title: 1113000_non-B


title: 1113000_B

status: Public on Apr 20 2019

type: RNA

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

country: USA

institute: MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: B-cell fraction of follicular lymphoma

label_protocol: 300 ng of total RNA was reverse-transcribed, amplified, and biotin-labeled using an Illumina TotalPrep RNA Amplification kit (Ambion).

extract_protocol: Total RNA was extracted using the RNAqueous kit (Ambion, Austin, TX).

treatment_protocol: Cell suspensions were quickly thawed, washed and pelleted from cryopreservation solution, and magnetically sorted by negative selection into nominal B (CD3-depleted) and non-B (NB; CD19- and CD20-depleted) fractions. The desired enrichment of the respective fractions was determined by flow cytometry for CD19+ and/or CD20+ cells in the B fraction, and CD3+ cells in the NB fraction, as well as by depletion of CD20+ B cells from the NB fraction. Total RNA was extracted from fractions, and then the RNA integrity number (RIN) was determined on an Agilent Bioanalyzer. Only those samples with an RIN >= 6.6 proceeded to labeling and hybridization.

tag: patient id

tag: tissue source

value: untreated follicular lymphoma

tag: cell fraction

value: B cells


title: Time 0 Repeat 2

city: Frederick

first: Barry

middle: Richard

last: O'Keefe

state: Maryland

address: Bldg. 562, Rm. 201, NCI at Frederick

department: Center for Cancer Research

institute: National Cancer Institute

description: bPGN treated

scan_protocol: NanoString Technology

data_processing:
Platform used was: nCounter® PanCancer Pathways Panel, CAT# XT-CSO-PATH1-12, nSOLVER, Advanced Analysis. Data were normalized to Time 0 for each repeat.
RCC files include Raw number of mRNA molecules per 100 ng of total RNA

source_name: HCT-116 human cell line

growth_protocol: RPMI 10%FBS

extract_protocol: miRVANA Paris RNA extraction

treatment_protocol: small molecule treatment. 50 nM bPGN

tag: cell line

tag: time


title: DLD cells charging 0h pol3 inhibition

city: Oxford

first: Irina

last: Chelysheva

address: Roosevelt Dr

department: NDM

country: United Kingdom

institute: University of Oxford

description: Biological replicate 1 of 1.

hyb_protocol: 1. Fluorescently labeled tRNAs were hybridized on the microarrays for 16 h at 60°C in a Hyb4 microarray hybridization system (Digilab) supplemented with polyA (0.17 mg/ml) and salmon sperm DNA (0.17 mg/ml). 2. Microarrays were washed once in 2× SSC/0.1% SDS (50°C), once in 1× SSC/0.1% SDS (42°C) and then three times in 0.1× SSC (42°C). 3. Arrays were dried and stored in the dark at 4°C.

scan_protocol: Arrays were scanned with a GenPIX 4200A (Molecular Devices) instrument.

data_processing:
1. TIF-files of scanned arrays were analyzed using the GenePix Pro 7 (Molecular Devices) software.
2. Ratios of  Cy3/Atto635 fluorescence signals were calculated for individual spots based on mean fluorescence signal (background fluorescence substraction).
3. Cy3 532/Atto635 ratios were normalized to Cy3 532/Atto635 values of tRNA standards (e.g. median Cy3 532/Atto635 ratios of the four tRNA standards E. coli tRNALys2, yeast tRNAAla5, E. coli tRNATyr2, Yeast tRNAPhe3) for individual blocks.
4. Normalized Cy3 532/Atto635 ratios for individual blocks were averaged, representing final Cy3 532/Atto635 ratios.

source_name: cultivated cells

label_protocol:
1. Equal amounts of in vitro synthesized tRNA standards (4 pmol each; E. coli tRNALys2, E. coli tRNATyr2, yeast tRNAAla5, yeast tRNAPhe3) were added to 2 µg extracted total RNA prior to deacetylation.
2. For  abundance arrays total RNA was deacylated for 45 min at 37°C with 100 mM Tris-HCl (pH 9); For tRNA charging arrays total RNA  was oxidized with periodate and thereafter treated for 45 min at 37°C with 100 mM Tris-HCl (pH 9) for tRNA deacetylation; tRNA standards were added prior the deacylation step.
3. Cy3 or Atto653 containing oligonucleotides (Microsynth) were ligated to tRNA 3'-CCA ends using 20 U/μl T4 DNA ligase (New England Biolabs) for 16h at 16°C in the presence of 15% DMSO (Sigma-Aldrich).

growth_protocol:
Cells were cultivated at 37°C and 5% CO2 supplemented with 10% FCS (PAN Biotech) and 2 mM L-glutamine (Gibco) until 70 to 80% confluency.
Cell were grown independently for each biological experiment and checked frequently for mycoplasma contamination.

extract_protocol: Total RNA for total tRNA arrays was extracted using TriReagent (Sigma-Aldrich) and for arrays to determine the charged fraction with acidic phenol (pH 4.5) according to manufacturer's protocol

treatment_protocol: Cells were treated with 4-hydroxytamoxifen to activate c-myc.

value: DLD-1 (ATCC CCL-221)

tag: treatment

value: charging 0h pol3 inhibition

tag: patient identifier

value: untreated


title: Time 24 Repeat 1

description: bPGN treated


title: Time 1 Repeat 1

description: bPGN treated


title: DLD cells charging 4h DMSO

description: Biological replicate 1 of 1.

value: charging 4h DMSO


title: DLD cells charging 0h DMSO

description: Biological replicate 1 of 1.

value: charging 0h DMSO


title: 1113073_B


title: 1113056_B_2


title: 1113054_B_2


title: 1113073_non-B

source_name: non-B-cell fraction of follicular lymphoma

value: non-B cells


title: 1113056_non-B_2


title: 1112961_B_2


title: DLD cells -Leu replicate 2

description: Biological replicate 2 of 3.

value: -Leu


title: 1112961_non-B_2


title: Dermal Fibroblasts_Rep3

type: SRA

city: Seoul

first: Seungkwon

last: You

address: Anam-dong Sungbuk-go

country: South Korea

institute: Korea University

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Dermal fibroblasts

growth_protocol: Fibroblasts were grown in DMEM supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen), and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
TruSeq Stranded mRNA Sample prep kit

tag: cell type

value: Dermal fibroblasts


title: Dermal Fibroblasts_Rep2


title: 1112971_B


title: Dermal Fibroblasts_Rep1


title: 1112988_B


title: DLD cells 8h treatment replicate 3

description: Biological replicate 3 of 3.

value: 4-hydroxytamoxifen for 8h


title: DLD cells -Leu replicate 3

description: Biological replicate 3 of 3.


title: 1112971_non-B


title: 1113054_non-B_2


title: DLD cells 8h treatment replicate 2

description: Biological replicate 2 of 3.


title: 1112988_non-B


title: 1113051_B


title: 1113051_non-B


title: 1113075_non-B


title: 1113075_B


title: Time 0 Repeat 1

description: bPGN treated


title: 1166768_non-B


title: DLD cells -Leu replicate 1

description: Biological replicate 1 of 3.


title: OLIG2::eGFP Fibroblasts_Rep2

source_name: OLIG2::eGFP ESCs

value: OLIG2::eGFP ESCs


title: MEF A2S D2 Rep A

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

data_processing:
BCL files were converted to FASTQ using bcl2fastq v2.19
Sequences were aligned to Mus musculus 10 (mm10) genome using Spliced Transcripts Alignment to a Reference (STAR), available through the SureCell RNA Single Cell App v1.1.0 in Illumina Basespace.
Droplets containing only single were selected using double knee plot in BaseSpace
Genome_build: mm10
Supplementary_files_format_and_content: .csv files containing UMI counts per genes (columns) for single cell (row).
Supplementary_files_format_and_content: The file 'IrrMEFs_CellID.csv' contains barcode information ("CellID") and sample information ("Sample", "Treatment", and "Timepoint") for each irradiated mouse embryonic fibroblast. These cells were removed before performing downstream Monocle analysis.

organism: Mus musculus

source_name: Mouse Embryonic Fibroblasts

growth_protocol:
MEF or mESCs were cultured in ESC Media (knockout DMEM, 15% FBS, L-glutamine, Pen/Strep, NEAA, 2-mercaptoethanol, and leuemia inhibitory factor) with or without small molecules (Ascorbic acid, SGC0946, CHIR-99021, and PD-032501).
Postnatal brain cells were cultured in neural basal medium supplmented with B27 (wo/ Vit A), Pen/Strep, L-glutamine, NEAA, 20ng/mL EGF, and 20ng/mL FGF2.  Postnatal brain cells repogramming was done in ESC media with small molecules.

extract_protocol:
Cells were resuspended into single cell suspension and encapsulated into droplets containing library components via Bio-Rad ddSeq Single-Cell Isolator.
Library were prepared using Illumina Bio-Rad SureCell WTA 3' Library Kit according to manufacturer's instruction.
Single-Cell RNA Sequencing

treatment_protocol: Reprogramming cultures were plated on irradiated MEFs and treated with 2ug/mL doxycycline, 50ug/mL ascorbic acid, and 5uM of SGC09456 on Day 0. CHIR-99021 and PD-0325901 (2i) was added 12 hours later. Media containing chemicals and doxycycline was replaced on day 2 and day 4 of reprogramming.

tag: timepoint

value: Day 2

tag: age

value: Embryonic


title: 1112924_non-B


title: OLIG2::eGFP Fibroblasts_Rep1


title: 1166768_B


title: DLD cells 4h treatment replicate 5

description: Biological replicate 5 of 5.

value: 4-hydroxytamoxifen for 4h


title: 1113003_non-B


title: DLD cells 8h treatment replicate 1

description: Biological replicate 1 of 3.


title: SOX10+ iOPCs_Rep3

source_name: SOX10::eGFP fibroblasts

value: SOX10::eGFP fibroblasts


title: SOX10+ iOPCs_Rep2


title: SOX10+ iOPCs_Rep1


title: OLIG2+ iOPCs_Rep3

source_name: OLIG2::eGFP fibroblasts

value: OLIG2::eGFP fibroblasts


title: DLD cells 4h treatment replicate 3

description: Biological replicate 3 of 5.


title: 1112932_B

value: untreated follicular lymphoma


title: DLD cells 4h treatment replicate 4

description: Biological replicate 4 of 5.


title: DLD cells 4h treatment replicate 2

description: Biological replicate 2 of 5.


title: 1112961_non-B


title: DLD cells 4h treatment replicate 1

description: Biological replicate 1 of 5.


title: 1113066_non-B


title: 1112932_non-B


title: 1113066_B

value: B cells


title: 1113078_non-B


title: DLD cells 2h treatment replicate 2

description: Biological replicate 2 of 2.

value: DLD-1 (ATCC CCL-221)

value: 4-hydroxytamoxifen for 2h


title: 1112990_B


title: 1112967_B


title: Hd tm1

city: Changsha

first: Yongting

last: Yu

address: No 348, Xianjiahu West Rd.

