title: Kc167_p65_Rep2

first: Vanja

last: Haberle

address: Campus-Vienna-Biocenter 1

institute: The Research Institute of Molecular Pathology (IMP)

description:
PCR amplified cDNA (STAP-seq transcript)
Kc167_p65_spikein_normalized.uniq.start.ps.bw
Kc167_p65_spikein_normalized.uniq.start.ns.bw
Kc167_Unique_tagcounts_per_oligo_all_reps.txt
Kc167_Normalized_tagcounts_per_oligo_merged_reps.txt

data_processing:
Library strategy: STAP-seq
Basecalls where performed using CASAVA 1.9.1
Paired-end COF-STAP-seq reads were trimmed to 46 bp, with the first 10 bp of the forward read as the unique molecular barcode identifier (UMI). The reads were mapped using the remaining 36 bp as paired-end to a reference containing 133bp long sequences of all 72,000 CP candidates and to D. pseudoobscura (dp3) genome (for spike-in controls) using Bowtie version 0.12.9. The spike-in control D. pseudoobscura CP sequences were selected from their D. melanogaster orthologs such that the reads could unambiguously be mapped to dp3 genome with the same mapping parameters. Multi-mapping was allowed and only mappings with reverse reads mapping to the end of the oligo sequence were kept ensuring they correspond to reporter transcripts transcribed from that particular cloned CP candidate. Read pairs that still mapped to more than one oligo sequence were randomly assigned to one position. For paired-end reads that mapped to the same positions, we collapsed those that have identical UMIs as well as those for which the UMIs differed by 1 nucleotide to ensure the counting of unique reporter transcripts. Tag counts at each position represent the sum of the 5′-most position of collapsed fragments.
Unique tags mapping to any position within the CP candidate were summed to obtain tag count per CP candidate. We did the same for the 9 spike-in D. pseudoobscura CPs, and the counts were used to calculate normalization factors between the datasets. For each spike-in CP we first assigned factor 1 to the dataset with the lowest count and then calculated down-scaling factors for all other datasets based on their counts for that CP. Final normalization factors were calculated as median of factors for individual spike-in CPs and were used to normalize raw tag counts for each sample. For each cofactor, normalized tag counts across the 3 biological replicates were averaged.
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited text files include genomic coordinates of 72,000 core promoter candidates from the Drosophila melanogaster genome and tag counts at those 72,000 candidates as follows: 1) Raw tag counts in each individual replicate of 23 cofactors and 2 controls is provided in All_reps_raw_tagcounts_per_oligo.txt file and 2) Normalized counts (normalized to spike-in) after merging replicates per cofactor are provided in the Merged_reps_spikein_normalized_tagcounts_per_oligo.txt file. Analogously, counts for the same 72,000 candidates for COFs tested in OSC and Kc167 cells are provided in the files OSC_Merged_reps_spikein_normalized_tagcounts_per_oligo.txt and Kc167_Merged_reps_spikein_normalized_tagcounts_per_oligo.txt, respectively. BigWig files contain normalized tag count per genomic position averaged across 3 biological replicates and separated by strand for each cofactor in different cell lines.

organism: Drosophila melanogaster

source_name: Kc167 cells

extract_protocol: The UAS STAP-seq screening vector was generated from pSTAP-seq_fly-ctrl (Addgene ID 86380) by cloning an array of 4 upstream activating sequences (UAS) (obtained from pSGE_91_4xUAS_dCP (Addgene ID 71169)) upstream of the library insertion site (position of the core promoter) between the XhoI and BglII restriction sites. The core promoter candidate library was cloned from a pool of 72,000 synthesized 200-mer oligonucleotides obtained from Twist Biosciences Inc. The CP candidates spanned 133bp total, centered on the candidates major (+1) TSS, flanked by the Illumina i5 (33bp) and i7 (34bp) adapter sequences upstream and downstream, respectively, serving as constant linkers for amplification and cloning. To comprehensively amplify the oligonucleotide pool (diluted to 1ng/µl) and thereby create the CP candidate library insert we performed 40 PCR reactions (98°C for 45 seconds (s); followed by 15 cycles of 98°C for 15s, 65°C for 30s, 72°C for 10s) with 1µl diluted oligonucleotide pool as template, using KAPA Hifi Hot Start Ready Mix (KAPA Biosystems; cat. no. KK2602) and primers (fw: TAGAGCATGCACCGGACACTCTTTCCCTACACGACGCTCTTCCGATCT and rev: GGCCGAATTCGTCGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) that add extra 15bp to each of the adapters, serving as homology arms for directional cloning of the CP candidate library insert using In-Fusion HD (Clontech; cat. no. 639650). All PCR reactions were pooled and purified with Agencourt AMPureXP DNA beads (ratio beads/PCR 1.4; cat. no. A63881). Directional cloning of the library insert (amplified oligonucleotide pool) into the UAS-STAP-seq screening vector was performed using In-Fusion HD (Clontech; cat. no. 639650) recombination.

value: Kc167 cells

tag: cofactor


title: mMSC shlSLR no.2

status: Public on May 15 2019

type: RNA

city: Nagoya

first: Yasuyuki

last: Mizutani

state: Aichi

address: showa-ku, turumai-cho, 65

department: Gastroenterology

country: Japan

institute: Nagoya University Graduate School of Medicine

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D).

data_processing: The scanned images were analyzed with  Agilent Feature Extraction (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

molecule: total RNA

organism: Mus musculus

source_name: mMSC shlSLR no.2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug 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.

extract_protocol: Total RNA was extracted using RLT buffer (Qiagen) and an RNeasy Mini Kit (Qiagen) and was treated with RNase-free DNase (Qiagen).

treatment_protocol: Three different target sequences used for shRNA-mediated knockdown of mouse Meflin. These Meflin shRNAs were transduced to primary cultured mouse MSCs by a retroviral expression system

tag: cell type

value: primary MSCs

tag: passage


title: Kc167_p65_Rep1

type: SRA

city: Vienna

country: Austria

library_source: transcriptomic

molecule: polyA RNA


title: Kc167_p65_Rep3


title: PAPZFW blood 1

type: genomic

city: New York

first: Gonzalo

last: Lopez

state: NY

address: 1399 Park avenue

department: Genetics and Genomic Sciences

country: USA

institute: Mount Sinai School of Medicine

description: Genomic DNA extracted from primary neuroblastoma and matched blood samples

hyb_protocol: Standard Illumina HumanHap550 Genotyping BeadChip v1, v3, v3duo, Human610-Quad v1.0 & HumanOmniExpress-12v1 BeadChip protocol

data_processing: IDATS were imported into Illumina's Genome Studio, along with pertinent manifest and cluster files for array versions HumanHap550 v1, v3, v3duo, Human610-Quad v1.0 & HumanOmniExpress-12v1

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: neuroblastoma

extract_protocol: DNA was extracted with Qiagen DNA extraction kit protocol

tag: usi

value: PAPZFW

tag: tissue

value: blood

tag: gender

value: male

tag: cog risk

value: high

tag: inss stage

tag: mycn status

value: non-amp

tag: ploidy

value: hyperdiploid (>1.0)

tag: ploidy value


title: PAMKPM blood 1

scan_protocol: Standard Illumina HumanHap550 Genotyping BeadChip v1, v3, v3duo, Human610-Quad v1.0 & HumanOmniExpress-12v1 BeadChip protocol

value: PAMKPM

value: female

value: amp


title: PALJVX blood 1

label_protocol: Standard Illumina HumanHap550 Genotyping BeadChip v1, v3, v3duo, Human610-Quad v1.0 & HumanOmniExpress-12v1 BeadChip protocol

value: PALJVX


title: huc1_p5_ctrl_18 [ctr_s_59]

city: shanghai

first: Yufang

last: Shi

state: Shanghai

address: 320 Yueyang Road

country: China

institute: Chinese Academy of Science

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie and single-end clean reads were aligned to the reference genome using TopHat. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. For unigene DGE, Bowtie was used to aligned single-end clean reads to the unigene sequences.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilo base of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazaviet al., 2008). For unigene DGE, we used RSEM to count the reads numbers mapped to each unigene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.10.1). DESeq provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P value less than 0.05 were considered significantly enriched by differential expressed genes.
A signed network was constructed by using any gene that was expressed at an FPKM value of 0.1 or higher in at least one of the samples. Soft power parameter was estimated and used to derive a pairwise distance matrix for selected genes using the topological overlap measure, and the dynamic hybrid cut method was used to detect clusters. The node centrality, defined as the sum of within-cluster connectivity measures, was used to rank genes for ‘‘hub-ness’’ within each cluster. For visual analysis of the constructed networks by hard thresholding of edge distances, the closest 150 edges were represented using Cytoscape 3.0.0.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited table includes raw read counts for all samples

growth_protocol: Umbilical cord was harvested from fetus with natural labor from Changzhou Maternal and Child Health Care Hospital, temporally preserved in saline added with 100 U/mL penicillin, 100 U/mL streptomycin and 0.54% sodium citrate anticoagulant. Cells were isolated as described below. Umbilical cord was washed with saline supplement with antibiotics. After the blood vessels were removed, the tissue was excised into pieces with diameter around 1 cm. The tissue clumps were cultured in the petri dish with low glucose DMEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 U/mL streptomycin. Half of culture medium was changed at day 4. At day 12, all the clumps were removed and cells were cultured for one more week. When cells reached around 80% confluency, cell can be passaged and cultured under the condition mentioned above. Samples are all qualified for microbiology and virology tests.

extract_protocol:
MSCs were captured on a large microfluidic chip (designed for cells from 17–25 μm) using the Fluidigm C1 Autoprep System. Capturing efficiency was evaluated by microscopic observation, each capture site was manually confirmed with single cell and processed further. RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the Nano Photometer spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500 platform and 50bp single-end reads were generated. These procedures were achieved by Novogene company.

treatment_protocol: those samples labeled with "sti" were cultured under normal medium plus 10ng/ml IFNγ plus TNFα

tag: donor id

value: umbilical cord derived mesenchymal stem cell (MSC)

tag: treatment

value: naïve


title: Kc167_gfzf_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
Kc167_gfzf_spikein_normalized.uniq.start.ps.bw
Kc167_gfzf_spikein_normalized.uniq.start.ns.bw
Kc167_Unique_tagcounts_per_oligo_all_reps.txt
Kc167_Normalized_tagcounts_per_oligo_merged_reps.txt

value: gfzf


title: PAPZWS blood 1

value: PAPZWS

value: diploid (=1.0)


title: 3T3-p53-Com1

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 East Duarte Road

department: Department of Computational & Quantitative Medicine

institute: Beckman Research Institute of City of Hope, Center for Informatics

data_processing:
Basecalls performed using CASAVA version 1.8
The RNA-seq sequence reads were mapped to mouse genome assembly mm10 using open source RNA-seq alignment tool HISAT2 (ver 2.0.4)
The alignment results were converted to RNA-seq gene expression measurement as RPKM (reads/kilo base of total exon length/million mapped) using Partek Genome Suite (version 6.6) with NCBI RefSeq database.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all Samples

source_name: MEF p53 null_complete

growth_protocol: Cell lines cultured in standard (25 mM glucose, 2 mM L-glutamine) DMEM

extract_protocol:
RNA from cell culture was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit V2 was used with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared with TruSeq SR Cluster V3 kits (Illumina).

