title: No_Fe_with_Zn_shoot3 (Replication 3)

city: new delhi

first: M G

last: MALLIKARJUNA

address: Indian Council of Agricultural Research

department: Division of Genetics

country: India

institute: ICAR-Indian Agricultural Research Institute

hyb_protocol: Array hybridizations were carriedout using the GeneChip® Hybridization, Wash, and Stain Kit as per usuer manual.

scan_protocol: GeneChips® were scanned using the GeneChip® Fluidics Station 450 (scanning on Affymetrix GSC3000)

data_processing:
The raw CEL were imported into the R platform using affy package. The GeneChip® Robust Multiarray Average algorithm was used for background correction, normalization, and probe set summarization. The arrayQualityMetrics package was employed to generate microarray quality metrics reports and linear modelling of microarray data and identification of DEGs was performed with limma package.
p-value of <0.05 and fold change value of >2.0

label: biotin

organism: Zea mays

source_name: 12 DAT old maize shoot (iron starvation)

label_protocol: ~300 ng of total RNA was biotin-labeled for GeneChip® analysis  as per manufacturer's guidelines

growth_protocol: Plants are grown in hydroponic solution at National Phytotron Facility, IARI, New Delhi. The plant are grown in hydroponic solution in complete medium, under Zn starvation, Fe starvation and both Fe an Zn starvation

extract_protocol: RNeasy Mini Kit (Qiagen, Hilden, North Rhine-Westphalia, Germany) was used to isolated total RNA from control and stress treated roots and shoots  as per to manufacturer’s guidelines

treatment_protocol: Experiment was designed as a two-factor experiment with the four possible treatments among iron and zinc combination viz., 1) +Fe+Zn, 2) +Fe–Zn, 3) –Fe+Zn and 4) –Fe–Zn

value: shoot;

tag: treatment (nutrient solution)

value: hydroponic solution lacking Iron;

tag: time point

value: after 12 days of transplantation to nutrient solution


title: Mouse_thyroid_wild-type_rep2

status: Public on Jan 04 2021

type: RNA

city: Greifswald

first: Janine

last: Golchert

address: Felix-Hausdorff-Str. 8

department: Department of Functional Genomics

country: Germany

institute: University Medicine Greifswald

hyb_protocol: 2.5 µg of fragmented and biotinylated cDNA were hybridized for 16 hr at 45°C on GeneChip Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing:
Quality of hybridizations was assessed using Expression Console software and microarray data were analyzed using Rosetta Resolver software including RMA normalization.
affymetrix-algorithm-name = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label: Biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Biotinylated cDNA were prepared according to the GeneChip® Whole Transcript PLUS Reagent Kit manual starting from 200 ng total RNA.

extract_protocol: Extraction of total RNA was performed with TRIzol reagent and homogenization in a bead mill dismembrator. After purification of total RNA, quality control was performed using an Agilent 2100 Bioanalyzer.

treatment_protocol: Ctsk-/-/Mct8-/y/Mct10-/- was generated by crossbreeding sexually mature mice at the age of 6 to 8 weeks to generate homozygous littermates. Thyroid tissue of male mice at 5 to 8 months of age was isolated and snap-frozen in liquid nitrogen.

tag: strain background

tag: genotype/variation

value: wild type

tag: tissue

value: thyroid tissue


title: Mouse_thyroid_wild-type_rep3


title: RNA_FE1

type: SRA

city: xiamen

first: kunzhao

last: du

address: jimei

country: China

institute: huaqiao university

description:
RNA_FE1 represents the Fto(f/f，Emx1-cre) sample biological repeat 1 of RNA-seq
RNA-seq_ read_count.txt
RNA-seq_ RPKM.txt

library_source: transcriptomic

data_processing:
For RNA-seq, In first step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reads mapping to the reference genome was performed.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool,and three sets of raw reads were obtained.
For Ribo-seq, Ribo-seq used TopHat2 for genome mapping.
Quantification of mapped results to gene level was carried out using HTSeq.
For samples with biological replicates, DESeq2 R package (1.14.1) was used for differential expression analysis. DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution.
Genome_build: mm10
Supplementary_files_format_and_content: Ribo-seq_ read_count.txt include raw gene count for each Sample in Ribo-seq
RNA-seq_ read_count.txt include raw gene count for each Sample in RNA-seq
Ribo-seq_ FPKM.txt include FPKM values for each Sample in Ribo-seq
Ribo-seq_ RPKM.txt include RPKM for each Sample in RNA-seq

source_name: cerebral cortex

extract_protocol:
For RNA-seq, cerebral cortices of mice were removed, and RNA was harvested using Trizol reagent.NEBNext® UltraTM RNA Library Prep Kit for Illumina® (Cat#E7530L) was used with 1 ug of total RNA for the construction of sequencing libraries.  For Ribo-Seq, three groups of E15.5 mouse cerebral cortices were rapidly washed twice in ultra-pure water, and grind thoroughly with liquid nitrogen to powder. Sample was treated with specific lysis buffer with cycloheximide (50mg/mL) to acquire the lysate. Concentration of the lysate was measured by the NanoDrop™ 2000 Spectrophotometer. To digest the RNA other than RPFs, cell or tissue lysate was treated with unspecific endoribonuclease RNase I. Isolation of monosomes was performed by size-exclusion chromatography with MicroSpin S-400 HR columns. The RNA samples were then treated with rRNA depletion kit to deplete the samples of as much rRNA contamination as possible before PAGE purification of the relatively short (20~38 nt) RPFs. Following PAGE purification, the both ends of RPF were phosphorylated and ligated with 5’ and 3’ adapters respectively. Then the fragments were reversely transcribed to the cDNAs and amplified by PCR. After library construction, the concentration of library was measured by The Qubit® 2.0 Fluorometer and adjusted to 1ng/uL. Agilent 2100 Bioanalyzer was deployed to examine the insert size of the acquired library. At last, the accurate concentration of cDNA library was again examined using qPCR. Once the insert size and concentration of the library was identical, the samples can then be subjected for sequencing. Raw data (raw reads) of FASTQ format were firstly processed through cut adapt.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: cerebral cortex

tag: age

value: embryonic day 15.5

tag: genotype

value: Fto(f/f, Emx1-cre)

tag: rna fraction

value: total RNA


title: case.no6_CC

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

department: Pathology

country: South Korea

institute: Asan Medical Center

data_processing:
Sequenced reads were removed low quality and adapter sequence before analysis. Then th raw RNA-seq data were analyzed using TCGA RNAseq RSEMv2 pipeline.
Mapping by MapSplice v2.2.1 and gene expression estimation after filtering by RSEM v1.3.0, and fixed upper quartile normaliztion for gene expression.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file include column head with sample name, and row name with gene symbol, and upper quartile normalized log2 values for each sample.

organism: Homo sapiens

source_name: gestational trophoblastic neoplasm

extract_protocol:
Total RNA was extracted using Trizol reagent from formalin-fixed parffin-embedded tissue. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina protocols.
RNA-seq was performed using Illumina HiSeq 2500 plafform.

treatment_protocol: formalin-fixed and paraffin-embedded tissue

value: tumor

tag: tissue type

value: choriocarcinomas (CC)


title: Mouse_thyroid_knockout_rep1

value: Ctsk-/-/Mct8-/y/Mct10-/- knockout


title: No_Fe_No_Zn_shoot3 (Replication 3)

source_name: 12 DAT old maize shoot (iron and zinc starvation)

value: hydroponic solution lacking both iron and zinc;


title: No_Fe_No_Zn_shoot1 (Replication 1)


title: RNA_ME1

description:
RNA_ME1 represents the Mettl3(f/f，Emx1-cre) sample biological repeat 1 of RNA-seq
RNA-seq_ read_count.txt
RNA-seq_ RPKM.txt

value: Mettl3(f/f, Emx1-cre)


title: RNA_ME2

description:
RNA_ME2 represents the Mettl3(f/f，Emx1-cre) sample biological repeat 2 of RNA-seq
RNA-seq_ read_count.txt
RNA-seq_ RPKM.txt


title: No_Fe_with_Zn_shoot1 (Replication 1)


title: case.no4_ETT

value: epithelioid trophoblastic tumors (ETT)


title: Mouse_thyroid_knockout_rep2


title: No_Fe_with_Zn_shoot2 (Replication 2)


title: No_Fe_No_Zn_shoot2 (Replication 2)


title: RNA_WT3

description:
RNA_WT3 represents the wild-type sample biological repeat 3 of RNA-seq
RNA-seq_ read_count.txt
RNA-seq_ RPKM.txt


title: case.no10_ETT


title: case.no7_PSTT

value: placental site trophoblastic tumors (PSTT)


title: RNA_WT1

description:
RNA_WT1 represents the wild-type sample biological repeat 1 of RNA-seq
RNA-seq_ read_count.txt
RNA-seq_ RPKM.txt


title: case.no5_PSTT


title: RNA_WT2

description:
RNA_WT2 represents the wild-type sample biological repeat 2 of RNA-seq
RNA-seq_ read_count.txt
RNA-seq_ RPKM.txt


title: RNA_ME3

description:
RNA_ME3 represents the Mettl3(f/f，Emx1-cre) sample biological repeat 3 of RNA-seq
RNA-seq_ read_count.txt
RNA-seq_ RPKM.txt


title: RIBO_FE3

description:
RIBO_FE3 represents the Fto(f/f，Emx1-cre) sample biological repeat 3 of ribo-seq
Ribo-seq_ read_count.txt
Ribo-seq_ FPKM.txt

data_processing:
Library strategy: Ribo-Seq
For RNA-seq, In first step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reads mapping to the reference genome was performed.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool,and three sets of raw reads were obtained.
For Ribo-seq, Ribo-seq used TopHat2 for genome mapping.
Quantification of mapped results to gene level was carried out using HTSeq.
For samples with biological replicates, DESeq2 R package (1.14.1) was used for differential expression analysis. DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution.
Genome_build: mm10
Supplementary_files_format_and_content: Ribo-seq_ read_count.txt include raw gene count for each Sample in Ribo-seq
RNA-seq_ read_count.txt include raw gene count for each Sample in RNA-seq
Ribo-seq_ FPKM.txt include FPKM values for each Sample in Ribo-seq
Ribo-seq_ RPKM.txt include RPKM for each Sample in RNA-seq

value: mRNA


title: RIBO_ME2

description:
RIBO_ME2 represents the Mettl3(f/f，Emx1-cre) sample biological repeat 2 of ribo-seq
Ribo-seq_ read_count.txt
Ribo-seq_ FPKM.txt


title: case.no8_PSTT


title: RIBO_FE1

description:
RIBO_FE1 represents the Fto(f/f，Emx1-cre) sample biological repeat 1 of ribo-seq
Ribo-seq_ read_count.txt
Ribo-seq_ FPKM.txt


title: RIBO_ME3

description:
RIBO_ME3 represents the Mettl3(f/f，Emx1-cre) sample biological repeat 3 of ribo-seq
Ribo-seq_ read_count.txt
Ribo-seq_ FPKM.txt


title: With_Fe_No_Zn_shoot3 (Replication 3)

source_name: 12 DAT old maize shoot (zinc starvation)

value: shoot;

value: hydroponic solution lacking zinc;


title: RIBO_ME1

description:
RIBO_ME1 represents the Mettl3(f/f，Emx1-cre) sample biological repeat 1 of ribo-seq
Ribo-seq_ read_count.txt
Ribo-seq_ FPKM.txt


title: case.no9_ETT


title: RIBO_WT2

description:
RIBO_WT2 represents the wild-type sample biological repeat 2 of ribo-seq
Ribo-seq_ read_count.txt
Ribo-seq_ FPKM.txt


title: case.no1_ETT


title: RIBO_WT3

description:
RIBO_WT3 represents the wild-type sample biological repeat 3 of ribo-seq
Ribo-seq_ read_count.txt
Ribo-seq_ FPKM.txt


title: RIBO_WT1

description:
RIBO_WT1 represents the wild-type sample biological repeat 1 of ribo-seq
Ribo-seq_ read_count.txt
Ribo-seq_ FPKM.txt


