title: Liver-control-1 (A517_2)

data_processing:
Illumina Casava1.7 software used for basecalling.
After filtering contaminant (aligned) reads, sequenced reads were then mapped to mm9 genome, RefSeq exons, splicing junctions using BWA v0.7.3 alignment algorithm
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Huber et al., Journal of immunology, 2012. In short, uniquely aligned reads to the exon and splicing-junction sites for each transcript  were counted and normalized by the size of the transcript and by the size of the library.
RNA for RNA-seq was extracted from livers collected from 2 control and 3 treated animals. Expression was compared between control and treated mice matched by weight at the beginning of the treatment ( A517_2/A517_1, A517_2/A517_3 and A517_4/A517_5). Expression change expressed as log2ratio for the 3 comparisons was then averaged.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Liver

extract_protocol:
Livers were removed, flash frozen, and RNA was harvested using Trizol reagent.
RNA-seq libraries were prepared from Tryzol extracted RNA samples from which rRNA was removed using Ribo-ZeroTM and following the TruSeq Stranded Total RNA Sample Prep kit protocol (Illumina).

value: liver


title: ire1b_TM_rep2

status: Public on Mar 31 2018

type: SRA

city: Ames

first: Stephen

last: Howell

state: Iowa

address: 1035A Roy J. Carver Co-Laboratory 1111 WOI Road

department: Department of Genetics, Development and Cell Biology

country: USA

institute: Plant Sciences Institute

description: Arabidopsis thaliana 7-days Seedlings

library_source: transcriptomic

data_processing:
All paired end data with read length 250 bp were aligned to Arabidopsis TAIR10 genome, using STAR (version 2.4.0 with parameters “--outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.10”)
Subsequently, reads count of each annotated gene was calculated by htseq-count (version 0.6.0 with parameters “-t mRNA -m intersection-nonempty --stranded no”).
Next, significantly differently expressed genes (DEGs) between each two samples were extracted with cutoff FDR (false discovery rate) < 0.01 using DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: txt files, count

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana 7-days Seedlings

growth_protocol: Seeds from WT, ire1b and ire1a ire1b were germinated and vertically grown on 100 mm × 100 mm square plates (Fisher Scientific) with 1/2 MS-0 media for 7 days.

extract_protocol:
Samples were harvested by sucking out the liquid with paper towel, and immediately ground into powder in liquid nitrogen. Total RNA extraction was extracted by using RNeasy Plant Mini Kit (QIAGEN, Cat. No. 74904).
RNA-seq libraries were prepared with paired-end and 250 nt

treatment_protocol: Seedlings with similar size were picked up and treated with DMSO (as the control) or with 5μg/mL TM in 6-well cell culture plates with liquid 1/2 MS-0 media (2.2g/L, 5% sucrose) for 6h.

tag: tissue

value: seedlings

tag: genotype

value: ire1b mutant

tag: replicate


title: Liver-MS417-3 (A517_5)

city: New York

first: Martin

middle: J.

last: Walsh

state: NY

address: One Gustave L. Levy Pl.

department: Structural and Chemical Biology

institute: Mount Sinai School of Medicine

molecule: total RNA

organism: Mus musculus

growth_protocol: Male ob/ob B6 mice were obtained from Taconic. They were single caged and pair fed a regular chow diet where the amount of food given to each control mouse corresponded to the mean amount ate by treated mice, fed ad libitum, the previous day.

treatment_protocol: At 10 weeks of age mice were being injected, by IP injection, with vehicle only (DMSO diluted in PBS) or MS417.  For the first 15 days mice were injected with a lower dose of 2.5mg/kg. For the remaining 2 weeks the higher 5mg/kg dose of MS417 was used.

tag: age

value: 14 weeks

tag: strain

tag: treatment


title: Liver-MS417-2 (A517_3)


title: Liver-MS417-1 (A517_1)


title: Brd4_ChIP-seq+MS417

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
read sequences were done QC filtering by FASTX ( -q 20 -p 90 )
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2
Peaks were called using SICER version 0.0.1 with setting: Redundancy Threshold (2), Window size (200), Fragment size (150), Effective genome fraction (0.74), Gap size (600), Statistic threshold value (FDR=0.01). To identify Brd4 bound MS417 sensitive binding sites from the 3T3-L1 Brd4_ChIP-seq the Brd4_ChIP-seq+MS417 ChIP was used as a control sample for the analysis.
Genome_build: mm9
Supplementary_files_format_and_content: wig and bed files was generated using SICER

molecule: genomic DNA

growth_protocol: Mouse 3T3-L1 cell line was maintained in DMEM containing 10% fetal bovine serum and 5% penicillin/streptomycin. At 2 days post-confluence 3T3-L1 pre-adipocytes were differentiated into adipocytes using differentiation inducing cocktail of 1μM Dexamethasone (Dex), 0.5mM isobutyl-methyl-xanthine (IBMX) and 167nM insulin in DMEM with 10% FBS. After three and five days of induction cells were washed with PBS and complete medium containing 167nM insulin was added. The ChIP experiment was performed on DMSO control and MS417 treated differentiating 3T3-L1 cells 5 days post differentiation induction.

extract_protocol:
Lysates were clarified from sonicated nuclei and Brd4-DNA complexes were isolated with antibody.
ChIP-DNA was end repaired with T4 DNA polymerase and polynucleotide kinase. An A-base was added to the end-repaired DNA fragments. Solexa adaptors were ligated to the ChIP DNA fragments and 200-300bp size fractions were excised from 2% agarose gel stained with GelStar. Adaptor-modified fragments were enriched by 16 cycles of PCR amplification. The DNA library prep was validated in Bioanalyzer for quantity and size.

treatment_protocol: Cells were treated with 1μM MS417 or as control with 1μL/1mL DMSO in parallel with the differentiation.

tag: cell type

value: adipocytes differentiated for 5 days

tag: cell line

value: MS417 BET-inhibitor

tag: antibody

value: Brd4 (Bethyl IHC-00396)


title: 32+29N-MSCs [32_B]

city: LAUSANNE

first: Mathieu

last: Quinodoz

state: Vaud

address: Rue du Bugnon 27

department: DBC

country: Switzerland

institute: Université de Lausanne

description:
32_B
normcount-32_B

data_processing:
mapping to reference genome with TopHat
table of counts with HTSeq
normalization and DE with edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including normalized counts for each Sample

organism: Homo sapiens

source_name: Tumor cells

growth_protocol: Primary lung cancer cells were isolated from tumor tissues removed by surgical resection at Centre Universitaire Hospitalier Vaudois (CHUV) with the agreement of the Swiss ethic committee (project authorization n° 131/12) from patients 21 and 32 diagnosed with lung squamous cell carcinoma. After tissue dissociation, single cell tumor bulk were cultured as spheres in ultra-low attachment flasks (Corning, Falcon) in KO medium: IMDM+GlutaMAX completed with 20% knockout serum (Gibco), 20 ng/mL leukemia inhibitory factor (LIF, Prospec), 20 ng/mL recombinant human (rh) epidermal growth factor (EGF, Prospec), 20 ng/mL fibroblast growth factor (FGF, Prospec) and 1% penicillin streptomycin (PS, Gibco). Depending on proliferation speed and size, spheres were dissociated by pipetting in PBS1x and half of the medium refreshed, or split at a 1:3 dilution. Primary mesenchymal stem cells (MSCs) were isolated from tumor tissue (-T) or normal adjacent tissue (N-) from the same patient or from patient 29. MSCs were cultured in adherent conditions in MSC medium: IMDM+GlutaMAX (Gibco) supplemented with 10% fetal bovine serum (FBS, PAN Biotech), 1% PS, 1% non-essential amino acids (NEAA, Gibco) and 10 ng/mL platelet-derived growth factor (PDGF, Prospec). Upon reaching 80% confluence, cells were split 1:4 - 1:6 using trypsin-EDTA 0.25 mg/ml (Lonza, USA).

extract_protocol:
RNA was extracted using miRCURY RNA isolation kit (Exiqon) including a DNAse step with RNAse-Free DNase set (QIAGEN) following the manufacturer’s instructions.
TruSeq stranded mRNA; polyA capture

treatment_protocol: Sphere-forming tumor cells from patients 21 and 32 were dissociated as single cells and seeded in ultra-low attachment six well plates (Costar, Corning) in transwell culture at 50000 cells/well with N- or T-MSCs from the same patient or from patient 29. Co-cultures were performed at 1:1 tumor:MSC cell ratios for 5 days. MSC cells were seeded into 1,0 µm-pore insert of PET-membrane (Corning, Falcon). Controls were tumor cells cultured alone. Cells were cultured in 4 ml of KO medium, half of which was refreshed at day 3. After removal of the upper chamber containing MSC cells, tumor cells were harvest, washed twice in ice-cold PBS, snap frozen and stored at -80°C until RNA extraction.

tag: patient id #

tag: patient status

value: moderately differentiated squaous cell lung carcinoma

value: Primary lung cancer cells

tag: passages

tag: cocultured with

value: mesenchymal stem cells (MSCs) isolated from the tumor tissue (T-)

tag: mscs isolated from

value: patient 29


title: 32_alone [32_A]

description:
32_A
normcount-32_A

value: none (alone)


title: 3T3-L1_diff

data_processing:
Illumina Casava1.7 software used for basecalling.
After filtering contaminant (aligned) reads, sequenced reads were then mapped to mm9 genome, RefSeq exons, splicing junctions using BWA v0.7.3 alignment algorithm
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Huber et al., Journal of immunology, 2012. In short, uniquely aligned reads to the exon and splicing-junction sites for each transcript  were counted and normalized by the size of the transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Mouse 3T3-L1 cell line was maintained in DMEM containing 10% fetal bovine serum and 5% penicillin/streptomycin. At 2 days post-confluence 3T3-L1 pre-adipocytes were differentiated into adipocytes using differentiation inducing cocktail of 1μM Dexamethasone (Dex), 0.5mM isobutyl-methyl-xanthine (IBMX) and 167nM insulin in DMEM with 10% FBS. After three and five days of induction cells were washed with PBS and complete medium containing 167nM insulin was added.

extract_protocol:
Total RNA for each condition was Trizol-extracted.
RNA-seq libraries were prepared from Tryzol extracted RNA samples from which rRNA was removed using Ribo-ZeroTM and following the TruSeq Stranded Total RNA Sample Prep kit protocol (Illumina).

treatment_protocol: Cells were treated with 1μM MS417 or as control with 1μL/1mL DMSO in parallel with the differentiation. RNA-seq was used to measure gene expression levels in control differentiating (5 days post-induction of differentiation) and MS417 treated differentiating (the inhibitor was added to the differentiation media 12h post induction) 3T3-L1 adipocytes.

tag: differentiation stage

value: 5 days post induction

value: DMSO control


title: 3T3-L1_diff_417


title: 21_alone [21_A]

description:
21_A
normcount-21_A

value: moderately differentiatied squamous cell lung carcinoma


title: 21+29N-MSCs [21_B]

description:
21_B
normcount-21_B


title: Brd4_ChIP-seq

value: DMSO-control


title: 32+29T-MSCs [32_C]

description:
32_C
normcount-32_C

value: mesenchymal stem cells (MSCs) isolated from normal lung tissues (N-)


title: 32+32N-MSCs [32_2]

description:
32_2
normcount-32_2

value: patient 32


title: 21+21T-MSCs [21_3]

description:
21_3
normcount-21_3

value: patient 21


title: 21_alone [21_1]

description:
21_1
normcount-21_1


title: Liver-control-2 (A517_4)

value: liver

value: DMSO


title: 3T3-L1_ndnt

value: non differentiated preadipocytes

value: no treatment


title: 32_alone [32_1]

description:
32_1
normcount-32_1


title: IRBB67 120hpi Xoo High temperature rep 2

city: Metro Manila

first: Sylvestre Gerbert

last: Dossa

address: DAPO Box

department: Genetics and Biotechnology

country: Philippines

institute: International Rice Research Institute

description:
Biological replication 2
Xoo (Xanthomonas oryzae pv. oryzae, strain PXO145 from the Philippines)

data_processing:
Demultiplexing: CASAVA v1.8.2, 1MM allowed for index
Alignment: The reads of each sample were mapped to the rice genome version 7 of the Rice Genome Annotation Project (RGAP) at MSU using clc biogenomics workbench v7.0.4 with the following parameters: 2 for mismatch cost, 3 for insertion cost and deletion cost, 0.5 for length fraction and 0.8 for similarity fraction.
The expression data for each sample was exported from clc biogenomics workbench and analyzed in the R/Bioconductor environment loading DESeq2, gplot, ggplot2 packages.
The differentially expressed genes based on a generalized linear model likelihood ratio test assuming negative binomial data distribution was done via DESeq2 and candidate genes were filtered to a minimum of 4X fold change and FDR-corrected p-value<0.05.
Genome_build: MSU7
Supplementary_files_format_and_content: csv files were generated from clc biogenomics workbench v7.0.4

organism: Oryza sativa

source_name: leaf

growth_protocol: Rice genotypes IR24 (susceptible), and IRBB67 (Xa4+Xa7) seeds were pre-germinated for 4 days at 37°C and transferred in pot for further growth under greenhouse conditions (12h light and 12h dark). Two weeks old healthy plants were then transferred into indoor growth chambers under two temperature regimes (29/21 °C and 35/31 °C; day/night temperatures) and 70% of relative humidity and inoculated at 21 days old. Philippines Xoo race 7, strain PXO145 (avrXa4+avrXa7) inoculums was prepared from 3 days old culture. Seedling of IR24 and IRBB67 at 21 days old were syringe needless inoculated with PXO145 and sterilized demineralized water (Mock) for RNA-Seq gene expression analysis. Leaf at the second position of the main tiller was inoculated and leaves were sampled at 3, 72 and 120 hours post inoculation (hpi). A pulled leaves from 5 plants for each rice genotype treatment at each time point and immediately frozen in liquid nitrogen, and stored at -80°C until total RNA extraction.