treatment_protocol: Cell lines were cultured in two conditions using DMEM without L-glutamine (glutamine-free) or with 2 mM L-glutamine added into the DMEM (control) for 18 hours

tag: cell line

value: mouse embryonic fibroblast (MEF)

tag: genotype/variation

tag: culture condition

value: DMEM + 2 mM L-glutamine


title: huc1_p5_ctrl_23 [r6_6]


title: huc1_p5_ctrl_17 [ctr_s_57]


title: 3T3-p53-Q1

source_name: MEF p53 null_Glutamine-free

value: DMEM without L-glutamine (glutamine-free)


title: 3T3-WT-Q3

source_name: MEF WT_Glutamine-free

value: wildtype p53


title: PAMIZA blood 1

value: PAMIZA

value: blood


title: PALPGG blood 1

value: PALPGG

value: high


title: 3T3-WT-Q2


title: huc1_p5_ctrl_15 [ctr_n_92]


title: Kc167_Nej_p300_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
Kc167_Nej_p300_spikein_normalized.uniq.start.ps.bw
Kc167_Nej_p300_spikein_normalized.uniq.start.ns.bw
Kc167_Unique_tagcounts_per_oligo_all_reps.txt
Kc167_Normalized_tagcounts_per_oligo_merged_reps.txt

value: Kc167 cells


title: Repetition 3 of female gonad in developmental stage II [Asib3Ms-F]

city: Shenzhen

first: Jianwei

last: Chen

address: Yantian

institute: BGI-Shenzhen

data_processing:
Removed low quality reads based on the following conditions: (i) adaptors, (ii) a high proportion of unknown nucleotides (N) (larger than 5%), and (iii) low quality reads ≥ 20% (q-value ≤ 20).
Assembly by the Trinity program (version: release-2013-08-14) with default settings except the ‘--path_reinforcement_distance’: minimum overlap of reads with growing transcript was 85, and the ‘--min_kmer_cov’: 3 k-mers was assembled by three modules including Inchworm, Chrysalis and Butterfly
We clustered transcripts that were just longer than 200 bp using TGICL to minimize redundancy.
Genome_build: de novo assembly submitted at TSA database - provisional accession number GGYF00000000
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Acipenser sinensis

source_name: female gonad in developmental stage II

extract_protocol:
Three kinds of tissues (hypothalamus (H), pituitary (P) and gonad (G)) were collected from each individual, flash frozen in liquid nitrogen and stored at -80 °C for RNA extraction.Total RNA was extracted with TRIzol reagent (Invitrogen) following the manufacturer’s instructions.
Total RNA samples (5 μg) were then subjected to cDNA construction following Illumina truSeq stranded mRNA sample preparation protocol. Next, forty-five libraries were sequenced using Illumina HiSeqTM2000/4000 with 2 × 90 or 100 bp paired-end sequencing.

tag: Sex

value: Female

tag: developmental stage

value: Stage II

value: Gonad


title: Kc167_gfzf_Rep1

tag: cell type

tag: cofactor


title: 3T3-WT-Q1


title: Kc167_Nej_p300_Rep2


title: huc1_p5_ctrl_13 [ctr_n_86]

value: umbilical cord derived mesenchymal stem cell (MSC)

tag: passage


title: Kc167_Nej_p300_Rep1


title: Repetition 3 of female hypothalamus in developmental stage II [Asib3Mh-F]

tag: tissue

value: Hypothalamus


title: huc1_p5_ctrl_14 [ctr_n_87]

value: naïve


title: 3T3-WT-Com2

source_name: MEF WT_complete


title: Repetition 3 of female pituitary in developmental stage II [Asib3Mp-F]

value: Pituitary


title: huc1_p5_ctrl_12 [ctr_n_85]


title: Kc167_gfzf_Rep2

value: gfzf


title: huc1_p5_ctrl_11 [ctr_n_81]


title: Repetition 2 of female gonad in developmental stage II [Asib2Ms-F]


title: Kc167_Mof_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
Kc167_Mof_spikein_normalized.uniq.start.ps.bw
Kc167_Mof_spikein_normalized.uniq.start.ns.bw
Kc167_Unique_tagcounts_per_oligo_all_reps.txt
Kc167_Normalized_tagcounts_per_oligo_merged_reps.txt

value: Mof


title: 3T3-WT-Com1

value: mouse embryonic fibroblast (MEF)

value: DMEM + 2 mM L-glutamine


title: Kc167_Mof_Rep2


title: huc1_p5_ctrl_10 [ctr_n_79]


title: ATAC_tgiILC1_infected_rep3

city: Saint Louis

first: Eugene

last: Park

state: MO

address: 4616 Lindell Blvd, Apt 201

institute: Washington University

library_source: genomic

data_processing:
Basecalls performed with CASAVA
ATAC-seq: reads were aligned to mm10 using Bowtie2, samtools was used to filter reads with q<30, and PicardTools was used to remove duplicate reads. Peaks were called with default commands in MACS2 and -q 0.05
RNA-seq: pseudoalignments to mm10 and abundance measurements with kallisto
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-seq: bigwig files; RNA-seq: abundance tsv files

source_name: splenic ILC1

extract_protocol: samples were prepared as previously described (Buenrostro et al 2015). 50,000 cells were lysed in 10mM Tris-Cl, 10 mL NaCl, 3mM MgCl2, 0.1% NP-40. Pellets were resuspended in 50 uL Transposition mix (Illumina) and incubated for 30 minutes at 37 C. Samples were purified with MinElute spin columns (Qiagen). Libraries were prepared with Nextera intext adapters and purified with AMPure XP beads (Beckman-Coulter). Sequencing was performed with 2x50 reads on a Illumina HiSeq 2500.

value: spleen

tag: strain

tag: infection status

value: infected d35


title: Kc167_Mof_Rep1


title: Repetition 2 of female hypothalamus in developmental stage II [Asib2Mh-F]


title: Repetition 2 of female pituitary in developmental stage II [Asib2Mp-F]


title: Kc167_Med25_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
Kc167_Med25_spikein_normalized.uniq.start.ps.bw
Kc167_Med25_spikein_normalized.uniq.start.ns.bw
Kc167_Unique_tagcounts_per_oligo_all_reps.txt
Kc167_Normalized_tagcounts_per_oligo_merged_reps.txt


title: huc1_p5_ctrl_16 [ctr_s_2]


title: huc1_p5_ctrl_9 [ctr_n_77]


title: Kc167_Med25_Rep2


title: ATAC_tgiILC1_infected_rep1


title: ATAC_tgiILC1_infected_rep2


title: shCT2

city: Hong Kong

first: Weicheng

last: Liang

address: Area 39

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Primary sequencing data is subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences. QC of alignment is performed to determine if resequencing is needed. The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio. If alignment result passes QC, we will proceed with downstream analysis including gene expression and deep analysis based on gene expression (PCA/correlation/screening differentially expressed genes and so on).
We define "dirty" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads. They need to be removed before downstreamanalysis to decrease data noise.
We use Bowtie2  to map clean reads to reference gene and use HISAT to reference genome.
Genome_build: hg19
Supplementary_files_format_and_content: Text files include RPKM values for each Sample

source_name: PLC/PRF/5 cell

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver cancer cell line

tag: passages


title: ATAC_cNK_infected_rep3

source_name: splenic cNK

value: cNK

value: uninfected


title: huc1_p5_ctrl_8 [ctr_n_76]


title: huc1_p5_ctrl_22 [r6_5]


title: shNC


title: ATAC_cNK_infected_rep2


title: huc1_p5_ctrl_7 [ctr_n_70]


title: 3T3-WT-Com3

value: wildtype p53


title: Kc167_Med25_Rep1

value: Kc167 cells


title: ATAC_cNK_infected_rep1


title: Kc167_Lpt_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
Kc167_Lpt_spikein_normalized.uniq.start.ps.bw
Kc167_Lpt_spikein_normalized.uniq.start.ns.bw
Kc167_Unique_tagcounts_per_oligo_all_reps.txt
Kc167_Normalized_tagcounts_per_oligo_merged_reps.txt

value: Lpt


title: 30min2

city: Nizwa

first: Abdul Latif

last: Khan

address: Barkatulmouz

country: Oman

institute: University of Nizwa

description: processed data file: gene_exp.diff.annot.xls

data_processing:
Next-generation sequencing machine IONS5 was used for sequencing.
Trinity was used for assembly.
The de novo assembled transcripts of B. sacra were annotated by performing a BLAST search with the software Blast2GO v.2.6.0.
By using TopHatper sample method, the original reads were mapped back against the reference transcriptome using default values.
Cuffdiff v.2.2.156 to identify differentially expressed genes (DEGs).
Genome_build: Trinity.fasta (de novo transcriptome assembly)
Supplementary_files_format_and_content: gene_exp.diff.annot.xls: Treated and control conditions differentially expressed genes (DEGs), p and q values by using Cuffdiff.

organism: Boswellia sacra

source_name: Wounded stem

extract_protocol:
Total RNA were extracted from the stem of B. sacra plant collected after 0 day and 30min of wounding stress (two biological replicates), using the Pure Link Plant RNA reagent kit (Life Technologies, USA) with some modifications and in-house developed HMW RNA extraction method.
The cDNA libraries were prepared for the ribominus total RNA were constructed using the Ion total RNA-seq kit V2, ERCC RNA spike- In control mixes were added according to the manufacturer protocol for 100ng. The total RNA were fragmented using RNases III followed by the purification, the yield was checked on the Bioanalyzer, followed by the amplification of cDNA, the yield was checked on the Bioanalyzer.
The Ion One Touch 2 system (Life Technologies, USA) was used for the emulsion PCR of cDNA, which was followed by the Ion One Touch ES for the enrichment of template. The enriched template was loaded into Ion 540 Chips for the transcriptome sequencing on Ion Torrent S5.

value: Stem

value: Wounding


title: 30min1


title: Control2

source_name: Control stem

value: Control


title: ATAC_cNK_uninfected_rep3


title: Kc167_Lpt_Rep2


title: huc1_p5_ctrl_5 [ctr_n_65]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: ATAC_cNK_uninfected_rep2


title: huc1_p5_ctrl_3 [ctr_n_56]


title: huc1_p5_ctrl_6 [ctr_n_67]


title: huc1_p5_ctrl_4 [ctr_n_62]


title: Kc167_Lpt_Rep1


title: Kc167_GFP_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
Kc167_GFP_spikein_normalized.uniq.start.ps.bw
Kc167_GFP_spikein_normalized.uniq.start.ns.bw
Kc167_Unique_tagcounts_per_oligo_all_reps.txt
Kc167_Normalized_tagcounts_per_oligo_merged_reps.txt

value: GFP


title: ATAC_cNK_uninfected_rep1


title: huc1_p5_ctrl_1 [ctr_n_48]


title: Kc167_GFP_Rep2


title: Kc167_GFP_Rep1


title: Control1


title: Macros-d7-4

city: Barcelona

first: Anna

last: Esteve-Codina

address: Carrer Baldiri Reixac 4-8

country: Spain

institute: CNAG-CRG

data_processing:
RNA-seq reads were mapped with STAR
Genes were quantified with RSEM
Differential expression was performed with DESeq2
Genome_build: gencode.vM18.primary_assembly
Supplementary_files_format_and_content: Raw counts gene quantifications (text file)

source_name: Monocytic cells

growth_protocol: Six week-old C57BL/6 (male) mice were infected intraperitoneally with  2x10E2  plaque forming units (pfu) of the strain Docile of LCMV to induce an acute infection.

