title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B2_AD007_indexed


title: DA1

status: Public on Aug 25 2020

type: SRA

city: Bloemfontein

first: Oluwasegun

middle: Olalekan

last: Kuloyo

address: 200 Nelson mandela drive, Park west

department: Microbial Biochemical and Food Biotechnology

country: South Africa

institute: University of the Free State

description:
DMSO_Ethanol_and_DMSO_AA.xlsx
DEvsDA.xlsx

library_source: transcriptomic

data_processing:
Quality of sequences was analysed with FastQC v0.11.5
Low quality reads (<Q30) were discarded using PRINSEQ-lite v0.20.4
Sequences were aligned using TopHat2 v2.2.1 modified with fr-secondstrand, -r 250 mate-std- I 10000 -G option (Dutton et al., 2016), which gave a much better alignment rate.
Gene expression count tables were built from BAM files, created with TopHat2 using the BEDTools multicov command
Counts were used to evaluate the differential expression of genes with DESeq2; Cuffdiff  was also used to generate differential expression data using aligned reads obtained from TopHat2 which were assembled with Cufflinks and merged with Cuffmerge.
Genome_build: C. albicans SC5314 genome assembly 21 (Skrzypek et al., 2017)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample for Cuffdiff and a count table for DESeq2

molecule: total RNA

organism: Candida albicans

source_name: cultures

growth_protocol: Preculture of Candida albicans SC5314  in yeast nitrogen base was grown under biofilm forming conditions in RPMI medium

extract_protocol:
Total RNA was extracted using the RNeasy protect mini kit (Qiagen), while the DNA present was removed with RNase-Free DNase Set (Qiagen). For the preparation of sequencing library, ribosomal RNA was removed from 1 µg of RNA per sample, using the Illumina Ribo-zero rRNA removal kit, and purified with an Agencourt RNAClean XP kit.
Indexed libraries were prepared using the ScriptSeqTM v2 RNA-Seq Library Preparation Kit and ScriptSeqTM Index PCR Primers-Set 1 (Illumina). The library size was profiled with the Bioanalyzer High Sensitivity Assay Kit (Agilent) and quantified with the Qubit HS DNA Assay Kit. The samples were diluted and spiked with a Phix control library (Illumina).

treatment_protocol: Biofilms were treated differently with arachidonic acid (dissolved in EtOH) and DMSO; fluconazole (dissolved in DMSO) and EtOH; fluconazole (dissolved in DMSO) and arachidonic acid (dissolved in EtOH) and DMSO and EtOH.

tag: strain

tag: developmental stage

value: Biofilm

tag: treatment


title: 244-day 97 PI spleen

type: RNA

city: New Haven

first: Hanah

last: Georges

state: Connecticut

address: 333 Cedar St

country: USA

institute: Yale University

hyb_protocol: Contracted to UC Denver Anschutz Genomics and Microarray Core

data_processing: Results were analyzed in R using the limma package

label: biotin

organism: Bos taurus

source_name: day 97 PI spleen

growth_protocol: BVDV  naïve heifers were inseminated (day 0) and confirmed pregnant by ultrasound

extract_protocol: 100 ug of splenic tissue was homogenized and RNA was extracted using TRI-Reagent per manufacturer's instructions.

treatment_protocol: Pregnant heifers were innoculated with media (Control) or BVDV (PI) on day 75 of gestation. Control and PI fetuses were collected on either day 82 or 97 of gestation.

tag: tissue

value: spleen

tag: gender

value: Male


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B2_AD004_indexed

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: Sex

value: male

tag: brain region

value: PIR

tag: age


title: Sample 47_HE12W2-FL

city: Beijing

first: Yuanyuan

last: Fu

address: 5 Yiheyuan Road

country: China

institute: BIOPIC, Peking University

data_processing:
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling
Read 2 was used to obtain the cell barcodes to further split the reads according to the cell IDs(barcode) and the same time recorded the UMI sequences
Read 1 was picked in each cell and these raw reads were trimmed to remove TSO or polyA sequence
Adaptor contamination and low-quality reads were discarded from the trimmed Read1 raw data
TopHat(version 2.0.14) with default settings were used for sequence alignment and uniquely mapped reads were kept.
Uniquely mapped reads were counted by HTSeq package (version 0.6.0), in which reads with same UMI info were assigned as “1”. Finally, for each given individual cell, cell-gene matrices with UMI counts values were generated.
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly hg19
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each Cell

organism: Homo sapiens

source_name: embryonic brain

extract_protocol:
The dissected tissue sections were digested in 2mg/ml collagenase IV (Gibco, 17104-019), 1 mg/ml papain (Sigma, P4762) and 10 U/μl DNase I (NEB, M0303L) with rough pipetting and then vortex on thermocycler at 37°C for 15 min to get single cells.
We did barcoded single cell transcritome library preparation the same as previous studies. The 3’ end of the mRNAs were captured in the libraries. Specifically, 4 cycles of pre-amplification with 98°C 20s, 65°C 30s and 72°C 5min was carried out before 14 cycles of cDNA amplification with  98°C 20s, 67°C 15s and 72°C 5min in this study.
barcoded-single cell RNA-seq

treatment_protocol: The aborted embryos were immediately dissected for the four brain regions and pons.

tag: embryonic stage

tag: brain structure

value: frontal lobe


title: Sample 46_HE12W-PONS

value: pons


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B2_AD002_indexed


title: Sample 45_HE12W-TL

value: temporal lobe


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B2_AD001_indexed


title: 846-day 97 PI spleen

scan_protocol: Contracted to UC Denver Anschutz Genomics and Microarray Core

value: Female


title: 822-day 97 PI spleen

label_protocol: Contracted to UC Denver Anschutz Genomics and Microarray Core


title: 8133-day 97 PI spleen


title: Sample 44_HE12W-OL

value: occipital lobe


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B1_AD008_indexed


title: Sample 43_HE12W-PL

value: parietal lobe


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B1_AD007_indexed


title: 294-day 97 control spleen

source_name: day 97 control spleen


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B1_AD006_indexed


title: 251-day 97 control spleen


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B2_AD012_indexed


title: 837-day 97 control spleen


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B1_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B2_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B1_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B12_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B5_AD004_indexed


title: 807-day 97 control spleen


title: Sample 40_HE11W-PONS2


title: Sample 41_HE12W-FL1


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B12_AD007_indexed


title: Sample 39_HE11W-PONS1


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B1_AD012_indexed


title: 835-day 82 PI spleen

source_name: day 82 PI spleen


title: Sample 38_HE11W-TL


title: 273-day 82 PI spleen


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B12_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B12_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B12_AD004_indexed


title: 267-day 82 PI spleen


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B12_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B12_AD002_indexed


title: GFP-positive (Cy5)/GFP-negative (Cy3)

city: Kyoto city

first: Seisuke

last: Tanigawa

state: Kyoto

address: 465 Kajii-cho,Kawaramachi-Hirokoji

department: Neurosurgery

country: Japan

institute: Kyoto prefectural university of medicine

hyb_protocol: 300 ng of Cy3 or Cy5-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 1 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver1.0 2color (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Microarray Scanner

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software (v 10.7.3.1) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method.

source_name: GFP-positive (Cy5)

label_protocol: Cyanine3 (Cy3) or Cyanine5(Cy5) labeled cRNA was prepared from 50 ng Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy mini spin columns (QIAGEN).

growth_protocol: The glioblastoma stem cell line was established with the neurosphere method from SB transposon-mediated de novo murine glioblastomas.The tumor tissues were minced with scalpels and digested with accutase at 37℃ for 20-30 min, then washed and incubated with serum free neural stem cell culture medium of Neurobasal Medium with B27 and N2 supplements (Gibco, Grand Island, NY, USA) and 10 ng/ml of EGF and bFGF (Minneapolis, MN, USA). The neurospheres were dissociated with accutase (Innovative Cell Technologies, San Diego, CA, USA) and maintained with the neural stem cell culture medium at 37 ºC in 5% CO2 atmosphere..

extract_protocol: Total RNA was extracted from the cells lysed with Trizol and purified with the RNeasy mini kit according to the manufacturer’s protocol.

treatment_protocol: GFP-positive and negative cells were collected using a fluorescence activated cell sorter.

tag: cell type

value: murine gliolbastoma stem cell line

tag: cell subtype

value: GFP-positive

source_name: GFP-negative (Cy3)

tag: cell fraction

value: GFP-negative


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B11_AD012_indexed


title: Sample 37_HE11W-OL_TL

value: occipital lobe and temporal lobe


title: Sample 36_HE11W-OL


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B11_AD010_indexed


title: 306-day 82 control spleen

source_name: day 82 control spleen


title: Sample 35_HE11W-PL


title: Sample 42_HE12W-FL2


title: 862-day 82 control spleen


title: Sample 34_HE11W-FL_PL

value: frontal  lobe and parietal lobe


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B11_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B11_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B11_AD006_indexed


title: Sample 33_HE11W-FL


title: 284B-day 82 control spleen


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B10_AD004_indexed


title: 8108-day 82 control spleen


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B10_AD012_indexed


title: Sample 32_HE10W3-PONS3


title: Sample 31_HE10W3-PONS2


title: Sample 30_HE10W3-PONS1


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B10_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B10_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B11_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B10_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B10_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B11_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B10_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A9_AD012_indexed


title: Sample 29_HE10W3-TL


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B11_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A9_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A9_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B1_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A9_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A9_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A9_AD002_indexed


title: Sample 26_HE10W3-PL


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A9_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A8_AD010_indexed


title: Sample 24_HE10W3-FL


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A8_AD012_indexed


title: Sample 23_HE10W-PONS


title: Sample 28_HE10W3-OL_TL


title: Syncytiotrophoblasts, rep2

city: SAN FRANCISCO

first: Susan

last: Fisher

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

institute: UCSF

hyb_protocol: Sample processing and hybridization were done according to protocols that were devised by the UCSF Gladstone (NHLBI) Genomics Core Facility.

scan_protocol: GeneChips were scanned using a GeneArray Scanner

data_processing: Gene expression data quality was confirmed, normalized (RMA) and annotated using the oligo package and the Bioconductor tools in the R programming environment. Significant differential expression between the trophoblast subtypes was determined using limma (BH adjusted p < 0.05, absolute linear fold change >=2).

source_name: human placenta, mid-gestation

label_protocol: Samples were prepared using the Ambion Whole-Transcript (WT) Expression kit, used in conjunction with the Affymetrix GeneChip  WT Terminal Labeling and Controls Reagent kit

extract_protocol: Total RNA was extracted using Qiagen RNeasy Plus Micro

treatment_protocol: Laser microdissection enabled the isolation of samples that were enriched for syncytiotrophoblasts, villus cytotrophoblasts or endovascular cytotrophoblasts.