extract_protocol:
Total RNA was extracted from syringe needless inoculated leaves using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer protocol. Total RNA was then treated with DNase (Promega) and quantified using NanoDrop. RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). For each time point and condition, two biological replicates and cleaned total RNA.
Libraries were prepared according to Illumina's instructions. Briefly, Single-end fragment library of 100bp length was generated from cleaned total RNA following the TruSeq RNA Sample Preparation kit.  Cluster generation of the produced libraries was performed using Illumina_ TruSeq SR Cluster Kit v3 - cBot - HS, and sequenced on a HiSeq 2000 platform (Illumina) with single-end 100-bp reads.

tag: innoculation

value: Leaf

value: 21 days old

tag: temperature

value: high

tag: collection time point


title: 21+21N-MSCs [21_2]

description:
21_2
normcount-21_2

value: Primary lung cancer cells

value: mesenchymal stem cells (MSCs) isolated from the tumor tissue (T-)


title: IR24 120hpi Xoo High temperature rep 2

tag: tissue

tag: genotype


title: 21+29T-MSCs [21_C]

description:
21_C
normcount-21_C

value: patient 29


title: IRBB67 120hpi Xoo Low temperature rep 2

tag: age

value: low


title: IRBB67 72hpi Xoo High temperature rep 2


title: IR24 120hpi Xoo Low temperature rep 2


title: IRBB67 72hpi Xoo Low temperature rep 2


title: IR24 3hpi Xoo High temperature rep 2


title: IRBB67 3hpi Xoo High temperature rep 2


title: IR24 72hpi Xoo Low temperature rep 2


title: IRBB67 120hpi Mock High temperature rep 2

description:
Biological replication 2
Mock (sterile demineralized water)

value: Water


title: IRBB67 3hpi Xoo Low temperature rep 2


title: IRBB67 120hpi Mock Low temperature rep 2


title: IR24 120hpi Mock Low temperature rep 2


title: I2

city: Hangzhou

first: Yujian

last: Jin

state: Zhejiang

address: Chaowang Road 18

country: China

institute: Zhejiang University of Technology

description: ion Al treatment

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using tophat v2.0.12 with default parameters
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using HTseq v0.6.0. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: ion Al treatment

extract_protocol:
Root samples were frozen in the liquid N2 as soon as harvested, and were stored at -80 °C for further processing. Total RNA was extracted using Trizol Reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina®(#E7530L，NEB)was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype

value: Columbia

value: wild type

tag: developmental stage

value: vegetative stage

value: root


title: IR24 3hpi Xoo Low temperature rep 2


title: N2

description: nAl2O4 treatment

source_name: nAl2O4 treatment


title: 32+32T-MSCs [32_3]

description:
32_3
normcount-32_3

value: moderately differentiated squaous cell lung carcinoma

tag: cell type

value: mesenchymal stem cells (MSCs) isolated from normal lung tissues (N-)

value: patient 32


title: IR24 120hpi Mock High temperature rep 2


title: C1

description: Control group

source_name: Control group


title: IRBB67 3hpi Mock High temperature rep 2


title: IR24 72hpi Mock High temperature rep 2


title: IR24 72hpi Mock Low temperature rep 2


title: C2

description: Control group


title: IRBB67 72hpi Mock Low temperature rep 2


title: IR24 72hpi Xoo High temperature rep 2


title: IR24 3hpi Mock High temperature rep 2


title: IRBB67 72hpi Mock High temperature rep 2


title: IR24 3hpi Mock Low temperature rep 2


title: IRBB67 3hpi Mock Low temperature rep 2


title: IRBB67 120hpi Xoo High temperature rep 1

description:
Biological replication 1
Xoo (Xanthomonas oryzae pv. oryzae, strain PXO145 from the Philippines)


title: IR24 120hpi Xoo High temperature rep 1


title: I1

description: ion Al treatment


title: IRBB67 120hpi Xoo Low temperature rep 1


title: IRBB67 72hpi Xoo High temperature rep 1


title: IR24 72hpi Xoo High temperature rep 1


title: IRBB67 72hpi Xoo Low temperature rep 1


title: IR24 72hpi Xoo Low temperature rep 1


title: IR24 120hpi Xoo Low temperature rep 1


title: N1

description: nAl2O3 treatment

source_name: nAl2O3 treatment


title: IR24 3hpi Xoo High temperature rep 1


title: IRBB67 3hpi Xoo High temperature rep 1


title: YS5

city: Charlestown

first: Yuya

last: Sugano

state: MA

address: 149 13th Street

department: Nephrology

institute: Massachusetts General Hospital

data_processing:
none provided by the submitter
Genome_build: n/a
Supplementary_files_format_and_content: raw counts

organism: Danio rerio

source_name: DL segments

extract_protocol:
DL segments were manually micro-dissected from Tg(slc12a3:mCherry) and RNAs were extracted using the RNA extraction kit (Machery-Nagel).
Apaptor-ligated cDNA libraries were constructed using Ovation Single Cell RNA-seq System (NuGEN).

tag: transgene

value: mCh+

value: adult


title: IR24 3hpi Xoo Low temperature rep 1

value: Leaf


title: YS3


title: YS1


title: IRBB67 72hpi Mock High temperature rep 1

description:
Biological replication 1
Mock (sterile demineralized water)

value: 21 days old


title: IR24 72hpi Mock Low temperature rep 1


title: IRBB67 72hpi Mock Low temperature rep 1


title: IRBB67 3hpi Mock High temperature rep 1

value: high


title: IR24 120hpi Mock High temperature rep 1


title: YS2

source_name: Mesonephros - DL

value: mCh-


title: IRBB67 120hpi Mock Low temperature rep 1


title: IR24 120hpi Mock Low temperature rep 1


title: YS4


title: IRBB67 3hpi Xoo Low temperature rep 1


title: IRBB67 120hpi Mock High temperature rep 1


title: IR24 3hpi Mock Low temperature rep 1


title: IR24 72hpi Mock High temperature rep 1


title: YS6


title: IR24 3hpi Mock High temperature rep 1


title: IRBB67 3hpi Mock Low temperature rep 1


title: WT-G60-BR2

city: Wuhan

first: Jianmei

last: Long

state: Hubei

address: shizishan street NO.1

institute: Huazhong Agricultural University

description: replicate 2 for transgenic samples at 60 DAI

data_processing:
The raw reads were filtered by removing low-quality reads, contaminants and trimming adaptor sequences, leaving the primary clean reads.
First 11 bp nucleotides were trimmed by trimmomatic to obtaining high-quality clean reads.
The high-quality clean reads were mapped to reference genome of clementine (version10.0,) with two mismatches allowed using HISAT2 followed by assembled with StringTie (Pertea et al., 2016).
Raw counts of each gene were caculated by Htseq-count
Differentially expressed genes were indentified by edgeR according to the criteria of absolute log2-fold change ≥1.0 and false discovery rate (FDR) < 0.05.
Genome_build: the genome assemblies of Clementine mandarin (Citrus reticulata,  http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV10 )

organism: Citrus hindsii

source_name: callus with somatic embryos presence

extract_protocol:
Total RNA was extracted by Trizol method
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer's instruction and index codes were added to attribute suqence to each sample.

treatment_protocol: The transgenic and wild type callus were moved from MT growth medium (Murashige and Tucker, 1969) with 4% sucrose to MT medium with 2% glycerol  to induce somatic embryos. The callus were collected at 40 and 60 DAI, respectively.

tag: common name

value: Hongkong kumquat

value: callus with somatic embryos presence

tag: genotype/variation


title: WT-G60-BR1

description: replicate 1 for transgenic samples at 60 DAI


title: OE-G40-BR1

description: replicate 1 for transgenic samples at 40 DAI

source_name: callus without somatic embryos presence

value: callus without somatic embryos presence

value: overexpressing csi-miR156a


title: OE-G60-BR2


title: WT-G40-BR1


title: OE-G40-BR2

description: replicate 2 for transgenic samples at 40 DAI


title: WT-G40-BR2


title: MtbA rep2

city: New Delhi

first: Sheetal

last: Gandotra

address: Sukhdev Vihar, Mathura Road

department: Chemical and System Biology

country: India

institute: CSIR-Institute of Genomics and Integrative Biology

data_processing:
Raw sequence data were collected from Illumina MiSeq
Quality checked reads were aligned to Mycobacterium tuberculosis H37Rv reference genome using bowtie2
Using Tuberculist annotations, read count per gene was calculated using HTSEQ
Differential expression analysis was performed using DESeq2
Genome_build: Mycobacterium tuberculosis H37Rv
Supplementary_files_format_and_content: Raw read counts per gene in csv format

organism: Mycobacterium tuberculosis H37Rv

source_name: Mtb isolated from infected 3T3L1 adipocytes

growth_protocol: Infection performed for 24h at MOI1 followed by removal of extracellular bacteria. RNA isolated from bacteria at d10 post infection. Equal number of bacteria inoculated in complete DMEM meduim

extract_protocol:
Bacteria were extracted from infected cells after treatmentw ith equal volume of GITC. Bacterial pellet was resuspended in Trizol LS for RNA extraction.DNA free RNA was depleted of 16S rRNA prior to library preparation
Purified RNA was DNase treated using Turbo DNAse (Ambion, AM2238) for 1h at 37°C. RNA was qualitatively and quantitatively estimated using Agilent 2100 Bioanalyzer. Subsequently, ribosomal RNA was depleted using Ribo-Zero Magnetic Gold Kit (Epidemiology), followed by sequencing library preparation using ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre). Samples were sequenced on an Illumina MiSeq platform) using 150-cycle paired-end chemistry with v3 kits.

tag: host cell line

tag: time point

value: d10 post infection

tag: replicate


title: MtbC rep1

source_name: Mtb in DMEM media

value: in vitro


title: MtbP rep2

source_name: Mtb isolated from infected 3T3L1 preadipocytes


title: M3_PFC_NeuN-_RNA_R2

status: Public on Mar 30 2018

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

data_processing:
Sequencing reads were trimmed by trim galore 0.3.7 with default setting.
ChIP-seq reads were aligned using bowtie 1.1.1. RNA-seq reads were aligned by TopHat v2.1.1.
ChIP-seq reads are extended to 250 bp and normalized based on the sequencing depth
Input signals are subtracted from ChIP-seq signals
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: bedgraph files of CpG methylation were generated using bismark_methylation_extractor. fpkm_tracking files were generated by Cufflinks.

source_name: NeuN- from prefrontal cortex

growth_protocol: GM12878 cells were cultured in RPMI 1640 medium (11875-093, Gibco) plus 15% fetal bovine serum (26140-079, Gibco) and 100 U/ml penicillin-streptomycin (15140-122, Gibco) at 37 ℃ in a humidified incubator with 5% CO2. Cells were sub-cultured every 2-3 days to maintain them in exponential growth phase.

