title: Spleen def diet 04

description: Spleen deficient diet 4 weeks


title: Spleen reg diet 03

status: Public on Jun 29 2018

type: SRA

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

country: USA

institute: Coriell Institute for Medical Research

description: Spleen regular diet 4 weeks

library_source: genomic

data_processing:
Library strategy: DREAM
Illumina fastq files were aligned to the Rattus norvegicus genome (rn4) using Bowtie2. Uniquely mapped reads were sorted into bam files using samtools.
We used a python script to map aligned sequencing reads to target CCCGGG sites in the Rattus norvegicus genome (rn4) and enumerate signatures corresponding to methylated (starting with CCGGG) and unmethylated (starting with GGG) CpG for each target site.
We used an R script to calculate methylation levels at each SmaI/XmaI site based on the following formula: let sm be the number of tags corresponding to methylated CpG (i.e., tags starting with CCGGG) and u be the number of tags corresponding to unmethylated CpG (i.e., tags starting with GGG), the methylation value was calculated as 100%*(c*sm/(c*sm+u)), where c is the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: rn4
Supplementary_files_format_and_content: tab delimited text file with numbers of reads and percent methylation at individual CCCGGG sites

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Spleen

extract_protocol:
spinal nerve ligation protocol: Spinal nerve ligation (SNL) in male Sprague-Dawley rats (8-9 weeks old, ± 220 g; Harlan Sprague-Dawley, Indianapolis, IN) was used for this study as the neuropathic pain model. Animals were anesthetized with 2-3% isoflurane, and the left L5 and L6 spinal nerves were isolated and ligated tightly with 4.0-silk suture under a surgical microscope. Sham surgery (without nerve ligation) was performed on the contralateral side as the control.
chemotherapy-induced neuropathy: Four intraperitoneal injections of the chemotherapeutic agent paclitaxel (2 mg/kg, every two days) were performed, and vehicle (cremophor ethanol 1:1)-treated rats were used as the control group.
intrathecal cathetrization: Under anesthesia with 2% isoflurane, an intrathecal catheter (a PE-10 tubing) was surgically inserted through an incision made in the cisternal membrane. The catheter is directed to the lumbar region of the spinal cord, and the external opening was sealed. Rats displaying signs of the motor or neurological dysfunction were excluded and terminated immediately with an overdose of phenobarbital (200 mg/kg, i.p.). The animals were allowed to recover for five days before intrathecal injections. Ten micrograms of N-phthaloyl-L-tryptophan (RG108, Tocris Bioscience, Bristol, UK) or vehicle (10% DMSO; saline) were injected intrathecally in a 5 µl volume followed by 10 µl saline flush.(Chestnut et al. 2011). Animals received intrathecal injections for four consecutive days.
neuronal enrichment: To prepare a neuronal nuclear enrichment, fresh whole DRG samples were cut and mashed onto an ice-cold petri dish. Mashed tissue from 3 DRGs was pooled in one 1.5 ml tube. The tissue was resuspended in buffer NAME (20 mM Tris pH8, 20 mM KCl, 1.5 mM MgCl2) with a cocktail of protease and phosphatase inhibitors cocktails (Pierce), 0.5 mM DTT and 1 mM PMSF (Sigma-Aldrich, MO) to obtain a single cell suspension. Cells were incubated on ice for 5 min before to be spincentrifuged at 3,000 rpm at 4 °C for 2 min. The pPellet was resuspended in buffer NAME containing 0.15% NP-40. Cells were incubated on a rotator overnight to isolate nuclei. Neuronal nuclei were immunoprecipitated using anti-Fox3 (neuronal nuclear marker, Abcam #104225) in PBS. Then, classical and genomic DNA extraction was performed. Neuronal nuclei were lysed with lysis buffer (0.1 M Tris pH 8, 5 mM EDTA, 0.2% SDS, 0.2 M NaCl and, proteinase K) overnight and precipitated with isopropanol. Genomic DNA pellet was washed with 75% ethanol, dried and re-suspended in TE buffer (Tris 10 mM pH8, 1 mM EDTA). The isolation purity was validated by western blot analysis. Nuclear proteins were extracted from one batch. Cytoplasm/nucleus separation was validated by western blot using anti-histone H3 (Cell Signaling Technology#9715; 1/4000) and neuronal enrichment was validated by western blot using the neuronal marker anti-Fox3 (Abcam #104225) and the satelite/glia markers anti-g Glutamine sSynthetase (Millipore #MAB302; 1/200) and anti-GFAP (Abcam #7260; 1/4000).
Genomic DNA extracted from tissue samples was spiked with methylation standards and sequentially digested with two restriction endonucleases recognizing CCCGGG sites in DNA. SmaI cleaved only unmethylated sites resulting in blunt ended fragments starting with 5’-GGG. Next, XmaI cleaved the remaining methylated sites creating 5’-CmeCGG overhang sequences. Exonuclease-deficient Klenow fragment DNA polymerase was then used to fill in the 3’ recesses left by XmaI and add 3’-dA overhangs to the ends of all fragments. Thus, specific signatures 5’-GGG and 5’-CCGGG were created at unmethylated and methylated CpG sites, respectively. Illumina sequencing adapters were then ligated to the enzyme-treated DNA; sequencing libraries were generated according to Illumina protocols and run on an Illumina HiSeq 2500 instruments at Fox Chase Cancer Center Genomics facility. Sequencing data were aligned to the rat genome (rn4), and the reads with unmethylated and methylated signatures were counted at individual CCCGGG sites. Methylation levels were calculated as the ratio of reads with the methylated signature to all reads mapping to each respective site. DNA methylation values at individual CpG sites were adjusted based on spiked in standards and filtered for the minimum sequencing depth of 100 reads.

