title: WT_Rep2_BS-Seq

first: Huang

last: Huan

address: No. 3888 Chenhua Road

description: treated with bisulfite

data_processing:
Low-quality sequences (q < 20) and adapters were trimmed using trimmomatic.
Reads were mapped to TAIR10 using BSMAP 2.87 with parameters -g 1
methratio.py python script of BSMAP was used to extract metylation ratios from BSMAP results with parameters -z and -r
Genome_build: TAIR10
Supplementary_files_format_and_content: wig

organism: Arabidopsis thaliana

source_name: Seedlings

extract_protocol: Genomic DNA was extracted from 14-d-old seedlings and sent to Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China)  for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.

value: wild type


title: arp6-4_Rep2_BS-Seq

status: Public on Dec 06 2020

type: SRA

city: Shanghai

department: Shanghai Center for Plant Stress  Biology

country: China

institute: Chinese Academy of Sciences

description: treated with bisulfite

library_source: genomic

molecule: genomic DNA

tag: genotype/variation


title: idm1-9_Rep2_BS-Seq

description: treated with bisulfite


title: idm1-9_Rep1_BS-Seq

description: treated with bisulfite


title: atmbd9-4npx1-4_Rep2_BS-Seq

description: treated with bisulfite


title: ros1-14_Rep2_BS-Seq

description: treated with bisulfite


title: atmbd9-4npx1-4_Rep1_BS-Seq

description: treated with bisulfite


title: ros1-14_Rep1_BS-Seq

description: treated with bisulfite


title: 35S_SUC2_Rep1_BS-Seq

description: treated with bisulfite


title: 35S_SUC2_Rep2_BS-Seq

description: treated with bisulfite


title: h2a.z-2_Rep2_BS-Seq

description: treated with bisulfite


title: h2a.z-2_Rep1_BS-Seq

description: treated with bisulfite


title: pie1-6_Rep2_BS-Seq

description: treated with bisulfite


title: idm1-9_input

data_processing:
 Low-quality sequences (q < 20) and adapters were trimmed using trimmomatic.
The paired-end reads were mapped to the TAIR10 genome of Arabidopsis thaliana with BWA(0.7-13) with defauilg parameter
To remove potential PCR duplicates, rmdup from SAMtools (Li et al., 2009) was used
Regions of H2A.Z enrichment were defined by computing the log2 ratios of the output of H2A.Z to input genomic DNA
Genome_build: TAIR10
Supplementary_files_format_and_content: tdf

growth_protocol: Plants were grown at 22°C in a growth chamber with 16 h of light and 8 h of darkness on 1/2 MS medium with 0.8% glucose and were harvested at 14-days old.

extract_protocol:
ChIP was performed according to a previously published protocol (Wierzbicki et al., 2008).
ChIP samples were sent to the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) for library construction and Illumina sequencing.

tag: antibody


title: pie1-6_Rep1_BS-Seq

description: treated with bisulfite


title: arp6-4_Rep1_BS-Seq

description: treated with bisulfite


title: WT_Rep1_BS-Seq

description: treated with bisulfite


title: pie1-6-H2A.Z


title: 35S_SUC2_input


title: 35S_SUC_H2A.Z


title: arp6-4_input


title: ros1-14_input


title: SUM149 Migratory

city: Ann Arbor

first: Yu-Chih

last: Chen

state: MI

address: 1301 Beal Ave.

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
Drop-seq_tools-1.12
Read 1 (R1) contains the barcode. Position 1-12 are cell barcodes, and Position 13-20 are molecular barcodes.
STAR
Genome_build: hg19 genome
Supplementary_files_format_and_content: Digital gene expression table of individual wild-type and migratory breast cancer cells

molecule: total RNA

organism: Homo sapiens

source_name: Breast cancer cell line

growth_protocol: MDA-MB-231 and GUM36 cells were cultured in DMEM (Gibco 11965) with 10% FBS (Gibco 10082) and 1% penicillin/streptomycin (Gibco 15070). SUM149 and SUM159 cells  were cultured in F-12 (Gibco 11765) media supplemented with 5% FBS (Gibco 10082), 1% Pen/Strep (Gibco 15070), 1% GlutaMax (Gibco 35050), 1 μg/mL hydrocortisone (Sigma H4001), and 5 μg/mL insulin (Sigma I6634).

extract_protocol:
We performed high-throughput single-cell barcoding transcriptome sequencing based on Drop-Seq protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Isolate migratory breast cancer cells from microfluidic chip and expand the number of sequencing

tag: cell line

tag: phenotype

value: migratory


title: GUM36 WT

value: WT


title: GUM36 Migratory


title: arp6-4_H2A.Z


title: pie1-6_input


title: idm1-9_H2A.Z


title: MDA-MB-231 WT


title: sgRNA_sorafenib_resistant_circRNA_screen_Sorafenib_rep1

city: Torino

first: Pier Paolo

last: Pandolfi

state: TO

address: 8 Via Verdi

institute: University of Torino

data_processing:
Library strategy: DNA-Seq
For screening studies, DNA-Seq reads were trimmed, counted and analyzed with MAGeCK v0.5.8
For RNA-Seq, reads were aligned and quantified with Salmon v0.13.1 then normalized with DESeq2 v1.26.0
Genome_build: hg38
Supplementary_files_format_and_content: text files contain normalized read count data for each set of sequencing experiments

source_name: hepatocellular carcinomas

extract_protocol:
For gRNA/shRNA screening screening experiments, genomic DNA was extracted from screened cells using Qiagen Blood and Tissue Kit. For RNA-Seq, RNA was extract with Trizol
For gRNA/shRNA screening libraries, custom primers compatible with Illumina sequencing primers were used to amplified gRNA/shRNA sequences from the genome. For RNA-Seq, RNA libraries were prepared according to Illumina's protocol, conducted by the Molecular Biology Core Facilities at Dana-Farber Cancer Institute

tag: cell type

value: hepatocellular carcinomas

tag: treatment

value: 2.5uM Sorafenib


title: SUM159 Migratory


title: ros1-14_H2A.Z


title: sgRNA_sorafenib_resistant_circRNA_screen_DMSO_rep1

value: DMSO


title: ESM1

city: Taipei City

first: KeFan

last: Pan

state: Please Select

address: Rm. 539, 5F., No.1, Sec. 1, Ren’ai Rd.

country: Taiwan

institute: National Taiwan University

description:
Vector-ESM1.xlsx
P-ESM1

data_processing:
Sequencing and base-calling services were provided by Genomics BioSci & Tech. Co. Ltd. (Taiwan).
Low quality bases and sequencing adapters in raw data which generated from Illumina sequencer was removed using program Trimmomatic, then the reads were aligned to reference transcript sequences using Bowtie2.
Gene expression level was calculated by RSEM with Maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model.
Differentially expressed genes (DEGs) are calculated by EBSeq
Genome_build: hg19
Supplementary_files_format_and_content: Files include FPKM values for each Sample.

source_name: prostate cancer cells

growth_protocol: 22Rv1 cells were grown in RPMI-1640 medium containing 10% FBS, and supplemented with penicillin and streptomycin.

extract_protocol:
Cell medium were removed and RNA was harvested using Rneasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were incubated at 37C in 5% CO2 and grown to 60-70% confluence before adding the lenti virus. After 72 hours, cells were collected and total RNA were harvested.

value: 22Rv1 human prostatic carcinoma cell line

value: prostate epithelial cells

tag: genotype

value: ESM1 overexpression


title: sgRNA_sorafenib_resistant_circRNA_screen_Sorafenib_rep2


title: CD34_cells_tripletB

status: Public on Dec 07 2020

type: genomic

city: Solna

first: Klas

last: Strååt

address: Akademiska stråket 1

department: Medicine

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Bisulphite converted DNA was eluted in 15 microliters according to the manufacturer's protocol, evaporated to a volume of <4 microliters, and used for methylation analysis using the Illumina Methylation EPIC array.

scan_protocol: Arrays were imaged using Illumina's iScan system

data_processing: Idat files were processed using minfi R package v1.28.4. Idat files were read with the read.metharray.exp function. Detection P values were generated using the detectionP function. Methylated and unmethylated signals were generated using the preprocessIllumina function with parameters bg.correct=TRUE and no normalization. Beta values were extracted using the getBeta function on methylated/unmethylated values.

label: Cy5 and Cy3

source_name: CD34+ cells, triplet B, Hodgkins lymphoma

label_protocol: Bisulphite conversion was performed using the EZ DNA Methylation Kit from Zymo Research with 250 ng of DNA per sample.

extract_protocol: Genomic DNA was isolated from CD34+ cells and from Naïve, marginal zone-like and switched memory B cells using the Dneasy Blood & Tissue Kit (Qiagen) in accordance with the manufacturer's protocol.

tag: disease state

value: Hodgkins lymphoma

tag: triplet

value: B

tag: cell population

value: CD34+ cells


title: sgRNA_sorafenib_resistant_circRNA_screen_DMSO_rep2


title: SUM159 WT


title: Patient 26 Post reduced activity 0 baseline [Ribo-Seq]

city: Salt Lake City

first: Michael

middle: T

last: Howard

state: UT

department: Human Genetics

institute: University of Utah

description: ribosome protected RNA fragments

data_processing:
Library strategy: Ribo-Seq
Adapter sequences were trimmed (FASTX- Toolkit hannonlab.cshl.edu/fastx_toolkit/) and contaminating rRNA sequences were removed (alignment to the human 45s rRNA repeat sequence using bowtie). Uniquely mapping sequences were identified by alignments using bowtie to Reference Sequence database (RefSeq) mRNA entries obtained from the University of California, Santa Cruz browser (Hg38 human genome reference assembly) in which all mRNAs derived from the same gene were reduced to a single entry corresponding to the longest isoform.
Normalization factors based on the trimmed mean of M-values were determined the Bioconductor package edgeR for ribosome profiling and RNA-Seq. Dispersion estimates were obtained prior to likelihood ratio tests (glmFit and glmLRT functions of edgeR) to determine significance of the log2 fold change in RPFs or RNA for all transcripts with ≥1 count/million in all samples.
Genome_build: Hg38
Supplementary_files_format_and_content: logFC
Supplementary_files_format_and_content: logCPM

source_name: Patient 26

extract_protocol:
Muscle biopsies were disrupted using a bead beater homogenizer. Total RNA was extracted in qiazol and Ribosomes isolated in a buffer containing 10mM MgCl2.
NEBNext rRNA removal kit was used to remove rRNA. Heat fragmented total RNA for RNA-Seq and ribosome protected RNA fragments were treated with T4 PNK and libraries constructed using the NEBNext Small RNA Library kit. Libraries were size selected for 25-35 nt fragments by native PAGE.