extract_protocol:
The mouse line C57Bl/6 was bred and maintained in groups of 3-4 per cage with food ad libitum. 8-10 week old mice were anesthetized with isoflurane and decapitated. The cerebellum was rapidly dissected and frozen on dry ice and stored at -80 ℃ until used for nuclei isolation.  Cerebellum was placed in 5 ml ice-cold nuclei extraction buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM Tris-HCl and 0.1% Triton X-100) with freshly added 50 μl protease inhibitor cocktail (P8340, Sigma-Aldrich), 5 μl 100 mM PMSF and 5 μl 1 M DTT. In addition, 7.5 μl 40 U/μl RNase inhibitor (N2611, Promega) was also added when RNA-seq was conducted. Once thawed, the tissue was homogenized by slowly doucing for 15 times with a loose pestle (D9063, Sigma-Aldrich) and 25 times with a tight pestle (D9063, Sigma-Aldrich). The homogenate was transferred into an ultracentrifugation tube (355631, Beckman Coulter) and underlayered with 9.5 ml sucrose cushion (1.8 M sucrose, 3 mM Mg(Ac)2 and 10 mM Tris-HCl). The homogenate was centrifuged at 32,300 rpm (107,164g) for 2.5 h at 4 ℃ with 70 Ti rotor (Optima L-90K Ultracentrifuge, Beckman Counter). The spinning was slowly braked to avoid disturbing the nuclei pellet. All the supernatant was removed and the nuclei was gently resuspended in 0.4 ml 10% normal goat serum (50062Z, Life Technologies) and 1.6 ml Dulbecco's phosphate-buffered saline (14190144, Life Technologies). For RNA-seq, 3 μl 40 U/μl RNase inhibitor was added into nuclei suspension. The integrity and the number of nuclei were checked under the microscope. 32 μl 2 ng/μl anti-NeuN antibody conjugated with Alexa 488 (MAB377X, EMD Millipore) was incubated with the nuclei suspension (2 ml) for 1 h at 4 ℃ on an end-to-end rotator. The stained samples were sorted using a FACS (BD FACSAria, BD Biosciences) with 50,000 to 100,000 unlabeled nuclei used as non-staining control. Human genomic DNA was purified from GM 12878 cells using QIAamp DNA Blood Mini Kit (Qiagen) following the manufacturer’s protocol and suspended in 50 µl EB buffer. Mouse genomic DNA was purified using QIAamp DNA Blood Midi Kit (Qiagen) from nuclei and suspended in 200 µl AE buffer (10 mM Tris-Cl, 0.5 mM EDTA, pH 9.0). The eluate was reloaded on the column membrane and spun to maximize DNA yield. Mouse DNA was concentrated by ethanol precipitation to 20 µl EB buffer. RNA was extracted from ~10,000 nuclei using RNeasy Mini Kit (Qiagen). DNase treatment step was included following kit instructions to remove gDNA contamination.
SurfaceChIP-seq library construction. The sequencing libraries were constructed using TruePLEX DNA-seq kit (Rubicon Genomics) or Accel-NGS 2S plus DNA library kit (Swift bioscience). GM12878 samples starting with ≥ 100 cells using DNA oligo linker were prepared using TruePLEX kit. The other samples are prepared using Accel-NGS 2S plus kit following instructions. mRNA-seq library construction. RNA was extracted from ~100,000 nuclei using RNeasy Mini Kit (Qiagen). DNase treatment was included following manufacturer instructions to remove gDNA contamination. mRNA-seq libraries were prepared using SMART-seq v4 Ultra Low Input RNA kit (Clontech) and Nextera XT DNA library prep kit (Illumina) following instructions.

value: NeuN- from prefrontal cortex

value: 8-10 weeks

tag: strain


title: MtbP rep1


title: MtbA rep1


title: M3_Cerebellum_NeuN-_RNA_R2

source_name: NeuN- from cerebellum

value: NeuN- from cerebellum


title: M3_Cerebellum_NeuN-_H3K4me3_1k_R2


title: M3_PFC_NeuN+_RNA_R2

source_name: NeuN+ from prefrontal cortex

value: NeuN+ from prefrontal cortex


title: M3_Cerebellum_NeuN-_RNA_R1


title: M3_Cerebellum_NeuN-_H3K27me3_1k_R2


title: M3_Cerebellum_NeuN-_H3K27ac_1k_R2


title: M3_Cerebellum_NeuN+_H3K4me3_1k_R2

source_name: NeuN+ from cerebellum

value: NeuN+ from cerebellum


title: M3_Cerebellum_NeuN+_RNA_R1


title: M3_Cerebellum_NeuN+_H3K4me3_1k_R1


title: M3_Cerebellum_NeuN-_H3K4me3_1k_R1


title: OE-G60-BR1


title: M3_PFC_NeuN-_RNA_R1


title: MtbC rep2


title: M3_Cerebellum_NeuN+_RNA_R2


title: M3_Cerebellum_NeuN+_H3K27me3_1k_R2


title: M3_Cerebellum_NeuN-_H3K27ac_1k_R1


title: M3_PFC_NeuN-_H3K4me3_1k_R1


title: M3_Cerebellum_NeuN+_H3K27me3_1k_R1


title: M3_PFC_NeuN-_H3K27me3_1k_R1


title: M3_PFC_NeuN-_H3K27me3_1k_R2


title: M3_Cerebellum_NeuN+_H3K27ac_1k_R1


title: M3_Cerebellum_NeuN+_H3K27ac_1k_R2


title: M3_PFC_NeuN-_H3K27ac_1k_R2


title: M3_PFC_NeuN-_H3K27ac_1k_R1


title: M3_PFC_NeuN+_H3K27me3_1k_R2


title: M3_PFC_NeuN+_H3K27me3_1k_R1


title: M3_PFC_NeuN+_RNA_R1


title: M3_PFC_NeuN+_H3K4me3_1k_R2


title: M3_PFC_NeuN+_H3K4me3_1k_R1


title: M3_Cerebellum_NeuN-_H3K27me3_1k_R1


title: M3_PFC_NeuN+_H3K27ac_1k_R2


title: M2_Cerebellum_NeuN-_input


title: M2_Cerebellum_NeuN-_H3K27me3_1k_R1


title: M2_Cerebellum_NeuN-_H3K4me3_1k_R2


title: M2_Cerebellum_NeuN-_H3K27me3_1k_R2


title: M2_Cerebellum_NeuN-_H3K4me3_1k_R1


title: M2_Cerebellum_NeuN-_H3K4me3_100_R2


title: M2_Cerebellum_NeuN-_H3K27me3_100_R2


title: M3_PFC_NeuN-_H3K4me3_1k_R2


title: M2_Cerebellum_NeuN+_input


title: M2_Cerebellum_NeuN-_H3K27ac_1k_R1


title: M2_Cerebellum_NeuN-_H3K27ac_100_R2


title: M2_Cerebellum_NeuN-_H3K27ac_1k_R2


title: M2_Cerebellum_NeuN-_H3K27ac_100_R1


title: M2_Cerebellum_NeuN+_H3K4me3_1k_R2


title: M2_Cerebellum_NeuN+_H3K4me3_100_R1


title: M2_Cerebellum_NeuN+_H3K4me3_1k_R1


title: M2_Cerebellum_NeuN+_H3K4me3_100_R2


title: M2_Cerebellum_NeuN+_H3K27me3_1k_R1


title: M3_PFC_NeuN+_H3K27ac_1k_R1


title: M2_Cerebellum_NeuN+_H3K27me3_100_R1


title: M2_Cerebellum_NeuN+_H3K27me3_1k_R2


title: M2_Cerebellum_NeuN+_H3K27me3_100_R2


title: M2_Cerebellum_mix_H3K4me3_1k_R2

source_name: Cerebellum

value: Cerebellum


title: M2_Cerebellum_NeuN+_H3K27ac_1k_R2


title: M2_Cerebellum_NeuN-_H3K27me3_100_R1


title: M2_Cerebellum_mix_input


title: M2_Cerebellum_NeuN+_H3K27ac_1k_R1


title: M2_Cerebellum_NeuN+_H3K27ac_100_R1


title: M2_Cerebellum_NeuN+_H3K27ac_100_R2


title: M2_Cerebellum_mix_H3K4me3_10k_R1


title: M2_Cerebellum_mix_H3K4me3_1k_R1


title: M2_Cerebellum_mix_H3K4me3_10k_R2


title: M2_Cerebellum_mix_H3K27me3_1k_R2


title: M2_Cerebellum_mix_H3K4me3_100_R1


title: M2_Cerebellum_mix_H3K27me3_1k_R1


title: M2_Cerebellum_mix_H3K27me3_10k_R2


title: M2_Cerebellum_mix_H3K4me3_100_R2


title: M2_Cerebellum_mix_H3K27ac_1k_R1


title: M2_Cerebellum_mix_H3K27ac_1k_R2


title: M2_Cerebellum_mix_H3K27me3_100_R1


title: M2_Cerebellum_mix_H3K27ac_100_R2


title: M2_Cerebellum_mix_H3K27ac_10k_R2


title: M2_Cerebellum_mix_H3K27me3_10k_R1


title: M2_Cerebellum_mix_H3K27ac_10k_R1


title: M1_PFC_NeuN-_H3K4me3_1k_R1


title: M1_PFC_NeuN-_H3K4me3_1k_R2


title: M1_PFC_NeuN-_input


title: M1_PFC_NeuN-_H3K4me3_100_R2


title: M1_PFC_NeuN-_H3K4me3_100_R1


title: M1_PFC_NeuN-_H3K27me3_1k_R1


title: M1_PFC_NeuN-_H3K27me3_100_R1


title: M1_PFC_NeuN-_H3K27ac_1k_R2


title: M1_PFC_NeuN-_H3K27me3_100_R2


title: M1_PFC_NeuN+_H3K4me3_1k_R2


title: M1_PFC_NeuN-_H3K27ac_1k_R1


title: M2_Cerebellum_mix_H3K27ac_100_R1


title: M1_PFC_NeuN-_H3K27ac_100_R1


title: M1_PFC_NeuN+_H3K4me3_100_R2


title: M2_Cerebellum_mix_H3K27me3_100_R2


title: M1_PFC_NeuN+_input


title: M1_PFC_NeuN+_H3K4me3_100_R1


title: M1_PFC_NeuN+_H3K27me3_1k_R2


title: M1_PFC_NeuN+_H3K4me3_1k_R1


title: M1_PFC_NeuN+_H3K27me3_100_R2


title: M2_Cerebellum_NeuN-_H3K4me3_100_R1


title: M1_PFC_NeuN+_H3K27me3_1k_R1


title: M1_PFC_NeuN+_H3K27me3_100_R1


title: M1_PFC_NeuN+_H3K27ac_1k_R2


title: M1_PFC_mix_H3K4me3_10k_R2

source_name: Prefrontal cortex

value: Prefrontal cortex


title: M1_PFC_NeuN+_H3K27ac_1k_R1


title: M1_PFC_NeuN+_H3K27ac_100_R2


title: M1_PFC_mix_H3K27me3_1k_R2


title: M1_PFC_mix_input


title: M1_PFC_mix_H3K4me3_100_R1


title: M1_PFC_mix_H3K4me3_1k_R2


title: M1_PFC_NeuN-_H3K27me3_1k_R2


title: M1_PFC_mix_H3K4me3_1k_R1


title: M1_PFC_mix_H3K4me3_10k_R1


title: M1_PFC_mix_H3K27me3_1k_R1


title: M1_PFC_mix_H3K27me3_10k_R2


title: M1_PFC_mix_H3K27me3_100_R1


title: M1_PFC_mix_H3K27me3_10k_R1


title: 2013_MA_t5_rep2

first: Qiang

last: Li

state: Saskatchewan

address: #1 Shizishan Street

data_processing:
Trimming using Trimmomatics
Read mapping using STAR
Alignment using Cufflinks
Raw counts and normalized counts using HT-Seq
Differentially expression analysis using DESeq2
Genome_build: IWGSC1
Supplementary_files_format_and_content: normalized counts

organism: Triticum aestivum

growth_protocol: Plants were grown under field conditions at Saskatoon, SK, Canada from September to November in 2010 and 2013.

extract_protocol:
Total RNA from crowns were extracted using a Plant RNA Isolation Mini Kit (Agilent Technologies, Mississauga, ON).
80 cDNA libraries were constructed using the TruSeq RNA Sample Preparation Kit v2 (Illumina) with two replicates for each lines at each time point in 2010 and 2013, respectively.

treatment_protocol: Crown tissue (less than a 1 cm long section at the base of the crown) for RNA extraction was collected from 40 to 60 plants in each treatment and replicate, flash frozen in liquid nitrogen, and stored in a -80oC freezer.

value: crown

tag: line

value: MA

tag: sampling data


title: 2013_SN_t5_rep1

value: SN


title: 2013_SN_t5_rep2


title: GM_8C_device2_H3K27me3_100_C8

data_processing:
Sequencing reads were trimmed by trim galore 0.3.7 with default setting.
ChIP-seq reads were aligned using bowtie 1.1.1. RNA-seq reads were aligned by TopHat v2.1.1.
ChIP-seq reads are extended to 250 bp and normalized based on the sequencing depth
Input signals are subtracted from ChIP-seq signals
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: bigwig files are converted by wigToBigWig. fpkm_tracking files were generated by Cufflinks.

