title: Sample 8-exp1 [TN1801R4091]

description:
14_180117
processed data file: 8expression.genes


title: 293_KO_Input1_Norm_

status: Public on Feb 03 2021

type: SRA

city: Granada

first: Juan

middle: Manuel

last: Marti

address: Avda. del Conocimiento 17

country: Spain

institute: CSIC

library_source: genomic

data_processing:
Quality assessment and sample alignment were performed using the miARma-Seq pipeline (Andres-Leon, Nunez-Torres et al. 2016).
fastqc were applied to gather the overall sequence quality and possible adapter accumulation.
Then, all samples were aligned to the reference Human GRCH38 genome from the GENCODE portal, version 28.
All samples were aligned using Burrows-Wheeler Aligner software (Li and Durbin 2009).
PCR duplicates were removed using samtools markdup with options –s –r (Li, Handsaker et al. 2009). Peak calling was performed using MACS2 (Zhang, Liu et al. 2008) with option –f BAM –g hs –s 75 –B –SPMR –nomodel.
Genome_build: Human GRCH38 genome from the GENCODE portal, version 28
Supplementary_files_format_and_content: Processed data is presented using wig format.

molecule: genomic DNA

organism: Homo sapiens

source_name: HEK293T K.O. PARP-1 cells

growth_protocol: Cells were cultured on DMEM high glucose growth medium supplemented with FBSi 10%.

extract_protocol:
Cellular lysates were treated with micrococcal nuclease in order to digest genomic DNA. HIF-1α-DNA complexes were isolated with antibody.
Library preparation and Illumina sequencing were performed by the IPBLN Genomics Core Facility (CSIC, Granada, Spain). ChIP-seq libraries were generated from 30 ng of DNA using the NEBNext Ultra II DNA library preparation kit for Illumina (NEB), and following manufacturer´s instructions with some modifications. A 10-fold dilution of adaptor was used in ligation reaction and no size selection was applied to the adaptor-ligated DNA clean up step, as recommended for Micrococcal Nuclease digested chromatin ChIP assays. A total of 5 cycles of amplification were used to complete adaptor sequences and introduce unique indices for sample multiplexing. Final libraries were quantified on the Qubit® fluorometer (Thermo) and run on a Bioanalyzer HS DNA chip to verify quality and size distribution. Equimolecular library pool was prepared, then diluted and denatured as recommended by Illumina NextSeq 500 library preparation guide. The 75 nt single-end sequencing was conducted on a NextSeq 500 sequencer (Illumina). An average of 24 million reads per sample was obtained.

treatment_protocol: Cells were exposed to hypoxia using a sealed hypoxic workstation (Ruskinn, Bridgend, UK). Cells exposed to 1% O2, 5% CO2 at 37ºC. Hypoxic duration is 4 hours.

tag: cell line

tag: cell type

value: human embryonic kidney cells

tag: passages

tag: genotype/variation

value: PARP-1 K.O.

tag: condition

value: Normoxia

tag: chip antibody


title: Sample 7-con2 [TN1712R1468]

city: Seoul

first: PI EN

last: CHANG

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Department of Orthodontics

country: South Korea

institute: Yonsei University College of Dentistry

description:
20171211_44
processed data file: 7expression.genes

library_source: transcriptomic

data_processing:
Base calling was performed by bcl2fastq 2.0
The read length Hiseq2500 platform 100PE was used to put fastqc files.
Total Bases of sequencing statistics in raw data divided by Total Reads (=101): Progress with Hiseq2500 platform 100PE
Genome_build: GRCh37(hg19)
Supplementary_files_format_and_content: FPKM

molecule: total RNA

source_name: adult PDL_untreated

extract_protocol:
PDL cells were washed with cold PBS after gentle scrapping from the extracted premolar. Total RNA was extracted from PDL cells using TRIzol Reagent. The RNA was stored at −70 °C and measured at an optical density of 260 nm. The mixtures of total RNA were incubated with Oligo dT. Real-time PCR was performed for the selected upregulated and downregulated genes to verify RNA-seq results.
The library was constructed, sequenced using an Illumina HiSeq2500 sequencer, and the data obtained through RNA-seq.

treatment_protocol: To stimulate the PDL, orthodontic force was applied to the first or second premolar on one side for 3 weeks, whereas the tooth on the other side was left untreated.

tag: age

tag: treatment

value: untreated

tag: tissue

value: adult tooth premolar periodontal ligment (PDL)


title: 293_KO_Input1_Hyp_

value: Hypoxia


title: test05

city: Haikou

first: Yandu

last: Lu

state: China

address: State Key Laboratory of Marine Resource Utilization in the South China Sea, College of Oceanology

department: College of Oceanology

country: China

institute: Hainan University

description:
The hlr1 mutant in high light for 144 hour
test05_control05.anno.xls

data_processing:
Raw reads containing adapter, poly-N, and low-quality reads were filtered and the effective data were mapped with the Nannochloropsis reference genome using TopHat (version 2.0.12). After excluding the ribosomal RNA or transfer RNA, we estimated the abundance of the transcripts using RPKM (Reads per Kilo bases per Million reads)
The p values were adjusted using the Benjamini and Hochberg method 63. Corrected p value﹤0.05 and fold change more than two were set as the threshold for significant difference in expression.
GO annotations of the data provided by our RNA-Seq analysis were performed using PANTHER (www.pantherdb.org/pathway/)
Genome_build: The BioProject accessions for assembled genomes were: PRJNA202418 for N. oceanica IMET1
Supplementary_files_format_and_content: Text file with FPKM values of three replicates, FoldChange, Log2FoldChange, pval, padj, Significant, GeneName, Biotype, Position, NR:Seq-id,NR:Score, NR:Evalue, NR:Description

organism: Nannochloropsis oceanica

growth_protocol: Nannochloropsis oceanica strain IMET1 was maintained in dim light at 4°C on solid modified f/2 medium, which was prepared with 35 g·L-1 sea salt, 1 g·L-1 NaNO3, 67 mg·L-1 NaH2PO4·H2O, 3.65 mg·L-1 FeCl3·6H2O, 4.37 mg·L-1 Na2EDTA·2H2O, trace metal mix (0.0196 mg·L-1 CuSO4·5H2O, 0.0126 mg·L-1 NaMoO4·2H2O, 0.044 mg·L-1 ZnSO4·7H2O, 0.01 mg·L-1 CoCl2, and 0.36 mg·L-1 MnCl2·4H2O), and vitamin mix (2.5 µg·L-1 VB12, 2.5 µg·L-1 biotin, and 0.5 µg·L-1 thiamine HCl) 28. For inoculation, cells were picked into liquid medium and were maintained under illumination at 50 μmol·photons·m-2·s-1 at 25 °C with a light/dark cycle (12 h/12h).

extract_protocol:
Total RNA of the algal cells was prepared using an RNA miniprep kit (CWBIO) and the concentrations were measured using the NanoDrop 2000 spectrophotometer (Thermo).
Libraries were constructed and then sequenced using the HiSeq 2500 (Illumina), which generated about 18 million read pairs per sample (ANNOROAD).

treatment_protocol: Mid-logarithmic phase algal cells were collected and equal numbers of cells were re-inoculated in liquid media at 25°C and dark adapted overnight. Then cells were transferred to continuous illumination at 200 μmol·photons·m-2·s-1.

tag: strain

tag: genotype

value: hlr1 mutant; defect in HLR1 gene

tag: light treatment

value: high light for 144 hour


title: test04

description:
The hlr1 mutant in high light for 96 hour
test04_control04.anno.xls

value: high light for 96 hour


title: test01

description:
The hlr1 mutant in dark incubation overnight
test01_control01.anno.xls

value: dark incubation overnight


title: test02

description:
The hlr1 mutant in high light for 1 hour
test02_control02.anno.xls

value: high light for 1 hour


title: test03

description:
The hlr1 mutant in high light for 6 hour
test03_control03.anno.xls

value: high light for 6 hour


title: Sample 7-con1 [TN1711R2047]

description:
20171123_14
processed data file: 7expression.genes


title: 293_KO_Chip2_Hyp_

value: Anti-HIF-1 alpha antibody - ChIP Grade (ab2185)


title: control 05

description:
WT in high light for 144 hour
test05_control05.anno.xls

value: wild type


title: 293_KO_Chip1_Norm_


title: WT-CTX-3

type: RNA

city: Albuquerque

first: Nora

last: Perrone-Bizzozero

state: NM

address: 1 University of New Mexico MSC08 4740

department: Neurosciences

country: USA

institute: University of New Mexico

description: total RNA

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Arrays v2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: A series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 1 out of 6 samples have

organism: Mus musculus

source_name: cortex

label_protocol: Briefly, mRNA and lncRNAs were purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a mixture of oligo(dT) and random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

growth_protocol: Adult mouse neocortex

extract_protocol: Trizol

treatment_protocol: KHSRP KO and wild type (WT) mice

value: Adult

tag: Sex

value: male

value: WT littermate mice


title: Sample 6-con [TN1711R1756]

description:
TN1711R1756_24
processed data file: 6expression.genes


title: Sample 7-exp2 [TN1712R2469]

description:
20171211_34
processed data file: 7expression.genes

source_name: adult PDL_orthodontic force stimulate

value: orthodontic force stimulate for 3 wks


title: control 03

description:
WT in high light for 6 hour
test03_control03.anno.xls


title: 293_KO_Chip1_Hyp_

value: human embryonic kidney cells

value: PARP-1 K.O.


title: control 02

description:
WT in high light for 1 hour
test02_control02.anno.xls


title: Sample 7-exp1 [TN1711R2048]

description:
20171123_24
processed data file: 7expression.genes


title: WT-CTX-1

description: total RNA


title: control 04

description:
WT in high light for 96 hour
test04_control04.anno.xls


title: KHSRP-KO-CTX-2

description: total RNA

value: KHSRP-KO mice


title: WT-CTX-2

description: total RNA


title: input DNA

city: Villejuif

first: Valeria

last: Naim

address: 114 rue Edouard Vaillant

department: Genome Stability and Oncogenesis

country: France

institute: CNRS UMR8200 University Paris Sud, Gustave Roussy

data_processing:
Reads were aligned to the human genome (hg19) using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format.
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. Duplicate reads are removed.
Aligned reads (tags) are extended in silico using Active motif proprietary software to a length corresponding to the average fragment length of the size-selected library (200 bp). Fragment density is determined by the number of extended tags assigned to 32 nt bins along the genome.
Peaks were called using either the MACS (v1.4.2) or SICER (v1.1) algorithms. MACS default cutoff is pvalue 1e-7 for narrow peaks and 1e-1 for broad peaks, and SICER default cutoff is FDR 1e-10 with gap parameter of 600 bp. Peak filtering was performed by removing false ChIP-Seq peaks as defined within the ENCODE blacklist.c
Spike-in protocols and normalization were used. For comparative analysis, the number of test tags are adjusted by a factor that would result in the same number of usable spike-in Drosophila tags for each sample within a normalization group. The normalization is im- plemented through random deletion of test sample tags (down-sampling). The normalization factor shows the adjustment relative to standard normalized tag numbers (where the usable tags for each sample within a normalization group would be adjusted to the same number).
Genome_build: hg19
Supplementary_files_format_and_content: The histograms of fragment densities (genomic “signal maps”) are stored in bigWig files.

source_name: HCT116 cells

growth_protocol: HCT116 cells were routinely cultured in McCoy’s 5A medium (ATCC) supplemented with 10% fetal bovine serum (FBS), 1 mM sodium pyruvate, 100 U/mL penicillin and 100 µg/mL streptomycin.