tag: tissue

value: muscle biopsy

tag: time point

value: Post reduced activity 0 baseline


title: Patient 26 Post reduced activity 60 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: Patient 26 Pre reduced activity 180 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: Vector-1

description:
Vector-ESM1.xlsx
P-Vector

value: control


title: Patient 26 Post reduced activity 180 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: NK cells day 0 sample 2

city: Houston

first: Katy

last: Rezvani

state: Texas

address: 1400 Pressler St

department: Stem Cell Transplantation

institute: University of Texas MD Anderson Cancer Center

description: D0NK _2

data_processing:
read were aligned to the transcriptome using TOPHAT2 v2.0.13 and gene level read counts were obtained using HTSEQ
Genome_build: hg38

source_name: Natural Killer cells freshly isolated day 0

growth_protocol: UCB–derived NK cells, with (CAR) or without CAR (NT), were expanded by co-culturing with uAPC helper cells

extract_protocol:
RNA isolation by Qiagen kit
Libraries were prepared according to Illumina's protocol for RNA-seq

treatment_protocol: NK cells were either freshly isolated {day 0) or harvested after co-cultured with uAPC (day 15)

value: UCB-derived Natural Killer cells

value: freshly isolated day 0


title: NK cells non-transduced sample 3

description: NT _3

source_name: Natural Killer cells non-transduced day 15

value: non-transduced day 15


title: Patient 26 Pre reduced activity 0 baseline [Ribo-Seq]

description: ribosome protected RNA fragments

value: Pre reduced activity 0 baseline


title: NK cells day 0 sample 1

description: D0NK _1


title: CD34_cells_tripletC

source_name: CD34+ cells, triplet C, no Hodgkins lymphoma

value: No Hodgkins lymphoma

value: C


title: naive_Bcells_tripletA

source_name: naïve B cells, triplet A, Hodgkins lymphoma

value: A

value: naïve B cells


title: switched_mem_tripletA

source_name: switched memory B cells, triplet A, Hodgkins lymphoma

value: switched memory B cells


title: Patient 26 Post reduced activity 180 min after Leucine [RNA-Seq]

description: RNA

data_processing:
Adapter sequences were trimmed (FASTX- Toolkit hannonlab.cshl.edu/fastx_toolkit/) and contaminating rRNA sequences were removed (alignment to the human 45s rRNA repeat sequence using bowtie). Uniquely mapping sequences were identified by alignments using bowtie to Reference Sequence database (RefSeq) mRNA entries obtained from the University of California, Santa Cruz browser (Hg38 human genome reference assembly) in which all mRNAs derived from the same gene were reduced to a single entry corresponding to the longest isoform.
Normalization factors based on the trimmed mean of M-values were determined the Bioconductor package edgeR for ribosome profiling and RNA-Seq. Dispersion estimates were obtained prior to likelihood ratio tests (glmFit and glmLRT functions of edgeR) to determine significance of the log2 fold change in RPFs or RNA for all transcripts with ≥1 count/million in all samples.
Genome_build: Hg38
Supplementary_files_format_and_content: logFC
Supplementary_files_format_and_content: logCPM


title: NK cells non-transduced sample 2

description: NT _2


title: Patient 26 Post reduced activity 60 min after Leucine [RNA-Seq]

description: RNA


title: SUM149 WT

value: WT


title: NK cells non-transduced sample 1


title: Patient 26 Post reduced activity 0 baseline [RNA-Seq]

description: RNA


title: NK cells + CD19CAR D15 sample 2

source_name: Natural Killer cells + CAR19 transduced

value: CAR19 transduced day 15


title: Patient 26 Pre reduced activity 60 min after Leucine [RNA-Seq]

description: RNA


title: NK cells + CD19CAR D15 sample 1


title: Patient 26 Pre reduced activity 0 baseline [RNA-Seq]

description: RNA


title: switched_mem_tripletC

source_name: switched memory B cells, triplet C, no Hodgkins lymphoma


title: Patient 26 Pre reduced activity 60 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: CD34_cells_tripletA

source_name: CD34+ cells, triplet A, Hodgkins lymphoma

value: Hodgkins lymphoma


title: Patient 25 Post reduced activity 180 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments

source_name: Patient 25


title: NK cells day 0 sample 3

description: D0NK _3


title: Patient 26 Pre reduced activity 180 min after Leucine [RNA-Seq]

description: RNA


title: marginal_zone_tripletB

source_name: marginal zone-like B cells, triplet B, Hodgkins lymphoma

value: B

value: marginal zone-like B cells


title: Patient 25 Post reduced activity 60 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments

value: muscle biopsy


title: Patient 25 Post reduced activity 0 baseline [Ribo-Seq]

description: ribosome protected RNA fragments

value: Post reduced activity 0 baseline


title: GC3-TT17

first: Sibo

last: Zhu

state: China

address: songhulu 2005

institute: Fudan University

data_processing:
Library strategy: scRNA-seq
HiSeq 2500 instrument (Illumina) and single-end 50-bp read flow cells were used in this study
Sequenced reads were trimmed for adaptor sequence by trimmomatic(v0.36), then mapped to human genome(hg19) by Hisat2(V2.0.5), and counted by featureCounts(v1.5.2)
data was filterd under the standization that a gene expressed at least in 3 cells and a cells must express at leat 200 features
Genome_build: hg19
Supplementary_files_format_and_content: csv file include raw count values for each cell

source_name: tumor tissue

extract_protocol:
Tissues were digested for 60 minutes at 37°C and then pipetted up and down every ten times every 10 minutes. The tissue suspensions were then filtered with a 70um nylon mesh (ThermoFisher Scientific, USA) and were centrifuged at 450g for 5 minutes. Pellets were resuspended for live cell staining using CFSE incubation for 5 minutes
Single cells from each tissue were manually picked under fluorescent microscopy (X71, Olympus, Japan) using mouth pipette. Each of the harvested single cells was transferred into 2uL of CLB (cell lysis buffer) in 0.2mL PCR tubes. Libraries of isolated single cells were then prepared as per the Smart-seq2 protocol15 with modifications on reverse transcription and amplification cycles.  Oligo-dT primed RT (reverse transcription) was performed by Smartscribe (Takara, Japan) reverse transcriptase and locked TSO oligonucleotide (Exiqon, Danmark) upon single cells. Full-length cDNA amplification was conducted by PCR amplification for 22 cycles with Hifi HotStart ReadyMix reagent (KAPA Biosystems, USA) and purified by 0.6x AMPure beads (BD, USA). Barcoded libraries were fragmented and segmented with Library Prep kit (Nextera XT, Illumina, USA). Pooled libraries with unique N5-N7 barcodes were sequenced with a Hiseq 2500 sequencer (Illumina, USA) and 50SE reads flow cell.

treatment_protocol: Biopsy, metastatic tumor or para-tumor tissues were dissected and transferred to a 2 ml tube (Axygen, China) each containing 1 ml pre-warmed M199-media (ThermoFisher Scientific, USA), 2 mg/ml collagenase P (Roche, USA) and 10U/ul DNase I (Roche, USA) as was described by Tirosh et al

value: tumor tissue

value: gastric cancer


title: GC3-LN4

source_name: lymph node

value: lymph node


title: Patient 25 Pre reduced activity 60 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: GC3-LN11


title: GC3-TT15


title: Patient 25 Pre reduced activity 0 baseline [Ribo-Seq]

description: ribosome protected RNA fragments


title: GC3-TT14


title: GC3-TT12


title: NK cells + CD19CAR D15 sample 3

value: UCB-derived Natural Killer cells


title: naive_Bcells_tripletB

source_name: naïve B cells, triplet B, Hodgkins lymphoma


title: Patient 25 Pre reduced activity 180 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: Patient 25 Post reduced activity 60 min after Leucine [RNA-Seq]

description: RNA


title: Patient 25 Post reduced activity 180 min after Leucine [RNA-Seq]

description: RNA


title: GC1-TT19


title: marginal_zone_tripletC

source_name: marginal zone-like B cells, triplet C, no Hodgkins lymphoma


title: marginal_zone_tripletA

source_name: marginal zone-like B cells, triplet A, Hodgkins lymphoma


title: Patient 25 Pre reduced activity 180 min after Leucine [RNA-Seq]

description: RNA


title: Patient 25 Post reduced activity 0 baseline [RNA-Seq]

description: RNA


title: switched_mem_tripletB

source_name: switched memory B cells, triplet B, Hodgkins lymphoma


title: Patient 25 Pre reduced activity 60 min after Leucine [RNA-Seq]

description: RNA


title: GC1-TT15


title: GC1-TT11


title: GC1-TT8


title: GC1-TT7


title: naive_Bcells_tripletC

source_name: naïve B cells, triplet C, no Hodgkins lymphoma


title: Patient 25 Pre reduced activity 0 baseline [RNA-Seq]

description: RNA

value: Pre reduced activity 0 baseline


title: MDA-MB-231 Migratory

source_name: Breast cancer cell line

value: migratory


title: Patient 23 Post reduced activity 180 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments

source_name: Patient 23


title: Patient 23 Post reduced activity 60 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: GC1-TT1


title: GC1-TT17


title: GC1-TT4


title: Patient 23 Pre reduced activity 180 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: GC2-TT26


title: Patient 23 Pre reduced activity 60 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: GC2-TT27


title: Patient 23 Post reduced activity 0 baseline [Ribo-Seq]

description: ribosome protected RNA fragments


title: GC2-TT23


title: Patient 23 Post reduced activity 0 baseline [RNA-Seq]

description: RNA


title: Patient 23 Pre reduced activity 0 baseline [Ribo-Seq]

description: ribosome protected RNA fragments


title: GC2-TT24


title: Patient 23 Post reduced activity 180 min after Leucine [RNA-Seq]

description: RNA


title: GC2-TT21


title: GC2-TT22


title: Patient 23 Pre reduced activity 180 min after Leucine [RNA-Seq]

description: RNA


title: Patient 23 Pre reduced activity 60 min after Leucine [RNA-Seq]

description: RNA


title: Patient 23 Pre reduced activity 0 baseline [RNA-Seq]

description: RNA


title: GC2-TT20


title: GC2-TT19


title: GC2-TT18


title: Patient 21 Post reduced activity 0 baseline [Ribo-Seq]

description: ribosome protected RNA fragments

source_name: Patient 21


title: GC3-TT13


title: GC3-TT16


title: Patient 21 Post reduced activity 60 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: GC2-TT25


title: Patient 23 Post reduced activity 60 min after Leucine [RNA-Seq]

description: RNA


title: GC3-TT11


title: Patient 21 Pre reduced activity 180 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: GC3-TT10


title: GC3-TT9


title: Patient 21 Pre reduced activity 60 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: Patient 21 Pre reduced activity 0 baseline [Ribo-Seq]

description: ribosome protected RNA fragments


title: GC2-TT17


title: Patient 21 Post reduced activity 180 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: Patient 21 Post reduced activity 0 baseline [RNA-Seq]

description: RNA


title: GC2-TT14


title: Patient 21 Post reduced activity 180 min after Leucine [RNA-Seq]

description: RNA


title: Patient 21 Post reduced activity 60 min after Leucine [RNA-Seq]

description: RNA


title: GC2-TT15


title: GC2-TT16


title: Patient 21 Pre reduced activity 60 min after Leucine [RNA-Seq]

description: RNA


title: GC2-TT12


title: GC2-TT13


title: Patient 21 Pre reduced activity 0 baseline [RNA-Seq]

description: RNA


title: Patient 21 Pre reduced activity 180 min after Leucine [RNA-Seq]

description: RNA


title: GC2-TT10


title: GC2-TT11


title: Patient 20 Post reduced activity 180 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments

source_name: Patient 20


title: GC1-TT16


title: Patient 20 Post reduced activity 0 baseline [Ribo-Seq]

description: ribosome protected RNA fragments


title: Patient 20 Post reduced activity 60 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: Patient 20 Pre reduced activity 180 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: GC1-TT3


title: GC1-TT6


title: GC3-TT8


title: Patient 20 Pre reduced activity 0 baseline [Ribo-Seq]

description: ribosome protected RNA fragments


title: Patient 20 Pre reduced activity 60 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: Patient 20 Post reduced activity 180 min after Leucine [RNA-Seq]

description: RNA


title: Patient 20 Post reduced activity 60 min after Leucine [RNA-Seq]

description: RNA


title: GC3-TT18


title: GC3-TT7


title: GC3-TT6


title: Patient 20 Post reduced activity 0 baseline [RNA-Seq]

description: RNA


title: Patient 20 Pre reduced activity 180 min after Leucine [RNA-Seq]