country: China

data_processing:
RNA-Seq: the cDNA library with a fragment length range of 300 bp (±25 bp) was constructed and the paired-end sequencing was performed by using the Illumina sequencing platform (HiSeqTM 2500).
Filtering: Adapter sequences were removed, higher N rate sequences, and low-quality reads (less than 13 bp or reads with unknown nucleotides larger than 5%) were filtered with the SeqPrep and Sickle software.
Gene annotation: High-quality reads were mapped to the tobacco (cultivar K326) genome (https://www.ncbi.nlm.nih.gov/assembly/GCA_000715075.1/) using Hisat2 (http://ccb.jhu.edu/software/hisat2/index.shtml) and annotated based on the tobacco genome sequence. The mapped reads were then assembled using Stringtie v1.3.3b (http://ccb.jhu.edu/software/stringtie/) with default parameters, and gffcompare utility was used to determine how many assembled transcripts match annotated genes and how many are novel transcripts. Functional annotation of new transcripts was performed through a match search against SWISS-Prot and GenBank-NR database using DIAMOND (e-value of 1e-5).
Gene Expression Analysis: Gene expression levels were measured in the RNA-Seq analysis as fragments per kilobase of exon model per million mapped reads (FPKM). The DEseq software was used to identify differentially expressed genes in pair-wise comparison, and the results of all statistical tests were corrected for multiple testing with the Benjamini–Hochberg false discovery rate (FDR < 0.01).
Supplementary_files_format_and_content: The .txt files contain the gene name, fpkm value, the number of total reads and the number of unique reads

organism: Nicotiana tabacum

source_name: Honghuadajinyuan

growth_protocol: Resistant (R line, Yanyan 97,Yy97) and susceptible (S line, Honghuadajinyuan，Hd) tobacco cultivars were used in this study. For each germplasm, ca. 100 seeds were surface-sterilized by immersion in 2% sodium hypochlorite (NaClO) for 5 min, followed by three rinses in sterile water. Subsequently, the seeds were plated in Petri dishes (9 cm in diameter) on Whatman No. 3 filter paper moistened with sterile water. Then the seeds were cultivated at 28±1ºC in dark in a chamber. After germination, the plantlet were individually transplanted into plastic pot (9 cm in diameter and 10 cm in depth) filled with pasteurized nutritious soils (clay: sand: organic matter = 3:1:1, v/v). The seedlings were grown at 25 ± 1°C with a 12 h photoperiod，80% ± 1 RH , under light intensity of 5000 lux, in a greenhouse of Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science (IBFC, CAAS).Resistant (R line, Yanyan 97,Yy97) and susceptible (S line, Honghuadajinyuan，Hd) tobacco cultivars were used in this study (Ji et al., 2000). For each germplasm, ca. 100 seeds were surface-sterilized by immersion in 2% sodium hypochlorite (NaClO) for 5 min, followed by three rinses in sterile water. Subsequently, the seeds were plated in Petri dishes (9 cm in diameter) on Whatman No. 3 filter paper moistened with sterile water. Then the seeds were cultivated at 28±1ºC in dark in a chamber. After germination, the plantlet were individually transplanted into plastic pot (9 cm in diameter and 10 cm in depth) filled with pasteurized nutritious soils (clay: sand: organic matter = 3:1:1, v/v). The seedlings were grown at 25 ± 1°C with a 12 h photoperiod，80% ± 1 RH , under light intensity of 5000 lux, in a greenhouse of Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science (IBFC, CAAS).

extract_protocol:
To prepare samples for Illumina sequencing, total RNA of each sample was extracted using an EASYspin plus Total RNA kit (Aidlab, Beijing, China) following the protocol. Quality and yield of RNA were determined by agarose gel electrophoresis and Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA), respectively.
Total RNA was extracted from the stem samples with TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) and purified with Plant RNA Purification regent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. The concentration and purity of total RNA was determined using NanoDrop2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA), and RNA integrity was examined by Agilent2100 bioanalyzer (Agilent, Santa Clara, CA, USA).Illumina sequencing was performed at Majorbio Bio-pharm Technology Co. Ltd, Shanghai, China (http://www.majorbio.com/). For transcriptome sequencing, eight individual libraries (Yy97ck1, Yy97ck2, Yy97tm1, Yy97tm2, Hdck1, Hdck2, Hdtm1 and Hdtm2) were constructed using 5 μg of total RNA. Briefly, poly (A) mRNA was extracted from the total RNA sample using Oligo (dT) magnetic beads. mRNA was fragmented into 200–500 nt pieces by adding a fragmentation buffer. First-strand cDNA was synthesized using SuperScript II reverse transcriptase (Life Technologies, Inc.) and random hexamer primers. After generation of second-strand cDNA, the double-strand cDNA was end-repaired, and a single ‘A’ base and indexed adapters were ligated to the fragments. The cDNA library was constructed with the Illumina Paired End Sample Prep kit (Illumina, USA), quantified by TBS380 (Picogreen, Invitrogen, USA) and was then sequenced on the Illumina HiSeqTM2500 (2×150 bp read length) platform.

treatment_protocol: Pathogen inoculation was performed at 4 to 5 true leaves. Virulence R. solanacearum strain CQPs-1 (kindly supplied by Pro. Wei Ding, College of Plant Protection, Southwest University) was used. This pathogen is belongs to phylotype I (Liu et al. 2017). The bacterium was reproduced in B medium (Boucher et al. 1985) at 28 ±1°C, 180 rpm in a ZHWY-2102C shaking incubator (Shanghai ZHICHENG Analytical Instrument Manufacturing CO., LTD, Shanghai, China) for 24 hours. The bacterial suspension was adjusted to an OD600 of 0.1 with sterile deinonized water. For pathogen inoculation, to each plant, diluted pathogen suspension of 20 ml was poured to the stem base. For control plants, equal volume of sterile water was added with the same method. There were at least 24 plants for each treatment. After inoculation, both the control and inoculated plants were grown at same condition as described above with except temperature was adjusted to 28 ± 1°C.

tag: cultivar

value: Honghuadajinyuan

tag: tissue

value: stem

tag: developmental stage

value: 5-6 leaf stage

tag: infection

value: Ralstonia solanacearum


title: Hd ck2

institute: Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science

value: control


title: 1112953_non-B

value: non-B cells


title: 1112953_B


title: 1112990_non-B


title: 1112961_B


title: OLIG2+ iOPCs_Rep1


title: Hd ck1


title: DLD cells 2h treatment replicate 1

description: Biological replicate 1 of 2.

value: untreated


title: Hd tm2


title: Yy97 tm2


title: Yy97 tm1


title: Yy97 ck2


title: Yy97 ck1


title: A2B5+ iOPCs(DF)_Rep3

value: Dermal fibroblasts


title: A2B5+ iOPCs(DF)_Rep2


title: DLD cells charging -Leu replicate 3

description: Biological replicate 3 of 3.

value: charging -Leu


title: OLIG2+ iOPCs_Rep2


title: 5-tag species mixing

city: St Louis

first: Samantha

last: Morris

state: Missouri

address: Department of Developmental Biology, Washington University School of

institute: Washington University in St Louis

description:
5tag
polyA RNA
Cells were encapsulated and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v2 chemistry). BAM files and Gene-barcode matrices were generated using 10X Genomics Cellranger version 3.0.2.

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to mm10 or hg19 genome build via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Genome_build: mm10 or hg19
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

organism:
Homo sapiens
Mus musculus

source_name: E13.5 mouse embryonic fibroblasts, HEK293T cell line

extract_protocol: 10x Genomics Chromium single cell preparation.

tag: mouse cell type

value: E13.5 mouse embryonic fibroblasts

tag: human cell line


title: 2-tag species mixing

description:
2tag
polyA RNA
Cells were encapsulated and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v2 chemistry). BAM files and Gene-barcode matrices were generated using 10X Genomics Cellranger version 2(?).


title: A2B5+ iOPCs(DF)_Rep1


title: DLD cells charging -Leu replicate 2

description: Biological replicate 2 of 3.


title: DLD cells charging -Leu replicate 1

description: Biological replicate 1 of 3.


title: O4+ iOPCs(D60)_Rep3

source_name: Foreskin fibroblasts

value: Foreskin fibroblasts


title: DLD cells charging 8h treatment replicate 5

description: Biological replicate 5 of 5.

value: charging 4-hydroxytamoxifen for 8h


title: O4+ iOPCs(D60)_Rep1


title: O4+ iOPCs(D40)_Rep3


title: DLD cells charging 8h treatment replicate 2

description: Biological replicate 2 of 5.


title: DLD cells charging 8h treatment replicate 3

description: Biological replicate 3 of 5.


title: O4+ iOPCs(D40)_Rep2


title: O4+ iOPCs(D40)_Rep1


title: DLD cells charging 8h treatment replicate 1

description: Biological replicate 1 of 5.


title: O4+ iOPCs(D60)_Rep2


title: Hippocampus Aged Saline Replicate 3

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

description: hippocampus from aged animal treated with intranasal saline for 3 months

hyb_protocol: Following fragmentation, cRNA was hybridized for 16hr at 45 degrees C, on Clariom_S_Rat Affymetrix arrays (Affymetrix Fluidics Station 450)

scan_protocol: Scanning performed according to vendor instructions on Affymetrics GCS 3000 7G scanner. .CEL files produced were used for subsequent analyses.

data_processing: .CEL files were processed with Partek software to RMA (log2) estimates of signal intensity.

organism: Rattus

source_name: hippocampus saline 3 months

label_protocol: Biotinylated cRNA prepared according to standard Affymetrix protocol

extract_protocol: Hippocampi were thawed on ice and homogenized in RiboZol™ Extraction Reagent (#97064-948; VWR®, Radnor, PA). RNA was precipitated with chloroform and isopropanol, then resuspended in a 75% ethanol solution.

treatment_protocol: All rats were treated with intranasal insulin aspart or saline (control) for 3 months, and were subjected to the Morris water maze task prior to hippocampus removal.

tag: strain

tag: Sex

value: male

value: hippocampus

tag: start age

value: 18 months

tag: end age

value: 21 months

tag: rin

value: intranasal saline for 3 months


title: Hippocampus Aged Saline Replicate 8


title: DLD cells charging 4h treatment replicate 4

description: Biological replicate 4 of 5.

tag: cell line

value: DLD-1 (ATCC CCL-221)

value: charging 4-hydroxytamoxifen for 4h


title: DLD cells charging 4h treatment replicate 5

description: Biological replicate 5 of 5.

tag: treatment


title: Hippocampus Aged Saline Replicate 7


title: Hippocampus Aged Saline Replicate 4


title: DLD cells charging 8h treatment replicate 4

description: Biological replicate 4 of 5.

tag: patient identifier


title: A2B5+ iOPCs(BJ)_Rep3

tag: cell type


title: Hippocampus Aged Saline Replicate 6


title: Hippocampus Aged Saline Replicate 2


title: Hippocampus Aged Insulin Replicate 6

description: hippocampus from aged animal treated with intranasal insulin for 3 months

source_name: hippocampus insulin 3 months

value: intranasal insulin for 3 months


title: Hippocampus Aged Insulin Replicate 7


title: Hippocampus Aged Insulin Replicate 4


title: A2B5+ iOPCs(BJ)_Rep2


title: Hippocampus Aged Saline Replicate 1


title: DLD cells charging 4h treatment replicate 3

description: Biological replicate 3 of 5.


title: Hippocampus Aged Saline Replicate 5


title: Hippocampus Aged Insulin Replicate 3


title: Hippocampus Aged Insulin Replicate 5


title: Hippocampus Aged Insulin Replicate 2


title: 1112967_non-B

tag: patient id

tag: tissue source

value: untreated follicular lymphoma

tag: cell fraction


title: A2B5+ iOPCs(BJ)_Rep1


title: Hippocampus Aged Insulin Replicate 1

tag: tissue


title: DLD cells charging 4h treatment replicate 2

description: Biological replicate 2 of 5.


title: Hippocampus Young Saline Replicate 6

description: hippocampus from young animal treated with intranasal saline for 3 months

value: 2 months

value: 5 months


title: DLD cells charging 4h treatment replicate 1

description: Biological replicate 1 of 5.

value: untreated


title: Hippocampus Young Saline Replicate 5


title: Hippocampus Young Saline Replicate 4


title: DLD cells charging 2h treatment replicate 2

description: Biological replicate 2 of 2.

value: charging 4-hydroxytamoxifen for 2h


title: Hippocampus Young Saline Replicate 2


title: DLD cells charging 2h treatment replicate 1

description: Biological replicate 1 of 2.


title: Hippocampus Young Saline Replicate 3


title: Bel-7404 with GTSE1-knockdown, biological rep3

city: Beijing

first: Jingyu

last: Wang

state: Select State

address: 4204, Biotechnology Building, Tsinghua University

department: Medical School

institute: Tsinghua University

description: gene expression data from GTSE1-knockdown cell line Bel-7404

hyb_protocol: Hybridization of the aRNA and the GeneChip® PrimeviewTM Human Gene Expression Array was conducted with GeneChip Hybridization Wash and Stain Kit.