extract_protocol:
Cells were fixed in 1% formaldehyde for 15 min, then quenched in 125mM glycine. After cell lysis, 30 µg of chromatin was used for immunoprecipitation using a FANCD2 antibody (Novus, NB100-182).
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.
Libraries were prepared according to Active Motif proprietary protocols.

treatment_protocol: FANCD2+APH sample was treated with 0.3 µM APH (Sigma A0781) for 20 hr.

value: human colon carcinoma cell line ATCC

tag: chip antibodies


title: KHSRP-KO-CTX-3

description: total RNA


title: KHSRP-KO-CTX-1

description: total RNA


title: control 01

description:
WT in dark incubation overnight
test01_control01.anno.xls


title: FANCD2+APH ChIP-seq

value: NB100-182 Novus


title: Sample 5-con [TN1710R1826]

description:
24
processed data file: 345expression.genes

value: untreated

value: adult tooth premolar periodontal ligment (PDL)


title: FANCD2-APH ChIP-seq


title: 95_iNSLC

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
Sequenced reads were trimmed using trimmomatic based on reads quality and adaptor sequence
The resulting reads were mapped to cj1700 using STAR version 2.6.0c
Reads mapped to exon regions were counted using featureCount version 1.5.1.
Raw count data was loaded to R software and normalized using Seurat version 3.0.0.
Genome_build: cj1700
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each Sample.

organism: Callithrix jacchus

source_name: E01F A2 iNSLC

extract_protocol:
Cells were sorted into 96 well plate with a flow cytometer SH800 (SONY) and dissolved with single cell lysis buffer
Library were constructed using GenNext RamDA-seqTM Single Cell Kit and Netera XT library prep kit

value: iNSLC


title: Sample 4-con [TN1710R1830]

description:
25_PSX
processed data file: 345expression.genes


title: 92_iNSLC


title: 94_iNSLC


title: scaRNA-seq K562 cells

city: Oxford

first: Martin

middle: Stephen Charles

last: Larke

state: Oxfordshire

address: Headley Way

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Total RNA <300nt in length (PAGE size selected)
k562_24.fwd.tss.bw
k562_24.rev.tss.bw
k562_24.fwd.tes.bw
k562_24.rev.tes.bw
K562 cells obtained from the WIMM transgenics facility were grown in RPMI media supplemented with 15% FBS (37C, 5% CO2). Cell density was maintained <=106/ml. Cell density and viability were determined using the nucleocounter platform (chemometec). 5x10^6 cells were harvested by pelleting before lysis in TRI regent and stoage at -80C until use

data_processing:
alignment (bowtie/0.1.19 -m 2 -p 4 --maxins 1000 --best --strata --chunkmb 256)
convert to .bam file iof properly paired read pairs  (samtools/0.1.19 view -f 3)
remove reads mapping to annotated (UCSC) ncRNA (even by 1bp) or annotated (UCSC) 3' splice sites (bedtools/2.25.0 intersect -v -wa -s -split)
convert to bedpe (bedtools/2.25.0 bamtobed -mate1) and grep chr | cut -f 1,2,3,5,6,9
convert to bed file of fragments using awk.
count millions of mapped reads (wc -l)
make coverage tracks, subsampling to sample woith lowest read coverage (bedtools/2.25.0 genomecov -bg -strand (+/-) -ibam)
conversion of bedGraphs to bigwig (ucsctools bedGraphToBigWig)
merging of bigwigs from same time point and strand (ucsctools bigWIgMerge)
Genome_build: mm9/hg19
Supplementary_files_format_and_content: strand specific bigWigs of transcription start sites (tss) and transcription ends sites (tes). Each replicate subsampled to sample with lowest number of RNA fragments. Biological triplicate merged.

source_name: K562 cells

growth_protocol: Mouse fetal livers were harvested at E12.5 and disaggregated in expansion media (StemPro (ThermoFisher)) supplemented with Epo (1U/ml), SCF (50ng/ml), Dexamethosone (1μM)). Cells from individual fetal livers were grown for 6 days, maintaining a constant erythroblast cell count of <= 1 x10^6. Cells were genotyped as wildtype, homozygous R1R2 or homozygous HS2HS3 during expansion. Cells were counted using the nucleocounter before selection for CD117 positive cells using magnetic assisted cell separation LS columns (130-042-401 - Milltenyi) following the manufacturers protocol. Cells were left to recover for 6h in expansion media at a density of 1x106 cells/ml. Aliquots of 5x106 cells were harvested as the ‘0h’ timepoint corresponding to early erythropoiesis whilst the remaining cells were re-suspended in differentiation media (which is expansion media with the following changes: increased levels of Epo (5U/ml) and transferrin (0.5mg/ml), SCF and Dexamethasone removed). To induce erythroid differentiation cells were grown for 24h before harvesting for the ‘24h’ timepoint. Cell morphology was examined and immunophenotype determined by flow assisted cell sorting (FACS) (Attune NxT – Thermo Fisher Scientific) with markers for CD117 and Ter119 at the 0h and 24h timepoints. 0h of erythropoiesis was defined as (CD117+,Ter119-) and 24h as (CD117-, Ter119+) and cells isolated were confirmed as having these appropriate erythroid stage markers (Edling and Hallberg 2007; Hay et al. 2016; McGrath, Catherman, and Palis 2017)

extract_protocol:
isolation protocol: 5x10^6 cells were aliquoted per replicate, pelleted by centrifugation (500g, 5min, R.T) and washed once in 5mL 1xPBS before lysis in TRI Reagent (Merck) by repeated pipetting. Samples were snap frozen and transferred to storage at -80°C until use.
Samples in TRI reagent were thawed on ice before extraction according to the manufacturers protocol. Samples were Dnase treated for 30mins at 37C using Turbe DNase before phenol chloroforom extraction and ethanol precipitation.
RNA <=300nt was size selected using a 10% denatuiring poly arcylamide gel. RNA was extracted and subjected to a modified veriosn of the NEB Next Small RNa for Illumna library rep kit (NEB), wherin after 3' adapter ligation matierla is phosphatase treated and decapped before continuing with 5' adapter ;igation and the remained opf the protocol according to the manufactureers protocol.

value: K562 cells


title: 91_iNSLC


title: Sample 5-exp [TN1710R1827]

description:
34
processed data file: 345expression.genes


title: 96_iNSLC


title: mNET-seq K562 cells

description:
RNA immunopreciptated with Pol2
mNET.k562.fwd.fullfrag.bw
mNET.k562.rev.fullfrag.bw
K562 cells obtained from the WIMM transgenics facility were grown in RPMI media supplemented with 15% FBS (37C, 5% CO2). Cell density was maintained <=106/ml. Cell density and viability were determined using the nucleocounter platform (chemometec). 5x10^6 cells were harvested by pelleting and snap frozen in a dry ice ethanol bath and stored at -80C until use

data_processing:
Library strategy: mNET-seq
alignment (bowtie/0.1.19 -m 2 -p 4 --maxins 1000 --best --strata --chunkmb 256)
isolate proper read pairs and convert to .bam (samtools/0.1.19 view -bS -f 3)
PCR duplicates removed (samtools/0.1.19 rmdup)
remove reads mapping to annotated (UCSC) ncRNA (even by 1bp) or annotated (UCSC) 3' splice sites (bedtools/2.25.0 intersect -v -wa -s -split)
convert to bedpe (bedtools/2.25.0 bamtobed -mate1) and grep chr | cut -f 1,2,3,5,6,9
convert to bed file of fragments using awk.
count millions of mapped reads (wc -l)
make reads per million normalised strand specific coverage tracks (bedtools/2.25.0 genomecov -bg -strand (+/-) -ibam)
conversion of bedGraphs to bigwig (ucsctools bedGraphToBigWig)
Genome_build: mm9
Supplementary_files_format_and_content: bigWigs of stranded full RNA fragments, biological duplicate merged
Supplementary_files_format_and_content: bigWigs of stranded 3' ends of RNA (Pol2 active site, with 2nt window to improve coverage) coverage, biological duplicate merged

growth_protocol: Mouse fetal livers were harvested at E12.5 and disaggregated in expansion media (StemPro (ThermoFisher)) supplemented with Epo (1U/ml), SCF (50ng/ml), Dexamethosone (1μM)). Cells from individual fetal livers were grown for 6 days, maintaining a constant erythroblast cell count of <= 1 x106. Cells were genotyped as wildtype, homozygous R1R2 or homozygous HS2HS3 during expansion. Cells were counted using the nucleocounter before selection for CD117 positive cells using magnetic assisted cell separation LS columns (130-042-401 - Milltenyi) following the manufacturers protocol. Cells were left to recover for 6h in expansion media at a density of 1x106 cells/ml. Aliquots of 5x106 cells were harvested as the ‘0h’ timepoint corresponding to early erythropoiesis whilst the remaining cells were re-suspended in differentiation media (which is expansion media with the following changes: increased levels of Epo (5U/ml) and transferrin (0.5mg/ml), SCF and Dexamethasone removed). To induce erythroid differentiation cells were grown for 24h before harvesting for the ‘24h’ timepoint. Cell morphology was examined and immunophenotype determined by flow assisted cell sorting (FACS) (Attune NxT – Thermo Fisher Scientific) with markers for CD117 and Ter119 at the 0h and 24h timepoints. 0h of erythropoiesis was defined as (CD117+,Ter119-) and 24h as (CD117-, Ter119+) and cells isolated were confirmed as having these appropriate erythroid stage markers (Edling and Hallberg 2007; Hay et al. 2016; McGrath, Catherman, and Palis 2017)

extract_protocol:
isolation protocol5x10^6 cells were aliquoted per replicate, pelleted by centrifugation (500g, 5min, R.T) and washed once in ice cold 5mL 1xPBS before snap freezing in a dry ice ethanol bath. Samples were snap frozen and transferred to storage at -80°C until use.  The antibody used for the mNET-seq samples is no longer commercially available. Antibody used in this study was kindly provided by Dr. Hiroshi Kimura. The antibody targets Pol II total CTD.
mNET-seq was performed as in (Nojima et al. 2015) but with a starting input cell number of 5x10^6
NEB small RNA for Illumina


title: 89_iNSLC


title: Sample 6-exp [TN1810R4796]

description:
TN1810R4796_34
processed data file: 6expression.genes


title: AtWW_G_dg

city: Urrbrae

first: Haipei

last: Liu

state: South Australia

address: PMB1 Waite Building, School AFW

country: Australia

institute: The University of Adelaide

description:
degradome-seq processed data.xlsx
AtWW_G

data_processing:
Library strategy: degradome-seq
sRNA-Seq: Small RNA sequencing analysis was performed using the ACGT101-miR program (LC Sciences, TX, USA). Raw reads were first processed by removing low-quality reads and adapter sequences to obtain clean sequences. Reads with a nucleotide (nt) length <18 nt or >25 nt were removed. Non-coding (nc) RNA families (rRNA, tRNA, snRNA and snoRNA), repeats and mRNA sequences were discarded using RFam, Repbase and durum wheat NCBI mRNA entries as references. Unique sRNA sequences were then obtained for each library. Conserved mature miRNAs and 5p- or 3p-derived miRNA variants were identified using BLAST search against the plant miRBase (Release 22.1). MIR (microRNA gene locus) and miRNA sequences from common plant species in the miRBase were used as references. Sequences mapped to the mature miRNA in the hairpin were identified as conserved mature miRNAs. Sequences mapped to the opposite arm of mature miRNA in the hairpin were identified as 5p- or 3p-derived variants. Single mismatch within the sequence and length variation at both 5p and 3p were allowed in the alignment. All the mapped miRNAs were aligned to the durum wheat genome (NCBI UID 3439611, assembly Svevo.v1) to determine their genomic location. The remaining unmatched sRNA sequences were used to identify novel durum miRNAs. Sequences were BLASTed to the durum wheat genome. To identify miRNA precursors, secondary hairpin structures containing matched sequences were predicted using RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi) from 120nt of flanking genome sequences.
mRNA-Seq: Prior to sequence assembly, low quality reads (those containing primer or adaptor sequence, and those with a sequencing quality score < 20) were removed. Clean reads were aligned to the durum reference genome using the HISAT package (V2.0). Aligned reads of each library were assembled and the transcript abundance were obtained using StringTie (V1.3.0). Normalised relative abundance was expressed in FPKM (Fragments Per Kilobase Million).
Degradome-Seq: Raw sequencing reads were processed using the ACGT101-DEG program (V4.1, LC Sciences) to remove low-quality reads, reads with adaptor and primer contamination, and reads that can be annotated as non-coding RNA families. The remaining clean reads were used to identify the degraded fragments of mRNAs that are targets of known and novel durum miRNAs with the CleaveLand package V4.0  and the ACGT101-DEG program (LC Sciences, TX, USA). The mRNA cleavage sites at the 10th position of miRNA alignment with P value < 0.05 were considered as significant.
Genome_build: Durum wheat genome (NCBI UID 3439611, assembly Svevo.v1)
Supplementary_files_format_and_content: Matrix table with abundance measurements of microRNAs (sRNA-seq), mRNAs (mRNA-seq) and mRNA targets (degradome-seq)

organism: Triticum turgidum subsp. durum

source_name: Developing grain tissue

growth_protocol: Durum wheat variety DBA Artemis plants were grown in controlled glasshouse conditions as previously described (Liu et al., 2019). The standard growing conditions were 22°C/12°C (day/night) with a 12h photoperiod.