title: 2007-601RNAseq

city: Indianapolis

first: Jing

last: Su

state: Indiana

address: 410 W. 10th Street, HITS 3000

department: Department of Biostatistics

country: USA

institute: Indiana University School of Medicine

data_processing:
RNA-Seq analysis was performed following the standard pipeline established by The Cancer Genome Atlas (TCGA) and the National Cancer Institute Genomic Data Commons (GDC). Briefly, quality of raw sequencing reads was assessed by FASTQC analysis (Babraham Bioinformatics). Sequence reads were aligned using the Spliced Transcripts Alignment to a Reference (STAR) sequence aligner with a two-pass approach and gene counts determined using HTSeq software. The RNA-Seq data was reported as raw counts, FPKM (Fragments Per Kilobase of transcript per Million mapped reads), and FPKM-UQ (Upper 75% Quantile).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: Brain metastatic tissue from solid tumor

extract_protocol:
Prior to analysis, frozen tumor block was assessed by a board-certified pathologist (SQ) to assess for adequate tumor content. Total RNA was purified from tumor specimens using the RNeasy Plus Micro Kit (Qiagen) with genomic DNA removal. RNA integrity (RIN) was determined by electrophoretic tracing using an Agilent Bioanalyzer. RNAseq libraries were constructed from samples (RIN >7.0) using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero rRNA depletion. Indexed libraries were sequenced on an Illumina NextSeq 500 DNA sequencer using 150x150-nt paired end reads, generating >40 million reads per sample (12 samples per flow cell) with >80% of sequences achieving >Q30 Phred quality scores. RNA-Seq analysis was performed following the standard pipeline established by The Cancer Genome Atlas (TCGA) and the National Cancer Institute Genomic Data Commons (GDC). Briefly, quality of raw sequencing reads was assessed by FASTQC analysis (Babraham Bioinformatics). Sequence reads were aligned using the Spliced Transcripts Alignment to a Reference (STAR) sequence aligner with a two-pass approach and gene counts determined using HTSeq software. The RNA-Seq data was reported as raw counts, FPKM (Fragments Per Kilobase of transcript per Million mapped reads), and FPKM-UQ (Upper 75% Quantile).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain Metastatic Tissue

tag: gender

value: Female

tag: survival time

tag: survival

tag: prognostic subtype

value: Others


title: case.no3_CC


title: RIBO_FE2

description:
RIBO_FE2 represents the Fto(f/f，Emx1-cre) sample biological repeat 2 of ribo-seq
Ribo-seq_ read_count.txt
Ribo-seq_ FPKM.txt

value: cerebral cortex


title: Tumor_T4_HiC

city: Chicago

first: Feng

last: Yue

state: IL

address: 303 E. Superior Simpson Querrey 7-518

department: Biochemistry and Molecular Genetics

institute: Northwestern University

library_source: genomic

data_processing:
HiC reads were aligned to hg19 genome assembly using BWA with runHiC pipeline using the default settings (https://pypi.org/project/runHiC/)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each RNA-Seq sample; the narrowPeak files included the peaks for each ATAC-seq and ChIP-seq sample; The cool file were the matrix of Hi-C for each Sample.

molecule: genomic DNA

source_name: Cell

growth_protocol: Bladder cancer cell lines were cultured in growth medium containing media + 10% fetal bovine serum and 1% penicillin and streptomycin (Corning). RT4, SW780, SCABER and HT1376 cells were cultured in McCoy’s 5A (Gibco), RPMI-1640 (Corning), Eagle minimum essential medium (MEM; GE life sciences), and Eagle MEM with 1% non-essential amino acids (Corning), respectively.

extract_protocol:
Hi-C was performed using the Arima-HiC kit as per the manufacturer’s protocol. Briefly, 1 million fresh and detached cells or 20mg tumor tissue (frozen and pulverized) was cross-linked with 1% formaldehyde, restriction enzyme digested, Biotin-14-dATP end-labeled , and subsequently ligated.  Ligated chromatin product was then reverse-crosslinked, sonicated (Covaris E220) to 300–500 bp fragments, pulled down with dynabeads Streptavidin  C1 beads.
Hi-C DNA was then processed using Kapa Hyper Prep Kit where it was end repaired, adenylated, adaptor ligated, and PCR amplified with KAPA DNA library prepare kit. Pair-end 2x50/2x100/2x150 bp high-throughput sequencing was performed using HiSeq/NovaSeq platform (Illumina).

tag: sample type

value: tissue;  Patient Tumor T4; Bladder Cancer

tag: chip-seq antibody


title: with_Fe_with_Zn_shoot3 (Replication 3)

source_name: 12 DAT old maize shoot (control)

value: Shoot

value: complete hydroponic solution

value: after 12 days of transplantation to nutrient solution


title: Tumor_T5_HiC

value: tissue;  Patient Tumor T5; Bladder Cancer


title: case.no2_PSTT1

value: tumor


title: With_Fe_No_Zn_shoot2 (Replication 2)


title: Tumor_T3_HiC

value: tissue;  Patient Tumor T3; Bladder Cancer


title: No_Fe_No_Zn_Root3 (Replication 3)

source_name: 12 DAT old maize root (iron and zinc starvation)

value: root

value: hydroponic solution lacking both iron and zinc


title: Tumor_T5_H3K27ac-ChIPSeq_1

data_processing:
ChIP-seq samples were aligned to human hg19 genome using Encode-DCC chip-seq-pipeline2 using the default settings (https://github.com/ENCODE-DCC/chip-seq-pipeline2)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each RNA-Seq sample; the narrowPeak files included the peaks for each ATAC-seq and ChIP-seq sample; The cool file were the matrix of Hi-C for each Sample.

extract_protocol:
10-20 M cells were cross-linked with 2% FA for 10 mins on ice where Glycine was used to quench the reaction.  Cross-linked chromatin was then extracted with cell lysis buffer (1% SDS, 50 mM Tris-HCl pH 8, 20 mM EDTA) and sonicated to 100-300 bp (Covaris E220).  5 ug chromatin was used as input control and 20ug chromatin was used for pull-down experiments. Fragmented chromatin was incubated with bead-antibody complex with either anti-mouse IgG dynabeads (ThermoFisher, 11201D) or sheep anti-rabbit IgG dynabeads (ThermoFisher, 11203D) with 4ug of anti-H3K27ac (Active motif, 39133) or 8ug of anti-GATA3 (Santa Cruz, sc268),  at 4°C for overnight in rotator. Pulled down chromatin was stringently washed and used for making libraries
IP DNA or control inputs were then processed using Kapa Hyper Prep Kit where they were end repaired, adenylated, adaptor ligated, and PCR amplified with KAPA DNA library prepare kit. Pair-end 2x50/2x100 bp high-throughput sequencing was performed using HiSeq/NovaSeq platform (Illumina).

value: H3K27ac(Active motif, 39133)


title: Tumor_T4_H3K27ac-ChIPSeq_1


title: Input_Differentiated [SLX-11527.A020]

city: London

first: Shamith

last: Samarajiwa

address: ICTEM Building, Hammersmith Campus, Du Cane Road,

department: Genetics and Genomics Section  Department of Metabolism, Digestion and Reproduction

country: United Kingdom

institute: Imperial College London

data_processing:
Reads were mapped to the human reference (hg19). ChIP-seq and ATAC-seq samples were mapped using BWA (version 0.7.12) and RNA-seq samples using STAR aligner (version 2.6.0c).
Low quality reads (mapping quality less than 20) as well as known adapter contamination were filtered out using Cutadapt (version 1.10.0).
H3K27AC, H3K27me3 and ATAC-seq samples: Average fragment size was determined using the ChIPQC Bioconductor package, and peak calling was performed with MACS2 (version 2.1.0), using fragment size as an extension size (--extsize parameter).
H3K9me3 samples: Enriched domains were called with EDD
ChIP-seq and ATAC-seq normalised coverage files (.bw) were generated using THOR.
RNA-seq counts were calculated using Rsubread.
Genome_build: hg19
Supplementary_files_format_and_content: .bw = coverage files
Supplementary_files_format_and_content: .narrowPeak/.bed = peak files
Supplementary_files_format_and_content: .txt = counts

growth_protocol: Keratinocytes were cultured in Epilife (Gibco) suppremented with human keratinocyte growth supprement (HKGS, Gibco).

extract_protocol:
For ChIP-seq, lysates were cralified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For RNA-seq, RNA was purified from using the Qiagen RNeasy plus kit according to the manufacturer's instructions.
For ChIP-seq, libraries were prepared using the NEB-Next Ultra II DNA Library Prep Kit (E7645, New England Biolabs) according to the manufacturer's instructions. For RNA-seq, libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: To induce differentiation in culture, keratinocytes were treated with 500 nM of phorbol 12-myristate 13-acetate (PMA, Sigma, P8139) for 48 h after become confluent.

tag: cell type

value: Skin-derived primary keratinocyte

tag: passage

tag: condition

value: Differentiated


title: Tumor_T3_H3K27ac-ChIPSeq_1


title: with_Fe_with_Zn_shoot1 (Replication 1)

tag: treatment (nutrient solution)

tag: time point


title: with_Fe_with_Zn_shoot2 (Replication 2)

tag: tissue


title: With_Fe_No_Zn_shoot1 (Replication 1)

value: Shoot;

value: hydroponic solution lacking zinc;


title: Tumor_T5_RNASeq_1

data_processing:
RNA-seq samples were aligned to human hg19 genome using Encode-DCC rna-seq-pipeline using the default settings (https://github.com/ENCODE-DCC/rna-seq-pipeline/blob/master/docs/reference.md)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each RNA-Seq sample; the narrowPeak files included the peaks for each ATAC-seq and ChIP-seq sample; The cool file were the matrix of Hi-C for each Sample.

molecule: polyA RNA

extract_protocol:
Total RNAs were extracted from 1-2 million cells using RNeasy Mini Kit (Qiagen).
The cDNA libraries were prepared using RNA Library Preparation Kit (Agilent). PolyA RNA was purified and enriched total RNA using oligo (dT) beads (Invitrogen), fragmented, reverse transcribed, end repaired, adenylated, ligated for  sequencing adaptors and PCR amplified. Pair-end 2x50/2x100 bp high-throughput sequencing was performed using HiSeq/NovaSeq platform (Illumina).


title: No_Fe_No_Zn_Root2 (Replication 2)


title: Tumor_T4_RNASeq_1


title: No_Fe_No_Zn_Root1 (Replication 1)


title: H3K27Ac_Differentiated_ChIP-seq [SLX-11527.A021]

tag: antibody


title: Tumor_T3_RNASeq_1


title: H3K27Ac_Differentiated_ChIP-seq [SLX-11527.A013]


title: 2009-451RNAseq

value: Brain Metastatic Tissue

value: Female

tag: age

value: Good


title: RT4_GATA3_ChIPSeq_1

description:
ChIP-seq
RT4_GATA3_ChIPSeq_1.narrowPeak.gz

value: Cell Line; RT4; Bladder Cancer

value: GATA3 antibody(Santa Cruz, sc268)


title: No_Fe_with_Zn_Root3 (Replication 3)

source_name: 12 DAT old maize root (iron starvation)

value: hydroponic solution lacking iron


title: Tumor_T2_HiC

description:
Hi-C(Arima)
Tumor_T2_HiC.mcool

value: Tissue; Patient Tumor T2; Bladder Cancer


title: No_Fe_with_Zn_Root2 (Replication 2)

value: after 12 days of transplantation to nutrient solution


title: H3K27Ac_Growing_ChIP-seq [SLX-11527.A010]

value: Growing


title: HT1376_HiC

description:
Hi-C(Arima)
HT1376_HiC.mcool

value: Cell Line; HT1376; Bladder Cancer


title: With_Fe_No_Zn_Root3 (Replication 3)

source_name: 12 DAT old maize root (zinc starvation)

value: root

value: hydroponic solution lacking zinc


title: No_Fe_with_Zn_Root1 (Replication 1)


title: H3K27Ac_Growing_ChIP-seq [SLX-11527.A011]


title: SW780_HiC

description:
Hi-C(Arima)
SW780_HiC.mcool

value: Cell Line; SW780; Bladder Cancer


title: Tumor_T1_HiC

description:
Hi-C(Arima)
Tumor_T1_HiC.mcool

value: Tissue; Patient Tumor T1; Bladder Cancer


title: Input_Growing [SLX-11527.A019]

value: Skin-derived primary keratinocyte


title: SW780_ATACSeq_2

data_processing:
ATAC-seq samples were aligned to human hg19 genome using Encode-DCC atac-seq-pipeline using the default settings (https://github.com/ENCODE-DCC/atac-seq-pipeline)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each RNA-Seq sample; the narrowPeak files included the peaks for each ATAC-seq and ChIP-seq sample; The cool file were the matrix of Hi-C for each Sample.