scan_protocol: Microarrays were read with GeneChip Scanner 3000.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Bel-7404 with GTSE1-knockdown

label_protocol: Amplified RNA was obtained via GeneChip 3’IVT PLUS Kit (Affymetrix) and labeled with biotin.

growth_protocol: Human hepatoma cell BEL-7404 were cultured in Roswell Park Memorial Institute 1640 medium supplemented with FBS and 5 μg/ml puromycin (Clontech, USA), and cells grew in suspension at 37 °C with 5% CO2.

extract_protocol: Total RNA extraction was performed with Trizol Reagent according to standard procedures.

treatment_protocol: Small interfering RNA (siRNA) target sites (psc34526: CTACTCCTACAAATCAATT; psc34528: GCGAGATTCCTGTCTAAAT) were designed against GTSE1 gene. Double-strand DNA oligos were then synthesized based on the short hairpin RNA (shRNA) interference sequences, and subcloned into lentiviral plasmids GV115 cloning vectors in TOP10 cells. Lentiviruses were harvest from 239T cells into which cotransfected with the recombinant plasmids, pHelper1.0 and pHelper2.0. Virus titer was determined by fluorescence method. In addition, lentivirus vectors inserted with scramble sequence (TTCTCCGAACGTGTCACGT) were simultaneously prepared as a negative control (shCtrl).

tag: tumor

value: Hepatoma cell line


title: Bel-7404 with GTSE1-knockdown, biological rep2


title: DLD cells charging control replicate 4

description: Biological replicate 4 of 5.

value: charging control


title: DLD cells charging control replicate 3

description: Biological replicate 3 of 5.


title: Bel-7404, biological rep3

description: gene expression data from wildtype hepatoma cell line Bel-7404


title: DLD cells charging control replicate 2

description: Biological replicate 2 of 5.


title: Bel-7404, biological rep2


title: DLD cells charging control replicate 5

description: Biological replicate 5 of 5.


title: OLIG2::eGFP Fibroblasts_Rep3

value: OLIG2::eGFP ESCs


title: Hippocampus Young Saline Replicate 1


title: DLD cells charging control replicate 1

description: Biological replicate 1 of 5.


title: Bel-7404, biological rep1


title: Hippocampus Young Insulin Replicate 4

description: hippocampus from young animal treated with intranasal insulin for 3 months


title: Hippocampus Young Insulin Replicate 2


title: Hippocampus Young Insulin Replicate 5


title: Bel-7404 with GTSE1-knockdown, biological rep1

description: gene expression data from GTSE1-knockdown hepatoma cell line Bel-7404


title: Hippocampus Young Insulin Replicate 1


title: NUGC3_siVGLL1_rep1

city: Daejeon

first: Bo-Kyung

last: Kim

address: Kwahag-ro

institute: KRIBB

description:
GE1_1100_4
Gene expression of cells treated with siVGLL1.

hyb_protocol: Labeled cRNA was applied microarray (Agilent Technologies, 8x60K) using Agilent’s Gene Expression Hybridization Kit.

scan_protocol: The microarray chip was scanned using Agilent’s DNA microarray scanner and the raw signal density was acquired from Feature Extraction software.

data_processing: The differential gene expression was classified by Benjamini-Hochberg's false discovery ratio method. GeneSpring GX12 software. Gene ontology and KEGG pathway for the differential expressed genes was analyzed using GeneSpring GX 12 (Agilent Technologies, San Carlos, CA) and DAVID Bioinformatics tools (National Institute of Allergy and Infectious Diseases, NIH).

label_protocol: Cyanine 3-labeled cRNA (complementary RNA) was generated from Agilent’s Low RNA Input Linear Amplification kit with 500ng total RNA. Labeled cRNA was also measured using Nanodrop spectrophotometer.

growth_protocol: Cells were cultured in an atmosphere of 5% CO2 at 37 °C.

extract_protocol: Total RNA from cell was isolated using Trizol Reagent (Molecular Research Center, Cincinnati, OH, USA), according to the manufacturer’s instructions.

treatment_protocol: NUGC3 cells were treated with 20nM siSC or siVGLL1 for 48h.

value: gastric cancer cells

tag: sirna


title: Hippocampus Young Insulin Replicate 3

value: male


title: NUGC3_siSC_rep1

description:
GE1_1100_3
Gene expression of cells treated with siSC.

value: siSC


title: SAMPLE_452 normal colon

status: Public on Apr 19 2019

type: genomic

city: Seattle

first: Sean

last: Maden

state: WA

address: 1100 Fairview Ave N

department: Clinical Research

institute: Fred Hutch

description:
9426020059_R05C02
SAMPLE_452

hyb_protocol: Illumina Infinium HD Methylation protocol

scan_protocol: Imaged with iScan+ using Methylation NXT scan setting

data_processing:
GenomeStudio v2011.1 with Methylation Module v1.9.0; preprocessing using SWAN normalization and Illumina background correction method using in minfi v1.22.1
matrix_signal.csv reports unmethylated and methylated signal intensities.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Tissue core or slide

extract_protocol: DNA from formalin fixed paraffin-embedded (FFPE) cores or tissue sections

