeq R package)
A Variance stabilizing transformation was applied
Genome_build: Transcript database consisting of all NM and NR mouse transcripts in RefSeq (Release 67)

source_name: brain, right hemisphere

extract_protocol:
Libraries were constructed using the Illumina TruSeq Small RNA Sample Prep kit (Illumina, San Diego, CA, USA).  Fragments between 20-35 bp were size selected
small RNA sequencing

treatment_protocol: Storage in RNA later

tag: sequencing batch

tag: experimental treatment

tag: extraction protocol

value: RNA was collected from whole brain (right hemisphere) using the RNeasy Plus Universal Midi, Mini, and minElute kits for RNA sequencing (Qiagen, Valencia, CA, USA).


title: LTS17-LQ32: polysome 4A-15 submergence

city: Taipei

first: Hsing Yi

last: Cho

state: Select One

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: ABRC

country: Taiwan

institute: Academia sinica, Taiwan

data_processing: The data analysis is described in Cho et al.,2018, New phytologist

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Germination and growth of Arabidopsis plants were described previously (Hsu et al., 2013).

extract_protocol:
The RNA loading on the polysome was isolated and quantified as previous described (Liu et al., 2012).
The cDNA libraries of total RNA and heavy polysome bound RNA were constructed and sequenced at High Throughput Genomics Core of biodiversity research center in Academia Sinica, Taipei, according to the instruction of Illumina HiSeq2000.

treatment_protocol: 9 d old seedlings were treated with 3 h submergence plus dark and 3 h dark, at room temperature according to (Cho et al.,2018).

tag: development stage

value: 9-day old seedling

tag: treatment

value: dark plus submergence treatment

tag: fraction

value: Polysome fraction


title: ETX-C-Side2

city: Shanghai

first: Ran

last: Wang

address: 320 Yue Yang Road

department: Shanghai Institute of Biochemistry and Cell Biology

country: China

institute: Chinese Academy of Sciences

description: Cells selected from the posterior domain of ETX-embryo

data_processing:
Raw reads were mapped to mm10 version of the mouse genome using the Tophat2 v2.0.4 program.
We calculated fragment per kilobase per million (FPKM) as expression level using Cufflinks v2.0.2 with default parameters.
Genes with the FPKM value > 1.0 in at least one sample across all samples were retained for further analysis.
The expression levels were transformed to logarithmic space by using log2(FPKM+1).
Genome_build: mm10
Supplementary_files_format_and_content: Textfile include FPKM values for each Sample

growth_protocol: Cell suspension seeded in aggregation plates. Grown in sequencial media (IVC; cell guidance systems).

extract_protocol:
To collect RNA for RNA-Seq, ETX-embryos generated using a T/Brachyury-GFP reporter line were collected and TSC compartments were dissected away. The ESC compartment was further dissected in half on the long side and each half was analysed separately under a fluorescent microscope to identify GFP+ve (prospective posterior) and GFP-ve (prospective anterior) cells. Samples were collected in lysis buffer (2.3μl of 0.2 % Triton X-100 (Sigma) supplemented with 1U/μl RNAsIN (Ambion)) and stored at -80 C until library preparation.
Low-input RNA-seq was performed using the Smart-seq2 protocol using 18 cycles of amplification in the PCR-preamplification step. A pool of indexed libraries was sequenced on a HiSeq 2500 in rapid run mode. Reads were mapped to the M. musculus genome (Ensembl version 38.77) and quantified using the HTSeq-count.

treatment_protocol: no treatment was used.

value: embryo

tag: domain

value: posterior


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS8 mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS8_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS8 mice (rep. A, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS8_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS94 mice (rep. C, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS94_HIGH_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS93 mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS93_HIGH_B


title: LTS17-LQ31: polysome 4A-15 control

value: dark treatment


title: ETX-B-Side2

source_name: Cells selected from the posterior domain of ETX-embryo


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS93 mice (rep. A, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS93_HIGH_A


title: LTS17-LQ28: polysome i4g1-2 submergence


title: ETX-A-Side2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS90 mice (rep. C, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS90_MED_C


title: LTS17-LQ27: polysome i4g1-2 control


title: ETX-C-Side1

description: Cells selected from the anterior domain of ETX-embryo

value: anterior


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS90 mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS90_MED_B


title: LTS17-LQ26: polysome Col-0 submergence


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS66 mice (rep. C, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS66_LOW_C


title: ETX-B-Side1

source_name: Cells selected from the anterior domain of ETX-embryo


title: LTS17-LQ25: polysome Col-0 control


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS66 mice (rep. A, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS66_LOW_A


title: ETX-A-Side1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS7 mice (rep. C, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS7_MED_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS49 mice (rep. A, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS49_LOW_A


title: LTS17-LQ21a: 4A-15 control

value: total mRNA


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS5 mice (rep. A, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS5_MED_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS46 mice (rep. C, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS46_LOW_C


title: LTS17-LQ20a: i4g1-2 submergence


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS43 mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS43_MED_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS43 mice (rep. C, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS43_MED_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS34 mice (rep. C, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS34_HIGH_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS92 mice (rep. C, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS92_MED_C


title: LTS17-LQ22a: 4A-15 submergence


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS34 mice (rep. A, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS34_HIGH_A


title: LTS17-LQ19a: i4g1-2 control


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS49 mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS49_LOW_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS32 mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS32_HIGH_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS32 mice (rep. A, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS32_HIGH_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS34 mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS34_HIGH_B


title: LTS17-LQ17a: Col-0 control


title: LTS17-LQ18a: Col-0 submergence


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS25 mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS25_HIGH_B


title: LTS17-LQ14: polysome 4A-15 submergence


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS25 mice (rep. A, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS25_HIGH_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS24 mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS24_LOW_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS66 mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS66_LOW_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS24 mice (rep. C, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS24_LOW_C


title: wt control 0 hours OS 2

city: Nijmegen

first: Human

last: Riahi Asl

state: Gelderland

address: Geert Grooteplein Zuid 10

department: Human Genetics

institute: Radboud UMC

description: G9a wild type heads after 0 hours oxidative stress exposure (paraquat)

data_processing:
Sequenced reads were aligned with Burrows-Wheeler algorithm (BWA) (Li & Durbin, 2010) to the Drosophila reference genome (BDGP.5, http://www.fruitfly.org/).
Per gene read counts were generated with HTSeq count (Anders et al, 2015) with following paramenters: intersection non-empty, non-stranded, quality filter = 15.
DESeq (Anders & Huber, 2010) was used to obtain library size-normalized read counts and to calculate differential expression of genes in 4 pairwise comparisons: 0 h versus 6 h and 0 h versus 12 h after OS in both G9a mutants and controls (fold change ≥1.5, adjusted p-value≤ 0.05, Benjamini-Hochberg).
Genome_build: Drosophila_melanogaster.BDGP5.70.gtf
Supplementary_files_format_and_content: Tab delimited file table of normalized count data. Tab delimited DESeq output files of  4 pairwise comparisons: wildtype 0 hours versus wildtype 6 hours (wt0VSwt6) and 12 hours (wt0VSwt12) after paraquat exposure. G9aDD1 mutant 0 hours versus G9aDD1 mutant 6 hours (mt0VSmt6) and 12 hours (mt0VSmt12) after paraquat exposure.

organism: Drosophila melanogaster

source_name: male fly head

growth_protocol: Flies were reared on standard medium (cornmeal/sugar/yeast) at 25 °C and 70 % humidity with a 12-h light/dark cycle. Flies were collected after eclosion and allowed to recover from CO2 exposure for 5 days prior to paraquat exposure.

extract_protocol:
200 fly heads per sample were used for total RNA extraction using QIAGEN lipid mini tissue kit.
mRNA libraries where prepared from 100 ng total RNA using Truseq RNA library prep v2 (Illumina). Samples where indexed and 4 samples where multiplexed on one sequencing lane. Samples 1, 2, 4 and 5 contain True-seq barcode 4, samples 19, 20, 22, 23 contain True-seq barcode 5 and samples 25, 26, 28, 29 contain True-seq barcode 6.

treatment_protocol: Flies (5-9 days) were transferred to paraquat containing food (50 mM) and incubated at 25 °C and 70 % humidity. At each time point, samples for RNA-seq were collected by flash freezing flies in liquid nitrogen followed by vortexing and filtering through a series of sieves to isolate heads from other body parts.

value: wildtype control

value: no treatment

tag: duration

value: 0 hours post treament

tag: age

value: 5-9 days

value: head


title: LTS17-LQ13: polysome 4A-15 control


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS19 mice (rep. C, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS19_LOW_C


title: LTS17-LQ12: polysome i4g1-2 submergence


title: LTS17-LQ11: polysome i4g1-2 control


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS13 mice (rep. C, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS13_MED_C


title: LTS17-LQ10: polysome Col-0 submergence


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS26 mice (rep. A, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS26_HIGH_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS114 mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS114_LOW_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS13 mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS13_MED_B


title: LTS17-LQ09: polysome Col-0 control


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS114 mice (rep. C, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS114_LOW_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS110 mice (rep. C, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS110_LOW_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS110 mice (rep. A, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS110_LOW_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS103 mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS103_HIGH_B


title: Hela CCL2 - Laboratory 12 (50 passages) Hela14_Rep3

city: West Haven

first: Yansheng

last: Liu

state: CT

address: 840 West Campus Drive, Fl 3rd Ste Cancer

department: School of Medicine

institute: Yale

data_processing:
RNAseq reads were checked with FastQC (v0.11.4) and read were quality controlled with Trimmomatic (v 0.35).
Reads were aligned to the GRCh38 reference genome using STAR (v 2.4.2a)
SNPs were called for every cell line using the GATK framework. Duplicate reads were marked with the Picard tools (v 2.0.1) "MarkDuplicates" function, followed by GATK (v 3.7) using SplitNCigarReads, HaplotypeCaller, and VariantFiltration. Variants were filtered if they had Fisher Strand values above 30, Quality by Depth values greater than 2, and with no more than 2 variants within a 35 bp window.
Genome_build: hg19
Supplementary_files_format_and_content: The tab-delimited text file includes raw counts and RPKM values for each sample.