extract_protocol:
Total RNA from splenic monocytic cells was directly extracted after cell sorting by RNeasy Micro kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Monocytic cells

tag: infection

value: 2x10E2 pfu of LCMV strain Docile

tag: day post-infection


title: Macros-d7-3


title: Kc167_Chro_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
Kc167_Chro_spikein_normalized.uniq.start.ps.bw
Kc167_Chro_spikein_normalized.uniq.start.ns.bw
Kc167_Unique_tagcounts_per_oligo_all_reps.txt
Kc167_Normalized_tagcounts_per_oligo_merged_reps.txt

value: Chro


title: Kc167_Chro_Rep2


title: Macro-d0-2

value: control


title: leaves_DTT+TUDCA (C)_2

city: zhengzhou

first: Xing

last: Yu

state: Henan

address: 95 Wenhua Road

institute: Henan Agricultural University

data_processing:
Illumina software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: iwgsc_refseqv1.0 RefSeq v1.0
Supplementary_files_format_and_content: File includes FPKM values for each Sample (the gene IDs of EPlTAEG*, Traes* and TRAES* can be found in the Ensembl plants, the URL is as follows: http://mar2016-plants.ensembl.org/Triticum_aestivum/Info/Index)

organism: Triticum aestivum

source_name: leaves_DTT+TUDCA cotreatment

extract_protocol:
Total RNA was extracted using TRNzol® Reagent (Tiangen Biotech, Beijing, China), according to the manufacturer’s instructions.
The RNA-seq libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and 150 bp paired-end reads were generated.

value: seedling

value: DTT+TUDCA cotreatment

tag: time

value: 2 days of treatment

value: leaf


title: leaves_DTT+TUDCA (C)_1


title: OSC_p65_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
OSC_p65_spikein_normalized.uniq.start.ps.bw
OSC_p65_spikein_normalized.uniq.start.ns.bw
OSC_Unique_tagcounts_per_oligo_all_reps.txt
OSC_Normalized_tagcounts_per_oligo_merged_reps.txt

source_name: OSC cells

value: OSC cells


title: leaves_DTT (C)_3

value: DTT


title: CD8CD44d7-4

source_name: CD8 T cells

value: CD8 T cells


title: CD8CD44d7-3


title: leaves_DTT (C)_2


title: huc1_p5_ctrl_2 [ctr_n_52]

tag: donor id


title: Kc167_Chro_Rep1

source_name: Kc167 cells

value: Kc167 cells


title: T. salsuginea, 72h low-oxygen treatment

city: Seoul

first: JiHye

last: Hwang

address: 52, Ewhayeodae-gil

country: South Korea

institute: Ewha Womans University

description: Analysis used RNA of A.thaliana under normal condition as control samples for comparison to the experimental samples(Brassicaceae species under low-oxygen treatment).

hyb_protocol: The labeled cDNA was hybridized on Operon Arabidopsis Version 3.0 microarray which consists of 26,173 probes spotted with synthetic 70-mer oligonucleotides on aminosilane-coated slides by the David Galbraith lab, University of Arizona.

scan_protocol: The slides were scanned using an ArrayWoRx (Applied Precision, Issaquah, WA, USA).

data_processing: Intensity values were quantified from the pairs of TIFF image files from each channel using version 5.6 ImaGene software (BioDiscovery, Los Angeles, CA, USA). The mean values from each channel were log2 transformed and normalized using the LOWESS algorithm to remove intensity dependent effects within the calculated values. Normalised values were used to calculate the Cy3/Cy5 fluorescence ratios from experimental with all replicates combined.

organism: Arabidopsis thaliana

source_name: root samples of A. thaliana under normal condition

label_protocol: Total RNA (5 ug) from root samples was reverse transcribed using reverse transcription (RT) primer tagged with either Cy3-3DNA or Cy5-3DNA capture sequence of Array 900 MPX Expression Array Detection Kits (Genisphere, Hatfield, PA, USA).

growth_protocol: The plants were grown for 2~3 weeeks in an environmentally controlled growth chamber at 23℃ under constant light (approximately 100 µmol m-2s-1).

extract_protocol: Total RNA was isolated using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany), following the manufacturer's instructions.

treatment_protocol: Two-week-old Arabidopsis or three-week-old closely related species were transferred into an airtight vacuum chamber in an environmentally controlled growth cabinet. The low-oxygen gas mixture (0.1% O2/99.9% N2) was supplied continuously into the airtight vacuum chamber to retain low O2 conditions during treatment.

tag: treatment

value: normal condition

value: root

organism: Eutrema salsugineum

source_name: root samples of T. salsuginea exposed for 72 h to low-oxygen

value: 72 h to low-oxygen


title: OSC_p65_Rep2


title: CD8CD44-d0-2


title: T. salsuginea, 8h low-oxygen treatment

source_name: root samples of T. salsuginea exposed for 8 h to low-oxygen

value: 8 h to low-oxygen


title: leaves_DTT+TUDCA (C)_3


title: leaves_DTT (C)_1


title: T. salsuginea, 24h low-oxygen treatment

source_name: root samples of T. salsuginea exposed for 24 h to low-oxygen

value: 24 h to low-oxygen


title: Macros-d0-1

value: Monocytic cells


title: leaves_control (C)_3


title: OSC_gfzf_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
OSC_gfzf_spikein_normalized.uniq.start.ps.bw
OSC_gfzf_spikein_normalized.uniq.start.ns.bw
OSC_Unique_tagcounts_per_oligo_all_reps.txt
OSC_Normalized_tagcounts_per_oligo_merged_reps.txt

value: gfzf


title: CD8CD44-d0-1


title: R. islandica, 24h low-oxygen treatment

organism: Rorippa islandica

source_name: root samples of R. islandica exposed for 24 h to low-oxygen


title: LN-LEC_SL107999

city: Charlottesville

first: Alexander

middle: Fritz

last: Koeppel

state: VA

address: 1640 Jefferson Park Avenue

department: School of Medicine

institute: University of Virginia

data_processing:
Trimming with fastx-trimmer
Alignment with STAR
Quantitation with featureCounts
Genome_build: mm9
Supplementary_files_format_and_content: Output of featureCounts software.  Text table of raw counts for all samples.

source_name: LN-LEC

extract_protocol:
Cells were sorted by flow cytometry directly into RNA Protect (Qiagen). Total RNA extraction was performed using RNAeasy mini kit (Qiagen) as per manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: age

value: 6-8 weeks

value: pooled inguinal, axillary, brachial, cervical, and mesenteric LNs

value: lymph node-derived lymphatic endothelial cell (LN-LEC)


title: OSC_gfzf_Rep2


title: leaves_control (C)_2

value: seedling

value: control


title: aly1-2 - cytoplasm - rep2 [mRNA-seq]

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: Cytoplasmic polyA RNA

data_processing:
Raw RNA-seq paired-end reads were processed to remove adapter sequences from both 3' and 5' ends using BBDuk2 program from BBTools package (https://jgi.doe.gov/data-and-tools/bbtools/) with the following parameters: “k=23 mink=11 hdist=1 tbo”. Adapter-trimmed reads were further processed to remove bases below the Phred quality score Q30 at both 3' and 5' ends by using BBDuk2.
The resulting quality-trimmed reads were aligned to reference TAIR10 Arabidopsis thaliana genome using STAR version 2.5.1b (Dobin et al., PMID: 23104886) with the parameters “--outMultimapperOrder Random --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMunmapped Within KeepPairs --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100”. To improve accuracy of STAR alignment, Arabidopsis gene and TE annotations from Araport11 (https://www.araport.org/) were also provided along with the reference genome sequence.
Read alignments against Arabidopsis genes and TEs were counted using featureCounts (Liao et al., PMID: 24227677) from the Subread package version 1.6.1 with the parameters “ -p -B -C -g gene_id -M --fraction -s 2”. The resulting read counts were used for all subsequent analyses.
Genome_build: TAIR10
Supplementary_files_format_and_content: *_geneCounts.tsv: Raw counts of reads for each gene or TE as calculated using featureCounts (described in data processing above), is provided.

growth_protocol: Plants were grown under 16-hour day conditions at 22ºC in a growth chamber. All tissue is inflorescence (stage 1-12) immature flower buds.

extract_protocol:
Total, Nuclear, and Cytoplasmic cell extracts were obtained as in the Cellular Fractionation protocol from Park et al., PMID: 15738428, with the following modification: Miracloth was substituted for using a 100 µm cell strainer. RNA was extracted using the Trizol LS protocol (Invitrogen) and enriched for poly(A)+ mRNAs using the NEBNext Poly(A) mRNA Magnetic Isolation Module.
Libraries were prepared using the NEBNext Ultra II Directional RNA library prep kit and dual-indexed.
Multiplexed libraries were sequenced on a HiSeq4000.

tag: ecotype/background

value: Columbia

tag: genotype/variation

tag: fraction

value: cytoplasmic


title: OSC_gfzf_Rep1

value: OSC cells


title: OSC_Nej_p300_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
OSC_Nej_p300_spikein_normalized.uniq.start.ps.bw
OSC_Nej_p300_spikein_normalized.uniq.start.ns.bw
OSC_Unique_tagcounts_per_oligo_all_reps.txt
OSC_Normalized_tagcounts_per_oligo_merged_reps.txt


title: R. islandica, 72h low-oxygen treatment

source_name: root samples of R. islandica exposed for 72 h to low-oxygen


title: T. salsuginea, 1h low-oxygen treatment

source_name: root samples of T. salsuginea exposed for 1 h to low-oxygen

value: 1 h to low-oxygen


title: LN-BEC_SL107998

source_name: LN-BEC

value: lymph node-derived blood endothelial cell (LN-BEC)


title: T. salsuginea, normal condition

value: normal condition

source_name: root samples of T. salsuginea under normal condition


title: aly1-2 - cytoplasm - rep1 [mRNA-seq]

description: Cytoplasmic polyA RNA

source_name: inflorescence (stage 1-12) immature flower buds


title: D-LEC_SL107997

source_name: D-LEC

value: mechanical and enzymatic digestion of D tissues

value: diaphragm-derived lymphatic endothelial cell (D-LEC)


title: OSC_p65_Rep1


title: OSC_Nej_p300_Rep2


title: D-LEC_SL107995


title: R. islandica, 3h low-oxygen treatment

value: root

source_name: root samples of R. islandica exposed for 3 h to low-oxygen

value: 3 h to low-oxygen


title: R. islandica, 8h low-oxygen treatment

source_name: root samples of R. islandica exposed for 8 h to low-oxygen

value: 8 h to low-oxygen


title: D-LEC_SL107996


title: wt Col - cytoplasm - rep2 [mRNA-seq]