extract_protocol:
Total RNA was extracted using the Tri reagent (Sigma-Aldrich) and treated with TURBO DNase (ThermoFisher Scientific). RNA concentration, quality and integrity was assessed by NanoDrop, gel electrophoresis and Bioanalyzer.
The sRNA libraries were constructed using the NEBNext® Multiplex Small RNA Library Prep Kit. The transcriptome libraries were constructed using the Illumina mRNA-Seq sample preparation kit. For degradome-seq, mRNA was enriched using oligo-d(T) magnetic beads. The enriched mRNA was mixed with biotinylated random primers and were ligated to 5' adaptors. First-strand cDNA was reverse-transcribed from ligated mRNA products and then amplified with PCR.

treatment_protocol: The treatment groups are: AtCC (DBA Artemis control group parents, progenies treated with control), AtCW (DBA Artemis control group parents, progenies treated with water-deficit stress), AtWC (DBA Artemis water-deficit stress group parents, progenies treated with control), AtWW (DBA Artemis water-deficit stress group parents, progenies treated with water-deficit stress). L represents flag leaf libraries, G represents developing grain libraries. All plants were well-watered from germination to booting. Water-deficit stress was applied by maintaining the soil water content at 6% (half of the field capacity) from booting until harvest. Flag leaf and developing grain samples were collected at 5 DPA (days post anthesis).

value: DBA Artemis

tag: origin of the parental plants

value: Water-deficit stress group parents

tag: progeny treatment

value: Water-deficit stress group


title: Sample 4-exp1 [TN1710R1831]

description:
15_PSX
processed data file: 345expression.genes


title: WT.Treg.CD45.1.L1#1

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a.
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts (subread 2.0.0) with GENCODE annotation (vM25).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Genes_count_table.tsv: Tab-delimited text file includes raw read counts.

source_name: CD4 TReg Cell

extract_protocol:
On day 50, 1000 CD45.1 or LNGFR+ CD4+ T cells were double-sorted from lymph nodes by a SH800, into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma). Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter).
Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

treatment_protocol: Lymph nodes were collected from 10-day-old scurfy mice, and CD4+ T cells were transfected with Human FOXP3 or an empty vector (LNGFR). In 10-day-old scurfy mice, Cyclophosphamide was injected i.p. at 50mg/kg 1. On day 14, CD4+CD25+ CD45.1+ cells or engineered CD4+ T cells from scurfy mice were injected i.p.. Human IL-2 was injected i.p. at 1000 IU/g once a day for 5 days and then once a week.

value: Lymph nodes

value: Scurfy - FOXP3 KO


title: AtWC_G_dg

description:
degradome-seq processed data.xlsx
AtWC_G

value: Control group


title: WT.Treg.CD45.1.G4#2


title: Sample 3-con [TN1710R1833]

description:
24_KTX
processed data file: 345expression.genes


title: Sample 3-exp [TN1710R1832]

description:
14_KTX
processed data file: 345expression.genes


title: 86_iNSLC


title: Sample 4-exp2 [TN1710R1828]

description:
44_PSX
processed data file: 345expression.genes


title: 87_iNSLC


title: 85_iNSLC


title: 93_iNSLC


title: 88_iNSLC


title: AtCC_G_dg

description:
degradome-seq processed data.xlsx
AtCC_G

value: Control group parents


title: WT.Treg.CD45.1.G4#1


title: 83_iNSLC


title: AtWC_L_dg

description:
degradome-seq processed data.xlsx
AtWC_L

source_name: Flag leaf tissue


title: AtWW_L_dg

description:
degradome-seq processed data.xlsx
AtWW_L


title: Sample 2-con [TN1709R0327]

description:
34_170905
processed data file: 2expression.genes


title: Sample 2-exp [TN1709R0329]

description:
24_170905
processed data file: 2expression.genes

value: orthodontic force stimulate for 3 wks


title: WT.Treg.CD45.1.E2#2


title: 84_iNSLC


title: WT.Treg.CD45.1.E2#1


title: WT.Treg.CD45.1.L1#2


title: AtCW_L_dg

description:
degradome-seq processed data.xlsx
AtCW_L


title: Sample 1-con [TN1708R0898]

description:
35
processed data file: 1expression.genes


title: T.4.LNGFR.G3#2

source_name: CD4 Tconv Cell


title: AtCW_G_dg

description:
degradome-seq processed data.xlsx
AtCW_G


title: 81_iNSLC


title: Sample 1-exp [TN1708R0897]

description:
25
processed data file: 1expression.genes


title: 80_iNSLC


title: AtCC_L_dg

description:
degradome-seq processed data.xlsx
AtCC_L


title: T.4.LNGFR.G2#2


title: 78_iNSLC


title: T.4.LNGFR.G2#1


title: T.4.LNGFR.G3#1


title: BT549_DOXplus_1

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (GRCh38.p7) by STAR (version 2.7.3a).
The number of fragments in each known gene from GENCODE (version 25) was quantified using STAR QuantMode (GeneCounts) function.
The differential gene expression was analyzed by R/Bioconductor package DESeq2 (version 1.24.0).
Genome_build: GRCh38.74
Supplementary_files_format_and_content: processed data is in supplementary file, which is a comma-separated text file containing a matrix of raw read counts for each gene accession number and sample

source_name: TNBC cell line

growth_protocol: Human BT-549 (ATCC) cells were cultured in RPMI1640 medium (Thermo Fisher Scientific) containing 10% fetal bovine serum, 100 μg/ml µg/mL streptomycin, 100 U/ml U/mL penicillin and 10 μg/ml µg/mL insulin.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using Trizol reagent
TruSeq Stranded mRNA (Illumina) was used for library preparation.

treatment_protocol: Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml ng/mL doxycycline.

tag: shRNA

value: MISSION shRNA TRCN0000122938

tag: gender

value: female

value: 500 ng/ml doxycycline


title: LCL_Input_G2M

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Sequencing was carried out on the Illumina Genome Analyzer GAIIx and HiSeq 1000 platforms.
Data collection was performed using Sequencing Control Software v2.6.
Real-time Analysis (RTA) 1.5-1.8 were used for base calling.
Mapping of ChIP-Seq data was performed using Bowtie (v0.12.8; options -n 1 -m 1 --best --strata --chunkmbs  1024) against the human GRCh37 assembly.
Genome_build: GRCh37
Supplementary_files_format_and_content: Seqmonk Probe reports (tab-delimited text) from cell cycle sorted HeLa cells (H3K9ac ChIP in G1, G2M and M) and LCLs (H3K4me3, H3K9ac, H3K27me3 ChIP in G1 and G2M) using 5000bp rolling windows, corrected for read count, log2 transformed.

source_name: Lymphoblastoid cell line (AH)

growth_protocol: The AH-LCL lymphoblastoid cell line was cultured in RPMI 1640 medium, 10% foetal bovine serum, supplemented with L-glutamine (2mM) and penicillin/streptomycin (all reagents from Life Technologies) at 37°C, 5% CO2). HeLa cells were cultured in DMEM medium supplemented with 10% foetal bovine serum (Sigma), supplemented with L-glutamine (2mM) and penicillin/streptomycin (Life Technologies).

extract_protocol:
Acetone-fixed cells were washed twice in cold PBS and resuspended in digestion buffer (0.32M sucrose, 50mM Tris/HCl (pH7.4), 4mM MgCl2, 1mM CaCl2, 5mM Na Butyrate, 0.1mM PMSF). Micrococcal nuclease was added to 25units/ml and chromatin digested at 37°C for 5 minutes. The reaction was stopped by the addition of EDTA to 5mM. Chromatin was pre-cleared by incubation with protein A sepharose beads and incubated overnight with antibodies to H3K9ac (in house, R607), H3K4me3 (in house, R612) and H3K27me3 (Millipore, 07-449). Antibody-bound material was isolated on Protein A-Sepharose beads (Invitrogen, UK) and DNA from antibody-bound and input chromatin was purified by PCR purification kit (Qiagen).
Sequencing libraries were prepared from 100ng DNA per sample using the NEBNext Library preparation kit for Illumina (NEB).  Samples were barcoded using the system described by Bronner et al. (2014).  Fragments were PCR amplified with 12–18 cycles using adaptor specific primers (Illumina); fragments ranging between 300 and 500 bp in size were gel-purified before cluster generation and sequencing.

treatment_protocol: Cells were sorted into cell-cycle phase by several protocols: Fluorescence-activated cell sorting: Lymphoblastoid cells were treated with 0.1µg/ml colcemid for 4 hours to enrich the mitotic fraction. Cells were then harvested by centrifugation, washed three times in PBS and ice cold acetone was added dropwise before freezing to -20°C for at least 2 hours. Cells were then washed and resuspended in ice cold PBS. Propidium iodide was added to a concentration of 10µg/ml and incubated for 30 minutes at 4°C. Cells were sorted into G1 and G2M fraction based on Propidium iodide fluorescence using a MoFlo cell sorter (DakoCytomation). Centrifugal elutriation: a JE-5.0 elutriating centrifuge (Beckman Coulter) was used. HeLa cells were trypsinised, washed in culture medium and resuspended in 10ml of elutriation buffer (5mM EDTA, 1% bovine serum albumin in 0.75x PBS). Cells were passaged through an 18G needle and loaded into the elutriation chamber.Optima G1 fractions were achieved loading at 15ml/min, 1800rpm and the purest G2M fraction at 11ml/min, 1300 rpm. Cell cycle fractions were eluted by gradually increasing the flow rate and collecting 200ml fractions. Eluted cells were centrifuged and acetone-fixed as above for ChIP-seq. Mitotic shak off: HeLa cells in culture were shaken on an orbital shaker at 200 rpm for 1 minute. Medium containing shaken-off cells was collected and cells pelleted by centrifugation. Cells were acetone-fixed as above for ChIP-seq.