value: Chorionic villus syncytium

value: Syncytiotrophoblasts


title: Syncytiotrophoblasts, rep1


title: Syncytiotrophoblasts, rep3


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A8_AD008_indexed


title: Syncytiotrophoblasts, rep4


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A8_AD002_indexed


title: Endovascular cytotrophoblasts, rep3

value: Uterine spiral arterioles

value: Endovascular cytotrophoblasts


title: Endovascular cytotrophoblasts, rep1


title: Endovascular cytotrophoblasts, rep4


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A9_AD006_indexed

value: male


title: Endovascular cytotrophoblasts, rep2


title: Sample 27_HE10W3-OL


title: Sample 22_HE10W-OL_TL


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A8_AD001_indexed

value: PIR


title: Sample 25_HE10W3-FL_PL


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A7_AD012_indexed


title: Sample 20_HE9W2-PONS2


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A7_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A7_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A8_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A7_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A7_AD007_indexed


title: Sample 19_HE9W2-PONS1


title: Cytotrophoblasts, rep4

value: Chorionic villus cell columns

value: Cytotrophoblasts


title: Cytotrophoblasts, rep3


title: Malonyl-CoA rep5

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

description:
M5
Purified HSPCs 7 days in culture

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8)
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.9.3)
Remaining reads were further filtered for low complexity with reaper (v. 15-065)
Reads were aligned to the Mus musculus.GRCm38.86 genome using STAR (v. 2.5.2b)
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7)
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1)
Genome_build: Mus musculus GRCm38.86
Supplementary_files_format_and_content: Tab-separated .txt files with gene-level read count estimates, computed by the htseq-count software package

source_name: Hematopoietic stem/progenitor cells (HSPCs)

growth_protocol: Freshly isolated murine HSPCs were cultured in serum-free media (Stemline II Hematopoietic Stem Cell Expansion Medium, Sigma, S0192) supplemented with 100ng/ml SCF (Recombinant Murine SCF, PeproTech, 250-03), 2ng/ml Flt3 ligand (Recombinant Mouse Flt-3 Ligand, R&D, 427-FL) and 1% P/S (Penicillin Streptomycin, Gibco, 15140-122) with or without 100μM malonyl-CoA (CoALA Bioscience, MC01) for 7 days.  A half medium change was performed after 3 or 4 days. 10’000 murine HSPCs (Lin-Sca1+cKit+)  were seeded per well of a 48-well plate (Falcon, 353078).

extract_protocol:
The progeny of 10’000 initially seeded and cultured LKS cells were collected, RNA isolated with RNeasy Micro Kit (Qiagen, 74004) and checked for integrity.
Libraries were prepared with 350 ng total RNA using Illumina TruSeq Stranded Total RNA Library Prep.

tag: 100micromolar malonyl-coa treatment

value: Yes


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A7_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A7_AD004_indexed


title: Sample 17_HE9W2-OL


title: Sample 16_HE9W2-PL


title: Malonyl-CoA rep3

description:
M3
Purified HSPCs 7 days in culture

treatment_protocol: with or without 100μM malonyl-CoA (CoALA Bioscience, MC01) for 7 days

value: Hematopoietic stem/progenitor cells (HSPCs)


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A5_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A7_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A5_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A5_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A5_AD004_indexed


title: Control rep5

description:
C5
Purified HSPCs 7 days in culture

value: No


title: Malonyl-CoA rep1

description:
M1
Purified HSPCs 7 days in culture


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A5_AD002_indexed


title: Sample 15_HE9W2-FL

value: frontal lobe


title: Sample 14_HE9W-PONS2

value: pons


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A5_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A4_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A4_AD012_indexed


title: Control rep3

description:
C3
Purified HSPCs 7 days in culture


title: Malonyl-CoA rep4

description:
M4
Purified HSPCs 7 days in culture


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A4_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A5_AD010_indexed


title: Cytotrophoblasts, rep2


title: Cytotrophoblasts, rep1


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A4_AD007_indexed


title: Sample 12_HE8W-PONS2


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A4_AD006_indexed


title: Sample 11_HE8W-PONS1


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A4_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A4_AD004_indexed


title: Sample 10_HE8W-R2

value: right hemisphere


title: Sample 9_HE8W-R1


title: Control rep4

description:
C4
Purified HSPCs 7 days in culture


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A3_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A4_AD001_indexed


title: CBESVNI2

city: Ness-Ziona

first: Einat

middle: B.

last: Vitner

state: Israel

address: Ness-Ziona

country: Israel

institute: Israel institute for Biological Research

data_processing:
60bp single reads were sequenced on 1 lanes of an Illumina hiseq
Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt; any reads shorter than 30bp were discarded
Reads were then mapped to the M. musculus GRCm38 reference genome using STAR (Dobin et al., 2013), supplied with gene annotations downloaded from Ensembl (and with EndToEnd option and outFilterMismatchNoverLmax was set to 0.04).
Expression levels for each gene were quantified using htseq-count (Anders et al., 2015) (“HTSeq,” n.d.). TPM values were estimated independently using Kallisto (Bray et al. 2016).
Genome_build: GRCm38

source_name: CBE + SVNI_half brain

extract_protocol:
Mice were sacrificed on p27-28; half brains were removed, flash frozen on dry ice, and RNA was harvested using Rneasy RNA mini kit (Qiagen, Hilden, Germany) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
CBE protocol: C57BL/6 mice were injected daily intraperitoneal (i.p.) with 35mg/kg/day of conduritol β epoxide (CBE) starting from day 13 of age for a duration of 15 days.
SVNI protocol and CBE + SVNI protocol: Half of the CBE-injected group was given a lethal one-time injection i.p. with 30 pfu of neuroadapted Sindbis virus on p21 (called CBE+SVNI), while an additional group that received no CBE injections also received 30 pfu of SVNI by i.p. injection (called "SVNI")

value: post natal day 28

tag: genotype/variation

value: wild type

value: CBE + SVNI

value: saggital half brain, homogenate


title: CBESVNI3


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A3_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A3_AD006_indexed


title: CBESVNI1


title: Sample 13_HE9W-PONS1


title: Sample 8_HE8W-L2

value: left hemisphere


title: SVNI3

source_name: SVNI_half brain

value: SVNI (Sindbis virus)


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A3_AD004_indexed


title: Control rep1

description:
C1
Purified HSPCs 7 days in culture


title: Sample 7_HE8W-L1


title: Sample 6_HE7W-R3


title: SVNI2


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A3_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A3_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A2_AD008_indexed


title: Sample 5_HE7W-R2


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A2_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A2_AD010_indexed


title: Sample 4_HE7W-R1


title: CBE3

source_name: CBE_half brain

value: CBE (Conduritol β epoxide)


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A2_AD004_indexed

value: male


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A2_AD002_indexed

value: PIR


title: SVNI1


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A3_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A2_AD001_indexed


title: Sample 2_HE7W-L2


title: CBE2


title: Control3

source_name: control_half brain

value: untreated; Control


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A1_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A1_AD010_indexed


title: CBE1


title: Sample 3_HE7W-L3


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A1_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A1_AD004_indexed


title: Sample 1_HE7W-L1


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A1_AD012_indexed


title: Control2


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A1_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B1_AD004_indexed


title: Control1


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A12_AD004_indexed


title: U2OS

city: Wen Zhou

first: zhi guo

last: liu

address: Wenzhou medical university of  higher education park  chashan town

institute: Wenzhou Medical University

data_processing:
Illumina HiSeq 1000 reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Read quality was checked for each sample using FastQC v0.10.1.  High-quality reads were then imported into TopHat v2.0.8 for alignment into BAM files.
BAM files were imported into the RNA-Seq pipeline of Partek Genomics Suite, version 6.6 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq release 2013-5-10). Exclusions included a minimum RPKM value of 1.0 in at least two of the 16 samples (potentially duplicates of one sample group). RPKM values were log2-transformed with an offset value of 1.0.
Genome_build: Alignment was initially to the transcriptome (hg19, GRCh37.72), and then to the genome (hg19, GRCh37).
Supplementary_files_format_and_content: ProcessedDataMatrix_Final.txt: Tab-delimited text file includes RPKMs (log2-transformed with an offset value of 1.0) for each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: bone

growth_protocol: Remove and discard culture medium.Briefly rinse the cell layer with 0.25% (w/v) Trypsin- 0.53 mM EDTA solution to remove all traces of serum that contains trypsin inhibitorAdd 2.0 to 3.0 mL of Trypsin-EDTA solution to flask and observe cells under an inverted microscope until cell layer is dispersed (usually within 1 to 15 minutes). Add 6.0 to 8.0 mL of complete growth medium and aspirate cells by gently pipetting. Add appropriate aliquots of the cell suspension to new culture vessels. Incubate cultures at 37°C. Atmosphere: air, 95%; carbon dioxide (CO2), 5%.Temperature: 37°C.

extract_protocol:
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.  1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x100 paired end flow cell.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Treated with active compound B5 at the concentration of 10μM for 48 hours.

tag: cell line

value: Bone osteosarcoma epithelial cells

value: bone

value: untreated


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A12_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A12_AD007_indexed


title: MG63

value: Osteoblast-like cells


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A12_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A12_AD002_indexed


title: RBSDV1 [JNIRB1]

city: Hangzhou

first: Tianze

last: Zhang

address: Yuhangtang Road 866

institute: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were was performed by removing reads containing adapter or poly-N and the low-quality bases using the FastQC program, And then, reads derived from ribosomal RNAs were removed by mapping reads to the Ribosomal Database Project (http://rdp.cme.msu.edu/) with Bowtie2 v2.2.4
Reads were aligned to the reference genome database using the TopHat v2.1.1 software with  -p 4 --b2-very-sensitive   --segment-length 30 --segment-mismatches 2 -r 20 --mate-std-dev 20
Transcript abundances of mRNAs and lncRNAs were quantified using the normalized expression values as FPKM by using the Cuffdiff (v2.1.1) software
Genome_build: Oryza_sativa version_7.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM of mRNA or lncRNA values for each Sample

organism: Oryza sativa

growth_protocol: Rice seedlings were grown inside an insect-free greenhouse at 28 °C and with a 16/8 h (light/dark) photoperiod.

extract_protocol:
Leaf tissues were collected from individual assayed plants, frozen in liquid nitrogen,total RNA was extracted from individual samples using TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RBSDV 1-3 were inoculated with RBSDV using viruliferous small brown planthoppers（SBPHs）for 3 days，MOCK1-3 were inoculated with non-viruliferous SBPHs

tag: cultivar

value: 40 days post sowing

value: RBSDV-infected

value: leaf

tag: molecule type

value: mRNA&lncRNA


title: RBSDV2 [JNIRB2]


title: MG63_B5

value: active compound B5


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_B10_AD002_indexed

tag: strain


title: MOCK2 [JNICK2]

tag: treatment

value: non-infected


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A10_AD012_indexed


title: U2OS_B5

tag: tissue


title: MOCK3 [JNICK3]


title: MOCK1 [JNICK1]