tag: tissue type

value: normal colon

tag: age

tag: gender

value: F

tag: anatomic location


title: SAMPLE_31314 normal colon

description:
101130760056_R01C01
SAMPLE_31314

label_protocol: Illumina Infinium HD Methylation protocol

value: M

value: rectum


title: SAMPLE_32238 normal colon

description:
200107460030_R06C01
SAMPLE_32238


title: SAMPLE_32214 normal colon

description:
200053730224_R04C02
SAMPLE_32214


title: SAMPLE_31719 normal colon

description:
101130760056_R02C02
SAMPLE_31719


title: SAMPLE_31713 normal colon

description:
101130760063_R06C02
SAMPLE_31713


title: SAMPLE_32232 normal colon

description:
200091640104_R04C02
SAMPLE_32232


title: SAMPLE_448 normal colon

description:
9426020071_R05C01
SAMPLE_448


title: SAMPLE_32070 normal colon

description:
200107460034_R02C02
SAMPLE_32070


title: SAMPLE_32109 normal colon

description:
200107460034_R04C02
SAMPLE_32109


title: SAMPLE_32169 normal colon

description:
200053730224_R01C02
SAMPLE_32169


title: SAMPLE_32028 normal colon

description:
101130760056_R03C01
SAMPLE_32028


title: SAMPLE_31368 normal colon

description:
101130760063_R05C02
SAMPLE_31368


title: SAMPLE_31647 normal colon

description:
200107460013_R06C02
SAMPLE_31647


title: SAMPLE_31377 normal colon

description:
200107460013_R04C02
SAMPLE_31377


title: SAMPLE_31602 normal colon

description:
101070190142_R05C01
SAMPLE_31602


title: SAMPLE_31554 normal colon

description:
200107460013_R03C01
SAMPLE_31554


title: SAMPLE_31749 normal colon

description:
200053730224_R04C01
SAMPLE_31749


title: SAMPLE_32268 normal colon

description:
101130760015_R06C01
SAMPLE_32268


title: SAMPLE_31728 normal colon

description:
200091640116_R04C02
SAMPLE_31728


title: SAMPLE_31998 normal colon

description:
200107460049_R04C01
SAMPLE_31998


title: SAMPLE_31857 normal colon

description:
200091640104_R06C01
SAMPLE_31857


title: SAMPLE_32280 normal colon

description:
101130760034_R02C01
SAMPLE_32280


title: SAMPLE_31401 normal colon

description:
101130760034_R05C01
SAMPLE_31401


title: SAMPLE_31740 normal colon

description:
200107460010_R05C01
SAMPLE_31740


title: SAMPLE_31581 normal colon

description:
101070190142_R02C01
SAMPLE_31581


title: SAMPLE_32079 normal colon

description:
101070190142_R01C02
SAMPLE_32079


title: SAMPLE_31266 normal colon

description:
101130760043_R05C02
SAMPLE_31266


title: SAMPLE_31644 normal colon

description:
200091640104_R03C02
SAMPLE_31644


title: SAMPLE_32217 normal colon

description:
200107460049_R02C01
SAMPLE_32217


title: SAMPLE_31668 normal colon

description:
200091640116_R01C02
SAMPLE_31668


title: SAMPLE_31437 normal colon

description:
200091640116_R03C01
SAMPLE_31437


title: SAMPLE_32274 normal colon

description:
101130760027_R03C02
SAMPLE_32274


title: SAMPLE_31869 normal colon

description:
200053730224_R06C01
SAMPLE_31869


title: SAMPLE_31302 normal colon

description:
101130760063_R03C01
SAMPLE_31302


title: SAMPLE_31521 normal colon

description:
200053730163_R03C02
SAMPLE_31521


title: SAMPLE_31854 normal colon

description:
101070190143_R03C02
SAMPLE_31854


title: SAMPLE_31221 normal colon

description:
101130760027_R04C02
SAMPLE_31221


title: SAMPLE_32196 normal colon

description:
101130760063_R03C02
SAMPLE_32196


title: SAMPLE_31866 normal colon

description:
101130760027_R02C02
SAMPLE_31866


title: SAMPLE_31827 normal colon

description:
101070190143_R04C01
SAMPLE_31827


title: SAMPLE_31821 normal colon

description:
101130760015_R04C01
SAMPLE_31821


title: SAMPLE_32100 normal colon

description:
101130760063_R06C01
SAMPLE_32100


title: SAMPLE_31275 normal colon

description:
200091640104_R01C01
SAMPLE_31275


title: SAMPLE_32010 normal colon

description:
200107460010_R05C02
SAMPLE_32010


title: SAMPLE_31383 normal colon

description:
200107460030_R03C01
SAMPLE_31383


title: SAMPLE_32193 normal colon

description:
101130760063_R04C01
SAMPLE_32193


title: SAMPLE_31704 normal colon

description:
200107460030_R04C02
SAMPLE_31704


title: SAMPLE_31614 normal colon

description:
101130760063_R05C01
SAMPLE_31614


title: SAMPLE_31131 normal colon

description:
200053730224_R05C01
SAMPLE_31131


title: SAMPLE_31386 normal colon

description:
101070190142_R06C02
SAMPLE_31386


title: SAMPLE_31860 normal colon

description:
200091640118_R03C01
SAMPLE_31860


title: SAMPLE_31404 normal colon

description:
101070190142_R04C01
SAMPLE_31404


title: SAMPLE_31689 normal colon

description:
101130760056_R01C02
SAMPLE_31689


title: SAMPLE_32103 normal colon

description:
200091640116_R06C01
SAMPLE_32103


title: SAMPLE_31143 normal colon

description:
101130760043_R03C01
SAMPLE_31143


title: SAMPLE_31716 normal colon

description:
101130760015_R04C02
SAMPLE_31716


title: SAMPLE_32067 normal colon

description:
200053730224_R02C02
SAMPLE_32067


title: SAMPLE_31413 normal colon

description:
200091640118_R05C02
SAMPLE_31413


title: SAMPLE_32178 normal colon

description:
200107460013_R03C02
SAMPLE_32178


title: SAMPLE_31536 normal colon

description:
200107460030_R01C02
SAMPLE_31536


title: SAMPLE_32115 normal colon

description:
101130760063_R04C02
SAMPLE_32115


title: SAMPLE_31686 normal colon

description:
200091640104_R04C01
SAMPLE_31686


title: SAMPLE_31122 normal colon

description:
200107460013_R04C01
SAMPLE_31122


title: SAMPLE_31296 normal colon

description:
101130760027_R01C01
SAMPLE_31296


title: SAMPLE_32250 normal colon

description:
101130760043_R04C01
SAMPLE_32250


title: SAMPLE_31623 normal colon

description:
200091640116_R05C02
SAMPLE_31623


title: SAMPLE_31248 normal colon

description:
101130760027_R04C01
SAMPLE_31248


title: SAMPLE_32064 normal colon

description:
200107460010_R06C01
SAMPLE_32064


title: SAMPLE_31803 normal colon

description:
101130760056_R02C01
SAMPLE_31803


title: SAMPLE_32142 normal colon

description:
200107460013_R02C02
SAMPLE_32142


title: SAMPLE_31572 normal colon

description:
200053730163_R02C01
SAMPLE_31572


title: SAMPLE_31281 normal colon

description:
200053730163_R06C01
SAMPLE_31281


title: SAMPLE_31584 normal colon

description:
200107460013_R01C02
SAMPLE_31584


title: SAMPLE_31620 normal colon

description:
200107460030_R04C01
SAMPLE_31620


title: SAMPLE_31662 normal colon

description:
101130760027_R05C01
SAMPLE_31662


title: SAMPLE_32190 normal colon

description:
200107460049_R01C01
SAMPLE_32190


title: SAMPLE_32166 normal colon

description:
101130760027_R06C01
SAMPLE_32166


title: SAMPLE_31206 normal colon

description:
101130760027_R03C01
SAMPLE_31206


title: SAMPLE_31419 normal colon

description:
200107460010_R04C01
SAMPLE_31419


title: SAMPLE_31785 normal colon

description:
200107460010_R02C02
SAMPLE_31785


title: SAMPLE_31830 normal colon

description:
200091640116_R03C02
SAMPLE_31830


title: SAMPLE_31587 normal colon

description:
200107460034_R05C01
SAMPLE_31587


title: SAMPLE_31485 normal colon

description:
200107460013_R05C02
SAMPLE_31485


title: SAMPLE_31776 normal colon

description:
200107460013_R06C01
SAMPLE_31776


title: SAMPLE_31635 normal colon

description:
101130760027_R02C01
SAMPLE_31635


title: SAMPLE_31881 normal colon

description:
101130760043_R02C02
SAMPLE_31881


title: SAMPLE_31725 normal colon

description:
101130760063_R02C01
SAMPLE_31725


title: SAMPLE_31215 normal colon

description:
101130760015_R03C01
SAMPLE_31215


title: SAMPLE_31674 normal colon

description:
101130760063_R01C02
SAMPLE_31674


title: SAMPLE_31839 normal colon

description:
101130760027_R01C02
SAMPLE_31839


title: SAMPLE_32151 normal colon

description:
200107460010_R02C01
SAMPLE_32151


title: SAMPLE_31245 normal colon

description:
200091640116_R02C02
SAMPLE_31245


title: SAMPLE_32058 normal colon

description:
200107460030_R05C02
SAMPLE_32058


title: SAMPLE_31359 normal colon

description:
200107460030_R05C01
SAMPLE_31359


title: SAMPLE_31362 normal colon

description:
200053730163_R01C01
SAMPLE_31362


title: SAMPLE_32127 normal colon

description:
101070190142_R03C02
SAMPLE_32127


title: SAMPLE_32175 normal colon

description:
101130760034_R03C02
SAMPLE_32175


title: SAMPLE_32001 normal colon

description:
200107460030_R02C02
SAMPLE_32001


title: SAMPLE_31158 normal colon

description:
200107460013_R02C01
SAMPLE_31158


title: SAMPLE_31473 normal colon

description:
101130760034_R04C02
SAMPLE_31473


title: SAMPLE_31254 normal colon

description:
101070190143_R03C01
SAMPLE_31254


title: SAMPLE_31197 normal colon

description:
200107460034_R05C02
SAMPLE_31197


title: SAMPLE_31119 normal colon

description:
200091640104_R03C01
SAMPLE_31119


title: SAMPLE_32076 normal colon

description:
200091640116_R02C01
SAMPLE_32076


title: SAMPLE_31335 normal colon

description:
200053730163_R05C02
SAMPLE_31335


title: SAMPLE_31149 normal colon

description:
200107460010_R03C01
SAMPLE_31149


title: SAMPLE_32253 normal colon

description:
101130760015_R01C02
SAMPLE_32253


title: SAMPLE_31449 normal colon

description:
101130760056_R05C02
SAMPLE_31449


title: SAMPLE_32223 normal colon

description:
101130760034_R02C02
SAMPLE_32223


title: SAMPLE_31695 normal colon

description:
200053730224_R01C01
SAMPLE_31695


title: SAMPLE_31269 normal colon

description:
101130760063_R02C02
SAMPLE_31269


title: SAMPLE_31752 normal colon

description:
200091640116_R06C02
SAMPLE_31752


title: SAMPLE_32040 normal colon

description:
200091640104_R05C01
SAMPLE_32040


title: SAMPLE_31191 normal colon

description:
200107460030_R02C01
SAMPLE_31191


title: SAMPLE_31287 normal colon

description:
101130760015_R05C01
SAMPLE_31287


title: SAMPLE_31332 normal colon

description:
200053730163_R05C01
SAMPLE_31332


title: SAMPLE_32124 normal colon

description:
200107460034_R01C02
SAMPLE_32124


title: SAMPLE_32091 normal colon

description:
101070190143_R05C01
SAMPLE_32091


title: SAMPLE_31779 normal colon

description:
101070190142_R03C01
SAMPLE_31779


title: SAMPLE_32091_2 normal colon

description:
101130760056_R05C01
SAMPLE_32091_2


title: SAMPLE_31284 normal colon

description:
101130760015_R05C02
SAMPLE_31284


title: SAMPLE_31659 normal colon

description:
101130760015_R02C02
SAMPLE_31659


title: SAMPLE_31227 normal colon

description:
101130760034_R01C02
SAMPLE_31227


title: SAMPLE_31680 normal colon

description:
101130760034_R03C01
SAMPLE_31680


title: SAMPLE_31479 normal colon

description:
101070190143_R01C01
SAMPLE_31479


title: SAMPLE_31557 normal colon

description:
101130760043_R02C01
SAMPLE_31557


title: SAMPLE_31272 normal colon

description:
200053730224_R06C02
SAMPLE_31272


title: SAMPLE_31212 normal colon

description:
101130760043_R03C02
SAMPLE_31212


title: SAMPLE_31164 normal colon

description:
200107460034_R06C02
SAMPLE_31164


title: SAMPLE_32205 normal colon

description:
101130760034_R06C02
SAMPLE_32205


title: SAMPLE_31200 normal colon

description:
101130760034_R01C01
SAMPLE_31200


title: SAMPLE_31323 normal colon

description:
101070190143_R01C02
SAMPLE_31323


title: SAMPLE_32145 normal colon

description:
200053730163_R01C02
SAMPLE_32145


title: SAMPLE_31338 normal colon

description:
200053730163_R04C02
SAMPLE_31338


title: SAMPLE_31707 normal colon

description:
200091640104_R05C02
SAMPLE_31707


title: SAMPLE_31389 normal colon

description:
200107460030_R06C02
SAMPLE_31389


title: SAMPLE_32088 normal colon

description:
101130760056_R06C02
SAMPLE_32088


title: SAMPLE_31161 normal colon

description:
101130760056_R04C02
SAMPLE_31161


title: SAMPLE_32157 normal colon

description:
200107460049_R03C01
SAMPLE_32157


title: SAMPLE_31407 normal colon

description:
101070190143_R05C02
SAMPLE_31407


title: SAMPLE_32106 normal colon

description:
200091640118_R04C02
SAMPLE_32106


title: SAMPLE_31467 normal colon

description:
200091640116_R01C01
SAMPLE_31467


title: SAMPLE_31236 normal colon

description:
200107460034_R03C02
SAMPLE_31236


title: SAMPLE_32136 normal colon

description:
101130760015_R02C01
SAMPLE_32136


title: SAMPLE_31548 normal colon

description:
200107460010_R04C02
SAMPLE_31548


title: SAMPLE_287 normal colon

description:
9426020072_R01C02
SAMPLE_287


title: SAMPLE_31224 normal colon

description:
101130760043_R04C02
SAMPLE_31224


title: SAMPLE_232 normal colon

description:
9426020059_R01C01
SAMPLE_232


title: SAMPLE_32034 normal colon

description:
101130760015_R03C02
SAMPLE_32034


title: SAMPLE_231 normal colon

description:
9426020060_R01C01
SAMPLE_231


title: SAMPLE_239 normal colon

description:
9426020070_R02C02
SAMPLE_239


title: SAMPLE_243 normal colon

description:
9426020072_R05C01
SAMPLE_243


title: SAMPLE_244 normal colon

description:
9426020072_R06C01
SAMPLE_244


title: SAMPLE_31416 normal colon

description:
200107460010_R01C01
SAMPLE_31416


title: SAMPLE_31593 normal colon

description:
101130760056_R04C01
SAMPLE_31593


title: SAMPLE_233 normal colon

description:
9426020059_R04C02
SAMPLE_233


title: SAMPLE_371 normal colon

description:
9426020071_R02C02
SAMPLE_371


title: SAMPLE_236 normal colon

description:
9426020059_R04C01
SAMPLE_236


title: SAMPLE_246 normal colon

description:
9426020072_R04C02
SAMPLE_246


title: SAMPLE_234 normal colon

description:
9426020070_R05C02
SAMPLE_234


title: SAMPLE_31761 normal colon

description:
101130760015_R01C01
SAMPLE_31761


title: sc6-LV

first: Zhou

last: Zhou

address: Beilishi Street 167, Xi Cheng District

institute: Fuwai Hospital, the Chinese Academy of Medical Sciences

data_processing:
The raw sequencing reads were subjected to adapter trimming and base quality filtering by fastp v0.7.0
Clean reads obtained were aligned to the human reference genome (GRCh37) using hisat2 v2.1.0 under default settings
Transcript de novo assembly for each sample was performed using StringTie v1.3.4b
The expression of the transcripts was quantified with kallisto v0.43.1 under default settings
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: Myocardial tissue

extract_protocol:
Total RNA was isolated with TRIzolTM reagent (Invitrogen, USA) according to the manufacturer’s instruction. RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Fluorometer (Life Technologies, CA, USA)
Strand-specific RNA-seq libraries were generated using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s instructions.