tag: cell line

value: AH-LCL lymphoblastoid cell line

tag: sorting method

value: fluorescence-activated cell sorting

tag: cell cycle phase


title: BT549_DOXplus_3


title: T.4.LNGFR.G1#2


title: LCL_H3K4me3_G2M


title: 82_iNSLC

tag: cell type


title: T.4.LNGFR.G1#1


title: 76_iNSLC


title: LCL_H3K4me3_G1

tag: chip antibody


title: LCL_H3K27me3_G2M


title: T.4.LNGFR.FOXP3.N3#2


title: BT549_DOXminus_2

value: DMSO


title: 75_iNSLC


title: BT549_DOXminus_1


title: 79_iNSLC


title: BT549_DOXplus_2


title: LCL_H3K27me3_G1


title: 74_iNSLC


title: T.4.LNGFR.FOXP3.N3#1


title: T.4.LNGFR.FOXP3.N2#2


title: LCL_Input_G1


title: Early-passage PDX / PDX passaged in mouse for 0 time (passage 0)

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

data_processing:
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and  employed a single-end, 50 base read length (SE50) sequencing strategy.
Reads were aligned to human hg38 and mouse mm10 genomes using TopHat2. Alignments matching hg38 with a higher fidelity than mm10 were retained, where fidelity is measured by the number of mismatches against the reference genome and counted for gene associations against the UCSC genes database with HTSeq.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

source_name: patient-derived xenograft (pdx)

growth_protocol: Tissues were obtained as frozen chunks, and manually pulverized before lysis

extract_protocol:
RNA was extracted from cell cultures every two weeks during the exponential growth phase; RNA was isolated from 0.5-1.0×106 cells. Total RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: muscle-invasive bladder cancer

tag: culture method

value: patient-derived xenograft (pdx)

tag: passage

value: early-passage


title: LCL_H3K9ac_G1


title: 73_iNSLC

value: iNSLC


title: 77_iNSLC


title: CoCaB organoids developed from late-passage PDX (passage 9)_1

source_name: organoids

value: organoids

value: late-passage


title: BT549_DOXminus_3

tag: treatment


title: CoCaB organoids developed from late-passage PDX (passage 9)_2


title: 71_iNSLC


title: T.4.LNGFR.FOXP3.N2#1

tag: strain

tag: tissue

value: Lymph nodes


title: CoCaB organoids developed from early-passage PDX (passage 2)_2


title: T.4.LNGFR.FOXP3.F5#2

tag: genotype

value: Scurfy - FOXP3 KO


title: T.4.LNGFR.FOXP3.F5#1


title: T.4.LNGFR.FOXP3.F2#2


title: 69_iNSLC


title: 68_iNSLC


title: LCL_H3K9ac_G2M


title: Late-passage PDX / PDX passaged in mouse for 8 times (passage 8)


title: T.4.LNGFR.FOXP3.F2#1


title: Late-passage PDX / PDX passaged in mouse for 7 times (passage 7)


title: 72_iNSLC


title: Late-passage PDX / PDX passaged in mouse for 6 times (passage 6)


title: T.4.LNGFR.FOXP3.F1#2


title: Early-passage PDX / PDX passaged in mouse for 2 times (passage 2)


title: T.4.LNGFR.FOXP3.F1#1


title: Early-passage PDX / PDX passaged in mouse for 1 time (passage 1)


title: 66_iNSLC


title: 65_iNSLC


title: 67_iNSLC


title: 64_iNSLC


title: CoCaB organoids developed from early-passage PDX (passage 2)_1


title: 63_iNSLC


title: roots_reil1-1 reil2-2_20°C->10°C_1w_replicate2

city: Docklands

first: Bo Eng

last: Cheong

state: VIC

department: School of BioSciences

institute: University of Melbourne

description: gene expression of mixotrophic hydroponic roots of the reil1-1 reil2-2 double mutant acclimating 7 days to 10°C

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturers instructions. Then Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-015059 Arabidopsis 3 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed and dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides. The scanned images were analyzed with GeneSpring (Agilent). Percentile normalization (75 percentile) was performed for each chip.

data_processing: The processing of this quantile normalized log2-transformed signal intensity matrix was performed using the normalize.quantile function of the preprocessCore package (https://github.com/bmbolstad/preprocessCore) on R statistical computing and graphics language (https://www.r-project.org/); Ben Bolstad (2019). preprocessCore: A collection of pre-processing functions. R package version 1.46.0.

organism: Arabidopsis thaliana

source_name: pools of complete root systems harvested develompental stage >1.10, i.e. plants with 10 leaves

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 µg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Generation of seed batches, storage, sterilization, and in vitro pre-cultivation of Arabidopsis thaliana Col-0 were as described previously (Schmidt et al., 2013, doi: 10.1104/pp.113.223925). In the current study circular white glass containers with glass lids were used for mixotrophic hydroponic culture. The glass containers had a slightly tapered bottom with 10.0 cm top diameter and 7.5 cm bottom diameter. The containers had a total volume of ~ 580 mL. Each contained 250 mL of liquid MS media with 2% sucrose (w/v) adjusted to pH 5.7 (Murashige and Skoog, 1962, doi: 10.1111/j.1399-3054.1962.tb08052.x). Sucrose addition reduced developmental and growth-differences between mutants and Col-0 wild type. The liquid was first poured into the jar, then a sterilized stainless steel wire mesh insert of 9 cm diameter, with mesh size 1.40 mm and wire thickness 0.25 mm was adjusted level with the top of the liquid. Four small ~1 cm³-blocks of solid MS media that contained 0.8 % (w/v) agar were placed on top of the mesh before applying single sterilized Arabidopsis seeds to each block. Four plants were routinely cultivated per container. The containers were closed tightly, but not airtight. Glass lids were fixed to the container by stainless steel clamps before transfer to a controlled-environment chamber for growth. The seeds were allowed to germinate and grow under sterile conditions in a long day photoperiod with a 16h/8h - day/night cycle. External temperature settings of the chamber were controlled. External light intensity was 100 - 150 µmol photons m-2 s-1. External relative humidity was 60% - 70%. The standard temperature regime was 20°C during the day and 18°C during night.

extract_protocol: Total RNA was isolated from root tissue using the RNeasy Plant Mini Kit and RNase free DNAse (Qiagen, Limburg, Netherlands). RNA integrity number (RIN) was evaluated and calculated by microfluidic electrophoresis using an Agilent 2100 Bioanalyzer and 2100 Expert software (Agilent Technologies GmbH & Co. KG, Waldbronn, Germany). RNA samples with RIN > 8.0 were sent to the 4×44K Agilent expression profiling service of ATLAS Biolabs GmbH (Berlin, Germany).

treatment_protocol: Plants were pre-cultivated at 20°C standard conditions to developmental stage ~1.10 (Boyes et al., 2001, doi: 10.1105/TPC.010011). At this stage, the plants were transferred carefully within their hydroponic containers from standard conditions to a second controlled-environment chamber with 10°C temperature during the day and 8°C during the night, but otherwise equal external light cycle, light intensity, and relative humidity settings. Non cold acclimated roots were harvested immediately before temperature shift. Following cold shift, 10°C acclimating root samples were harvested after one day, or one week. Each harvested biological replicate was the pool of complete root material from four plants of a single container. Three independent biological replicates were harvested for microarray based transcriptome analyses.

tag: ecotype

value: root

value: acclimating to 10°C for 1 week

tag: time point

value: 1 week

tag: genotype/variation

value: reil1-1 reil2-2 double T-DNA mutant


title: 62_iNSLC


title: roots_reil1-1 reil2-2_20°C->10°C_1w_replicate3


title: roots_reil1-1 reil2-2_20°C->10°C_1d_replicate2

description: gene expression of mixotrophic hydroponic roots of the reil1-1 reil2-2 double mutant acclimating 1 day to 10°C

source_name: pools of complete root systems harvested develompental stage ~1.10, i.e. plants with 10 leaves

value: acclimating to 10°C for 1 day

value: 1 day


title: 61_iNSLC


title: sample_DKO-m6A-rep1

city: Dallas

first: harini

last: ramalingam

state: Texas

address: 5323 Harry Hines Boulevard

department: IMN

institute: UTSW

data_processing:
The reads from FASTQ files were aligned to the mouse genome (mm10) using STAR, a splice-aware aligner for RNA-seq data
The peaks were called using MACS2 (v2.1.0)
The peaks were annotated using ChIPseeker
The motif analysis was performed using HOMER (v4.7.2)
differential expression analysis of input RNA samples was performed using EdgeR
The BAM files were input normalized using the bamCompare module of deepTools (v3.1.1)
The differentially bound m6A sites between groups of samples (control, Pkd1F/RC-KO and Pkd1F/RC;Mettl3F/F-DKO) were analyzed using Diffbind
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values.

source_name: kidney

extract_protocol:
Kidneys were removed from mice and flash frozen. Total RNA was isolated using the miRNeasy Mini kit from Qiagen (catalog #217004).
RNA libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit (catalog E7530S, New England Biolabs).
Immunoprecipitated (anti-m6A) and the corresponding input RNA were used to prepare libraries for sequencing using the Illumina NextSeq 500.

treatment_protocol: m6A RNA IP using the Magna MeRIP™ m6A Kit (EMD Millipore, catalog #17-10499) was performed on P18 wildtype, Pkd1F/RC-KO and Pkd1F/RC-Mettl3-DKO mouse kidney samples.

tag: Sex

value: female

value: kidney

tag: age

value: postnatal day 18

tag: sample type

value: m6A IP


title: sample_DKO-m6A-rep2

value: male


title: sample_SKO-m6A-rep1


title: ventral_SNpc_HC5

city: Cardiff

first: Jimena

last: Monzón-Sandoval

address: Maindy Road

institute: UK Dementia Research Institute at Cardiff University

description: ~100 LCM captured nigral cells

data_processing:
Reads were mapped to cDNA sequences from Homo sapiens GRCh38 release 85 available through the Ensembl FTP site.
Kallisto version 0.42.4 was used to create an index and estimate counts and transcript abundances; default parameters were used except for the number of bootstraps, which was set to 100. Finally, the tximport function in R was used to summarize transcript abundances for all protein-coding genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_abundance.tvs contain transcript abundances estimated with kallisto (target_id, length, eff_length, est_counts, tpm)

molecule: polyA RNA

source_name: substantia nigra pars compacta neurons (ventral tier)

extract_protocol:
RNA was extracted from ~100 pooled LCM neurons from each tier using PicoPure RNA isolation Kit (Arcturus, Mountain View, CA) with DNAse digestion step (RNAse-Free DNAse Set; QIAGEN, Hilden, Germany).
The cDNA was prepared for the sequencing using the SMARTer Kit (Clontech Laboratories, Mountain View, CA). Samples were sequenced (HiSeq4000 75bp paired-end) across 2 lanes

value: substantia nigra pars compacta neurons

tag: origin

tag: tier

value: ventral

value: F

tag: rin


title: sample_SKO-m6A-rep2


title: dorsal_SNpc_HC5

description: ~100 LCM captured nigral cells

source_name: substantia nigra pars compacta neurons (dorsal tier)

tag: cell type

value: dorsal


title: ventral_SNpc_HC4

description: ~100 LCM captured nigral cells

value: M


title: roots_reil1-1 reil2-2_20°C->10°C_1d_replicate1


title: roots_reil1-1 reil2-2_20°C_replicate3

description: gene expression of mixotrophic hydroponic roots of the reil1-1 reil2-2 double mutant at 20°C