organism: Homo sapiens

source_name: Hela CCL2

growth_protocol: Hela cells were grown in DMEM with penicillin, streptomycin, and glutamine stock solution (Gibco).

extract_protocol:
RNA was harvested using TRIzol
RNA libraries were prepared for sequencing 4 µg of total RNA using TrueSeq RNA kit (Illumina)

value: Hela cells

tag: passages


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS103 mice (rep. A, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS103_HIGH_A


title: LTS17-LQ06: 4A-15 submergence


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS103 mice (rep. C, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS103_HIGH_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) ISS mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
ISS_HIGH_B_Ctl3_4

value: ISS/IbgTejJ


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS14 mice (rep. A, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS14_MED_A


title: Hela CCL2 - Laboratory 12 (50 passages) Hela14_Rep2


title: LTS17-LQ04: i4g1-2 submergence


title: EpCAM+ EGFR-

type: RNA

city: Toronto

first: Frances

last: Wong

state: ON

address: 1 King's College Circle, MSB3360

country: Canada

institute: University of Toronto

hyb_protocol: Hybridization was performed by the Princess Margaret Genomics Center (Toronto, Canada) as per Affymetrics protocol.

scan_protocol: Scanning was performed by the Princess Margaret Genomics Center (Toronto, Canada) as per Affymetrics protocol.

data_processing: Data was processed, RMA normalized, and coverted into log2 values in R 3.1.2 using the Affy library from Bioconductor.

label: biotin

label_protocol: Biotinylated cDNA was prepared by the Princess margaret Genomics Center (Toronto, Canada) as per Affymetrics protocol.

extract_protocol: All samples were processed in a single batch. RNA was expreacted using the Norgen Biotek RNA extraction kit. RNA purity and integrity were determined using 28S to 18S rRNA ratio (Agilent Bioanalyzer)

treatment_protocol: First trimester human placentas were in PBS to remove containing maternal blood and digested in trypsin for a trophoblast enriched fraction. Cells are frozen in -80. When sufficent sample is collected, cells are thawed and labeled with target antibodies in preparation for fluorescence actived cell sorting to isolated target homogenous subpopulations.

tag: gestational age


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS80 mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS80_MED_B_Ctl2_3

tag: strain


title: EpCAM- CDCP1-


title: EpCAM- EGFR-


title: Hela CCL2 - Laboratory 12 (50 passages) Hela14_Rep1


title: EpCAM+ CDCP1-


title: LTS17-LQ05: 4A-15 control


title: EpCAM+ EGFR+


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS22 mice (rep. C, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS22_MED_C


title: EpCAM- CDCP1+


title: EpCAM+ CDCP1+


title: LTS17-LQ02: Col-0 submergence


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS41 mice (rep. C, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS41_LOW_C_Ctl4_3


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS5 mice (rep. C, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS5_MED_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS5 mice (rep. B, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS5_MED_B


title: Hela CCL2 - Laboratory 13 Hela13


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) ILS mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
ILS_MED_B_Ctl1_3

value: ILS/IbgTejJ


title: Hela CCL2 - Laboratory 12 (7 passages) Hela12_Rep3


title: EpCAM- EGFR+


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS7 mice (rep. B, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS7_MED_B

value: RNA was collected from whole brain (right hemisphere) using the RNeasy Plus Universal Midi, Mini, and minElute kits for RNA sequencing (Qiagen, Valencia, CA, USA).


title: Hela CCL2 - Laboratory 12 (7 passages) Hela12_Rep1


title: Hela CCL2 - Laboratory 12 (7 passages) Hela12_Rep2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS7 mice (rep. A, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS7_MED_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) ISS mice (rep. B, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
ISS_HIGH_B_Ctl3_3


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS107 mice (rep. A, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS107_LOW_A


title: LTS17-LQ03: i4g1-2 control

value: 9-day old seedling


title: LTF_GG07 Polysome K48M control

data_processing:
For sequencing data mapping, reference transcript data set (TAIR 10 cDNA update) including cDNA for 41,672 annotated protein-coding gene sequences was retrieved from the Arabidopsis Information Resources database (TAIR: https://www.arabidopsis.org/).
The raw reads were preprocessed and normalization by empirical analysis of DGE of CLC bio software workbench 6 (Qiagen) statistically.
Genome_build: TAIR 10 cDNA update
Supplementary_files_format_and_content: Excel file including each RPKM values for each sample

treatment_protocol: 9 d old seedlings were treated with 3 h submergence plus dark and 3 h dark, at room temperature according to (Hsu et al., 2013).

tag: genotype

value: Overexpressed SnRK1.1K48M in Col-0


title: LTF_GG06 Polysome Col-0 submergence

value: dark plus submergence treatment

value: Polysome fraction


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS46 mice (rep. A, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS46_LOW_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS41 mice (rep. C, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS_41_LOW_C_Ctl4_2


title: Hela CCL2 - Laboratory 11 Hela11


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) ILS mice (rep. B, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
ILS_MED_B_Ctl1_2


title: LTF_GG05 Polysome Col-0 control


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS3 mice (rep. B, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS3_HIGH_B1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS80 mice (rep. B, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS80_MED_B_Ctl2_2


title: Hela CCL2 - Laboratory 9 Hela9


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS43 mice (rep. A, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS43_MED_A1


title: Hela CCL2 - Laboratory 7 Hela7


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS90 mice (rep. A, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS90_MED_A


title: LTF_GG03 K48M control


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS22 mice (rep. A, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS22_MED_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS93 mice (rep. C, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS93_HIGH_C1


title: LTS17-LQ01: Col-0 control


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS114 mice (rep. A, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS114_LOW_A


title: LTF_GG08 Polysome K48M submergence


title: Hela Kyoto - Laboratory 10 Hela10

source_name: Hela Kyoto


title: LTF_GG02 Col-0 submergence


title: LTF_GG04 K48M submergence


title: LTF_GG01 Col-0 control


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS49 mice (rep. C, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS49_LOW_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS46 mice (rep. B, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS46_LOW_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS110 mice (rep. B, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS110_LOW_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS19 mice (rep. B, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS19_LOW_B1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS24 mice (rep. A, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS24_LOW_A1


title: Hela Kyoto - Laboratory 8 Hela8


title: Hela Kyoto - Laboratory 4 Hela4


title: ST_FR57 Polysome K48M control


title: ST_FR58 Polysome K48M submergence


title: Hela CCL2.2 - Laboratory 5 Hela5

source_name: Hela CCL2.2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS19 mice (rep. A, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS19_LOW_A


title: Hela Unlabeled (Appears to be Kyoto) - Laboratory 3 Hela3

source_name: Hela Unlabeled (Appears to be Kyoto)


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS94 mice (rep. A, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS94_HIGH_A


title: ST_FR56 Polysome Col-0 submergence


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS22 mice (rep. B, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS22_MED_B1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS26 mice (rep. C, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS26_HIGH_C1


title: Hela Kyoto - Laboratory 1 Hela1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS14 mice (rep. B, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS14_MED_B1


title: ST_FR95 Polysome Col-0 control


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS13 mice (rep. A, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS13_MED_A


title: ST_FR54 K48M submergence


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS92 mice (rep. A, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS92_MED_A1


title: Hela CCL2 - Laboratory 2 Hela2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS92 mice (rep. B, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS92_MED_B


title: ST_FR53 K48M control


title: Ovarian cancer cells

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description:
High coverage deep sequencing of the transcriptome
PA1Control

data_processing:
Samples were aligned using TOPHAT
Cufflinks was used to assemble the individual transcripts from RNA-seq reads that have been aligned to the genome, and quantifies their expression
Cuffmerge was used to merge the transcripts assembled from individual samples and produces a unified transcriptome file for using in down-stream analysis. It also performs reference GTF based annotation for the unified transcriptome.
Cuffdiff was used for differential gene expression analysis. It compared expression levels of genes and transcripts in RNA-Seq experiments, stating the up- or down-regulated genes between two or more conditions, along with the genes that are differentially spliced or are undergoing other types of isoform-level regulation.
Genome_build: Homo_sapiens_UCSC_hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Ovarian cancer cells

growth_protocol: DMEM+ 10%FBS+1% antibiotic at 37oC at 5%CO2

extract_protocol:
Total RNA was isolated and harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The sequencing library is prepared by random fragmentation of the cDNA sample, followed by 5' and 3' adapter ligation, after end-repair and the addition of an ‘A’ base and SPRI cleanup. The prepared cDNA library was amplified using PCR for the enrichment of the adapter-ligated fragments. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. . The individual libraries were quantified using a NanoDrop spectrophotometer (Thermo Scientific) and validated for quality with a Bioanalyzer (Agilent Technologies). Adapter-ligated fragments are then PCR amplified and gel purified

treatment_protocol: Transient transfection using interferrin transfection reagent

tag: disease

value: Ovarian cancer

tag: tissue

value: Ovary

tag: Sex

value: Female

value: Ovarian cancer cells


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS99 mice (rep. A, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS99_LOW_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) ISS mice (rep. D, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
ISS_HIGH_D2


title: ST_FR52 Col-0 submergence

value: total mRNA


title: Hela CCL2 - Laboratory 6 Hela6

tag: cell type


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS32 mice (rep. C, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS32_HIGH_C1

tag: sequencing batch


title: Immortalized normal ovarian cells

description:
High coverage deep sequencing of the transcriptome
IOSE_Control

source_name: Immortalized normal ovarian cells

value: Normal

value: Immortalized normal ovarian cells


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS99 mice (rep. C, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS99_LOW_C1

tag: experimental treatment


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS107 mice (rep. C, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS107_LOW_C1

tag: extraction protocol


title: ST_FR51 Col-0 control

tag: development stage

value: dark treatment


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS107 mice (rep. B, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS107_LOW_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS3 mice (rep. C, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS3_HIGH_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS99 mice (rep. B, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS99_LOW_B1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS25 mice (rep. C, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS25_HIGH_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS94 mice (rep. B, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS94_HIGH_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS26 mice (rep. B, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS26_HIGH_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS14 mice (rep. C, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS14_MED_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS112 mice (rep. A, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS112_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) ISS mice (rep. D, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
ISS_HIGH_D1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS41 mice (rep. B, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS41_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS80 mice (rep. A, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS80_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) ILS mice (rep. B, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
ILS_MED_B_Ctl1_1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS3 mice (rep. A, sequencing batch 2)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS3_HIGH_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) ISS mice (rep. B2, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
ISS_HIGH_B_Ctl3_2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS112 mice (rep. B, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS112_B


title: Third instar larval ovary dissociated with Trypsin and Collagenase rep 3

city: Bethesda

first: Justin

middle: Matthew

last: Fear

state: MD

address: 50 South Drive

department: LCDB

institute: NIDDK, NIH

description:
SV-6-10X-Ov
Drosophila melanogaster (7227)
Female organism (FBbt:00007011)
scRNA-Seq
*R1_001.fastq.gz: FASTQ file containing the 26bp cell barcode.
*R2_001.fastq.gz: FASTQ file containing the 98 bp RNA sequence.
*I1_001.fastq.gz: FASTQ file containing the 8 bp sample index.