source_name: GM12878 cell line

tag: cell line


title: M1_PFC_NeuN+_H3K27ac_100_R1


title: M1_PFC_mix_H3K27ac_1k_R2


title: M1_PFC_mix_H3K27ac_100_R2


title: M1_PFC_mix_H3K27me3_100_R2


title: M1_PFC_mix_H3K27ac_10k_R2


title: M1_PFC_mix_H3K27ac_1k_R1


title: 2013_WM_t5_rep2

value: WM


title: 2013_MA_t5_rep1


title: 2013_WM_t4_rep2


title: 2013_WM_t4_rep1


title: M1_PFC_mix_H3K4me3_100_R2


title: 2013_NO_t5_rep2

value: NO


title: M1_PFC_mix_H3K27ac_100_R1


title: M1_PFC_mix_H3K27ac_10k_R1


title: 2013_NO_t5_rep1


title: GM_8C_device2_H3K27me3_100_C7


title: GM_8C_device2_H3K4me3_100_C3


title: GM_8C_device2_H3K27me3_100_C6


title: 2013_MA_t4_rep2


title: GM_8C_device2_H3K4me3_100_C4


title: 2013_WM_t5_rep1


title: 2013_NO_t4_rep1


title: 2013_SN_t4_rep2


title: 2013_WM_t3_rep2


title: GM_8C_device1_H3K27me3_100_C7


title: 2013_WM_t3_rep1


title: 2013_MA_t4_rep1


title: GM_8C_device2_H3K4me3_100_C1


title: GM_8C_device2_H3K4me3_100_C2


title: 2013_SN_t4_rep1


title: GM_8C_device1_H3K27me3_100_C8


title: 2013_SN_t3_rep2


title: 2013_MA_t3_rep2


title: GM_8C_device1_H3K27me3_100_C6


title: 2013_MA_t3_rep1


title: GM_8C_device1_H3K27me3_100_C5


title: GM_8C_device1_H3K4me3_100_C4


title: GM_8C_device2_H3K27me3_100_C5


title: 2013_NO_t4_rep2


title: GM_8C_device1_H3K4me3_100_C2


title: 2013_SN_t3_rep1


title: 2013_WM_t2_rep2


title: GM_8C_device1_H3K4me3_100_C3


title: GM_8C_device1_H3K4me3_100_C1


title: GM_AGP_H3K4me3_500_8min_R1

extract_protocol:
The mouse line C57Bl/6 was bred and maintained in groups of 3-4 per cage with food ad libitum. 8-10 week old mice were anesthetized with isoflurane and decapitated. The cerebellum was rapidly dissected and frozen on dry ice and stored at -80 ℃ until used for nuclei isolation.  Cerebellum was placed in 5 ml ice-cold nuclei extraction buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM Tris-HCl and 0.1% Triton X-100) with freshly added 50 μl protease inhibitor cocktail (P8340, Sigma-Aldrich), 5 μl 100 mM PMSF and 5 μl 1 M DTT. In addition, 7.5 μl 40 U/μl RNase inhibitor (N2611, Promega) was also added when RNA-seq was conducted. Once thawed, the tissue was homogenized by slowly doucing for 15 times with a loose pestle (D9063, Sigma-Aldrich) and 25 times with a tight pestle (D9063, Sigma-Aldrich). The homogenate was transferred into an ultracentrifugation tube (355631, Beckman Coulter) and underlayered with 9.5 ml sucrose cushion (1.8 M sucrose, 3 mM Mg(Ac)2 and 10 mM Tris-HCl). The homogenate was centrifuged at 32,300 rpm (107,164g) for 2.5 h at 4 ℃ with 70 Ti rotor (Optima L-90K Ultracentrifuge, Beckman Counter). The spinning was slowly braked to avoid disturbing the nuclei pellet. All the supernatant was removed and the nuclei was gently resuspended in 0.4 ml 10% normal goat serum (50062Z, Life Technologies) and 1.6 ml Dulbecco's phosphate-buffered saline (14190144, Life Technologies). For RNA-seq, 3 μl 40 U/μl RNase inhibitor was added into nuclei suspension. The integrity and the number of nuclei were checked under the microscope. 32 μl 2 ng/μl anti-NeuN antibody conjugated with Alexa 488 (MAB377X, EMD Millipore) was incubated with the nuclei suspension (2 ml) for 1 h at 4 ℃ on an end-to-end rotator. The stained samples were sorted using a FACS (BD FACSAria, BD Biosciences) with 50,000 to 100,000 unlabeled nuclei used as non-staining control. Human genomic DNA was purified from GM 12878 cells using QIAamp DNA Blood Mini Kit (Qiagen) following the manufacturer’s protocol and suspended in 50 µl EB buffer. Mouse genomic DNA was purified using QIAamp DNA Blood Midi Kit (Qiagen) from nuclei and suspended in 200 µl AE buffer (10 mM Tris-Cl, 0.5 mM EDTA, pH 9.0). The eluate was reloaded on the column membrane and spun to maximize DNA yield. Mouse DNA was concentrated by ethanol precipitation to 20 µl EB buffer. RNA was extracted from ~10,000 nuclei using RNeasy Mini Kit (Qiagen). DNase treatment step was included following kit instructions to remove gDNA contamination.
SurfaceChIP-seq library construction. The sequencing libraries were constructed using TruePLEX DNA-seq kit (Rubicon Genomics) or Accel-NGS 2S plus DNA library kit (Swift bioscience). GM12878 samples starting with ≥ 100 cells using DNA oligo linker were prepared using TruePLEX kit. The other samples are prepared using Accel-NGS 2S plus kit following instructions. mRNA-seq library construction. RNA was extracted from ~100,000 nuclei using RNeasy Mini Kit (Qiagen). DNase treatment was included following manufacturer instructions to remove gDNA contamination. mRNA-seq libraries were prepared using SMART-seq v4 Ultra Low Input RNA kit (Clontech) and Nextera XT DNA library prep kit (Illumina) following instructions.
ChIP-seq and mRNA-seq


title: GM_AGP_H3K4me3_500_8min_R2


title: 2013_NO_t3_rep2


title: 2013_NO_t3_rep1


title: GM_AGP_H3K4me3_500_4min_R1


title: GM_AGP_H3K4me3_500_4min_R2


title: 2013_MA_t2_rep2


title: 2013_WM_t2_rep1


title: GM_AGP_H3K4me3_500_2min_R2


title: GM_AGP_H3K4me3_500_1min_R2


title: 2013_SN_t2_rep2


title: GM_AGP_H3K4me3_100_4min_R2


title: GM_AGP_H3K4me3_500_2min_R1


title: GM_AGP_H3K4me3_500_1min_R1


title: 2013_MA_t2_rep1


title: 2013_SN_t2_rep1


title: 2013_WM_t1_rep2


title: 2013_NO_t2_rep2


title: 2013_SN_t1_rep2


title: GM_4C_device_H3K27me3_500_C3


title: GM_4C_device_H3K4me3_500_C2


title: GM_4C_device_H3K27me3_500_C4


title: 2013_WM_t1_rep1


title: GM_4C_device_H3K4me3_500_C1


title: 2013_SN_t1_rep1


title: GM_input_H3K27me3


title: 2013_MA_t1_rep1


title: 2013_NO_t1_rep2


title: GM_H3K27me3_10k_R2


title: 2013_MA_t1_rep2


title: 2013_NO_t1_rep1


title: GM_H3K27me3_10k_R1


title: GM_H3K27me3_5k_R2


title: GM_H3K27me3_5k_R1


title: 2010_WM_t5_rep1


title: GM_H3K27me3_1k_R2


title: 2010_WM_t5_rep2


title: 2010_SN_t5_rep2


title: 2013_NO_t2_rep1


title: GM_H3K27me3_1k_R1


title: 2010_MA_t5_rep2


title: GM_AGP_H3K4me3_100_4min_R1


title: 2010_MA_t5_rep1


title: 2010_SN_t5_rep1


title: GM_H3K27me3_500_R1


title: GM_H3K27me3_100_R2


title: GM_H3K27me3_500_R2


title: 2010_NO_t5_rep2


title: 2010_NO_t5_rep1


title: GM_input_H3K4me3


title: GM_H3K27me3_100_R1


title: 2010_WM_t4_rep2


title: 2010_SN_t4_rep1


title: GM_H3K4me3_1k_R2


title: GM_H3K4me3_5k_R1


title: GM_H3K4me3_500_R2


title: GM_H3K4me3_5k_R2


title: GM_H3K4me3_1k_R1


title: GM_H3K4me3_500_R1


title: GM_H3K4me3_100_R1


title: GM_H3K4me3_100_R2


title: GM_H3K4me3_60_R2


title: 2010_NO_t4_rep2


title: 2010_NO_t4_rep1


title: 2010_WM_t3_rep1


title: GM_H3K4me3_60_R1


title: 2010_SN_t3_rep2


title: GM_H3K4me3_30_R1


title: 2010_SN_t3_rep1


title: 2010_MA_t3_rep2


title: 2010_WM_t4_rep1


title: 2010_MA_t3_rep1


title: 2010_NO_t3_rep2


title: 2010_NO_t3_rep1


title: 2010_SN_t4_rep2


title: 2010_WM_t2_rep2


title: GM_H3K4me3_30_R2


title: 2010_SN_t2_rep2


title: 2010_MA_t4_rep2


title: 2010_WM_t2_rep1


title: 2010_MA_t2_rep2


title: 2010_SN_t2_rep1


title: M1_PFC_NeuN-_H3K27ac_100_R2


title: 2010_WM_t3_rep2


title: 2010_NO_t2_rep2


title: 2010_NO_t2_rep1


title: 2010_MA_t2_rep1


title: 2010_MA_t4_rep1


title: 2010_WM_t1_rep2


title: 2010_SN_t1_rep2


title: 2010_MA_t1_rep1


title: 2010_NO_t1_rep2


title: 2010_MA_t1_rep2


title: 2010_WM_t1_rep1


title: 2010_SN_t1_rep1


title: 2010_NO_t1_rep1


title: R5_prim_Scar

city: Utrecht

first: Anna

last: Alemany

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institue

description:
Scarred GFP
each plate contains 384 sorted cells

data_processing:
In scar libraries, first read contains cell barcode (8 first nucleotides) and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries, first read contains UMI (6 first nucleotides) and cell barcode (from 7 to 14 nucleotides) and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome.
Genome_build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9, ensemble 74, extended with ERCC92
Supplementary_files_format_and_content: *scarclones.txt: tabular separated files, with scar percentage (columns) per cell (rows). Cells from the same fish have been named according to barcode ID, plate and organ of origin.  Last column (hclust) referes to ID for the clone (cells sharing hclust label have the same scar pattern). *transcriptome.txt.gz: tabular separated files, with transcript count (rows) per cell (columns). Cells in each file are labeled according to barcode ID, plate, organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained after running RaceID (Grun, D. et al. Nature 525, 251-255, 2015) and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.

source_name: primary fin single cells

extract_protocol:
After organ isolation, live single cells are sorted into 384 well plates containing mineral oil, uniquely barcoded cell specific primers for independent scar and mRNA detection, Spike-in controls and and RNAse inhibitor.
Scartrace
Illumina TruSeq adapaters

tag: cas9 injection

value: mRNA

tag: FISH id

value: primary fin

tag: sorted plates


title: R5_prim_Trans

description:
full mRNA
each plate contains 384 sorted cells

tag: tissue


title: R4_wkm_Trans

source_name: wkm single cells

value: whole kidney marrow


title: R5_sec_Trans

source_name: secondary fin single cells

value: secondary fin


title: R5_sec_Scar


title: R4_terv_Trans

source_name: tertiary ventral fin single cells

value: tertiary fin


title: R4_terv_Scar


title: R4_terd_Trans

source_name: tertiary dorsal fin single cells


title: R4_terd_Scar

source_name: teritary dorsal fin single cells


title: R4_prim_Trans


title: R4_prim_Scar


title: R3_right-midbrain_Trans

source_name: right midbrain single cells

value: right midbrain


title: R4_sec_Scar


title: R3_left-midbrain_Trans

source_name: left midbrain single cells

value: left midbrain


title: R3_right-eye_Trans

source_name: right eye single cells

value: right eye


title: R3_right-midbrain_Scar


title: R3_left-midbrain_Scar


title: R3_hindbrain_Scar

source_name: hindbrain single cells

value: hindbrain


title: R3_right-eye_Scar


title: R3_forebrain_Trans

source_name: forebrain single cells

value: forebrain


title: No antibody iCLIP control, spermatogenic worms 3

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

data_processing:
Library strategy: iCLIP
The first 9 nucleotides of the read (the random barcode) were removed and stored in the read name.
Reads were mapped to the C. elegans WS235 genome using STAR (for peak calls, reads-per-gene counts) or novoalign (CIMS/CITS).
Multimapping reads and those with a mapping score below 20 were removed.
PCR duplicates were removed using the random barcode stored in the read name.
Peaks were called by custom CLIP-seq processing scripts or by the CIMS/CITS methods.
Genome_build: WS235
Supplementary_files_format_and_content: [.txt] file reports the number of reads mapped to each gene.