value: not cold acclimated, 20°C

value: 0 day


title: roots_reil1-1 reil2-2_20°C->10°C_1w_replicate1

value: root

value: acclimating to 10°C for 1 week


title: sample_wt-m6A-rep2

value: wildtype


title: dorsal_SNpc_HC4

description: ~100 LCM captured nigral cells


title: 60_iNSLC

value: iNSLC


title: 59_iNSLC


title: sample_DKO-input-rep2

value: input


title: ventral_SNpc_HC3

description: ~100 LCM captured nigral cells


title: dorsal_SNpc_HC3

description: ~100 LCM captured nigral cells


title: roots_reil1-1 reil2-2_20°C_replicate2

value: reil1-1 reil2-2 double T-DNA mutant


title: roots_reil1-1 reil2-2_20°C->10°C_1d_replicate3

value: acclimating to 10°C for 1 day

value: 1 day


title: 58_iNSLC


title: roots_reil1-1 reil2-1_20°C->10°C_1w_replicate3

description: gene expression of mixotrophic hydroponic roots of the reil1-1 reil2-1 double mutant acclimating 7 days to 10°C

value: 1 week

value: reil1-1 reil2-1 double T-DNA mutant


title: roots_reil1-1 reil2-1_20°C->10°C_1w_replicate2


title: sample_DKO-input-rep1

value: female

value: kidney

value: postnatal day 18


title: roots_reil1-1 reil2-1_20°C->10°C_1w_replicate1


title: 57_iNSLC


title: sample_SKO-input-rep2

value: male


title: roots_reil1-1 reil2-2_20°C_replicate1


title: 56_iNSLC


title: sample_SKO-input-rep1


title: dorsal_SNpc_HC7

description: ~100 LCM captured nigral cells

value: substantia nigra pars compacta neurons

value: dorsal

value: M


title: ventral_SNpc_HC7

description: ~100 LCM captured nigral cells

value: ventral


title: ventral_SNpc_HC1

description: ~100 LCM captured nigral cells


title: sample_wt-m6A-rep1

value: m6A IP


title: 55_iNSLC


title: roots_reil1-1 reil2-1_20°C->10°C_1d_replicate3

description: gene expression of mixotrophic hydroponic roots of the reil1-1 reil2-1 double mutant acclimating 1 day to 10°C

value: root


title: sample_wt-input-rep2

value: wildtype


title: roots_reil1-1 reil2-1_20°C->10°C_1d_replicate2


title: 54_iNSLC

value: iNSLC


title: dorsal_SNpc_HC1

description: ~100 LCM captured nigral cells


title: sample_wt-input-rep1

value: input


title: 50_iNSLC


title: dorsal_SNpc_HC6

description: ~100 LCM captured nigral cells


title: ventral_SNpc_HC6

description: ~100 LCM captured nigral cells


title: roots_reil1-1 reil2-1_20°C->10°C_1d_replicate1

value: acclimating to 10°C for 1 day


title: roots_reil1-1 reil2-1_20°C_replicate3

description: gene expression of mixotrophic hydroponic roots of the reil1-1 reil2-1 double mutant at 20°C

value: not cold acclimated, 20°C

value: 0 day


title: 52_iNSLC


title: scaRNA-seq Mouse HS2HS3 fetal liver cells late erythroid (24h) replicate 3

description:
Total RNA <300nt in length (PAGE size selected)
hs2hs3_24.fwd.tss.bw
hs2hs3_24.rev.tss.bw
hs2hs3_24.fwd.tes.bw
hs2hs3_24.rev.tes.bw

source_name: Differentiated CD117+ mouse fetal liver erythroid cells

tag: cell markers


title: roots_reil1-1 reil2-1_20°C_replicate2

value: reil1-1 reil2-1 double T-DNA mutant


title: roots_reil1-1 reil2-1_20°C_replicate1


title: scaRNA-seq Mouse HS2HS3 fetal liver cells late erythroid (24h) replicate 2

value: Differentiated CD117+ mouse fetal liver erythroid cells


title: scaRNA-seq Mouse HS2HS3 fetal liver cells late erythroid (24h) replicate 1


title: 47_iNSLC


title: 48_iNSLC


title: 49_iNSLC


title: scaRNA-seq Mouse R1R2 fetal liver cells late erythroid (24h) replicate 2

description:
Total RNA <300nt in length (PAGE size selected)
r1r2_24.fwd.tss.bw
r1r2_24.rev.tss.bw
r1r2_24.fwd.tes.bw
r1r2_24.rev.tes.bw


title: Patient 2

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

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

description:
Single-cell RNA-seq of Embryonic Skin
CellAnnotation_AllCells.tsv
CellAnnotation_Tcells.tsv
raw_gene_bc_matrices_h5.h5

data_processing:
Raw sequencing data were demultiplexed using the function mkfastq in Cell Ranger (version 2.1.0).
Sequencing data were aligned to the reference genome with Cell Ranger count and merged with Cell Ranger aggr.
Genome_build: GRCh38/h38
Supplementary_files_format_and_content: raw_gene_bc_matrices_h5.h5; read count matrix with cells / barcodes (columns) and genes (rows)
Supplementary_files_format_and_content: CellAnnotation_AllCells.tsv; mapping of cell types to barcodes across samples
Supplementary_files_format_and_content: CellAnnotation_Tcells.tsv; mapping of T cells to barcodes; prediction T cell subsets

source_name: Embryonic Skin

extract_protocol:
For the preparation of single cell suspensions of fetal organs, a dissociation kit in combination with an automatic tissue dissociator (gentleMACS Octo dissociater, Miltenyi Biotec) was used according to the manufacturer´s instruction. Briefly, the dissociation kit samples (3 biopsies à 4 mm) were put onto gentleMACS for mechanical treatment. The “h_skin_01” preinstalled program was used. Cell clumps and tissue debris were removed with a 70 μm nylon cell strainer and remaining cells were further processed for indicated procedures.
Single-cell RNA-seq was performed using the Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics) according to the manufacturer’s protocol. Briefly, viable CD3+ T cells (up to 5.000 cells/fetus) were FACS-sorted from single cell suspensions of four fetal (17-22 weeks EGA) skin donors. In order to get a more complete resolution of human skin development, we additionally sort-purified up to 10.000 total skin cells and mixed them with the CD3+ T cell population. Cells were pelleted by centrifuging for 5 min at 4°C at 300 × g and resuspended in PBS with 0.04% BSA. Up to 10.000 cells suspended in reverse transcription reagents, along with gel beads, were segregated into aqueous nanoliter-scale Gel Beads in Emulsion (GEMs). The GEMs were then reverse-transcribed in a C1000 Thermal Cycler (Bio-Rad) programmed at 53°C for 45 min, 85°C for 5 min, and hold at 4°C. After reverse transcription, single-cell droplets were broken, and the single-strand cDNA was isolated and cleaned with Cleanup Mix containing Dynabeads MyOne SILANE (Thermo Fisher Scientific). cDNA was then amplified with a C1000 Thermal Cycler programmed at 98°C for 3 min, 10 cycles of (98°C for 15 s, 67°C for 20 s, 72°C for 1 min), 72°C for 1 min, and hold at 4°C. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, and index adapter ligated, with cleanup in-between steps using SPRIselect Reagent Kit (Beckman Coulter). Post-ligation product was amplified with a T1000 Thermal Cycler programmed at 98°C for 45 s, 10 cycles of (98°C for 20 s, 54°C for 30 s, 72°C for 20 s), 72°C for 1 min, and hold at 4°C. The sequencing-ready library was cleaned up with SPRIselect beads and sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 3000/4000 platform and the 75 bp paired-end configuration.

tag: estimated gastational age

value: 17 weeks


title: scaRNA-seq Mouse R1R2 fetal liver cells late erythroid (24h) replicate 1


title: roots_Col-0_20°C->10°C_1w_replicate1

description: gene expression of mixotrophic hydroponic roots of Arabidopsis thaliana (Col-0) acclimating 7 days to 10°C

value: acclimating to 10°C for 1 week

value: 1 week

value: wild type (Col-0)


title: roots_Col-0_20°C->10°C_1w_replicate3


title: 44_iNSLC

source_name: E01F A2 iNSLC


title: dorsal_SNpc_HC2

description: ~100 LCM captured nigral cells

value: substantia nigra pars compacta neurons

value: dorsal

value: F


title: Patient 1

value: 20 weeks


title: roots_Col-0_20°C->10°C_1d_replicate3

description: gene expression of mixotrophic hydroponic roots of Arabidopsis thaliana (Col-0) acclimating 1 day to 10°C

value: root

value: 1 day


title: Patient 3

value: 22 weeks


title: ventral_SNpc_HC2

description: ~100 LCM captured nigral cells

value: ventral


title: 42_iNSLC

value: iNSLC


title: scaRNA-seq Mouse Wildtype fetal liver cells late erythroid (0h) replicate 3

description:
Total RNA <300nt in length (PAGE size selected)
wt_0.fwd.tss.bw
wt_0.rev.tss.bw
wt_0.fwd.tes.bw
wt_0.rev.tes.bw

source_name: Undifferentiated CD117+ mouse fetal liver erythroid cells

value: wildtype


title: roots_Col-0_20°C->10°C_1w_replicate2


title: 41_iNSLC


title: scaRNA-seq Mouse Wildtype fetal liver cells late erythroid (0h) replicate 2

value: Undifferentiated CD117+ mouse fetal liver erythroid cells


title: scaRNA-seq Mouse R1R2 fetal liver cells late erythroid (24h) replicate 3


title: PA-15-SM

city: Lyon

first: Antoine

last: Marçais

address: 21 avenue Tony Garnier

institute: Inserm

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto hg38 assembly of human genome using STAR 2.5.3a.
Quantification : Gene expression was quantified using HTSeq v0.6.1p1 (union mode) and Ensembl release 97 annotations.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated values file containing raw read counts in each sample.

source_name: NK cells

extract_protocol:
RNA was extracted from cell-sorted NK cells using Direct-Zol RNA Microprep Kit (Ozyme) according to the manufacturer instructions.
Libraries were constructed following the protocol developped by Picelli et al (Nature Protocols, 2014; PMID: 24385147).

tag: disease state

value: chronic hepatitis B

value: PBMC


title: roots_Col-0_20°C->10°C_1d_replicate1

tag: treatment

value: acclimating to 10°C for 1 day


title: scaRNA-seq Mouse Wildtype fetal liver cells late erythroid (0h) replicate 1


title: 40_iNSLC


title: roots_Col-0_20°C_replicate3

description: gene expression of mixotrophic hydroponic roots of Arabidopsis thaliana (Col-0) at 20°C

value: not cold acclimated, 20°C

value: 0 day


title: roots_Col-0_20°C->10°C_1d_replicate2

value: wild type (Col-0)


title: 45_iNSLC


title: PA-16-BK


title: PA-13-HE


title: 39_iNSLC


title: scaRNA-seq Mouse Wildtype fetal liver cells late erythroid (24h) replicate 3

description:
Total RNA <300nt in length (PAGE size selected)
wt_24.fwd.tss.bw
wt_24.rev.tss.bw
wt_24.fwd.tes.bw
wt_24.rev.tes.bw

value: Differentiated CD117+ mouse fetal liver erythroid cells


title: 38_iNSLC


title: VS-10-MA

value: control healthy donor


title: scaRNA-seq Mouse Wildtype fetal liver cells late erythroid (24h) replicate 1


title: ATAC-seq Mouse HS2HS3 fetal liver cells replicate 3

description:
Genome-wide library of transposase acccessible fragments
atac.24h.hs2hs3.rpm.bw