description: Cytoplasmic polyA RNA

value: wt

value: inflorescence (stage 1-12) immature flower buds


title: LN-LEC_SL107994

value: 6-8 weeks

value: pooled inguinal, axillary, brachial, cervical, and mesenteric LNs


title: OSC_Nej_p300_Rep1

source_name: OSC cells


title: wt Col - cytoplasm - rep1 [mRNA-seq]

description: Cytoplasmic polyA RNA


title: OSC_Mof_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
OSC_Mof_spikein_normalized.uniq.start.ps.bw
OSC_Mof_spikein_normalized.uniq.start.ns.bw
OSC_Unique_tagcounts_per_oligo_all_reps.txt
OSC_Normalized_tagcounts_per_oligo_merged_reps.txt

value: Mof


title: leaves_control (C)_1

tag: developmental stage

value: seedling

value: control

value: 2 days of treatment

value: leaf


title: LN-LEC_SL107993

tag: cell type

value: lymph node-derived lymphatic endothelial cell (LN-LEC)


title: R. islandica, 1h low-oxygen treatment

source_name: root samples of R. islandica exposed for 1 h to low-oxygen

value: 1 h to low-oxygen


title: A. stelleri, 24h low-oxygen treatment

value: normal condition

organism: Arabis stelleri

source_name: root samples of A. stelleri exposed for 24 h to low-oxygen

value: 24 h to low-oxygen


title: OSC_Mof_Rep2

value: OSC cells

tag: cofactor


title: LN-LEC_SL107992


title: OSC_Mof_Rep1


title: aly1-2 - nuclear - rep1 [mRNA-seq]

description: Nuclear polyA RNA

value: Columbia

value: nuclear


title: LN-BEC_SL107991

value: lymph node-derived blood endothelial cell (LN-BEC)


title: R. islandica, normal condition

source_name: root samples of A. thaliana under normal condition

value: root

source_name: root samples of R. islandica under normal condition


title: wt Col - nuclear - rep2 [mRNA-seq]

description: Nuclear polyA RNA

value: wt

value: inflorescence (stage 1-12) immature flower buds


title: wt Col - nuclear - rep1 [mRNA-seq]

description: Nuclear polyA RNA


title: LN-BEC_SL107990

value: 6-8 weeks

value: pooled inguinal, axillary, brachial, cervical, and mesenteric LNs


title: OSC_Med25_Rep2

description:
PCR amplified cDNA (STAP-seq transcript)
OSC_Med25_spikein_normalized.uniq.start.ps.bw
OSC_Med25_spikein_normalized.uniq.start.ns.bw
OSC_Unique_tagcounts_per_oligo_all_reps.txt
OSC_Normalized_tagcounts_per_oligo_merged_reps.txt


title: A. stelleri, 3h low-oxygen treatment

source_name: root samples of A. stelleri exposed for 3 h to low-oxygen

value: 3 h to low-oxygen


title: A. stelleri, 8h low-oxygen treatment

source_name: root samples of A. stelleri exposed for 8 h to low-oxygen

value: 8 h to low-oxygen


title: aly1-2 - rep3 [mRNA-seq]

description: PolyA RNA

value: total


title: OSC_Med25_Rep3


title: aly1-2 - rep2 [mRNA-seq]

description: PolyA RNA


title: OSC_Lpt_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
OSC_Lpt_spikein_normalized.uniq.start.ps.bw
OSC_Lpt_spikein_normalized.uniq.start.ns.bw
OSC_Unique_tagcounts_per_oligo_all_reps.txt
OSC_Normalized_tagcounts_per_oligo_merged_reps.txt

value: Lpt


title: A. stelleri, normal condition

source_name: root samples of A. stelleri under normal condition


title: aly1-2 - nuclear - rep2 [mRNA-seq]

description: Nuclear polyA RNA


title: A. stelleri, 1h low-oxygen treatment

source_name: root samples of A. stelleri exposed for 1 h to low-oxygen


title: A. thaliana, 24h low-oxygen treatment

source_name: root samples of A. thaliana exposed for 24 h to low-oxygen


title: wt Col - rep3 [mRNA-seq]

description: PolyA RNA


title: 28346: Hindlimbs E16.5 Osx-Cre, Tgfbr2flfl Ai9, biological rep 1

first: Grazia

last: Abou-Ezzi

address: 660 South Euclid Avenue

institute: Washington Univeristy in Saint Louis

description: Hindlimbs from OsxCre, Tgfbr2flfl

hyb_protocol: Following fragmentation and labeling, 2.5 ug of cDNA were hybridized onto the Affymetrix Clariom S arrays and placed in GeneChip Hybridization Oven 640 for 18 hr at 45C. Gene Chip’s were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

label: biotin

source_name: OsxCre,Tgbr2flfl, Hindlimbs

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cells isolated directly from mice

extract_protocol: TdTomato+ lineage- (stromal cells) from E16.5 hindlimbs  were sorted directly into  lysis buffer using the NucleoSpin® RNA XS kit (Takaara), as  per manufacturer’s recommendations.

value: Hindlimbs

tag: genotype

value: OsxCre, Tgbr2flfl Ai9

value: stromal cells


title: 28338: Hindlimbs E16.5 Osx-Cre, Tgfbr2flfl Ai9, biological rep 1

description: Hindlimbs from OsxCre, Tgfbr2flfl

tag: tissue


title: wt Col - rep2 [mRNA-seq]

description: PolyA RNA


title: A. thaliana, 72h low-oxygen treatment

value: normal condition

source_name: root samples of A. thaliana exposed for 72 h to low-oxygen

value: 72 h to low-oxygen


title: A. thaliana, 8h low-oxygen treatment

source_name: root samples of A. thaliana exposed for 8 h to low-oxygen


title: 28345: Hindlimbs E16.5 Osx-Cre, Tgfbr2flfl Ai9, biological rep 1

description: Hindlimbs from OsxCre, Tgfbr2flfl


title: aly1-2 - rep1 [mRNA-seq]

description: PolyA RNA

source_name: inflorescence (stage 1-12) immature flower buds

value: Columbia


title: OSC_Lpt_Rep1

value: OSC cells


title: OSC_Lpt_Rep2


title: OSC_Med25_Rep1


title: A. thaliana, 3h low-oxygen treatment

source_name: root samples of A. thaliana exposed for 3 h to low-oxygen


title: OSC_GFP_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
OSC_GFP_spikein_normalized.uniq.start.ps.bw
OSC_GFP_spikein_normalized.uniq.start.ns.bw
OSC_Unique_tagcounts_per_oligo_all_reps.txt
OSC_Normalized_tagcounts_per_oligo_merged_reps.txt

value: GFP


title: Repetition 1 of female hypothalamus in developmental stage II [Asib1Mh-F]

tag: Sex

value: Female

value: Stage II

value: Hypothalamus


title: wt Col - rep1 [mRNA-seq]

description: PolyA RNA

value: wt

value: inflorescence (stage 1-12) immature flower buds


title: A. thaliana, 1h low-oxygen treatment

value: root

source_name: root samples of A. thaliana exposed for 1 h to low-oxygen

value: 1 h to low-oxygen


title: OSC_GFP_Rep2


title: 28344: Hindlimbs E16.5 Osx-Cre, Ai9, biological rep 1

description: Hindlimbs from Wt

source_name: Wild-type, Hindlimbs

value: OsxCre, Ai9


title: A. stelleri, 72h low-oxygen treatment

source_name: root samples of A. stelleri exposed for 72 h to low-oxygen


title: Repetition 1 of female pituitary in developmental stage II [Asib1Mp-F]

value: Pituitary


title: OSC_GFP_Rep1

source_name: OSC cells


title: Repetition 1 of female gonad in developmental stage II [Asib1Ms-F]

source_name: female gonad in developmental stage II

value: Gonad


title: L32-4

city: Calgary

first: Chinju Therese

last: Johnson

state: Alberta

department: Production Animal Health

country: Canada

institute: University of Calgary

data_processing:
Base calling and demultiplexing were done with CASAVA 1.9 (Illumina) with default settings. Initial quality control, conducted with FastQC detected no adapter sequences, base qualities and other parameters were excellent.
Sequenced reads were aligned to the bovine genome (Bos taurus, UMD3.1.87, downloaded from Illumina iGENOME website) using TopHat, with Bowtie2 as an internal aligner.
FeatureCounts program was used to count number of reads on each exon by transcript meta-feature
To conduct a “per-gene” analysis, the most expressed transcript over all conditions was selected by the provided ad hoc python script (select_protein_coding_transcripts.py).
Count-tables obtained with FeatureCounts was loaded, and the count in each sample normalised by library size. Normalised counts on protein coding genes were used for analysis of differential expression with DESeq2 in R package (version 1.14.1) via SARTools6 (Version 1.4.0) package
Genome_build: Bos taurus, UMD3.1.87
Supplementary_files_format_and_content: rawcounts contain raw counts of reads mapping to features.

organism: Bos taurus

source_name: Bovine testes parenchyma

extract_protocol:
A small portion of testicular parenchyma (~75 mg) from each bull (n=28) was homogenised and total RNA extracted. Trizol reagent-mediated extraction was performed as per manufacturer’s instructions. For each sample (n=28) total RNA (1 µg) was used to create mRNA libraries using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: diet

value: Low (12% Crude Protein, 64.4% Total Digestible Nutrients)

tag: age at castration

value: 32 weeks

value: testes


title: L32-3


title: OSC_Chro_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
OSC_Chro_spikein_normalized.uniq.start.ps.bw
OSC_Chro_spikein_normalized.uniq.start.ns.bw
OSC_Unique_tagcounts_per_oligo_all_reps.txt
OSC_Normalized_tagcounts_per_oligo_merged_reps.txt

value: Chro


title: 28342: Hindlimbs E16.5 Osx-Cre, Ai9, biological rep1

description: Hindlimbs from Wt

value: Hindlimbs

value: stromal cells


title: Repetition 6 of male hypothalamus in developmental stage II [Asib6Mh]

value: Male


title: L32-1


title: Repetition 6 of male pituitary in developmental stage II [Asib6Mp]


title: OSC_Chro_Rep1

value: OSC cells


title: OSC_Chro_Rep2


title: 28343: Hindlimbs E16.5 Osx-Cre, Ai9, biological rep1

description: Hindlimbs from Wt


title: L32-2


title: Repetition 5 of male gonad in developmental stage II [Asib5Ms]

source_name: male gonad in developmental stage II

value: Stage II


title: 28337: Hindlimbs E16.5 Osx-Cre, Tgfbr2flfl Ai9, biological rep 1

description: Hindlimbs from OsxCre, Tgfbr2flfl

value: OsxCre, Tgbr2flfl Ai9


title: 28341: Hindlimbs E16.5 Osx-Cre, Ai9, biological rep1

description: Hindlimbs from Wt


title: GFP_Rep6

description:
PCR amplified cDNA (STAP-seq transcript)
Unique_tagcounts_per_oligo_all_reps.txt

source_name: S2 cells

value: S2 cells

value: GFP


title: L24-8

value: 24 weeks


title: L24-7


title: Repetition 6 of male gonad in developmental stage II [Asib6Ms]


title: 28340: Hindlimbs E16.5 Osx-Cre, Ai9, biological rep1

description: Hindlimbs from Wt


title: GFP_Rep5


title: 28339: Hindlimbs E16.5 Osx-Cre, Ai9, biological rep1

description: Hindlimbs from Wt


title: Repetition 5 of male pituitary in developmental stage II [Asib5Mp]


title: GFP_Rep4


title: L24-6


title: Repetition 4 of male gonad in developmental stage II [Asib4Ms]


title: L24-5


title: pzg_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
pzg_spikein_normalized.uniq.start.ps.bw
pzg_spikein_normalized.uniq.start.ns.bw
Unique_tagcounts_per_oligo_all_reps.txt
Normalized_tagcounts_per_oligo_merged_reps.txt

value: pzg


title: Vehicle_B16-OVA_2

city: Pamplona

first: Maria

middle: Angela

last: Aznar

address: Pio XII num 55

institute: Center for applied medical research (CIMA)

description: Gene expression data from whole B16-OVA cell line

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix Mouse Clariom S array according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: Data was normalized using Bioconductor software and RMA algorithm.

label: Biotin

source_name: B16-OVA cell line incubated with Vehicle replicate 2

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: B12-OVA cells were cultured in RPMI 1640 containing 10% fetal bovine serum, 2mM glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, and 50 µM 2-mercaptoethanol and 400µg/mL Geneticin (Gibco).