organism: Caenorhabditis elegans

source_name: Spermatogenic (fem-3(gf)), adult hermaphrodites worms

growth_protocol: iCLIP was performed on C. elegans worms grown to early adult phase at 25 degrees.

extract_protocol: Cells were lysed by ball milling, and libraries prepared by the iCLIP method.

value: spermatogenic hermaphrodite adults

tag: antibody

value: No-antibody control


title: No antibody iCLIP control, spermatogenic worms 1


title: R2_wkm_Trans


title: R4_wkm_Scar


title: No antibody iCLIP control, oogenic worms 1

source_name: Oogenic, adult hermaphrodite worms

value: oogenic hermaphrodite adults


title: No antibody iCLIP control, oogenic worms 2


title: R1_wkm_Trans


title: FBF-2 iCLIP, oogenic worms 3

value: anti-FLAG

tag: molecule subtype

value: RNA fragments crosslinked to protein (iCLIP)


title: R1_wkm_Scar


title: FBF-2 iCLIP, oogenic worms 2


title: R4_sec_Trans


title: R1_right-midbrain_Scar


title: FBF-2 iCLIP, oogenic worms 1


title: R1_right-midbrain_Trans


title: FBF-1 iCLIP, oogenic worms 3


title: R1_right-eye_Trans


title: R2_wkm_Scar


title: FBF-1 iCLIP, oogenic worms 1


title: FBF-1 iCLIP, oogenic worms 2


title: R1_right-eye_Scar


title: No antibody iCLIP control, spermatogenic worms 2


title: R1_left-midbrain_Scar

source_name: midbrain single cells


title: R1_left-midbrain_Trans


title: R3_left-eye_Scar

source_name: left eye single cells

value: left eye


title: FBF-2 iCLIP, spermatogenic worms 2


title: R3_forebrain_Scar


title: FBF-2 iCLIP, spermatogenic worms 3


title: FBF-2 iCLIP, spermatogenic worms 1


title: No antibody iCLIP control, oogenic worms 3


title: FBF-1 iCLIP, spermatogenic worms 3


title: R1_left-eye_Scar


title: FBF-1 iCLIP, spermatogenic worms 2


title: R1_hindbrain_Trans


title: R1_forebrain_Trans


title: FBF-1 iCLIP, spermatogenic worms 1


title: R1_forebrain_Scar


title: P1_primary-fin_Scars

data_processing:
In scar libraries, first read contains cell barcode (8 first nucleotides) and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to -1; and extending gap penalty to -0.1. Subsequently, we pool scars per cell and by cigar. For each scar library, a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next, scars were filtered according to their frequency of detection in the full library. For each cell, reads are normalized to 100 and scars representing less than 3.5% are removed.                                       ~
Genome_build: In scar libraries: eGFP sequence extended with ERCC92
Supplementary_files_format_and_content: *scarclones.txt: tabular separated files, with scar percentage (columns) per cell (rows). Cells from the same fish have been named according to barcode ID, plate and organ of origin.  Last column (hclust) referes to ID for the clone (cells sharing hclust label have the same scar pattern)

value: protein


title: R1_left-eye_Trans

value: mRNA


title: P1_left-eye_Scars


title: P1_right-midbrain_Scars


title: P1_right-eye_Scars


title: P1_left-midbrain_Scars


title: P1_hindbrain_Scars


title: P1_forebrain_Scars


title: P1_wkm_Scars


title: BCL11A_HUDEP2_CRISPR_115edit_rep3_60min

city: Boston

first: Stuart

last: Orkin

address: 1 Blackfan Circle

department: Hematology and Oncology

institute: Boston Children's Hospital

description: hg19 custom

data_processing:
Note that reads are aligned to custom hg19 where there is 1-bp deletion at chr11:5271199 and 13-bp deletion at chr11:5276109, corresponding to distal TGACCA motif deletion of HBG1/2.
Reads are of size 42bp.
Trimmomatic v.0.33 was run to trim away adapter sequences (ILLUMINACLIP:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25)
Untrimmed reads were further removed 6bp from the 3’ end to further rid of remaining adapter bases not trimmed by Trimmomatic. Deposited raw reads (FASTQ) have been trimmed.
Bowtie2 was used to align reads to reference genome assembly (hg19) with settings -p 2 --dovetail –phred33
Aligned reads are marked for duplicates with Picard MarkDuplicates function.
Afterward, the BAM file was filtered with SAMtools to discard reads, mates that were unmapped, or PCR/optical duplicates (-f 3 –F 4 –F 8 –F 1024). Fragments of size less than 120bp were kept
MACS version 2.1 was used to call peaks from the fragment-size selected and duplicate-removed reads with narrowPeak setting, P-value cutoff of 1e-5, and with –SPMR which normalizes the signal intensity to facilitate comparison between tracks. Peaks that are centered on repeat-masked region of the genome were removed. Other low-complexity regions as outlined in the ENCODE blacklist file were also removed.
NOTE that for CRISPR 115-edit experiments, the reads are aligned to a custom hg19 genome where two places are deleted (1-bp deletion at chr11:5271199, and 13-bp deletion at chr11:5276109). These coordinates correspond to distal TGACCA motif deletion of HBG1/2.
Genome_build: hg19, hg19 custom
Supplementary_files_format_and_content: Bigwig – pile up generated with MACS v2, and normalized for read coverage (--SPMR in MACS).
Supplementary_files_format_and_content: Frag.ends.bigwig – fragment ends were determined with BEDtools bamtobed -BEDPE and piled up to bigwig.
Supplementary_files_format_and_content: NarrowPeak – peaks generated with MACS v2 (callpeak -g hs -f BAMPE -q 0.01) and we filtered peaks centered on RepeatMask regions or blacklisted regions (ENCODE)
Supplementary_files_format_and_content: bed – log-odds of BCL11A binding for TGACCA occurrences. Col1-3: coordinates of TGACCA. Col7: log-odds. Computed with CENTIPEDE.

source_name: human umbilical cord blood-derived erythroid progenitor (HUDEP)

extract_protocol:
CUT&RUN experiments were carried out as described(Skene and Henikoff, 2017) with minor changes. Briefly, nuclei from 2 million cells were isolated and incubated with primary antibody for 2 hours. After washing away unbound antibody, protein A-MNase was added at a 1:1000 ratio and incubated for 1 hour. The nuclei were washed again and placed in a 0°C metal block. To activate protein A-MNase, CaCl2 was added to a final concentration of 2mM. The reaction was carried out for different time courses and stopped by chelating Ca2+. The protein-DNA complex was released by centrifugation and then digested by proteinase K at 50°C overnight. DNA was extracted by ethanol precipitation, followed by Qubit and bioanalyzer quality control. Protein A-MNase (batch 5) was kindly provided by Dr. Steve Henikoff.  The antibodies used were: GATA1, ab11852, abcam; CTCF, 07-729, Millipore; BCL11A, ab191401, abcam; normal rabbit IgG, 12-370, Millipore.
For library preparation, we modified the protocol of NEBNext® Ultra™ II DNA Library Prep Kit, NEB (Ipswich, USA), aiming to preserve small DNA fragments (30-80bp). Briefly, dA-tailing temperature was decreased to 50°C to avoid DNA melting, and the reaction time was increased to 1 hour to compensate for lower enzymatic activity. After adapter ligation, 2.1x volume of AMPure XP beads was added to the reaction to ensure high recovery efficiency of small fragments. After 12 cycle of PCR amplification, the reaction was cleaned up with 1.2x volume of AMPure XP beads. 16-24 barcoded libraries were quantified, mixed and denatured according to the standard protocol from Illumina. 1.3mL of 1.8pM diluted library was loaded to a NextSeq® 500/550 High Output Kit v2 (75 cycles), and sequenced in the NextSeq 500 platform with paired-end sequencing.

value: erythroid

value: Crispr edited HUDEP2 clone D3

tag: digestion time

tag: differentiation days


title: BCL11A_HUDEP2_CRISPR_115edit_rep1_60min

description: hg19 custom


title: BCL11A_HUDEP2_CRISPR_115edit_rep2_60min

description: hg19 custom


title: GATA1_HUDEP2_rep1_30min

data_processing:
Reads are of size 42bp.
Trimmomatic v.0.33 was run to trim away adapter sequences (ILLUMINACLIP:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25)
Untrimmed reads were further removed 6bp from the 3’ end to further rid of remaining adapter bases not trimmed by Trimmomatic. Deposited raw reads (FASTQ) have been trimmed.
Bowtie2 was used to align reads to reference genome assembly (hg19) with settings -p 2 --dovetail –phred33
Aligned reads are marked for duplicates with Picard MarkDuplicates function.
Afterward, the BAM file was filtered with SAMtools to discard reads, mates that were unmapped, or PCR/optical duplicates (-f 3 –F 4 –F 8 –F 1024). Fragments of size less than 120bp were kept
MACS version 2.1 was used to call peaks from the fragment-size selected and duplicate-removed reads with narrowPeak setting, P-value cutoff of 1e-5, and with –SPMR which normalizes the signal intensity to facilitate comparison between tracks. Peaks that are centered on repeat-masked region of the genome were removed. Other low-complexity regions as outlined in the ENCODE blacklist file were also removed.
NOTE that for CRISPR 115-edit experiments, the reads are aligned to a custom hg19 genome where two places are deleted (1-bp deletion at chr11:5271199, and 13-bp deletion at chr11:5276109). These coordinates correspond to distal TGACCA motif deletion of HBG1/2.
Genome_build: hg19, hg19 custom
Supplementary_files_format_and_content: Bigwig – pile up generated with MACS v2, and normalized for read coverage (--SPMR in MACS).
Supplementary_files_format_and_content: Frag.ends.bigwig – fragment ends were determined with BEDtools bamtobed -BEDPE and piled up to bigwig.
Supplementary_files_format_and_content: NarrowPeak – peaks generated with MACS v2 (callpeak -g hs -f BAMPE -q 0.01) and we filtered peaks centered on RepeatMask regions or blacklisted regions (ENCODE)
Supplementary_files_format_and_content: bed – log-odds of BCL11A binding for TGACCA occurrences. Col1-3: coordinates of TGACCA. Col7: log-odds. Computed with CENTIPEDE.


title: GATA1_CD34_Day9_30min

source_name: CD34+ HSPC derived erythroid precursors


title: GATA1_HUDEP2_rep2_30min


title: CD34_Day9_IgG

value: IgG


title: BCL11A_HUDEP2_KO

value: BCL11A KO HUDEP-2 cells


title: GATA1_CD34_Day7_30min


title: BCL11A_HUDEP2_rep4_60min


title: R1_hindbrain_Scar


title: BCL11A_HUDEP2_rep3_60min


title: BCL11A_CD34_Day9_90min


title: BCL11A_CD34_Day7_15min


title: BCL11A_HUDEP2_rep4_30min


title: BCL11A_CD34_Day9_15min


title: BCL11A_CD34_Day7_60min


title: BCL11A_CD34_Day5_60min


title: BCL11A_CD34_Day5_90min


title: BCL11A_CD34_Day5_30min


title: BCL11A_HUDEP2_rep2_60min


title: BCL11A_CD34_Day3_90min


title: BCL11A_CD34_Day7_90min


title: BCL11A_CD34_Day7_30min


title: BCL11A_HUDEP2_rep1_60min


title: BCL11A_CD34_Day9_60min


title: CD34_Day7_IgG


title: BCL11A_CD34_Day3_30min


title: CTCF_HUDEP2_30min

value: CTCF


title: BCL11A_CD34_Day3_60min


title: Amp_treated_SK36 strain_T20_Rep3

city: Richmond

first: Fadi

middle: Elias

last: El-Rami

address: 521 N 11th Str, wood bldg, room 424

department: Microbiology & Immunology

institute: Virginia Commonwealth University

description: replicate 3

data_processing:
Standard Illumina pipeline. Real Time Analysis (RTA v. 1.18.66.3) software used for image processing, intesity extraction and basecalling based on intensities. CHASTITY software used for quality filter of basecalling.
Reads obtained from RNA-sequencing were aligned against the Streptococcus sanguinis SK36 genome using  using Rockhopper v. 2.03
Analyses were run on default parameter settings to obtain expression data of the treated samples compared to untreated SK36. Significance was represented by a q-value ≤ 0.01 adjusted for a false discovery rate of 1%.
Genome_build: Streptococcus sanguinis reference genome; NC_009009.1
Supplementary_files_format_and_content: tab-delimited text file includes transcription and translation start/stop site, strand direction, gene name and ID, gene product, raw and normalized counts for each replicate, Reads Per Kilobase of exon per Megabase of library size (RPKM), expression, p-value and Rockhopper's adjusted q-value for the mutant expression vs. the wild-type SK36 expression

organism: Streptococcus sanguinis

source_name: Ampicillin-treated SK36 after 20 min

growth_protocol: Untreated cells were incubated at 37°C under anaerobic conditions in brain-heart infusion media and harvested at late-log phase. Treated cells were exposed to sub-inhibitory Ampicillin dose at late-log phase for either 10, 20, or 30 minutes.