data_processing:
Mapping : bowtie/0.1.19 -m 2 --maxins 1000, --chunkmbs 256 --best --strata mm9
PCR duplicates removed (samtools/0.1.19 rmdup)
convert to bedpe (bedtools/2.25.0 bamtobed -mate1) and grep chr | cut -f 1,2,3,5,6,9
convert to bed file of fragments using awk (awk used to adjust fragment size to compensate for Tn5 transposase cutting (forward strand fragments shift +4, reverse strand shift -5bp))
remove reads mapping to chromosomes X Y and M (grep -v chr[a-zA-Z])
conversion to scaled reads per million bedGraph (bedtools/2.25.0 genome cov -bg) based on fragments per million coverage over consensus peaks
conversion to scaled bigwig, one pairi for each comparison e.g. Wt vs R1R2 (ucsctools bedGraphToBigWig)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file of fragment coverage (PCR duplicates removed), scaled by fragments per million, biological triplicate merged

extract_protocol:
isolation protocol: 50,000 cells were pelleted and resuspended in ATAC lysis buffer (Beunrostro et al 2013)
MinElute PCR purification kit
ATAC-seq (Buenrostro et al 2013)

tag: strain

value: Fetal liver cultured ex vivo

tag: developmental stage

value: late erythroid


title: VS-06-FN

tag: tissue


title: 35_iNSLC


title: 36_iNSLC


title: scaRNA-seq Mouse Wildtype fetal liver cells late erythroid (24h) replicate 2

tag: genotype


title: VS-07-TE


title: NC-1

city: Wuhu

first: wei

middle: cheng

last: wu

address: 2 Zheshan West Road, Jinghu District

institute: Yijishan Hospital of Wannan Medical College

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Ensembl
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: All cells were cultured in RPMI-1640 (Gibco, USA) containing 10% fetal bovine serum and 100 μg/mL streptomycin (Gibco, USA) at 37 ˚C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549 cells transfected with si-NC and si-ENC1

tag: cell line

value: lung cancer cells

value: transfected with si-NC


title: ENC1-2

tag: genotype/variation

value: transfected with si-ENC1


title: NC-3


title: ATAC-seq Mouse HS2HS3 fetal liver cells replicate 2


title: VS-03-FX


title: ATAC-seq Mouse HS2HS3 fetal liver cells replicate 1


title: roots_Col-0_20°C_replicate1

tag: ecotype

value: root

tag: time point


title: 33_iNSLC

value: iNSLC


title: ENC1-3


title: PA-12-KM


title: ATAC-seq Mouse Wildtype fetal liver cells replicate 3

description:
Genome-wide library of transposase acccessible fragments
atac.24h.wt.rpm.bw

value: wildtype


title: 34_iNSLC


title: 32_iNSLC


title: roots_Col-0_20°C_replicate2


title: ENC1-1


title: ATAC-seq Mouse Wildtype fetal liver cells replicate 2


title: NC-2


title: 31_iNSLC


title: ATAC-seq Mouse Wildtype fetal liver cells replicate 1


title: 30_iNSLC


title: VS-05-GJ


title: Atrophy

city: New Haven

first: Leyuan

last: Xu

state: CT

address: 300 Cedar Street, Ste S255B

department: Internal Medicine/Section of Nephrology

institute: Yale University

description: Named "atrophy" in the combined processed data

data_processing:
Cell Ranger version 3.0.0 was used to process Chromium single cell 3’ RNA-seq output and align the Read to the mouse reference transcriptome (mm9).
A downstream data analysis was performed using Seurat v3.1.0 R package
Red blood cells, cells with transcriptome <200 (likely cell fragments) or > 3,500 (potentially cell duplets) and cells with mitochondrial gene percentage >50% were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include gene counts, data, and scaled data for each cell and each sample

source_name: Kidney

extract_protocol:
Injured kidneys were harvested, minced into approximately 1 mm3 cubes, and digested using Liberase™ (100 µg/mL) and DNase I (10 µg/mL) (Roche Diagnostics) for 25 min at 37 °C. Reaction was deactivated by adding chilled DMEM with 10% FBS. The solution was then passed through a 40-µm cell strainer. After centrifugation at 1,000 RPM for 10 min at 4 °C, the cell pellet was resuspended in chilled DMEM with 10% FBS and passed through another 40-µm cell strainer. Cell number and viability were analyzed using trypan blue staining (Invitrogen). This method generated single cell suspension with greater than 70% viability.
The scRNA-seq library and sequencing were performed at the Yale Center for Genome Analysis (YCGA).

value: Kidney

tag: age

value: 11-week old

value: Wild-type

value: Unilateral IRI with contralateral kidney intact


title: 29_iNSLC


title: mNET-seq Mouse HS2HS3 fetal liver cells late erythroid (24h) replicate 2

description:
RNA immunopreciptated with Pol2
HS2HS3.fwd.fullfrag.bw
HS2HS3.rev.fullfrag.bw


title: 28_iNSLC


title: Repair

description: Named "repair" in the combined processed data

value: Unilateral IRI with contralateral nephrectomy


title: mNET-seq Mouse HS2HS3 fetal liver cells late erythroid (24h) replicate 1


title: SmallRNA_Tv03

city: Beijing

first: Zhensheng

last: Wang

address: Dongdan santiao

department: Microbiology and Parasitology

institute: Peking Union Medical College

data_processing:
Raw sequencing data  generated from Illumina  NextSeq 500
The quality of raw sequencing data was evaluated by FastQC (v0.11.7).  The 3' and 5' adaptors were trimmed and reads shorter than 18 nt or longer than 40 nt were filtered out by Cutadapt (v1.17) and Python2 (v2.7.5)
The dataset was further mapped to the genome of T. vaginalis G3 strain (TrichDB, release 47, http://trichdb.org/trichdb/) using BLASTN to remove any contamination and yielded a clean data pool.
Genome_build: T. vaginalis G3 strain (TrichDB, release 47, http://trichdb.org/trichdb/)

organism: Trichomonas vaginalis

source_name: Trophozoites of Trichomonas vaginalis

growth_protocol: Three in vitro adapted T. vaginalis strains (Tv01-03) were maintained in Diamond’s media supplemented with 10% heat-inactivated bovine serum, penicillin (1000 units/ml) and streptomycin (0.1mg/ml) at 37℃ in tri-gas incubator (5% CO2, 5% O2, 90% N2)

extract_protocol:
Total RNA of each isolate was extracted employing TRIzol Reagent (Invitrogen, Shanghai, China) and treated with DNase I to remove any genomic DNA contamination.
Small RNA molecules were ligated to 5' and 3' adaptors consecutively and then converted to cDNA by reverse transcription followed by polymerase chain reaction (PCR) amplifications. Approximately 2.34 femtomole of reverse transcription - PCR (RT-PCR) products per sample were sequenced directly by Illumina NextSeq 500 system (Illumina, USA) at 50 base pairs (bp) single-read by Aksomics Inc (Shanghai, China)


title: mNET-seq Mouse R1R2 fetal liver cells late erythroid (24h) replicate 2

description:
RNA immunopreciptated with Pol2
R1R2.fwd.fullfrag.bw
R1R2.rev.fullfrag.bw


title: 27_iNSLC

data_processing:
Sequenced reads were trimmed using trimmomatic based on reads quality and adaptor sequence
The resulting reads were mapped to cj1700 using STAR version 2.6.0c
Reads mapped to exon regions were counted using featureCount version 1.5.1.
Raw count data was loaded to R software and normalized using Seurat version 3.0.0.
Genome_build: cj1700
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each Sample.

extract_protocol:
Cells were sorted into 96 well plate with a flow cytometer SH800 (SONY) and dissolved with single cell lysis buffer
Library were constructed using GenNext RamDA-seqTM Single Cell Kit and Netera XT library prep kit


title: SmallRNA_Tv02


title: 26_iNSLC


title: HDM+c-di-GMP5

city: Auburn

first: Amarjit

last: Mishra

state: AL

address: 1130 Wire Road, 264 Greene Hall

department: Pathobiology

institute: Auburn University

description: Gene expression data from house dust mite and c-di-GMP group

hyb_protocol: After fragmentation and terminal labelling, cRNA were hybridized on GeneChip Mouse Genome Array (Further GeneChip was washed and stained in Fluidics Station 450)

scan_protocol: GeneChips Array scanning was performed according to the manufacturer's instruction.

data_processing:
Data was processed using Transcriptome Analysis Console (TAC) 4.0.1 instructions.
#%result_name=Auburn_1
#%array_type=Clariom_S_Mouse_HT
#%annotation=Clariom_S_Mouse_HT.r1.na36.mm10.a1.transcript.csv
#%comparison=1 vs 2

label: biotin

source_name: Mice lung from House dust mite and c-di-GMP received group

label_protocol: Biotinylated cRNA were prepared according to the standard Array protocol (GeneChip Whole Transcriptome Array, Thermo Fisher Scientific).

growth_protocol: Six to eight weeks old naïve C57BL/6 J mice were purchased from Jackson Laboratory (Bar Harbor, MA) and all animal procedures and experimental protocols were approved by the Auburn University Animal Care and Use Committee.

extract_protocol: Extraction of total RNA was performed using Invitrogen PureLink RNA Mini Kit according to the manufacturer's instructions.

treatment_protocol: For Th1-Th17 asthma model, mice were sensitized with 50 μg HDM (Greer Laboratories) and 0.5 μg c-di-GMP (Biolog Inc.) on days 1, 3, and 5 intranasal. After 5 days of rest, mice were subjected to 3 challenge sets each with 3 consecutive challenges with HDM & c-di-GMP with a rest of 3 days between each set. The c-di-GMP and HDM was instilled only on the first day of each challenge set, followed by HDM. Similarly, Th2 model followed the same sensitization and challenge protocol where 50 μg HDM was instilled except c-di-GMP.

value: 6-8 week old

value: house dust mite and c-di-GMP group

value: lung


title: SmallRNA_Tv01


title: 25_iNSLC


title: mNET-seq Mouse Wildtype fetal liver cells late erythroid (24h) replicate 2

description:
RNA immunopreciptated with Pol2
wt.fwd.fullfrag.bw
wt.rev.fullfrag.bw

data_processing:
Library strategy: mNET-seq
alignment (bowtie/0.1.19 -m 2 -p 4 --maxins 1000 --best --strata --chunkmb 256)
isolate proper read pairs and convert to .bam (samtools/0.1.19 view -bS -f 3)
PCR duplicates removed (samtools/0.1.19 rmdup)
remove reads mapping to annotated (UCSC) ncRNA (even by 1bp) or annotated (UCSC) 3' splice sites (bedtools/2.25.0 intersect -v -wa -s -split)
convert to bedpe (bedtools/2.25.0 bamtobed -mate1) and grep chr | cut -f 1,2,3,5,6,9
convert to bed file of fragments using awk.
count millions of mapped reads (wc -l)
make reads per million normalised strand specific coverage tracks (bedtools/2.25.0 genomecov -bg -strand (+/-) -ibam)
conversion of bedGraphs to bigwig (ucsctools bedGraphToBigWig)
Genome_build: mm9
Supplementary_files_format_and_content: bigWigs of stranded full RNA fragments, biological duplicate merged
Supplementary_files_format_and_content: bigWigs of stranded 3' ends of RNA (Pol2 active site, with 2nt window to improve coverage) coverage, biological duplicate merged

extract_protocol:
isolation protocol5x10^6 cells were aliquoted per replicate, pelleted by centrifugation (500g, 5min, R.T) and washed once in ice cold 5mL 1xPBS before snap freezing in a dry ice ethanol bath. Samples were snap frozen and transferred to storage at -80°C until use.  The antibody used for the mNET-seq samples is no longer commercially available. Antibody used in this study was kindly provided by Dr. Hiroshi Kimura. The antibody targets Pol II total CTD.
mNET-seq was performed as in (Nojima et al. 2015) but with a starting input cell number of 5x10^6
NEB small RNA for Illumina