data_processing:
We called bases using RTA v1.13 (Illumina, San Diego, CA), and demultiplexed and converted BCLs to FASTQs using Cell Ranger mkfastq v2.0.0 (10X Genomics, Pleasanton, CA). We aligned reads to FlyBase r6.16 and generated gene level counts using Cell Ranger count v2.1.1. We forced the number of cells (--force-cells=3000) because our cell population had a large dynamic range of RNA concentration due to the presence of the germline. We combined the three replicates using Seurat’s multiple CCA method and called cell type clusters and differential expression from the merged data set.
Genome_build: Drosophila melanogaster Release 6 plus ISO1 MT (GCA_000001215.4).
Supplementary_files_format_and_content: combined.biomarkers.tsv: Differential expression among cell clusters using Seurat v2.3.1.
Supplementary_files_format_and_content: combined.counts.tsv: Merged raw counts table with replicates 1, 2, and 3.
Supplementary_files_format_and_content: *.barcodes.tsv, *.genes.tsv, *.matrix.mtx: Filtered raw counts output by Cell Ranger count --force-cells=3,000 (v2.1.1).

molecule: polyA RNA

source_name: Dissociated cells from pools of third instar larval ovaries

growth_protocol: We grew w[1118] flies (FBst0005905; Bloomington Drosophila Stock Center, Bloomington, IN) on fly food A (LabExpress Ann Arbor, MI) under constant light, at 25°C and 60% relative humidity. We collected eggs every 8-16 hr from six mated females and let them develop into late third instar larvae. We fed larvae with yeast/water paste containing 0.5mg/ml Sulforhodamine B sodium salt (Sigma-Aldrich, Cat. No. S1402-25G. St. Louis, MO). We collected gonads from late third instar larvae (immobilized with no anterior spiracle extension, with 50% gut clearance).

extract_protocol:
We dissected and washed late third instar larvae in PBS (Gibco Life Technologies, Carlsbad, CA) at 22°C. We removed larval fat body attached to the gonads by treating with 0.1% Trypsin (Thermo Fisher, Walkersville, MD) and 0.075 mg/ml Collagenase (Sigma-Aldrich, St. Louis, MO) in PBS for three minutes. In order to remove the fat body, we gently vortexed 1.5 ml eppendorf tubes containing the enzyme mix with gonads by flicking the tube with a forefinger. We rinsed the ovaries with 5 ml PBS, twice and incubated in 100 μl 0.5% Trypsin (w/v) and 2 mg/ml Collagenase in PBS in a watch glass wells for 30 minutes at 22°C. During incubation we observed the ovaries under dissecting scope and gently teased them apart with tungsten needles (Fine Scientific Tools, Foster City, CA) and pipetted the cells, several times to achieve maximum dissociation. To stop dissociation, we incubated in 1% (w/v) FBS (Gibco Life Technologies, Carlsbad, CA) for two minutes and added 0.04% (w/v) BSA (MP, Santa Ana, CA). We filtered the cell suspensions, through a 35 μm filter (Thermo Fisher, Walkersville, MD) pre-coated with 0.5% BSA solution and washed the watch glass and filter with 50 μl PBS, 0.04% BSA and transferred filtrate to 200 μl PCR tubes. On a table top centrifuge we pelleted cells at 0.9 g for 5 minutes (Thermo Fisher Scientific, Walkersville, MD) and resuspended in 25 μl PBS, 0.04% BSA. To estimate the number of cells in the sample, we imaged 1 μl of cell suspension and counted the cells between 5 μm to 25 μm. We pooled 20 ovaries to generate SV-2-10X-Ov, 21 for SV-4-10X-Ov-2 and 41 for SV-6-10X-Ov-3. We ran two batches, with SV-1-10X-Te and SV-2-10X-Ov in one batch and the rest in the other.
We loaded the dissociated cells onto the 10X Chromium system for barcoding and library preparation following the user guide for Single Cell 3’ Reagent Kits v2 (10X Genomics, Pleasanton, CA). We quantified libraries with Quant-iT PicoGreen (Life Technologies, Carlsbad, CA) and confirmed 300-500 bp insert sizes on a TapeStation 2200 (Agilent Technologies Inc, MD).

value: Late third instar larval stage:immobilized, partial gut clearance as dyed yeast paste exist partly in midgut and hindgut, prior to anterior spiracle eversion

value: Chromium Single Cell 3' Library & Gel Bead Kit v2, 16 rxns PN-120237

value: Chromium Single Cell A Chip Kit, 48 rxns PN-120236

value: Chromium i7 Multiplex Kit, 96 rxns PN-120262


title: Third instar larval ovary dissociated with Trypsin and Collagenase rep 2

description:
SV-4-10X-Ov
Drosophila melanogaster (7227)
Female organism (FBbt:00007011)
scRNA-Seq
*R1_001.fastq.gz: FASTQ file containing the 26bp cell barcode.
*R2_001.fastq.gz: FASTQ file containing the 98 bp RNA sequence.
*I1_001.fastq.gz: FASTQ file containing the 8 bp sample index.


title: Third instar larval testes dissociated with Trypsin and Collagenase rep 2

description:
SV-3-10X-Te-2
Drosophila melanogaster (7227)
Male organism (FBbt:00007004)
A pool of 22 testes dissected from late third instar larva. Testes were cleaned of fatbody and dissociated into single cells.
scRNA-Seq
*R1_001.fastq.gz: FASTQ file containing the 26bp cell barcode.
*R2_001.fastq.gz: FASTQ file containing the 98 bp RNA sequence.
*I1_001.fastq.gz: FASTQ file containing the 8 bp sample index.

data_processing:
We called bases using RTA v1.13 (Illumina, San Diego, CA), and demultiplexed and converted BCLs to FASTQs using Cell Ranger mkfastq v2.0.0 (10X Genomics, Pleasanton, CA). We aligned reads to FlyBase r6.16 and generated gene level counts using Cell Ranger count v2.1.1. We forced the number of cells (--force-cells=3000) because our cell population had a large dynamic range of RNA concentration due to the presence of the germline. Each replicate was independently analyzed using Seurat v2.3.1 to generate cell type clusters with their corresponding biomarkers. We also combined replicates 1, 2, and 3 using Seurat’s multiple CCA method and called cell type clusters from the merged data.
Genome_build: Drosophila melanogaster Release 6 plus ISO1 MT (GCA_000001215.4).
Supplementary_files_format_and_content: *.biomarkers.tsv: Differential expression among cell clusters using Seurat v2.3.1.
Supplementary_files_format_and_content: *.barcodes.tsv, *.genes.tsv, *.matrix.mtx: Filtered raw counts output by Cell Ranger count --force-cells=3,000 (v2.1.1).
Supplementary_files_format_and_content: combined.counts.tsv: Merged raw counts table with replicates 1, 2, and 3.

source_name: Dissociated cells from pools of third instar larval testes

growth_protocol: We used w[1118] flies (FBst0005905; Bloomington Drosophila Stock Center, Bloomington, IN) grown on fly food A (LabExpress Ann Arbor, MI) at 25°C under constant light and 60% relative humidity. We dissected larvae from 8-16 hr after egg collection from six mated females. Larvae were provided with yeast paste with 0.5 mg/ml Sulforhodamine B sodium salt (Sigma-Aldrich, St. Louis, MO) and collected when they were immobile with 50% gut clearance, but before eversion of the anterior spiracle.

extract_protocol:
We washed and dissected late third instar larvae in PBS (Gibco Life Technologies, Carlsbad, CA) at 22°C. We removed residual larval fat body cells attached to the testes by treating with 0.1% Trypsin (Thermo Fisher, Walkersville, MD) and 0.075 mg/ml Collagenase (Sigma-Aldrich, St. Louis, MO) in PBS for three minutes in 1.5 ml eppendorf tubes and gentle vortexing by flicking the tube with a forefinger. We rinsed the gonads twice with 5 ml PBS and incubated in 100 μl 0.5% Trypsin (w/v) and 2 mg/ml Collagenase in PBS in watch glass wells for 30 minutes at 22°C. During incubation we gently teased apart the testes with tungsten needles (Fine Scientific Tools, Foster City, CA) under dissecting scope observation and cells were pipetted several times to achieve maximum dissociation. To stop dissociation, we incubated in 1% (w/v) FBS (Gibco Life Technologies, Carlsbad, CA) for two minutes and added 0.04% (w/v) BSA (MP, Santa Ana, CA). We filtered cell suspensions, and washed with 50 μl PBS, 0.04% BSA, through a 35 μm filter (Thermo Fisher, Walkersville, MD) pre-coated with 0.5% BSA solution and transferred filtrate to 200 μl PCR tubes. We pelleted cells at 0.9 g for 5 minutes on a table top centrifuge (Thermo Fisher Scientific, Walkersville, MD) and resuspended in 25 μl PBS, 0.04% BSA. We imaged 1 μl of cell suspension and counted the cells between 5 μm to 25 μm to estimate the number of cells in the sample. We pooled a total of 22 testes for SV-1-10X-Te and SV-3-10X-Te-2, 55 for SV-5-10X-Te-3, and 50 for SV-8-10X-Te-4. We ran three batches, with SV-1-10X-Te in the first batch, SV-3-10X-Te-2 and SV-5-10X-Te-3 in the second batch, and SV-8-10X-Te-4 in the last batch.
We loaded the dissociated cells onto the 10X Chromium system for barcoding and library preparation following the user guide for Single Cell 3’ Reagent Kits v2 (10X Genomics, Pleasanton, CA). We quantified libraries with Quant-iT PicoGreen (Life Technologies, Carlsbad, CA) and confirmed 300-500bp insert sizes on a TapeStation 2200 (Agilent Technologies Inc, MD). Each library was placed in a single lane on an Illumina HiSeq 2500 (Illumina, San Diego, CA).