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: B16-OVA cells were incubated either with BO-112 at 0.5 µg/mL (n=3) or identical volumes of vehicle (5%glucose, n=3). After 24h, cells were collected and total RNA was isolated in two steps using TRIzol (Life technologies) and Rneasy Mini-Kit (Quiagen) purification, following manufacturer`s RNA cleanup protocol.

value: B16-OVA cell line


title: L16-9

value: 16 weeks


title: pzg_Rep2

first: Vanja

last: Haberle

institute: The Research Institute of Molecular Pathology (IMP)

data_processing:
Library strategy: STAP-seq
Basecalls where performed using CASAVA 1.9.1
Paired-end COF-STAP-seq reads were trimmed to 46 bp, with the first 10 bp of the forward read as the unique molecular barcode identifier (UMI). The reads were mapped using the remaining 36 bp as paired-end to a reference containing 133bp long sequences of all 72,000 CP candidates and to D. pseudoobscura (dp3) genome (for spike-in controls) using Bowtie version 0.12.9. The spike-in control D. pseudoobscura CP sequences were selected from their D. melanogaster orthologs such that the reads could unambiguously be mapped to dp3 genome with the same mapping parameters. Multi-mapping was allowed and only mappings with reverse reads mapping to the end of the oligo sequence were kept ensuring they correspond to reporter transcripts transcribed from that particular cloned CP candidate. Read pairs that still mapped to more than one oligo sequence were randomly assigned to one position. For paired-end reads that mapped to the same positions, we collapsed those that have identical UMIs as well as those for which the UMIs differed by 1 nucleotide to ensure the counting of unique reporter transcripts. Tag counts at each position represent the sum of the 5′-most position of collapsed fragments.
Unique tags mapping to any position within the CP candidate were summed to obtain tag count per CP candidate. We did the same for the 9 spike-in D. pseudoobscura CPs, and the counts were used to calculate normalization factors between the datasets. For each spike-in CP we first assigned factor 1 to the dataset with the lowest count and then calculated down-scaling factors for all other datasets based on their counts for that CP. Final normalization factors were calculated as median of factors for individual spike-in CPs and were used to normalize raw tag counts for each sample. For each cofactor, normalized tag counts across the 3 biological replicates were averaged.
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited text files include genomic coordinates of 72,000 core promoter candidates from the Drosophila melanogaster genome and tag counts at those 72,000 candidates as follows: 1) Raw tag counts in each individual replicate of 23 cofactors and 2 controls is provided in All_reps_raw_tagcounts_per_oligo.txt file and 2) Normalized counts (normalized to spike-in) after merging replicates per cofactor are provided in the Merged_reps_spikein_normalized_tagcounts_per_oligo.txt file. Analogously, counts for the same 72,000 candidates for COFs tested in OSC and Kc167 cells are provided in the files OSC_Merged_reps_spikein_normalized_tagcounts_per_oligo.txt and Kc167_Merged_reps_spikein_normalized_tagcounts_per_oligo.txt, respectively. BigWig files contain normalized tag count per genomic position averaged across 3 biological replicates and separated by strand for each cofactor in different cell lines.

extract_protocol: The UAS STAP-seq screening vector was generated from pSTAP-seq_fly-ctrl (Addgene ID 86380) by cloning an array of 4 upstream activating sequences (UAS) (obtained from pSGE_91_4xUAS_dCP (Addgene ID 71169)) upstream of the library insertion site (position of the core promoter) between the XhoI and BglII restriction sites. The core promoter candidate library was cloned from a pool of 72,000 synthesized 200-mer oligonucleotides obtained from Twist Biosciences Inc. The CP candidates spanned 133bp total, centered on the candidates major (+1) TSS, flanked by the Illumina i5 (33bp) and i7 (34bp) adapter sequences upstream and downstream, respectively, serving as constant linkers for amplification and cloning. To comprehensively amplify the oligonucleotide pool (diluted to 1ng/µl) and thereby create the CP candidate library insert we performed 40 PCR reactions (98°C for 45 seconds (s); followed by 15 cycles of 98°C for 15s, 65°C for 30s, 72°C for 10s) with 1µl diluted oligonucleotide pool as template, using KAPA Hifi Hot Start Ready Mix (KAPA Biosystems; cat. no. KK2602) and primers (fw: TAGAGCATGCACCGGACACTCTTTCCCTACACGACGCTCTTCCGATCT and rev: GGCCGAATTCGTCGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) that add extra 15bp to each of the adapters, serving as homology arms for directional cloning of the CP candidate library insert using In-Fusion HD (Clontech; cat. no. 639650). All PCR reactions were pooled and purified with Agencourt AMPureXP DNA beads (ratio beads/PCR 1.4; cat. no. A63881). Directional cloning of the library insert (amplified oligonucleotide pool) into the UAS-STAP-seq screening vector was performed using In-Fusion HD (Clontech; cat. no. 639650) recombination.


title: Repetition 4 of male pituitary in developmental stage II [Asib4Mh]

value: Pituitary


title: Repetition 3 of male gonad in developmental stage II [Asib3Ms]

value: Gonad


title: Repetition 5 of male hypothalamus in developmental stage II [Asib5Mh]

value: Hypothalamus


title: pzg_Rep1


title: brm_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
brm_spikein_normalized.uniq.start.ps.bw
brm_spikein_normalized.uniq.start.ns.bw
Unique_tagcounts_per_oligo_all_reps.txt
Normalized_tagcounts_per_oligo_merged_reps.txt

value: brm


title: L16-12

value: Low (12% Crude Protein, 64.4% Total Digestible Nutrients)

value: testes


title: L16-11


title: BO112_B16-OVA_3

source_name: B16-OVA cell line incubated with BO-112 replicate 3


title: Vehicle_B16-OVA_1

source_name: B16-OVA cell line incubated with Vehicle replicate 1


title: Repetition 4 of male hypothalamus in developmental stage II [Asib4Mp]


title: L16-10


title: BO112_B16-OVA_1

source_name: B16-OVA cell line incubated with BO-112 replicate 1


title: brm_Rep2


title: brm_Rep1


title: Repetition 3 of male pituitary in developmental stage II [Asib3Mp]


title: Repetition 2 of male gonad in developmental stage II [Asib2Ms]


title: BO112_B16-OVA_2

source_name: B16-OVA cell line incubated with BO-112 replicate 2


title: Vehicle_mouse_4

description: Gene expression data from whole subcutaneos B16OVA tumors

source_name: B16OVA tumors intratumorally injected with Vehicle

growth_protocol: 5x10^5 B16-OVA cells line were subcutaneously injected in B6 mice

extract_protocol: Tumors were excissed, Total RNA was isolated in two steps using TRIzol (Life technologies) and Rneasy Mini-Kit (Quiagen) purification, following manufacturer`s RNA cleanup protocol.

treatment_protocol: Intratumoral BO-112 or identical volumes of vehicle (5%glucose)

value: B16OVA tumor


title: L8-16

value: 8 weeks


title: L8-14


title: Repetition 2 of male pituitary in developmental stage II [Asib2Mp]

value: Male


title: Repetition 2 of male hypothalamus in developmental stage II [Asib2Mh]

value: Stage II


title: L8-15


title: L8-13


title: Tip60_Rep1

description:
PCR amplified cDNA (STAP-seq transcript)
Tip60_spikein_normalized.uniq.start.ps.bw
Tip60_spikein_normalized.uniq.start.ns.bw
Unique_tagcounts_per_oligo_all_reps.txt
Normalized_tagcounts_per_oligo_merged_reps.txt


title: Repetition 1 of male gonad in developmental stage II [Asib1Ms]


title: H32-43

value: High (20% crude protein, 71.6% Total Digestible Nutrients)

value: 32 weeks


title: Vehicle_mouse_5


title: Gcn5_pCAF_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
Gcn5_pCAF_spikein_normalized.uniq.start.ps.bw
Gcn5_pCAF_spikein_normalized.uniq.start.ns.bw
Unique_tagcounts_per_oligo_all_reps.txt
Normalized_tagcounts_per_oligo_merged_reps.txt

value: S2 cells


title: Repetition 1 of male hypothalamus in developmental stage II [Asib1Mh]


title: H32-42


title: Vehicle_mouse_2


title: Gcn5_pCAF_Rep2


title: Tip60_Rep3


title: Repetition 1 of male pituitary in developmental stage II [Asib1Mp]


title: Gcn5_pCAF_Rep1


title: H32-41


title: Tip60_Rep2


title: BO112_mouse_4

source_name: B16OVA tumors intratumorally injected with BO112


title: BO112_mouse_5


title: Vehicle_mouse_3


title: Repetition 6 of unknown sex gonad in developmental stage I [Asia6s]

value: not determined

value: Stage I


title: BO112_mouse_3


title: Vehicle_mouse_1


title: H24-48

value: 26 weeks


title: Br140_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
Br140_spikein_normalized.uniq.start.ps.bw
Br140_spikein_normalized.uniq.start.ns.bw
Unique_tagcounts_per_oligo_all_reps.txt
Normalized_tagcounts_per_oligo_merged_reps.txt


title: H24-47

value: 25 weeks


title: Br140_Rep2


title: Repetition 5 of unknown sex gonad in developmental stage I [Asia5s]


title: Repetition 4 of unknown sex gonad in developmental stage I [Asia4s]


title: BO112_mouse_2


title: H24-46

value: 24 weeks


title: HCT116_p65_Rep2

description:
PCR amplified cDNA (STAP-seq transcript); polyA+ RNA
HCT116_P65_spikein_normalized.uniq.start.ps.bw
HCT116_P65_spikein_normalized.uniq.start.ns.bw
Unique_tagcounts_per_oligo_all_reps.txt
Normalized_tagcounts_per_oligo_merged_reps.txt