value: Differentiated CD117+ mouse fetal liver erythroid cells


title: mNET-seq Mouse R1R2 fetal liver cells late erythroid (24h) replicate 1


title: mNET-seq Mouse Wildtype fetal liver cells late erythroid (24h) replicate 1


title: RNA-seq Mouse Wildtype fetal liver cells early erythroid (0h) replicate 3

description:
poly adenylated RNA (ribo and globin RNA depleted)
RNAseq.0h.plus.rpm.bw
RNAseq.0h.minus.rpm.bw

data_processing:
alignment (bowtie/0.1.19 -m 2 -p 4 --maxins 1000 --best --strata --chunkmb 256)
convert to .bam file (samtools/0.1.19 view -bS)
find read pairs mapping 100% to an annotated intron (bedtools/2.25.0 intersect -s -split -f 1)
remove reads mapping to exons and ncRNA (even by 1bp) (bedtools/2.25.0 intersect -v -wa -s -split)
find read pairs mapping 100% to an annotated intron (bedtools/2.25.0 intersect -s -split -f 1)
sort by coordinate (samtools/0.1.19 sort)
count millions of mapped reads (samtools/0.1.19 flagstat)
make reads per million normalised strand specific coverage tracks (bedtools/2.25.0 genomecov -bg -strand (+/-) -ibam)
conversion of bedGraphs to bigwig (ucsctools bedGraphToBigWig)
merging of bigwigs from same time point and strand (ucsctools bigWIgMerge)
Genome_build: mm9
Supplementary_files_format_and_content: strand specific bigWigs of Intronic RNA fragment coverage scaled by fragments per million, biological triplicate merged

extract_protocol:
isolation protocol: 5x10^6 cells were aliquoted per replicate, pelleted by centrifugation (500g, 5min, R.T) and washed once in 5mL 1xPBS before lysis in TRI Reagent (Merck) by repeated pipetting. Samples were snap frozen and transferred to storage at -80°C until use.
Samples in TRI reagent were thawed on ice before extraction using the Direct-zol RNA Miniprep Kit (Zymo) according to the manufacturers protocol and including an on column DNase digestion step for an increased incubation time of 30mins.
2.0mg of high quality Total RNA (RIN>9.6 - Tapestation Agilent), quantified using Qubit (Thermo Fisher Scientific) was depleted of ribosomal and globin RNA species with the Globin-Zero Gold rRNA Removal Kit (Illumina). polyA+ RNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). polyA+ RNA was made into a strand specific library using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) (utilising a 15 minute fragmentation step, 12 cycles of PCR with single indexing).

value: Undifferentiated CD117+ mouse fetal liver erythroid cells


title: 14_ES

source_name: No.40 ESC

value: ESC


title: KO_llog_2

city: Pittsburgh

first: Thomas

middle: Alexander

last: Hooven

state: PA

address: 4401 Penn Ave., Rangos Research Bldg #8128

department: Pediatrics

institute: University of Pittsburgh

description: The log2-fold change values in the associated processed data file represent knockout expression relative to wild type for each growth phase

data_processing:
Trimmed and demultiplexed reads were aligned to the 10/84 genome using Bowtie 2
BAM alignments were used for statistical analysis using DESeq
Genome_build: NZ_CP006910
Supplementary_files_format_and_content: DESeq statistical data in XLSX format

organism: Streptococcus agalactiae

source_name: Laboratory-grown bacteria

growth_protocol: Samples were grown stationary at 37 C

extract_protocol:
ThermoFisher Ribopure Bacterial RNA Purifcation Kit
Ribo-Zero Plus rRNA Depletion Kit followed by Illumina TruSeq total RNA Kit Library Preparation

value: CNCTC 10/84 mrvR deletion mutant

tag: growth phase

value: late log

tag: replicate


title: KO_s_1

value: stationary


title: 12_ES

city: Shinjuku

first: Sho

last: Yoshimatsu

institute: Keio University School of Medicine


title: KO_llog_1


title: RNA-seq Mouse Wildtype fetal liver cells early erythroid (0h) replicate 1

city: Oxford

first: Martin

last: Larke

institute: University of Oxford


title: 11_ES


title: KO_elog_2

value: early log


title: KO_s_2


title: 10_ES


title: 19_iPS

source_name: E01F A-2-2 iPSC

value: iPSC


title: HDM+c-di-GMP3


title: HDM+c-di-GMP1


title: KO_elog_1


title: 02_fiblo

source_name: E01F fibroblast

value: Fibroblast


title: RNA-seq Mouse Wildtype fetal liver cells late erythroid (24h) replicate 3

description:
poly adenylated RNA (ribo and globin RNA depleted)
RNAseq.24h.plus.rpm.bw
RNAseq.24h.minus.rpm.bw

value: wildtype


title: RNA-seq Mouse Wildtype fetal liver cells late erythroid (24h) replicate 2


title: RNA-seq Mouse Wildtype fetal liver cells early erythroid (0h) replicate 2


title: HDM+c-di-GMP2


title: WT_s_2

value: CNCTC 10/84 wild type


title: HDM5

description: Gene expression data from house dust mite group

source_name: Mice lung from House dust mite received group

value: house dust mite group


title: HDM+c-di-GMP4


title: RNA-seq Mouse Wildtype fetal liver cells late erythroid (24h) replicate 1


title: WT_s_1


title: adult mouse pituitary 2

city: La Jolla

first: Michal

last: Krawczyk

address: 9500 Gilman Dr

department: Ophthalmology

institute: UCSD

description: 10X single cell ATAC library V1

data_processing:
Raw sequencing data were converted to fastq format using cell ranger atac mkfastq (10x Genomics, v.1.0.0).
Read counts of single library were aligned to mm10 reference genome for quantification and analyzed by cellranger-atac count (10x Genomics, v.1.0.0).
Cellranger-atac aggr was used on integrated libraries to normalize both sample data to equal sequencing depth
Genome_build: mm10
Supplementary_files_format_and_content: filtered peak matrix, h5, ATACseq peaks
Supplementary_files_format_and_content: filtered tf matrix, h5, transcription factor motifs
Supplementary_files_format_and_content: peak annotation, tsv, gene annotations for identified ATAC peaks

source_name: dissected pituitary gland

growth_protocol: mice were housed under standard conditions. Pituitaries were collected by dissection postmortem

extract_protocol:
Pituitaries were collected from two adult male mice. Nuclei isolation for scATAC-seq was performed following the instruction provided by 10xGenomics (scATAC-V1) with some modifications. 100,000 cells were added to a 2 mL microcentrifuge tube and centrifuged (300 x g for 5 min at 4°C). The supernatant was removed without disrupting the cell pellet. Lysis Buffer [10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% Digitonin, and 1% BSA] was diluted by Lysis Dilution Buffer [10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA] to make 0.1x Lysis Buffer. 100 μL chilled 0.1x Lysis Buffer was added to the cell pellet, and then pipette-mixed 10 times. The microcentrifuge tube was then incubated on ice for 5 min. Next, 1 mL of chilled Washing Buffer [10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, and 1% BSA] was added and gently pipette-mixed 5 times. Nuclei were centrifuged (500 x g for 5 min at 4°C) to remove the supernatant, and the wash was repeated. An appropriate volume of chilled Diluted Nuclei Buffer (10xGenomics) was added to resuspend nuclei at 2,500 nuclei/μL to retrieve/target 6,000 nuclei per library following the standard protocol provided by Chromium Single Cell ATAC Library and Gel Bead kit (10x Genomics, v1).
Libraries were constructed using standard protocol provided by Chromium Single Cell ATAC Library and Gel Bead kit (10x Genomics, v1). Each sample was uniquely barcoded
Libraries were then pooled and loaded on a NovaSeq Illumina sequencer and sequenced to ~50% saturation

value: adult

tag: Sex

value: male


title: ChIP-seq Input Mouse Wildtype fetal liver

description:
Genome-wide library of DNA fragments
input_24h.bw
input_24h.bw

data_processing:
Mapping : bowtie/0.1.19 -m 2 --maxins 1000, --chunkmbs 256 --best --strata mm9
Read pairs with samflag -3 isolated (proper pairs) (samtools/0.1.19 view -f3 )
PCR duplicates removed (samtools/0.1.19 rmdup)
convert to bedpe (bedtools/2.25.0 bamtobed -mate1) and grep chr | cut -f 1,2,3,5,6,9
convert to bed file of fragments using awk.
peaks called (macs2/2.0.10)
coverage of fragments over peaks determined (bedtools/2.25.0 coverage -counts)
normalisation based on fragments per million mapped fragments under peaks (all peaks merged to form consensus from a given comparison, e.g 3x Wildtype vs 3 x R1R2 KO)
conversion to scaled bedGraph (bedtools/2.25.0 genome cov -bg) based on fragments per million coverage over consensus peaks
conversion to scaled bigwig, one pair for each comparison e.g. Wt vs R1R2 (ucsctools bedGraphToBigWig)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file of fragment coverage (PCR duplicates removed), scaled by fragments per million over consensus peak calls, biological triplicate merged

growth_protocol: Mouse fetal livers were harvested at E12.5 and disaggregated in expansion media (StemPro (ThermoFisher)) supplemented with Epo (1U/ml), SCF (50ng/ml), Dexamethosone (1μM)). Cells from individual fetal livers were grown for 6 days, maintaining a constant erythroblast cell count of <= 1 x10^6. Cells were genotyped as wildtype, homozygous R1R2 or homozygous HS2HS3 during expansion. Cells were counted using the nucleocounter before selection for CD117 positive cells using magnetic assisted cell separation LS columns (130-042-401 - Milltenyi) following the manufacturers protocol. Cells were left to recover for 6h in expansion media at a density of 1x10^6 cells/ml. Aliquots of 5x10^6 cells were harvested as the ‘0h’ timepoint corresponding to early erythropoiesis whilst the remaining cells were re-suspended in differentiation media (which is expansion media with the following changes: increased levels of Epo (5U/ml) and transferrin (0.5mg/ml), SCF and Dexamethasone removed). To induce erythroid differentiation cells were grown for 24h before harvesting for the ‘24h’ timepoint. Cell morphology was examined and immunophenotype determined by flow assisted cell sorting (FACS) (Attune NxT – Thermo Fisher Scientific) with markers for CD117 and Ter119 at the 0h and 24h timepoints. 0h of erythropoiesis was defined as (CD117+,Ter119-) and 24h as (CD117-, Ter119+) and cells isolated were confirmed as having these appropriate erythroid stage markers (Edling and Hallberg 2007; Hay et al. 2016; McGrath, Catherman, and Palis 2017)

extract_protocol:
isolation protocol: 5 million Mouse Fetal Liver cells were pelleted (500g, 5 mins, RT) before resuspension in 9ml of RPMI media (+10% FBS) and addition of 1ml fixation solution (50mM HEPES pH 8.0, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 100mM NaCl, 10% formaldehyde). Samples were incubated on the roller at room temperature for 10 mins and fixation reactions quenched by the addition of 1.25ml of fresh glycine solution (1M). Samples were incubated on the roller for 5 mins before spinning down at (300g, 5 mins, 4°C), washing 1 x in 10mls of ice-cold PBS and snap freezing the pellet in a dry ice ethanol bath. All samples were stored at -80°C until use.
DNA was purified by phenol-chloroform extraction with PhaseLock tubes (5Prime) and ethanol precipitation with NaOAc, and 2 µl GlycoBlue (Invitrogen).
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs) - 12 cycles of PCR utilised

value: Fetal liver cultured ex vivo

value: late erythroid

tag: antibody conditions


title: adult mouse pituitary 1

description: 10X single cell ATAC library V1


title: WT_llog_2


title: ChIP-seq Pol2 Mouse HS2HS3 fetal liver cells replicate 3

description:
Genome-wide library of Immunoprecipitated fragments
bhom.rpmpeaks.bw
bhom.rpmpeaks.bw