description: RNA


title: GC3-TT5


title: GC3-TT4


title: GC3-TT19


title: GC1-TT18


title: Patient 19 Post reduced activity 60 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments

source_name: Patient 19


title: GC3-TT2


title: GC3-TT3


title: Patient 19 Post reduced activity 0 baseline [Ribo-Seq]

description: ribosome protected RNA fragments


title: Patient 19 Pre reduced activity 180 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: Patient 19 Pre reduced activity 60 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: GC2-TT8


title: Patient 19 Post reduced activity 180 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: Patient 19 Pre reduced activity 0 baseline [Ribo-Seq]

description: ribosome protected RNA fragments


title: GC2-TT7


title: Patient 20 Pre reduced activity 0 baseline [RNA-Seq]

description: RNA


title: GC3-TT1


title: Patient 19 Post reduced activity 180 min after Leucine [RNA-Seq]

description: RNA


title: GC2-TT6


title: GC2-TT5


title: Patient 19 Post reduced activity 60 min after Leucine [RNA-Seq]

description: RNA


title: GC2-TT9


title: Patient 20 Pre reduced activity 60 min after Leucine [RNA-Seq]

description: RNA


title: Patient 19 Post reduced activity 0 baseline [RNA-Seq]

description: RNA


title: GC2-TT4


title: Patient 19 Pre reduced activity 180 min after Leucine [RNA-Seq]

description: RNA


title: GC2-TT3


title: Patient 19 Pre reduced activity 0 baseline [RNA-Seq]

description: RNA


title: Patient 19 Pre reduced activity 60 min after Leucine [RNA-Seq]

description: RNA


title: GC2-TT2


title: GC1-TT14


title: Patient 18 Post reduced activity 60 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments

source_name: Patient 18


title: GC1-TT2


title: Patient 18 Post reduced activity 0 baseline [Ribo-Seq]

description: ribosome protected RNA fragments


title: GC1-TT13


title: GC1-TT5


title: GC1-TT12


title: Hnrnpll_KO_H8_EBD8

city: Beijing

first: Jia

last: Yu

address: Dong Dan San Tiao 5, Dongcheng District

institute: Peking Union Medical College

description: Hnrnpll KO EB-differentiation day 8

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences and low quality sequences with trimmomatics (version 0.36) with default parameters, then mapped to mm10 whole genome of GENCODE vM12 using hisat v2.0.5 with parameters --dta -t -p 8.
Both transcripts per kilobase of exon per million reads (TPM) and non-normalized raw counts were calculated using stringtie v1.3.3b with parameters -e -B -p 8.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM and non-normalized raw counts values for each sample.

molecule: polyA RNA

organism: Mus musculus

source_name: Hnrnpll KO EB-differentiation day 8

growth_protocol: ESC were culture in ES cell culture medium supplemented with 15% fetal bovine serum, 1000U/ml leukemia inhibitory factor. EBs were formed from ES cells by using handing drop culture method and collect the samples every other day.

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols; illumina polyA+ RNA-seq library

value: embryoid body

value: Hnrnpll-/-

tag: time

value: day 8


title: Patient 18 Pre reduced activity 60 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: Hnrnpll_KO_G6_EBD8

description: Hnrnpll KO EB-differentiation day 8


title: Hnrnpll_KO_H8_EBD4

description: Hnrnpll KO EB-differentiation day 4

source_name: Hnrnpll KO EB-differentiation day 4

value: day 4


title: Patient 18 Pre reduced activity 0 baseline [Ribo-Seq]

description: ribosome protected RNA fragments


title: Hnrnpll_KO_G6_EBD4

description: Hnrnpll KO EB-differentiation day 4


title: GC2-TT1


title: Patient 18 Post reduced activity 180 min after Leucine [RNA-Seq]

description: RNA


title: Hnrnpll_KO_G6_ESC

description: Hnrnpll KO EB-differentiation day 0

source_name: Hnrnpll KO EB-differentiation day 0

value: embryonic stem cell

value: day 0


title: GC1-TT9


title: Hnrnpll_KO_H8_ESC

description: Hnrnpll KO EB-differentiation day 0


title: Patient 18 Post reduced activity 180 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: WT_EBD8

description: Wild type EB-differentiation day 8

source_name: Wild type EB-differentiation day 8

value: wild type


title: GC3-LN10


title: Patient 18 Post reduced activity 0 baseline [RNA-Seq]

description: RNA


title: WT_ESC

description: Wild type EB-differentiation day 0

source_name: Wild type EB-differentiation day 0


title: sgRNA_essential_circRNA_screen_Day14_rep2

source_name: hepatocellular carcinomas

value: hepatocellular carcinomas

value: Day 14


title: Patient 18 Pre reduced activity 180 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments

value: muscle biopsy


title: Patient 18 Pre reduced activity 180 min after Leucine [RNA-Seq]

description: RNA


title: GC3-LN7

source_name: lymph node


title: GC3-LN8


title: sgRNA_essential_circRNA_screen_Day0_rep1

value: Day 0


title: GC1-TT10

source_name: tumor tissue

value: tumor tissue


title: shRNA_essential_circRNA_screen_Day14_rep2


title: shRNA_essential_circRNA_screen_Day14_rep1


title: GC3-LN5

value: gastric cancer


title: shRNA_essential_circRNA_screen_Day0_rep2


title: GC3-LN9

value: lymph node


title: shRNA_essential_circRNA_screen_Day0_rep1


title: Patient 18 Post reduced activity 60 min after Leucine [RNA-Seq]

description: RNA


title: WT_EBD4

description: Wild type EB-differentiation day 4

source_name: Wild type EB-differentiation day 4


title: Patient 17 Post reduced activity 180 min after Leucine [RNA-Seq]

description: RNA

source_name: Patient 17


title: GC2-LN13


title: Patient 17 Post reduced activity 60 min after Leucine [RNA-Seq]

description: RNA


title: sgRNA_essential_circRNA_screen_Day14_rep1


title: GC2-LN12


title: Patient 17 Post reduced activity 0 baseline [RNA-Seq]

description: RNA

value: Post reduced activity 0 baseline


title: GC2-LN11


title: CPB011-MUF-08h

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

institute: University of California, San Diego (UCSD)

description: leukocyte expression profile from CPB011-MUF-08h

data_processing:
Basecalling, demultiplexing, and adapter trimming was performed using Illumina's bcl2fastq (v2.17.1.14)
RNA-seq reads were aligned to the GRCh38/hg38 assembly of the human genome using STAR (version 2.5.2a) using default parameters
Gene expression values were calculated across RefSeq defined transcript exons using HOMER. Read totals were normalized to 10 million reads per sample
Genome_build: hg38
Supplementary_files_format_and_content: normalized counts per gene (tab-delimited text) Columns: RefSeqID, chr, start, end, strand, transcript length, copies in genome, gene symbol, annotation, sample1, sample2…)

source_name: circulating leukocytes

growth_protocol: Pediatric patients less than 1 month old with different congenital heart defects requiring repair utilizing cardiopulmonary bypass (CPB) were enrolled in our study at Mercy’s Children Hospital, Kansas City, MO. T  A standard cardiopulmonary bypass protocol was utilized in all of the patients.  Approach in all cases was via median sternotomy.  Aortic cannulation was used for the arterial access with either single venous cannula being placed in the right atrium or bicaval cannulation, depending on the type of the defect requiring repair.  The CPB circuit was blood-primed.  Standard additives included Solumedrol, Sodium Bicarbonate, Cefazolin and Tranexamic Acid.  After initiation of CPB, the patients were cooled to 18 to 28 degrees Centigrade. Mean perfusion pressure (MAP) was maintained at 25-35 mmHg and the minimum Hct was kept at 24%.  Upon completion of repair, the patients were rewarmed and weaned from CPB.  Modified ultrafiltration (MUF) was performed in all of the patients after weaning from CPB.

extract_protocol:
Total RNA from the nucleated cells was extracted using either the MirVana RNA extraction kit (Invitrogen) or PAXgene Blood RNA Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Blood samples of 2.5mL were collected from an indwelling patient line or from the CPB pump, dependent upon the time of the blood draw (i.e. for blood draws performed while the patient was on CPB, these samples were pulled from the CPB pump). These samples were collected in EDTA tubes at 7 time points: before CPB (CPB-0h), 1h into CPB (CPB-1h), end of CPB (CPB-end), end of modified ultrafiltration (MUF-end), and 1h (MUF-1h), 8h (MUF-8h), 24h (MUF-24h) during postoperative recovery.

tag: donor

value: 8h into postoperative recovery

value: leukocyte


title: CPB011-MUF-24h

description: leukocyte expression profile from CPB011-MUF-24h

value: 24h into postoperative recovery


title: CPB011-MUF-01h

description: leukocyte expression profile from CPB011-MUF-01h

value: 1h into postoperative recovery


title: Patient 18 Pre reduced activity 60 min after Leucine [RNA-Seq]

description: RNA


title: CPB011-MUF-00h

description: leukocyte expression profile from CPB011-MUF-00h

value: end of modified ultrafiltration


title: CPB011-CPB-01h

description: leukocyte expression profile from CPB011-CPB-01h

value: 1h into CPB


title: Patient 17 Pre reduced activity 180 min after Leucine [RNA-Seq]

description: RNA


title: GC3-LN6


title: CPB011-CPB-00h

description: leukocyte expression profile from CPB011-CPB-00h

value: before CBP


title: GC2-LN10


title: sgRNA_essential_circRNA_screen_Day0_rep2


title: Patient 18 Pre reduced activity 0 baseline [RNA-Seq]

description: RNA

value: Pre reduced activity 0 baseline


title: CPB010-MUF-24h

description: leukocyte expression profile from CPB010-MUF-24h


title: Patient 17 Pre reduced activity 60 min after Leucine [RNA-Seq]

description: RNA


title: CPB010-MUF-08h

description: leukocyte expression profile from CPB010-MUF-08h


title: CPB010-MUF-01h

description: leukocyte expression profile from CPB010-MUF-01h


title: CPB010-MUF-00h

description: leukocyte expression profile from CPB010-MUF-00h


title: GC1-LN4


title: Patient 17 Post reduced activity 180 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: CPB011-CPB-end

description: leukocyte expression profile from CPB011-CPB-end

value: end of CPB


title: Patient 17 Pre reduced activity 0 baseline [RNA-Seq]

description: RNA


title: CPB010-CPB-end

description: leukocyte expression profile from CPB010-CPB-end


title: GC2-LN8


title: Patient 17 Post reduced activity 60 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: CPB010-CPB-00h

description: leukocyte expression profile from CPB010-CPB-00h


title: CPB004-MUF-24h

description: leukocyte expression profile from CPB004-MUF-24h


title: GC2-LN7


title: Patient 17 Post reduced activity 0 baseline [Ribo-Seq]

description: ribosome protected RNA fragments


title: Patient 17 Pre reduced activity 180 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: GC2-LN5


title: Patient 17 Pre reduced activity 60 min after Leucine [Ribo-Seq]

description: ribosome protected RNA fragments


title: GC2-LN9


title: GC2-LN4


title: CPB004-MUF-01h

description: leukocyte expression profile from CPB004-MUF-01h


title: CPB004-MUF-00h

description: leukocyte expression profile from CPB004-MUF-00h


title: CPB004-CPB-01h

description: leukocyte expression profile from CPB004-CPB-01h


title: CPB004-CPB-end

description: leukocyte expression profile from CPB004-CPB-end


title: GC2-LN3


title: CPB004-MUF-12h

description: leukocyte expression profile from CPB004-MUF-12h

value: 12h into postoperative recovery


title: CPB004-CPB-00h

description: leukocyte expression profile from CPB004-CPB-00h


title: X_3

city: Mengzi

first: shuang

last: yang

address: Caoba street

institute: Institute of Sericulture and Apiculture, Yunnan Academy of Agriculture