tag: group

value: Healthy

tag: Sex


title: SAMPLE_514 normal colon

description:
9426020070_R06C01
SAMPLE_514


title: SAMPLE_322 normal colon

description:
9426020126_R02C02
SAMPLE_322


title: SAMPLE_443 normal colon

description:
9426020060_R01C02
SAMPLE_443


title: SAMPLE_556 normal colon

description:
9426021037_R03C01
SAMPLE_556


title: SAMPLE_521 normal colon

description:
9426020060_R05C01
SAMPLE_521


title: sc5-LV

value: female


title: ND2


title: sc2-LV


title: SAMPLE_527 normal colon

description:
9426020070_R02C01
SAMPLE_527


title: SAMPLE_502 normal colon

description:
9426021037_R01C01
SAMPLE_502


title: N105-LV


title: ND1-LV


title: SAMPLE_516 normal colon

description:
9426020060_R03C02
SAMPLE_516


title: SAMPLE_490 normal colon

description:
9426020060_R04C02
SAMPLE_490


title: N104-LV


title: SAMPLE_548 normal colon

description:
9426020126_R04C02
SAMPLE_548


title: SAMPLE_546 normal colon

description:
9426020071_R03C02
SAMPLE_546


title: N103-LV


title: SAMPLE_518 normal colon

description:
9426020070_R05C01
SAMPLE_518


title: SAMPLE_474 normal colon

description:
9426020072_R06C02
SAMPLE_474


title: N102-LV


title: HCM591

value: hypertrophic cardiomyopathy


title: SAMPLE_537 normal colon

description:
9426020070_R01C01
SAMPLE_537


title: HCM562


title: HCM552


title: HCM533


title: SAMPLE_499 normal colon

description:
9426020070_R01C02
SAMPLE_499


title: HCM518


title: HCM541


title: SAMPLE_473 normal colon

description:
9426020126_R02C01
SAMPLE_473


title: SAMPLE_31173 normal colon

description:
200091640118_R06C02
SAMPLE_31173


title: SAMPLE_540 normal colon

description:
9426020126_R03C02
SAMPLE_540


title: HCM515


title: HCM506


title: HCM504


title: HCM498


title: SAMPLE_482 normal colon

description:
9426021037_R02C02
SAMPLE_482


title: SAMPLE_520 normal colon

description:
9426020059_R02C02
SAMPLE_520


title: HCM491


title: SAMPLE_459 normal colon

description:
9426020072_R05C02
SAMPLE_459


title: HCM490


title: SAMPLE_484 normal colon

description:
9426021037_R01C02
SAMPLE_484


title: SAMPLE_557 normal colon

description:
9426020059_R06C02
SAMPLE_557


title: HCM486


title: HCM493


title: SAMPLE_478 normal colon

description:
9426020126_R05C01
SAMPLE_478


title: SAMPLE_507 normal colon

description:
9426020126_R05C02
SAMPLE_507


title: SAMPLE_497 normal colon

description:
9426020060_R05C02
SAMPLE_497


title: SAMPLE_558 normal colon

description:
9426020126_R03C01
SAMPLE_558


title: HCM483


title: HCM460


title: SAMPLE_536 normal colon

description:
9426020070_R03C02
SAMPLE_536


title: SAMPLE_554 normal colon

description:
9426020060_R06C01
SAMPLE_554


title: HCM456


title: HCM443


title: SAMPLE_492 normal colon

description:
9426020071_R04C01
SAMPLE_492


title: HCM439


title: SAMPLE_509 normal colon

description:
9426021037_R04C01
SAMPLE_509


title: HCM437


title: SAMPLE_538 normal colon

description:
9426020072_R01C01
SAMPLE_538


title: HCM429


title: SAMPLE_531 normal colon

description:
9426020059_R05C01
SAMPLE_531


title: HCM431


title: SAMPLE_512 normal colon

description:
9426020072_R02C02
SAMPLE_512


title: SAMPLE_517 normal colon

description:
9426020059_R03C01
SAMPLE_517


title: HCM405


title: SAMPLE_481 normal colon

description:
9426020071_R06C02
SAMPLE_481


title: SAMPLE_495 normal colon

description:
9426020070_R04C01
SAMPLE_495


title: HCM395


title: HCM420


title: SAMPLE_470 normal colon

description:
9426020071_R04C02
SAMPLE_470


title: SAMPLE_479 normal colon

description:
9426020071_R03C01
SAMPLE_479


title: SAMPLE_477 normal colon

description:
9426020059_R01C02
SAMPLE_477


title: HCM282


title: SAMPLE_486 normal colon

description:
9426020126_R01C01
SAMPLE_486


title: HCM273


title: SAMPLE_534 normal colon

description:
9426021037_R04C02
SAMPLE_534


title: SAMPLE_461 normal colon

description:
9426020059_R03C02
SAMPLE_461


title: HCM269


title: SAMPLE_454 normal colon

description:
9426020060_R02C02
SAMPLE_454


title: OLEOp:GmPSKγ1tc

city: Shanghai

first: Liangliang

address: 381 Nanchen Road, Baoshan District

institute: Shanghai University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Ensemblg plants
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Seed

extract_protocol:
Total RNA from Arabidopsis seeds at 10 DAP was extracted using an RNAprep pure plant kit (Tiangen, Beijing, China) according to the manufacturer's instructions, followed by clean-up and DNase I treatment with RNeasy mini kit (QIAGEN, GmBH, Germany) in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: 10 DAP

tag: genotype/variation

value: Developing seed


title: Mo THP-1_WGBS

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute

description:
HCF2FALXX_3_JW_27_Other_AGTTCC_R_170307_SHANAI_WGBSLIB_M003
processed data: THP1_monocyte_macrophage.tsv

library_source: genomic

data_processing:
For RNA-seq data: The original raw data from Illumina CASAVA v1.8 software are transformed to Sequenced Reads by base calling.
Raw reads are filtered to remove reads containing adapters or reads of low quality reads, then were mapped to Ensembl human reference genome (GRCh38.v86) using STAR_2.5.2a.
Quantification of intron retention (IR) and Differential IR analysis were run by IRFinder (v1.2.3) and its built-in script via Audic and Claverie test respectively.
Gene-leve expression was measured using featureCounts (1.5.0-p3).Differential expression was assessed with Deseq2 (1.22.2)
For WGBS data: Bisulphite reads were processed and aligned to the human genome reference using Meth10X, https://github.com/luuloi/Meth10X (Nair et al., 2018).
Genome_build: GRCh38.v86 (Ensembl)
Supplementary_files_format_and_content: Tab delimited txt file including rlog normalized counts for ND_M0_M1 and differetial IR quantification. A count table and bigwig files of methylated and coverage at each CpG site in the genome.

source_name: THP-1 monocytic cells_Mo

growth_protocol: Human THP-1 monocytic cells were maintained in RPMI medium supplemented with 2 mM L-glutamine, 25 mM HEPES, 10% (v/v) FBS, 1 mM sodium pyruvate, 1% (v/v) non-essential amino acids, and 0.1 mg/mL penicillin/streptomycin at 37°C in the presence of 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol. Genomic DNA was extracted using standard phenol-chloroform method.
Poly-A-enriched mRNA libraries were prepared from 2 μg of TURBOTM DNase-treated, total RNA using the TruSeq® Stranded Library Preparation Kit (Illumina), according to the manufacturers’ instructions. mRNA sequencing was performed on each cell population in triplicates by Novogene (China). A total of 100 million paired-end strand-specific reads were sequenced per sample on an Illumina HiSeq 2500 Platform.Whole-genome bisulphite sequencing (WGBS) was performed on a HiSeq X Ten platform (Illumina) following library preparation using the TruMethyl WG method v.1.9 (Cambridge Epigenetix).

treatment_protocol: 1.5 × 10^7 cells per 75 cm2 culture flask of THP-1 cells were differentiated using phorbol-12-myristate 13-acetate (PMA) into macrophages. Resting macrophages are further polarised into pro-inflammatory macrophages using lipopolysaccharide (LPS) and interferon gamma (IFN-γ). To inhibit nuclear degradation by the RNA exosome, THP-1 macrophages were transfected with 300 nM EXOSC10 siRNA (sense: 5′ – GAAGGCAGCUGAGCAAACAdTdT – 3′, antisense: 5′ – UGUUUGCUCAGCUGCCUUCdTdT). ON-TARGETplus non-targeting siRNA (GE Dharmacon) was used as a negative control.

tag: cell line

value: Monocytic cell line


title: SAMPLE_453 normal colon

description:
9426021037_R06C01
SAMPLE_453


title: SAMPLE_515 normal colon

description:
9426020060_R06C02
SAMPLE_515


title: SAMPLE_455 normal colon

description:
9426020126_R01C02
SAMPLE_455


title: JH047_whole_brain_7d_hypoxia_R2

city: Baltimore

first: Jacob

middle: S

last: Heng

state: MD

address: 725 North Wolfe Street

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: Whole brain

data_processing:
scRNA-seq data were pre-processed using the Cell Ranger pipeline (v2.1.0; 10x Genomics) with default settings.  The normalized gene x cell matrix was used as input for the MonocleR/Bioconductor package (Trapnell et al., 2014).  Log-normalized expression estimates (with a pseudocount of 1) were used as input for a modified dpFeature analysis.  For preliminary cell clustering, PCA was performed on the high variance genes, and appropriate components were visualized in two dimensions using UMAP.  Initial clusters were identified from the 2-D embedding using k-means clustering.  Cell type identity was determined by cross-referencing clusters with expression of multiple known cell type markers.
RiboTag, whole retina, and whole brain RNA-seq data were pseudoaligned to the mouse genome (mm10) using the Kallisto software (Bray et al., 2016). Aligned counts were obtained for differential gene expression analysis using EBseq (Leng et al., 2013) and posterior probability ³0.95 that a gene/transcript is differentially expressed was considered statistically significant.
Genome_build: mm10

source_name: adult whole brain, 7-day hypoxia

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
Total RNA was extracted from homogenized whole brain using the TRIzol  reagent (ThermoFisher)  as per the manufacturer's protocol. Extracted RNA was further purified using the RNeasy Mini kit (74104, QIAGEN, Venlo, Netherlands) as per the manufacturer's protocol/
Libraries were constructed using the NuGEN single cell RNA-seq library preparation kit as per the manufacturer's protocol.

tag: genotype

value: WT

tag: strain

value: 2 month

value: Male

value: brain

tag: treatment

value: Mouse was exposed to 7 days of 7.5% oxygen in a normobaric chamber


title: SAMPLE_549 normal colon

description:
9426020071_R01C02
SAMPLE_549


title: Mϕ THP-1_WGBS

description:
HCF2FALXX_4_JW_28_Other_ATGTCA_R_170307_SHANAI_WGBSLIB_M003
processed data: THP1_monocyte_macrophage.tsv

source_name: THP-1 macrophage_Mϕ

tag: cell type


title: JH046_whole_brain_7d_hypoxia_R1

description: Whole brain


title: JH045_whole_brain_48h_hypoxia_R3

description: Whole brain

source_name: adult whole brain, 48-hour hypoxia

value: Mouse was exposed to 48 hours of 7.5% oxygen in a normobaric chamber


title: SAMPLE_526 normal colon

description:
9426020060_R04C01
SAMPLE_526


title: SAMPLE_506 normal colon

description:
9426021037_R02C01
SAMPLE_506


title: SAMPLE_491 normal colon

description:
9426021037_R03C02
SAMPLE_491


title: BSC120L: H3K27ac_B1_2

city: San Antonio

first: Rong

last: Li

state: TX

address: 7703 Floyd Curl Drive

department: Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

data_processing:
H3K27ac ChIP-seq was aligned to the human genome by BWA and only unique mapped reads were saved. BELT, a bin based peak calling algorism that applies a statistical method to control false discovery rate (FDR), was used to call peaks. Super-enhancers were identified using ROSE.
Genome_build: hg19
Supplementary_files_format_and_content: bed files with super enhancers

source_name: Normal breast tissue

extract_protocol:
Primary human breast epithelial cells were crosslinked with 1% formaldehyde at room temperature for 10 min, followed by incubation with 125 mM glycine for an additional 5 min. All following steps were carried out in buffers containing protease inhibitors in 4 °C until elution. Cells were pelleted by centrifugation at 1,000 g for 5 min, washed with PBS twice, then lysed in lysis buffer (5 mM HEPES, pH 7.9, 85 mM KCl, 0.5% Triton X-100) for 10 min. Nuclei were pelleted by centrifugation at 1,600 g for 5 min, and lysed in nuclei lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS). Chromosomal DNA was sonicated using a Bioruptor Pico to obtain < 300 bp fragments. 10% of sonicated DNA was saved as input, and the rest was incubated with H3K27ac antibody overnight (Abcam; ab4729). Dynabeads Protein A (Thermo Fisher Scientific; 10002D) was added the following day and incubated for additional 4 hr before washing. Washing was performed twice in TE sarcosyl buffer (50 mM Tris-HCl, pH 8.0, 2 mM EDTA, 0.2% sarcosyl), twice in TSE1 buffer (150 mM sodium chloride, 20 mM Tris-HCl pH 8.0, 2 mM EDTA, 0.1% SDS, 1% Triton-X-100), twice in TSE2 buffer (500 mM sodium chloride, 20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 0.1% SDS, 0.1% Triton X-100), twice in TSE3 buffer (250 mM lithium chloride, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1% sodium deoxycholate, 1% NP-40) and twice in TE buffer (50 mM Tris-HCl, pH 8.0, 2 mM EDTA). DNA was subsequently eluted from Dynabeads, reverse-crosslinked, and ethanol-precipitated.
H3K27ac ChIP-seq libraries were constructed using a MicroPlex Library Preparation Kit (Diagenode; C05010011) following the manufacturer’s guide. After a total of 10 cycles of PCR amplification, libraries were purified using Agencourt AMPure XP System (Beckman Coulter; A63880). Quality and quantity of the libraries were measured by a Qubit dsDNA HS Assay Kit (Life Technologies; Q32851) using a Bioanalyser 2100. Libraries with different index sequences were pooled together and then sequenced with a single-end 50 bp module using an Illumina Hiseq 3000 system. De-multiplexing was performed by CASAVA to generate FASTQ files for each sample. Between 38 and 92 million unique mapped reads were obtained for each sample.