treatment_protocol: modified diet treatment: To manipulate DNA methylation levels, we altered the intake of methyl group donors (folate and vitamin B12) by feeding the rats with modified diets. The original diet AIN-93M (normal folate and vitamin B12 doses are 2.1 ppm and 28 µg/kg, respectively) was modified by Purina Animal Nutrition LLC Technical Services to make a folate and vitamin B12 deficient diet (0.1 ppm and 3 µg/kg respectively) and a diet 5 times enriched in folate and vitamin B12 (10.5 ppm and 140 µg/kg respectively). Five-week-old rats (weighing ~120 g) were randomly placed in new cages with ad libitum regular, deficient and enriched diets, respectively. The animals were kept on the diets for four weeks before SNL surgery, followed by three weeks after SNL.

tag: strain

value: Sprague-Dawley

tag: tissue

value: Spleen

tag: age

value: adult

tag: procedure

value: regular diet 4 weeks


title: Spleen reg diet 01

description: Spleen regular diet 4 weeks


title: Spleen rich diet 02

description: Spleen enriched diet 4 weeks

value: enriched diet 4 weeks


title: Spleen reg diet 07

description: Spleen regular diet 4 weeks


title: Spleen def diet 09

description: Spleen deficient diet 4 weeks

value: deficient diet 4 weeks


title: Spleen reg diet 06

description: Spleen enriched diet 4 weeks


title: Spleen def diet 10

description: Spleen deficient diet 4 weeks


title: Prefrontal cortex def diet 21

description: Prefrontal cortex deficient diet 7 weeks, 3 weeks after SNL

source_name: Prefrontal cortex

value: Prefrontal cortex


title: Prefrontal cortex reg diet 20

description: Prefrontal cortex regular diet 7 weeks, 3 weeks after SNL

value: regular diet 7 weeks, 3 weeks after SNL


title: Spleen rich diet 08

description: Spleen enriched diet 4 weeks


title: Prefrontal cortex rich diet 18

description: Prefrontal cortex rich diet 7 weeks, 3 weeks after SNL

value: rich diet 7 weeks, 3 weeks after SNL


title: Prefrontal cortex def diet 19

value: deficient diet 7 weeks, 3 weeks after SNL


title: Prefrontal cortex rich diet 16


title: Prefrontal cortex def diet 10 [d90_FC_10]

description: Prefrontal cortex deficient diet 4 weeks


title: Prefrontal cortex rich diet 14


title: Prefrontal cortex reg diet 15


title: Prefrontal cortex reg diet 17


title: Prefrontal cortex def diet 09 [d90_FC_9]