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A10_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A11_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A11_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A1_AD002_indexed


title: E12.5 fetal liver Eto2 mut-6

city: bethesda

first: Xiang

last: Guo

state: MD

address: 50 south drive, blg50

department: NIDDK

institute: NIH

data_processing:
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg38 and mm10  whole genome using hisat2 v2.1.0 with default parameters respectively. Multimappnig reads were filtered using samtoools 1.9, uniquely aligned reads were then mapped to gene features using Subread featureCounts v1.6.4
Differential expression between groups of samples was tested using R version 3.5.1 with DESeq2 1.22.1
Genome_build: hg38 , mm10
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample ...

molecule: polyA RNA

source_name: Fetal liver

growth_protocol: Primary CD34+ umbilical cord cells were obtained from Lonza (cat. 2C-101) and were cultured as described (Wilber et al., 2010). Control C57BL/6J and Eto2 KO mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Fetal livers isolated from E8.5 and E12.5 control and knockout mice.

extract_protocol:
Total RNA was isolated using the Purelink RNA Mini Kit and PicoPure RNA isolation kit.
RNA sequencing libraries were generating from 1 ug total RNA from mouse E8.5 yolk sac/E12.5 fetal liver cells,  or 10 ng total RNA from CD34+ cord blood cells, respectively, using the Illumina TruSeq Stranded mRNA Library Preparation kit (20020594) following manufacturer’s protocol.

value: Fetal liver

value: embryonic day 12.5

tag: genotype


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A10_AD010_indexed

tag: Sex


title: Sample 18_HE9W2-TL

value: temporal lobe


title: RBSDV3 [JNIRB3]


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A11_AD004_indexed

tag: brain region


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A10_AD007_indexed

tag: age


title: E12.5 fetal liver Eto2 mut-5


title: E.coli_DH10B_circuit Ribo-seq - induction state 7

city: Boston

first: Jing

state: MA

address: 610 Commonwealth Avenuce

institute: Boston University

description:
Ribosome protected mRNA
Ribosome profiling on E.coli carrying 0x41 circuit plasmid (pAN3945) and reporter plasmid (pAN4023) induced by aTc and Arabinose

data_processing:
Reads were trimmed of adapter sequence CTGTAGGCACCATCAATATCTCGTATGCCGTCTTCTGCTTG using cutadapt. Only reads longer than 10 nt after trimming were selected.
Trimmed reads were aligned to the E. coli DH10B genome (NC_010473.1) and the circuit and reporter plasmids using the ‘bowtie’ function with parameters ‘-v1 -m2 -k1’
Reads that didn't align to RepBase were aligned to hg19 using STAR v2.4.01 and a splice junction database derived from GENCODE v19
Transcription profiles and ribosome occupancy profiles were generated using an in-house Python script.
Genome_build: NC_010473.1
Supplementary_files_format_and_content: Adaptor-trimmed sequences are in FASTQ files. Transcription and ribosome occupancy profiles of genome, circuit and reporter plasmid are stored in wig file format.

organism: Escherichia coli

source_name: Escherichia coli DH10B cells

growth_protocol: Cultures were incubated at 37°C and 200 rpm for 5 to 7 hours until OD600 reached to 0.3

extract_protocol:
Cells were filtered and flash frozen. Ribosome protected mRNA and total RNA were extracted according to the protocol in the manuscript.
Libraries were constructed using an in-house method described in the manuscript.
Libraries were multiplexed and sequenced on Illumina HiSeq2000 to generate 50nt read

treatment_protocol: Cultures were induced in the presence or absence of 1 mM IPTG, 2 ng/ml (4.32 nM) aTc, and 5 mM Ara

value: 4.32 nM  aTc, 5 mM Ara


title: E.coli_DH10B_circuit Ribo-seq - induction state 8

description:
Ribosome protected mRNA
Ribosome profiling on E.coli carrying 0x41 circuit plasmid (pAN3945) and reporter plasmid (pAN4023) induced by IPTG, aTc and Arabinose

value: 1 mM IPTG, 4.32 nM  aTc, 5 mM Ara


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A11_AD010_indexed

value: male

value: PIR


title: E.coli_DH10B_circuit Ribo-seq - induction state 6

description:
Ribosome protected mRNA
Ribosome profiling on E.coli carrying 0x41 circuit plasmid (pAN3945) and reporter plasmid (pAN4023) induced by IPTG and Arabinose

value: 1 mM IPTG, 5 mM Ara


title: E.coli_DH10B_control Ribo-seq

description:
Ribosome protected mRNA
Ribosome profiling on E.coli carrying a circuit backbone plasmid (pAN871) and reporter plasmid (pDV4-pBAD-yfp) with no induction

value: pAN871, pDV4-pBAD-yfp

value: no induction


title: E12.5 fetal liver Eto2 mut-4


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A10_AD001_indexed


title: E.coli_DH10B_circuit Ribo-seq - induction state 5

description:
Ribosome protected mRNA
Ribosome profilingon E.coli carrying 0x41 circuit plasmid (pAN3945) and reporter plasmid (pAN4023) induced by Arabinose

value: 5 mM Ara


title: E12.5 fetal liver Eto2 mut-1


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A11_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A11_AD002_indexed


title: HeLa_hypoxia_24h_RNA-seq

city: Guangzhou

first: Yan-Jie

last: Wang

address: 107, West Yanjiang Road

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

data_processing:
Sequencing reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR (version 020201)
For meRIP-seq data, exomePeak software (version 3.10) was used for m6A peak calling, and m6A peaks were annotated by Homer (version 4.9)
Genome_build: hg19
Supplementary_files_format_and_content: bw and FPKM data for RNA-seq samples

source_name: Cervical cancer cells

growth_protocol: HeLa cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1 × penicillin-streptomycin (Beyotime) and maintained in a 5% CO2 and 95% air incubator [20% (vol/vol) O2]. For hypoxia exposure, cells were placed in a modular incubator chamber (MART) filled with a hypoxic gas mixture containing 1% O2, 5% CO2, and 94% N2 for various time periods.

extract_protocol: For meRIP-seq, the libraries were constructed by Truseq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions and quantified by BioAnalyzer High Sensitivity DNA chip, and then deeply sequenced on the Illumina HiSeq X10 to generate 150-bp paired-end reads. For RNA-seq library, mRNA enrichment, cDNA synthesis, adaptor addition, circularization, PCR amplification and library examination were performed on the BGIseq 500 at Beijing Genome Institute (BGI; Shenzhen, China)

treatment_protocol:
Total RNA from the indicated samples was extracted using TRIZol reagent (Invitrogen Life Technologies) according to the manufacturer’s instruction. All samples were treated with DNase I to avoid genomic DNA contaminations.
poly(A)+ RNA was isolated from total RNA using Oligotex mRNA Kits and subsequently fragmented into around 150 nt fragments using the RNA fragmentation buffer (20 mM Tris-HCl, pH 7.4, 20 mM ZnCl2) at 94 ℃ for 40 s. The reaction was then stopped with 0.05 M EDTA. For m6A-IP, 2 μg fragmented RNA was incubated with 3 μg anti-m6A antibody (Abcam) in immunoprecipitation buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.5% Igepal CA-630) supplemented with RNase inhibitor for 2 h at 4 ℃. Then the above mixture was incubated with 20 μl protein A/G beads (Thermo Fisher Scientific, #88803) for additional 2 h at 4 ℃ on a rotating wheel. After washing 5 times with immunoprecipitation buffer, bound RNA was extracted by proteinase K digestion, phenol-chloroform extraction followed by standard ethanol precipitation.

value: HeLa

value: Cervical cancer cells

tag: merip antibody


title: E12.5 fetal liver Eto2 mut-2


title: E.coli_DH10B_circuit Ribo-seq - induction state 4

description:
Ribosome protected mRNA
Ribosome profiling on E.coli carrying 0x41 circuit plasmid (pAN3945) and reporter plasmid (pAN4023) induced by IPTG and aTc

value: 1 mM IPTG, 4.32 nM  aTc


title: HeLa_hypoxia_6h_RNA-seq


title: HeLa_hypoxia_12h_RNA-seq


title: E12.5 fetal liver wt-6


title: Suc_R1_automated_L002

city: Cambridge

first: Lena

last: van Giesen

address: 16 Divinity Avenue

department: MCB

institute: Harvard University

data_processing:
Adaptors were trimmed using trim galore
Reads were aligned to the available genome () using Rsubread
Reads were normalized
Transcriptome was assembled using Trinity
Transcriptome was indexed and reads aligned to Transcriptome using Kallisto
Genome_build: Transcriptome was used or genome available on NCBI (GCA_001194135.1 Octopus_bimaculoides_v2_0) to align reads
Supplementary_files_format_and_content: O.bim_Counts.depth.norm.csv, normalized counts after aligning to the genome, the two lanes of the same data set were were merged for this processing
Supplementary_files_format_and_content: Trinity_obim_assembly.fa, assembled transcriptome, fasta file (used for protein sequence confirmation)

organism: Octopus bimaculoides

source_name: whole sucker cup from arm R1

extract_protocol:
Bulk tissues were manually dissected and RNA extracted with phenol chlorophorm standard protocol
libraries were built with the Kapa mRNA HyperPlus kit

tag: tssue

value: whole sucker cup from arm R1


title: Suc_R1_manual_L002


title: E12.5 fetal liver wt-5


title: HeLa_normoxia_RNA-seq

tag: cell type


title: Stat_L002

source_name: Statocyst tissue

value: Statocyst tissue


title: E.coli_DH10B_circuit Ribo-seq - induction state 1

description:
Ribosome protected mRNA
Ribosome profiling on E.coli carrying 0x41 circuit plasmid (pAN3945) and reporter plasmid (pAN4023) with no inducer


title: E.coli_DH10B_circuit Ribo-seq - induction state 3

description:
Ribosome protected mRNA
Ribosome profiling on E.coli carrying 0x41 circuit plasmid (pAN3945) and reporter plasmid (pAN4023) induced by aTc

value: 4.32 nM aTc


title: Skin_L002

source_name: Skin from mantle

value: Skin from mantle


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A10_AD006_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A10_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_1_CEMBA180326_3E_2_A11_AD008_indexed


title: E12.5 fetal liver Eto2 mut-3

value: Fetal liver

value: embryonic day 12.5


title: E12.5 fetal liver wt-4


title: Olfactory_L002

source_name: Olfactory organ

value: Olfactory organ


title: Eye_L002

source_name: Eye

value: Eye


title: Brain_L002

source_name: Brain tissue from optic lobe

value: Brain tissue from optic lobe


title: 8_Suckers_cells_L002

source_name: sucker rims, disscociated cells

value: sucker rims, disscociated cells


title: E.coli_DH10B_circuit RNA-seq - induction state 8

description:
mRNA
RNA-seq on E.coli carrying 0x41 circuit plasmid (pAN3945) and reporter plasmid (pAN4023) induced by IPTG, aTc, Arabinose