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.
Raw data of fastq format were firstly processed through in-house perl scripts. Clean data were obtained by removing reads containing adapter, reads containing poly-N, and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequences duplication level of the clean data were calculated.
Genome_build: reference sequence used for read alignment.

organism: Galleria mellonella

source_name: antennae

growth_protocol: Newly emerged adult wax moths were used to maintain the stock culture. All G. mellonella larvae were reared on old combs in an incubator at 34 ± 1°C with 65 ± 5% relative humidity in constant darkness in the laboratory.

extract_protocol:
Total RNA was extracted from the antennae using TRIzol™ reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. Residual DNA in the total RNA was removed using DNase (Promega, Madison, WI, USA). The quality of RNA was assessed using 1% agarose gel electrophoresis.
The RNA-Seq library construction and Illumina sequencing of the samples (using the Illumina HiseqTM 2000 platform) were performed by Novogene Bioinformatics Technology Co. Ltd., Beijing, China.

treatment_protocol: For transcriptome sequencing, antennae (approximately 300 samples for each sex) were collected from freshly eclosed female and male moths. All collected antennae samples were immediately frozen in liquid nitrogen and then stored at -80°C until RNA extraction.

value: antennae

tag: developmental stage

value: adult

tag: Sex

value: male


title: X_2


title: GC2-LN2


title: X_1


title: BCG 3

city: Nanjing

first: Chen

last: Zhao

state: Jiangsu

address: 22nd Hankou Road

institute: Nanjing University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter;
(2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;
(3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12)
The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni
Genome_build: Homo_sapiens：GCF_000001405.38_GRCh38.p12
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: cell line

growth_protocol: The THP-1 cell line was maintained in medium 1640 supplemented with 10% (v/v) fetal calf serum, 2mM glutamine, 1mM sodium pyruvate, and 0.05mM 2-mercaptoethanol in a humidiﬁed 5% carbon dioxide atmosphere at 37°C.

extract_protocol:
The total RNA extraction was prepared from M.tb infected THP-1 cells with RNA Miniprep kit reagent as described by the manufacturer Vazyme biotech, Nanjing, China.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The THP-1 was differentiated for 24 h using a culture medium containing 40 ng/ml phorbol 12-myristate 13-acetate. The cells were then washed with fresh culture medium and incubated for 48 h. Rapidly grown M. tuberculosis H37Rv, H37Ra and BCG were pelleted (3,200 rpm, 10 min), washed twice with PBS (phosphate-buffered saline), and re-suspended in a THP-1 culture medium. Differentiated THP-1 cells were infected with Mycobacterium tuberculosis at a multiplicity of infection 5 (MOI) for 24h. The experiments were divided into four groups include; control, H37Rv, H37Ra, and BCG infected groups respectively.

value: monocyte

tag: treament

value: treated with PMA for 24h and infected BCG strain for 24h


title: CPB010-CPB-01h

description: leukocyte expression profile from CPB010-CPB-01h


title: CPB003-MUF-24h

description: leukocyte expression profile from CPB003-MUF-24h


title: C_3

value: female


title: BCG 2


title: CPB003-MUF-10h

description: leukocyte expression profile from CPB003-MUF-10h

value: 10h into postoperative recovery


title: CPB003-MUF-01h

description: leukocyte expression profile from CPB003-MUF-01h


title: C_2


title: GC1-LN2

value: lymph node

value: gastric cancer


title: C_1


title: GC2-LN1


title: BCG 1


title: H37Ra 3

value: treated with PMA for 24h and infected H37Ra strain for 24h


title: Patient 17 Pre reduced activity 0 baseline [Ribo-Seq]

description: ribosome protected RNA fragments

value: muscle biopsy


title: GC1-LN1


title: GC3-LN3


title: H37Ra 2


title: CPB003-MUF-00h

description: leukocyte expression profile from CPB003-MUF-00h

value: end of modified ultrafiltration

value: leukocyte


title: CPB003-CPB-end

description: leukocyte expression profile from CPB003-CPB-end


title: H37Ra 1


title: H37Rv 3

value: treated with PMA for 24h and infected H37Rv strain for 24h


title: CPB003-CPB-00h

description: leukocyte expression profile from CPB003-CPB-00h

value: before CBP


title: GC3-LN1


title: GC3-LN2


title: CPB003-CPB-01h

description: leukocyte expression profile from CPB003-CPB-01h

value: 1h into CPB


title: ZD9-Deg

city: hangzhou

first: zhilan

last: ye

state: zhejiang

address: yuhangtang road

institute: zhejiang university

description: Small RNA

data_processing:
Library strategy: Degradome sequencing
Raw sequencing reads were obtained using Illumina’s software to remove adaptors and low quality reads.
The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline.
The degradome reads were matched to transcriptome to generate the degradome density file. In addition, the targeted mRNA sequences of the miRNAs were predicted using TargetFinder software (http://targetfinder.org/). The overlapped mRNAs of the predicted target mRNAs and the mRNAs in degradome density file were considered as the target genes of the miRNAs.
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release-44/plants/fasta/hordeum_vulgare/dna
Supplementary_files_format_and_content: excel,expression profiles

organism: Hordeum vulgare

source_name: Hordeum vulgare L.

growth_protocol: Seeds were sterilized with 3% H2O2 for 30 min and rinsed three-times with deionized water, then soaked for 3 h at room temperature. A hydroponic experiment was carried out in a growth chamber at Zijingang Campus, Zhejiang University, Hangzhou, China (Hangzhou, 120.2° E, 30.5° N). After one week of germination, the uniform seedlings were selected for hydroponic incubation in 15-L black rectangular pots with aerated 1/5 Hoagland solution according to Ye et al (2017). The hydroponic solution's pH was adjusted to 5.8 using 1M HCl or NaOH, as required, and the solution was renewed every three days.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Poly(A) RNA is purified from plant total RNA(20ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Because of the 3′ cleavage product of the mRNA contains a 5′-monophosphate，the 5' adapters were ligated to the 5' end of the 3′ cleavage product of the mRNA by the RNA ligase. The next step is reverse transcription to make the first strand of cDNA with a 3′-adapter random primer. and size selection was performed with AMPureXP beads.Then the cDNA were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 15cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 200-400 bp. At last, we performed the 50bp single-end sequencing on an Illumina Hiseq 2500 (LC Bio, China) following the vendor's recommended protocol.

treatment_protocol: The two-leaf-old seedlings were subjected to K treatments consisting of two levels, 0.01mM (low K) and 1mM (normally used as control).

tag: cultivar

value: shoot


title: XZ153_T_7d_2

description: Small RNA

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release-44/plants/fasta/hordeum_vulgare/dna
Supplementary_files_format_and_content: excel,expression profiles

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA libraries according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: The two-leaf-old seedlings were subjected to K treatments consisting of two levels, 0.01mM (low K) and 1mM (normally used as control, CK).

value: low K tolerant

value: low K

value: 7 days


title: CPB002-MUF-28h

description: leukocyte expression profile from CPB002-MUF-28h

value: 28h into postoperative recovery


title: XZ153_T_7d_3

description: Small RNA


title: XZ153-Deg

description: Small RNA


title: GC3-LN12


title: GC1-LN3


title: H37Rv 1

value: monocyte


title: CPB002-MUF-08h

description: leukocyte expression profile from CPB002-MUF-08h

value: 8h into postoperative recovery


title: GC2-LN6


title: XZ153_T_7d_1

description: Small RNA


title: HEK293t KO

city: West Haven

first: Sarah

middle: A

last: Slavoff

state: Connecticut

address: Yale University West Campus-Building 600

department: Chemistry

institute: Yale University- West Campus

data_processing:
Basecalls were performed with CASAVA version 1.8.2
75bp paired end reads were aligned to the hg19 genome and GRCh37.p13 transcriptome using tophat version 2.0.12 with default parameters
Gene expression was quantified using cufflinks version 2.2.1 with the cuffdiff command using the GRCh37.p13 transcriptome as reference and default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file which contains FPKM values and statistical comparison between WT and KO gene expression

source_name: HEK293T cells with CRISPR knockout of alt-RPL36

growth_protocol: the cells were grown at 37 C/5% CO2 in DMEM supplemented with 10% FBS/1% Pen-strep

extract_protocol:
whole RNA was extracted from 1 T-25 flask using the Qiagen Rneasy Kit, according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: with CRISPR knockout of alt-RPL36


title: Control 3

value: treated with PMA for 24h

tag: cell line


title: XZ153_CK_7d_2

description: Small RNA

tag: phenotype

value: control


title: XZ153_CK_7d_3

description: Small RNA


title: XZ153_CK_7d_1

description: Small RNA


title: Control 1

tag: cell type


title: CPB002-CPB-end

description: leukocyte expression profile from CPB002-CPB-end

value: end of CPB


title: ZD9_T_7d_3

description: Small RNA

value: low K sensitive

tag: treatment


title: ESM1-NES

description:
Vector-NLS-NES.xlsx
22Rv1-P-NES

source_name: prostate cancer cells

value: 22Rv1 human prostatic carcinoma cell line

value: prostate epithelial cells

tag: genotype

value: ESM1-NES overexpression


title: H37Rv 2

value: treated with PMA for 24h and infected H37Rv strain for 24h


title: ZD9_T_7d_2

description: Small RNA


title: csrB csrC csrD pgaC pBR322-CsrB C

city: Gainesville

first: Anastasia

middle: Haley

last: Potts

state: FL

address: 1355 Museum Drive, Bldg. 981

department: Department of Microbiology and Cell Science

institute: University of Florida

data_processing:
Basecalls were made with Casava
Reads were aligned to the E. coli rRNA sequences with bowtie with default parameters and unaligned reads were retained
Reads were aligned to the E. coli genome and plasmid sequences with bowtie using default parameters.
Read counts per gene were calculated with Htseq Count
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Raw count matrix

organism: Escherichia coli K-12

source_name: bacterial cells

growth_protocol: Strains were grown in Kornberg medium (1.1% K2HPO4, 0.85% KH2PO4, 0.6% yeast extract, 0.5% glucose) to stationary phase (OD600 = 2.0)

extract_protocol: RNA samples were depleted or rRNA with Ribozero then libraries constructed with Kappa stranded library preparation kit (Roche cat. # 07277261001)

tag: strain

value: csrB csrC csrD pgaC

tag: plasmid


title: ESM1-NLS

description:
Vector-NLS-NES.xlsx
22Rv1-P-NLS

value: ESM1-NLS overexpression


title: CPB002-CPB-01h

description: leukocyte expression profile from CPB002-CPB-01h

value: 1h into CPB

value: leukocyte


title: csrB csrC csrD pgaC pBR322-empty C


title: CPB002-MUF-00h

description: leukocyte expression profile from CPB002-MUF-00h

value: end of modified ultrafiltration


title: csrA csrD pgaC pBR322-csrD C

value: csrA csrD pgaC


title: Liver5-RNAseq-HighTemperature

city: Barcelona

first: Dafni

last: Anastasiadi

address: Pg. Marítim de la Barceloneta 37-49

department: Renewable Marine Resources

country: Spain

institute: Institute of Marine Sciences-CSIC

data_processing:
RRBS-seq: RRBS raw reads were quality trimmed by the Timmomatic v. 0.32 with the following parameters SLIDINGWINDOW:4:15 MAXINFO:20:0.50 MINLEN:18
RRBS-seq: Trimmed reads were aligned to the reference genome dicLab v1.0c using BSMAP v. 2.90 in RRBS mode with the following parameters -D C-CGG -w 100 -v 0.08 -r 1 -p 4 -n 0 -s 12 -S 0 -f 5 -q 0 -u -V 2
RRBS-seq: Methylation calling was performed by the methratio.py python script that accompanies BSMAP.
Supplementary_files_format_and_content: RRBS-seq: Output of methratio.py was converted using awk to methylkit input. Tab-delimited files contain the coverage and the frequency of Cs (methylated cytosines) and of Ts (unmethylated cytosines) per CpG (chromosome, base, strand) covered
RNA-seq: RNA-seq reads were decontaminated by BBDuk (v. 37.61) using the following parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=30 minlen=23
RNA-seq: Reads were aligned to the genome by HISAT2 (v. 2.1.0) using the core hisat2 function with default parameters
RNA-seq: Reads were counted at the gene level by feature Counts of the Subread package
Supplementary_files_format_and_content: RNA-seq: For each tissue, one plain text file is provided with the feature counts per gene per sample
Genome_build: dicLab v1.0c (June 2012); http://seabass.mpipz.mpg.de/

organism: Dicentrarchus labrax

source_name: Liver

growth_protocol: Eggs fertilizated in a commercial hatchery and raised at the Aquarium facilities of the Institute of Marine Sciences (CSIC). Temperature increased from 13.5±1°Cto 20.5±1°C at a rate of ~0.5°C/day starting at 7 days post fertilization (dpf) and maintained until 68 dpf. After this period and until fish were 3 years old, they were maintained under natural conditions of temperature and photoperiod.