title: Prefrontal cortex def diet 04 [d90_FC_4]


title: Prefrontal cortex reg diet 07 [d90_FC_7]

description: Prefrontal cortex regular diet 4 weeks


title: Prefrontal cortex rich diet 02 [d90_FC_2]

description: Prefrontal cortex enriched diet 4 weeks


title: Prefrontal cortex rich diet 06 [d90_FC_6]

description: Prefrontal cortex enriched diet 4 weeks


title: Prefrontal cortex def diet 09 [d34_FC_9]


title: Prefrontal cortex reg diet 01 [d90_FC_1]

description: Prefrontal cortex regular diet 4 weeks


title: Prefrontal cortex def diet 10 [d34_FC_10]


title: Prefrontal cortex rich diet 08 [d34_FC_8]

description: Prefrontal cortex enriched diet 4 weeks


title: Prefrontal cortex rich diet 08 [d90_FC_8]

description: Prefrontal cortex enriched diet 4 weeks


title: Prefrontal cortex def diet 04 [d33_FC_4]


title: Prefrontal cortex reg diet 07 [d33_FC_7]

description: Prefrontal cortex regular diet 4 weeks


title: Prefrontal cortex rich diet 06 [d33_FC_6]

description: Prefrontal cortex enriched diet 4 weeks


title: Prefrontal cortex rich diet 02 [d32_FC_2]

description: Prefrontal cortex enriched diet 4 weeks


title: Prefrontal cortex reg diet 03 [d32_FC_3]

description: Prefrontal cortex regular diet 4 weeks


title: Prefrontal cortex reg diet 01 [d32_FC_1]

description: Prefrontal cortex regular diet 4 weeks


title: Spinal cord Sham def diet 19

description: Spinal cord deficient diet 7 weeks, 3 weeks after sham operation

source_name: Spinal cord

value: Spinal cord


title: Spinal cord Sham reg diet 17

description: Spinal cord regular diet 7 weeks, 3 weeks after sham operation


title: 24hrs treated_2

status: Public on Jun 30 2018

city: Los Angeles

first: vineela

last: gangalapudi

state: CALIFORNIA

address: 8723 Alden drive

department: Biomedical sciences

institute: Cedars- sinai Medical center

library_source: transcriptomic

data_processing:
We used the STAR aligner to map the samples, and Qced them using Rseqc then used DEseq2 for DE to get the significantly differentially expressed genes between the control  and  treated samples at each time point
Genome_build: GRCh38 version 23
Supplementary_files_format_and_content: Excel table includes count values for lincRNA and protein-coding genes for each Sample calculated by STAR.

molecule: total RNA

organism: Chlorocebus aethiops

source_name: Vero cell line

growth_protocol: Vero cells from three different time points(12hr,24hr, 48hr) were used.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Quiagen)
Total RNA was quantified using both the NanoDrop to assess sample contamination by proteins or carryover reagents from RNA isolation, and the Qubit fluorometer (Invitrogen). Samples were then qualified using the Fragment Analyzer (Advanced Analytical Technologies, Ankeny, IA) that analyzes the integrity of the total RNA by measuring the ratio between the 18S and 28S ribosomal peaks. Libraries were constructed using SMARTer Ultra Low Input RNA v3 kit (Clontech), indexed using Nextera indices (Illumina). Final libraries were again quantitated with the Qubit fluorometer and checked for size via the Fragment Analyzer. Libraries were diluted to 4nM and pooled in equal volumes for denaturation, hybridization, and sequencing on an Illumina NextSeq 500 (Illumina) with single end 75bp sequencing chemistry.

treatment_protocol: Vero cell line was maintained in DMEM medium which was supplemented in 10% fetal bovine serum (FBS), penicillin (100 units/ml), streptomycin (100 mg/ml), 10 mM Hepes, and 2 mM L-glutamine.The following day, Zika viral inoculum was prepared in serum-free base media at an MOI of 1.