value: 1 mM IPTG, 4.32 nM  aTc, 5 mM Ara


title: E.coli_DH10B_control RNA-seq

description:
mRNA
RNA-seq on E.coli carrying a circuit backbone plasmid (pAN871) and reporter plasmid (pDV4-pBAD-yfp) with no induction

value: pAN871, pDV4-pBAD-yfp


title: E12.5 fetal liver wt-3


title: E12.5 fetal liver wt-2


title: E.coli_DH10B_circuit Ribo-seq - induction state 2

description:
Ribosome protected mRNA
Ribosome profiling on E.coli carrying 0x41 circuit plasmid (pAN3945) and reporter plasmid (pAN4023) induced by IPTG

value: 1 mM IPTG


title: E.coli_DH10B_circuit RNA-seq - induction state 6

description:
mRNA
RNA-seq on E.coli carrying 0x41 circuit plasmid (pAN3945) and reporter plasmid (pAN4023) induced by IPTG and Arabinose

value: 1 mM IPTG, 5 mM Ara


title: Stat_L001


title: Suc_R1_manual_L001


title: Suc_R1_automated_L001


title: E.coli_DH10B_circuit RNA-seq - induction state 7

description:
mRNA
RNA-seq on E.coli carrying 0x41 circuit plasmid (pAN3945) and reporter plasmid (pAN4023) induced by aTc and Arabinose

value: 4.32 nM  aTc, 5 mM Ara


title: E8.5 fetal liver Eto2 mut-6

value: embryonic day 8.5


title: Olfactory_L001


title: E.coli_DH10B_circuit RNA-seq - induction state 5

description:
mRNA
RNA-seq on E.coli carrying 0x41 circuit plasmid (pAN3945) and reporter plasmid (pAN4023) induced by Arabinose

value: 5 mM Ara


title: Eye_L001


title: E.coli_DH10B_circuit RNA-seq - induction state 4

description:
mRNA
RNA-seq on E.coli carrying 0x41 circuit plasmid (pAN3945) and reporter plasmid (pAN4023) induced by IPTG and aTc

value: 1 mM IPTG, 4.32 nM  aTc


title: E8.5 fetal liver Eto2 mut-4


title: Skin_L001


title: Brain_L001


title: E8.5 fetal liver Eto2 mut-5


title: low-fiber offspring3

city: chongqing

first: yu

last: linchao

address: No.136 Zhongshan Second Road, Yuzhong District, Chongqing

institute: children's hospital of chongqing medical university

data_processing:
Library strategy: 16s rDNA-sequencing
Raw fastq files were demultiplexed, quality-filtered by Trimmomatic and merged by FLASH
Operational taxonomic units (OTUs) were clustered with 97% similarity cutoff using UPARSE
chimeric sequences were identified and removed using UCHIME
The taxonomy of each 16S rRNA gene sequence was analyzed by RDP Classifier algorithm against the Silva (SSU123) 16S rRNA database using confidence threshold of 70%
Genome_build: METAGENOMIC, FASTA of OTU on series record.
Supplementary_files_format_and_content: OTU counts

organism: feces metagenome

source_name: feces

extract_protocol:
DNA was extracted, isolated and purified using QIAamp DNA stool mini kit (Qiagen) according to the manufacturer’s protocols.
libraries were prepared for sequencing using standard Illumina protocols

tag: diet

value: low fiber

tag: developmental stage

value: offspring at weaning

value: pup's feces


title: E8.5 fetal liver Eto2 mut-3

value: Fetal liver


title: low-fiber offspring2


title: E.coli_DH10B_circuit RNA-seq - induction state 3

description:
mRNA
RNA-seq on E.coli carrying 0x41 circuit plasmid (pAN3945) and reporter plasmid (pAN4023) induced by aTc

value: 4.32 nM aTc


title: E.coli_DH10B_circuit RNA-seq - induction state 2

description:
mRNA
RNA-seq on E.coli carrying 0x41 circuit plasmid (pAN3945) and reporter plasmid (pAN4023) induced by IPTG


title: E8.5 fetal liver Eto2 mut-2


title: normal offspring3

value: normal fiber


title: E12.5 fetal liver wt-1

value: embryonic day 12.5


title: low-fiber offspring1


title: normal offspring2


title: E.coli_DH10B_circuit RNA-seq - induction state 1

description:
mRNA
RNA-seq on E.coli carrying 0x41 circuit plasmid (pAN3945) and reporter plasmid (pAN4023) with no induction

value: no induction


title: low fiber5

value: mother at E18.5

value: maternal feces


title: E8.5 fetal liver Eto2 mut-1


title: E8.5 fetal liver wt-5


title: low fiber3


title: low fiber4


title: E8.5 fetal liver wt-6


title: low fiber2


title: E8.5 fetal liver wt-4


title: normal fiber5


title: 8_Suckers_cells_L001

value: sucker rims, disscociated cells


title: low fiber1


title: normal fiber4


title: ATACseq_Gorlin_rep2

city: Stanford

first: Anthony

last: Oro

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

data_processing:
bowtie used for alignment.
duplicate fragments were removed using samtools
macs2 used for peak calling
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

source_name: human BCC_Gorlin

extract_protocol:
ATAC-seq cell lysis and transposition with Tn5 was carried out based on published protocol by Buenrostro et. al (Nature Methods, 2013). DNA was purified using the Qiagen MinElute columns per manufacturer's instructions.
Libraries were generated using custom Nextera PCR primers and PCR conditions from published protocol by Buenrostro et. al (Nature Methods, 2013).

treatment_protocol: tumors were minced and digested in 0.5% collagenase in HBSS for 1 hour, and 0.05% trypsin for 15 minutes. Cells were strained through a 70 um filter, then stained with the following antibodies for FACS: anti-LYPD3 (Sino Biological 11836-R213-P), anti-Trop2/TACSTD2 (R&D systems FAB650-V), anti-LY6D (E4881, courtesy of Dr. Ruud Brakenhoff), and anti-CD49f/ItgA6 (Millipore MAB1378).

tag: protein expression


title: BCC_2 ATACseq_ItgA6+LYPD3-TACSTD2-LY6D-_rep2

source_name: human BCC_2

value: ItgA6+ LYPD3+ TACSTD2+ LY6D+/-


title: ATACseq_Gorlin_rep1


title: BCC_2 ATACseq_ItgA6+LYPD3-TACSTD2-LY6D-_rep1


title: E8.5 fetal liver wt-3


title: E8.5 fetal liver wt-2


title: normal fiber3


title: normal fiber1


title: BCC_2 ATACseq_ItgA6+LYPD3+TACSTD2+LY6D+_rep2

value: ItgA6+ LYPD3- TACSTD2- LY6D-


title: BCC_2 ATACseq_ItgA6+LYPD3+TACSTD2+LY6D+_rep1


title: BCC_1 ATACseq_ItgA6+LYPD3+TACSTD2+LY6D+_rep2

source_name: human BCC_1


title: normal fiber2


title: E8.5 fetal liver wt-1


title: normal offspring1


title: BCC_1 ATACseq_ItgA6+LYPD3+TACSTD2+LY6D+_rep1


title: BCC_1 ATACseq_ItgA6+LYPD3-TACSTD2-LY6D-_rep2


title: SE2

city: Davis

first: Tom

last: Glaser

address: One Shields Ave

institute: University of California Davis

data_processing:
Adapter sequences were removed using Cutadapt (Martin, 2011) and bases with quality scores <30 were trimmed from 3’ read ends using sickle (github.com/najoshi/sickle, version 85e5117). Trimmed reads <30 bp were discarded. After quality control, the final read counts were 69.5±12.6 million (WT) and 70.2±3.8 million (SE) per replicate. These were mapped to the mouse genome GRCm38 (mm10) genome using BWA (Burrows-Wheeler Alignment tool) (Li, 2013).  Peaks were called using the Genrich v0.5 algorithm (github.com/jsh58/Genrich) from Harvard Informatics Group. Bigwig alignment files were generated for all peaks using bedtools (version 2.27.0) and displayed as a genome browser track using the bedGraphToBigWig script from UCSC (github.com/ucscGenomeBrowser/kent). Differential binding analysis was performed using voom software in the limma package (Law et al., 2014) based on the number of reads overlapping each peak region.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig and narrowpeak

source_name: Retina

extract_protocol:
Pairs of E14.5 +/+ and SE/SE retinas (n=3 per genotype) were dissected in sterile Opti‑MEM media (Thermo Fisher) and processed into a single cell suspension by rinsing in cold PBS, and digesting extracellular matrix in TrypLE (Thermo Fisher) for 10 min at 37oC and extracellular DNA in Opti‑MEM with 0.2 U/µL DNaseI (Roche) at room temperature for 10 min.  Between steps, retinas were diluted in Opti‑MEM and centrifuged at 500×g for 5 min at 4oC.  Cells were resuspended in DMEM, dispersed by centrifugation through a pre‑wet 40 µm strainer for 2 min at 500×g at 4oC, and counted (Countess, Thermo Fisher).  Approximately 100,000 cells were washed in cold PBS, resuspended in cold cell lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.3% NP-40) and immediately centrifuged for 10 min at 500×g at 4oC.  The resulting nuclear pellets were exposed to Tn5 transposase and genomic DNA (gDNA) was extracted according to the original ATAC‑seq protocol (Buenrostro et al., 2015), scaled for 100,000 cells, with the Nextera DNA Library Prep Kit (Illumina, San Diego, CA).
The ATAC‑seq library was amplified using one shared primer and one unique primer, barcoded for each of six biological replicates, and half of the transposed gDNA (50,000 cell equivalents). PCR conditions and total cycle numbers were determined using previous guidelines (Buenrostro et al., 2015).  Replicates were amplified for 17, 18 and 19 cycles (wild-type) or 15, 16 and 16 cycles (SE).  Following library amplification, sample quality was assessed by polyacrylamide gel electrophoresis, Qubit DNA HS assay (Thermo Fisher) and high sensitivity DNA bioanalyzer (Agilent, Santa Clara, CA). Molar concentrations were calculated using the average fragment length and qPCR results (KAPA Library Quantification kit, Roche, Indianapolis, IN). The six sample libraries were pooled equally (300 nM each) and size-selected to remove primer and adapter dimers (SPRI beads with 1.8x ratio, Beckman Coulter, Brea, CA).  The pooled library was 1.9 ng/µL (17.5 nM) with mean fragment size ~170 bp.  This was sequenced using an Illumina HiSeq2500 instrument with a paired-end 100 format (Novogene, Sacramento, CA).

tag: retina

value: retina

value: Atoh7 SE/SE


title: SE1


title: BCC_1 ATACseq_ItgA6+LYPD3-TACSTD2-LY6D-_rep1


title: WT3

value: Atoh7 +/+


title: WT2


title: WT1


title: SE3


title: hBCC2 RNAseq_ItgA6+LYPD3+TACSTD2+LY6D+_rep1

data_processing:
Tophat used for alignment.
Homer is used to calculate raw counts and FPKM values
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

extract_protocol:
RNA isolated using the QIAGEN RNeasy Mini Kit according to the manufacturer's protocol.
The RNA-seq libraries were constructed by TruSeq Stranded mRNA Library Prep kit (Illumina) per manufacturer's protocol and sequenced using the Illumina Hiseq2000 platform.


title: hBCC2 RNAseq_ItgA6+LYPD3+TACSTD2+LY6D+_rep2


title: hBCC2 RNAseq_ItgA6+LYPD3-TACSTD2-LY6D-_rep1


title: hBCC2 RNAseq_ItgA6+LYPD3-TACSTD2-LY6D-_rep2


title: naive B cell of SLE 3

city: Sendai

first: Hiroshi

last: Fujii

state: MIyagi

address: Seiryo 1-1, Aoba-ku

department: Department of Hematotology and Rheumatology

institute: Tohoku University, School of Medicine

description: freshly isolated from PBMC

hyb_protocol: Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 degree) to Agilent Whole Human Genome Oligo Microarrays 8x60K V2.

scan_protocol: The array slides were scanned by Agilent’s Microarray Scanner System (Agilent Technologies)

data_processing: The Agilent Feature Extraction Software (FES) was used to read put and process the microarray image files.

source_name: naive B cell

label_protocol: After targeted cRNA was amplified and labelled with Cyanine-3 using Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

extract_protocol: After isolation of each B cell subset, total RNA was extracted in each B cell subset using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy Mini Kit (QIAGEN, Hilden, Germany).