extract_protocol:
Cell nuclei were isolated from 30-50K cells in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Nuclei were then incubated nuclei with Tn5 transpose (Illumina, FC-121-1030) at 37oC for 30 mins.
DNA library was then purified, PCR amplified and subsequently verified for nucleosome pattern size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent). Pair-end 2x50/2x100/2x150 bp high-throughput sequencing was performed using HiSeq/NovaSeq platform (Illumina).


title: SCABER_HiC

description:
Hi-C(Arima)
SCABER_HiC.mcool

value: Cell Line; SCABER; Bladder Cancer


title: H3K27me3_Differentiated_ChIP-seq [SLX-11527.A004]

value: Differentiated


title: SW780_ATACSeq_1


title: Tumor_T1_input-ChIPSeq_1

description:
ChIP-seq
Tumor_T1_H3K27ac-ChIPSeq.narrowPeak.gz


title: RT4_HiC

description:
Hi-C(Arima)
RT4_HiC.mcool


title: SW780_input-ChIPSeq_2

description:
ChIP-seq
SW780_H3K27ac-ChIPSeq_pool.narrowPeak.gz


title: H3K27me3_Differentiated_ChIP-seq [SLX-11527.A003]


title: HT1376_input-ChIPSeq_1

description:
ChIP-seq
HT1376_H3K27ac-ChIPSeq_pool.narrowPeak.gz


title: H3K27me3_Growing_ChIP-seq [SLX-11527.A002]


title: With_Fe_No_Zn_Root2 (Replication 2)


title: HT1376_input-ChIPSeq_2


title: SCABER_input-ChIPSeq_2

description:
ChIP-seq
SCABER_H3K27ac-ChIPSeq_pool.narrowPeak.gz


title: H3K27me3_Growing_ChIP-seq [SLX-11527.A001]


title: SW780_input-ChIPSeq_1


title: With_Fe_No_Zn_Root1 (Replication 1)


title: H3K9me3_Differentiated_ChIP-seq [SLX-11527.A018]


title: RT4_input-ChIPSeq_2

description:
ChIP-seq
RT4_H3K27ac-ChIPSeq_pool.narrowPeak.gz


title: H3K9me3_Differentiated_ChIP-seq [SLX-11527.A016]


title: Tumor_T1_H3K27ac-ChIPSeq_1

value: H3K27ac(Active motif, 39133)


title: HT1376_H3K27ac-ChIPSeq_2


title: RT4_input-ChIPSeq_1


title: H3K9me3_Growing_ChIP-seq [SLX-11527.A015]


title: with_Fe_with_Zn_Root1 (Replication 1)

source_name: 12 DAT old maize root (control)

value: complete hydroponic solution


title: with_Fe_with_Zn_Root2 (Replication 2)


title: HT1376_H3K27ac-ChIPSeq_1


title: with_Fe_with_Zn_Root3 (Replication 3)


title: H3K9me3_Growing_ChIP-seq [SLX-11527.A014]


title: SCABER_H3K27ac-ChIPSeq_2


title: SCABER_H3K27ac-ChIPSeq_1


title: RT4_H3K27ac-ChIPSeq_2


title: SCABER_input-ChIPSeq_1


title: RT4_H3K27ac-ChIPSeq_1


title: HT1376_ATACSeq_2

description:
ATAC-seq
HT1376_ATACSeq_pool.narrowPeak.gz


title: HT1376_ATACSeq_1


title: SCABER_ATACSeq_1

description:
ATAC-seq
SCABER_ATACSeq_pool.narrowPeak.gz


title: SCABER_ATACSeq_2


title: RT4_ATACSeq_2

description:
ATAC-seq
RT4_ATACSeq_pool.narrowPeak.gz


title: RT4_ATACSeq_1

description:
ATAC-seq
RT4_ATACSeq_pool.narrowPeak.gz


title: SW780_H3K27ac-ChIPSeq_2


title: HT1376_RNASeq_2

description:
RNA-seq
HT1376_RNASeq_2.genes.results


title: 7029 gene

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Human Exon 1.0 ST arrays were hybridized with 4,7µg of labelled DNA, during 17hours, at 45°C under a 60rpm rotation in Affymetrix Oven.

scan_protocol: Affymetrix 7G scanner was scanned microarrays

data_processing:
Raw data were normalized and controlled with Expression console (Affymetrix).
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: breast cancer tissue

label_protocol: 100ng of total RNA were amplified and labbelled according Affymetrix recommandations. Briefly, total RNA were reverse transcribed, and amplified durintg an in vitro transcription step using the WT expression Kit (Ambion). Complementary RNA were converted into sense-oriented cDNA and molecules were fragmented and labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit. 5,5µg of sens DNA were fragmented and labelled prior hybridization.

extract_protocol: Rneasy (Qiagen)

value: Inflammatory


title: SW780_RNASeq_2

description:
RNA-seq
SW780_RNASeq_2.genes.results


title: 7040 gene


title: 7032 gene


title: HT1376_RNASeq_1

description:
RNA-seq
HT1376_RNASeq_1.genes.results


title: 7034 gene


title: SW780_RNASeq_1

description:
RNA-seq
SW780_RNASeq_1.genes.results


title: SCABER_RNASeq_2

description:
RNA-seq
SCABER_RNASeq_2.genes.results


title: SW780_H3K27ac-ChIPSeq_1


title: 4535 exon

value: Non-Inflammatory


title: 7027 gene


title: 5161 exon


title: 5082 exon


title: 5162 exon


title: RT4_RNASeq_2

description:
RNA-seq
RT4_RNASeq_2.genes.results

value: Cell Line; RT4; Bladder Cancer


title: Tumor_T1_RNASeq_1

description:
RNA-seq
Tumor_T1_RNASeq_1.genes.results


title: 5128 exon


title: SCABER_RNASeq_1

description:
RNA-seq
SCABER_RNASeq_1.genes.results


title: MTA1 rep2

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:TGGAATTCTCGGGTGCCAAGG;end2:GATCGTCGGACTGTAGAACT) trimmed with fastx_clipper
Reads were mapped using tophat2 -N 2. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
Reads with overlap region on the locus of genome were clustered. The read number (N), read length and observed max depth were then counted for each cluster. For each gene, a same number of reads with coincident lengths were generated using computational simulation. The outputting reads were further randomly placed to same genes to generate max peak height from overlapping reads. The whole process was repeated for 500 times. All the observed peaks with heights higher than those of random max peaks (p value ＜ 0.01) were selected, while the FTO peaks that have an overlap with control peaks were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: bed files include MTA1 binding peaks for each sample

source_name: Cell line HCT116

extract_protocol:
Formaldehyde crosslinked cells were lysed on ice by resuspending and repeated pipetting with 10 cell pellet volumes of lysis buffer (1× PBS, 0.1% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate). Then, add 1% (vol/vol) 40U/ul Recombinant RNase Inhibitor（Takara,2313A） and 2% (vol/vol) 10mg/ml PMSF to the cell lysate, mix and rotate the mixture end over end at 4 °C for 30 min. Add 10 X RQ I buffer and DNase I(Promega,M610A). Incubate the tubes at 37 °C for 3 min,shaking at 1,000rpm. Immediately afterward a Stop solution was added to the lysates to quench DNase. Then, centrifuge 10,000 rpm for 10 min at 4 °C. Carefully collect the supernatant. Prepare a 1/50000 dilution of MNase(Thermo,EN0181).
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to illumina NextSeq 500 system for 151 nt pair-end sequencing by ABlife. Inc (Wuhan, China) and Illumina GAIIx (Illumina, San Diego, CA, USA) 150 nt paird-end sequencing .

value: colon

tag: morphology

value: epithelial

tag: disease

value: colorectal carcinoma


title: 7026 gene


title: 5195 exon


title: 5174 exon


title: 7025 gene


title: 4470 exon


title: 5173 exon


title: 7030 gene


title: 7024 gene


title: RT4_RNASeq_1

description:
RNA-seq
RT4_RNASeq_1.genes.results


title: Ctrl rep2


title: 6604 gene


title: 5020 exon


title: HEK-293T UT Int3 Input

city: New Haven

first: Nicolle

middle: A.

last: Rosa-Mercado

state: CT

address: 295 Congress Avenue

department: Molecular Biophysics and Biochemistry

institute: Yale University

data_processing:
Samples were mapped to the hg38 genome using Bowtie2 version 2.3.4.1-foss-2016b.
Read counts were generated using bedtools multicov and normalized to input using factors calculated with edgeR (normalizeChIPtoInput).
Peaks were called using MACS2 version 2.1.1.20160309-foss-2016b-Python-2.7.13
To visualize genome coverage, normalized bigwig files (ChIP/Input) were generated using deepTools (bamCompare --operation ratio)
Supplementary_files_format_and_content: Peaks called by MACS2 and normalized bigwig files generated using deepTools.

source_name: HEK-293T cells

growth_protocol: HEK-293T cells were cultured at 37ºC in DMEM supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin, and 1% L-glutamine.

extract_protocol:
Cells were sonicated and DNA  was isolated with an antibody against Integrator subunits 3 or 11.
KAPA hyper prep kit was used to prepare libraries.

treatment_protocol: Hyperosmotic stress was induced with 80 mM KCl for 1 hour.

tag: stress

tag: chip antibody


title: 6603 gene


title: SB3: Sample 6_SA187_Rep3_MMS

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

data_processing:
Sequenced reads were quality-checked using FASTQC and trimmed using Trimmomatic to have a minimum length of 36 bp and Phred quality score >30. Leading and trailing bases were removed with base quality below 3.
Trimmed reads aligned against Enterobacter sp. SA187 genome by using TopHat 2.0
Differentially expressed genes were calculated by using Cufflinks 2.2.1. Cut-off of 2-fold change and p <= 0.05 were used.
Genome_build: contig.1.cir

organism: Enterobacter sp. SA187

source_name: bacterial cells

growth_protocol: Sterilized seeds were stratified for 3 days and then plated on ½ MS agar plates (Murashige and Skoog basal salts, Sigma), grown vertically for 5 days at 22 C and 16h light, then transferred to fresh ½ MS agar plates with (samples SPB) or without (samples PB) 100 mM NaCl (6 seedlings per plate) and cultivated for additional 12 days. Bacterial pure culture were grown overnight in LB, then washed and transferred to ½ MS  broth wih (samples SB) or without (samples B) 100 mM NaCl

extract_protocol:
Total RNA was extracted from 17-day-old seedlings flash frozen in liquid nitrogen, using NucleoSpin® RNA Plant extraction kit (Macherey-Nagel) following manufacturer's instructions,  was used with 1 ug of total RNA for the construction of sequencing libraries. Total RNA from bacteria pure culture was extracted by using RiboPure™ RNA Purification Kit (Invitrogen), following manufacturesr's intructions with some minor modifications
Total RNA from bacteria and dual (plant + bacteria) samples was treated with Ribo-Zero Magnetic Gold Kit to remove ribosomal rRNA (rRNA). For rRNA depletion of bacteria samples (B and SB), rRNA Removal solution from Ribo-Zero Gold kit (Epidemiology) was used. For rRNa depletion of dual samples (B and BS), rRNA Removal solution from Ribo-Zero Magnetic kit (Plant Leaf) and rRNA Removal Solution from Ribo-Zero Gold kit (Epidemiology) were mixed in a ratio 1:1. An amount of 1 ug of total RNA was used for the contruction of RNA-Seq libraries. Pair-end sequencing of the 6 dual (plant + bacteria) RNA-Seq libraries was performed by using Illumina Genome Analyzer IIx (GAIIx), while Pair-end sequencing of the 6 bacteria RNA-Seq libraries was performed by using Illumina HiSeq 2500. Read length was 101 bp