tag: treatment

value: zika infected

tag: cell line

value: vero


title: 5_eos_Sto_1mth

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

data_processing:
Reads were aligned with STAR STAR-2.5.1b with the options --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Alignments were counted with the R method Rsubread::featureCounts
Genome_build: GRCm38
Supplementary_files_format_and_content: text files holding gread counts per gene

organism: Mus musculus

growth_protocol: Eosinphils were sorted by flow-cytometry from the mouse gastric lamina propria.

extract_protocol:
RNA was isolated using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems, Thermofisher Scientific).
Library Prep was done using the NuGEN Ovation SoLo RNA-seq kit

value: Stomach

value: H. pylori-infected


title: 9_eos_Sto_1mth


title: 17_eos_Sto_ctrl

value: uninfected


title: 8_eos_Sto_1mth


title: 6_eos_Sto_1mth


title: 4_eos_Sto_1mth


title: 13_eos_Sto_ctrl


title: Spinal cord Sham rich diet 18

description: Spinal cord enriched diet 7 weeks, 3 weeks after sham operation


title: 3_eos_Sto_1mth


title: 2_eos_Sto_1mth


title: Spinal cord Sham rich diet 16

value: enriched diet 7 weeks, 3 weeks after sham operation


title: 18_eos_Sto_ctrl


title: 15_eos_Sto_ctrl


title: Spinal cord Sham reg diet 20

value: Sprague-Dawley

value: regular diet 7 weeks, 3 weeks after sham operation


title: 1_eos_Sto_1mth


title: Spinal cord Sham reg diet 15

value: adult


title: Spinal cord Sham rich diet 14


title: Spinal cord Sham def diet 13

value: deficient diet 7 weeks, 3 weeks after sham operation


title: 12_eos_Sto_ctrl


title: 11_eos_Sto_ctrl


title: Spinal cord Sham def diet 21


title: Spinal cord SNL reg diet 20

description: Spinal cord regular diet 7 weeks, 3 weeks after spinal nerve ligation


title: Spinal cord rich diet 08

description: Spinal cord enriched diet 4 weeks

value: enriched diet 4 weeks


title: Spinal cord SNL rich diet 16

description: Spinal cord enriched diet 7 weeks, 3 weeks after spinal nerve ligation


title: Spinal cord SNL def diet 19

description: Spinal cord deficient diet 7 weeks, 3 weeks after spinal nerve ligation