value: Primary human mammary epithelial cells (HMECs)

value: BRCA1 mutation carrier


title: BSC113: H3K27ac_B1_3


title: SAMPLE_510 normal colon

description:
9426020071_R06C01
SAMPLE_510

value: normal colon

value: F


title: JH044_whole_brain_48h_hypoxia_R2

description: Whole brain


title: SAMPLE_539 normal colon

description:
9426020072_R04C01
SAMPLE_539

value: M


title: SAMPLE_469 normal colon

description:
9426020071_R01C01
SAMPLE_469


title: BSC121R: H3K27ac_NC_3

value: Non-carrier


title: BSC107L: H3K27ac_B1_1

value: female


title: SAMPLE_446 normal colon

description:
9426020126_R06C01
SAMPLE_446


title: SAMPLE_508 normal colon

description:
9426020070_R06C02
SAMPLE_508


title: JH043_whole_brain_48h_hypoxia_R1

description: Whole brain


title: JH042_whole_brain_normoxia_R3

description: Whole brain

source_name: adult whole brain, normoxia

value: Mouse was exposed to normoxic conditions


title: BSC122L: H3K27ac_NC_2


title: JH041_whole_brain_normoxia_R2

description: Whole brain


title: BSC112: H3K27ac_NC_1


title: AR84_retina_Ndp_R2

description: Multiple whole retinas

source_name: adult NdpKO whole retina

extract_protocol:
6-8 retinas were homogenized in a Dounce homogenizer in 500 μL polysome buffer [50 mM Tris, pH 7.5, 250 mM sucrose, 100 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1 mM DTT, 200 U/mL RNasin Plus (Promega), 1 mg/mL heparin, 100 g/mL cycloheximide, 0.5 mM spermidine (Sigma),  complete EDTA-free protease inhibitor cocktail (Roche)].  Homogenates were centrifuged at 10,000xg for 10 min to create a postmitochondrial supernatant.  Five μL mouse monoclonal anti-HA antibody (HA.11, ascites fluid; Covance) were added to the supernatants (400 μL) and rotated for 4 hours at 4 °C. 100 μL protein G magnetic beads (Dynabeads; Invitrogen) were washed twice with polysome buffer and added directly to the antibody-coupled polysomes and rotated overnight at 4 °C.  The following day, samples were placed in a magnet on ice and the beads were washed 4x5 minutes in high salt buffer (50 mM Tris, pH 7.5, 300 mM KCl, 12 mM MgCl 2, 1% Nonidet P-40, 1 mM DTT, 20 μg/mL cycloheximide).  To prepare total RNA, 350 μL of Qiagen RLT buffer were added to the beads or to 50 μl of the input samples. Total RNA was prepared according to manufacturer’s instructions using RNeasy Plus Micro kit (Qiagen) and the quantity and quality of the RNA were assessed using Bioanalyzer (Agilent).
Libraries were constructed using the NuGEN single cell RNA-seq library preparation kit as per the manufacturer's protocol.

value: Mixed

value: retina


title: SAMPLE_547 normal colon

description:
9426020072_R03C01
SAMPLE_547


title: ALSCs rep2

city: Hohhot

first: Chen

last: Yanglin

address: Xilin road

institute: Inner Mongolia University

data_processing:
Illumina Casava1.8 software used for basecalling.
Fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ..

source_name: AF stem cells

extract_protocol:
Blastocysts from Sv129 mice × GOF/GFP mice were cultured in KSOM for 2 days. 24-well plates were coated by fibronectin at least 0.5 hour before use. The embryos were placed in Tyrode’s solution to remove the zona pellucida. Embryos without zona pellucida were moved into AF derivation medium. AF Derivation medium included Act A, bFGF and basic medium，basic medium including DMEM/F12, 2 mM L-glutamine, 1×MEM nonessential amino acids, 0.1 mM β-mercaptoethanol, supplemented with N2 and B27. Formed outgrowth was cut by glass needle into small pieces before moved in fresh AF medium. Then, these structures could be passaged by Accutase every 2 or 3 days. These cells were called AFSCs. AFSCs were passaged into AL culture medium or AB culture medium over 5 times to convert to ALSCs or ABSCs. AFSCs in AL culture medium over passage 5 were called ALSCs; AFSCs in AB culture medium over passage 5 were called ABSCs. AB culture medium was Act A and leukemia inhibitory factor (LIF) in basic medium. ABSCs culture medium was Act A and BMP4 in basic medium. All collected cells were treated with RNeasy Mini Kit to obtain mRNA. Purified mRNA was used as templates for cDNA synthesis after fragmentation. The cDNA libraries were sequenced using Illumina HiSeq 2000.
RNeasy Micro Kit (Qiagen)was used to isolate total RNA of ALSCs. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H - ). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Sv129 x GOF/GFP F1

value: AFSCs-derived stem cell

tag: passage


title: ALSCs rep3


title: JH048_whole_brain_7d_hypoxia_R3

description: Whole brain

value: WT

value: 2 month


title: JH040_whole_brain_normoxia_R1

description: Whole brain

value: Male

value: brain


title: AR83_retina_Ndp_R1

description: Multiple whole retinas


title: SAMPLE_553 normal colon

description:
9426020059_R02C01
SAMPLE_553


title: AR60_MC_Ndp_R2

description: Affinity captured polyribosomes from multiple retinas

source_name: adult NdpKO Muller glia Ribotag pulldown

value: NdpKO


title: AR58_MC_Ndp_R1


title: ABSCs rep2

value: AFSCs-derived TSCs like cell


title: SAMPLE_445 normal colon

description:
9426020072_R02C01
SAMPLE_445


title: ABSCs rep1


title: SAMPLE_468 normal colon

description:
9426020060_R03C01
SAMPLE_468


title: ABSCs rep3


title: AR49_retina_WT_R1

description: Multiple whole retinas

source_name: adult WT whole retina


title: AFSCs rep3

source_name: Blastocyst

value: Blastocyst-derived EpiSCs like cell


title: SAMPLE_449 normal colon

description:
9426020059_R06C01
SAMPLE_449

value: normal colon


title: SAMPLE_447 normal colon

description:
9426020126_R06C02
SAMPLE_447

value: F


title: SAMPLE_494 normal colon

description:
9426020070_R03C01
SAMPLE_494


title: AR53_retina_WT_R2

description: Multiple whole retinas


title: SAMPLE_465 normal colon

description:
9426020071_R05C02
SAMPLE_465


title: AFSCs rep2


title: IL17RAKO FRC rep 2

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

institute: University of Pittsburgh

data_processing:
Analysis was performed on Illumina NextSeq500
Sequenced Reads were trimmed for adapter sequence using Trimmomatic with default parameters
Reads were mapped to mm9 genome version using TopHat2.1.1 and gene expression values (FPKM) were calculated using Cufflinks2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-deliminated text file includes FPKM values for each gene (rows) for all samples (columns)

source_name: Skin draining lymph node

extract_protocol:
Skin draining lymph nodes were removed, digested in presense of liberase and DNase1, and stained with fluorescently labeled CD45, CD31 and gp38 antibodies. Then the Live CD45-CD31-Gp38+ FRC were sorted with help of fluorescence assisted cell sorter directly into lysis buffer.
Libraries were prepared using SMARTer cDNA prep and NexteraXT library prep kits.

value: Skin draining lymph node

value: Fibroblastic reticular cells

value: Day 12 post immunization


title: AR39_MC_WT_R2

source_name: adult WT Muller glia Ribotag pulldown


title: 2_Index-9.PRY-1_mu38_L1_T_RNA_2

city: boston

first: Ayush

middle: Vasant

last: Ranawade

state: MA

address: 360 Huntington Ave

department: Bioengineering

institute: Northeastern University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.  The sequence reads that passed quality filters were analyzed using ce6 with Burrows–Wheeler Aligner (BWA) with default parameters followed by eXpress to estimate transcript abundances. Differentially-expressed genes were called at a false discovery rate (FDR) of 0.05% using the DESeq package in R.
Genome_build: C elegans mirbase cel.gff3
Supplementary_files_format_and_content: counts

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Standard NGM growth media condition at 20 degrees

extract_protocol:
Synchronized L1 stage animals were obtained by bleach treatment and RNA was isolated using the Trizol RNA extraction method
On size selection for small RNA,  libraries were prepared for sequencing using standard Illumina  TruSeq RNA Sample Preparation v2 high-throughput (HT) protocol.
RNA-Seq 50 bp cDNA library

treatment_protocol: Twice bleached synchronized

tag: developmental stage


title: SAMPLE_285 normal colon

description:
9426020060_R02C01
SAMPLE_285

source_name: Tissue core or slide

value: M

value: cecum


title: 2_Index-3.PRY-1_mu38_L1_T_RNA_1


title: ALSCs rep1


title: SAMPLE_458 normal colon

description:
9426020070_R04C02
SAMPLE_458


title: IL17RAKO FRC rep 1

tag: tissue


title: AFSCs rep1


title: 2_Index-6.N2_L1_T_RNA_2

value: N2 wildtype


title: SAMPLE_456 normal colon

description:
9426020071_R02C01
SAMPLE_456


title: WT FRC rep 2


title: SAMPLE_296 normal colon

description:
9426020072_R03C02
SAMPLE_296


title: 1533 pBIC Lymphoma

city: Pamplona

first: SERGIO

last: ROA

address: Irunlarrea, 1

department: Biochemistry and Genetics

country: Spain

institute: University of Navarra

description: Deep-sequencing from leader to constant IgH regions including VDJ sequences

data_processing:
Library strategy: IgH VDJC-seq
Preprocessing,  including assembly of raw paired-end reads and error-correction, was performed using the SHMPrep program (http://www.ams.sunysb.edu/~maccarth/software.html)
Supplementary_files_format_and_content: FASTA format with aligned paired-end error-corrected sequences and headers indicating unique sequence ID, primer usage (VPRIMER, CPRIMER), barcode usage, DUPCOUNT (number of the same aligned sequences, except for the barcode and primer regions that have the same CONSCOUNT) and CONSCOUNT (number of aligned sequences that share the same barcodes).

source_name: Lymphoma B cells from spleen

extract_protocol:
Murine spleens were submitted to cellular disggregation, followed by lysis of erythrocytes using ACK buffer. Then, single-cell preparations were stained for B220, CD38 and Fas and submitted to fresh cellular sorting in a FACSAria Ilu sorter (BD) after exclusion of dead cells with 7AAD. Intracellular YFP or GFP expression results from CRE-mediated recombination of corresponding reporter alleles at the ROSA26 locus of YC or BIC/pBIC mice, respectively. Total RNA was extracted from sorted cells using TRIzol (Invitrogen) as described in manufacturer´s protocol and quality control of extracted RNA was measured using Agilent Bioanalyzer.
As described in Vergani et al. Front Immunol 8, 1157 (2017), with specific murine primers indicated in Supplemental Information of the publication associated with this dataset.