extract_protocol:
Cells were lysed and RNA was extracted by FastPrep lysing matrix beads. Clean-up and DNase I treatment was conducted by QIAGEN RNeasy mini kit, according to the manufacterer's protocol. Illlumina RiboZero Magnetic Kit for bacteria was used to deplete ribosomal RNA from 2 µg of total RNA.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) was used for the RNA-seq library preparation according to the manufacturer’s protocol. Briefly, ribosomal-depleted RNA was fragmented followed by first-strand cDNA synthesis from random primers using ProtoScript II Reverse Transcriptase (New England BioLabs). Second strand cDNA was synthesized and purified. End repair was performed on the double-stranded cDNA and primed with the addition of 5’-phosphorylated dA-tailed ends using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase (New England BioLabs). This was immediately followed by adaptor ligation (New England BioLabs) and purified. Samples were PCR-amplified for 12 cycles with Phusion HiFi polymerase (New England Biolabs) with paired-end primers and a randomly chosen unique barcode (NEB Next Multiplex Oligs for Illumina - Index Primers 2,3,4,5,6,8,10,11,12,13,15,16). Agencourt AMPure XP Beads (Beckman Coulter) were used for all purification steps.

tag: growth phase

value: late-log

tag: treated with

value: 0.125 µg/ml of Ampicillin for 20min


title: Amp_treated_SK36 strain_T30_Rep2

description: replicate 2

source_name: Ampicillin-treated SK36 after 30 min

value: 0.125 µg/ml of Ampicillin for 30min


title: Amp_treated_SK36 strain_T30_Rep1

description: replicate 1


title: Amp_treated_SK36 strain_T10_Rep3

description: replicate 3

source_name: Ampicillin-treated SK36 after 10 min

value: 0.125 µg/ml of Ampicillin for 10min


title: Amp_treated_SK36 strain_T20_Rep2

description: replicate 2


title: BCL11A_HUDEP2_rep4_90min


title: Amp_treated_SK36 strain_T20_Rep1

description: replicate 1


title: Amp_treated_SK36 strain_T10_Rep2

description: replicate 2


title: Amp_treated_SK36 strain_T10_Rep1

description: replicate 1


title: Untreated_SK36 strain_Rep3

description: replicate 3

source_name: Untreated SK36

value: none (untreated)


title: BCL11A_CD34_Day9_30min


title: Untreated_SK36 strain_Rep1

description: replicate 1


title: Untreated_SK36 strain_Rep2

description: replicate 2


title: induced iSLK.219 cells input rep 2

status: Public on Mar 29 2018

city: Berkeley

first: Britt

last: Glaunsinger

address: 1951 Oxford Street

department: Plant and Microbial Biology

institute: UC Berkeley

description: processed data file: human_Union_induced_FC4_genes.txt

data_processing:
library strategy: MeRIP-seq
Reads were mapped to reference human and KSHV transcriptomes using Bowtie.
m6A peaks were called and analyzed using the model-based analysis of ChIP-seq (MACS) peak-calling algorithm.
Human and viral peaks were considered significant if their MACS-assigned fold change was greater than four (FC>4) and individual False Discovery Rate value less than 5% (FDR>5%). For reference, we have included a full list of FC>2 peaks in the virus.
The above data processing steps were performed as described previously: Dominissini D, Moshitch-Moshkovitz S, Salmon-Divon M, Amariglio N, Rechavi G. Transcriptome-wide mapping of N(6)-methyladenosine by m(6)A-seq based on immunocapturing and massively parallel sequencing. Nat Protoc. 2013 Jan;8(1):176–89.
Genome_build: Human: University of California, Santa Cruz (UCSC) Dec. 2013 (GRCh38/hg38) KSHV: University of California, Santa Cruz (UCSC) KSHV Feb 2012 Assembly
Supplementary_files_format_and_content: Processed data files contain the genomic coordinates and transcript names for m6A peaks that map back to the human or KSHV transcriptome.  Each processed data file is derived from the corresponding input and m6A IP conditions (uninduced1, induced1, uninduced2, induced2).    For each of these conditions, two outputs are generated: m6A peaks in human transcripts and m6A peaks in viral transcripts. An additional output, "Human Union Induced" and "Human Union Uninduced" files refer to the human m6A peaks that occur in both biological replicates of the indicated treatment condition.   "Chr" refers to chromosome number for m6A peaks occuring on human transcripts.  KSHV is a non-segmented virus, so all m6A peaks mapping to KSHV by default occur on "chr1."   "Peak_start" and "Peak_end" indicate the coordinates of the start and end of the m6A peak within the reference transcriptome.  For m6A peaks in human transcripts, the RefSeq ID and gene symbol is provided.  For m6A peaks in viral transcripts, the parameters "gene_start" and "gene_end" refer to the annotated start and stop sites for the viral open reading frame (ORF) containing the m6A peak. In cases where a single m6A peak spans more than one viral ORF, all of the annotated ORFs contained within that peak are listed. "Strand" indicates whether the indicated viral transcript is encoded on the positive or negative sense strand of the virus. "dist_middle_TSS" refers to the distance between the middle of the indicated m6A peak and the start of its respective ORF.  "dist_middle_end" refers to the distance from the middle of the peak to the end of the ORF.  FC refers to the "Fold Change" (m6A IP/input) for each peak.  While only peaks with a fold change of four or greater (FC>4) were considered significant, for reference, all peaks of fold change two or greater (FC>2) are listed for KSHV transcripts.

source_name: induced iSLK.219 cells input

growth_protocol: iSLK.219 cells were cultured in DMEM containing 10% Fetal Bovine Serum and 1% Pen-Strep

extract_protocol:
RNA was isolated and DNAse treated as in the m6A RIP, except the RNA was first fragmented to lengths of ~100 nt prior to immunoprecipitation with anti-m6A antibody (Synaptic Systems).
Immunoprecipitated RNA fragments and comparable amounts of input were subjected to first-strand cDNA synthesis using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Sequencing was carried out on Illumina HiSeq2500 according to the manufacturer’s instructions, using 10 pM template per sample for cluster generation, TruSeq SR Cluster kit v3 (Illumina), TruSeq SBS Kit v3-HS (Illumina) and TruSeq Multiplex Sequencing primer kit (Illumina).

treatment_protocol: 2.5 mg total cellular RNA was prepared from iSLK.219 cells that were either uninduced (latent virus), or induced for five days with doxycycline to allow KSHV lytic replication.  2 separate biological replicates for the uninduced and induced samples were used per treatment condition.

tag: cell type

value: KSHV-positive renal carcinoma cell line

tag: genotype/variation

tag: passages

tag: induced with

value: doxycyclin for 5 days

tag: rip antibody

value: Total RNA


title: induced iSLK.219 cells m6A IP rep 2

source_name: induced iSLK.219 cells m6A IP

value: anti-m6A (Synaptic Systems)

value: m6A-modified RNA


title: uninduced iSLK.219 cells input rep 2

description: processed data file: human_Union_uninduced_FC4_genes.txt

source_name: uninduced iSLK.219 cells input

value: none (uninduced)


title: Amp_treated_SK36 strain_T30_Rep3

description: replicate 3

tag: strain


title: uninduced iSLK.219 cells m6A IP rep 2

source_name: uninduced iSLK.219 cells m6A IP

tag: cell line


title: induced iSLK.219 cells m6A IP rep 1


title: Restricted 1 TP2 [EOSJ2-38]

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
EOSJ2-38

data_processing:
Basecalls performed using CASAVA version 1.4
RNAseq reads were aligned to UMD3.1 genome using Bowtie (--very-senstive setting, --solexa1.3-quals), sorted and possible PCR duplicates were removed using Samtools.
Raw counts were enumerated using HTSEQ-count (settings: mode = union)
The raw read counts were normalized using scaling factors estimated by the Trimmed mean of M-Values (TMM) method implemented  the edgeR software package. The normalised values represent read counts per million mapped reads, adjusted for sample library size
Genome_build: UMD 3.1
Supplementary_files_format_and_content: Tab delimited txt files
Supplementary_files_format_and_content: First row contains the ENSEMBL gene IDs and second row the raw number of reads that map to each gene

organism: Bos taurus

source_name: jejunal epithelium

growth_protocol: Purebred Holstein Friesian bulls were assigned to one of two feeding treatments (i) restricted feed allowance for 125 days (n=9) followed by ad libitum access to feed for a further 55 days (n=10) or (ii) a control group with ad libitum access to feed through out the 180 days trial (n=19).  The first 125 days of the trial were denoted as Peirod 1, during which treatment groups were fed differentially. the subsequent 55 days, denoted as Period 2 during which all bulls were fed ad libitum. All bulls received the same diet of 70% concentrate 30% grass silage through out the experimental trial,with the amount of feed provided different dependent on each treatment group. restricted fed animals were fed to grow at 0.6 kg /day during Peirod 1, with ad libitum animals expected to gain in excess of 1.5 to 2 kg/day

extract_protocol:
Total RNA was extracted from frozen muscle tissue by homogenisation using the Qiagen Rneasy RNA isolation kit.
Single-end mRNA-seq libraries were constructed using the Illumina Truseq sample prep kit.

treatment_protocol: 19 bulls fed a restricted diet for 125 days to grow at 0.6kg/day, after which they were fed ad libitum for a further 55 days. The remaining 19 bulls in the control group were fed ad libitum throughout

tag: diet

value: 70% concentrate, 30% grass silage diet

value: jejunal epithelium

tag: breed

value: Holstein Friesian

tag: time point (biopsy day)

value: day 55 of Period 2

tag: feeding period

value: Realimentation period


title: Restricted 3 TP2 [EOSJ2-44]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
EOSJ2-44

tag: tissue


title: Restricted 7 TP2 [EOSJ1-56]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
EOSJ1-56


title: Restricted 6 TP2 [EOSJ3-53]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
EOSJ3-53


title: Restricted 4 TP2 [EOSJ1-45]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
EOSJ1-45


title: Restricted 10 TP2 [EOSJ4-46]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
EOSJ4-46


title: Restricted 2 TP2 [EOSJ3-41]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
EOSJ3-41


title: Restricted 9 TP2 [EOSJ4-57]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
EOSJ4-57


title: uninduced iSLK.219 cells m6A IP rep 1

tag: molecule subtype


title: Restricted 5 TP2 [EOSJ2-55]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
EOSJ2-55


title: Restricted 8 TP2 [EOSJ3-35]

description:
Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2
EOSJ3-35


title: Restricted 9 TP1 [EOSJ1-25]

description:
Experimental: day 125 with restricted diet Period 1
EOSJ1-25

value: day 125 of Period 1

value: Differential feeding


title: Restricted 6 TP1 [EOSJ2-9]

description:
Experimental: day 125 with restricted diet Period 1
EOSJ2-9


title: Restricted 7 TP1 [EOSJ1-30]

description:
Experimental: day 125 with restricted diet Period 1
EOSJ1-30


title: Restricted 8 TP1 [EOSJ1-11]

description:
Experimental: day 125 with restricted diet Period 1
EOSJ1-11


title: Restricted 10 TP1 [EOSJ3-6]

description:
Experimental: day 125 with restricted diet Period 1
EOSJ3-6


title: uninduced iSLK.219 cells input rep 1


title: Restricted 5 TP1 [EOSJ1-27]

description:
Experimental: day 125 with restricted diet Period 1
EOSJ1-27


title: SIGAG8

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

data_processing:
Reads aligned to mm10 and processed using Cell Ranger 1.3
Counts extracted using R-package (library: cellrangerRkit_1.1.0)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Counts: Mapped read counts per gene, per cell. Column headers are cell barcodes.

extract_protocol:
The femora, tibiae, and ilia of C57BL/6 mice of W41/W41 mice were crushed and the bone marrow cells were released and the red blood cells were lysed with ammonium chloride solution (STEMCELL Technologies). The cells were stained with the fluorophore-conjugated monoclonal antibodies, and sorted using an Influx cell sorter (BD Biosciences) equipped with five lasers. The cells were sorted into 1.5 ml tubes containing PBS + 2% FCS.
Sorted cells were harvested, resuspended in 0.04% BSA (Thermo Fisher) and counted. Cells were processed using the 10x Chromium™ Single Cell 3’ kit, following manufacturers instructions

treatment_protocol: Samples were lineage depleted using EasySep™ Mouse Hematopoietic Progenitor Cell Isolation Kit (STEMCELL Technologies).