title: Spinal cord rich diet 06

description: Spinal cord enriched diet 4 weeks


title: Spinal cord SNL rich diet 18

value: enriched diet 7 weeks, 3 weeks after spinal nerve ligation


title: Spinal cord def diet 04

description: Spinal cord deficient diet 4 weeks

value: deficient diet 4 weeks


title: Spinal cord SNL def diet 21

value: deficient diet 7 weeks, 3 weeks after spinal nerve ligation


title: 7_eos_Sto_1mth


title: Spinal cord SNL def diet 13


title: Spinal cord reg diet  07

description: Spinal cord regular diet 4 weeks

value: regular diet 4 weeks


title: Spinal cord SNL rich diet 14


title: Spinal cord SNL reg diet 15

value: regular diet 7 weeks, 3 weeks after spinal nerve ligation


title: Spinal cord SNL reg diet 17

value: Spinal cord


title: Spinal cord Taxol control 02

description: Spinal cord paclitaxel control

value: paclitaxel control


title: Spinal cord rich diet 02

description: Spinal cord enriched diet 4 weeks


title: Spinal cord Taxol treatment 01

description: Spinal cord paclitaxel treatment

value: paclitaxel treatment


title: Spinal cord Taxol treatment 02

description: Spinal cord paclitaxel treatment


title: Spinal cord reg diet 01

description: Spinal cord regular diet 4 weeks


title: Spinal cord def diet 10

description: Spinal cord deficient diet 4 weeks


title: Spinal cord Taxol control 03

description: Spinal cord paclitaxel control


title: Spinal cord Sham week 3 05

description: Spinal cord 3 weeks after sham operation

value: 3 weeks after sham operation


title: Spinal cord SNL week 3 06

description: Spinal cord 3 weeks after spinal nerve ligation

value: 3 weeks after spinal nerve ligation


title: Spinal cord Sham week 3 04


title: Spinal cord SNL week 3 05


title: Spinal cord SNL week 3 04


title: Spinal cord reg diet 03

description: Spinal cord regular diet 4 weeks


title: Spinal cord Sham week 3 03


title: Spinal cord Sham week 3 02


title: Spinal cord Sham week 3 01


title: Spinal cord Taxol control 01

description: Spinal cord paclitaxel control


title: DRG SNL week 3 014

description: DRG 3 weeks after spinal nerve ligation

source_name: DRG

value: dorsal root ganglion


title: Spinal cord Sham week 3 06


title: Spinal cord SNL week 3 03


title: DRG SNL week 3 013

description: DRG 3 weeks after spinal nerve ligation


title: DRG neonatal 01

description: DRG neonatal DRGs

value: neonatal

value: neonatal DRGs


title: Spinal cord SNL week 3 01

value: Sprague-Dawley


title: Spinal cord SNL week 3 02

value: adult


title: DRG neonatal 02

description: DRG neonatal DRGs


title: RD_99-31391415

city: London

first: Guillermo

last: Carbajosa

address: Guy’s Hospital, St Thomas Street

department: Medical and Molecular Genetics

country: United Kingdom

institute: King's College London

data_processing:
Illumina NextSeq 500 platform 76bp reads.
RNA-seq reads were aligned to the mouse GRCm38 rel 79 reference transcriptome using Kallisto version 0.42.4.
Genome_build: GRCm38.rel79
Supplementary_files_format_and_content: *tsv: Tab-delimited text files include TPM values and counts for each Sample.

source_name: cortex, WT, 8m

extract_protocol:
The hippocampus and cortex were dissected from the left hemisphere of each mouse brain, and snap frozen in liquid nitrogen. Tissues were homogenized in Qiazol reagent and total RNA isolated using the RNeasy Plus Universal Mini Kit according to the manufacturer's protocol (Qiagen). RNA integrity (RIN) was measured for all samples using the Bioanalyser Agilent 2100 series using RNA nano chip. All sequencing libraries analyzed were generated from RNA samples measuring a RIN score >= 8.9.
The Illumina TruSeq mRNA stranded protocol was used to obtain poly-A mRNA from all samples. 100ng of isolated mRNA was used to construct RNA-seq libraries. Libraries were quantified and normalized using the NEBNext® mRNA Library prep kit for Illumina.

tag: strain/background

tag: genotype/variation

value: WT

tag: gender

value: male

value: cortex

tag: sample id


title: RD_98-31389429


title: DRG fetal 02

description: DRG fetal DRGs one day before expected delivery

value: fetal


title: DRG fetal 01

value: fetal DRGs one day before expected delivery


title: RD_98-30893058


title: RD_97-31388425


title: RD_99-30904986


title: DRG RG108 treatment 03

description: DRG RG108 treatment

value: RG108 intrathecal application


title: DRG Sham week 3 014

description: DRG 3 weeks after sham operation


title: DRG RG108 control 01

description: DRG control for RG108 treatment

value: vehicle intrathecal application


title: RD_97-30888992


title: DRG RG108 control 02

description: DRG control for RG108 treatment


title: DRG RG108 treatment 02

description: DRG RG108 treatment


title: DRG Sham week 3 013

description: DRG 3 weeks after sham operation


title: RD_9-30976063

source_name: hippocampus, TREM2KO, 4m

value: hippocampus


title: RD_9-30772752


title: DRG RG108 treatment 01

description: DRG RG108 treatment


title: DRG RG108 control 03

description: DRG control for RG108 treatment


title: RD_80-31441450

source_name: hippocampus, TREM2KO, 8m


title: RD_8-30916086

source_name: hippocampus, WT, 4m


title: RD_80-30874902


title: DRG Neurons SNL 02

description: purified DRG neurons

source_name: DRG neurons


title: RD_79-30869901


title: DRG Neurons SNL 01

description: purified DRG neurons


title: DRG Sham siRNA control 03

description: DRG 3 weeks after sham operation, control siRNA intrathecally


title: DRG Input SNL 01

description: DRG input control for neuron purification


title: DRG Input Sham 01


title: RD_78-31412455


title: RD_78-30877898


title: RD_77-31440458


title: RD_8-30773754


title: RD_77-30862906


title: RD_76-30875917


title: DRG SNL siGadd45a 04

description: DRG 3 weeks after spinal nerve ligation, Gadd45a siRNA intrathecally