value: Male


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) ILS mice (rep. A, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
ILS_A

value: ILS/IbgTejJ

value: RNA was collected from whole brain (right hemisphere) using the RNeasy Plus Universal Midi, Mini, and minElute kits for RNA sequencing (Qiagen, Valencia, CA, USA).


title: Third instar larval ovary dissociated with Trypsin and Collagenase rep 1

description:
SV_2_10X_Ov
Drosophila melanogaster (7227)
Female organism (FBbt:00007011)
scRNA-Seq
*R1_001.fastq.gz: FASTQ file containing the 26bp cell barcode.
*R2_001.fastq.gz: FASTQ file containing the 98 bp RNA sequence.
*I1_001.fastq.gz: FASTQ file containing the 8 bp sample index.


title: OxGlu-lim_rep3 MC WT

city: Mölndal

first: David

last: Bergenholm

state: SWEDEN

address: Axgatan 139

country: Sweden

institute: Chalmers tekniska högskola

data_processing:
RNA sequencing reads (R1 & R2 reads) were mapped to reference genome assembly with Bowtie2 using default settings to generate SAM files.
SAM files were treated with SAMtools option –q 20 to remove low-quality reads and then converted to sorted BAM files.
Bedtools Genomcov function was used to generate read counts
Genome_build: R64-2-1 of S. cerevisiae S288C
Supplementary_files_format_and_content: Excel .xlsx file containing Systematic name, common name, three lines of raw reads, three lines of CPM, one line for mean and one for std, this was done for all conditions and all experiments

organism: Saccharomyces cerevisiae

source_name: MC

growth_protocol: Cells were cultivated in four different limited media in chemostat: n-lim, glu-lim, et-lim and oxy.glu-lim

extract_protocol:
Cells cultivated in chemostats were sampled for RNA-seq analysis after steady state was achieved(OD600, dissolved oxygen and off-gas profiles became constant) for 48 to 60 hours. Rapidly withdrawing 10 OD of culture and put into a precooled 50 ml falcon tube, the samples were immediately centrifuged at 4000 rpm for 5 min at −20 °C. The supernatant was discarded, the pellet was frozen in liquid nitrogen and stored at −80 °C until further analysis. The RNA extraction was performed using the RNeasy Mini Kit (QIAGEN).
The sequencing libraries were prepared in three replicates using a TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold, RS122-2303, + Ribo-Zero magnetic Gold Kit from Epicentre

value: CEN.PK 113-5D

tag: carbon source

value: 1% (w/v) glucose


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS80 mice (rep. C, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS80_C


title: Third instar larval testes dissociated with Trypsin and Collagenase rep 1

description:
SV-1-10X-Te
Drosophila melanogaster (7227)
Male organism (FBbt:00007004)
A pool of 22 testes dissected from late third instar larva. Testes were cleaned of fatbody and dissociated into single cells.
scRNA-Seq
*R1_001.fastq.gz: FASTQ file containing the 26bp cell barcode.
*R2_001.fastq.gz: FASTQ file containing the 98 bp RNA sequence.
*I1_001.fastq.gz: FASTQ file containing the 8 bp sample index.


title: Third instar larval testes dissociated with Trypsin and Collagenase rep 4

description:
SV-8-10X-Te-4
Drosophila melanogaster (7227)
Male organism (FBbt:00007004)
A pool of 50 testes dissected from late third instar larva. Testes were cleaned of fatbody and dissociated into single cells.
scRNA-Seq
*R1_001.fastq.gz: FASTQ file containing the 26bp cell barcode.
*R2_001.fastq.gz: FASTQ file containing the 98 bp RNA sequence.
*I1_001.fastq.gz: FASTQ file containing the 8 bp sample index.


title: Third instar larval testes dissociated with Trypsin and Collagenase rep 3

description:
SV-5-10X-Te-3
Drosophila melanogaster (7227)
Male organism (FBbt:00007004)
A pool of 55 testes dissected from late third instar larva. Testes were cleaned of fatbody and dissociated into single cells.
scRNA-Seq
*R1_001.fastq.gz: FASTQ file containing the 26bp cell barcode.
*R2_001.fastq.gz: FASTQ file containing the 98 bp RNA sequence.
*I1_001.fastq.gz: FASTQ file containing the 8 bp sample index.


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) ISS mice (rep. B1, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
ISS_HIGH_B_Ctl3_1

value: ISS/IbgTejJ


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS41 mice (rep. A, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS41_LOW_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS112 mice (rep. C, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS112_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) ILS mice (rep. C, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
ILS_C


title: Glu-lim_rep3 MC WT

value: 0.75% (w/v) glucose


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS41 mice (rep. C, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS41_LOW_C_Ctl4_1


title: OxGlu-lim_rep1 MC WT


title: Glu-lim_rep2 MC WT


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS80 mice (rep. B, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS80_MED_B_Ctl2_1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS72 mice (rep. A, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS72_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS72 mice (rep. C, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS72_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS72 mice (rep. B, sequencing batch 1)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS72_B


title: Et-lim_rep3 MC WT

value: 0.5% (w/v) ethanol


title: OxGlu-lim_rep2 MC WT


title: Et-lim_rep1 MC WT


title: Et-lim_rep2 MC WT


title: N-lim_rep3 MC WT

value: 6% (w/v) glucose


title: Glu-lim_rep1 MC WT


title: dmem.3

city: Philadelphia

first: david

last: smith

state: Pennsylvania

address: 3501 Civic Center Blvd

institute: CHOP

data_processing:
raw read quality was assessed using FASTQC and filtered using TRIMMOMATIC
processed reads were aligned to the UCSC mm10 genome using TopHat2
Alignments were compressed using SAMtools, and the reads were counted with HTSeq
Read counts were normalized and differential expression was estimated with DESeq
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited counts

source_name: LPS-stimulated murine peritoneal macrophages

growth_protocol: BALB/c male mice, 6-8 weeks old, were injected with 1ml of thioglycollate medium into the peritoneum. After 4 days, the peritoneum was lavaged and cells were plated.

extract_protocol:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834554/
Total macrophage RNA was extracted using TRIreagent (Cat. No. T9424, Sigma-Aldrich). RNA content was precipitated and depleted of rRNA using NEBNext rRNA Depletion Kit (Cat. No. E6310, New England BioLabs). cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (Cat. No. 7240, New England BioLabs).

treatment_protocol: Adherent cells were washed, and media was replaced with either media or media supplemented with 200 µM 10(Z)-hexadecenoic acid.

value: BALB/c

value: male

value: primary murine peritoneal macrophages

tag: treatment

value: vehicle (media)


title: 10h.2

value: media supplemented with 200 µM 10(Z)-hexadecenoic acid


title: 10h.3


title: dmem.1


title: 10h.1


title: N-lim_rep1 MC WT


title: PGF3-15,Type 3

city: Boston

first: Grace

last: Daher

address: 1 Joslin Place

institute: Joslin Diabetes Center

hyb_protocol: Chips were hybridized overnight for 16 hours at 40 C

scan_protocol: Chips were scanned using the GeneChip scanner from Affymetrix.

data_processing: Data were normalized using MAS 5.0

source_name: white adipose tissue_Type 3

label_protocol: cRNA were biotin labeled, from 250 ng starting total RNA

growth_protocol: Immortomouse™ clonal preadipocyte cell lines were created from the stromovascular fraction (SVF) of the subcutaneous and perigonadal fat of a single 8 week-old male mouse. The SVF cells were isolated by collagenase digestion of subcutaneous and perigonadal fat, plated and grown at 33°C in preadipocyte growth media (Macotela et al., 2012) supplemented with 10 units/mL interferon-gamma (Peprotech). After 2 passages, 190 individual cells were sorted without gating using an Aria flow cytometer (BD Biosciences), and one cell was placed in each well. Cells were grown at 33°C with 10 units/mL Interferon γ into clonal cell lines. Adipogenic capacity of cell lines was assessed by lipid accumulation by Oil Red O staining after the induction of differentiation.

extract_protocol: Total RNA was isolated using an RNeasy minikit (Qiagen)

tag: cell line

tag: tissue source

tag: adipocyte type

value: Type 3

tag: differentiation score  (1-4)

tag: media acidification (1-4)


title: OxGlu-lim_rep3 MC Hap1-tagged

tag: strain

value: HAP1-TAP constructed from CEN.PK 113-5D by adding a C-terminal CBP-ProtA tag to Hap1p


title: PGF3-11,Type 1

source_name: white adipose tissue_Type 1

treatment_protocol: Adipogenic capacity of cell lines was assessed by lipid accumulation by Oil Red O staining after the induction of differentiation.

value: Immortomouse™ clonal preadipocyte cell line

value: stromovascular fraction (SVF) of the subcutaneous and perigonadal fat

value: Type 1


title: dmem.2


title: PGF3-6,Other

source_name: white adipose tissue_Other

value: Other


title: N-lim_rep2 MC WT

value: CEN.PK 113-5D


title: OxGlu-lim_rep1 MC Hap1-tagged

value: 1% (w/v) glucose


title: PGF3-3,Type 3


title: Glu-lim_rep3 MC Hap1-tagged


title: PGF3-4,Type 1


title: PGF2-5,Type 3


title: PGF2-8,Type 1


title: Glu-lim_rep2 MC Hap1-tagged


title: Glu-lim_rep1 MC Hap1-tagged


title: SCF3-16,Other


title: PGF3-5,Other


title: PGF2-2,Type 3


title: BLK6_noDVT (Sham)

city: Ann Arbor

first: Anuli

middle: Caroline

last: Anyanwu

state: MI

address: 2344 Cardiovascular Center SPC 5853 ; 1500 E. Medical Center Drive

department: Cardiology and Internal Medicine

institute: University of Michigan Medical School

description: Gene expression data from C57BLK6 WT mouse no IVC ligation

hyb_protocol: Following fragmentation, 3.7 ug of cDNA were hybridized for 20 hr at 48C on Mouse Gene ST 1.1 strip arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267).