extract_protocol:
Trizol RNA extraction
mRNA-Seq sample preparation kit (TruSeq Stranded mRNA LT Sample Prep Kit, Illumina)

treatment_protocol: Tissues dissected were immediately snap frozen in liquid nitrogen. All samples were then kept at -80ºC until DNA/RNA extraction

tag: FISH

value: European sea bass

tag: age

value: 3-years old

tag: developmental temperature

value: HighTemperature (reared in aquarium facilities)

value: Liver


title: csrB csrC csrD pgaC pBR322-CsrD C


title: ZD9_CK_7d_3

description: Small RNA

tag: tissue

value: shoot

value: control

tag: time

value: 7 days


title: Vector-2

description:
Vector-NLS-NES.xlsx
22Rv1-P-vector

value: 22Rv1 human prostatic carcinoma cell line


title: CPB002-CPB-00h

description: leukocyte expression profile from CPB002-CPB-00h

tag: donor

tag: time point

value: before CBP


title: DM_B.TCGGAATGT

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

description: CD3e+CD8a+CD44-PD1- cells isolated from the spleen of 18 months old mouse (biological replicate 4)

data_processing:
Data were sequenced on HiSeq 2500 instrument (Illumina, San Diego, CA) using 41bpX11bp pair-end sequencing on two lanes. Second mate was used for sample demultiplexing, at which point individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outReadsUnmapped Fastx --outSAMstrandField All.
Gene expression was obtained using in-house scripts bassed on MACS and HTSeq (https://github.com/ctlab/quant3p).
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file that includes raw count data for each sample

source_name: CD3e+CD8a+CD44-PD1- cells

extract_protocol:
Mice were aged to 18 months of age in a SPF facility. Upon tissue harvest, mice were euthanized and perfused with 25 ml of cold PBS. The spleen was dissected and splenocytes isolated by using mechanical dissociation. The cell suspension was filtered through a 70 um filter to remove debris. Viable splenic CD3e+CD8a+CD44-PD1-, CD3e+CD8a+CD44+PD1- and CD3e+CD8a+PD1+ cells were sorted using BD Aria II cell sorter, and pelleted at 400 x g 10 min at +4 C. The cell pellet was resuspended in PBS + 0.04% BSA at 1000 cells/uL. mRNA was isolated directly from cell pellets with RNeasy Micro Kit (QIAGEN).
mRNA was isolated directly from cell pellets with RNeasy Micro Kit (QIAGEN) and cDNA synthesized using custom oligo-dT primer with a barcode and adaptor-linker sequence (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15). Samples were pooled based on Actb qPCR values, RNA-DNA hybrids degraded with acid-alkali treatment and a second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated with T4 ligase (NEB). After SPRI-beads clean-up (Agencourt AMPure XP, BeckmanCoulter). the mixture was PCR-enriched (12 cycles) and SPRI-purified yielding final strand-specific RNA-seq libraries.

tag: mouse genotype

value: wt

value: Splenic CD8 T cells


title: Liver4-RNAseq-HighTemperature


title: Control 2

value: monocyte

tag: treament

value: treated with PMA for 24h


title: csrA csrD pgaC pBR322-csrA C


title: ZD9_T_7d_1

description: Small RNA

tag: cultivar

value: low K sensitive

value: low K


title: ZD9_CK_7d_2

description: Small RNA


title: DM_B.GGTCCAGAT

description: CD3e+CD8a+CD44-PD1- cells isolated from the spleen of 18 months old mouse (biological replicate 3)


title: HEK293t WT

source_name: HEK293T cells

tag: cell line

tag: genotype/variation

value: WT


title: Liver3-RNAseq-HighTemperature


title: csrA csrD pgaC pBR322-empty C

value: csrA csrD pgaC


title: ZD9_CK_7d_1

description: Small RNA

tag: phenotype


title: csrB csrC pgaC pBR322-empty C

value: csrB csrC pgaC


title: DM_B.GCACATCTT

description: CD3e+CD8a+CD44-PD1- cells isolated from the spleen of 18 months old mouse (biological replicate 2)


title: XZ153_T_2d_3

description: Small RNA

value: low K tolerant

tag: treatment

value: 2 days


title: Liver2-RNAseq-HighTemperature

value: European sea bass

value: 3-years old

value: HighTemperature (reared in aquarium facilities)

value: Liver


title: XZ153_T_2d_2

description: Small RNA

value: shoot


title: Brain5-RNAseq-HighTemperature

source_name: Brain

value: Brain


title: XZ153_T_2d_1

description: Small RNA


title: csrA pgaC pBR322-empty C

tag: genotype

value: csrA pgaC


title: Liver1-RNAseq-HighTemperature


title: Brain4-RNAseq-HighTemperature


title: XZ153_CK_2d_3

description: Small RNA

value: control


title: Brain3-RNAseq-HighTemperature


title: XZ153_CK_2d_2

description: Small RNA


title: DM_A.TTGAGCCTT

description: CD3e+CD8a+CD44+PD1- cells isolated from the spleen of 18 months old mouse (biological replicate 4)

source_name: CD3e+CD8a+CD44+PD1- cells

tag: strain

value: wt

value: Splenic CD8 T cells


title: DM_A.TTCGCTGAT

description: CD3e+CD8a+CD44+PD1- cells isolated from the spleen of 18 months old mouse (biological replicate 3)


title: DM_B.AGCAATTCT

description: CD3e+CD8a+CD44-PD1- cells isolated from the spleen of 18 months old mouse (biological replicate 1)


title: DM_A.CCAGTTAGT

description: CD3e+CD8a+CD44+PD1- cells isolated from the spleen of 18 months old mouse (biological replicate 2)


title: WT pgaC pBR322-empty C

value: WT pgaC

tag: plasmid


title: DM_A.ACACGATCT

description: CD3e+CD8a+CD44+PD1- cells isolated from the spleen of 18 months old mouse (biological replicate 1)


title: csrB csrC csrD pgaC pBR322-CsrB B

value: csrB csrC csrD pgaC


title: Brain2-RNAseq-HighTemperature

tag: FISH


title: XZ153_CK_2d_1

description: Small RNA


title: Brain1-RNAseq-HighTemperature

tag: age


title: DM_B.CATGCTTAT

description: CD3e+CD8a+PD1+ cells isolated from the spleen of 18 months old mouse (biological replicate 4)

source_name: CD3e+CD8a+PD1+ cells


title: DM_B.AGTTGCTTT

description: CD3e+CD8a+PD1+ cells isolated from the spleen of 18 months old mouse (biological replicate 3)


title: ZD9_T_2d_3

description: Small RNA

value: low K sensitive

value: low K


title: csrD pgaC pBR322-empty C

value: csrD pgaC


title: Testis5-RNAseq-HighTemperature

source_name: Testis

tag: developmental temperature

value: Testis


title: CPB002-MUF-01h

description: leukocyte expression profile from CPB002-MUF-01h

value: 1h into postoperative recovery

tag: cell type

value: leukocyte


title: csrA csrD pgaC pBR322-csrD B

value: csrA csrD pgaC


title: ZD9_T_2d_2

description: Small RNA

tag: tissue

tag: time

value: 2 days


title: csrB csrC csrD pgaC pBR322-CsrD B


title: DM_A.AACTTGACT

description: CD3e+CD8a+PD1+ cells isolated from the spleen of 18 months old mouse (biological replicate 2)


title: ZD9_T_2d_1

description: Small RNA


title: csrA csrD pgaC pBR322-empty B


title: Testis3-RNAseq-HighTemperature

value: European sea bass

value: 3-years old

value: HighTemperature (reared in aquarium facilities)


title: csrA csrD pgaC pBR322-csrA B


title: ZD9_CK_2d_3

description: Small RNA

value: shoot


title: ZD9_CK_2d_2

description: Small RNA

value: control


title: Testis1-RNAseq-HighTemperature


title: csrB csrC csrD pgaC pBR322-empty B


title: csrD pgaC pBR322-empty B


title: Testis2-RNAseq-HighTemperature


title: ZD9_CK_2d_1

description: Small RNA


title: csrA pgaC pBR322-empty B

value: csrA pgaC


title: Muscle5-RNAseq-HighTemperature

source_name: Skeletal muscle

value: Skeletal muscle


title: OL_rep3 (RNA-seq)

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

data_processing:
Reads were aligned to the mm9 genome using TopHat v2.0.6 without providing a reference transcriptome.
Abundance of transcripts from the iGenomes hg19 RefSeq reference were measured using Cufflinks v2.0.2.
FPKMs were quantile normalized.
Genome_build: mm9
Supplementary_files_format_and_content: genes.fpkm_tracking files from cufflinks v2.0.2

source_name: oligodendrocyte progenitor cells

growth_protocol: OPCs were cultured as described previously, with the exception that SHH was not used for maintenance or differentiation (Najm et al., 2011).

extract_protocol:
10^6 cells were pelleted, resuspended in TRIzol, and frozen at -80 degrees Celsius. Total RNA was isolated using the Qiagen Rneasy Mini Kit (ThermoFisher #15596026), beginning with chloroform extraction and separation by PhaseLock gel tubes (5 Prime #2302830).
1ug of each sample was rRNA depleted (Ribo-Zero Gold, Illumina #MRZG12324), fragmented, and indexed using the TruSeq Stranded mRNA Library Preparation Kit (Illumina #RS-122-2103) per the manufacturer’s protocol.

treatment_protocol: Cells were plated and allowed to attach for 1hr prior to addition of compounds. T3 was added an hour after compound addition.

value: oligodendrocyte progenitor cells

value: oligodendrocytes differentiated using protocol from Najm et al., Nat Methods. 2011 Nov; 8(11):957–962.


title: OL_JQ1_rep1 (RNA-seq)

value: oligodendrocytes differentiated in the presence of JQ1 using protocol from Najm et al., Nat Methods. 2011 Nov; 8(11):957–962.


title: OL_JQ1_rep3 (RNA-seq)


title: CD45.1+CD3e+CD8a+ cells isolated from the spleen of 25 months old mouse (young donor CD8 T cells) [ALAW-4]