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were  freshly isolated from healthy donors or SLE patients by Ficoll (GE Healthcare, Uppsala, Sweden) gradient centrifugation. For microarray analysis, first,  B cells were positively isolated with CD19 microbeads  (Miltenyi Biotec, Auburn, CA, USA), then  CD19+CD27-CD38-CD43-CD3-CD14-CD16-(naive B cell) CD19+CD27+CD38-CD43CD3-CD14-CD16- (memory B cell) and CD19+CD38+CD43+CD3-CD14-CD16- (CD38+CD43+ B cell) were  gated and isolated with FACSAria II (BD). For B cell cultures, B cells were isolated from PBMC using B Cell Isolation Kit II (Miltenyi Biotec, Auburn, CA, USA).

tag: individual

value: SLE patient 3

value: whole blood

value: PBMC

tag: cell subset

value: naive B cell


title: memory B cell of SLE 3

description: freshly isolated from PBMC

source_name: memory B cell

value: memory B cell


title: naive B cell of SLE 2

description: freshly isolated from PBMC

value: SLE patient 2


title: naive B cell of SLE 4

description: freshly isolated from PBMC

value: SLE patient 4


title: hBCC1 RNAseq_ItgA6+LYPD3+TACSTD2+LY6D+_rep2


title: plasmablast of SLE 3

description: freshly isolated from PBMC

source_name: plasmablast

value: plasmablast


title: naive B cell of healthy donor 4

description: freshly isolated from PBMC

value: healthy donor 4


title: plasmablast of SLE 1

description: freshly isolated from PBMC

value: SLE patient 1


title: plasmablast of healthy donor 4

description: freshly isolated from PBMC


title: plasmablast of SLE 4

description: freshly isolated from PBMC


title: naive B cell of healthy donor 2

description: freshly isolated from PBMC

value: healthy donor 2


title: memory B cell of SLE 1

description: freshly isolated from PBMC


title: plasmablast of healthy donor 3

description: freshly isolated from PBMC

value: healthy donor 3


title: plasmablast of healthy donor 2

description: freshly isolated from PBMC


title: memory B cell of healthy donor 4

description: freshly isolated from PBMC


title: naive B cell of healthy donor 3

description: freshly isolated from PBMC


title: memory B cell of healthy donor 3

description: freshly isolated from PBMC


title: naive B cell of SLE 1

description: freshly isolated from PBMC


title: plasmablast of SLE 2

description: freshly isolated from PBMC


title: hBCC1 RNAseq_ItgA6+LYPD3-TACSTD2-LY6D-_rep2


title: hBCC1 RNAseq_ItgA6+LYPD3-TACSTD2-LY6D-_rep1


title: memory B cell of SLE 2

description: freshly isolated from PBMC


title: memory B cell of healthy donor 2

description: freshly isolated from PBMC


title: memory B cell of SLE 4

description: freshly isolated from PBMC


title: human K562 ETO2 ChIP-2

data_processing:
ChIP-seq reads were aligned to the GENCODE v25 genome assembly using Bowtie2 v2.3.4.1
Multimapping reads removed with samtools v1.7 using “view” subcommand and the additional argument “-q 20”, duplicated reads were removed with Picard v2.18.0
peaks were called using  MACS2 version 2.1.1
Genome_build: GENCODE v25
Supplementary_files_format_and_content: bed files were generated using MACS2 version 2.1.1

source_name: human K562 cells

growth_protocol: Human K562 cells were cultured in RPMI 1640 medium containing 10 % fetal bovine serum.

extract_protocol:
Briefly, 30X106 K562 cells were fixed with 1% formaldehyde, sonicated and immunoprecipitated with antibodies against LDB1 or ETO2 . Chromatin was pulled down using Dynabeads Protein G, washed twice with RIPA-LS, RIPA-HS, LiCL washing buffer, followed by one wash with 10mM TrisHCl pH8.0. Precipitated DNA was tagmentated on magnetic beads with 0.2ul of tagmentation enzyme (Nextera XT DNA Library Preparation Kit, Illumina # FC-131-1024) for 10 minutes at 37 degree while shaking. The beads with tagementated DNA were washed twice with RIPA-LS and TE buffers. The DNA was eluted and de-crosslinked in ChIP elution buffer (20 mM Tris, pH 7.5, 5 mM EDTA, pH 8.0, 50 mM NaCl, 1% SDS, and 50 μg/mL proteinase K) for 1 hour at 55 degree and incubated at degree  overnight.
ChIP Libraries were prepared using Nextera XT DNA Library Preparation Kit, Illumina # FC-131-1024. Eluted DNA was purified using SRI beads (1.8x) and PCR amplified with Nextera primers. Libraries were purified (1.8x) and size selected (0.65x/ 0.15x) with SRI beads.

tag: antibodies

value: ETO2 (santa cruz, sc-9739x)

value: wild type


title: human K562 LDB ChIP-2

value: LDB1 (santa cruz, sc-11198x)


title: human K562 input-2


title: plasmablast of healthy donor 1

description: freshly isolated from PBMC

value: healthy donor 1


title: memory B cell of healthy donor 1

description: freshly isolated from PBMC


title: naive B cell of healthy donor 1

description: freshly isolated from PBMC


title: human K562 LDB ChIP-1


title: human K562 ETO2 ChIP-1


title: human K562 input-1


title: hBCC1 RNAseq_ItgA6+LYPD3+TACSTD2+LY6D+_rep1

value: ItgA6+ LYPD3+ TACSTD2+ LY6D+/-


title: Axl LacZ/LacZ High #1

city: Bergen

first: Pouda

middle: Panahandeh

last: Strømland

address: Jonas Lies Vei 91

country: Norway

institute: University of Bergen

description:
101036360057_E
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: mammary gland

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

growth_protocol: AXL-expressing cells were enriched  from dissociated Axl+/LacZ and AxlLacZ/LacZ adult mammary glands by FACS using the fluorogenicβ -galactosidase substrate fluorescein Di-β-D-galactopyranoside (FDG). An FDGhigh gate (highest 5%) was used to enrich for AXL-expressing cells, while AXL-negative cells were sorted using an FDGlow gate (lowest 65%). Transcriptomes from FACS sorted FDGhigh and FDGlow cells isolated from Axl+/LacZ adult mammary glands.

extract_protocol: RNA was extracted with RNeasy Mini Kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

value: mammary gland

value: Axl LacZ/LacZ High


title: Axl LacZ/LacZ Low #2

description:
101036360057_H
replicate 2

value: Axl LacZ/LacZ Low


title: Axl LacZ/+ High #2

description:
101036360057_B
replicate 2

value: Axl LacZ/+ High


title: Axl LacZ/LacZ High #2

description:
101036360057_F
replicate 2


title: Axl LacZ/LacZ Low #1

description:
101036360057_G
replicate 1


title: Axl LacZ/+ High #1

description:
101036360057_A
replicate 1


title: Axl LacZ/+ Low #2

description:
101036360057_D
replicate 2

value: Axl LacZ/+ Low


title: Ch-MSC-PCL-bone_replicate_1

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
Run on NextSeq500 using v2 chemistry. RTA Version 2.4.6. BCL files were converted to fastq using bcl2fastq. Indexes were split using custom scripts allowing 1 mismatch
RNAseq reads were preprocessed to remove Nugen adapters using Trimomatic version 0.32. Trimmed reads were then aligned with bowtie version 1.01 to a target containing the bovine (bt8), rat (rn4) and human (hg38) genomes with a custom gene annotation file consisting of the longest transcript at each locus for each genome and gene expression was then quantified using RSEM version 1.2.15.
Genome_build: combined hg38/bt8/rn4 - see supplemental file combined_genome.fa
Supplementary_files_format_and_content: combined_genome.fa.gz is a fasta file consisting of 3 genomes - human hg38, rat rn4 and cow bt8
Supplementary_files_format_and_content: annotation.gtf.gz is a simplified gene annotation file consisting of the longest gene model per locus for each gene in each genome assembly. Original gene models were obtained from the May 2016 refGene tables provided by UCSC genome informatics.
Supplementary_files_format_and_content: counts

organism:
Homo sapiens
Bos taurus
Rattus norvegicus

source_name: Human Mesenchymal Stem Cells, rat stromal cells and cow bone

growth_protocol: Chondrogenically pre-cultured adult human mesenchymal stem cells (hMSC) seeded on poly(ε-caprolactone) scaffolds (3D woven PCL) sutured to bovine bone and implanted into info nude rats for 8 weeks

extract_protocol:
Qiagen RNAeasy
Nugen

value: 8 week culture


title: Axl LacZ/+ Low #1

description:
101036360057_C
replicate 1


title: human K562 rescued ETO2 full length without ZF (D4)-3

data_processing:
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg38 and mm10  whole genome using hisat2 v2.1.0 with default parameters respectively. Multimappnig reads were filtered using samtoools 1.9, uniquely aligned reads were then mapped to gene features using Subread featureCounts v1.6.4
Differential expression between groups of samples was tested using R version 3.5.1 with DESeq2 1.22.1
Genome_build: hg38 , mm10
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample

growth_protocol: Human K562 cells were cultured in RPMI 1640 medium containing 10 % fetal bovine serum.  Control C57BL/6J and Eto2 KO mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Fetal livers isolated from E14.5 control and knockout mice.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (human K562 cells) and PicoPure RNA isolation kit (fetal liver cells)
RNA sequencing libraries were generating from 1 ug (K562 cells and total fetal liver cells) or 10 ng (FACS sorted fetal liver cells) of RNA using Illumina TruSeq  mRNA Library Preparation kit following manufacturer’s protocol.