value: Antibody:2ug of Anti Rbp1 (Pol2) - Santa Cruz Biotechnology (sc899)


title: WT_llog_1


title: WT_elog_1


title: WT_elog_2


title: 6_S129: PL-Train-6d_rep3

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
RNA-Seq was run on an Illumina HiSeq 4000 as paired end 150 reads.
Alignments were guided by a Gene Transfer File (Ensembl GTF Rnor_6.0.84) and the mean read insert sizes and their standard deviations were calculated using Picard tools (v.1.126)
The Read Per Million (RPM) normalized BigWig files were generated using BEDTools (v2.17.0) and bedGraphToBigWig tool (v4).
DESeq2 was used to generate gene count tables and differential gene analysis.
Genome_build: Rnor_6.0.84
Supplementary_files_format_and_content: count table (txt), bigWig (bw)

organism: Rattus norvegicus

source_name: Prelimbic Cortex

extract_protocol:
Rats were euthanized by decapitation. Their brains were quickly dissected and snap-frozen in pre-chilled isopentane on dry ice. PL (bregma +3.7mm to +2.2mm) and dHC (bregma -2.3mm to -4.52mm) tissue was isolated by punches in a cryostat using a Neuro Punch (19 gauge, Fine Science Tools, Foster City, CA) as described previously (Milekic et al., 2007) and immediately submerged into Qiazol (Qiagen, Venlo, Netherlands). Total RNA was isolated using the RNAeasy Plus Universal Kit following the manufactureâ€™s protocol (Qiagen, Venlo, Netherlands). 500 ng of RNA was reverse-transcribed using QuantiTect Reverse Transcription Kit (Qiagen, Venlo, Netherlands) in order to perform real-time polymerase chain reaction (RT-PCR) on all individual samples to validate immediate early gene c-Fos induction in trained vs. naÃ¯ve animals. RNA samples for naÃ¯ve and both groups of trained animals were pooled into 3 biological replicates (n=5/group per condition) and submitted to the New York University School of Medicine Genome Technology Center for further quality control, quantification and normalization. RNA integrity was tested on an Agilent 2100 Bioanalyzer before library preperation.
RNA-Seq library preps were made using the Illumina TruSeqÂ® Stranded mRNA LT kit (Cat #RS- RS-122-2101 or RS-122-2102), on a Beckman Biomek FX instrument, using 200 ng of total RNA as input, amplified by 12 cycles of PCR, and run on an Illumina 4000, as paired end 150 reads.

value: Long-Evans

value: Brain

value: Adult


title: Top3-Flag replicate input

type: genomic

city: Milan

first: Dana

last: Branzei

address: Via Adamello 16

country: Italy

institute: IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation

description: Binding pattern of Top3 by ChIP-on-chip after arrest of cells in G2/M with Nocodazole (replicate)

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner.

data_processing: BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

label: Dynabeads Protein A invitrogen

organism: Saccharomyces cerevisiae

source_name: G2/M arrest with Nocodazole

label_protocol: Sample preparation and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol.

growth_protocol: Cells were grown in YP+Glucose 2% (YPD) media at 25°C in 500 ml flask for a density of 1.2×10^7 cells/ml.

extract_protocol: Binding profiles by ChIP-on-chip were determined as described in (Bermejo et al., 2009).

treatment_protocol: G2/M synchronization was performed by 10-20 μg/ml Nocodazole for 120-180 minutes at 25°C and validated by microscopy. Cells were treated with 0.2 mg/ml of Auxin (stock 50 mg/ml) during the arrest, if mentioned. Cells were collected and fixed with 1% formaldehyde for 30 min at room temperature for further ChIP.

tag: strain genotype

value: W303 MATa RAD5+, Top3-10FLAG::KANMX4

tag: antibody

value: Anti-FLAG M2 F1804 (SIGMA)


title: 4_S127: PL-Train-6d_rep1


title: 5_S128: PL-Train-6d_rep2


title: smc6-56 Top3-Flag input

description: Binding pattern of Top3 in smc6-56 background by ChIP-on-chip after arrest of cells in G2/M with Nocodazole

value: W303 MATa smc6-56-13myc::KAN, Top3-10FLAG::KANMX4


title: smc6-56-sup Top3-Flag input

description: Binding pattern of Top3 in smc6-56-sup background by ChIP-on-chip after arrest of cells in G2/M with Nocodazole

value: W303 MATa smc6-56-sup-13myc::KAN, Top3-10FLAG::KANMX4


title: smc6-56-sup Top3-Flag


title: Top3-Flag replicate


title: smc6-56 Top3-Flag


title: ChIP-seq Pol2 Mouse R1R2 fetal liver cells replicate 1

address: Headley Way

description:
Genome-wide library of Immunoprecipitated fragments
ahom.rpmpeaks.bw
ahom.rpmpeaks.bw


title: ChIP-seq Pol2 Mouse R1R2 fetal liver cells replicate 2


title: ChIP-seq Pol2 Mouse R1R2 fetal liver cells replicate 3


title: ChIP-seq Pol2 Mouse HS2HS3 fetal liver cells replicate 2


title: ChIP-seq Pol2 Mouse HS2HS3 fetal liver cells replicate 1


title: HA-Mms4 input

description: Binding pattern of Mms4 by ChIP-on-chip after arrest of cells in G2/M with Nocodazole

value: W303 MATa RAD5+, mms4::pADH1-tc3-3xHA-Mms4::HPHMX

value: anti-HA (F-7) Santa Cruz Biotechnology


title: ChIP-seq Pol2 Mouse Wildtype fetal liver cells replicate 3

description:
Genome-wide library of Immunoprecipitated fragments
wt_vs_ahom.rpmpeaks.bw
wt_vs_bhom.rpmpeaks.bw

value: wildtype


title: 3_S126: PL-Naive_rep3


title: HA-Mms4


title: 24_S147: dHC-Train-1hr_rep3

source_name: Dorsal hippocampus


title: ChIP-seq Pol2 Mouse Wildtype fetal liver cells replicate 2

source_name: Differentiated CD117+ mouse fetal liver erythroid cells


title: HDM3

value: 6-8 week old

value: lung


title: 6HA-Sgs1 input

description: Binding pattern of Sgs1 by ChIP-on-chip after arrest of cells in G2/M with Nocodazole

value: W303 MATa RAD5+, sgs1::pADH1-tc3-6xHA-Sgs1 (KanMX4)


title: ChIP-seq Pol2 Mouse Wildtype fetal liver cells replicate 1


title: NG-Capture-C Mouse HS2HS3 fetal liver cells replicate 3

description: Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture

data_processing:
Library strategy: Capture-C
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment: Bowtie 2
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Processing: Combining data from multiple replicates (custom scripts)
Processing: Removal of ploidy regions and off target capture (custom scripts)
Genome_build: mm9
Supplementary_files_format_and_content: custom format: coordinates_fragment_tested, counts_biorep1, counts_biorep2, counts_biorep3

growth_protocol: Mouse fetal livers were harvested at E12.5 and disaggregated in expansion media (StemPro (ThermoFisher)) supplemented with Epo (1U/ml), SCF (50ng/ml), Dexamethosone (1μM)). Cells from individual fetal livers were grown for 6 days, maintaining a constant erythroblast cell count of <= 1 x106. Cells were genotyped as wildtype, homozygous R1R2 or homozygous HS2HS3 during expansion. Cells were counted using the nucleocounter before selection for CD117 positive cells using magnetic assisted cell separation LS columns (130-042-401 - Milltenyi) following the manufacturers protocol. Cells were left to recover for 6h in expansion media at a density of 1x10^6 cells/ml. Aliquots of 5x10^6 cells were harvested as the ‘0h’ timepoint corresponding to early erythropoiesis whilst the remaining cells were re-suspended in differentiation media (which is expansion media with the following changes: increased levels of Epo (5U/ml) and transferrin (0.5mg/ml), SCF and Dexamethasone removed). To induce erythroid differentiation cells were grown for 24h before harvesting for the ‘24h’ timepoint.

extract_protocol:
3C Libraries were generated according to the NG Capture-C protocol (Davies et al. 2016). Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 70%. DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies)
5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Nextseq 500 (150 bp paired-end reads)

value: Mixed

value: homozygous deletion of HS2 and HS3 beta-globin enhancers


title: high elevation lake water microbial gene_6

city: Nanjing

first: Huabing

last: Li

address: East Beijing Road 73

institute: Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences

description: sample in lake HHZ

hyb_protocol: The dried and labeled DNA was resuspended in 42 μl hybridization solution, which included 1 × HI-RPM hybridization buffer, 1 × a CGH blocking agent, 0.05 μgμl-1 Cot-1 DNA, 10 pM universal standard, and 10% formamide (final concentrations). Hybridizations were performed at 67°C for 24 h with a rotation of 20 rpm in a hybridization oven.

scan_protocol: The scanned images of hybridized GeoChips were converted and extracted by using Agilent Feature Extraction 11.5 software (Agilent Technologies, Inc., CA, USA)

data_processing: Raw data were uploaded to the microarray analysis pipeline (http://ieg.ou.edu/microarray/). In brief, the following steps were performed: (i) spots with a signal to noise ratio (SNR) less than 2 were removed due to poor quality; (ii) for each sample, intensities plus 1 were transformed to logarithm and divided by mean signal intensity.

organism: uncultured microorganism

source_name: water

label_protocol: DNA (500 ng) was labeled with the fluorescent dye Cy-3 (GE Healthcare, CA, USA) by random priming.

extract_protocol: The whole microbial DNA was extracted and puriﬁed using the Wizard DNA clean-up kit.

treatment_protocol: In this study, to investigate the influence of elevation  on microbial functional genes in aquatic environments, we focused on four shallow freshwater lakes at comparable elevations, two HELs (at 4,652 m and 4,608 m, respectively) and two LELs (at 530 m and 525 m, respectively), at Siguniang Mountain in Sichuan province, China. Six sampling sites were set in each lake. At each site, approximately 1 L of water was collected from surface waters (top 50 cm) for microbial Geochip analyses

value: lake at 4608 m


title: HDM2

value: house dust mite group


title: Saline control3

description: Gene expression data from saline control lung

source_name: Mice lung from PBS control

value: saline control lung


title: high elevation lake water microbial gene_7

description: sample in lake BHZ

value: lake at 4652 m


title: high elevation lake water microbial gene_9

description: sample in lake BHZ


title: 23_S146: dHC-Train-1hr_rep2

value: Long-Evans

value: Brain

value: Adult


title: Saline control4


title: 22_S145: dHC-Train-1hr_rep1


title: 6HA-Sgs1


title: high elevation lake water microbial gene_5

description: sample in lake HHZ


title: Saline control1


title: Saline control2


title: high elevation lake water microbial gene_8

description: sample in lake BHZ


title: high elevation lake water microbial gene_12

description: sample in lake BHZ


title: high elevation lake water microbial gene_4

description: sample in lake HHZ


title: high elevation lake water microbial gene_2

description: sample in lake HHZ


title: HDM4


title: NG-Capture-C Mouse HS2HS3 fetal liver cells replicate 2

value: Fetal liver cultured ex vivo

value: late erythroid


title: HDM1


title: high elevation lake water microbial gene_10

description: sample in lake BHZ


title: high elevation lake water microbial gene_11

description: sample in lake BHZ


title: high elevation lake water microbial gene_3

description: sample in lake HHZ


title: 2_S125: PL-Naive_rep2


title: low elevation lake water microbial gene_12

description: sample in lake BGY

value: lake at 530 m