treatment_protocol: Initial plates for sterilized seeds germination containing bacterial strain SA187 (2·10E+5 cfu·mL-1) were used to prepare plant-associated samples PB and SPB. Free-living samples B and SB were obtained from pure bacterial cultures. 100 mM NaCl was added to the synthetic plant agar and bacterial liquid growth media fo treated samples

value: bacterial cells

tag: life-style

value: pure culture (free-living)

value: 4 hours

tag: genotype

value: wild type


title: HEK-293T KCl Int3 Input

value: 1 hour 80 mM KCl


title: HEK-293T KCl Int3 ChIP

value: Anti-Int3 (Bethyl A-302-050A)


title: SB2: Sample 5_SA187_Rep2_MMS


title: 4457 exon


title: HEK-293T UT Int3 ChIP


title: 4436 exon


title: 4412 exon


title: 4405 exon


title: 4533 exon


title: SB1: Sample 4_SA187_Rep1_MMS


title: HEK-293T KCl anti-Int11 Input rep1


title: HEK-293T KCl anti-Int11 Input rep2


title: B3: Sample 3_SA187_Rep3_MM


title: HEK-293T KCl anti-Int11 ChIP rep2


title: 1807 exon


title: HEK-293T KCl anti-Int11 ChIP rep1


title: B1: Sample 1_SA187_Rep1_MM


title: 6596 gene


title: H37Rv_48h

city: Chongqing

first: Fake

last: Li

state: Chongqing

address: Changjiangzhilu 10 Yuzhong District

department: Clinical Laboratory Medicine

institute: Daping Hospital

data_processing:
Quality control analysis of the raw sequence files was conducted with FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The quality-checked reads for each condition were first mapped to the latest UCSC transcript set using Bowtie2 (version 2.1.0)
Then the gene expression level was estimated using RSEM (RNA-Seq by Expectation Maximization, v1.2.15) and normalized with TMM (trimmed mean of M-values) to identify differentially expressed genes (DEGs) using the edgeR package.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include TMM values for each Sample ...

source_name: THP-1 macrophages

growth_protocol: Human monocyte cell line THP-1 cells were cultured in RPMI 1640 basic medium (Gibco, life technologies, USA) supplemented with 2 mM L-glutamine, Penicillin (100 U/ml)-Streptomycin (100 µg/ml) Solution and 10% fetal bovine serum (FBS) (Catalog No. 04-121-1A, Biological Industries, Israel) at cultural density of 5 × 105 - 1 × 106/ml.

extract_protocol:
The total RNA were isolated with RNeasy mini kit (Qiagen, Germany) according to the manufacturer's instructions
Both rRNA and mitochondrial RNA was removed with Ribo-Zero Gold Removal Magnetic Kit for human/mouse/rat (Epicentre, now Illumina) according to the manufacturer’s instructions. The libraries were prepared with KAPA RNA-Seq Kit for Illumina (Kapa biosystems, USA) following the manufacturer's procedure. The RNA was fragmented to the desired size (about 300 bp) by heating in the presence of Mg++. The 1st strand cDNA was synthesized with random primers. The 2nd strand cDNA synthesis converted cDNA:RNA hybrid to double strand cDNA (dscDNA), while marking the 2nd strand with dUTP. Then dAMP was added to 3’-end of dscDNA fragments. Following by ligation of 3’-dTMP adapters (10 nM) to 3’-dAMP library fragments, and PCR amplification (14 cycles) of the adapter-ligated library DNA. The dUTP-marked strand was not amplified. Library fragment size distribution was confirmed by electrophoresis and library concentration was determined with Qubit 2.0 Fluorometric Quantitation (Thermo Fisher Scientific, USA). These libraries were sequenced using the Illumina Hiseq 3000 Sequencer (50 cycles, single read lane).

treatment_protocol: THP-1 macrophages were uninfected or infected with Mycobacteria tuberculosis H37Rv and H37Ra at MOI=3 for 1 h, 4 h, 12 h, 24 h or 48 h. Cells were placed in a humidified, 37℃ 5% CO2 incubator.

value: THP-1 macrophages

tag: agent


title: HEK-293T UT anti-Int11 Input rep2


title: 6597 gene


title: 1256 exon


title: H37Rv_24h


title: HEK-293T UT anti-Int11 Input rep1


title: 6589 gene


title: 6594 gene


title: 6598 gene


title: H37Rv_12h


title: 6595 gene


title: HEK-293T UT anti-Int11 ChIP rep2


title: B2: Sample 2_SA187_Rep2_MM


title: 6588 gene


title: 6586 gene


title: H37Rv_4h


title: HEK-293T UT anti-Int11 ChIP rep1


title: 1222 exon


title: 6585 gene


title: 6583 gene


title: 553 exon


title: 6582 gene


title: 150 exon


title: 7034 exon


title: Fetal epithelium sample pool 3 - Second Tag Hashing Antibody Library

city: Oxford

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

description:
Hashing antibody (EPCAM) library of single cells from 8 fetal intestinal epithelial samples from 12, 13 and 16 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Epithelial_pool_3_HTO2

data_processing:
Raw sequence data for mRNA libraries were processed using 10x Genomics cellranger pipeline, version 3.1.0
Raw sequence data from hashing libraries were processed using CITE-Seq-Count, version 1.4.3
Genome_build: hg38
Supplementary_files_format_and_content: compressed raw UMI counts matrices from Cellranger outputs for mRNA libraries. Compressed raw UMI matrices from CITE-Seq-Count for antibody oligo tag counts.

source_name: Small and large fetal intestine

extract_protocol:
fetal intestinal samples were digested using either EDTA chelation protocol (EpCAM+/ epithelial pools) or milteyni umbilical cord digestion kit (EpCAM- / stromal pools) and then stained with either a oligonucleotide conjugated antibody to B2M/Cd298 (biolegend) or in EpCAM+ cells an additional EpCAM+ oligo conjugated antibody. In the case of the first pool 3 samples were digested fully without separation. All these libraries are 3 prime, scRNA seq processed using 10x v3 single cell RNA seq protocol and co-ordinate with a HTO library (in the case of single stain) or a HTO and ADT library (in EpCAM+ cells case) for demultiplexing
RNA libraries were processed as per 10x v3 single cell RNA seq protocol library preparation for illumina i7 sample indexes (CG000183, Rev C), HTO and ADT libraries were extracted from the protocol during SPRI clean up and amplified with custom tru-seq primers as per description in published protocol: https://doi.org/10.1186/s13059-018-1603-1

value: EPCAM+ intestinal epithelial cells

tag: post-conceptual weeks


title: 129 exon


title: H37Ra_48h


title: Fetal epithelium sample pool 2 - Second Tag Hashing Antibody Library

description:
Hashing antibody (EPCAM) library of single cells from 8 fetal intestinal epithelial samples from 8, 10, 17, 18 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Epithelial_pool_2_HTO2


title: 7040 exon


title: H37Ra_24h


title: Fetal stromal sample pool 4 - Hashing Antibody Library

description:
Hashing antibody (TotalSeq Human HTO) library of single cells from 9 fetal intestinal stromal samples from 10, 15 and 22 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Stromal_pool_4_HTO

value: EPCAM- intestinal stromal cells


title: Fetal epithelium sample pool 1 - Second Tag Hashing Antibody Library

description:
Hashing antibody (EPCAM) library of single cells from 9 fetal intestinal epithelial samples from 8, 9, 13 and 22 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Epithelial_pool_1_HTO2


title: H37Ra_4h


title: Fetal epithelium sample pool 4 - Hashing Antibody Library

description:
Hashing antibody (TotalSeq Human HTO) library of single cells from 9 fetal intestinal epithelial samples from 10, 15 and 22 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Epithelial_pool_4_HTO


title: H37Rv_1h


title: H37Ra_1h


title: 6544 gene


title: 6575 gene


title: H37Ra_12h


title: Fetal stromal sample pool 3 - Hashing Antibody Library

description:
Hashing antibody (TotalSeq Human HTO) library of single cells from 8 fetal intestinal stromal samples from  8, 10, 17, 18  post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Stromal_pool_3_HTO


title: 7030 exon


title: THP-1 macrophages uninfected_48h


title: Fetal stromal sample pool 2 - Hashing Antibody Library

description:
Hashing antibody (TotalSeq Human HTO) library of single cells from 8 fetal intestinal stromal samples from 12, 13 and 16 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Stromal_pool_2_HTO


title: 6318 gene


title: 7029 exon


title: 7032 exon


title: 6316 gene


title: Fetal epithelium sample pool 3 - Hashing Antibody Library

description:
Hashing antibody (TotalSeq Human HTO) library of single cells from 8 fetal intestinal epithelial samples from 12, 13 and 16 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Epithelial_pool_3_HTO


title: Fetal stromal sample pool 1 - Hashing Antibody Library

description:
Hashing antibody (TotalSeq Human HTO) library of single cells from 9 fetal intestinal stromal samples from 8, 9, 13 and 22 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Stromal_pool_1_HTO


title: THP-1 macrophages uninfected_12h


title: 6309 gene


title: THP-1 macrophages uninfected_24h


title: THP-1 macrophages uninfected_4h


title: 6311 gene


title: THP-1 macrophages uninfected_1h


title: Fetal epithelium sample pool 1 - Hashing Antibody Library

description:
Hashing antibody (TotalSeq Human HTO) library of single cells from 9 fetal intestinal epithelial samples from 8, 9, 13 and 22 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Epithelial_pool_1_HTO


title: 7027 exon


title: Fetal epithelium sample pool 2 - Hashing Antibody Library

description:
Hashing antibody (TotalSeq Human HTO) library of single cells from 8 fetal intestinal epithelial samples from 8, 10, 17, 18 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Epithelial_pool_2_HTO


title: 7025 exon


title: 6307 gene


title: THP-1 macrophages uninfected_0h


title: 7024 exon


title: 6604 exon


title: Fetal stromal sample pool 4 - Gene Expression

description:
Gene expression of single cells from 9 fetal intestinal stromal samples from 10, 15 and 22 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Stromal_pool_4_GEX


title: 6597 exon


title: 6598 exon


title: s_10_ESC_EED226_S90

city: Hachioji

first: Shoko

last: Nishihara

state: Tokyo

address: 1-236 Tangi-machi

department: Bioinformatics

country: Japan

institute: Soka University, Graduate School of Engineering

description: 200923_NovaSeq_truseqUD_l1_0090_B12_Dr_Murakami_10_ESC_EED226_S90

data_processing:
Illumina bcl2fastq2-v2.20 software was used to demultiplex data and convert BCL files from Novaseq6000 systems running RTA versions v3.4.4 to standard FASTQ file formats for downstream analysis.
To remove the reads derived from ribosomal RNA (rRNA), the reads were aligned to rRNA sequence obtained from Ensembl by bowtie (v2.2.4).
The remaining reads were aligned to the reference mouse genome with the guide of RefSeq transcript model by STAR (v2.6.0a).
Read count was performed using featureCounts (v1.6.2). TPM values of each gene was calculated as a gene expression value.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx

source_name: Embryonic stem cells treated with EED226

extract_protocol:
RNA was purified using a RNeasy Mini Kit with an RNase-free DNase Set (QIAGEN), according to the supplier’s manual.
The libraries were prepared using TruSeq Stranded mRNA  Prep Kit (Illumina), according to the supplier's manual.