value: ETO2+/+ without domain ZF


title: human K562 rescued ETO2 full length without HHR (D2)-3

value: ETO2+/+ without domain HHR


title: human K562 rescued ETO2 full length without ZF (D4)-1


title: human K562 rescued ETO2 full length without ZF (D4)-2


title: Ch-MSC-PCL-bone_replicate_3


title: C_Th22

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

country: Germany

institute: BIH at Charité

data_processing:
HiSeq Control Software 2.2.58,  Basecall: RTA 1.18.64.0
FastQ generation: bcl2fastq 1.8.4, FastQ trimming: Trimmomatic 0.36 (ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:3:20 MINLEN:36), alignment: tophat 2.1.0 with bowtie2 2.2.5 and samtools 0.1.19 (--no-novel-juncs)
Reads were summarized per gene using the featureCount algorithm implemented in the R package Rsubread (v1.16.1).
Raw counts of protein-coding genes were normalized using normTransform function of the DESeq2 package (v1.6.3) (pseudocount=1, log2-transformation).
Normalized data were batch compensated to remove CD4/CD8 and donor differences using combat algorithm implemented in the sva package (v3.12.0).
Genome_build: iGenome Homo_sapiens/Ensembl/GRCh37
Supplementary_files_format_and_content: Raw counts - tab-deliminated file with reads summerized per gene.
Supplementary_files_format_and_content: Normalized data - tab-deliminated file with normelized data of protein-coding genes
Supplementary_files_format_and_content: Compensated data - tab-deliminated file with normelized and batch compensated data

source_name: T lymphocytes

growth_protocol: Ex vivo sort from human PBMC

extract_protocol:
RNA was isolated from sorted cells using Macherey&Nagel RNA isolation kit according to the manufacturers protocol. The quality of total RNA isolates was analyzed using the Agilent RNA 6000 Nano Kit.
Poly-(A)-selection was performed utilizing the NEBNext Poly(A)mRNA Magnetic Isolation Module (NEB) according to the manufacturers requirements. mRNA libraries were prepared with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB). All libraries were analyzed with the Agilent DNA 1000 Kit and quantified using the Qubit® dsDNA BR Assay Kit (ThermoFisher). After equimolar pooling all samples were sequenced on an Illumina HiSeq 1500 system with High Output chemistry v4 (50 cycles, single-read)

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were separated from heparinized whole blood by density centrifugation (Biocoll, Biochrom). Cells were cultured in RPMI 1640 medium (Gibco) supplemented with 100 U/mL penicillin, 0.1 mg/mL streptomycin, 0.3 mg/mL glutamine, and 10% inactivated human AB serum (Pan Biotec).

tag: donor

value: C

value: CD4+ T lymphocytes


title: C_Th17+1


title: C_Th17


title: Ch-MSC-PCL-bone_replicate_2


title: human K562 rescued ETO2 full length without HHR (D2)-1


title: human K562 rescued ETO2 full length without TAF110 (D1)-3

value: ETO2+/+ without domain TAF110


title: human K562 rescued ETO2 full length without HHR (D2)-2


title: human K562 rescued ETO2 full length without TAF110 (D1)-2


title: human K562 rescued ETO2 full length-3


title: C_Th2


title: human K562 rescued ETO2 full length-2


title: C_Th1


title: PBMC CD3+ T-cells Ctrl 200256300094_R06C02

type: genomic

city: Toronto

first: Patrick

last: McGowan

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: University of Toronto Scarborough

description: PBMC CD3+ T-cells Ctrl

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Minfi R package standard protocol

label: Cy5 and Cy3

source_name: PBMC CD3+ T-cells

label_protocol: Standard Illumina Protocol

extract_protocol: CD3+ T-cells were isolated from PBMC samples using flurescently labelled antibodies and a FACSAria flow cytometer. Genomic DNA was extracted by MasterPure Complete DNA and RNA Purification Kit (Epicentre)

tag: sample group

value: control


title: human K562 rescued KO control-3


title: human K562 rescued ETO2 full length-1


title: PBMC CD3+ T-cells Ctrl 200256300094_R05C02

description: PBMC CD3+ T-cells Ctrl


title: PBMC CD3+ T-cells Ctrl 200256300094_R04C02

description: PBMC CD3+ T-cells Ctrl


title: C_Tc17

tag: tissue

value: CD8+ T lymphocytes


title: human K562 rescued KO control-2

tag: genotype


title: C_Tc17+1


title: C_Tc2


title: C_Tc_22


title: PBMC CD3+ T-cells Ctrl 200256300094_R01C02

description: PBMC CD3+ T-cells Ctrl


title: PBMC CD3+ T-cells Ctrl 200256300094_R02C02

description: PBMC CD3+ T-cells Ctrl


title: human K562 rescued KO control-1


title: C_Tc1


title: PBMC CD3+ T-cells Ctrl 200256300074_R06C02

description: PBMC CD3+ T-cells Ctrl


title: human K562 rescued WT control-3


title: PBMC CD3+ T-cells Ctrl 200256300094_R06C01

description: PBMC CD3+ T-cells Ctrl


title: PBMC CD3+ T-cells Ctrl 200256300094_R03C02

description: PBMC CD3+ T-cells Ctrl


title: PBMC CD3+ T-cells CFS 200256300094_R04C01

description: PBMC CD3+ T-cells CFS

value: CFS


title: human K562 rescued WT control-2


title: PBMC CD3+ T-cells CFS 200256300094_R05C01

description: PBMC CD3+ T-cells CFS


title: B_Th17+1

value: B


title: PBMC CD3+ T-cells CFS 200256300094_R03C01

description: PBMC CD3+ T-cells CFS


title: human K562 rescued WT control-1


title: B_Th17


title: PBMC CD3+ T-cells CFS 200256300094_R02C01

description: PBMC CD3+ T-cells CFS


title: human K562 ETO2 KO-3


title: human K562 ETO2 KO-2


title: PBMC CD3+ T-cells CFS 200256300094_R01C01

description: PBMC CD3+ T-cells CFS


title: B_Tc_22


title: human K562 ETO2 KO-1


title: B_Th1


title: human K562 Control-3


title: B_Th2


title: AR_48: Control

city: Munich

first: sharmilee

last: vetrivel

state: Bayern

address: ziemssenstraße 1, DG

institute: Ludwig Maximilian University of Munich (Universität München)

data_processing:
The quality of sequencing reads was verified using FastQC0.11.5 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) before and after trimming. Adapters were trimmed using cutadapt. Reads with <15 bp and >40 bp insert sequences were discarded. Alignment of reads was performed using miRBase V21 with sRNAbench. For further analysis EdgeR and DeSeq in R was used.miRNAs with an at least 5 raw count per library were included. Disease groups were compared by unpaired Mann–Whitney test, and to decrease the false discovery rate, corrected p-value was calculated by Benjamini–Hochberg method. P adjusted < 0.05 and log2fold of change >1.5 was applied as cut-off for significance.
Reads with <15 bp and >40 bp insert sequences were discarded. Alignment of reads was performed using miRBase V21 with sRNAbench.
For further analysis EdgeR and DeSeq in R was used.miRNAs with an at least 5 raw count per library were included.
Disease groups were compared by unpaired Mann–Whitney test, and to decrease the false discovery rate, corrected p-value was calculated by Benjamini–Hochberg method.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Serum

extract_protocol:
Total RNA isolation was carried out from all serum samples (450 µl) by miRNeasy Serum/Plasma Kit (Qiagen GmbH, Hilden, Germany). The isolated RNA was held frozen at −80°C until further use.
RNA integrity and absence of DNA was confirmed by Bioanalyzer RNA Nano chips (Agilent Technologies, St. Louis, MO) and Qubit DNA High sensitivity kit, respectively. Sequencing libraries were prepared using the Illumina TruSeq Small RNA Library Preparation Kit. Next generation sequencing was performed on 2 lanes of an Illumina HiSeq2500 (Illumina, San Diego, CA) multiplexing all samples (single end read, 50 bp).

tag: disease group

value: Control

tag: time point

value: Not applicable

value: Serum


title: B_Tc17+1


title: AR_47: Control


title: human K562 Control-2


title: PBMC CD3+ T-cells Ctrl 200256300074_R04C02

description: PBMC CD3+ T-cells Ctrl


title: B_Th22


title: PBMC CD3+ T-cells CFS 200256300074_R05C02

description: PBMC CD3+ T-cells CFS


title: human K562 rescued ETO2 full length without TAF110 (D1)-1


title: AR_46: Control


title: B_Tc17


title: human K562 Control-1


title: PBMC CD3+ T-cells Ctrl 200256300074_R02C02

description: PBMC CD3+ T-cells Ctrl


title: B_Tc2


title: PBMC CD3+ T-cells Ctrl 200256300074_R01C02

description: PBMC CD3+ T-cells Ctrl


title: AR_45: Control


title: Sample_18-TM_tripletT

city: Athens

first: Eleni

last: Katsantoni

address: Soranou tou Ephessiou 4

department: Basic Research

country: Greece

institute: Biomedical Research Foundation, Academy of Athens

description: Transcriptomics_raw_Sample_18-TM_691240_TM-T

data_processing:
Primer and adapter sequencing were removed, and reads were trimmed if necessary using Trimmomatic (version 0.30).
RNA-seq reads were aligned to hg38 genome assembly using Tophat2 (version 2.0.10) with the following parameters: --b2-very-sensitive, --read-realign-edit-dist 0, -g 2, -G hg38.gtf, -M
Number of reads per gene were counted using the Htseq-count (version 0.5.4p5) with the following parameters: --mode=intersection-nonempty
DESeq2 (v1.8) was used for differential expression analysis and libraries were corrected for batch effect (subgroups of Healthy, TI, TM age- and sex-matched cultured together).
Genome_build: hg38
Supplementary_files_format_and_content: Number of reads per gene were generated using Htseq-count (txt files) Number of reads per gene were generated using Htseq-count (txt files) and differential expression was performed using DESeq2 (excel files).

source_name: Thalassemia Major_male_ErPCs

growth_protocol: Erythroid precursor cells (ErPCs) cultures were performed after isolation of peripheral blood mononuclear cells (PBMCs) from healthy subjects and β-thalassemia patients using the previously described Protocol C. Cell samples for RNA-seq analysis were collected at the 4th day of differentiation.

extract_protocol:
Cells were lysed using Tri Reagent (Sigma T9424) and total RNA was extracted.
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation kit v2 (Illumina RS-122-2001) using 1.5-2.0 ug total RNA according to manufacturer’s instructions.