tag: immunophenotype

tag: isolation

value: FACS-sorted cells


title: OLEOp:GmPSKγ1

source_name: Seed

value: 10 DAP

value: Developing seed


title: 2_Index-2.N2_L1_T_RNA_1


title: SAMPLE_316 normal colon

description:
9426020126_R04C01
SAMPLE_316

tag: tissue type


title: 2201 BIC Lymphoma

value: BIC, Blimp1F/FIKK2castopF/stopFCg1Cre/+


title: 1531 pBIC Lymphoma


title: 2254 BIC Lymphoma


title: 4129 YC GC cells

source_name: Germinal Center B cells from spleen

value: YC controls, YFPstopF/+Cg1Cre/+


title: 4128 YC GC cells


title: WT FRC rep 1

tag: age

value: WT


title: 4125 YC GC cells


title: 4129 YC naïve B cells

source_name: Naïve cells from spleen


title: Mϕ THP-1_EXOCS10_KD_RNA-seq [S_M0_EXOCX10_siRNA_F]

description:
S_M0_EXOCX10_siRNA_F
processed data file: EXOSC10_KD_Control.txt

molecule: polyA RNA

source_name: THP-1 macrophage_Mϕ EXOCS10 KD

value: THP-1-derived macrophage

value: EXOCS10 KD


title: SAMPLE_555 normal colon

description:
9426021037_R05C01
SAMPLE_555

tag: gender


title: 4128 YC naïve B cells


title: Mϕ THP-1_EXOCS10_KD_RNA-seq [S_M0_EXOCX10_siRNA_C]

description:
S_M0_EXOCX10_siRNA_C
processed data file: EXOSC10_KD_Control.txt


title: Mϕ THP-1_EXOCS10_KD_RNA-seq [S_M0_EXOCX10_siRNA_A]

description:
S_M0_EXOCX10_siRNA_A
processed data file: EXOSC10_KD_Control.txt


title: 4125 YC naïve B cells


title: 4126 YC GC cells


title: 4126 YC naïve B cells


title: OCI-Ly1 + s2 siRNA rep3

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: For analysis of microarray expression data, R and Bioconductor were used to perform preprocessing (quality control and extraction of intensity data from NimbleScan files) and log2 transformation of two-color array intensity signals, background correction, estimation of relative expression as log-Ratios, average between biological replicates, subtraction of averages from the negative (scramble siRNA) control and comparative t-tests.

source_name: OCI-Ly1 + FOXP1 #2 siRNA

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Human DLBCL OCI-Ly1 cells were grown in IMDM media containing 20% of human serum, 50microM Beta-mercaptoethanol and 2% penicillin/streptomycin.

extract_protocol: Total RNA was extracted from sorted cells using TRIzol (Invitrogen) as described in manufacturer´s protocol and quality control of extracted RNA was measured using Agilent Bioanalyzer.

treatment_protocol: Two different sequences targeting the 3’UTR region of hFOXP1 were used (siFOXP1#1: 5’-CAACTTAGCCAGCGCAATA-3’ and siFOXP1#2: 5’-GCCAAGGCCTTCTGACAATT-3’) to effectively knock-down FOXP1 expression in OCI-Ly10 compared to scramble siRNA. All siRNAs were transiently transfected into cells by nucleofection with Amaxa (Lonza) and harvested 48h later for RNA extraction and transcriptional analysis. Data collected from three replicates of each siRNA was averaged and normalized to the siRNA control group.

value: Diffuse large B-cell lymphoma (DLBCL) cell line

tag: sirna

source_name: Untransfected reference OCI-Ly1


title: OCI-Ly1 + s2 siRNA rep1


title: Small_KD_6-22

city: Nanjing

first: Suwen

last: Tian

address: 101Longmian Avenue

institute: Nanjing Medical University

description: small RNA

data_processing:
The quality of sequencing data was validated using KASAVA (version 1.8)
Raw reads were pre-processed using Fastx (fastx_toolkit-0.0.13.2) to achieve clean data by filtering rRNAs and trimming adaptors
Reads were mapped to miRBase (version 21.0) by CLC genomics workbench (version 5.5) without base mismatch
RNA expression values (TPM) were calculated by Cufflinks v2.1.1
Genome_build: miRBase (version 21.0)
Supplementary_files_format_and_content: tab-delimited text files include counts and TPM values

source_name: spermatogonial progenitor cells

extract_protocol:
RNA sample was extracted by the TruSeq Small RNA library prep kit (Illumina, USA) according to the manufacturer’s protocols
small RNA libraries was performed using Illumina Hiseq2500 according to the manufacturer’s instructions.

value: testis

value: spermatogonial progenitor cells

value: post natal day 6

value: Mov10 knockdown


title: Mϕ THP-1_EXOCS10_Con_RNA-seq [S_M0_EXOCX10_contC]

description:
S_M0_EXOCX10_contC
processed data file: EXOSC10_KD_Control.txt

source_name: THP-1 macrophage_Mϕ EXOCS10 control

value: EXOCS10 control


title: left tumor (LT) treated with CMP (A) at 1 wk, biological rep 4

city: New York

first: Nathan

last: Suek

state: NY

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Following fragmentation and labeling, 3.5ug of fragmented and labeled ss-cDNA was hybridized for 16hr at 45C on Clariom S Mouse HT array plates on the GeneTitan MultiChannel Instrument.

scan_protocol: After hybridization was completed the washing, staining and scanning of the arrays was completed on the GeneTitan MultiChannel Instrument.

data_processing: Data was analyzed using the rma() function in R package oligo

source_name: left tumor treated with CMP at 1 wk

label_protocol: Biotinylated sense-strand DNA targets are generated from 50ng of total RNA following standard protocol using the WT Plus Reagent kit (Applied Biosystems GeneChip WT Plus Reagent Kit Target Preparation Manual).

extract_protocol: not provided

treatment_protocol:
tumor implant protocol: Mice were implanted intradermally with 5x10^5 B16 tumor cells on Day 0.
Mice were injected intratumorally with MPL and CD40 and injected intraperitoneally with PD1 between Day 7-9. Other mice were injected intraperitoneally with PD1 alone. Treatment was given 2x/week and then sacrificed 1 week after start of trx.
organ harvest protocol: Mice were sacrificed and the distant tumors were dissected and mechanically dissociated into single cell suspensions.

tag: strain background

value: 8-10 weeks at time of organ harvest

value: tumor


title: OCI-Ly1 + s2 siRNA rep2


title: TAF_Dros_Inp

city: Mainz

first: Junaid

last: Akhtar

state: Rheinland-Pflaz

address: Johannes-Joachim-Becherweg, 32

department: Institute of Neurobiology and Developmental Biology

country: Germany

institute: University of Mainz

description:
IgG Control from 1000 Tum NSCs
Used as control while processing

data_processing:
De-multiplexing and fastq file conversion was performed using blc2fastq (v.1.8.4)
Mapping was performed using bowtie2 (v. 2.3.3) against ensembl release 84 of BDGP6 for Drosophila sample and K562 samples against hg38 (ensemble release 84).
The mapped bam files were normalized to RPKM using deepTools, and bigwig coverage file was generated
Genome_build: dm6 (Drosophila melanogaster), hg38 (K562 Cells)
Supplementary_files_format_and_content: UCSC compatible library size normalised bigwig tracks

organism: Drosophila melanogaster

source_name: Neural Stem Cells (Type II)

extract_protocol:
Conventional libraries: After precipitating and pelleting, DNA was dissolved in 30 μl of TE buffer pH 8.0. The recovered DNA was converted into libraries using NebNext Ultra II DNA library preparation kit, following manufacturer’s protocol.
TAF-ChIP: Fixed cells were directly sorted in 240 μl of 140mM RIPA (10mM Tris-Cl pH 8.0, 140mM NaCl, 0.1mM EDTA pH8.0, 1% Triton X-100, and 0.1% SDS), and sonicated with 3 cycles at low power settings for breaking the nuclei. 15 μl of Protein A and G Dynabeads were coupled to 1 μg of specific antibody in the blocking buffer (RIPA 140mM supplemented with 0.2 mg/ml BSA, 0.05 mg/ml of glycogen and 0.2 mg/ml of yeast t-RNA) for 3 hrs at 4°C. The unfragmented chromatin were centrifuged at 14000 rpm for 10 minutes at 4°C, and the supernatant was transferred to the tube with blocked and antibody coupled beads. The samples were incubated at 4°C overnight with head over tail rotations. The samples were then washed twice briefly with 300 μl of home made tagmentation buffer (20 mM Tris(hydroxymethyl)aminomethane pH 7.6; 10 mM MgCl2; 20% (vol/vol) dimethylformamide) using magnetic rack for beads separation. The washed beads were resupended in 20 μl of 1X tagmentation DNA buffer (Nextera XT Kit) containing 1 μl of Nextera DNA tagmentation enzyme and incubated at 37 °C for 40 minutes with constant shaking in a thermoblock at 500 rpm. Following the tagmentation, the beads were washed as following; once with 140mM RIPA (10mM Tris-Cl pH 8.0, 140mM NaCl, 0.1mM EDTA pH8.0, 1% Triton X-100, and 0.1% SDS), four times with 250mM RIPA (10mM Tris-Cl pH 8.0, 250mM NaCl, 0.1mM EDTA pH8.0, 1% Triton X-100, and 0.1% SDS) and twice with TE buffer pH8.0 (10mM Tris-Cl pH 8.0 and 0.1mM EDTA pH8.0). The samples after proteinase K treatment for reverse-crosslinking were subjected to phenol chloroform extraction. After precipitating and pelleting, DNA was dissolved in 30 μl of TE buffer pH 8.0. The DNA was amplified in a 100 μl reaction with 1X NEBNext High-Fidelity PCR Mix with primers containing molecular indices (listed in Table 1) with following program; 72 °C for 3min, {98 °C for 10 seconds, 63 °C for 30 seconds, 72 °C for 30 seconds} for 12 cycles, 72 °C for 5 minutes, and hold at 4 °C. The PCR reaction was purified with beads based size selection to remove any fragment that might be of larger than 1000 bp size. Ampure Xp beads were added to the PCR reaction in a ratio of 0.2X ratio to bind larger fragments. The magnetic beads were separated with the help of magnetic rack and supernatant was transferred to a fresh tube. Ampure Xp beads were added to the PCR reaction in a ration of 0.8X to bind the target library. After PCR purification, libraries were analyzed on Agilent Bioanalyzer for size distribution and the concentration was measured using Qubit fluorometer. The finished libraries were pooled in equimolar amounts and sequenced on illumina NextSeq 500.

value: Neural Stem Cells (Type II)

value: Larval brain

tag: ip target

value: IgG rabbit

tag: chip antibody


title: left tumor (LT) treated with CMP (A) at 1 wk, biological rep 2


title: OCI-Ly1 + s1 siRNA rep2

source_name: OCI-Ly1 + FOXP1 #1 siRNA

tag: cell line


title: left tumor (LT) treated with CMP (A) at 1 wk, biological rep 3

description:
E4-LT_1Wk
*Due to indexing anomaly, there is no E3 but rather skips to E4


title: EWAT Sample 3

first: Gregory

last: Putzel

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing with Illumina Casava 1.8.2
Adapter trimming using FLEXBAR (v2.4)
Alignment to mm10 reference genome using STAR version 2.3.0 with default settings
Reads per gene counted using Rsubread R package
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Entrez ID) in each sample

source_name: Sorted adipose stem and progenitor cells (ASPC)

extract_protocol:
Sorted cells were used to prepare RNAseq libraries using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).
Standard Illumina protocols


title: OCI-Ly1 + s1 siRNA rep3


title: OCI-Ly1 + s1 siRNA rep1


title: left tumor (LT) treated with PD1 (A) at 1 wk, biological rep 4

source_name: left tumor treated with PD1 at 1 wk


title: Mϕ THP-1_EXOCS10_Con_RNA-seq [S_M0_EXOCX10_contF]

description:
S_M0_EXOCX10_contF
processed data file: EXOSC10_KD_Control.txt

tag: genotype/variation


title: EWAT Sample 2

tag: strain


title: left tumor (LT) treated with CMP (A) at 1 wk, biological rep 1


title: stem_24hours_control_rep2

city: Ann Arbor

first: mehmet

last: tardu

state: MI

address: 930 N University Ave

department: Chemistry

institute: University of Michigan

data_processing:
Illumina data processing pipeline (v1.5) was used for base calling.
FastQC (v0.11.5) was used to evaluate the initial quality of the raw reads.
The following steps were performed to obtain high quality clean reads using Trimmomatic (v0.35) tool: 1) eliminate low quality reads (phred score <20) and 2) short reads with length <20 nucleotide
All downstream analyses were based on clean, high quality data. De novo assembly of the high quality reads was performed using Trinity, which is composed of three independent software modules: Inchworm, Chrysalis and Butterfly. By Inchworm, RNA-seq data was assembled into unique sequences through establishing a k-mer graph (K = 25). By Chrysalis, the contigs generated in the previous step were clustered, and a de Bruijn graph was constructed for each cluster. Subsequently, by Butterfly, these Bruijn graphs were processed in parallel and the paths were traced according to reads and pairs of reads within graphs to obtain full-length transcripts for alternative splicing isoforms and distinguish transcripts of paralogous genes. Finally, the distributed situation of length of result sequences was counted and analyzed using RSEM method. A Pearson’s correlation analysis was performed to obtain the transcript-level R2 between biological replicates.
For count-based differential expression testing between root and leaf tissues at different time-points, edgeR was used with the following arguments:  min_rowSum_counts of 10, false discovery rate (FDR) < 0.01 and the value of | log2 fold change| ≥ 1
Genome_build: De novo assembly
Supplementary_files_format_and_content: matrix text file (transcript count values of rsem output across samples). The stem samples were used only for de novo transcriptome assembly construction and are not included in the matrix file.