treatment_protocol: ESCs were cultured in ESC medium containing 10 μM EED226 or DMSO in the presence of LIF for 48h.

tag: strain

value: Embryonic stem cell

tag: treatment


title: 5622 gene


title: 5623 gene


title: Fetal epithelium sample pool 4 - Gene Expression

description:
Gene expression of single cells from 9 fetal intestinal epithelial samples from 10, 15 and 22 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Epithelial_pool_4_GEX

tag: cell type


title: 6603 exon

tag: condition


title: 6596 exon


title: Fetal stromal sample pool 3 - Gene Expression

description:
Gene expression of single cells from 8 fetal intestinal stromal samples from  8, 10, 17, 18  post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Stromal_pool_3_GEX


title: 6303 gene


title: s_8_EpiLC_S64_Mouse

description: 200923_NovaSeq_truseqUD_l1_0064_H08_Dr_Murakami_8_EpiLC_S64

source_name: Embryonic stem cell derived Epiblast-like stem cells

treatment_protocol: To induce EpiLC differentiation, ESCs maintained on MEF feeder cells were passaged on gelatin-coated 60-mm dishes, and cultured for 30 min in ESC medium containing LIF to completely remove MEF feeder cells 24h prior induction. Subsequently, supernatants containing ESCs were seeded at low density in gelatin-coated 60-mm dishes containing ESC medium in the presence of 1 μM PD0325901 (Wako), 3 μM CHIR99021 (Wako) and LIF. The following day, EpiLC induction was performed; ESC samples were collected for further analysis or seeded at 1 x 106 in gelatin-coated 60-mm dishes containing ESC medium without LIF for 24h. Subsequently, EpiLC medium, consisting of DMEM/F12 (Gibco) supplemented with 20% knockout serum replacement (KSR) (Gibco), 2 mM L-glutamine (Invitrogen), 1% penicillin/streptomycin (Gibco), 0.1 mM 2-mercaptoethanol (Gibco), 0.1 mM nonessential amino acids (Gibco), 30 ng/ml FGF2 (Wako) and 0.6 μM JAK inhibitor (JAKi) (Santa Cruz Biotechnology), was added. EpiLC medium was changed daily and EpiLCs were collected for further analysis 72h post-induction.

value: ESC-derived epiblast-like stem cells


title: Fetal stromal sample pool 2 - Gene Expression

description:
Gene expression of single cells from 8 fetal intestinal stromal samples from 12, 13 and 16 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Stromal_pool_2_GEX


title: 6317 gene

value: Inflammatory


title: s_7_ESC_S63_Mouse

description: 200923_NovaSeq_truseqUD_l1_0063_G08_Dr_Murakami_7_ESC_S63

source_name: Embryonic stem cell

treatment_protocol: ESC medium consisting of DMEM (Gibco) supplemented with 15% fetal bovine serum (FBS) (Nichirei Biosciences), 1% penicillin/streptomycin (Gibco), 0.1 mM 2-mercaptoethanol (Gibco), 0.1 mM nonessential amino acids (Gibco), and 1000 U/mL LIF (Chemicon International).


title: s_9_ESC_DMSO_S89

description: 200923_NovaSeq_truseqUD_l1_0089_A12_Dr_Murakami_9_ESC_DMSO_S89

source_name: Embryonic stem cells treated with vehicle

value: DMSO


title: 5440 gene


title: 5323 gene


title: Fetal stromal sample pool 1 - Gene Expression

description:
Gene expression of single cells from 9 fetal intestinal stromal samples from 8, 9, 13 and 22 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Stromal_pool_1_GEX


title: 6594 exon

value: Non-Inflammatory


title: 6595 exon


title: VGT3.5 [G709-26]

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
The final product was assessed for its size distribution and concentration using the BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). The libraries were pooled and diluted to 3 nM using 10 mM Tris-HCl (pH 8.5) and then denatured using the Illumina protocol. The denatured libraries were loaded onto an S1 flow cell on an Illumina NovaSeq 6000 (Illumina) and run for 2 x 50 cycles according to the manufacturer's instructions.
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read.
BBDuk (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/) was used to trim/filter low quality sequences using the “qtrim=lr trimq=10 maq=10” option.
Alignment of the filtered reads to the mouse reference genome (GRCm38) was performed using HISAT2 (version 2.1.0) and applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq by supplementing Ensembl gene annotation (GRCm38.78).
Gene expression values were calculated as transcripts per million (TPM) using custom R scripts.
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file, gene expression values in TPM

source_name: VGT3-positive inhibitory interneuron

extract_protocol:
Patch pipettes (1.5–2.0 MΩ) were filled with DEPC-treated internal solution containing (in mM): 140 K-methanesulfonate, 0.2 EGTA, 2 MgCl2 and 10 HEPES, pH-adjusted to 7.3 with KOH. RNase inhibitor (1U/μl, Ambion) was dissolved into the internal solution. Before filling the electrode with RNase inhibitor-containing solution (4.5 μl), the tip of the electrode was always loaded with a small volume of internal solution (~0.5 μl) to form a smooth seal. Immediately after establishing whole-cell mode, the cytosol of the recorded cell was aspirated into the patch pipette and immediately expelled into an RNase free 0.5-ml tube (Ambion).
The cDNA libraries were prepared using the SMART-Seq® HT Kit (TAKARA Bio) and Nextera XT DNA Library Prep Kit (Illumina) as per the manufacturer's instructions.

treatment_protocol: The cytosol of single cell VGT3-, Pv- and Sst-positive inhibitory interneuron washarvested using the whole cell patch-clamp technique.

value: postnatal 6- to 7-day-old

tag: tissue/cell type

value: VGT3-positive inhibitory interneuron


title: Fetal epithelium sample pool 2 - Gene Expression

description:
Gene expression of single cells from 8 fetal intestinal epithelial samples from 8, 10, 17, 18 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Epithelial_pool_2_GEX


title: 5322 gene


title: 6588 exon


title: 6586 exon


title: Sst.4 [G709-20]

source_name: Sst-positive inhibitory interneuron

value: Sst-positive inhibitory interneuron


title: Sst.3 [G709-19]


title: 5197 gene


title: Sst.5 [G709-21]


title: Sst.2 [G709-18]


title: HEK-293T KCl Pol II Inp rep1

data_processing:
Samples were mapped to the hg38 genome using Bowtie2 version 2.3.4.1-foss-2016b.
Read counts were generated using bedtools multicov and normalized to input using factors calculated with edgeR (normalizeChIPtoInput). DESeq2 was used to quantify differences in Pol II binding across gene bodies.
Peaks were called using MACS2 version 2.1.1.20160309-foss-2016b-Python-2.7.13.
To visualize genome coverage, normalized bigwig files (ChIP/Input) were generated using deepTools (bamCompare --operation ratio).
Supplementary_files_format_and_content: Peaks called by MACS2 and normalized bigwig files generated using deepTools are included.

extract_protocol:
Cells were sonicated for 10 cycles of 30 seconds on and 30 seconds off in a Diagenode Bioruptor Pico sonicator. DNA-bound Pol II was isolated with an antibody against Pol II.
KAPA hyper prep kit was used to prepare libraries.


title: 5195 gene


title: VGT3.4 [G709-24]


title: 5174 gene


title: Fetal epithelium sample pool 1 - Gene Expression

description:
Gene expression of single cells from 9 fetal intestinal epithelial samples from 8, 9, 13 and 22 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Epithelial_pool_1_GEX


title: 6582 exon


title: Fetal epithelium sample pool 3 - Gene Expression

description:
Gene expression of single cells from 8 fetal intestinal epithelial samples from 12, 13 and 16 post-conceptual weeks tagged with oligonucleotide-labelled antibodies, pooled and captured in a single 10x reaction
Epithelial_pool_3_GEX


title: HEK-293T KCl Pol II ChIP rep2

value: Anti-Pol II (Cell Signaling D8L4Y)


title: HEK-293T KCl Pol II Inp rep2


title: Sst.1 [G709-16]


title: HEK-293T KCl Pol II ChIP rep1


title: 6583 exon


title: Pv.5 [G709-11]

source_name: Pv-positive inhibitory interneuron

value: Pv-positive inhibitory interneuron


title: 5196 gene


title: HEK-293T UT Pol II Input rep1


title: HEK-293T UT Pol II Input rep2


title: Pv.2 [G709-05]


title: Pv.4 [G709-08]


title: 6575 exon


title: 6585 exon


title: 5173 gene


title: 6544 exon


title: 5162 gene


title: 5082 gene


title: 5128 gene


title: 5161 gene


title: HEK-293T UT Pol II ChIP rep1


title: Pv.3 [G709-06]


title: 5020 gene


title: Pv.1 [G709-04]


title: 6308 gene


title: TDE_2

city: Beijing

first: Wenfeng

last: Zeng

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
The RNA-Seq raw data were processed through the standard  RNA-Seq  analysis  pipeline.  Briefly,  read  alignment  was  examined  using  TopHat2 version  2.1.1.  Differential-expression  analysis  was   carried  out  with  DESeq2  version  1.24.0  in  R  v.3.3.1 (http://cran.r-project.org/). Genes were considered to be differentially expressed if the adjusted P  was  less  than  0.05.
Supplementary_files_format_and_content: raw counts

source_name: BMDC

growth_protocol: BMDCs were obtained by differentiating bone marrow cells with 20 ng/ml GM-CSF for 6 days

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

treatment_protocol: BMDCs were untreated or treated with either normal cell-derived exosomes or tumor cell-derived exosome for 24 hours

value: bone marrow

value: bone-marrow derived DC (BMDC)

value: wildtype

value: treated by exosomes from tumor cells for 24 hours


title: TDE_3


title: HEK-293T KCl TL control  rep1

data_processing:
TT-TL-seq data processing was performed as in Schofield et al. 2018 with the exception of generating read counts and normalization factors.
DoGFinder was used to identify regions of readthrough transcription (-minDoGLen 5000 -minDoGCov 0.8 -w 200 -mode F).
Normalization factors were calculated using edgeR (calcNormFactors "upperquartile" setting).
Gene counts were generated using bedtools multicov and normalized according to scale factors calculated using edgeR (calcNormFactors "upperquartile" setting).
IGVtools was used to generate TDF files for TT-TL-seq tracks.
Supplementary_files_format_and_content: Text files containing normalized counts for gene bodies or DoG regions; TT-TL-seq tracks in tdf format.

extract_protocol:
RNA was extracted using TRIzol and subjected to TimeLapse chemistry as described in Schofield et al. 2018. s4U-labeled RNAs were enriched as described in Duffy et al. 2015.
Clonetech SMARTer stranded total RNA pico kit was used.

treatment_protocol: For hyperosmotic stress, cells were treated with 80 mM KCl for 1 hour. For Int11 knockdown, cells were treated with siRNAs for 48 hours.

tag: sirna treatment

value: siC-transfected HEK-293T cells

value: 1 hour 80 mM KCl


title: HEK-293T KCl TL control rep2


title: 6589 exon


title: TDE_1

tag: tissue


title: HEK-293T siC TL control rep2


title: HEK-293T siC TL control  rep1


title: NE_3

value: treated by exosomes from NIH-3T3 cells for 24 hours


title: 6318 exon


title: NE_2


title: 4457 gene


title: 4470 gene


title: 6309 exon


title: HEK-293T siInt11 + WT TT-TL

description:
nascent RNA
siInt11_mRNA_counts
TT-TL-seq_DoGCounts

value: siInt11-transfected HEK-293T cells

tag: rescue

value: HEK-293T cells stably expressing siRNA-resistant wild-type Int11

value: 5 minutes 1 mM


title: 6317 exon

value: Inflammatory


title: 6308 exon


title: 6311 exon


title: 4436 gene

value: Non-Inflammatory


title: 5221 gene


title: 4412 gene


title: NE_1


title: 4405 gene


title: 6316 exon


title: 4533 gene


title: HEK-293T siInt11 + E203Q TT-TL

value: HEK-293T cells stably expressing siRNA-resistant E203Q mutant Int11


title: 6303 exon


title: HEK-293T siInt11 TT-TL rep2


title: 5623 exon


title: 1807 gene


title: CTR_3

value: no treatment


title: HEK-293T UT Pol II ChIP rep2


title: HEK-293T siInt11 TT-TL rep1


title: CTR_2


title: CTR_1


title: 5440 exon


title: HEK-293T KCl TT-TL rep1

description:
nascent RNA
KCl_counts_mRNA.txt
TT-TL-seq_DoGCounts


title: 1222 gene


title: 7026 exon


title: 1256 gene


title: 5622 exon


title: 553 gene


title: single cell replicate VGT3.2 [G556.07]

treatment_protocol: The cytosol of single cell VGT3-positive inhibitory interneuron washarvested using the whole cell patch-clamp technique.