title: RD_76-31438469


title: DRG SNL siGadd45a 05

value: 3 weeks after spinal nerve ligation, Gadd45a siRNA intrathecally


title: RD_75-31402460


title: DRG Sham siRNA control 02

value: 3 weeks after sham operation, control siRNA intrathecally


title: DRG SNL siGadd45a 03


title: DRG Neurons Sham 02

description: purified DRG neurons

value: 3 weeks after sham operation


title: DRG SNL siGadd45a 02


title: DRG SNL siGadd45a 01


title: DRG SNL siRNA control 03

description: DRG 3 weeks after spinal nerve ligation, control siRNA intrathecally


title: RD_75-30867920


title: RD_79-31412454


title: RD_74-31402461


title: DRG SNL siRNA control 02

value: 3 weeks after spinal nerve ligation, control siRNA intrathecally


title: DRG SNL siRNA control 01

value: dorsal root ganglion


title: DRG Sham siRNA control 01


title: DRG def diet Sham 021

description: DRG deficient diet 7 weeks, 3 weeks after sham operation


title: PGYLI1

city: Blacksburg

first: Stephen

last: Melville

state: Virginia

address: 217 LS1, Washington St.

department: Biological Sciences

institute: Virginia Tech

description: PGY liquid

data_processing:
Geneious version 9 with low sensitivity
Relative expression levels of annotated coding regions were calculated with units of transcripts per million (TPM). TPM, as proposed by Wagner (3) is calculated as: TPM= (coding Sequence read count x Mean read length x 106)/(Coding sequence length x Total transcript count). Differentially expressed genes were identified by a stringent cutoff of fold-change >4 when media conditions were compared against one another for each gene.
Genome_build: NC_003366
Supplementary_files_format_and_content: excel, raw and average RNA-seq data and compiled sRNA values

organism: Clostridium perfringens

source_name: Bacteria

growth_protocol: C. perfringens HN13 cells were grown in duplicate in six conditions: liquid culture to mid-log phase and 1% agar plates of PGY, BHI, and FABG media for 24 hours.  Liquid cultures were standardized to OD600=0.500 and cells were scraped from the outer edges of plate grown colonies and resuspended in DPBS to OD600=0.500.  Bacteria were pelleted and frozen in liquid nitrogen prior to RNA purification.

extract_protocol:
Cells were lysed in 500 μl Tri Reagent (Zymo Research) using high-impact zirconium beads in a Mini-Beadbeater (Biospec) for one minute and kept on ice.  RNA was then purified from cell lysate using a Direct-Zol RNA Mini-Prep Plus Kit according to the manufacturer’s protocol (Zymo Research), including an on-column DNA digestion. RNA integrity was measured using an Agilent BioAnalyzer 2100 (VBI), and samples with a RIN of 8.3 or greater were used for RNA sequencing.
Library construction was performed for Illumina sequencing by Virginia Bioinformatics Institute. All samples were processed with HiSeq Illumina sequencing (VBI) creating 100-bp paired-end reads, and the resulting data was aligned to C. perfringens strain 13 reference genome (NCBI, accession number NC_003366) using the bioinformatics mapper Geneious version 9 with low sensitivity