organism: Lens culinaris

source_name: stem, 24hours, control

growth_protocol: Seeds of lentil (Lens culinaris Medik. cv. Sultan) were kindly provided by the Southeastern Anatolia Agricultural Research Institute. The seeds were selected for size homogeneity, surface-sterilized for 2–3 min in 1% sodium hypochlorite, rinsed and soaked in distilled water.

extract_protocol:
Total RNA was isolated from 1 gr of root, stem and leaves of Lens culinaris using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions. BioAnalyzer (Agilent, USA) was used to measure the quality and the quantity of the isolated total RNAs. After that, total RNA samples were treated with RNase-free DNase I (Thermo Scientific, USA) at a concentration of 1 U/µg to eliminate the genomic DNA. Then, RNA-seq library preparation was performed using TruSeq Stranded RNA LT Kit (Illumina, USA) according to the manufacturer’s instructions.
mRNAs were purified from the 1 µg of total RNA using oligo (dT) magnetic beads and fragmented using fragmentation buffer. Afterthat, the cleaved short RNA fragments were used for first-strand cDNA synthesis using first strand synthesis mix, and the second strand was synthesized using second strand marking master mix. The double strand cDNAs were purified with AMPure XP beads (Beckman Coulter, USA) and eluted with resuspension buffer followed by 3’end adenine nucleotide addition. Finally, sequencing adaptors were ligated to the fragments and cDNA fragments were enriched by PCR amplification. Enriched cDNA libraries were used for cluster generation and sequencing. 100x2 paired-end sequencing of cDNA libraries for control and drought stress exposed samples (1st day and 4th day samples of root and leaf, and 1st day sample of stem) with two biological replicates were performed using the Illumina HiSeq4000 sequencing platform (Illumina, USA).

treatment_protocol: Seeds were surface-sterilized for 5 min in 1% sodium hypochlorite and rinsed with dH2O and then germinated on perlit medium with irrigated everyday by 50 ml Hoagland's nutrient solution (5 mM KNO3, 5 mMCa(NO3)2, 1 mM MgSO4, 5 mM KH2PO4, 0.1 mMFeEDTA, 46 mM H3BO3, 4.5 mM MnCl2, 3.8 mM ZnSO4, 0.3 mM CuSO4, 0.1 mM NH4MoO7). Seven days old seedlings were transferred to hydroponic medium. Control samples were kept in the Hoagland's nutrient solution for the entire hydroponic assay, the drought stress exposed samples were kept in the Hoagland's nutrient solution including 15% PEG 6000, for 5 days. All the experimental pods were aerated through the experiment by air pump and kept in a controlled climate chamber at a temperature of 25/18°C day/night; photoperiod was 16/8 h light/dark, with 10% humidity.

value: Medik. cv. Sultan

value: stem

tag: genotype

value: wild type


title: stem_24hours_control_rep1


title: left tumor (LT) treated with PD1 (A) at 1 wk, biological rep 2


title: left tumor (LT) treated with PD1 (A) at 1 wk, biological rep 1


title: Small_Ctrl_6-22

description: small RNA

tag: cell type

value: Mov10 Vector


title: OCI-Ly1 + sc siRNA rep3

source_name: OCI-Ly1 + scramble siRNA

value: Scramble Control


title: leaf_96hours_control_rep2

source_name: leaf, 96hours, control

value: leaf


title: left tumor (LT) treated with isotype control (A) at 1 wk, biological rep 4

source_name: left tumor treated with isotype at 1 wk


title: Mϕ THP-1_EXOCS10_Con_RNA-seq [S_M0_EXOCX10_contA]

description:
S_M0_EXOCX10_contA
processed data file: EXOSC10_KD_Control.txt

value: THP-1-derived macrophage


title: OCI-Ly1 + sc siRNA rep2

value: Diffuse large B-cell lymphoma (DLBCL) cell line


title: OCI-Ly1 + sc siRNA rep1


title: leaf_96hours_drought_rep2

source_name: leaf, 96hours, drought


title: leaf_96hours_control_rep1


title: left tumor (LT) treated with PD1 (A) at 1 wk, biological rep 3


title: JH17_Cerebral_cortex_hypoxia_scRNAseq

description: Dissociated cerebral cortical cells

source_name: adult dissociated cerebral cortex, 7-day hypoxia

extract_protocol:
Dissociated single cells were processed through the GemCode Single Cell Platform using the GemCode Gel Bead, Chip, and Library Kits (10X Genomics, Pleasanton) as per the manufacturer’s protocol.  In brief, single cells were sorted into 0.4% BSA–DPBS.  Approximately 14,000 single retinal cells were added to a channel.  The cells were then partitioned into Gel Beads in Emulsion in the 10x Genomics Chromium Controller, where cell lysis
Cell lysis was followed by barcoded oligo-DT priming and reverse transcription of poly-adenylated RNA, amplification, shearing and 5′ adaptor and sample index attachment.

value: WT

value: 2 month

tag: Sex

value: Male

value: cerebral cortex

tag: treatment

value: Mouse was exposed to normoxic conditions


title: JH18_Cerebral_cortex_normoxia_scRNAseq

description: Dissociated cerebral cortical cells

source_name: adult dissociated cerebral cortex, normoxia

tag: tissue

value: Mouse was exposed to 7 days of 7.5% oxygen in a normobaric chamber


title: JH30_WT_retina_scRNAseq_R1

description: Dissociated retinal cells

source_name: adult dissociated WT retina

value: retina


title: JH29_NdpKO_retina_scRNAseq_R1

description: Dissociated retinal cells

source_name: adult dissociated NdpKO retina

value: NdpKO


title: leaf_96hours_drought_rep1


title: leaf_24hours_control_rep2

source_name: leaf, 24hours, control


title: JH26_WT_retina_scRNAseq_R1

description: Dissociated retinal cells


title: JH25_NdpKO_retina_scRNAseq_R1

description: Dissociated retinal cells


title: leaf_24hours_control_rep1


title: leaf_24hours_drought_rep2

source_name: leaf, 24hours, drought


title: EWAT Sample 1


title: leaf_24hours_drought_rep1


title: D rep3

city: Harbin

first: Zhiyong

last: Wu

address: 600 Changjiang Road, Xiangfang District

institute: Northeast Agricultural University

description: E.coli infection

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2 with parameters v1.5.2, then mapped to Gallus_gallus-5.0 genome using bowtie2 v2. 2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: csv files include RPKM values for each Sample ...

organism: Gallus gallus

source_name: Lung

growth_protocol: Eighty (1 day old) commercial Leghorn chickens were obtained from Chia Chau Chicken Farm (Harbin, Heilongjiang, China) and were assigned randomly to four groups namely control group, co-infection group, MG group, E.coli group. The chickens were in healthy conditions, MG and E.coli-free and did not undergo vaccination and raised to the 10th day in four separate environmentally controlled chambers (named A, B, C and D).

extract_protocol:
Lungs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent(Invitrogen)
BGISEQ-500 RNA-Seq Library. Library was validated on the Agilent Technologies 2100 bioanalyzer.

treatment_protocol: Control group (A): No treatment control, fed with the same environment, keeping up with the end of the experiment.Co-infection group (B): The infectious dose was diluted into 0.2ml MG medium in left caudal thoracic air sac at the 7th day, and injected intraperitoneally with 0.1 ml of E.coli bacteria at day 10. MG group (C): The MG infection model was constructed one time by left caudal thoracic air sac inoculation with MG Rlow strain 0.2mL at the 7th day. E.coli group (D): The infectious dose was injected intraperitoneally with 0.1 ml of E.coli bacteria at day 10.

value: Lung

value: Leghorn chicken

value: 13 day old


title: pBIC_6

description: PolyA RNA

data_processing:
The quality of the samples was verified using FastQC software.
FASTQ files were mapped to mm10 mouse assembly using STAR with default parameters.
featureCounts software and Gencode M13 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions.
Obtained gene counts were normalized using edgeR and voom function of limma.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: B220+GFP+ cells from spleen

extract_protocol:
Murine spleens were submitted to cellular disaggregation, followed by lysis of erythrocytes using ACK buffer. Then, single-cell preparations were stained with B220 and submitted to fresh cellular sorting in a FACSAria Ilu sorter (BD) after exclusion of dead cells with 7AAD. Total RNA was extracted from sorted cells using TRIzol (Invitrogen) as described in manufacturer´s protocol and quality control of extracted RNA was measured using Agilent Bioanalyzer.
General transcriptome library preparation and massive sequencing were performed by BGI Tech (BGI, Shenzhen, China) using the Illumina HiSeq4000 platform with the paired-end 100-bp read option.

tag: murine model

value: ABC-DLBCL lymphoma (pBIC)

value: splenic B cells (B220+GFP+)


title: 2CLM2

city: Hong Kong

first: Kathy

last: Chan

address: 386, South Block, Science Center, The Chinese University of Hong Kong, Sha Tin

department: School of Life Sciences

institute: The Chinese University of Hong Kong

data_processing:
Illumina RTA 1.18.54 was used for base-calling
Fastp was used to filter out low quality and unclean reads and Hisat2 was used to align the  high quality and clear reads against the reference genome (Coprinopsis cinerea AmutBmut pab1-1 v1.0) from JGI.
Fragments per kilobase of transcript per million fragments mapped (FPKM) were calculated using Cufflinks protocol form Trapnell C., Nature Protocols, 2012
Genome_build: JGI Coprinopsis cinerea AmutBmut pab1-1 v1.0
Supplementary_files_format_and_content: text files include FPKM values for each Sample

organism: Coprinopsis cinerea

source_name: LiCl-treated, mycelium

growth_protocol: Grown on yeast extract-malt extract-glucose (YMG) medium solidified with 1.5% (w/v) agar

extract_protocol:
Control and LiCl treated samples in two time points of Coprinopsis cinerea were harvested, first one in the mycelium stage were harvested after 4 days of incubation in total darkness, before reaching the edge of plates, whereas second one in the hyphal knot stage were collected after 3-4 days of incubation under the 12/12 h light/dark cycle after the mycelium reached the edge of plates.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: a piece of mycelium 5 mm diameter punch from the stock plates was inoculated on plates spread with 3 μM LiCl and autoclaved water was added in the control plates

tag: developmental stage

value: mycelium

tag: sample type

value: LiCl


title: D rep2

description: E.coli infection

tag: age


title: pBIC_5

description: PolyA RNA


title: D rep1

description: E.coli infection