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v3.0.2)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v3.0.2)
barcode processing, Cell Ranger Single Cell Software Suite (v3.0.2)
single-cell 5′ gene counting , Cell Ranger Single Cell Software Suite (v3.0.2)
alignment, Cell Ranger Single Cell Software Suite (v3.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

extract_protocol:
Mice were aged to 3 or 24 months of age in a SPF facility. Upon tissue harvest, mice were euthanized and perfused with 25 ml of cold PBS. The spleen was dissected and splenocytes isolated by using mechanical dissociation. The cell suspension was filtered through a 70 um filter to remove debris. For cell transfer, total CD8 T cells were isolated from CD45.1 young mice using EasySep Mouse CD8+ T Cell Isolation Kit (Stemcell) [CD8 T cell purity was validated by flow cytometry as > 95%]. 1-month post transfer, viable splenic CD45.1+CD3e+CD8a+ and CD45.2+CD3e+CD8a+ cells were sorted using BD Aria II cell sorter, and pelleted at 400 x g 10 min at +4 C. The cell pellet was resuspended in PBS + 0.04% BSA at 1000 cells/uL.
For gene expression libraries (GEX), 50 ng of amplified cDNA was used for library preparation, consisting of fragmentation, end repair, A-tailing, adapter ligation and sample index PCR as per the manufacturer’s instructions. Libraries were sequenced on a NovaSeq S4 (300 cycle) flow cell, targeting 45,000 read pairs/cell. For TCR repertoire libraries, 2 uL of amplified cDNA underwent two rounds of Target Enrichment using nested primer pairs specific for mouse TCR constant regions. 50 ng of the target enrichment PCR product was used for library preparation, consisting of fragmentation, end repair, A-tailing, adapter ligation and sample index PCR as per the manufacturer’s instructions. Enriched libraries were sequenced on a NovaSeq S4 (300 cycle) flow cell, targeting 5,000 read pairs per cell.

value: wt

tag: tissue/cell type

value: Splenic CD8 T cells


title: OL_JQ1_rep2 (RNA-seq)


title: CD45.2+CD3e+CD8a+ cells isolated from the spleen of 25 months old mouse (old recipient CD8 T cells) [ALAW-3]

tag: mouse genotype


title: Muscle4-RNAseq-HighTemperature


title: Muscle3-RNAseq-HighTemperature


title: Testis4-RNAseq-HighTemperature

value: Testis


title: DM_A.AACGCATTT

description: CD3e+CD8a+PD1+ cells isolated from the spleen of 18 months old mouse (biological replicate 1)


title: Muscle2-RNAseq-HighTemperature


title: csrB csrC csrD pgaC pBR322-CsrB A

value: csrB csrC csrD pgaC


title: csrB csrC csrD pgaC pBR322-CsrD A


title: OPC_rep3 (RNA-seq)

value: OPCs grown using protocol from Najm et al., Nat Methods. 2011 Nov; 8(11):957–962.


title: csrB csrC pgaC pBR322-empty B

value: csrB csrC pgaC


title: CD45+ cells isolated from the spleen of 3-month-old wild type mice (samples pooled from 3 mice)

source_name: CD45+ cells from the spleen

extract_protocol:
Mice were aged to 3 or q7 months of age in a SPF facility. Upon tissue harvest, mice were euthanized and perfused with 25 ml of cold PBS. Peritoneal cavity was washed with 5 ml of PBS + 1% BSA and cells collected. The spleen was dissected and splenocytes isolated by using mechanical dissociation. The lungs and the liver were digested during 30 min at +37 C in DMEM + 0.5% BSA + 0.1% collagenase D. The cell suspension was filtered through a 70 um filter to remove debris, viable CD45+ cells sorted using BD Aria II cell sorter, and pelleted at 400 x g 10 min at +4 C. The cell pellet was resuspended in PBS + 0.04% BSA at 1000 cells/uL.
For gene expression libraries (GEX), 50 ng of amplified cDNA was used for library preparation, consisting of fragmentation, end repair, A-tailing, adapter ligation and sample index PCR as per the manufacturer’s instructions. Libraries were sequenced on a NovaSeq S4 (300 cycle) flow cell, targeting 45,000 read pairs/cell. For TCR and BCR repertoire libraries, 2 uL of amplified cDNA underwent two rounds of Target Enrichment using nested primer pairs specific for mouse TCR or BCR constant regions. 50 ng of the target enrichment PCR product was used for library preparation, consisting of fragmentation, end repair, A-tailing, adapter ligation and sample index PCR as per the manufacturer’s instructions. Enriched libraries were sequenced on a NovaSeq S4 (300 cycle) flow cell, targeting 5,000 read pairs per cell.

value: wildtype

value: CD45+ cells

value: spleen


title: OL_rep1 (RNA-seq)


title: OPC_rep2 (RNA-seq)


title: CD45+ cells isolated from the spleen of 17-month-old wild type mice (samples pooled from 3 mice)


title: Muscle1-RNAseq-HighTemperature

value: European sea bass

value: 3-years old

value: HighTemperature (reared in aquarium facilities)


title: csrA csrD pgaC pBR322-csrD A

value: csrA csrD pgaC


title: csrB csrC csrD pgaC pBR322-empty A


title: CD45+ cells isolated from peritoneal cavity of 17-month-old wild type mice (samples pooled from 3 mice)

source_name: CD45+ cells from peritoneal cavity

value: peritoneal cavity


title: Liver3-RRBS-HighTemperature

extract_protocol:
Phenol-Chlorofrom DNA extraction
RRBS library preparation using the Premium RRBS Kit from Diagenode (C02030037)

value: Liver


title: OPC_rep1 (RNA-seq)

value: oligodendrocyte progenitor cells


title: Liver2-RRBS-HighTemperature

extract_protocol:
Phenol-Chlorofrom DNA extraction
RRBS library preparation using the Premium RRBS Kit from Diagenode (C02030036)


title: WT pgaC pBR322-empty B

value: WT pgaC


title: csrA csrD pgaC pBR322-csrA A


title: csrA csrD pgaC pBR322-empty A


title: OL_S-JQ1_RNApolII (ChIP-seq)

data_processing:
The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) was used to remove adapter sequences and trim read ends using a quality score cutoff of 20.
ChIP-seq data were aligned to mm9 genome assemblies (retrieved from http://cufflinks.cbcb.umd.edu/igenomes.html), using Bowtie v0.12.9 (Langmead et al., 2009), allowing reads with ≤ 2 mismatches and discarding reads with > 1 reportable alignment ("-m 1" parameter).
Peaks were detected with MACS v1.4 (Zhang et al., 2008), using an aligned input DNA sample as control.
Genome_build: mm9
Supplementary_files_format_and_content: MACS called peaks

extract_protocol:
ChIPs were performed from 5x10^7 crosslinked cells as previously described (Schmidt et al., 2009).
Sequencing libraries were prepared as previously described (Schmidt et al., 2009).

tag: chip antibody

value: 8wg16 (Abcam ab817)

value: oligodendrocytes differentiated in the presence of (S)-JQ1 using protocol from Najm et al., Nat Methods. 2011 Nov; 8(11):957–962.


title: Liver1-RRBS-HighTemperature

extract_protocol:
Phenol-Chlorofrom DNA extraction
RRBS library preparation using the Premium RRBS Kit from Diagenode (C02030035)


title: CD45+ cells isolated from the lungs of 17-month-old wild type mice (samples pooled from 3 mice)

source_name: CD45+ cells from the lungs

value: lungs


title: OL_R-JQ1_RNApolII (ChIP-seq)

value: oligodendrocytes differentiated in the presence of (R)-JQ1 using protocol from Najm et al., Nat Methods. 2011 Nov; 8(11):957–962.


title: csrB csrC pgaC pBR322-empty A


title: CD45+ cells isolated from the liver of 3-month-old wild type mice (samples pooled from 3 mice)

source_name: CD45+ cells from the liver

value: liver


title: OPC_RNApolII (ChIP-seq)

value: OPCs grown using protocol from Najm et al., Nat Methods. 2011 Nov; 8(11):957–962.


title: Brain2-RRBS-HighTemperature

extract_protocol:
Phenol-Chlorofrom DNA extraction
RRBS library preparation using the Premium RRBS Kit from Diagenode (C02030033)

value: Brain


title: csrD pgaC pBR322-empty A

value: csrD pgaC


title: OPC_input control (ChIP-seq)


title: CD45+ cells isolated from the liver of 17-month-old wild type mice (samples pooled from 3 mice)

value: wildtype

value: CD45+ cells


title: CD45+ cells isolated from the lungs of 3-month-old wild type mice (samples pooled from 3 mice)


title: Brain1-RRBS-HighTemperature

extract_protocol:
Phenol-Chlorofrom DNA extraction
RRBS library preparation using the Premium RRBS Kit from Diagenode (C02030032)

value: European sea bass

value: 3-years old


title: CD45+ cells isolated from peritoneal cavity of 3-month-old wild type mice (samples pooled from 3 mice)


title: csrA pgaC pBR322-empty A

value: csrA pgaC


title: Testis3-RRBS-HighTemperature

extract_protocol:
Phenol-Chlorofrom DNA extraction
Custom RRBS library preparation with 100 ng of DNA, as in Klughammer et al., Cell 2015

value: HighTemperature (reared in aquarium facilities)

value: Testis


title: Testis2-RRBS-HighTemperature


title: WT pgaC pBR322-empty A


title: T02_Ctrl

city: Chengdu

first: Fanyuan

state: Sichuan

address: No.14, 3rd Section, Ren Min Nan Rd

department: Endodontics

institute: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence.
Filtered reads were mapped to mm10 reference genome by TopHat2.Cufflinks were used to assemble mapped reads and identify new genes.
Gene expression level was estimated by FPKM.Differential expession genes was analyzed by DESeq.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

source_name: Ctrl mice femurs

extract_protocol:
total RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
Libraries were prepared according to Illumina's instructions of RNA sample. Paired-end method was adopted for further processes.

treatment_protocol: To increase Wnt7b in bone we crossed 9.6kb DMP1-Cre mice and R26-Wnt7b mice. 9.6kb DMP1-Cre; R26-Wnt7b mice were set as OE mice meanwhile their littermates of R26-Wnt7b were controls (Ctrl). Owing to heterozygotes and homozygotes of OE mice didn’t show any different phenotypes all OE mice used in this study were homozygotes.

value: bone

value: Ctrl femurs free of cartilage and marrow cells

value: control


title: shRNA_essential_circRNA_screen_Day14_deep_sequencing_rep2

first: Pier Paolo

institute: University of Torino

data_processing:
Library strategy: DNA-Seq
For screening studies, DNA-Seq reads were trimmed, counted and analyzed with MAGeCK v0.5.8
For RNA-Seq, reads were aligned and quantified with Salmon v0.13.1 then normalized with DESeq2 v1.26.0
Genome_build: hg38
Supplementary_files_format_and_content: text files contain normalized read count data for each set of sequencing experiments

source_name: hepatocellular carcinomas

extract_protocol:
For gRNA/shRNA screening screening experiments, genomic DNA was extracted from screened cells using Qiagen Blood and Tissue Kit. For RNA-Seq, RNA was extract with Trizol
For gRNA/shRNA screening libraries, custom primers compatible with Illumina sequencing primers were used to amplified gRNA/shRNA sequences from the genome. For RNA-Seq, RNA libraries were prepared according to Illumina's protocol, conducted by the Molecular Biology Core Facilities at Dana-Farber Cancer Institute

value: hepatocellular carcinomas

value: Day 14


title: T01_Ctrl


title: shRNA_essential_circRNA_screen_Day14_deep_sequencing_rep1


title: T03_Ctrl


title: T03_OE

source_name: OE mice femurs

value: OE femurs free of cartilage and marrow cells

value: Wnt7b overexpression


title: Testis1-RRBS-HighTemperature


title: shRNA_essential_circRNA_screen_Day0_deep_sequencing_rep2

value: Day 0


title: T02_OE


title: shRNA_essential_circRNA_screen_Day0_deep_sequencing_rep1


title: Muscle2-RRBS-HighTemperature

value: Skeletal muscle


title: T01_OE


title: Muscle1-RRBS-HighTemperature


title: OL_rep2 (RNA-seq)

value: oligodendrocyte progenitor cells

value: oligodendrocytes differentiated using protocol from Najm et al., Nat Methods. 2011 Nov; 8(11):957–962.