tag: growth

value: PGY liquid


title: RD_74-30868936


title: RD_73-31429488


title: RD_73-30877899


title: RD_72-31416483

source_name: hippocampus, WT, 8m


title: RD_71-31441453


title: RD_72-30868937


title: DRG reg diet Sham 017

description: DRG regular diet 7 weeks, 3 weeks after sham operation


title: DRG rich diet Sham 016

description: DRG enriched diet 7 weeks, 3 weeks after sham operation


title: RD_71-30867921


title: DRG reg diet Sham 015

value: regular diet 7 weeks, 3 weeks after sham operation


title: DRG def diet SNL 021

description: DRG deficient diet 7 weeks, 3 weeks after spinal nerve ligation

value: Sprague-Dawley


title: RD_7-30766752


title: RD_70-30876913


title: RD_7-30985046


title: DRG def diet Sham 013

value: adult

value: deficient diet 7 weeks, 3 weeks after sham operation


title: RD_70-31416484

value: WT

value: male


title: DRG reg diet SNL 020

description: DRG regular diet 7 weeks, 3 weeks after spinal nerve ligation


title: RD_69-30874903


title: RD_69-31416486


title: DRG def diet SNL 019

value: deficient diet 7 weeks, 3 weeks after spinal nerve ligation


title: RD_68-31434445


title: DRG rich diet SNL 018

description: DRG enriched diet 7 weeks, 3 weeks after spinal nerve ligation


title: DRG def diet Sham 019


title: RD_68-30865920


title: DRG rich diet Sham 018

value: enriched diet 7 weeks, 3 weeks after sham operation


title: DRG reg diet SNL 015

value: regular diet 7 weeks, 3 weeks after spinal nerve ligation


title: RD_67-31401458


title: DRG rich diet Sham 014


title: DRG rich diet SNL 014

value: enriched diet 7 weeks, 3 weeks after spinal nerve ligation


title: RD_66-30865921

value: hippocampus


title: DRG reg diet Sham 020


title: RD_66-31438471


title: RD_67-30866930


title: DRG def diet 009

description: DRG deficient diet 4 weeks

value: deficient diet 4 weeks


title: RD_65-31444431


title: 10d-B37Htn1-4

city: Zürich

first: Coraline

middle: Rosalie

last: Praz

address: Zollikerstrasse 107

department: Institute of Plant and Microbial Biology

institute: University of Zürich

data_processing:
MAPPING: The RNA sequencing reads were mapped on the reference genome with STAR allowing one mismatch per 100 bp and no multimapper with the following command: STAR -outFilterMultiMapNmax 1 - outFilterMismatchNoverLmax 0.01 - alignIntronMax 10000.
COUNT: Read counts were determined from the mapping files with featureCounts 1.4.6.
Genome_build: The maize reference genome Zea_mays.AGPv3.27 and the corresponding annotation were downloaded (http://www.maizegdb.org/).
Supplementary_files_format_and_content: The processed data files are count table obtained from featureCount. The first column is the gene ID and the last column is the read count. Other columns are explained in the header of the files.

organism: Zea mays

source_name: B37Htn1, leaf, 10 days post inoculation

growth_protocol: Two or three maize seeds were sown in each Jiffy pot (ø 8cm), and fifteen pots were placed in one tray. Seedling plants were grown in a greenhouse condition of 16 h at 20°C in the day, 8 h at 18°C in the night and approximately 60% relative humidity. The second leaves of seedling plants were harvested with four biological replicates at 0, 9-hpi, 3-dpi and 10-dpi, which corresponded to before inoculation, the germination/penetration, biotrophic growth and necrotrophic growth, respectively.

extract_protocol:
Forty-eight samples (4 genotypes, 4 time points, 3 biological replicates) were subjected for total RNA extraction using SV Total RNA Isolation Kits (Promega, Dübendorf, Switzerland). 1 μl of total RNA was checked by Nanodrop 1000 Spectrophotometer to estimate the RNA concentration.
The quantity and quality in RNA sequencing were determined using Qubit® 1.0 Fluorometer (Thermo Fisher Scientific, Wilmington, USA) and Bioanalyzer 2100 (Agilent, Waldbronn, Germany). The TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., Hayward, USA) was used for library preparation. 1 μg of total RNA per sample was ribosome depleted and then subjected for synthesizing double-strand cDNA. Each cDNA sample was fragmented, end-repaired, polyadenylated and then ligated with TruSeq adaptor that contains the index for multiplexing. The cDNA fragments containing TruSeq adapters at the both ends were enriched with PCR reaction. The enriched libraries were quantified and qualified, and then normalized to 10nM. The TruSeq SR Cluster Kit v4 cBot (Illumina, Inc., Hayward, USA) was used for cluster generation using 8 pM of pooled normalized libraries. Sequencing was performed on the Illumina HiSeq2500 at single end 125 bp using the TruSeq SBS Kit v4.