tag: subject status

value: Thalassemia Major

tag: gender

value: male

value: peripheral blood

value: Erythroid precursor cells (ErPCs)


title: PBMC CD3+ T-cells CFS 200256300074_R04C01

description: PBMC CD3+ T-cells CFS


title: AR_43: Control


title: A_Th22

value: A


title: PBMC CD3+ T-cells Ctrl 200256300071_R06C02

description: PBMC CD3+ T-cells Ctrl


title: Sample_18-TI_tripletT

description: Transcriptomics_raw_Sample_18-TI_571760_TI-T

source_name: Thalassemia Intermedia_male_ErPCs

value: Thalassemia Intermedia


title: Sample_18-H_tripletT

value: Healthy


title: PBMC CD3+ T-cells CFS 200256300074_R06C01

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells CFS 200256300074_R05C01

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells Ctrl 200256300074_R03C02

description: PBMC CD3+ T-cells Ctrl


title: AR_42: Control


title: PBMC CD3+ T-cells CFS 200256300074_R03C01

description: PBMC CD3+ T-cells CFS


title: A_Th17+1


title: PBMC CD3+ T-cells CFS 200256300074_R01C01

description: PBMC CD3+ T-cells CFS


title: AR_44: Control


title: PBMC CD3+ T-cells CFS 200256300074_R02C01

description: PBMC CD3+ T-cells CFS


title: Sample_16-TITD_tripletJ

description: Transcriptomics_raw_Sample_16-TI_715976_TI-J


title: AR_41: Control


title: AR_40: Control


title: A_Th2


title: B_Tc1


title: PBMC CD3+ T-cells Ctrl 200256300071_R04C02

description: PBMC CD3+ T-cells Ctrl


title: Sample_16-H_tripletJ


title: AR_39: Control


title: A_Th1


title: Sample_16-TM_tripletJ

description: Transcriptomics_raw_Sample_16-TM_739723_TM-J


title: PBMC CD3+ T-cells Ctrl 200256300071_R05C02

description: PBMC CD3+ T-cells Ctrl


title: A_Tc_22


title: AR_38: Cushing Disease

value: Cushing Disease

value: postoperative


title: Sample_15-TM_tripletG

description: Transcriptomics_raw_Sample_15-TM_780873_TM-G


title: Sample_15-TITD_tripletG

description: Transcriptomics_raw_Sample_15-TI_781393_TI-G


title: PBMC CD3+ T-cells Ctrl 200256300071_R03C02

description: PBMC CD3+ T-cells Ctrl


title: A_Tc17+1


title: AR_34: Cushing Disease


title: Sample_14-TM_tripletA

description: Transcriptomics_raw_Sample_14-TM_882150_TM-A'


title: Sample_15-H_tripletG


title: A_Tc2


title: Sample_14-TI_tripletA

description: Transcriptomics_raw_Sample_14-TI_859725_TI-A'


title: A_Tc17


title: A_Tc1


title: PBMC CD3+ T-cells CFS 200256300071_R06C01

description: PBMC CD3+ T-cells CFS


title: Sample_14-H_tripletA


title: PBMC CD3+ T-cells Ctrl 200256300071_R01C02

description: PBMC CD3+ T-cells Ctrl


title: AR_30: Cushing Disease


title: PBMC CD3+ T-cells Ctrl 200256300071_R02C02

description: PBMC CD3+ T-cells Ctrl


title: Neuron_ok304_rep3

city: Brisbane

first: Steven

last: Zuryn

state: Queensland

address: 79 Upland Road

department: Queensland Brain Institute

country: Australia

institute: The University of Queensland

data_processing:
Basecalls performed using CASAVA (v1.8).
Read quality was assessed by FastQC (v0.11.8) and sequence adapters trimmed using Cutadapt (v2.10), default parameters.
Reads were mapped to the reference genome (WBcel235) using Hisat2 (v2.2.0), default parameters.
General genome arithmetic and index generation was performed using Samtools (v1.10).
Genes were annotated using FeatureCounts (Subread v2.0.0) and assessed for differential expression using edgeR (v3.11).
Significance threshold was set at P < 0.01 and logFC > 2. Only genes with a read count greater than 1CPM in at least two independent samples were considered for analysis.
Genome_build: WBcel235 (Ensemble release 96)
Supplementary_files_format_and_content: Matrix table with normalised read count

organism: Caenorhabditis elegans

source_name: Nervous system

growth_protocol: 50, 000-100, 000 synchronized L4 stage worms grown at 20 degrees, were snap frozen in liquid N2 and processed for immunoprecipitation.

extract_protocol:
Cell-type spedific polysome complexes were immunoprecipitated using FLAG conjugated magnetic beads. Immunocomplexes were eluted from beads using the FLAG peptide and mRNA purified using TRIzol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols adapted for low input samples.

treatment_protocol: standard

value: Neurons


title: PBMC CD3+ T-cells CFS 200256300071_R03C01

description: PBMC CD3+ T-cells CFS


title: Sample_13-TM_tripletS

description: Transcriptomics_raw_Sample_13-TM_643121_TM-S

source_name: Thalassemia Major_female_ErPCs

value: female


title: AR_26: Cushing Disease


title: Neuron_ok304_rep2


title: PBMC CD3+ T-cells CFS 200256300071_R04C01

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells CFS 200256300071_R05C01

description: PBMC CD3+ T-cells CFS


title: AR_36: Cushing Disease


title: Sample_13-TITD_tripletS

description: Transcriptomics_raw_Sample_13-TI_590845_TI-S

source_name: Thalassemia Intermedia_female_ErPCs


title: AR_24: Cushing Disease


title: Neuron_ok304_rep1


title: PBMC CD3+ T-cells CFS 200256300071_R02C01

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells CFS 200256300071_R01C01

description: PBMC CD3+ T-cells CFS


title: AR_22: Cushing Disease


title: Neuron_wt_rep3

value: wild type


title: Sample_13-H_tripletS


title: Neuron_wt_rep2


title: Sample_12-TITD_tripletW

description: Transcriptomics_raw_Sample_12-TI_660499_TI-W


title: Sample_12-TITD_exTM_tripletW

description: Transcriptomics_raw_Sample_12-TI_645976_exTM_TI-W


title: Neuron_wt_rep1


title: AR_37: Cushing Disease

value: preoperative


title: AR_35: Cushing Disease


title: N2_rep2

description: Immunoprecipitated small RNA

data_processing:
Basecalls performed using CASAVA (v1.8).
Read quality was assessed by FastQC (v0.11.8) and sequence adapters trimmed using Cutadapt (v2.10), default parameters.
Reads were mapped to the reference genome (WBcel235) using Bowtie2, default parameters.
General genome arithmetic and index generation was performed using Samtools (v1.10).
Known and novel miRNA annotation and quanitification was performed by miRDeep2 (v2.0.0.8), only miRNAs with > 3 score were considered significant.
Custom scripts were used to determine isomiR type from miRDeep2 output.
EdgeR (v3.11) was used to assess differential expression of miRNAs and isomiRs.
Only miRNAs with a read count greater than 1CPM and isomiRs with a read count greater than 50CPM in at least two independent samples were considered for analysis.
Significance threshold for miRNAs was set at P < 0.01 and logFC > 2. Significance threshold for isomiRs was set at FDR < 0.05 and logFC > 2.
Genome_build: WBcel235 (Ensemble release 96)
Supplementary_files_format_and_content: Matrix tables with normalised read count of miRNAs and all miRNAs/isomiRs.

source_name: wild type

extract_protocol:
RNA was purified from immunoprecipitated ALG:RNA complexes using TRIzol reagent (Invitrogen)
NextSeq libraries were constructed as per manufacturers instructions

treatment_protocol: Standard

value: non-transgenic

tag: treatment

value: Untreated


title: PBMC CD3+ T-cells Ctrl 200256300066_R06C02

description: PBMC CD3+ T-cells Ctrl

value: control


title: PBMC CD3+ T-cells Ctrl 200256300066_R05C02

description: PBMC CD3+ T-cells Ctrl


title: Sample_11-TM_tripletQ

description: Transcriptomics_raw_Sample_11-TM_652391_TM-Q

tag: cell type


title: Sample_12-H_tripletW


title: A_Th17

value: CD4+ T lymphocytes


title: AR_20: Cushing Disease

value: Serum


title: N2_rep1

description: Immunoprecipitated small RNA

value: Control


title: AR_33: Cushing Disease


title: Sample_11-TITD_tripletQ

description: Transcriptomics_raw_Sample_11-TI_609850_TI-Q

value: peripheral blood


title: AR_32: Cushing Disease


title: Muscle_ALG-2_rep2

description: Immunoprecipitated small RNA

value: Body wall muscle


title: AR_31: Cushing Disease


title: PBMC CD3+ T-cells Ctrl 200256300066_R03C02

description: PBMC CD3+ T-cells Ctrl


title: PBMC CD3+ T-cells Ctrl 200256300066_R04C02

description: PBMC CD3+ T-cells Ctrl


title: Muscle_ALG-2_rep1

description: Immunoprecipitated small RNA


title: AR_29: Cushing Disease


title: Sample_10-TI_tripletH

description: Transcriptomics_raw_Sample_10-TI_772072_TI-H

value: Erythroid precursor cells (ErPCs)


title: Sample_10-TM_tripletH

description: Transcriptomics_raw_Sample_10-TM_761707_TM-H

value: Thalassemia Major


title: PBMC CD3+ T-cells CFS 200256300066_R04C01

description: PBMC CD3+ T-cells CFS

value: CFS


title: PBMC CD3+ T-cells Ctrl 200256300066_R02C02

description: PBMC CD3+ T-cells Ctrl


title: Muscle_ALG-1_rep1

description: Immunoprecipitated small RNA


title: AR_27: Cushing Disease

value: Cushing Disease


title: AR_23: Cushing Disease


title: PBMC CD3+ T-cells CFS 200256300066_R05C01

description: PBMC CD3+ T-cells CFS


title: AR_25: Cushing Disease


title: Neuron_ALG-2_rep2

description: Immunoprecipitated small RNA

value: Nervous System


title: Sample_10-H_tripletH

value: Healthy


title: AR_21: Cushing Disease


title: Neuron_ALG-2_rep1

description: Immunoprecipitated small RNA


title: AR_19: Cushing Disease


title: Neuron_ALG-1_rep2

description: Immunoprecipitated small RNA


title: AR_28: Cushing Disease

value: postoperative


title: AR_12: Cortisol producing adenoma

value: Cortisol producing adenoma


title: PBMC CD3+ T-cells Ctrl 200256300065_R06C02

description: PBMC CD3+ T-cells Ctrl


title: AR_10: Cortisol producing adenoma


title: PBMC CD3+ T-cells Ctrl 200256300065_R05C02

description: PBMC CD3+ T-cells Ctrl


title: Neuron_ALG-1_rep1

description: Immunoprecipitated small RNA


title: PBMC CD3+ T-cells CFS 200256300066_R02C01

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells CFS 200256300066_R01C01