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system

data_processing: Data was analyzed using the oligo Bioconductor package implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: Wildtype C57BLK6 control no Inferior Vena Cava Ligation

label_protocol: cDNA were prepared according to the NuGen WT-Pico V2 kit protocol from 50 ng total RNA (Ovation PicoSL WTA System V2 P/N 3312). Biotinylated single-stranded cDNA were prepared from 3ug of cDNA (Encore Biotin Module P/N 4200-12, 4200-60, 4200-A01)

growth_protocol: All mice, WT and Cd39-/- were back bred at least 8 generations into the C57BL/6J background. For all experiments, WT and Cd39-/- mice were aged-matched, males or females (8 to 10 weeks). Venous stasis thrombosis was induced by complete or partial ligation of the infra-renal IVC and an operator blinded to animal genotype.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Briefly, mice were anesthetized and underwent midline laparotomy, the intestines were exteriorized and the IVC completely or partially ligated immediately below the renal veins. Side branches were ligated and back branches were cauterized to ensure complete stasis. The abdominal cavity was closed in a bilayer manner using 5-0 Vicryl sutures (Ethicon) for abdominal muscles, and surgical glue (Vetbond, 3M) for the skin. Sham-operated experiments consisted of median laparotomy and vena cava dissection without ligation of the IVC. At specified time-points, the thrombus-containing IVC was carefully removed, and weighed en toto. Following thrombus induction, the thrombosed IVC was either 1) weighed; 2) fixed in 10% formalin; or 3) thrombus and IVC were carefully separated, weighed, snap frozen, and stored at -80oC until used for biochemical analysis.

tag: background strain

tag: genotype

value: Wildtype

tag: stress

value: noDVT

value: Inferior vena cava


title: PGF3-2,Type 2

source_name: white adipose tissue_Type 2

value: Type 2


title: CD39-/-_DVT (48hrs)

description: Gene expression data from CD39 knockout mouse 48hrs post IVC ligation

source_name: CD39 knockout experimental Inferior Vena Cava Ligation for 48hrs

value: CD39 knockout

value: DVT

tag: tissue


title: CD39-/-_noDVT (Sham)

description: Gene expression data from CD39 knockout mouse no IVC ligation

source_name: CD39 knockout control no Inferior Vena Cava Ligation


title: PGF2-4,Other


title: SCF3-11,Type 2


title: BLK6_DVT (48hrs)

description: Gene expression data from C57BLK6 WT mouse 48hrs post IVC ligation

source_name: Wildtype C57BLK6 experimental Inferior Vena Cava Ligation for 48hrs


title: Et-lim_rep1 MC Hap1-tagged

value: 0.5% (w/v) ethanol


title: SCF3-8,Type 2


title: SCF3-1,Type 2


title: SCF3-6,Other


title: N-lim_rep3 MC Hap1-tagged

value: 6% (w/v) glucose


title: Et-lim_rep2 MC Hap1-tagged


title: N-lim_rep2 MC Hap1-tagged


title: OxGlu-lim_rep2 MC Hap1-tagged


title: SCF1-18,Other


title: siHBO1_SKOV-3_REP3

city: Houston

first: Paul

last: Webb

address: 6670 Bertner Ave

department: Genomic Medicine

institute: Houston Methodist Research Institute

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Unmodified microarray data obtained from GenomeStudio (Illumina) was background-substracted and quantile-normalized using the lumi package within R

source_name: SKOV-3 cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: SKOV-3 cell line was purchased from ATCC and maintained in rpmi-1640 (ATCC)

extract_protocol: Total RNA was extracted and prepared using Rneasy (Qiagen) in accordance with the protocol provided with the kit

treatment_protocol: Cells were plated in 12-well plates and transfected with HBO1 or scramble siRNA. Total RNA was collected after two days (48h)

tag: transfection


title: siHBO1_SKOV-3_REP1

description: replicate 1


title: siCTRL_UWB1.289_REP3

description: replicate 3

source_name: UWB1.289 cell line

growth_protocol: UWB1.289 cell line was purchased from ATCC and maintained in DMEM/F-12 + GlutaMAX (Gibco)

value: scramble


title: siHBO1_UWB1.289_REP2

description: replicate 2


title: siCTRL_UWB1.289_REP2

description: replicate 2


title: SCF3-9,Type 3

value: Type 3


title: N-lim_rep1 MC Hap1-tagged

value: HAP1-TAP constructed from CEN.PK 113-5D by adding a C-terminal CBP-ProtA tag to Hap1p


title: SCF1-23,Type 2

value: Immortomouse™ clonal preadipocyte cell line


title: siCTRL_SKOV-3_REP3

description: replicate 3


title: siHBO1_UWB1.289_REP3

description: replicate 3


title: OxGlu-lim_rep3 DASGIP Hap1-tagged

source_name: DASGIP 1 L


title: siCTRL_UWB1.289_REP1

description: replicate 1


title: siHBO1_SKOV-3_REP2

description: replicate 2


title: siCTRL_SKOV-3_REP1

description: replicate 1


title: SCF1-12,Type 3

value: stromovascular fraction (SVF) of the subcutaneous and perigonadal fat


title: SCF1-15,Type 3


title: siHBO1_UWB1.289_REP1

description: replicate 1


title: OxGlu-lim_rep2 DASGIP Hap1-tagged


title: SCF1-13,Type 3


title: OxGlu-lim_rep1 DASGIP Hap1-tagged


title: Et-lim_rep3 MC Hap1-tagged


title: Glu-lim_rep3 DASGIP Hap1-tagged

value: 0.75% (w/v) glucose


title: Glu-lim_rep2 DASGIP Hap1-tagged


title: SCF1-7,Other

value: Other


title: siHBO1 OVCAR-3_REP2

description: replicate 2

source_name: OVCAR-3 cell line

growth_protocol: OVCAR-3 cell line was purchased from ATCC and maintained in RPMI-1640 (ATCC)


title: siCTRL OVCAR-3_REP2

description: replicate 2


title: siHBO1 OVCAR-3_REP3

description: replicate 3


title: siHBO1 OVCAR-3_REP1

description: replicate 1


title: siHBO1 OVCAR-3_REP4

description: replicate 4


title: siCTRL OVCAR-3_REP4

description: replicate 4


title: siCTRL OVCAR-3_REP3

description: replicate 3


title: Glu-lim_rep1 DASGIP Hap1-tagged


title: Et-lim_rep3 DASGIP Hap1-tagged


title: siCTRL_SKOV-3_REP2

description: replicate 2


title: Et-lim_rep2 DASGIP Hap1-tagged


title: Uninfected rice plants, bio rep 2

city: Hyderabad

first: Ramesh

middle: V.

last: Sonti

state: Andhra Pradesh

address: Uppal Road

department: Plant Microbe Interactions

institute: Centre for cellular and molecular biology (CCMB)

description: Expression profile of uninfected rice plants, 24 and 72 hrs post infection.

hyb_protocol: The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rice Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450

scan_protocol: The gene chips were scanned on an Affymetrix Scanner 3000

data_processing: The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to GeneSpring 13.1 - GX - PA  (Agilent Technology) for further analysis. The PLIER 16 algorithm was used for data normalization

label: Biotin

organism: Oryza sativa

source_name: 25 days old rice seedlings

label_protocol: 250ng of total RNA from pooled sample was converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)

growth_protocol: Rice plants were grown in platic trays under green house conditions.

extract_protocol: 2 cm rice tissue was collected from the leaves below the point of Xoo inocluation and where the fungal spores were sprayed, 10-15 such leaf pieces for each biological replicate were collected and processed for RNA isolation using TRIZOL (Invitrogen). The tissue was collected and RNA was extracted at two time points 24 and 72 hrs post infection, RNA was then pooled from these two time points.

treatment_protocol: For bacterial blight infection, the rice leaves were clip inoculated with Xanthomonas oryzae pv. oryzae isolate (DX-020), by dipping the scissors in saturated culture of Xoo and cutting the leaf tips so that the cells are deposited at the site of incision. For blast infection, the fungal spore suspension of Magnaporthe oryzae isolate (SP-28) was sprayed in conditions of hight humidity to facilitate heavy infection.

value: Rice line carrying bacterial blight and blast resistance gene Xa21, xa13 and Pi54 respectively

tag: age

value: 25 days old rice seedlings

tag: infection

value: uninfected


title: N-lim_rep3 DASGIP Hap1-tagged


title: Magnaporthe oryzae and Xantomonas oryzae pv. oryzae infected rice plants, bio rep 1

description: Expression profile of infected rice plants, 24 and 72 hrs post infection.