value: bone marrow

value: Lin-cKit+

tag: genotype

value: Kit mutant (W41/W41)


title: SIGAH8


title: Restricted 4 TP1 [EOSJ3-13]

description:
Experimental: day 125 with restricted diet Period 1
EOSJ3-13


title: SIGAG1

value: WT bl6 mice (pool 6 mice)

value: WT


title: Restricted 2 TP1 [EOSJ2-5]

description:
Experimental: day 125 with restricted diet Period 1
EOSJ2-5


title: induced iSLK.219 cells input rep 1

description: processed data file: human_Union_induced_FC4_genes.txt

value: KSHV-positive renal carcinoma cell line

value: doxycyclin for 5 days


title: SIGAF1


title: Control 10 TP2 [EOSJ4-54]

description:
Control: day 55 with ad libitum diet Period 2
EOSJ4-54


title: SIGAB1

value: LSK


title: Control 8 TP2 [EOSJ2-31]

description:
Control: day 55 with ad libitum diet Period 2
EOSJ2-31


title: Control 4 TP2 [EOSJ3-51]

description:
Control: day 55 with ad libitum diet Period 2
EOSJ3-51


title: Control 5 TP2 [EOSJ4-42]

description:
Control: day 55 with ad libitum diet Period 2
EOSJ4-42


title: Control 7 TP2 [EOSJ4-36]

description:
Control: day 55 with ad libitum diet Period 2
EOSJ4-36


title: Restricted 3 TP1 [EOSJ4-19]

description:
Experimental: day 125 with restricted diet Period 1
EOSJ4-19


title: Control 1 TP2 [EOSJ3-59]

description:
Control: day 55 with ad libitum diet Period 2
EOSJ3-59


title: SIGAC1


title: GMP_46

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts(.txt)
Supplementary_files_format_and_content: extra_sequences.fa: Fasta file contains the sequences used for the customized index.

source_name: Bone marrow cells

extract_protocol:
Single cells were sorted into 96 well PCR plates containing 2.3 µl lysis buffer consisting of 2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton per well. Cells were processed for RNA-sequencing following Picelli et al (Nature Protocols 9, 171-181 (2014)). Briefly, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes, followed by cDNA synthesis using SuperScript™ II Reverse Transcriptase (Invitrogen 18064014). PCR was performed with 23 PCR cycles and products cleaned up using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter). ERCC Spike In Mix was included in each single cell reaction at 1: 3 000 000 dilution (ThermoFisher Scientific 4456740). Single cell cDNA library was eluted in 20 µl volume of EB Buffer (Qiagen).
Prior to library preparation, cDNA library was checked on Agilent Bioanalyser 2100 with Agilent High Sensitivity DNA Kit. Library preparation was performed using Illumina Nextera XT DNA Library Preparation Kit with 1.26 µl cDNA library and Nextera XT Index Kit v2 Set A and D. Single cell libraries were pooled for all indexed samples and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.2 ratio of cDNA: beads.   Pooled libraries were quantified with KAPA Library Quant Kit (KAPA Biosystems KK4824) and single-end 50 base pair sequencing was performed on the Illumina HiSeq 4000 platform.

tag: cell population

value: GMP

tag: sorting strategy

value: Live Lin- cKit+ Sca1- CD34+ CD16/32hi cells falling outside the BMCP gate


title: Control 6 TP2 [EOSJ1-37]

description:
Control: day 55 with ad libitum diet Period 2
EOSJ1-37

value: 70% concentrate, 30% grass silage diet


title: Control 3 TP2 [EOSJ1-40]

description:
Control: day 55 with ad libitum diet Period 2
EOSJ1-40

value: jejunal epithelium


title: GMP_45


title: SIGAH1


title: GMP_44


title: GMP_42


title: GMP_40


title: Control 10 TP1 [EOSJ1-1]

description:
Control: day 125 with ad libitum diet Period 1
EOSJ1-1

value: Holstein Friesian


title: GMP_39


title: Control 9 TP1 [EOSJ2-20]

description:
Control: day 125 with ad libitum diet Period 1
EOSJ2-20


title: Control 2 TP2 [EOSJ4-47]

description:
Control: day 55 with ad libitum diet Period 2
EOSJ4-47

value: day 55 of Period 2


title: Restricted 1 TP1 [EOSJ4-21]

description:
Experimental: day 125 with restricted diet Period 1
EOSJ4-21


title: GMP_41


title: GMP_38


title: Control 8 TP1 [EOSJ4-4]

description:
Control: day 125 with ad libitum diet Period 1
EOSJ4-4


title: Control 7 TP1 [EOSJ4-17]

description:
Control: day 125 with ad libitum diet Period 1
EOSJ4-17


title: SIGAD1


title: GMP_37


title: Control 9 TP2 [EOSJ2-34]

description:
Control: day 55 with ad libitum diet Period 2
EOSJ2-34

value: Realimentation period


title: GMP_47


title: GMP_43


title: Control 6 TP1 [EOSJ3-3]

description:
Control: day 125 with ad libitum diet Period 1
EOSJ3-3

value: day 125 of Period 1


title: GMP_35


title: Control 4 TP1 [EOSJ1-15]

description:
Control: day 125 with ad libitum diet Period 1
EOSJ1-15

value: Differential feeding


title: GMP_33


title: GMP_34


title: GMP_32


title: Control 2 TP1 [EOSJ3-28]

description:
Control: day 125 with ad libitum diet Period 1
EOSJ3-28


title: GMP_30


title: GMP_31


title: GMP_26


title: GMP_22


title: GMP_28


title: GMP_21


title: GMP_23


title: GMP_24


title: GMP_27


title: GMP_20


title: GMP_18


title: GMP_17


title: GMP_25


title: GMP_16


title: GMP_13


title: GMP_14


title: GMP_15


title: Control 5 TP1 [EOSJ3-2]

description:
Control: day 125 with ad libitum diet Period 1
EOSJ3-2


title: GMP_36


title: GMP_12


title: Control 1 TP1 [EOSJ2-12]

description:
Control: day 125 with ad libitum diet Period 1
EOSJ2-12


title: Control 3 TP1 [EOSJ2-23]

description:
Control: day 125 with ad libitum diet Period 1
EOSJ2-23


title: GMP_11


title: GMP_7


title: GMP_10


title: GMP_6


title: GMP_8


title: shNsd1.2 ChIP-seq H3K36me2

city: Dublin 2

first: Darren

middle: John

last: Fitzpatrick

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

institute: Trinity College Dublin

description:
Immuno-precipitation of chromatin using a specific antibody against H3K36me2 (Abcam 9049)
ChIP control
Cells were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin was precipitated with H3K27me3 and H3K36me2 antibody. IPs were performed using Protein A Sepharose beads and recovered DNA was used for high-throughput sequencing.

data_processing:
Alignment: Short reads were mapped onto the mouse reference genome (mm9) using Bowtie retaining only reads with unique alignment. For ChIP-rx experiments, sequence reads were also aligned to the Drosophila reference genome (dm6).
Peaks: Peak calling was performed with the Model-based Analysis of ChIP-Seq (MACS2) algorithm
Genome_build: mm9

source_name: E14 Embryonic stem cells

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: Mouse ES cells were grown in feeder-free culture in the presence of LIF. Cell were virally transduced, selected with puromycin and propagated for five days before harvested for chromatin isolation.


title: GMP_29


title: GMP_9


title: shNsd1.1 ChIP-seq H3K36me2


title: GMP_19


title: shNon-targeting control ChIP-seq H3K36me2


title: shNsd1.1 ChIP-rx H3K36me2

description:
Immuno-precipitation of chromatin using a specific antibody against H3K36me2 (Abcam cat. AB176921);  added 5% spike-in chromatin for normalization
ChIP
Cells were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin was precipitated with H3K27me3 and H3K36me2 antibody. IPs were performed using Protein A Sepharose beads and recovered DNA was used for high-throughput sequencing.

tag: spike-in reference organism

value: Drosophila melanogaster

tag: spike-in cell line

tag: spike-in mix ratio


title: GMP_4


title: GMP_2


title: GMP_5


title: GMP_3


title: GMP_1


title: shNsd1.2 ChIP-rx H3K27me3

description:
Immuno-precipitation of chromatin using a specific antibody against H3K27me3 (Cell signaling C36B11 9733); added 5% spike-in chromatin for normalization
ChIP
Cells were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin was precipitated with H3K27me3 and H3K36me2 antibody. IPs were performed using Protein A Sepharose beads and recovered DNA was used for high-throughput sequencing.


title: BMCP_94

value: BMCP

value: Live Lin- cKit+ Sca1- integrin beta7hi CD16/32hi cells


title: shNsd1.2 ChIP-rx H3K36me2


title: BMCP_92


title: shNsd1.1 ChIP-rx H3K27me3


title: shNon-targeting control ChIP-rx H3K36me2

description:
Immuno-precipitation of chromatin using a specific antibody against H3K36me2 (Abcam cat. AB176921); added 5% spike-in chromatin for normalization
ChIP
Cells were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin was precipitated with H3K27me3 and H3K36me2 antibody. IPs were performed using Protein A Sepharose beads and recovered DNA was used for high-throughput sequencing.


title: BMCP_93


title: BMCP_91


title: BMCP_89


title: BMCP_90


title: BMCP_87


title: BMCP_88


title: BMCP_86


title: BMCP_85


title: BMCP_84


title: BMCP_82


title: BMCP_81


title: BMCP_83


title: BMCP_80


title: BMCP_79


title: BMCP_75


title: BMCP_78


title: BMCP_74


title: BMCP_76


title: BMCP_77


title: BMCP_72


title: shNon-targeting control ChIP-rx H3K27me3


title: BMCP_73


title: BMCP_70


title: BMCP_67


title: BMCP_62


title: BMCP_63


title: BMCP_68


title: BMCP_71


title: BMCP_64


title: BMCP_65


title: BMCP_69


title: BMCP_61


title: BMCP_66


title: BMCP_60


title: BMCP_57


title: BMCP_58


title: BMCP_59


title: BMCP_56


title: BMCP_53


title: BMCP_54


title: BMCP_52


title: BMCP_51


title: BMCP_49


title: BMCP_47


title: BMCP_43


title: BMCP_46


title: BMCP_42


title: BMCP_40


title: BMCP_35


title: BMCP_48


title: BMCP_37


title: BMCP_34


title: BMCP_50


title: BMCP_36


title: BMCP_41


title: BMCP_39


title: BMCP_32


title: BMCP_45


title: BMCP_30


title: BMCP_28


title: BMCP_44


title: BMCP_55


title: BMCP_38


title: BMCP_29


title: BMCP_26


title: BMCP_27


title: BMCP_25


title: BMCP_24


title: BMCP_22


title: BMCP_20


title: BMCP_18


title: BMCP_33


title: BMCP_19


title: BMCP_31


title: BMCP_16


title: BMCP_13


title: BMCP_14


title: BMCP_17


title: C3A

first: Balazs

last: Balint

state: Csongrad

address: Vallalkozok street

country: Hungary

institute: Seqomics Ltd

data_processing:
Basecalls were performed using Abi Solid 5 ICS
Data was filtered based on read length. Minimum number of nucleotides in reads = 50, Software: CLC Genomics Workbench Tool 7.5.1
CLC Legacy RNA-Seq analysis was carried out. Min. length fraction = 0.8, Min. similarity fraction = 0.8, Additional upstream bases = 0, Additional downstream bases = 0, Maximum number of mismatches allowed (applies to short reads) = 2, Unspecific match limit = 10, Use colorspace encoding = Yes, Use strand specific assembly = No, Organism type = PROKARYOTE, Exon discovery = Yes, Minimum number of reads = 10, Minimum length of putative exons = 50, Create list of unmapped reads = No, Create report = Yes, Create fusion gene table = No, Expression level = Genes, Calculate RPKM for genes without transcripts = No, Expression value = Number of reads mapped to the gene, Software: CLC Genomics Workbench Tool 7.5.1
rRNA reads were discarded
Genes unexpressed in the majority of samples  were removed (expression threshold: at least 5 read counted in at least 21 samples)
TMM scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Batch effect removal was applied using non-treated controls samples as reference points.  Function:ComBat, Package: sva, version: 3.8.0
linear modeling with empirical Bayes moderation was built in limma. Package: limma, Version: 3.18.13
Genome_build: U00096.3 annoted with Blatner locus numbers, downloaded from EcoGene 3.0
Supplementary_files_format_and_content: Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool

organism: Escherichia coli

source_name: ancestor (BWk3)

growth_protocol: Strains were grown in Minimal salts (MS) medium supplemented with 0.1mM MgSO4, 0.54 μg/mL FeCl3, 1 μg/mL Tiamin, 0.2% Cas amino-acids and 0.2% glucose.