data_processing:
Library strategy: STAP-seq
Basecalls where performed using CASAVA 1.9.1
Paired-end COF-STAP-seq reads were trimmed to 46 bp, with the first 10 bp of the forward read as the unique molecular barcode identifier (UMI). The reads were mapped using the remaining 36 bp as paired-end to a reference containing 133bp long sequences of all 12,000 CP candidates and to M. musculus (mm9) genome (for spike-in controls) using Bowtie version 0.12.9 allowing 2 mis-matches. The spike-in control M. musculus CP sequences were selected from their H. sapiens orthologs such that the reads could unambiguously be mapped to mm9 genome with the same mapping parameters. Multi-mapping was allowed and only mappings with reverse reads mapping to the end of the oligo sequence were kept ensuring they correspond to reporter transcripts transcribed from that particular cloned CP candidate. Read pairs that still mapped to more than one oligo sequence were randomly assigned to one position. For paired-end reads that mapped to the same positions, we collapsed those that have identical UMIs as well as those for which the UMIs differed by 1 nucleotide to ensure the counting of unique reporter transcripts. Tag counts at each position represent the sum of the 5′-most position of collapsed fragments.
Unique tags mapping to any position within the CP candidate were summed to obtain tag count per CP candidate. We did the same for the 9 spike-in M. musculus CPs, and the counts were used to calculate normalization factors between the datasets. For each spike-in CP we first assigned factor 1 to the dataset with the lowest count and then calculated down-scaling factors for all other datasets based on their counts for that CP. Final normalization factors were calculated as median of factors for individual spike-in CPs and were used to normalize raw tag counts for each sample. For each cofactor, normalized tag counts across the 3 biological replicates were averaged.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include genomic coordinates of 12,000 core promoter candidates from the human genome and tag counts at those 12,000 candidates as follows: 1) Raw tag counts in each individual replicate of 5 cofactors and 2 controls is provided in All_reps_raw_tagcounts_per_oligo.txt file and 2) Normalized counts (normalized to spike-in) of merged replicates per cofactor are provided in the Merged_reps_spikein_normalized_tagcounts_per_oligo.txt file. BigWig files contain normalized tag count per genomic position averaged across 3 biological replicates for each cofactor and separated by strand.

source_name: HCT116 cells

extract_protocol: The UAS STAP-seq screening vector was generated from pSTAP-seq_fly-ctrl (Addgene ID 86380) by cloning an array of 4 upstream activating sequences (UAS) (obtained from pSGE_91_4xUAS_dCP (Addgene ID 71169)) upstream of the library insertion site (position of the core promoter) between the XhoI and BglII restriction sites. The core promoter candidate library was cloned from a pool of 12,000 synthesized 200-mer oligonucleotides obtained from Twist Biosciences Inc. The CP candidates spanned 133bp total, centered on the candidates major (+1) TSS, flanked by the Illumina i5 (33bp) and i7 (34bp) adapter sequences upstream and downstream, respectively, serving as constant linkers for amplification and cloning. To comprehensively amplify the oligonucleotide pool (diluted to 1ng/µl) and thereby create the CP candidate library insert we performed 20 PCR reactions (98°C for 45 seconds (s); followed by 15 cycles of 98°C for 15s, 65°C for 30s, 72°C for 10s) with 1µl diluted oligonucleotide pool as template, using KAPA Hifi Hot Start Ready Mix (KAPA Biosystems; cat. no. KK2602) and primers (fw: TAGAGCATGCACCGGACACTCTTTCCCTACACGACGCTCTTCCGATCT and rev: GGCCGAATTCGTCGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) that add extra 15bp to each of the adapters, serving as homology arms for directional cloning of the CP candidate library insert using In-Fusion HD (Clontech; cat. no. 639650). All PCR reactions were pooled and purified with Agencourt AMPureXP DNA beads (ratio beads/PCR 1.4; cat. no. A63881). Directional cloning of the library insert (amplified oligonucleotide pool) into the UAS-STAP-seq screening vector was performed using In-Fusion HD (Clontech; cat. no. 639650) recombination.

tag: cell line

value: HCT116 cells

tag: experimental procedure

value: STAP-Seq


title: HCT116_p65_Rep1


title: Br140_Rep1


title: Atac2_Rep3

description:
PCR amplified cDNA (STAP-seq transcript)
Atac2_spikein_normalized.uniq.start.ps.bw
Atac2_spikein_normalized.uniq.start.ns.bw
Unique_tagcounts_per_oligo_all_reps.txt
Normalized_tagcounts_per_oligo_merged_reps.txt


title: HCT116_MLL3_Rep3

description:
PCR amplified cDNA (STAP-seq transcript); polyA+ RNA
HCT116_MLL3_spikein_normalized.uniq.start.ps.bw
HCT116_MLL3_spikein_normalized.uniq.start.ns.bw
Unique_tagcounts_per_oligo_all_reps.txt
Normalized_tagcounts_per_oligo_merged_reps.txt


title: Repetition 3 of unknown sex gonad in developmental stage I [Asia3s]

value: Gonad


title: H16-52

value: 16 weeks


title: Atac2_Rep2


title: T. salsuginea, 3h low-oxygen treatment

description: Analysis used RNA of A.thaliana under normal condition as control samples for comparison to the experimental samples(Brassicaceae species under low-oxygen treatment).

source_name: root samples of A. thaliana under normal condition

value: normal condition

value: root

source_name: root samples of T. salsuginea exposed for 3 h to low-oxygen

value: 3 h to low-oxygen


title: HCT116_MLL3_Rep2


title: HCT116_p65_Rep3


title: Repetition 1 of unknown sex gonad in developmental stage I [Asia1s]


title: Atac2_Rep1


title: HCT116_MLL3_Rep1


title: H16-49

value: testes


title: Vehicle_B16-OVA_3

source_name: B16-OVA cell line incubated with Vehicle replicate 3

value: B16-OVA cell line


title: H16-50

value: High (20% crude protein, 71.6% Total Digestible Nutrients)


title: HCT116_MED15_Rep3

description:
PCR amplified cDNA (STAP-seq transcript); polyA+ RNA
HCT116_MED15_spikein_normalized.uniq.start.ps.bw
HCT116_MED15_spikein_normalized.uniq.start.ns.bw
Unique_tagcounts_per_oligo_all_reps.txt
Normalized_tagcounts_per_oligo_merged_reps.txt


title: Repetition 5 of unknown sex hypothalamus in developmental stage I [Asia5h]

value: Hypothalamus


title: H8-56

value: 8 weeks


title: HCT116_MED15_Rep2


title: H8-53


title: Repetition 4 of unknown sex hypothalamus in developmental stage I [Asia4h]

value: not determined


title: BO112_mouse_1

value: B16OVA tumor


title: Repetition 3 of unknown sex hypothalamus in developmental stage I [Asia3h]

value: Stage I


title: H24-45


title: Repetition 2 of unknown sex gonad in developmental stage I [Asia2s]


title: HCT116_MED15_Rep1


title: HCT116_GFP_Rep3

description:
PCR amplified cDNA (STAP-seq transcript); polyA+ RNA
HCT116_GFP_spikein_normalized.uniq.start.ps.bw
HCT116_GFP_spikein_normalized.uniq.start.ns.bw
Unique_tagcounts_per_oligo_all_reps.txt
Normalized_tagcounts_per_oligo_merged_reps.txt

value: GFP


title: clf0Rt3

city: Amherst

first: Jeeyon

last: Jeong

state: MA

address: 25 East Drive

department: Biology

institute: Amherst College

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were filgered to remove reads containing adapters or reads of low quality, then mapped to Arabidopsis TAIR10 reference genome using TopHat2 (TMR>70%; MMR<10%)
RPKM (Reads Per Kilo bases per Million reads) method (Mortazavi et al 2008)
Genome_build: TAIR10
Supplementary_files_format_and_content: RPKM

source_name: Root

growth_protocol: Germinated and grown for 12 days on B5, followed by 3 days on iron sufficient (+Fe) or iron deficient (-Fe) media; 16/8 light/dark cycle at 22°C

extract_protocol:
Total RNA was extracted from fresh Arabidopsis root tissue using Plant RNA Isolation Kit (Agilent) per manufacturer's instructions.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Grown for 3 days on iron sufficient (+Fe) or iron deficient (-Fe) media

value: clf

value: iron deficient


title: Repetition 6 of unknown sex hypothalamus in developmental stage I [Asia6h]


title: Repetition 2 of unknown sex hypothalamus in developmental stage I [Asia2h]


title: control_rep3

first: Zanxin

last: Wang

state: Guangdong

address: #12 Langshan Road, Nanshan District

institute: Shenzhen Sun Yat-sen Cardiovascular Hospital

description: Gene expression data from control rat

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  Affymetrix Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Rattus norvegicus

source_name: control rat

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Rats with the same age and weighing 250-290 g were used under the feeding conditions (temperature: 22 ± 2 °C, humidity: 40 ~ 70%; light cycle: 12 / 12 hours).

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

treatment_protocol: Rats were randomly averaged into three groups, including Sham, IRI and IRI+RPostC. 1% sodium pentobarbital was used for the anaesthesia of rats. After the endotracheal intubation, a small animal ventilator assisted breathing was connected. We cut the skin longitudinally along the sternum, bluntly separated the muscles with hemostatic forceps, exposed the 3rd to 5th ribs on the left side of the sternum, and open the chest in the 4th intercostal space on the left side of the chest. We then cut the pericardium and fixed the thorax with a self-made hook to fully expose the heart section. The needle was inserted from the left atrial appendage and placed under the conus of the pulmonary artery. The anterior descending branch was ligated with a 6/0 medical suture for 30 minutes, then loosened, and the thoracic cavity was sutured layer by layer.  In the Sham group, the blood vessels of the anterior descending branch were not blocked after threading, and the chest was closed after 60 minutes of threading. In the IRI group, the left anterior descending coronary artery was blocked and opened 45 minutes later. After 15 minutes of stabilization, the chest was closed. In the IRI+RPostC group, after 45 minutes of anterior descending coronary artery occlusion, RPostC was performed. Method: The left femoral artery clamp was clamped for 30 seconds, opened for 30 seconds, repeated three times, and the chest was closed after 15 minutes of stabilization.

value: control


title: Repetition 1 of unknown sex hypothalamus in developmental stage I [Asia1h]

extract_protocol:
Three kinds of tissues (hypothalamus (H), pituitary (P) and gonad (G)) were collected from each individual, flash frozen in liquid nitrogen and stored at -80 °C for RNA extraction.Total RNA was extracted with TRIzol reagent (Invitrogen) following the manufacturer’s instructions.
Total RNA samples (5 μg) were then subjected to cDNA construction following Illumina truSeq stranded mRNA sample preparation protocol. Next, forty-five libraries were sequenced using Illumina HiSeqTM2000/4000 with 2 × 90 or 100 bp paired-end sequencing.