title: illium lysoforte 1000 48-1476I

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

description: Gene expression data from illium lysoforte 1000 48-1476I

hyb_protocol: Mucosal cells, scraped from the jejunum and ileum segments, were homogenized with TriReagent and RNA was purified with Directzol RNA mini prep columns (Zymo Research Co., Irvine CA).  RNA was quantified with a Nanodrop ND 1000 spectrophotometer (Thermo Scientific, Wilmington, DE) and samples were shipped frozen to the University of Virginia for RNA quality and DNA microarray analyses in the Biomolecular Analysis Core facility. RNA quality was assessed with an Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA) and only samples with a RIN greater than 8.7 were used for microarray analysis.  Some tissue samples had to be re-extracted to recover RNA with a RIN > 8.7. Microarray analysis using the chicken genome 1.0 array (Affymetrix, Santa Clara, CA) was performed on the d10 samples (total of 50 samples: 5 treatments, 2 segments, 5 replicates).

data_processing: Data extraction, QC, and RMA normalization were performed with BioConductor software. Probes were annotated using the Bioconductor GeoQuery package. Differential expression was assessed with moderated ANOVA, using the BioConductor limma package; false discovery rate (FDR) estimates were calculated using the Benjamini-Hochberg method.

organism: Gallus gallus

source_name: chicken illium

growth_protocol: Day of hatch Cobb 500 male broilers were obtained from the Cobb hatchery in Wadesboro, NC and transported to the Virginia Tech Poultry Research Center.  125 chicks were weighed, wing-banded and placed in a room with adjoining floor pens (25/pen), separated by wire fencing. Broilers were individually weighed weekly (d7, d14, d21, and d28) to assess growth rates and not to generate statistically significant production data.

treatment_protocol: There were 5 experimental groups. Control group (T1) was provided feed without supplement and was compared to four treatment groups provided feed with either purified LPC, isolated from lysolecithin by column chromatography, (T2, T3) or lysolecithin (T4, T5), each at two different application levels.  T2 (LPC-low) contained 9.5 g/T of LPC supplemented as 500 g/T of purified LPC plus carrier.  T3 (LPC-high) contained 19 g/T of LPC supplemented as 1,000 g/T of purified LPC plus carrier. T4 (lysolecithin-low) contained 9.5 g/T of LPC supplemented as 250 g/T of lysolecithin. T5 (lysolecithin-high) contained 19 g/T of LPC supplemented as 500 g/T of lysolecithin. Lysoforte (as 50% w/w lysolecithin on carrier) and purified LPC were provided by Kemin Industries Inc., Des Moines, Iowa, USA. Pure LPC was applied to a carrier prior to mixing with feed to ensure homogeneous distribution within the feed.

value: illium

value: lysoforte 1000

tag: batch


title: Magnaporthe oryzae and Xantomonas oryzae pv. oryzae infected rice plants, bio rep 3


title: Magnaporthe oryzae and Xantomonas oryzae pv. oryzae infected rice plants, bio rep 2


title: Uninfected rice plants, bio rep 3


title: illium lysoforte 1000 47-1441I

description: Gene expression data from illium lysoforte 1000 47-1441I

scan_protocol: Mucosal cells, scraped from the jejunum and ileum segments, were homogenized with TriReagent and RNA was purified with Directzol RNA mini prep columns (Zymo Research Co., Irvine CA).  RNA was quantified with a Nanodrop ND 1000 spectrophotometer (Thermo Scientific, Wilmington, DE) and samples were shipped frozen to the University of Virginia for RNA quality and DNA microarray analyses in the Biomolecular Analysis Core facility. RNA quality was assessed with an Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA) and only samples with a RIN greater than 8.7 were used for microarray analysis.  Some tissue samples had to be re-extracted to recover RNA with a RIN > 8.7. Microarray analysis using the chicken genome 1.0 array (Affymetrix, Santa Clara, CA) was performed on the d10 samples (total of 50 samples: 5 treatments, 2 segments, 5 replicates).


title: jejunum lysoforte 1000 49-1441J

description: Gene expression data from jejunum lysoforte 1000 49-1441J

source_name: chicken jejunum

label_protocol: Mucosal cells, scraped from the jejunum and ileum segments, were homogenized with TriReagent and RNA was purified with Directzol RNA mini prep columns (Zymo Research Co., Irvine CA).  RNA was quantified with a Nanodrop ND 1000 spectrophotometer (Thermo Scientific, Wilmington, DE) and samples were shipped frozen to the University of Virginia for RNA quality and DNA microarray analyses in the Biomolecular Analysis Core facility. RNA quality was assessed with an Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA) and only samples with a RIN greater than 8.7 were used for microarray analysis.  Some tissue samples had to be re-extracted to recover RNA with a RIN > 8.7. Microarray analysis using the chicken genome 1.0 array (Affymetrix, Santa Clara, CA) was performed on the d10 samples (total of 50 samples: 5 treatments, 2 segments, 5 replicates).

value: jejunum


title: Uninfected rice plants, biological replicate 3

data_processing: The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to GeneSpring 13.1 - GX - PA  (Agilent Technology) for further analysis. The PLIER 16 was used for data normalization

source_name: 25 days old  rice seedlings

label_protocol: 250ng of total RNA from the pooled sample was converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)

extract_protocol: 2 cms rice tissue was collected from the leaves below the point of Xoo inocluation, 10-15 such leaf pieces were collected from each biological replicate and processed for RNA isolation using TRIZOL (Invitrogen). Similarly 2 cms rice tissue from the apical meristem where the larvae reside were collected and processed for RNA isolation using TRIZOL (Invitrogen). The tissue was collected from two time points 24 and 72 hrs post infection. The RNA from the two tissue samples and from the two time points were pooled for the experiment.

treatment_protocol: Gall midge biotype 1 (GMB1) is maintained on rice var. TN1 under greenhouse conditions. Test plants along with suitable controls were raised in trays and 21 day old plants were exposed to freshly emerged flies (30 females and 10 males) obtained from nucleus culture under mesh cage for 48h for oviposition.  Infested plants in the trays were later transferred to high humidity chamber and left for two days for the eggs to hatch.  On 5 th day after release of adults, plants were examined for the presence of maggots at apical meristem which was considered as ‘ 0 day’ of larval infestation. At '0 day' larval infestation the rice leaves were challenged with Xoo. For bacterial blight infection, the rice leaves were clip inoculated with Xanthomonas oryzae pv. oryzae isolate (DX-020), by dipping the scissors in saturated culture of Xoo and cutting the leaf tips so that the cells are deposited at the site of incision.

value: Rice line carrying bacterial blight and gall midge resistance gene Xa21, xa13, xa5 and Gm1, Gm4 Gm8, gm3 respectively.


title: jejunum lysoforte 500 46-1480J

description: Gene expression data from jejunum lysoforte 500 46-1480J

extract_protocol: Mucosal cells, scraped from the jejunum and ileum segments, were homogenized with TriReagent and RNA was purified with Directzol RNA mini prep columns (Zymo Research Co., Irvine CA).  RNA was quantified with a Nanodrop ND 1000 spectrophotometer (Thermo Scientific, Wilmington, DE) and samples were shipped frozen to the University of Virginia for RNA quality and DNA microarray analyses in the Biomolecular Analysis Core facility. RNA quality was assessed with an Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA) and only samples with a RIN greater than 8.7 were used for microarray analysis.  Some tissue samples had to be re-extracted to recover RNA with a RIN > 8.7. Microarray analysis using the chicken genome 1.0 array (Affymetrix, Santa Clara, CA) was performed on the d10 samples (total of 50 samples: 5 treatments, 2 segments, 5 replicates).

value: lysoforte 500


title: jejunum lysoforte 1000 50-1476J

description: Gene expression data from jejunum lysoforte 1000 50-1476J


title: illium lysoforte 500 45-1480I

description: Gene expression data from illium lysoforte 500 45-1480I


title: Orseola oryzae and Xanthomonas oryzae pv. oryzae infected rice plants, biological replicate 1

value: co-infection with insect Orseola oryza and pathogen Xanthomonas oryzae pv. oryzae


title: Orseola oryzae and Xanthomonas oryzae pv. oryzae infected rice plants, biological replicate 2


title: Et-lim_rep1 DASGIP Hap1-tagged

value: 0.5% (w/v) ethanol


title: jejunum lpc 1000 44-1496J

description: Gene expression data from jejunum lpc 1000 44-1496J


title: Orseola oryzae and Xanthomonas oryzae pv. oryzae infected rice plants, biological replicate 3


title: N-lim_rep2 DASGIP Hap1-tagged

value: 6% (w/v) glucose


title: N-lim_rep1 DASGIP Hap1-tagged


title: Saccharomyces cerevisiae-AR Biological Repeat-2

city: Stellenbosch

first: Kirti

last: Shekhawat

address: Alexander Street

country: South Africa

institute: IWBT

description:
S._cerevisiae_with_MIX_FPKM.txt
Sc-AR-2_S8

data_processing:
NS2500 next generation sequencing platform
The reads were aligned to the reference genomes with Tophat v2.0.13. The obtained bam files were further converted in to gff files to analyse the data further. The number of reads in the alignments that overlap with gene features were counted with feature Counts 1.4.6. The following parameters were chosen: -Q 0 –s 0 –t exon –g gene_id.
Gene expression levels were normalized using fragments per kilobase of exon per million mapped reads (FPKM). A negative binomial generalized linear model (GLM) was fitted against the normalized counts using the EdgeR 3.4.0 package of Bioconductor. The differential expression was tested with a GLM likelihood ratio test, also implemented in the EdgeR package. The resulting p-values were corrected for multiple testing with Benjamini-Hochberg to control the false discovery rate (FDR)
Genome_build: S. cerevisia S288C for S. cerevisiae reference genome and Lachancea thermotolerans cbs 6340 for Lachancea thermotolerans
Supplementary_files_format_and_content: Text files include FPKM values of L. thermotolerans and S. cerevisiae single fermentations with their mixed fermentations

source_name: Saccharomyces cerevisiae Yeast Cells

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

value: S. cerevisiae Cross evolution-285

value: Wine Yeast

value: Aerobic

tag: cell type

value: Yeast cells


title: Saccharomyces cerevisiae-AN Biological Repeat-1

description:
S._cerevisiae_with_MIX_FPKM.txt
Sc-R1-AN_S3

value: Anaerobic


title: Mutant 1

city: Calgary

first: Carol

last: Huang

state: Alberta

address: 3330 Hospital Drive NW

institute: University of Calgary

hyb_protocol: After 2nd strand cycle reaction, total 5.5ug ssDNA were biotin-labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Gene 1.0ST Array at 45°C for 16h.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G System.