tag: age

value: postnatal 6- to 7-day-old


title: 5197 exon


title: HEK-293T siC TT-TL rep2

description:
nascent RNA
KCl_counts_mRNA.txt
siInt11_mRNA_counts
TT-TL-seq_DoGCounts


title: 6307 exon


title: single cell replicate VGT3.3 [G556.10]


title: HEK-293T siC TT-TL rep1


title: 5322 exon


title: 5221 exon


title: 5323 exon


title: HT

status: Public on Jan 03 2021

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

country: Denmark

institute: Aalborg University

data_processing:
Read filtration via Fastp (0.20.1)  --trim_front1 7, --trim_tail1 7, --cut_front, --cut_tail, --overrepresentation_analysis, --detect_adapter_for_pe, --correction
Read alignment via STAR (2.7.5c)  --quantMode GeneCounts, --outSAMtype BAM SortedByCoordinate, --readFilesCommand zcat, --chimSegmentMin 20
Differential expression analysis was perfomred using edgeR . The Trimmed Mean of M-values (TMM) method was used to normalize the data.
Genome_build: Annotation with Ensembl Release 100, Ensembl GRCh38 reference genome build
Supplementary_files_format_and_content: fastp provided statistics on read quality, while outputting trimmed reads in fastq format  STAR aligner generated aligned reads in BAM format (not uploaded).  Gene counts were provided as read coverage in a tab-separated file

source_name: diffuse large B-cell lymphoma cell line

growth_protocol: The cell lines were cultured under standard conditions at 37 °C in humidified atmosphere of 95% air and 5% CO2 with RPMI-1640 medium containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S) for no longer than 20 passages.

extract_protocol:
Total RNA was extracted using a modified protocol combining TRIzol Reagent (Invitrogen, Paisley, UK) and mirVana miRNA Isolation Kit (Ambion/ThermoFisher Scientific, Grand Island, NY).
poly-A selected sequencing

tag: cell line

value: HT

tag: Sex

value: Male

tag: ethnicity

value: Caucasian

tag: phenotype

value: Resistant against rituximab


title: OCI-Ly8


title: single cell replicate VGT3.1 [G556.06]


title: 129 gene


title: NU-DHL-1

value: Sensitive to rituximab


title: E14 cells_Npac RNAi-rep2

city: singapore

first: SU E

last: YU

state: SINGAPORE

address: NUS, MD7, level 4

department: Biochemistry

country: Singapore

institute: NUS

description: Gene expression data from Npac RNAi (selected by puromycin for 3 days).

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed using RMA in the bioconducter and normalized using cross correlation.

source_name: E14 cells, Npac RNAi

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mouse ES cells (E14) were cultured in ES cell medium consisting of Glasgow Minimum Essential Medium (GMEM; Invitrogen), 15% ES cell qualified fetal bovine serum (FBS; Invitrogen), 0.055 mM β-mercaptoethanol (Sigma), 100 mM sodium pyruvate (Invitrogen), 0.1 mM MEM nonessential amino acid (NEAA, Invitrogen) and 1,000 units/ml of LIF (Millipore).

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

treatment_protocol: E14 cells were transfected with Npac shRNA by using Lipofectamine 2000 (Invitrogen) according to the manual provided. After transfection for 24 hours, cells were selected in 6-well culture plate for 3 days with puromycin. The cells were then harvested for either extraction of protein or RNA.

value: E14 murine embryonic stem cells

value: Npac Knockdown cells


title: MC-116

value: sensitive to rituximab


title: E14 cells_control RNAi-rep2

description: Gene expression data from control RNAi (selected by puromycin for 3 days).

source_name: E14 cells, control RNAi

value: Control Knockdown cells


title: 5196 exon

source_name: breast cancer tissue


title: CM4

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
CM3_CM4_US83300186_252665510917_S01_GE2_1200_Dec17_1_4.txt
Gene expression in cortex of adult female mouse

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two biological replicas were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) mouse (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction vs.11 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
normalized ratio of the background subtracted signal of that feature to the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal

source_name: Cortex of MRL/MpJ mouse_replicate 4

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a Thermo Scientific NanoDrop ND-2000 and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: cortex was isolated from adult female mice and  minced in ice

tag: strain/genotype

value: MRL/MpJ

value: female

value: cortex

tag: develomental stage

value: adult


title: CM3

source_name: Cortex of MRL/MpJ mouse_replicate 3


title: CM2

description:
CM1_CM2_US83300186_252665510917_S01_GE2_1200_Dec17_1_3.txt
Gene expression in cortex of adult female mouse

source_name: Cortex of MRL/MpJ mouse_replicate 2


title: CM1

source_name: Cortex of MRL/MpJ mouse_replicate 1


title: CL2

description:
CL1_CL2_US83300186_252665512245_S01_GE2_1200_Dec17_1_1.txt
Gene expression in cortex of adult female mouse

source_name: Cortex of MRL/lpr mouse_replicate 2

value: MRL/lpr


title: CK1

description:
CK1_CK2_US83300186_252665510916_S01_GE2_1200_Dec17_1_1.txt
Gene expression in cortex of adult female mouse

source_name: Cortex of Fn14koMRL mouse_replicate 1


title: E14 cells_Npac RNAi-rep1

tag: genotype


title: CL3

description:
CL3_CL4_US83300186_252665512245_S01_GE2_1200_Dec17_1_2.txt
Gene expression in cortex of adult female mouse

source_name: Cortex of MRL/lpr mouse_replicate 3


title: SU-DHL-4


title: CK4

description:
CK3_CK4_US83300186_252665510916_S01_GE2_1200_Dec17_1_2.txt
Gene expression in cortex of adult female mouse

source_name: Cortex of Fn14koMRL mouse_replicate 4


title: CK3

source_name: Cortex of Fn14koMRL mouse_replicate 3


title: E3_5_MUT.MUT_29

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

institute: Cerevance ltd

description: single cell

data_processing:
STAR alignment
htseq-count
Genome_build: mm10
Supplementary_files_format_and_content: counts (text file)

source_name: ICM

extract_protocol:
For E3.5 blastocysts, zona pellucidae were removed using acid tyrode’s solution (Sigma) and embryos subjected to immunosurgery using 20% anti-mouse whole antiserum (Sigma) in N2B27 in at 37oC, 7% CO2 for 30 minutes, followed by 3 rinses in M2, then 15 minutes in 20% non-heat inactivated rat serum (made in house) in N2B27 in at 37oC, 7% CO2. After 30 minutes in fresh N2B27 lysed trophectoderm was removed and placed in lysis buffer for genotyping. ICMs were incubated in 0.025% trypsin (Invitrogen) plus 1% chick serum (Sigma) for 5-10 minutes in small drops and dissociated by repetitive pipetting using a small diameter mouth-controlled flame-pulled Pasteur pipette. Individual ICM cells were transferred into single cell lysis buffer and snap frozen on dry ice.
Smart-seq2 libraries were prepared as described previously and sequenced on the Illumina platform in a 125 bp paired-end format.