title: HCT116_GFP_Rep2

address: Campus-Vienna-Biocenter 1

value: HCT116 cells

value: STAP-Seq


title: clf0Rt1


title: HCT116_GFP_Rep1


title: control_rep1

description: Gene expression data from control rat


title: control_rep2

description: Gene expression data from control rat


title: clf50Rt3

value: iron sufficient


title: Repetition 5 of unknown sex pituitary in developmental stage I [Asia5p]

value: Pituitary


title: clf50Rt2

value: root


title: HCT116_EP300_Rep3

description:
PCR amplified cDNA (STAP-seq transcript); polyA+ RNA
HCT116_EP300_spikein_normalized.uniq.start.ps.bw
HCT116_EP300_spikein_normalized.uniq.start.ns.bw
Unique_tagcounts_per_oligo_all_reps.txt
Normalized_tagcounts_per_oligo_merged_reps.txt


title: RpostC_IRI_rep3

description: Gene expression data from RpostC_IRI rat model

source_name: RpostC_IRI rat model


title: HCT116_EP300_Rep1


title: HCT116_EP300_Rep2


title: Repetition 3 of unknown sex pituitary in developmental stage I [Asia3p]


title: Repetition 4 of unknown sex pituitary in developmental stage I [Asia4p]


title: clf50Rt1


title: HCT116_EMSY_Rep3

description:
PCR amplified cDNA (STAP-seq transcript); polyA+ RNA
HCT116_EMSY_spikein_normalized.uniq.start.ps.bw
HCT116_EMSY_spikein_normalized.uniq.start.ns.bw
Unique_tagcounts_per_oligo_all_reps.txt
Normalized_tagcounts_per_oligo_merged_reps.txt

value: EMSY


title: Col00Rt3

value: wild type


title: RpostC_IRI_rep2


title: clf0Rt2


title: IRI_rep3

description: Gene expression data from IRI rat model

source_name: IRI rat model

value: IRI


title: Repetition 1 of unknown sex pituitary in developmental stage I [Asia1p]


title: Repetition 2 of unknown sex pituitary in developmental stage I [Asia2p]


title: RpostC_IRI_rep1


title: NE Rep 3

city: East Lansing

first: Thomas

last: Sharkey

state: MI

address: 612 Wilson Rd, Rm 210 Plant Biology Building

department: Biochemistry and Molecular Biology

institute: Michigan State University

data_processing:
Sequencing reads were cleaned and trimmed using Trimmomatic version 0.32 (Bolger et al., 2014)
Cleaned reads were examined with FASTQC (Andrews, 2012) for quality control
Reads were mapped to the reference genomes, Nicotiana tabacum (TN90) and Arbidopsis thaliana (TAIR10)
To calculate read counts for each gene, Rsubread version 3 (Liao et al., 2013) tool (featureCounts function) was used to build read count matrix.
Read count matrix was analyzed using the linear-model based Limma::Voom package (Law et al., 2014) to calculate the gene expression values (RPKM) and perform gene DE statistical analyses
Genome_build: TAIR10 and TN90. Please see the gff3 file on the series record with Nicotiana tabacum gene coordinates.
Supplementary_files_format_and_content: Excel files include RPKM values for each sample

organism: Nicotiana tabacum

source_name: leaves

growth_protocol: Plants were grown on Sure-Mix growing medium in greenhouses

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Hilden, Germany)
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA) following the manufacturer's recommendations

treatment_protocol: NE does not emit isoprene; IE emits isoprene

tag: cultivar

value: Samsun

value: leaves

value: 7 weeks since seeding

tag: isoprene emission phenotype

value: Non-emitting


title: HCT116_EMSY_Rep2

city: Vienna


title: HCT116_EMSY_Rep1


title: bi_GU

city: Warsaw

first: Agnieszka

last: Dzikowska

address: Pawinskiego 5A

country: Poland

institute: University of Warsaw

description:
total RNA depleted of rRNA
Illumina HiSeq 2000 at 2x100 bp paired-end sequencing

data_processing:
quality filtering and trimming, adapter removal
mapping withTophat v1.3.2 (Trapnell et al., 2009)
Mapped reads were filtered to retain only those where both reads of the pair (R1 and R2) aligned in the correct relative orientation
Genome_build: Aspergillus nidulans reference genome sequence A_nidulans_FGSC_A4 version “s09-m04-r07” downloaded from the Aspergillus Genome Database (AspGD) website (http://www.aspergillusgenome.org/)
Supplementary_files_format_and_content: Fragment counting was done using htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#count)
Supplementary_files_format_and_content: Differential gene expression was assesed using the R package edgeR (Robinson et al., 2010) and a nominal value of 0.3 for the ‘biological coefficient of variation’ (BCV)

organism: Aspergillus nidulans

source_name: mycelium grown on 1% glucose and 10 mM urea as a carbon and nitrogen source, respectively

growth_protocol: mycelia were grown in minimal medium for 9-12h at 37oC under carbon repressing (1% glucose) or non-repressing (0.1% fructose); and under nitrogen repressing (10 mM ammonium tartrate) or non-repressing (5mM urea) conditions.

extract_protocol:
Total RNA was isolated from mycelim using the mirVanaTMmiRNA Isolation Kit (Ambion) according to manufacturer’s instructions. Total RNA was depleted of rRNA usuing RiboMinus™ Eukaryote Kit for RNA-Seq (Ambion) and assessed by Agilent 2100 Bioanalyzer.
RNA–Seq libraries were prepared using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre).  17.5 ng of rRNA depleted RNA, according to quantification by Bioanalyzer, was used as input and   following 10 cycles of amplification, libraries were purified using AMPure XP beads. Each library was quantified using Qubit and the size distribution assessed using the Agilent 2100 Bioanalyser.


title: HCT116_BRD4_Rep3

description:
PCR amplified cDNA (STAP-seq transcript); polyA+ RNA
HCT116_BRD4_spikein_normalized.uniq.start.ps.bw
HCT116_BRD4_spikein_normalized.uniq.start.ns.bw
Unique_tagcounts_per_oligo_all_reps.txt
Normalized_tagcounts_per_oligo_merged_reps.txt


title: Col50Rt 3

tag: treatment


title: bi_GNH4

source_name: mycelium grown on 1% glucose and 10 mM ammonium tartrate as a carbon and nitrogen source, respectively


title: bi_FU

source_name: mycelium grown on 0.1% fructose and 10 mM urea as a carbon and nitrogen source, respectively


title: Col50Rt 2


title: NE Rep 4

tag: age


title: IE Rep 4

value: Isoprene emitting


title: HCT116_BRD4_Rep2


title: Col50Rt 1


title: IE Rep 2


title: Col00Rt1


title: NE Rep 2


title: IE Rep 3


title: Col00Rt2


title: bi_FNH4

source_name: mycelium grown on 0.1% fructose and 10 mM ammonium tartrate as a carbon and nitrogen source, respectively


title: Repetition 3 of male hypothalamus in developmental stage II [Asib3Mh]

first: Jianwei

last: Chen

institute: BGI-Shenzhen

data_processing:
Removed low quality reads based on the following conditions: (i) adaptors, (ii) a high proportion of unknown nucleotides (N) (larger than 5%), and (iii) low quality reads ≥ 20% (q-value ≤ 20).
Assembly by the Trinity program (version: release-2013-08-14) with default settings except the ‘--path_reinforcement_distance’: minimum overlap of reads with growing transcript was 85, and the ‘--min_kmer_cov’: 3 k-mers was assembled by three modules including Inchworm, Chrysalis and Butterfly
We clustered transcripts that were just longer than 200 bp using TGICL to minimize redundancy.
Genome_build: de novo assembly submitted at TSA database - provisional accession number GGYF00000000
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

value: Male

value: Stage II

value: Hypothalamus


title: HCT116_BRD4_Rep1


title: IRI_rep2

description: Gene expression data from IRI rat model


title: IRI_rep1

description: Gene expression data from IRI rat model


title: 66 Y Male run2626_lane12_read1 Cell_10

status: Public on May 14 2019

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN703-S502=Jun7_x_x_077_Cell_10

data_processing:
FASTQ sequence files were aligned to the human genome version 19 (hg19) using RSEM.
Single-cell were analyzed using RSEM to estimate transcripts per million mapped reads (TPM) for all genes.
Differentially expressed genes were identified using AltAnalyze using a FDR adjusted empirical Bayes moderated t-test p<0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values

source_name: Bone Marrow

extract_protocol:
Fluidigm C1 protocol
Nextera XT DNA Library Preparation Kit (Illumina Inc, Santa Clara, CA)
All aged (65-75 yo) samples were derived from femurs from individuals undergoing hip replacement surgery at the University of Michigan hospital. Donors had no known history of hematological malignancy. Bone marrow mononuclear cells (BM MNC) were isolated using ficoll based density centrifugation and cryopreserved. Additional bone marrow mononuclear cells were purchased from Allcells, Hemacare, Stemcell Technologies, University of Pennsylvania Stem Cell and Xenograft Core, and Cincinnati Children’s Hospital Processing Core for young (18-30 yo) and middle-aged (45-55 yo) donors. For scRNA-seq, bone marrow cells from healthy donors was obtained at Cincinnati Children’s Hospital Medical Center through informed consent under an approved institutional review board research protocol. Mononuclear cells were isolated with Ficoll-Paque (GE Healthcare), then enriched using CD34 MicroBeads on a Automacs Pro separator (Miltenyi, San Diego, CA). CD34+ cells were stained with lineage antibodies conjugated to PerCP-Cy™5.5: CD2 (Becton, Dickinson and Company, clone RPA-2.10), CD3 (Becton, Dickinson and Company, clone UCHT1), CD4 (Becton, Dickinson and Company, clone RPA-T4), CD7 (Becton, Dickinson and Company, clone M-T701), CD8 (Becton, Dickinson and Company, clone RPA-T8), CD10 (Becton, Dickinson and Company, clone HI10a), CD11b (Biolegend, clone ICRF44), CD14 (Becton, Dickinson and Company, clone M5E2), CD19 (eBioscience, clone HIB19), CD20 (eBioscience, clone 2H7), CD24 (Biolegend, clone ML5), CD56 (Becton, Dickinson and Company, clone B159), CD66b (Becton, Dickinson and Company, clone G10F5), Glycophorin A (Biolegend, clone HIR2) and CD90-biotin (eBioscience, clone 5E10). To isolate CD34+CD38- hematopoietic stem and progenitor cells (HSPC), lineage stained cells were stained with: Streptavidin APC-Cy7 (Becton, Dickinson and Company), CD123-PE (eBioscience, clone 6H6), CD34-APC (eBioscience, clone 4H11), CD38-PE-Cy7 (eBioscience, clone HIT2), CD45RA-FITC ( Invitrogen, clone MEM-56). Cell sorting was performed on a BD FACSAria II with a 100um nozzle.
cDNA was made with Clontech SMARTer® Kit “the mRNA Seq: RT + Amp (1771x), Libraries were constructed using Nextera XT DNA Library Preparation Kit
Single cells were separated using Fluidigm C1 system


title: 66 Y Male run2626_lane12_read1 Cell_82

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN711-S502=Jun7_x_x_270_Cell_82