data_processing:
affymetrix-algorithm-name = rma-gene-default (v.1.0)
program-name = Expression Console (v.1.2.0.20)
Array data files were generated with GeneChip® Command Console® Software (AGCC) and statistical significant analysis was carried out on software of GeneSpring (Agilent Technologies).  The Fold Change between treatment and control was based on the p<0.05 from unpaired T-test.

source_name: Mouse Islet from PrlR+/- heterozygous

label_protocol: Total RNA of 250 ng of each sample with RIN higher than 8.5 was labelled with Whole Transcript Sense kit (Ambion)

growth_protocol: Female wild type prolactin receptor null mice were set up for timed mating at age 12-16 weeks. On day 15 of pregnancy, mice were euthanized by cervical dislocation and islets were harvested from the mice.

extract_protocol: RNA was extracted using mirVana miRNA Isolation Kit (Ambion, Austin, USA) according to the manufacturer’s protocol.  Total RNA was purified with RNeasy Plus Micro Kit (Qiagen, Valencia, USA) to remove genomic DNA.

treatment_protocol: Female heterozygous prolactin receptor null mice were set up for timed mating at age 12-16 weeks. On day 15 of pregnancy, mice were euthanized by cervical dislocation and islets were harvested from the mice.

tag: strain background

tag: genotype/variation

tag: Sex

value: female

tag: tissue/cell type

value: Islet


title: Mutant 4

value: heterozygous prolactin receptor null mice


title: illium lpc 1000 42-1496I

description: Gene expression data from illium lpc 1000 42-1496I

tag: treatment


title: Control 2

source_name: Mouse Islet from PrlR+/+ wild type

value: wild type prolactin receptor null mice


title: Control 1


title: Uninfected rice plants, bio rep 1

value: Rice line carrying bacterial blight and blast resistance gene Xa21, xa13 and Pi54 respectively

value: 25 days old rice seedlings

value: uninfected


title: Uninfected rice plants, biological replicate 2

value: Rice line carrying bacterial blight and gall midge resistance gene Xa21, xa13, xa5 and Gm1, Gm4 Gm8, gm3 respectively.


title: Control 3


title: 3D_H_R2

city: Blacksburg

first: Chang

last: Lu

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

description: Mnase digested chromatin

library_source: genomic

data_processing:
AQUAS pipiline with parameter specified as: --type histone --species hg19 --final-stage idr --se
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file is compressed binary indexed files, and is useful for dense, continuous data that will be displayed in the Genome Browser as a graph.

molecule: genomic DNA

growth_protocol: U251 human glioblastoma cells (Sigma-Aldrich, St. Louis, MO) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% fetal bovine serum (FBS) (Life Technologies, Grand Island, NY), 1% penicillin/streptomycin. (Lonza), and 0.1% non-essential amino acids (VWR, Radnor, PA). The cells were maintained in a 37˚C humidified incubator with 5% CO2.

extract_protocol:
The day after U251s were seeded in the collagen hydrogels, media was refreshed and well plates or flasks were placed in an incubator at normoxic (21% O2) or hypoxic (1% O2) conditions. Samples were incubated for 72 hours. Cells in flasks were trypsinized, rinsed once in ice cold PBS, then re-suspended in ice cold PBS at 1,000 cell/μl. Cells seeded in collagen hydrogels were obtained by digesting the collagen in a solution of 0.5% collagenase (Thermo Fisher, Waltham, MA) and 1% FBS in Hanks Buffered Salt Solution (HBSS)( Lonza). Collagen scaffolds were submerged in collagenase solution and incubated at 37˚C and 5% CO2 for 2 hours. Digested collagen solution was collected, rinsed once in ice cold PBS, and re-suspended in ice cold PBS at 1,000 cell/μl. 1 μl of phenylmethyldulfonyl fluoride (PMSF) (Sigma-Aldrich, St. Louis, MO) and 1 μl of protease inhibitor cocktail (1X concentration) (Sigma-Aldrich, St. Louis, MO) were added to a 100 μl aliquot of cell suspension for each culture condition.
All ChIP-seq libraries were constructed using Accel-NGS 2S plus DNA library kit (Swift Bioscience) following the manufacturer’s instructions.

treatment_protocol: Cellularized collagen scaffolds were formed in (poly)-dimethylsiloxane (PDMS) wells (Sylgard® 184 Silicone Elastomer Kit, Dow Corning, Midland, MI) of 10 mm diameter and 1 mm thickness.  The PDMS wells were surface treated with 1% poly (ethylenimine) (PEI) for 10 minutes and 0.1 % glutaraldehyde for 20 minutes (Fisher Scientific, Pittsburg, PA) to crosslink the collagen to the PDMS. Excess glutaraldehyde was rinsed off of the wells with DI water. Hydrogels with a final concentration of 5 mg/ml collagen were created from the 10 mg/ml stock solution. U251s were seeded within the collagen hydrogels at a density of 1 million cells/ml.  The hydrogels were prepared by transferring the desired volume of collagen stock (50% of the final hydrogel volume) into a centrifuge tube kept on ice. Ice cold 10X DMEM (10% of final solution) and 1N NaOH (2% of final solution) were added to and mixed thoroughly with the collagen stock. In a separate centrifuge tube, U251s were added to 1X DMEM (volume needed to complete the remaining 50% of the final hydrogel volume). The U251 cell suspension was then added to the uncrosslinked collagen solution and slowly mixed on ice until cells were homogenously dispersed in the collagen solution. 10X DMEM and 1X DMEM were purchased from Sigma-Aldrich (St. Louis, MO) and NaOH was purchased from Fisher Scientific (Pittsburg, PA).  Using a syringe, the neutralized collagen solution was transferred to the PDMS wells and allowed to polymerize at 37˚C at 5% CO2 for 30 minutes. After collagen is crosslinked, sufficient media was added to the wells to completely submerge collagen scaffolds.

tag: cell line

tag: chip antibody

value: H3K4me3(Abcam ab8580)

tag: model

tag: condition

value: hypoxia


title: Mutant 3


title: Uninfected rice plants, biological replicate 1

tag: genotype


title: illium lpc 1000 41-1424I

description: Gene expression data from illium lpc 1000 41-1424I

value: illium


title: Mutant 2


title: jejunum lpc 1000 43-1424J

description: Gene expression data from jejunum lpc 1000 43-1424J

value: jejunum


title: WT-AI

city: Shang Hai

first: Daiming

last: Xiang

address: 225 Changhai Road, 200438 Shanghai, China

institute: Eastern Hepatobiliary Surgery Hospital/Institute, the Second Military Medical University

description: Gene expression data from DEN-induced hepatocellular carcinoma mice (wild-type)

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45°C on GeneChip® Gene mouse 1.0 ST Array. GeneChips were washed and stained in the GeneChip2 Fluidics Station 450 .

scan_protocol: GeneChips were scanned using the GeneChip2 Scanner 3000 7G

data_processing: Samples were corrected and normalized using standard  robustmulti-array analysis (RMA) procedure implemented in the Affymetrix Expression Console software.

source_name: carcinoma tissue from DEN-induced HCC mice (wild-type)

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol (GeneChip® WT Terminal Labeling Kit) from 0.5 ug total RNA

growth_protocol: HLF-deficient mice and WT mice were was induced with DEN

treatment_protocol: HCC tissue samples were collected from HLF-deficient mice and WT mice

value: WT

tag: agent

value: DEN

value: carcinoma tissue


title: jejunum lpc 500 39-1462J

description: Gene expression data from jejunum lpc 500 39-1462J

tag: tissue

value: lpc 500


title: jejunum lpc 500 40-1509J

description: Gene expression data from jejunum lpc 500 40-1509J


title: illium lpc 500 38-1509I

description: Gene expression data from illium lpc 500 38-1509I


title: XP-B/CS+XPB/GFP cell replicate 3-RNAseq

city: Illkirch

first: Frederic

last: Coin

address: 1, rue laurent fries

department: Functional Genomics and Cancer

country: France

institute: IGBMC

data_processing: Reads were mapped onto the hg19 assembly of the human genome. Read counting was performed with HOMER v4.8.3(65) and expression was estimated with EdgeR. Genome ontology was performed with The Database for Annotation and Integrated Discovery (DAVID) v6.7 (https://david.ncifcrf.gov).

source_name: Fibroblasts from XP-B/CS patients

extract_protocol:
GenElute Mammalian Total RNA Miniprep Kit (Sigma)
TruSeq Stranded mRNA Sample Preparation Kit following guide instructions and subsequently analyzed on an Illumina Hiseq 4000 as single-end 50 base reads following Illumina’s instructions

tag: mutation

value: ERCC3 c.296T>C mutant, pPhe99Ser (RefSeq accession number NM_000122.1)

value: wild-type XPB tagged with GFP


title: Villi, mutant, rep 1

city: Munich

first: Vladimir

last: Chubanov

state: Non-US/Canada

address: Goethestraße 33

department: Walther-Straub-Institut

country: Germany

institute: Ludwig-Maximilians-Universität München

hyb_protocol: 2.5 µg of fragmented and labeled ssDNA samples were hybridized for 16-18h hr at 45°C on GeneChip Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with DNASTAR ArrayStrar 11.0 software

source_name: Intestine

label_protocol: Biotinylated single-stranded DNA samples were prepared according to the standard Affymetrix protocol (Whole Transcript Expression arrays) from 100 ng total RNA using the WT terminal labeling kit

growth_protocol: Intestines from 5 days old Trpm7 deficient and control littermates were collected in RNAlater reagent (QIAGEN)

extract_protocol: Total RNA was extracted using the GenElute mammalian total RNA purification kit (Sigma-Aldrich).