extract_protocol:
RNA was isolated in late exponential phase (OD around 0.8-1). QIAGEN RNA Protect bacteria reagent was used for freezing of samples (Cat. Num.: 76506). Macherey-Nagel NucleoSpin RNA Plant kit was used for RNA isolation (Cat. Num.:  740949.50). And additional DNase treatment was carried out with Ambion DNase I (Cat. Num.: AM2222). All steps were carried out according to the Manufacturer's instructions.
Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria, Cat.Num.: MRZGN126) was used for RNA depletion. SOLiD Total RNA-Seq kit was used for sequencing library generation (Cat. Num.: PN 4445374). All steps were carried out according to the Manufacturer's instructions.

treatment_protocol:
Control: the ancestor strain from which the antibiotic adaptation started.
AMP: Parallel lineages were adapted to gradually increasing concentrations of ampicillin for 30 transfers (around 240 generations).
CHL:  Parallel lineages were adapted to gradually increasing concentrations of chloramphenicol for 48 transfers (around 384 generations).
CPR:  Parallel lineages were adapted to gradually increasing concentrations of ciprofloxacin for 48 transfers (around 384 generations).
DOX:  Parallel lineages were adapted to gradually increasing concentrations of doxycycline for 30 transfers (around 240 generations).
ERY:  Parallel lineages were adapted to gradually increasing concentrations of erythromycin for 33 transfers (around 264 generations).
FOX:  Parallel lineages were adapted to gradually increasing concentrations of cefoxitin for 48 transfers (around 384 generations).
KAN:  Parallel lineages were adapted to gradually increasing concentrations of kanamycin for 45 transfers (around 360 generations).
NAL:  Parallel lineages were adapted to gradually increasing concentrations of nalidixic acid for 48 transfers (around 384 generations).
NIT:  Parallel lineages were adapted to gradually increasing concentrations of nitrofurantoin for 30 transfers (around 240 generations).
TET:  Parallel lineages were adapted to gradually increasing concentrations of tetracycline for 39 transfers (around 312 generations).
TOB: Parallel lineages were adapted to gradually increasing concentrations of tobramycin for 45 transfers (around 360 generations).
TRM:  Parallel lineages were adapted to gradually increasing concentrations of trimethoprim for 36 transfers (around 288 generations).

value: ancestor (BWk3)

tag: resistance

value: Control, sensitive

value: Control


title: C4A


title: C3B


title: BMCP_15


title: C3C


title: C4B


title: BMCP_12


title: BMCP_21


title: C2C


title: BMCP_11


title: BMCP_10


title: C2A


title: BMCP_9


title: BMCP_8


title: BMCP_23


title: 67C

source_name: tetracycline adapted line 7

value: TET


title: BMCP_7


title: 67B


title: BMCP_6


title: 64C

source_name: tetracycline adapted line 1


title: BMCP_5


title: 64B


title: BMCP_4


title: C4C


title: 64A


title: BMCP_3


title: 62C

source_name: nitrofurantoin adapted line 7

value: NIT


title: BMCP_2


title: BMCP_1


title: C2B


title: 61C

source_name: nitrofurantoin adapted line 6


title: 62A


title: 67A


title: 56C

source_name: nalidixic acid adapted line 8

value: NAL


title: 61B


title: 54C

source_name: nalidixic acid adapted line 6


title: 56A


title: 61A


title: 48C

source_name: trimethoprim adapted line 6

value: TRM


title: 49B

source_name: trimethoprim adapted line 7


title: 49A


title: 54B


title: 56B


title: 48B


title: 48A


title: 46A

source_name: cefoxitin adapted line 8

value: FOX


title: 42C

source_name: cefoxitin adapted line 1


title: 46C


title: 40C

source_name: erythromycin adapted line 6

value: ERY


title: 42A


title: 62B


title: 40B


title: 42B


title: 49C


title: 54A


title: 38B

source_name: erythromycin adapted line 2


title: 38A


title: 36C

source_name: doxycycline adapted line 5

value: DOX


title: 33C

source_name: doxycycline adapted line 2


title: 36B


title: 36A


title: 33B


title: 31C

source_name: ciprofloxacin adapted line 9

value: CPR


title: 33A


title: 46B


title: 31B


title: 31A


title: 27C

source_name: ciprofloxacin adapted line 4


title: 25A

source_name: chloramphenicol adapted line 9

value: CHL


title: 25C


title: 27A


title: 27B


title: 21C

source_name: chloramphenicol adapted line 2


title: 21B


title: 21A


title: 40A


title: 20B

source_name: ampicillin adapted line 9

value: AMP


title: 25B


title: 18C

source_name: ampicillin adapted line 7


title: 38C


title: 20A


title: 18A


title: 18B


title: 20C


title: 11C

source_name: kanamycin adapted line 4

value: KAN


title: 11B


title: 10C

source_name: kanamycin adapted line 1


title: 11A


title: 8C

source_name: tobramycin adapted line 9

value: TOB


title: 10B


title: 7C

source_name: tobramycin adapted line 8


title: 8B


title: 10A


title: 7B


title: 7A


title: 8A


title: 1A

source_name: ancestor (BWk3)


title: Liver tissue of mice fed Western diet with carbon tetrachloride (CCl4) for 24 weeks, pool of 4 mice (WD_CCl4_24wk)

status: Public on Mar 28 2018

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Raw sequencing reads were aligned to mouse reference genome (mm10) by STAR 2-pass algorithm, and gene expression levels were calculated as count per million (CPM) normalized by trimmed mean of M-values (TMM) method.
Genome_build: mm10
Supplementary_files_format_and_content: gct files include normalized expression values for each sample

source_name: liver

extract_protocol:
Liver was removed, flash frozen on dry ice, and RNA was harvested using RNeasy Kit (Qiagen).
Illumina TruSeq RNA Sample Prep Kit was used with 200ng of total RNA for the construction of sequencing libraries. RNA-Seq libraries were prepared for sequencing using standard Illumina protocols.
Poly-A-based mRNA selection

value: liver

value: Western diet

tag: ccl4 treatment

tag: diet duration

value: 24 weeks


title: Liver tissue of mice fed normal diet with carbon tetrachloride (CCl4) for 24 weeks, pool of 4 mice (ND_CCl4_24wk)

value: Normal diet


title: Liver tissue of mice fed Western diet with oil (vehicle) for 24 weeks, pool of 4 mice (WD_oil_24wk)

value: Oil


title: Liver tissue of mice fed normal diet with oil (vehicle) for 24 weeks, pool of 4 mice (ND_oil_24wk)


title: Tumor tissue of mouse fed western diet with carbon tetrachloride (CCl4) for 24 weeks (WD_CCl4_HCC_1)

source_name: hepatocellular carcinoma

value: hepatocellular carcinoma


title: 1B

tag: strain

value: ancestor (BWk3)

value: Control, sensitive

value: Control


title: Liver tissue of mice fed Western diet with oil (vehicle) for 12 weeks, pool of 4 mice (WD_oil_12wk)

value: 12 weeks


title: Liver tissue of mice fed Western diet with carbon tetrachloride (CCl4) for 12 weeks, pool of 4 mice  (WD_CCl4_12wk)


title: NMR_B_LVR

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

description:
old naked mole-rat non-breeder
160208_nmr_B_Leber

data_processing:
Extraction of read information in FastQ format was done using the tool bcl2astq v1.8.4 (provided by Illumina).
Reads were mapped using STAR (v2.4.1d) with a maximum mismatch of 6% and a minimum aligned length of 90%. Reads mapped to multiple loci were discarded.
Reads per gene were counted using HTSeq framework (0.6.1p1)
Genome_build: genome (hetgla2, GCA_000247695.1) can be download from UCSC (ftp://hgdownload.cse.ucsc.edu/goldenPath/hetGla2/bigZips/)
Supplementary_files_format_and_content: The Excel sheet includes raw counts for all genes and each sample.

organism: Heterocephalus glaber

extract_protocol:
Extraction was done as described in Bens et al. 2016. (PMID:26763976)
Library preparation was done using Illumina's TruSeq RNA Library Prep Kit v2 kit following the manufacturer's description.

tag: Sex

value: male

tag: reproductive status

value: non-breeder

tag: age

value: 30 years


title: NMR_C_LVR

description:
old naked mole-rat non-breeder
160208_nmr_C_Leber

value: 20 years


title: Liver tissue of mice fed normal diet with carbon tetrachloride (CCl4) for 12 weeks, pool of 4 mice (ND_CCl4_12wk)

tag: diet


title: NMR_NM_4925_LVR [re-used]

description:
This is duplicated sample record of GSM2609152 for the convenient retrieval of the complete raw data from SRA
140912_nmr_4925_Leber

value: 3.7 years


title: NMR_NM_6206_LVR [re-used]

description:
This is duplicated sample record of GSM2609154 for the convenient retrieval of the complete raw data from SRA
140912_nmr_6206_Leber

value: 2.8 years


title: NMR_A_LVR

description:
old naked mole-rat non-breeder
merged_nmr_A_Leber


title: Liver tissue of mice fed normal diet with oil (vehicle) for 12 weeks, pool of 4 mice  (ND_oil_12wk)


title: NMR_NM_0713_LVR [re-used]

description:
This is duplicated sample record of GSM2609143 for the convenient retrieval of the complete raw data from SRA
140912_nmr_0713_Leber

value: 3.4 years


title: NMR_NM_3295_LVR [re-used]

description:
This is duplicated sample record of GSM2609149 for the convenient retrieval of the complete raw data from SRA
140912_nmr_3295_Leber

value: 4.1 years

value: liver


title: Exonic_amplicon_E10F-E8R

city: Newcastle Upon Tybe

first: Michael

last: Jackson

address: International Centre for Life

institute: Institute of Genetic Medicine

description:
FIRRE_amplicon_junctions_identified.xlsx
Amplicons generated using FIRRE exonic primers in divergent orientation to verify splice junctions within circRNAs

data_processing:
Library strategy: Amplicon sequencing
Base calling and demultiplexing were performed using Illumina's CASAVA software
For amplicon sequences only, splice sites were mapped to human genome using MapSplice
Genome_build: HG19
Supplementary_files_format_and_content: Excel spreadsheet with amplicon junctions

growth_protocol: Human embryonic stem cells (H9 line, passage 34-45), were plated in triplicate, expanded and differentiated for a minimum of 90 days according to the protocol of Mellough et al., 2012 (PMID: 22267304), with minor modifications outlined in Mellough et al., 2015 (PMID: 25827910).

extract_protocol:
Cells were harvested at three time points (days 0, 45 & 90) and RNA was extracted using the RNAeasy micro extraction kit with genomic DNA elimination columns (Qiagen), according to manufacturer’s recommendations. RNA quantitation was performed using the NanoDrop ND-1000 spectrophotometer (Thermo Scientific), and quality was assessed using the Agilent 2100 Bioanalyser (Agilent Technologies). RIN values indicated some reduction in RNA quality over time, with day 0 sample RIN values ranging from 9.8-10, day 45 samples ranging from 7.6-9.1 and day 90 samples ranging from 7.1-8.9
Amplicons were generated using a total RNA template extracted from an independent H9 day 0 replicate extracted as per extract protocol. Primers from FIRRE exons with illumina Nextera linkers attached were used in all cases, with sequencing primers and Illumina indexes being attached in a 2nd amplification using the Nextera DNA library preparation kit. These were then sequenced as paired ends using an Illumina nano DNA kit on the Illumina MiSeq platform according to manufacturers recommendations to target depths ranging from 1500-6000 reads per amplicon.

treatment_protocol: Cultures were supplemented with recombinant human IGF-1 (Sigma-Aldrich) at a concentration of 5ng/ml (to day 37) followed by 10ng/ml (after day 37).

tag: cell line

tag: cell type

value: human embryonic stem cells

tag: treatment

value: No treatment


title: Exonic_amplicon_E10F-E7R


title: 1C


title: Tumor tissue of mouse fed western diet with carbon tetrachloride (CCl4) for 24 weeks (WD_CCl4_HCC_2)

tag: tissue

value: Western diet

value: 24 weeks


title: Exonic_amplicon_E10F-E5R


title: Exonic_amplicon_E6F-E5R


title: Exonic_amplicon_E10F-E11R

description:
FIRRE_amplicon_junctions_identified.xlsx
Amplicons generated using FIRRE exonic primers to verify splice junctions


title: Exonic_amplicon_E7F-E6R


title: Exonic_amplicon_E10F-E13R


title: Exonic_amplicon_E8F-E11R


title: Exonic_amplicon_E5BF-E7R


title: Exonic_amplicon_E5F-E8R


title: Exonic_amplicon_E5F-E7R