title: 66 Y Male run2626_lane12_read1 Cell_94

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN704-S506=Jun7_x_x_270_Cell_94


title: 66 Y Male run2626_lane12_read1 Cell_54

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN711-S506=Jun7_x_x_270_Cell_54


title: 66 Y Male run2626_lane12_read1 Cell_66

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN709-S502=Jun7_x_x_270_Cell_66


title: 66 Y Male run2626_lane12_read1 Cell_12

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN705-S504=Jun7_x_x_077_Cell_12


title: 66 Y Male run2626_lane12_read1 Cell_43

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN702-S503=Jun7_x_x_077_Cell_43


title: 66 Y Male run2626_lane12_read1 Cell_30

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN709-S506=Jun7_x_x_077_Cell_30


title: 66 Y Male run2626_lane12_read1 Cell_74

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN710-S502=Jun7_x_x_270_Cell_74


title: 66 Y Male run2626_lane12_read1 Cell_35

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN707-S503=Jun7_x_x_077_Cell_35


title: 66 Y Male run2626_lane12_read1 Cell_67

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN710-S503=Jun7_x_x_270_Cell_67


title: 66 Y Male run2626_lane12_read1 Cell_1

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN701-S517=Jun7_x_x_077_Cell_1


title: 66 Y Male run2626_lane12_read1 Cell_84

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN701-S504=Jun7_x_x_270_Cell_84


title: 66 Y Male run2626_lane12_read1 Cell_87

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN704-S507=Jun7_x_x_270_Cell_87


title: 66 Y Male run2626_lane12_read1 Cell_17

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN703-S517=Jun7_x_x_077_Cell_17


title: 66 Y Male run2626_lane12_read1 Cell_49

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN706-S517=Jun7_x_x_270_Cell_49


title: 66 Y Male run2626_lane12_read1 Cell_6

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN706-S506=Jun7_x_x_077_Cell_6


title: 66 Y Male run2626_lane12_read1 Cell_19

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN705-S503=Jun7_x_x_077_Cell_19


title: 66 Y Male run2626_lane12_read1 Cell_92

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN702-S504=Jun7_x_x_270_Cell_92


title: 66 Y Male run2626_lane12_read1 Cell_50

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN707-S502=Jun7_x_x_270_Cell_50


title: 66 Y Male run2626_lane12_read1 Cell_63

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN701-S507=Jun7_x_x_270_Cell_63


title: 66 Y Male run2626_lane12_read1 Cell_33

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN705-S517=Jun7_x_x_077_Cell_33


title: 66 Y Male run2626_lane12_read1 Cell_36

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN708-S504=Jun7_x_x_077_Cell_36


title: 66 Y Male run2626_lane12_read1 Cell_16

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN709-S508=Jun7_x_x_077_Cell_16


title: 66 Y Male run2626_lane12_read1 Cell_73

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN709-S517=Jun7_x_x_270_Cell_73


title: 66 Y Male run2626_lane12_read1 Cell_45

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN704-S505=Jun7_x_x_077_Cell_45


title: 66 Y Male run2626_lane12_read1 Cell_81

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN710-S517=Jun7_x_x_270_Cell_81


title: 66 Y Male run2626_lane12_read1 Cell_11

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN704-S503=Jun7_x_x_077_Cell_11


title: 66 Y Male run2626_lane12_read1 Cell_78

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN702-S506=Jun7_x_x_270_Cell_78


title: 66 Y Male run2626_lane12_read1 Cell_68

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN711-S504=Jun7_x_x_270_Cell_68


title: 66 Y Male run2626_lane12_read1 Cell_37

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN709-S505=Jun7_x_x_077_Cell_37


title: 66 Y Male run2626_lane12_read1 Cell_58

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN708-S502=Jun7_x_x_270_Cell_58


title: 66 Y Male run2626_lane12_read1 Cell_61

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN711-S505=Jun7_x_x_270_Cell_61


title: 66 Y Male run2626_lane12_read1 Cell_75

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN711-S503=Jun7_x_x_270_Cell_75


title: 66 Y Male run2626_lane12_read1 Cell_60

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN710-S504=Jun7_x_x_270_Cell_60


title: 66 Y Male run2626_lane12_read1 Cell_9

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN702-S517=Jun7_x_x_077_Cell_9


title: 66 Y Male run2626_lane12_read1 Cell_29

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN708-S505=Jun7_x_x_077_Cell_29


title: 66 Y Male run2626_lane12_read1 Cell_14

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN707-S506=Jun7_x_x_077_Cell_14


title: 66 Y Male run2626_lane12_read1 Cell_44

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN703-S504=Jun7_x_x_077_Cell_44


title: 66 Y Male run2626_lane12_read1 Cell_55

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN712-S507=Jun7_x_x_270_Cell_55


title: 66 Y Male run2626_lane12_read1 Cell_5

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN705-S505=Jun7_x_x_077_Cell_5


title: 66 Y Male run2626_lane12_read1 Cell_31

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN710-S507=Jun7_x_x_077_Cell_31


title: 66 Y Male run2626_lane12_read1 Cell_77

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN701-S505=Jun7_x_x_270_Cell_77


title: 66 Y Male run2626_lane12_read1 Cell_4

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN704-S504=Jun7_x_x_077_Cell_4


title: 66 Y Male run2626_lane12_read1 Cell_2

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN702-S502=Jun7_x_x_077_Cell_2


title: 66 Y Male run2626_lane12_read1 Cell_41

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN712-S517=Jun7_x_x_077_Cell_41


title: 66 Y Male run2626_lane12_read1 Cell_80

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN704-S508=Jun7_x_x_270_Cell_80


title: 66 Y Male run2626_lane12_read1 Cell_20

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN706-S504=Jun7_x_x_077_Cell_20


title: 66 Y Male run2626_lane12_read1 Cell_57

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN707-S517=Jun7_x_x_270_Cell_57


title: 66 Y Male run2626_lane12_read1 Cell_25

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN704-S517=Jun7_x_x_077_Cell_25


title: 66 Y Male run2626_lane12_read1 Cell_18

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN704-S502=Jun7_x_x_077_Cell_18


title: 66 Y Male run2626_lane12_read1 Cell_69

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN712-S505=Jun7_x_x_270_Cell_69


title: 66 Y Male run2626_lane12_read1 Cell_95

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN705-S507=Jun7_x_x_270_Cell_95


title: 66 Y Male run2626_lane12_read1 Cell_96

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN706-S508=Jun7_x_x_270_Cell_96


title: 66 Y Male run2626_lane12_read1 Cell_59

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN709-S503=Jun7_x_x_270_Cell_59


title: 66 Y Male run2626_lane12_read1 Cell_83

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN712-S503=Jun7_x_x_270_Cell_83


title: Repetition 6 of unknown sex pituitary in developmental stage I [Asia6p]

address: Yantian

value: not determined

value: Stage I


title: 66 Y Male run2626_lane12_read1 Cell_72

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN703-S508=Jun7_x_x_270_Cell_72


title: 66 Y Male run2626_lane12_read1 Cell_79

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN703-S507=Jun7_x_x_270_Cell_79


title: 66 Y Male run2626_lane12_read1 Cell_3

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN703-S503=Jun7_x_x_077_Cell_3


title: 66 Y Male run2626_lane12_read1 Cell_7

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN707-S507=Jun7_x_x_077_Cell_7


title: 66 Y Male run2626_lane12_read1 Cell_91

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN701-S503=Jun7_x_x_270_Cell_91


title: 66 Y Male run2626_lane12_read1 Cell_70

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN701-S506=Jun7_x_x_270_Cell_70


title: 66 Y Male run2626_lane12_read1 Cell_34

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN706-S502=Jun7_x_x_077_Cell_34


title: 66 Y Male run2626_lane12_read1 Cell_93

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN703-S505=Jun7_x_x_270_Cell_93


title: 66 Y Male run2626_lane12_read1 Cell_76

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN712-S504=Jun7_x_x_270_Cell_76


title: 66 Y Male run2626_lane12_read1 Cell_64

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN702-S508=Jun7_x_x_270_Cell_64


title: 66 Y Male run2626_lane12_read1 Cell_86

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN703-S506=Jun7_x_x_270_Cell_86


title: 66 Y Male run2626_lane12_read1 Cell_47

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN706-S507=Jun7_x_x_077_Cell_47


title: 66 Y Male run2626_lane12_read1 Cell_89

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN711-S517=Jun7_x_x_270_Cell_89


title: 66 Y Male run2626_lane12_read1 Cell_85

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN702-S505=Jun7_x_x_270_Cell_85


title: 66 Y Male run2626_lane12_read1 Cell_88

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN705-S508=Jun7_x_x_270_Cell_88


title: 66 Y Male run2626_lane12_read1 Cell_27

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN706-S503=Jun7_x_x_077_Cell_27


title: 66 Y Male run2626_lane12_read1 Cell_21

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN707-S505=Jun7_x_x_077_Cell_21


title: 66 Y Male run2626_lane12_read1 Cell_71

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN702-S507=Jun7_x_x_270_Cell_71


title: 66 Y Male run2626_lane12_read1 Cell_53

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN710-S505=Jun7_x_x_270_Cell_53


title: 66 Y Male run2626_lane12_read1 Cell_42

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN701-S502=Jun7_x_x_077_Cell_42


title: 66 Y Male run2626_lane12_read1 Cell_28

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN707-S504=Jun7_x_x_077_Cell_28


title: 66 Y Male run2626_lane12_read1 Cell_39

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN711-S507=Jun7_x_x_077_Cell_39


title: 66 Y Male run2626_lane12_read1 Cell_26

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN705-S502=Jun7_x_x_077_Cell_26


title: 66 Y Male run2626_lane12_read1 Cell_38

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN710-S506=Jun7_x_x_077_Cell_38


title: 66 Y Male run2626_lane12_read1 Cell_90

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN712-S502=Jun7_x_x_270_Cell_90


title: 66 Y Male run2626_lane12_read1 Cell_62

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN712-S506=Jun7_x_x_270_Cell_62


title: 66 Y Male run2626_lane12_read1 Cell_32

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN711-S508=Jun7_x_x_077_Cell_32


title: 66 Y Male run2626_lane12_read1 Cell_56

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN701-S508=Jun7_x_x_270_Cell_56


title: 66 Y Male run2626_lane12_read1 Cell_40

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN712-S508=Jun7_x_x_077_Cell_40


title: 66 Y Male run2626_lane12_read1 Cell_24

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN710-S508=Jun7_x_x_077_Cell_24


title: 66 Y Male run2626_lane12_read1 Cell_15

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN708-S507=Jun7_x_x_077_Cell_15


title: 66 Y Male run2626_lane12_read1 Cell_22

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN708-S506=Jun7_x_x_077_Cell_22


title: 66 Y Male run2626_lane12_read1 Cell_48

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN707-S508=Jun7_x_x_077_Cell_48


title: 66 Y Male run2626_lane12_read1 Cell_23

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN709-S507=Jun7_x_x_077_Cell_23


title: 66 Y Male run2626_lane12_read1 Cell_46

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN705-S506=Jun7_x_x_077_Cell_46