treatment_protocol: Villi were mechanically disassociated and collected by centrifugation

tag: genetic background

value: Mutant

tag: age

value: 5 days

tag: gender

value: unknown


title: Villi, control, rep 2

value: Control


title: Villi, mutant, rep 2


title: KO-AI

description: Gene expression data from DEN-induced hepatocellular carcinoma mice (HLF-deficient)

source_name: carcinoma tissue from DEN-induced HCC mice (HLF-deficient)

value: HLF-deficient


title: Villi, mutant, rep 3


title: Villi, control, rep 3


title: XP-B/CS+XPB/GFP cell replicate 2-RNAseq


title: 3D_H_input

description: Mnase digested chromatin


title: 3D_H_R1

description: Mnase digested chromatin


title: Villi, control, rep 1


title: XP-B/CS cell replicate 3-RNAseq


title: XP-B/CS cell replicate 2-RNAseq


title: 3D_N_input

description: Mnase digested chromatin

value: normoxia


title: 3D_N_R2

description: Mnase digested chromatin


title: XP-B/CS cell replicate 1-RNAseq


title: 3D_N_R1

description: Mnase digested chromatin


title: 2D_N_input

description: Mnase digested chromatin


title: 2D_N_R2

description: Mnase digested chromatin


title: illium lpc 500 37-1462I

description: Gene expression data from illium lpc 500 37-1462I

tag: batch


title: jejunum control 36-1477J

description: Gene expression data from jejunum control 36-1477J

value: control


title: jejunum lysoforte 1000 34-1471J

description: Gene expression data from jejunum lysoforte 1000 34-1471J

value: lysoforte 1000


title: illium control 35-1477I

description: Gene expression data from illium control 35-1477I


title: 2D_N_R1

description: Mnase digested chromatin

value: H3K4me3(Abcam ab8580)


title: jejunum lysoforte 1000 33-1431J

description: Gene expression data from jejunum lysoforte 1000 33-1431J


title: siCTRL OVCAR-3_REP1

description: replicate 1

value: scramble


title: 2D_H_input

description: Mnase digested chromatin

value: hypoxia


title: 2D_H_R2

description: Mnase digested chromatin


title: jejunum lysoforte 500 30-1415J

description: Gene expression data from jejunum lysoforte 500 30-1415J

value: jejunum

value: lysoforte 500


title: 2D_H_R1

description: Mnase digested chromatin


title: Day3_Replicate2

city: Seattle

first: Elaine

middle: M.

last: Faustman

state: WA

address: 4225 Roosevelt Way NE, #100

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: gene expression in differentiating human neural progenitor cells in vitro

hyb_protocol: Purified RNA samples were then hybridized to Affymetrix Human 2.0 microarrays to measure global gene expression in each sample.

scan_protocol: Fragmented/Labeled DNA was combined with Hybridization cocktail 99C for 5 minutes according to Affymetrix hybridization kit protocol, then injected onto Affymetrix GeneChip Human Gene 2.0 ST array and incubated 16-18 hours 45C at 60rpm.

data_processing: Microarray CEL files were analyzed using R with the library packages, limma, oligo, NBclist, annotate and pd.hugene.1.0.st.v1.  Probe features were normalized with the rma() function. The getNetAffx() function was used to annotate probe features. Fitting of the expression values for replicates was performed by the lmFit() function.

source_name: human neural progenitor cells in differentiation conditions 3 days

label_protocol: Fragmented ssDNA was incubated with Affymetrix DNA Labeling Reagent 37°C 1 hour according to kit protocol

growth_protocol: Commercially available human neural progenitor cells (hNPCs) from ArunA Biomedical were expanded 8-10 passages in ENStem-A neural expansion medium (Millipore). At passages 8-10, cells were plated at a density of (200,000 cells/ml) in 35mm dishes coated in Matrigel (BD Biosciences) diluted 1:200 in DMEM/F-12.

extract_protocol: RNA from differentiating hNPC plates was harvested in Trizol 0, 1, 3, 7, 14, and 21 days following initiation of differentiation. RNA was then isolated using an RNA isolation kit (Ambion/mirVAna) according to kit protocol and samples were further purified with a cleanup kit (Qiagen) according to kit protocol. Expression data reflects replicate samples from 3 independent cell preparations.

treatment_protocol: Cells were allowed to attach and proliferate for 24 hours after plating, then medium was replaced with Hyclone neuronal differentiation medium (Thermo Scientific) in the absence of growth factor to initiate differentiation. Cells were maintained in differentiation conditions for up to 21 days, with half of the medium refreshed every two days.

tag: cell type

value: hNPCs derived from WA09 hESCs , maintained in differentiation conditions


title: illium lysoforte 1000 31-1431I

description: Gene expression data from illium lysoforte 1000 31-1431I

value: illium


title: Day0_Replicate3

source_name: human neural progenitor cells in differentiation conditions 0 days


title: Day1_Replicate3

source_name: human neural progenitor cells in differentiation conditions 1 day


title: HMLE TWIST emetine rep2

first: Samuel

middle: Emerson

last: Harvey

state: TEXAS

address: One Baylor Plaza

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

data_processing:
Paired-end RNA-seq reads for each sample were mapped to the human genome (GRCh37) and transcriptome (Gencode v24 backmapped to GRCh37) using STAR v2.5.3a using the following command: STAR --runThreadN 16 --alignEndsType EndToEnd –outSAMtype BAM SortedByCoordinate --readFilesCommand zcat
Alternative splicing quantification and differential analysis was conducted for all replicates using rMATS v3.2.5 using the following command: python RNASeq-MATS.py -gtf gencode.v24lift37.annotation.gtf -o output_dir  -t paired -len 100 -analysis U -libType fr-firststrand
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited files for differential skipped exons (SE) identified by rMATS analysis considering junction counts only as referenced above. rMATS_SE_MCF10A_control_compared_to_emetine.txt.gz contains a comparison of MCF10A control and MCF10A emetine treated samples. rMATS_SE_HMLE_TWIST_control_compared_to_emetine.txt.gz contains a comparison of HMLE_TWIST control and HMLE_TWIST emetine treated samples

source_name: HMLE-TWIST cells

growth_protocol: The maintenance of HMLE-TWIST and MCF10a cells was conducted as previously described (Brown et al., J Clin Invest. 2011;121(3):1064–1074. doi:10.1172/JCI44540)

extract_protocol:
Total RNA was extracted using standard Trizol extraction procedures
Stranded paired-end polyA-purified RNA sequencing libraries were prepared using Illumina TruSeq protocols

treatment_protocol: Cells were treated with DMSO or 10 µM emetine for 24 hours before collection

value: Immortalized breast epithelial cells overexpressing retrovirally integrated pBabe-TWIST

value: HMLE-TWIST

value: 10 µM emetine treatment for 24 hrs


title: Day14_Replicate3

source_name: human neural progenitor cells in differentiation conditions 14 days


title: Day21_Replicate 3

source_name: human neural progenitor cells in differentiation conditions 21 days


title: Day7_Replicate2

source_name: human neural progenitor cells in differentiation conditions 7 days


title: Day14_Replicate2


title: Day21_Replicate 2


title: HMLE TWIST emetine rep1


title: illium lysoforte 1000 32-1471I

description: Gene expression data from illium lysoforte 1000 32-1471I

source_name: chicken illium


title: Day3_Replicate3


title: Day21_Replicate 1


title: Day7_Replicate3


title: 24hpf_repeat3 [H24_3]

city: Shanghai

first: XiaoYuan

last: Zhang

address: 320 Yueyang road

institute: Shanghai Institute of Biochemistry and Cell Biology,CAS

data_processing:
Raw reads were pre-processed by Trimmomatic
Reads were mapped to danRer10 using HISAT2 version 2.0.5
Gene expression quantification was done by StringTie version 1.3.3 with annotation file(Danio_rerio.GRCz10.89.gtf) downloaded from Ensembl.
A Python script prepDE.py(http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#deseq) was used to calculate gene read count.
Genome_build: danRer10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Danio rerio

extract_protocol:
PGCs were picked out by green fluoresence
RNA-seq library was constructed with NexteraXT kits by Smart-Seq2.

tag: strain

value: AB

tag: developmental stage

value: 24hpf (prim-5 stage)

value: gonad

value: primordial germ cells (PGCs)


title: jejunum lysoforte 500 29-1465J

description: Gene expression data from jejunum lysoforte 500 29-1465J

source_name: chicken jejunum


title: 24hpf_repeat2 [H24_2]


title: Day1_Replicate2


title: 24hpf_repeat1 [H24_1]


title: Day7_Replicate1


title: Day3_Replicate1


title: illium lysoforte 500 27-1465I

description: Gene expression data from illium lysoforte 500 27-1465I


title: jejunum lpc 1000 26-1479J

description: Gene expression data from jejunum lpc 1000 26-1479J


title: 11hpf_repeat3 [H11_3]

value: 11hpf (3-somite stage)


title: HMLE TWIST control rep2

value: DMSO treated


title: HMLE TWIST control rep1


title: illium lysoforte 500 28-1415I

description: Gene expression data from illium lysoforte 500 28-1415I


title: illium lpc 1000 25-1479I

description: Gene expression data from illium lpc 1000 25-1479I


title: 11hpf_repeat2 [H11_2]


title: MCF10A emetine rep2

source_name: MCF10a cells

value: Non-tumorigenic breast epithelial cells


title: 11hpf_repeat1 [H11_1]


title: Day14_Replicate1


title: MCF10A emetine rep1


title: MCF10A control rep2


title: Day0_Replicate1


title: Day1_Replicate1


title: jejunum lpc 500 24-1443J

description: Gene expression data from jejunum lpc 500 24-1443J

value: lpc 500


title: jejunum lpc 500 23-1452J

description: Gene expression data from jejunum lpc 500 23-1452J


title: MCF10A control rep1


title: 6hpf_repeat2 [H6_2]

value: 6hpf (shield stage)


title: illium lpc 500 22-1443I

description: Gene expression data from illium lpc 500 22-1443I


title: 6hpf_repeat3 [H6_3]