title: Brain3-RRBS-HighTemperature

extract_protocol:
Phenol-Chlorofrom DNA extraction
RRBS library preparation using the Premium RRBS Kit from Diagenode (C02030034)

value: Brain


title: NT_1601

status: Public on Dec 05 2020

city: San Francisco

first: Srilaxmi

last: Nerella

state: CA

address: HSE1355A, 513 Parnassus ave

department: Department of Medicine

institute: UCSF

data_processing:
Adapter trimming on FASTQ - Cutadapt 1.2.1
Quality trimming on FASTQ - Sickle 1.29
Alignment - STAR 2.4.2a
Analysis - R package: DESeq2
Genome_build: Homo_sapiens.GRCh38.81

source_name: Human bronchial epithelial cells

extract_protocol:
Air-liquid-interface cultured human bronchial epithelial cells were harvested using Norgen Biotek lysis buffer (Cat. 47700) and stored at -80C until RNA extraction. RNA/DNA/Protein Purification Plus Kit (Norgen Biotek) was used for RNA extraction according to the manufacturer’s protocol.
NuGen Universal

value: Untreated

value: Non-targeting


title: NT_13_1828


title: 141KO_13_1721


title: 141KO_1721


title: 141KO_1601


title: NT_1721


title: NT_13_1601


title: 141KO_1828


title: NT_1828


title: 141KO_13_1734


title: NCI-H929 cells, transfected with control lentivirus sponges-3

type: RNA

first: Tian

last: Xia

description: Gene expression data from NCI-H929 cells transfected with control lentivirus sponges

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

label: biotin

source_name: NCI-H929 cells

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

growth_protocol: NCI- H929 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum in an atmosphere at 37°C with 5% CO2.

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

treatment_protocol: PRMT5-shRNA lentivirus were prepared by the co-transfection of 293T cells with pLKO.1 and packaging plasmids pMD2G and psPAX2. 48 h after transfection, the viral supernatants were collected. The NCI-H929 cells were incubated with viral supernatants in the presence of polybrene. The positive cells were selected with 1μg/mL puromycin. Lentivirus sponge PRMT5-downregulated NCI-H929 and normal NCI-H929 were collected at room temperature (RT) at the same timepoint.

tag: transfected with

value: control lentivirus sponges


title: NCI-H929 cells, transfected with PRMT5 downregulating lentivirus sponges-3

description: Gene expression data from NCI-H929 cells transfected with PRMT5 downregulating lentivirus sponges

tag: cell line

value: PRMT5 downregulating lentivirus sponges


title: 141KO_13_1601


title: NCI-H929 cells, transfected with control lentivirus sponges-2


title: NCI-H929 cells, transfected with PRMT5 downregulating lentivirus sponges-2


title: 141KO_13_1828


title: NT_13_1734


title: Muscle3-RRBS-HighTemperature

value: European sea bass

value: 3-years old

value: HighTemperature (reared in aquarium facilities)


title: NT_13_1721


title: BulkATAC_MCF10A-RepB

first: Michael

middle: Ryan

last: Corces

address: 1650 Owens Street

department: Neurological Disease

institute: Gladstone Institute

description:
Bulk ATAC-seq of MCF10A cells. Replicate B.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best

data_processing:
Raw sequencing data was converted to FASTQ format using cellranger-atac mkfastq (10x Genomics, version 1.0.0)
Single-cell ATAC-seq reads were aligned to the hg19 reference genome (https://support.10xgenomics.com/single-cell-atac/software/downloads/latest) and quantified using cellranger-count (10x Genomics, version 1.0.0)
Genotypes used to perform demuxlet were determined as follows for each cell line: Bulk ATAC-seq FASTQ files were processed and aligned using PEPATAC (http://code.databio.org/PEPATAC/) as described previously. Peaks were identified using MACS2 and a union set of variable-width accessible regions was identified using bedtools merge (version 2.26.0). These accessible regions were genotyped across all samples using samtools mpileup (version 1.5) and Varscan mpileup2snp (version 2.4.3) with the following parameters “--min-coverage 5 --min-reads2 2 --min-var-freq 0.1 --strand-filter 1 --output-vcf 1”. All positions containing a single nucleotide variant were compiled into a master set and then each cell line was genotyped at those specific single-base locations using samtools mpileup. The allelic depth at each position was converted into a quaternary genotype (homozygous A, heterozygous AB, homozygous B, or insufficient data to generate a confident call). Then, for each cell line, inferred genotype probabilities were created based on those quaternary genotypes and a VCF file was created for input to demuxlet using recommended parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Processed scATAC-seq data is provided as an R SummarizedExperiment object. This object contains row and column metadata corresponding to the individual cells and peak regions of chromatin accessibility. This object also contains a sparse matrix representing Tn5 transposase insertion counts per peak region:
CellLine_HighLoading.fragments.tsv.gz:  fragments
CellLine_LowLoading.fragments.tsv.gz:  fragments
CellLine_LowLoading-MotifMatrix-SE.rds:  SummarizedExperiment RDS (R data file)
CellLine_LowLoading-PeakMatrix-SE.rds:  SummarizedExperiment RDS (R data file)
CellLine_HighLoading-MotifMatrix-SE.rds:  SummarizedExperiment RDS (R data file)
CellLine_HighLoading-PeakMatrix-SE.rds:  SummarizedExperiment RDS (R data file)
demuxlet_CellLineHigh_mergedBAMs.best:  demuxlet.best
demuxlet_CellLineLow_mergedBAMs.best:  demuxlet.best

source_name: Immortalized cell line

extract_protocol:
Cultured cells were viably cryopreserved in aliquots of 100,000 cells using 100 ul of BAMBANKER freezing media (Wako Chemicals 302-14681) so that scATAC-seq could be performed on all cells at the same time. For each cell line, cells were thawed via the addition of 1 mL ice-cold resuspension buffer (RSB) [10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2] containing 0.1% Tween-20 (RSB-T). Cells were pelleted in a fixed-angle rotor at 300 RCF for 5 minutes at 4°C. The supernatant was removed, and the pellet was resuspended in 100 uL of ice-cold lysis buffer (RSB containing 0.1% Tween-20, 0.1% NP-40, and 0.01% digitonin) and incubated on ice for 3 minutes. To dilute lysis, 1 mL of chilled RSB-T was added to each tube and the cells were pelleted as before. The supernatant was removed and the pelleted nuclei were resuspended in Diluted Nuclei Buffer (10x Genomics). The nuclei stock concentration was determined for each cell line using Trypan Blue and a total of 5,000 nuclei from each cell line were pooled together and loaded into the 10x Genomics scATAC-seq (v1) transposition reaction.
scATAC-seq library preparation was performed as recommended by the manufacturer.

tag: source

value: ATCC

tag: growth media

value: DMEM/F12, 5% horse serum, 0.02 ug/ml human EGF, 0.5 ug/ml hydrocortisone, 0.1 ug/ml Cholera toxin, 10 ug/ml insulin from bovine pancreas, penicillin/streptomycin


title: BulkATAC_K562-RepB

description:
Bulk ATAC-seq of K562 cells. Replicate B.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best

value: RPMI-1640, 10% FBS, penicillin/streptomycin


title: BulkATAC_MCF7-RepA

description:
Bulk ATAC-seq of MCF7 cells. Replicate A.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best

value: EMEM, 10% FBS, penicillin/streptomycin


title: BulkATAC_T24-RepA

description:
Bulk ATAC-seq of T24 cells. Replicate A.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best

value: McCoy's 5A, 10% FBS, penicillin/streptomycin


title: BulkATAC_T24-RepB

description:
Bulk ATAC-seq of T24 cells. Replicate B.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best


title: BulkATAC_MCF10A-RepA

description:
Bulk ATAC-seq of MCF10A cells. Replicate A.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best


title: BulkATAC_THP1-RepA

description:
Bulk ATAC-seq of THP1 cells. Replicate A.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best


title: BulkATAC_THP1-RepB

description:
Bulk ATAC-seq of THP1 cells. Replicate B.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best


title: BulkATAC_MCF7-RepB

description:
Bulk ATAC-seq of MCF7 cells. Replicate B.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best


title: BulkATAC_K562-RepA

description:
Bulk ATAC-seq of K562 cells. Replicate A.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best


title: BulkATAC_Jurkat-RepB

description:
Bulk ATAC-seq of Jurkat cells. Replicate B.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best

value: Jurkat


title: BulkATAC_Jurkat-RepA

description:
Bulk ATAC-seq of Jurkat cells. Replicate A.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best


title: BulkATAC_HT1080-RepB

description:
Bulk ATAC-seq of HT1080 cells. Replicate B.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best

value: DMEM, 10% FBS, penicillin/streptomycin


title: BulkATAC_HT1080-RepA

description:
Bulk ATAC-seq of HT1080 cells. Replicate A.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best


title: BulkATAC_HeLa-RepA

description:
Bulk ATAC-seq of HeLa cells. Replicate A.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best

value: HeLa


title: BulkATAC_GM12878-RepB

description:
Bulk ATAC-seq of GM12878 cells. Replicate B.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best

value: Coriell


title: BulkATAC_HeLa-RepB

description:
Bulk ATAC-seq of HeLa cells. Replicate B.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best


title: NCI-H929 cells, transfected with PRMT5 downregulating lentivirus sponges-1

description: Gene expression data from NCI-H929 cells transfected with PRMT5 downregulating lentivirus sponges


title: BulkATAC_GM12878-RepA

description:
Bulk ATAC-seq of GM12878 cells. Replicate A.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best


title: BulkATAC_293T-RepA

description:
Bulk ATAC-seq of 293T cells. Replicate A.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best


title: BulkATAC_293T-RepB

description:
Bulk ATAC-seq of 293T cells. Replicate B.
demuxlet_CellLineHigh_mergedBAMs.best
demuxlet_CellLineLow_mergedBAMs.best


title: graft_donor

city: Oxford

first: Lucy

last: Garner

address: Experimental Medicine, Level 5, John Radcliffe Hospital

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
BCL files were converted to FASTQ files using cellranger mkfastq (v2.2.0)
Alignment, filtering, barcode counting and UMI counting were performed using cellranger count (v2.2.0)
Single-cell V(D)J sequences and annotations were generated using cellranger vdj (v2.2.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_gene_bc_matrices_h5.h5 output file from cellranger count (v2.2.0) - unfiltered gene-barcode matrices containing all barcodes in HDF5 format. filtered_contig_annotations.csv output file from cellranger vdj (v2.2.0) - high-level annotations of each high-confidence, cellular contig.