value: Mutant

tag: developmental stage


title: CL1

source_name: Cortex of MRL/lpr mouse_replicate 1


title: CL4

source_name: Cortex of MRL/lpr mouse_replicate 4


title: E3_5_MUT.MUT_28

description: single cell


title: CK2

source_name: Cortex of Fn14koMRL mouse_replicate 2


title: E3_5_WT_or_HET.WT_42

description: single cell

value: Wild-Type


title: E3_5_MUT.MUT_27

description: single cell


title: E3_5_WT_or_HET.WT_41

description: single cell


title: E3_5_WT_or_HET.WT_40

description: single cell


title: E3_5_WT_or_HET.WT_38

description: single cell


title: 4535 gene

value: Non-Inflammatory


title: E3_5_WT_or_HET.WT_39

description: single cell


title: E3_5_WT_or_HET.WT_37

description: single cell


title: SU-DHL-8m

source_name: diffuse large B-cell lymphoma cell line


title: E3_5_MUT.MUT_25

description: single cell


title: E3_5_MUT.MUT_23

description: single cell


title: E3_5_MUT.MUT_17

description: single cell


title: E3_5_MUT.MUT_16

description: single cell


title: E3_5_WT_or_HET.HET_15

description: single cell

value: Heterozygote


title: E3_5_MUT.MUT_18

description: single cell


title: E3_5_MUT.MUT_19

description: single cell


title: E3_5_MUT.MUT_21

description: single cell


title: E3_5_MUT.MUT_20

description: single cell


title: E3_5_WT_or_HET.HET_16

description: single cell


title: E3_5_WT_or_HET.HET_14

description: single cell


title: E3_5_WT_or_HET.HET_11

description: single cell


title: E3_5_WT_or_HET.HET_13

description: single cell


title: E3_5_WT_or_HET.HET_12

description: single cell


title: E3_5_MUT.MUT_26

description: single cell


title: E3_5_WT_or_HET.HET_10

description: single cell


title: E3_5_WT_or_HET.HET_9

description: single cell


title: E3_5_WT_or_HET.HET_8

description: single cell


title: E3_5_WT_or_HET.HET_7

description: single cell


title: E3_5_MUT.MUT_24

description: single cell


title: E3_5_WT_or_HET.HET_4

description: single cell


title: E3_5_WT_or_HET.HET_6

description: single cell


title: E3_5_MUT.MUT_22

description: single cell


title: E3_5_WT_or_HET.HET_5

description: single cell


title: E3_5_WT_or_HET.HET_3

description: single cell


title: E3_5_WT_or_HET.HET_2

description: single cell


title: E3_5_WT_or_HET.WT_36

description: single cell


title: E3_5_WT_or_HET.WT_32

description: single cell


title: E3_5_WT_or_HET.WT_34

description: single cell


title: E3_5_WT_or_HET.WT_29

description: single cell


title: E3_5_WT_or_HET.WT_30

description: single cell


title: E3_5_WT_or_HET.WT_28

description: single cell


title: E3_5_WT_or_HET.WT_31

description: single cell


title: E3_5_WT_or_HET.WT_33

description: single cell


title: E3_5_WT_or_HET.WT_35

description: single cell


title: E3_5_WT_or_HET.WT_24

description: single cell


title: E3_5_WT_or_HET.WT_22

description: single cell


title: E3_5_WT_or_HET.WT_27

description: single cell


title: E3_5_WT_or_HET.WT_20

description: single cell


title: E3_5_WT_or_HET.WT_26

description: single cell


title: E3_5_WT_or_HET.WT_23

description: single cell


title: E3_5_WT_or_HET.WT_19

description: single cell


title: E3_5_WT_or_HET.WT_21

description: single cell


title: E3_5_WT_or_HET.WT_25

description: single cell


title: E3_5_WT_or_HET.WT_17

description: single cell


title: E3_5_WT_or_HET.HET_1

description: single cell


title: E3_5_MUT.MUT_15

description: single cell


title: E3_5_WT_or_HET.WT_18

description: single cell


title: E3_5_MUT.MUT_12

description: single cell


title: E3_5_MUT.MUT_13

description: single cell


title: E3_5_MUT.MUT_11

description: single cell


title: E3_5_MUT.MUT_14

description: single cell


title: E3_5_MUT.MUT_10

description: single cell


title: E3_5_MUT.MUT_6

description: single cell


title: E3_5_WT_or_HET.WT_16

description: single cell


title: E3_5_MUT.MUT_9

description: single cell


title: E3_5_WT_or_HET.WT_15

description: single cell


title: E3_5_WT_or_HET.WT_13

description: single cell


title: E3_5_MUT.MUT_7

description: single cell


title: E3_5_MUT.MUT_8

description: single cell


title: E3_5_WT_or_HET.WT_14

description: single cell


title: E3_5_WT_or_HET.WT_12

description: single cell


title: HEK-293T KCl TT-TL rep2

source_name: HEK-293T cells

value: siC-transfected HEK-293T cells

tag: stress

value: 1 hour 80 mM KCl

value: 5 minutes 1 mM


title: E3_5_MUT.MUT_4

description: single cell


title: E3_5_MUT.MUT_3

description: single cell


title: E3_5_MUT.MUT_1

description: single cell


title: E3_5_WT_or_HET.WT_8

description: single cell


title: E3_5_WT_or_HET.WT_9

description: single cell


title: E3_5_MUT.MUT_2

description: single cell


title: E3_5_WT_or_HET.WT_5

description: single cell


title: E3_5_WT_or_HET.WT_6

description: single cell


title: E3_5_WT_or_HET.WT_4

description: single cell


title: E3_5_WT_or_HET.WT_7

description: single cell


title: E3_5_WT_or_HET.WT_3

description: single cell


title: E3_5_WT_or_HET.WT_2

description: single cell


title: E3_5_WT_or_HET.WT_1

description: single cell


title: E4_5_MUT.MUT_19

description: single cell


title: E4_5_MUT.MUT_18

description: single cell


title: E3_5_WT_or_HET.WT_11

description: single cell


title: E4_5_MUT.MUT_16

description: single cell


title: E4_5_MUT.MUT_17

description: single cell


title: E3_5_MUT.MUT_5

description: single cell


title: E4_5_WT_or_HET_EPI.HET_22

description: single cell

source_name: Epiblast


title: E4_5_MUT.MUT_13

description: single cell


title: E4_5_WT_or_HET_PRE.HET_22

description: single cell

source_name: Primitive Endoderm


title: E3_5_WT_or_HET.WT_10

description: single cell


title: E4_5_MUT.MUT_14

description: single cell


title: E4_5_WT_or_HET_EPI.HET_20

description: single cell


title: E4_5_WT_or_HET_PRE.HET_21

description: single cell


title: E4_5_WT_or_HET_PRE.HET_20

description: single cell


title: E4_5_WT_or_HET_EPI.HET_18

description: single cell


title: E4_5_WT_or_HET_PRE.HET_19

description: single cell


title: E4_5_WT_or_HET_EPI.HET_17

description: single cell


title: E4_5_WT_or_HET_EPI.HET_19

description: single cell


title: E4_5_WT_or_HET_PRE.HET_18

description: single cell


title: E4_5_WT_or_HET_EPI.HET_16

description: single cell


title: E4_5_WT_or_HET_EPI.WT_15

description: single cell


title: E4_5_WT_or_HET_PRE.WT_7

description: single cell


title: E4_5_WT_or_HET_PRE.WT_6

description: single cell


title: E4_5_WT_or_HET_EPI.WT_13

description: single cell


title: E4_5_WT_or_HET_EPI.WT_11

description: single cell


title: E4_5_WT_or_HET_EPI.WT_14

description: single cell


title: E4_5_MUT.MUT_15

description: single cell


title: E4_5_WT_or_HET_EPI.WT_12

description: single cell


title: E4_5_MUT.MUT_12

description: single cell


title: E4_5_WT_or_HET_EPI.WT_8

description: single cell


title: E4_5_WT_or_HET_EPI.HET_21

description: single cell


title: E14 cells_control RNAi-rep1

source_name: E14 cells, control RNAi


title: E4_5_WT_or_HET_PRE.WT_5

description: single cell


title: E4_5_WT_or_HET_EPI.WT_10

description: single cell


title: E4_5_WT_or_HET_PRE.WT_4

description: single cell


title: E4_5_WT_or_HET_EPI.WT_7

description: single cell


title: E4_5_WT_or_HET_EPI.WT_6

description: single cell


title: 150 gene

source_name: breast cancer tissue


title: E4_5_WT_or_HET_PRE.WT_1

description: single cell


title: E4_5_WT_or_HET_EPI.WT_5

description: single cell


title: E4_5_WT_or_HET_PRE.WT_3

description: single cell


title: E4_5_WT_or_HET_EPI.WT_4

description: single cell


title: E4_5_WT_or_HET_PRE.WT_2

description: single cell


title: E4_5_WT_or_HET_EPI.WT_2

description: single cell


title: E4_5_WT_or_HET_EPI.WT_1

description: single cell


title: E4_5_WT_or_HET_EPI.HET_15

description: single cell


title: E4_5_WT_or_HET_EPI.WT_3

description: single cell


title: E4_5_WT_or_HET_PRE.HET_17

description: single cell


title: E4_5_WT_or_HET_PRE.HET_15

description: single cell


title: E4_5_WT_or_HET_EPI.HET_13

description: single cell


title: E4_5_WT_or_HET_PRE.HET_14

description: single cell


title: E4_5_WT_or_HET_EPI.HET_14

description: single cell


title: E4_5_WT_or_HET_EPI.WT_9

description: single cell


title: E4_5_WT_or_HET_EPI.HET_12

description: single cell


title: E4_5_WT_or_HET_PRE.HET_13

description: single cell


title: E4_5_WT_or_HET_EPI.HET_10

description: single cell


title: E4_5_MUT.MUT_10

description: single cell


title: E4_5_MUT.MUT_8

description: single cell


title: E4_5_MUT.MUT_7

description: single cell


title: E4_5_MUT.MUT_11

description: single cell


title: E4_5_MUT.MUT_9

description: single cell


title: E4_5_WT_or_HET_EPI.HET_9

description: single cell


title: E4_5_MUT.MUT_4

description: single cell


title: E4_5_MUT.MUT_5

description: single cell


title: E4_5_MUT.MUT_6

description: single cell


title: E4_5_MUT.MUT_2

description: single cell


title: E4_5_WT_or_HET_PRE.HET_10

description: single cell


title: E4_5_WT_or_HET_PRE.HET_11

description: single cell


title: E4_5_WT_or_HET_EPI.HET_8

description: single cell


title: E4_5_MUT.MUT_3

description: single cell


title: E4_5_WT_or_HET_PRE.HET_12

description: single cell


title: E4_5_WT_or_HET_PRE.HET_9

description: single cell


title: E4_5_WT_or_HET_PRE.HET_16

description: single cell


title: E4_5_WT_or_HET_EPI.HET_7

description: single cell


title: E4_5_WT_or_HET_PRE.HET_8

description: single cell


title: E4_5_WT_or_HET_PRE.HET_7

description: single cell


title: E4_5_WT_or_HET_EPI.HET_6

description: single cell


title: E4_5_WT_or_HET_EPI.HET_5

description: single cell


title: E4_5_WT_or_HET_EPI.HET_11

description: single cell


title: E4_5_WT_or_HET_EPI.HET_4

description: single cell


title: E4_5_WT_or_HET_PRE.HET_5

description: single cell


title: E4_5_WT_or_HET_PRE.HET_6

description: single cell


title: E4_5_WT_or_HET_PRE.HET_4

description: single cell


title: E4_5_WT_or_HET_EPI.HET_3

description: single cell


title: E4_5_WT_or_HET_PRE.HET_2

description: single cell


title: E4_5_WT_or_HET_PRE.HET_3

description: single cell


title: E4_5_WT_or_HET_EPI.HET_2

description: single cell


title: E4_5_MUT.MUT_1

description: single cell


title: 7 week old WT 994_7WT

city: Philadelphia

first: yinfei

last: tan

address: 333 cottman ave

department: Genomic Core

institute: Fox Chase Cancer Center

description: 7 week old WT

data_processing:
fastq files was generated at the basespace cloud
fastq files was aligned to mm10 using tophat2 to get bam files
Differentially expressed gene list was obtained by using cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff

source_name: Cardiac cell

extract_protocol:
Illumina stranded mRNA library prep kit was used
mRNA was enriched by using polyT beads, heat fragmentated, then reverse transcribled to cDNA.  Illumina adapters were ligated to the cDNA and PCR was performed to get the final library.

value: WT


title: 7 week old KO 995_7KO

description: 7 week old KO

value: EGFR KO


title: 7 week old KO 992_7KO

description: 7 week old KO


title: E4_5_WT_or_HET_EPI.HET_1

description: single cell


title: 7 week old WT 991_7WT

description: 7 week old WT


title: 9 week old WT 973_WT

description: 9 week old WT


title: 9 week old KO 972_KO

description: 9 week old KO


title: 9 week old KO 964_9KO

description: 9 week old KO


title: 9 week old KO 971_KO

description: 9 week old KO


title: 9 week old WT 970_WT

description: 9 week old WT


title: 9 week old WT 963_9WT

description: 9 week old WT


title: 7 week old WT 986_7WT

description: 7 week old WT


title: snATAC_MOs_P_rep2

city: La Jolla

first: Rongxin

last: Fang

state: CA

institute: Ludwig Institute for Cancer Research

data_processing:
Using a custom python script, we first de-multicomplexed FASTQ files by integrating the cell barcode (reads in in I1.fastq) into the read name (R1.fastq and R2 fastq) in the following format: "@"+"barcode"+":"+"original_read_name".
Demulticomplexed reads were aligned to the corresponding reference genome (mm10) using bwa (0.7.13-r1126) in pair-end mode with default parameter settings. Alignments were then sorted based on the read name using samtools (v1.9).
Pair-end reads were converted into fragments and only those that are 1) properly paired (according to SMA flag value); 2) uniquely mapped (MAPQ > 30); 3) with length less than 1000bp were kept.
Since fragments were sorted by barcode (integrated into the read name), fragments belonging to the same cell (or barcode) were automatically grouped together which allowed for removing PCR duplicates for each cell separately.
Using remaining fragments, a snap-format (Single-Nucleus Accessibility Profiles) file was generated.
Genome_build: mm10
Supplementary_files_format_and_content: snap file is hierarchically structured hdf5 file that contains the following sessions: header (HD), cell-by-bin matrix (BM), cell-by-peak matrix (PM), cell-by-gene matrix (GM), barcode (BD) and fragment (FM). HD session contains snap-file version, date, alignment and reference genome information. BD session contains all unique barcodes and corresponding meta data. BM session contains cell-by-bin matrices of different resolutions (or bin sizes). PM session contains cell-by-peak count matrix. PM session contains cell-by-gene count matrix. FM session contains all usable fragments for each cell. Fragments are indexed for fast search. A detailed documentation of snap file can be found here (https://docs.google.com/document/d/1AGyn_WJTr0A1SKcfrEgum-jvAJjWd84jZ6DwbwiGRaQ/edit?usp=sharing)

source_name: posterior of secondary motor cortex

extract_protocol:
Nuclei were isolated from frozen mouse brain sections and permeabilized. Nuclei were tagmented with Tn5 in 96 wells to introduce a first barcode (T5 and T7). After pooling, 20 nuclei were sorted into 768 wells and a second barcode (i5 and i7) was introduced by PCR.
Nuclei were tagmented with Tn5 in 96 wells to introduce a first barcode (T5 and T7). After pooling, 20 nuclei were sorted into 768 wells and a second barcode (i5 and i7) was introduced by PCR. Libraries were sequenced on a HiSeq2500 (Illumina) with following read lengths: 50 + 16 + 16 + 50 (Read1 + Index1 + Index2 + Read2). The first 8 bpof Index1 correspond to the T7 barcode and the last 8 bp to the i7 barcode. The first 8 bp of Index2 correspond to the i5 barcode and the last 8 bp to the T5 barcode.