description: PBMC CD3+ T-cells CFS


title: Intestine_ALG-2_rep2

description: Immunoprecipitated small RNA

value: Intestine


title: PBMC CD3+ T-cells CFS 200256300066_R03C01

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells Ctrl 200256300065_R04C02

description: PBMC CD3+ T-cells Ctrl


title: Sample_09-H_tripletC

value: female


title: Sample_08-H_dNB


title: AR_8: Cortisol producing adenoma


title: PBMC CD3+ T-cells Ctrl 200256300066_R01C02

description: PBMC CD3+ T-cells Ctrl


title: Sample_07-TM_Fe29


title: Intestine_ALG-2_rep1

description: Immunoprecipitated small RNA

value: Untreated


title: AR_4: Cortisol producing adenoma


title: PBMC CD3+ T-cells CFS 200256300065_R06C01

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells Ctrl 200256300065_R03C02

description: PBMC CD3+ T-cells Ctrl

value: control


title: Intestine_ALG-1_rep2

description: Immunoprecipitated small RNA


title: Sample_07-TI_Fe77

value: Thalassemia Intermedia


title: AR_2: Cortisol producing adenoma

value: Serum


title: Sample_09-TITD_tripletC

description: Transcriptomics_raw_Sample_09-TI_845265_TI-C


title: Intestine_ALG-1_rep1

description: Immunoprecipitated small RNA


title: PBMC CD3+ T-cells Ctrl 200256300065_R01C02

description: PBMC CD3+ T-cells Ctrl


title: PBMC CD3+ T-cells CFS 200256300066_R06C01

description: PBMC CD3+ T-cells CFS


title: Sample_07-H_dLePe


title: Sample_08-TM_AVLTU


title: AR_11: Cortisol producing adenoma

value: preoperative


title: PBMC CD3+ T-cells Ctrl 200256300065_R02C02

description: PBMC CD3+ T-cells Ctrl


title: Sample_06-TM_Fe10

value: male

value: peripheral blood


title: Sample_09-TM_tripletC

description: Transcriptomics_raw_Sample_09-TM_880070_TM-C

value: Erythroid precursor cells (ErPCs)


title: PBMC CD3+ T-cells CFS 200256300065_R05C01

description: PBMC CD3+ T-cells CFS


title: Sample_06-TITD_Fe28


title: Sample_06-H_dGiAg


title: AR_3: Cortisol producing adenoma


title: AR_9: Cortisol producing adenoma


title: RNA-seq ASZ_con_rep4

data_processing:
Tophat used for alignment.
Homer is used to calculate raw counts and FPKM values
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: ASZ001 murine BCC cell line

growth_protocol: ASZ001 cells were cultured in 154CF medium (Life Technologies) supplemented with 2% chelated FBS and 0.05 mM CaCl2.

treatment_protocol: Experiments were carried out using low serum conditions with 154CF medium containing 0.2% chelated FBS and 0.05 mM CaCl2 for 24 hours.

value: DMSO


title: Sample_05-TM_Fe9

value: Thalassemia Major


title: PBMC CD3+ T-cells CFS 200256300065_R02C01

description: PBMC CD3+ T-cells CFS

value: CFS


title: PBMC CD3+ T-cells CFS 200256300065_R03C01

description: PBMC CD3+ T-cells CFS


title: AR_1: Cortisol producing adenoma


title: Sample_11-H_tripletQ


title: Sample_05-TITD_Fe80


title: RNA-seq ASZ_ALK5_inh_rep2


title: RNA-seq ASZ_ALK5_inh_rep3


title: Sample_05-H_dPF


title: sample.458_d6_ld

city: Saint Louis

first: Todd

last: Fehniger

state: Missouri

address: 660 South Euclid Avenue, Campus Box 8007

department: Medicine

institute: Washington University School of Medicine

description: 458_d6_ld.CGACGTACAC-TTACGTTCTC.CGACGTACAC-TTACGTTCTC_S50

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2
Genome_build: GRCh38
Supplementary_files_format_and_content: counts of uniquely aligned unambiguous reads per gene

source_name: NK_LD IL-15

growth_protocol: In 1 experiment, NK cells from 3 different donors were isolated, activated for 16hrs with low-dose IL-15 or IL12/15/18, and incubated for six days in 1ng/mL IL-15

extract_protocol:
RNA was isolated using the Direct-zol RNA MicroPrep kit (zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blood

value: NK cells

value: LD IL-15

value: Day 6


title: Muscle_ALG-1_rep2

description: Immunoprecipitated small RNA

value: Body wall muscle


title: RNA-seq ASZ_con_rep5


title: PBMC CD3+ T-cells CFS 200256300065_R04C01

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells CFS 200256300065_R01C01

description: PBMC CD3+ T-cells CFS


title: RNA-seq ASZ_ALK5_inh_rep1


title: PBMC CD3+ T-cells Ctrl 200256300061_R06C02

description: PBMC CD3+ T-cells Ctrl


title: RNA-seq ASZ_AP1_inh_rep1


title: RNA-seq ASZ_con_rep3


title: Sample_04-TITD_Fe50


title: sample.446_d6_ld

description: 446_d6_ld.CCGTGAACTG-TATGCAACTC.CCGTGAACTG-TATGCAACTC_S43


title: sample.446_d6_ciml

description: 446_d6_ciml.AATCCGAGTA-TTAGAATCGG.AATCCGAGTA-TTAGAATCGG_S11


title: RNA-seq ASZ_con_rep2


title: sample.445_d6_ld

description: 445_d6_ld.GCTCTGTGTC-ACCGCGCTAA.GCTCTGTGTC-ACCGCGCTAA_S64


title: sample.458_d6_ciml

description: 458_d6_ciml.GTATGGCTAA-GCCAGCTATC.GTATGGCTAA-GCCAGCTATC_S67


title: Sample_04-TM_Fe8


title: Sample_04-H_dTG

value: Healthy


title: RNA-seq ASZ_con_rep1


title: sample.445_d6_ciml

description: 445_d6_ciml.TCGTGACGAC-GATGAGCGGT.TCGTGACGAC-GATGAGCGGT_S78


title: PBMC CD3+ T-cells Ctrl 200256300061_R03C02

description: PBMC CD3+ T-cells Ctrl


title: ATAC-seq ASZ_AP1_inh_rep2

data_processing:
bowtie used for alignment.
duplicate fragments were removed using samtools
macs2 used for peak calling
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

extract_protocol:
ATAC-seq cell lysis and transposition with Tn5 was carried out based on published protocol by Buenrostro et. al (Nature Methods, 2013) with minor modifications for on-plate transposition. Briefly, 100,000 ASZ001 cells were plated per replicate in a 48-well plate, then serum starved with or without 20 µM AP-1 inhibitor T-5224 for 24 hours. Wells were washed with cold PBS and lysed using 0.1% NP40 in resuspension buffer for 10 minutes at 25°C. Wells were washed again, then 100 µl of transposition mixture was added per well and incubated for 37°C for 30 min, shaking at 1000 RPM using a thermoshaker. DNA was purified using the Qiagen MinElute columns per manufacturer's instructions.
Libraries were generated using custom Nextera PCR primers and PCR conditions from published protocol by Buenrostro et. al (Nature Methods, 2013).

treatment_protocol: Experiments were carried out using low serum conditions with 154CF medium containing 0.2% chelated FBS and 0.05 mM CaCl2 for 24 hours. 100,000 cells per replicate were treated with DMSO or 20 uM T-5224.


title: ATAC-seq ASZ_AP1_inh_rep1


title: Dengue Infection_Day5 follow-up [Sample_20464_F]

city: Faridabad

first: Abhay

middle: Deep

last: Pandey

address: 3rd Milestone, Faridabad-Gurgaon Expressway

department: Virology

country: India

institute: Regional Centre for Biotechnology

data_processing:
Inbuilt Illumina Casava 1.8.2 software used for basecalling.
QC of sequenced reads were done by FASTQC.
Adapter cutting were done by cutadapt.
Using mirdeep2 and edgeR packages, we have detected differentially expressed  microRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include Normalised count values for each Sample

source_name: Dengue Infection_Day5 follow-up_plasma

extract_protocol:
MicroRNA were isolated from 150 µl of plasma according to the miRNeasy RNA isolation protocol (Qiagen). Quality of isolated small RNA was checked using small RNA chips in 2100 Bioanalyzer (Agilent) for each sample and quantitation was performed in Qubit Fluorometer using micro RNA assay kit (Invitrogen). Small RNA sequencing library preparation was performed using Illumina® TruSeq® Small RNA Library Prep Kit according to the manufacturer’s instructions. Four nanogram of small RNA per sample was used for library preparation.
RNA-seq library preparation was performed using TruSeq® RNA library Prep Kit v2 (Illumina).

tag: subject status/time point

value: Day 5 Followup

value: Plasma


title: PBMC CD3+ T-cells Ctrl 200256300061_R05C02

description: PBMC CD3+ T-cells Ctrl

value: control


title: Sample_03-TM_Fe59

value: female


title: Sample_03-H_dZC


title: PBMC CD3+ T-cells Ctrl 200256300061_R02C02

description: PBMC CD3+ T-cells Ctrl


title: PBMC CD3+ T-cells Ctrl 200256300061_R01C02

description: PBMC CD3+ T-cells Ctrl


title: Dengue Infection_Day5 follow-up [Sample_20139_F]


title: ATAC-seq ASZ_con_rep2


title: Sample_02-TM_ALVT33


title: Dengue Infection_Day5 follow-up [sample_20035_F]


title: Sample_02-H_dRoDeAA


title: ATAC-seq ASZ_con_rep1


title: Dengue Infection_Day5 follow-up [Sample_20688_F]


title: PBMC CD3+ T-cells CFS 200256300061_R04C01

description: PBMC CD3+ T-cells CFS


title: Dengue Infection_Day5 follow-up [sample_20476_F]


title: fetal liver Eto2 mut-5

first: Xiang

institute: NIH

source_name: Fetal livers

tag: strain

value: Fetal livers

tag: age

value: embryonic day 14.5


title: PBMC CD3+ T-cells CFS 200256300061_R06C01

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells CFS 200256300061_R05C01

description: PBMC CD3+ T-cells CFS


title: PBMC CD3+ T-cells CFS 200256300061_R02C01

description: PBMC CD3+ T-cells CFS


title: Sample_03-TITD_Fe46

value: Thalassemia Intermedia

value: peripheral blood


title: Sample_01-TM_Fe6

value: Erythroid precursor cells (ErPCs)


title: Sample_01-TI_Fe73


title: fetal liver Eto2 mut-4


title: Dengue Infection_Day5 follow-up [Sample_20736_F]


title: AR_7: Cortisol producing adenoma

value: Cortisol producing adenoma

value: preoperative

value: Serum


title: fetal liver Eto2 mut-3


title: Dengue Infection_Day5 follow-up [Sample_20655_F]


title: Sample_01-H_dLCC