source_name: small intestine

extract_protocol:
Small intestinal biopsies were collected at the time of endoscopy and transported in R10 (RPMI-1640 [Lonza] + 10% FCS [Sigma-Aldrich] + 1% penicillin/streptomycin [Sigma-Aldrich]), before cryopreservation in freezing medium (10% DMSO [Sigma-Aldrich], 90% FCS [Sigma-Aldrich]). When required, samples were rapidly thawed in a 37°C water bath and washed in 20 ml R10 before tissue dissociation. Duodenal samples were incubated in R10 media with 1 mg/ml Collagenase D (Roche) and 100 μg/ml DNase (Thermo Fisher Scientific) for one hour in a shaking incubator at 37°C. Biopsies were then dissociated by vigorous agitation using a GentleMACS Dissociator (Miltenyi Biotec), then strained through a 70 μm filter. Cells were washed with R10 media. Mononuclear cells were isolated on a discontinuous 70% and 35% Percoll gradient (GE Healthcare) by centrifugation at 700 g for 20 minutes without brake. Mononuclear cells were collected from the interface and washed in R10. Live CD3+ graft donor T cells were sorted by FACS.
scRNAseq libraries were generated using 10x Genomics Chromium Single Cell V(D)J Reagents Kits (v1 Chemistry) following manufacturer’s instructions.

tag: donor

tag: disease state

value: intestinal transplant recipient


title: 294167

data_processing:
BCL files were converted to FASTQ files using bcl2fastq (v2.20.0)
Reads were trimmed using Trimmomatic (v0.36)
Trimmed reads were aligned to GRCh38 using STAR (v2.5.3a; --outFilterMismatchNoverLmax 0.04 --outFilterType BySJout --outMultimapperOrder Random)
Alignments were filtered using Samtools v1.6 to retain only primary alignments and properly paired reads
Ensembl gene counts were generated using featureCounts (v1.6.0; -C -B -p)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw gene counts: Ensembl gene IDs and raw gene counts for all samples and genes

extract_protocol:
Small intestinal biopsies were collected at the time of endoscopy and transported in R10 (RPMI-1640 [Lonza] + 10% FCS [Sigma-Aldrich] + 1% penicillin/streptomycin [Sigma-Aldrich]), before cryopreservation in freezing medium (10% DMSO [Sigma-Aldrich], 90% FCS [Sigma-Aldrich]). When required, samples were rapidly thawed in a 37°C water bath and washed in 20 ml R10 before tissue dissociation. Duodenal samples were incubated in R10 media with 1 mg/ml Collagenase D (Roche) and 100 μg/ml DNase (Thermo Fisher Scientific) for one hour in a shaking incubator at 37°C. Biopsies were then dissociated by vigorous agitation using a GentleMACS Dissociator (Miltenyi Biotec), then strained through a 70 μm filter. Cells were washed with R10 media. Mononuclear cells were isolated on a discontinuous 70% and 35% Percoll gradient (GE Healthcare) by centrifugation at 700 g for 20 minutes without brake. Mononuclear cells were collected from the interface and washed in R10. Single cells were index-sorted into 96-well plates with one cell per well in 2.3 μl lysis buffer (0.8% (vol/vol) Triton X-100 and 2 U/μL RNase inhibitor).
Smart-seq2 libraries were generated following the published protocol (S. Picelli et al., Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc. 9, 171–181 (2014)) with External RNA Controls Consortium RNA (1:100,000) added prior to sequencing.

value: CD8+ T cell

tag: cd103 status


title: 295177


title: 295179


title: 296108


title: 296191


title: 295120


title: 294165


title: 292143


title: 292156


title: 291131


title: 291168


title: 293155


title: 292141


title: 294132


title: 293144


title: 290180


title: 290117


title: 289105


title: 289192


title: 293153


title: 290119


title: 288190


title: 287178


title: 288109


title: 287176


title: 286133


title: 285154


title: 286164


title: 285152


title: 284157


title: 284142


title: 285145


title: 286166


title: 283169


title: 283128


title: 289107


title: 283130


title: 282181


title: 282118


title: 284140


title: 291129


title: 282116


title: 287121


title: 280189


title: 279177


title: 279122


title: 281106


title: 281193


title: 278134


title: 278165


title: 278163


title: 277153


title: 276158


title: 277151


title: 277146


title: 275170


title: 276139


title: 275129


title: 275127


title: 274115


title: 274182


title: 274117


title: 281104


title: 280110


title: 279175


title: 272188


title: 272111


title: 271176


title: 271123


title: 271174


title: 269152


title: 270135


title: 270164


title: NCI-H929 cells, transfected with control lentivirus sponges-1

description: Gene expression data from NCI-H929 cells transfected with control lentivirus sponges


title: 269147


title: 276141


title: 268140


title: 268138


title: 267171


title: 268159


title: 267128


title: 267126


title: 273105


title: 273194


title: 273103


title: 266114


title: 265195


title: 264112


title: 270162


title: 265102


title: 266116


title: 265104


title: 263173


title: 264187


title: 269150


title: 263175


title: 262163


title: 263124


title: 261151


title: 261149


title: 260160


title: 261148


title: 260139


title: 262136


title: 260137


title: 258184


title: 259127


title: 259125


title: 259172


title: 257196


title: 257103


title: 258113


title: 256186


title: 257101


title: 256101


title: 262161


title: 255174


title: 255113


title: 254125


title: 253137


title: 254162


title: 254172


title: 253150


title: 252149


title: 251126


title: 251161


title: 250173


title: 250124


title: 252148


title: 251136


title: 258115


title: 253160


title: 249185


title: 250114


title: 248185


title: 249102


title: 249112


title: 248102


title: 247173


title: 246171


title: 247114


title: 246161


title: 246126


title: 245138


title: 244150


title: 245159


title: 245149


title: 252138


title: 244147


title: 243162


title: 244137


title: 243125


title: 242123


title: 242113


title: 243135


title: 242174


title: 241186


title: 241101


title: 240103


title: 239184


title: 238172


title: 241111


title: 239115


title: 238170


title: 237160


title: 237158


title: 236151


title: 237139


title: 236148


title: 235163


title: 233187


title: 234124


title: 235134


title: 234122


title: 234175


title: 236146


title: 233112


title: 231183


title: 233110


title: 232104


title: 231116


title: 229159


title: 230128


title: 230169


title: 230171


title: 229157


title: 229140


title: 228152


title: 227164


title: 228145


title: RNA-seq aged CLP rep2

city: Minato-ku

first: Atsushi

last: Iwama

state: Tokyo

address: 4-6-1, Shirokanedai

department: Center for Stem Cell Biology and Regenerative Medicine

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

data_processing:
alignment:TopHat2 (version 2.0.13; with default parameters) and Bowtie2 (version 2.1.0) were used for alignment to the reference mouse genome (mm10 from the University of California, Santa Cruz Genome Browser;) with annotation data from iGenomes (Illumina)
Row count for each gene symbol are generated by StringTie
Data normalization:DESeq2
DESeq2 were used to perform statistical analysis for differentially expressed genes
Genome_build: mm10

source_name: 20 month common lymphoid progenitor

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro Kit (Qiagen)
Total RNA were subjected to reverse transcription and amplification with a SMARTer Ultra Low Input RNA Kit for Sequencing (Clontech). After sonication with an ultrasonicator (Covaris), the libraries for RNA-seq were generated from fragmented DNA with 8 cycles of amplification using a NEB Next Ultra DNA Library Prep Kit (New England BioLabs). After the libraries were quantified using the Bioanalyzer (Agilent), samples were subjected to sequencing with Hiseq1500 (Illumina) and 61 cycles of the sequencing reactions were performed.

value: Murine bone marrow derived CLPs

tag: surface markers

value: IL-7+ Lin- Sca-1 low c-kit low

tag: strain


title: RNA-seq aged CLP rep1

tag: age


title: Ezh2 KO HSC

data_processing:
alignment:TopHat2 (version 2.0.13; with default parameters) and Bowtie2 (version 2.1.0) were used for alignment to the reference mouse genome (mm10 from the University of California, Santa Cruz Genome Browser;) with annotation data from iGenomes (Illumina)
Row counts for each gene symbol are generated by StringTie
Normalization and statistical analysis were performed using DEGES-edgeR of TCC package, and 448 genes were selected using cutoff of q<0.05
For making tdf file, bedtools genomecov was used to make bedgraph file and
Genome_build: mm10

source_name: Ezh2 knock out hematopoietic stem cell

treatment_protocol: To generate a gene set upregulated in Ezh2-deficient HSCs, BM cells (1-5x106) from Cre-ERT;Ezh2+/+ and Cre-ERT;Ezh2fl/fl CD45.2 mice were transplanted into lethally irradiated CD45.1 recipient mice. Ezh2 was deleted by intraperitoneal injection of 100 μl of tamoxifen (10 mg/ml) a day for 5 consecutive days as previously described (Mochizuki et al., Blood 2015). HSCs (CD150+CD48–CD34–Flt3–LSK) were purified from recipient mice 1 months after tamoxifen injection, and were subjected to RNA-seq analysis.

tag: genotyping

value: Ezh2 Δ/Δ CreERT+/-

value: Lin- Sca-1+ c-kit+  CD34- CD150+ CD48- Flt3-


title: WT_HSC

source_name: WT hematopoietic stem cell

value: Ezh2 +/+ CreERT+/-


title: 235136

tag: cell type


title: 226176


title: RNA-seq aged MEP rep2

source_name: 20 month megakaryocyte-erythrocyte progenitors

value: Murine bone marrow derived MEPs

value: IL-7- Lin- Sca-1- c-kit+ FcgR- CD34-


title: RNA-seq aged GMP rep2

source_name: 20 month granulocyte-macrophage progenitors

value: Murine bone marrow derived GMPs

value: IL-7- Lin- Sca-1- c-kit+ FcgR+ CD34+


title: RNA-seq aged GMP rep1


title: RNA-seq aged MEP rep1


title: 226123


title: 225188


title: 232195


title: RNA-seq aged MPP4 rep2

source_name: 20 month multipotent progenitor 4s

value: Murine bone marrow derived MPP4s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150- CD48+ Flt3+


title: 225111


title: 225109


title: RNA-seq aged MPP3 rep2

source_name: 20 month multipotent progenitor 3s

value: Murine bone marrow derived MPP3s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150- CD48+ Flt3-


title: 223182


title: 224105


title: RNA-seq aged MPP3 rep1


title: RNA-seq aged MPP4 rep1


title: 224194


title: 223117


title: 227133


title: 222170


title: RNA-seq aged MPP1 rep1

source_name: 20 month multipotent progenitor 1s

value: Murine bone marrow derived MPP1s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150+ CD48- Flt3-


title: 227135

value: intestinal transplant recipient


title: RNA-seq aged HSC rep1

source_name: 20 month hematopoietic stem cells

value: Murine bone marrow derived HSCs

value: IL-7- Lin- Sca-1+ c-kit+  CD34- CD150+ CD48- Flt3-


title: RNA-seq aged HSC rep2


title: 222129

value: CD8+ T cell


title: 226121


title: 221158


title: RNA-seq young CLP rep2

source_name: 10 week common lymphoid progenitor

value: Murine bone marrow derived CLPs

value: IL-7+ Lin- Sca-1 low c-kit low


title: 222168


title: 221156


title: RNA-seq young CLP rep1


title: 220153


title: RNA-seq young MEP rep1

source_name: 10 week megakaryocyte-erythrocyte progenitors


title: RNA-seq young MEP rep2


title: 221141


title: 220146


title: RNA-seq aged MPP2 rep2

source_name: 20 month multipotent progenitor 2s

value: Murine bone marrow derived MPP2s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150+ CD48+ Flt3-


title: RNA-seq young GMP rep2

source_name: 10 week granulocyte-macrophage progenitors


title: 220144


title: RNA-seq aged MPP2 rep1


title: RNA-seq young MPP4 rep2

source_name: 10 week multipotent progenitor 4s


title: RNA-seq aged MPP1 rep2


title: RNA-seq young GMP rep1


title: 219165


title: 219134


title: RNA-seq young MPP3 rep2

source_name: 10 week multipotent progenitor 3s