tag: strain

value: Male


title: snATAC_MOs_A_rep2

source_name: anterior of secondary motor cortex


title: snATAC_MOs_M_rep2

source_name: middle of secondary motor cortex


title: snATAC_MOs_M_rep1


title: 3'-seq siRRP40xsiINTS11 xPAP rep 3

city: Aarhus C

first: Søren

last: Lykke-Andersen

address: C.F.Møllers Allé 3

department: Molecular Biology and Genetics

institute: Aarhus University

description: 4sU-labeled RNA

data_processing:
Illumina software used for basecalling (Casava) and demultiplexing
TT-seq/RNA-seq: the fastq files were mapped to the reference genome (GRCh38 + RNA spike-ins) using STAR aligner to generate the BAM alignment files
TT-seq/RNA-seq: the BAM files were filtered to contain only uniquely mapped reads with Samtools
TT-seq/RNA-seq: Size-factors for sequencing depth normalization were obtained using the DESeq2 algorithm from counts on reduced GenCode v21 annotation generated with HTSeq. The reads mapping to spike-ins were used to estimate antisense and contamination bias (contaminating unlabeled RNA in 4sU-labeledRNA).  TT- and RNA-seq data were corrected accordingly. The experiments were done in duplicates in two batches and the data were batch corrected using the limma package.
TT-seq/RNA-seq: TT-seq/RNA-seq: Size-factors for sequencing depth normalization were obtained using the DESeq2 algorithm from counts on reduced GenCode v21 annotation generated with HTSeq. The reads mapping to spike-ins were used to estimate antisense and contamination bias (contaminating unlabeled RNA in 4sU-labeledRNA).  TT- and RNA-seq data were corrected accordingly. The experiments were done in duplicates in two batches and the data were batch corrected using the limma package.
3'-seq: reads were trimmed using the bbduk.sh script from BBMAP and homopolymeric A-stretches removed from reads.
3'-seq: the data was mapped using STAR against a compound index composed of hg38 merged with ERCC spike-ins.
3'-seq: 5' ends of uniquely mapped reads were used for downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig; normalized and bias corrected coverage generated with…

source_name: tissue culture cells

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
TT-seq/RNA-seq: Six in vitro transcribed spike-in RNAs were added to the lysates (TRIzol, Thermo) followed by extraction of RNA according to the manufacturer’s protocol. The RNA was then sonicated and used as input for RNA-seq or for further purification of 4sU-labeled RNA. 4sU-labeled RNA was first biotinylated with EZ-Link HPDP-Biotin (Pierce) and isolated with µMACS Streptavidin Kit (Miltenyi). 4sU-labeld RNA was eluted by cleaving off the biotin with DTT. Both total RNA and 4sU-labeled RNA purified prior to libary preparation using the miRNeasy Micro Kit (Qiagen) including DNse I treatment to remove genomic DNA.
3'-seq:
TT-seq/RNA-seq RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded Total RNA Sample Prep kit).
3'-seq libraries were generated with standard and modified Lexogen 3'-seq protocols. The modified preapration included 3'end polydenylation in vitro using E.coli poly(A) polymerase ('xPAP') preceeding the NGS library preparation with the QuantSeq REV kit according to manufacturer's protocol (Lexogen).
RNA-Seq, paired-end; RNA 3'end seq, single-end

treatment_protocol: Two rounds of transfections were performed. The first transfections were performed using SilentFect (final dilution 1:1000) in RPMI 1640 medium. Two days after the first transfection, the media was changed, and the transfection was repeated using Lipofectamine 2000 (final dilution 1:1000) in RPMI 1640 medium. siRNAs were used at a final concentration of 15 nM of each siRNA. 24 hours after the second round of transfections, cells were labelled for 5 min or 10 min for TT-seq or 3'-seq, respectively, with 500 µM 4-thiouridine minutes and harvested.

value: HeLa Kyoto

value: cervix

tag: cell type

value: epithelial

tag: sirna

value: RRP40 + INTS11

tag: rna treatment

value: polydenylation with E.coli poly(A) polymerase ('xPAP')


title: E4_5_WT_or_HET_PRE.HET_1

description: single cell


title: 3'-seq siRRP40xsiINTS11 noPAP rep 3

description: 4sU-labeled RNA


title: 3'-seq siRRP40xsiINTS11 noPAP rep 2

description: 4sU-labeled RNA


title: 3'-seq siRRP40 xPAP rep 2

description: 4sU-labeled RNA


title: 7 week old KO 987_7KO

description: 7 week old KO


title: SLA23

city: Rome

first: Julie

last: Martone

address: P.le Aldo Moro 5

country: Italy

institute: "Sapienza" University

data_processing:
Illumina Casava 1.9 software was used for basecalling.
Trimmomatic software was used to remove adapter sequences, setting the simple clip threshold to 8. Reads whose length after trimming was less than 18 nucleotides were discarded.
Bowtie with parameters -v 0 --best --norc -m 1 was then used to align remaining reads to microRNA spike-in sequences. Reads mapping to both exogenous miRNAs were counted using a custom Python script. Since very few reads mapped on cel-miR-2, which was absent from most of the samples, we decided to use only cel-lin-4 for normalization.
We then used Bowtie with --best -v 0 switches to align reads not mapping to spike-in sequences to a sequence database derived from mirBase 21 and composed of canonical human microRNAs and their putative isoforms.
Isomirage software was used to count reads mapping on the template isoforms of each miRNA.
Genome_build: MirBase 21 human miRNAs.
Supplementary_files_format_and_content: Tab-separated raw count table.

source_name: SERUM

extract_protocol:
Circulating microRNAs were extracted from 200µl of serum by miRCURYTM RNA Isolation Kit-Biofluids.
Small RNA libraries were generated from total RNA using TruSeq Small RNA Library Preparation Kit.

tag: disease

value: ALS patient


title: 3'-seq siRRP40 xPAP rep 3

description: 4sU-labeled RNA

tag: tissue


title: 3'-seq siRRP40xsiINTS11 xPAP rep 1

description: 4sU-labeled RNA


title: 3'-seq siRRP40xsiINTS11 noPAP rep 1

description: 4sU-labeled RNA


title: SLA24


title: SLA22


title: snATAC_MOs_P_rep1


title: SLA21


title: snATAC_MOs_A_rep1


title: 3'-seq siRRP40 noPAP rep 1

description: 4sU-labeled RNA


title: SLA16


title: 3'-seq siRRP40 noPAP rep 3

description: 4sU-labeled RNA


title: SLA15


title: SLA10


title: Leukemia cells JOK1 replicate4

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

description: RhoH expression consequences in JOK1 cells, replicate4

hyb_protocol: Agilent-012391 Whole Human Genome Microarray 44K were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.9.1.3.1).

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction and LOWESS normalization.

label_protocol: manufacturer's instructions

growth_protocol: Cell lines were grown as described by Galiègue-Zouitina et al (2008) Cancer Res, 68, 4531-4540; Delestré et al (2011) Biochem J, 437, 75-88; Poret et al (2015) Cancer Res, 75, 3902-3911

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: Cell lines were treated as described by Galiègue-Zouitina et al (2008) Cancer Res, 68, 4531-4540; Delestré et al (2011) Biochem J, 437, 75-88; Poret et al (2015) Cancer Res, 75, 3902-3911

tag: treatment

value: RhoH vector

value: empty vector


title: 3'-seq siRRP40 noPAP rep 2

description: 4sU-labeled RNA


title: Leukemia cells JOK1 replicate3

description: RhoH expression consequences in JOK1 cells, replicate3


title: 3'-seq siINTS11 xPAP rep 3

description: 4sU-labeled RNA


title: 3'-seq siINTS11 xPAP rep 1

description: 4sU-labeled RNA


title: 3'-seq siRRP40xsiINTS11 xPAP rep 2

description: 4sU-labeled RNA


title: SLA6


title: Leukemia cells JOK1 replicate1

description: RhoH expression consequences in JOK1 cells, replicate1


title: 3'-seq siINTS11 noPAP rep 3

description: 4sU-labeled RNA


title: SLA8


title: SLA4


title: WT6

value: healthy


title: SLA2


title: 3'-seq siLUC xPAP rep 3

description: 4sU-labeled RNA

value: Luciferase


title: 3'-seq siINTS11 noPAP rep 2

description: 4sU-labeled RNA


title: WT5


title: SLA3


title: 3'-seq siLUC xPAP rep 2

description: 4sU-labeled RNA


title: WT4


title: 3'-seq siINTS11 noPAP rep 1

description: 4sU-labeled RNA


title: 3'-seq siLUC noPAP rep 3

description: 4sU-labeled RNA


title: 3'-seq siLUC xPAP rep 1

description: 4sU-labeled RNA


title: 3'-seq siINTS11 xPAP rep 2

description: 4sU-labeled RNA


title: 3'-seq siLUC noPAP rep 1

description: 4sU-labeled RNA


title: 3'-seq siLUC noPAP rep 2

description: 4sU-labeled RNA


title: WT3


title: WT2


title: Sham_6h_2

city: Wuhan

first: Dong

last: Chen

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description: lung tissue of rats collected at 6h after having surgery to marginally rotate their pancreas

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Qvalue < =0.05
Genome_build: rat_ensembl_v6
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

organism: Rattus norvegicus

source_name: lung tissue

growth_protocol: Sixty healthy male Sprague Dawley (SD) rats (specific pathogen-free, eight weeks old, 180–220 g) with animal license number SYXK (Liao) 2013-0003 were purchased from the Laboratory Animal Center of Dalian Medical University. Another animal license number, SCXK (Liao) 2013-0006 (with qualified number 211003700), was also acquired. The animals were housed in PVC cages. The temperature was controlled at 22 ± 2ºC in a room with 12 h light-dark cycles and free access to standard laboratory food and drinking water for one week prior to the experiments.

extract_protocol:
Total RNA of each lung tissue sample was extracted using TRIzol Reagent (Ambion) according to the manufacturer’s instructions. To eliminate any DNA present, RQ1 DNase (Promega) was added to the extracted total RNA. The absorbance of the purified RNA was measured to determine the quality and concentration with a Smartspec plus (BioRad, Hercules, USA) at 260 nm/280 nm (A260/A280). Agarose gel electrophoresis (1.5%) was conducted to verify the integrity of the RNA
For RNA-seq library preparation, 10 μg of purified total RNA of each sample was purified and concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen). Polyadenylated mRNAs were used for the construction of a directional RNA-seq library. Ion fragmentation of purified mRNAs was conducted at 95ºC following end repair and 5' adaptor ligation. The fragmented mRNAs were reverse-transcribed with RT primer, known 3' adaptors, and random hexamers. Then, purification and amplification of the cDNAs were conducted. The 200–500 bps of amplified cDNAs were collected. The cDNAs for each sample were quantified and stored at -80ºC until sequencing.

treatment_protocol: Animals were randomized into five groups (n = 12 per group); the control group, the sham-operated group, the SAP model group, the SAP-DEX treated group, and the SAP-emodin treated group. Furthermore, each group was sub-divided into 6 h and 24 h subgroups. Briefly, SD rats were denied food for 12 h but had free access to water and were then given 1% pentobarbital sodium anesthesia (intraperitoneal injection, 40 mg/100 g body weight) prior to the surgical operation. The SAP model was induced as previously described  by administering fresh 5.0% sodium taurocholate (0.1 mL/100 g body weight) into the biliopancreatic duct by standard retrograde infusion. This procedure induced SAP and eventually resulted in a SAP-induced ALI, which served as the model. Sterile saline of the same volume was given to the control group of animals. The sham group of animals had surgery to marginally rotate their pancreas. DEX (10 mg/kg body weight) was intravenously administered to the DEX group of animals at 2 h and 12 h post-operation, and an equivalent volume of sterile saline was intravenously administered to the other groups of animals. Emodin (40 mg/ kg body weight) was intragastrically given to the SAP-emodin group at 2 h and 12 h post-operation. An equal volume containing 0.5% carboxymethylcellulose sodium was intragastrically given to the other groups of animals. At 6 h and 24 h post-operation, blood samples were taken via the abdominal aorta for arterial blood gas analysis and serum harvesting, and then stored at -80ºC until used

value: lung


title: Sham_6h_3