tag: genotype

tag: line

value: Near isogenic lines with Htn1 gene

tag: infection

value: E. turcium

tag: time

value: 10 days post inoculation

value: Leaves


title: RD_6-30974038


title: DRG def diet 004

description: DRG deficient diet 4 weeks

value: dorsal root ganglion


title: DRG def diet SNL 013


title: DRG rich diet 008

description: DRG enriched diet 4 weeks

value: enriched diet 4 weeks


title: 10d-B37Htn1-2


title: DRG reg diet SNL 017

value: Sprague-Dawley


title: DRG reg diet 007

description: DRG regular diet 4 weeks

value: adult

value: regular diet 4 weeks


title: RD_6-30770754

value: WT


title: 10d-B37-4

source_name: B37, leaf, 10 days post inoculation

value: Recurrent parental line


title: DRG rich diet 006

description: DRG enriched diet 4 weeks


title: DRG reg diet 003

description: DRG regular diet 4 weeks


title: RD_65-30864911

value: male


title: 10d-B37Htn1-3


title: DRG reg diet 001

description: DRG regular diet 4 weeks


title: RD_5-30981049


title: RD_5-30754836


title: 10d-B37-3


title: 10d-B37-1


title: 10d-w22Htn1-4

source_name: w22Htn1, leaf, 10 days post inoculation


title: DRG Taxol control 03

description: DRG control for paclitaxel treatment

value: control for paclitaxel treatment


title: DRG def diet 010

description: DRG deficient diet 4 weeks


title: RD_48-31014061

source_name: cortex, TREM2KO, 4m

value: cortex


title: DRG Taxol control 02

description: DRG control for paclitaxel treatment


title: RD_47-31015049


title: 10d-w22Htn1-2


title: RD_46-31015048


title: DRG Taxol control 01

description: DRG control for paclitaxel treatment


title: 10d-w22Htn1-1


title: DRG Taxol treatment 03

description: DRG paclitaxel treatment

value: paclitaxel treatment


title: RD_46-30782125


title: 10d-w22-1

source_name: w22, leaf, 10 days post inoculation


title: DRG Taxol treatment 02

description: DRG paclitaxel treatment


title: DRG rich diet 002

description: DRG enriched diet 4 weeks


title: RD_45-30767165


title: RD_45-30998146


title: DRG Decitabine 003

description: DRG decitabine treatment

value: decitabine treatment


title: DRG Taxol treatment 01

description: DRG paclitaxel treatment


title: 3d-B37Htn1-3

source_name: B37Htn1, leaf, 3 days post inoculation

value: 3 days post inoculation


title: RD_44-31008060


title: 3d-B37Htn1-4

value: Near isogenic lines with Htn1 gene


title: 10d-w22-4

value: E. turcium


title: 3d-B37Htn1-1


title: RD_47-30767166


title: DRG Decitabine 001

description: DRG decitabine treatment


title: 3d-B37-4

source_name: B37, leaf, 3 days post inoculation


title: DRG Decitabine 002

description: DRG decitabine treatment


title: 3d-B37-3


title: RD_44-30782124


title: DRG Control 007

description: DRG control for decitabine treatment

value: control for decitabine treatment


title: RD_43-30999154


title: RD_42-30998145


title: 10d-w22-3

value: 10 days post inoculation

value: Leaves


title: DRG Control 006

description: DRG control for decitabine treatment

value: dorsal root ganglion


title: 3d-B37-1


title: RD_41-31009051


title: RD_43-30778132


title: 3d-w22-4

source_name: w22, leaf, 3 days post inoculation


title: 3d-w22Htn1-4

source_name: w22Htn1, leaf, 3 days post inoculation


title: DRG Control 005

description: DRG control for decitabine treatment

source_name: DRG

value: Sprague-Dawley


title: 3d-w22Htn1-1


title: 3d-w22-3


title: DRG Sham week 3 009

description: DRG 3 weeks after sham operation

value: adult

value: 3 weeks after sham operation


title: RD_40-31006053

source_name: cortex, WT, 4m

value: WT


title: RD_41-30768115


title: DRG Sham week 3 012

description: DRG 3 weeks after sham operation


title: 3d-w22-1

value: Recurrent parental line


title: DRG Sham week 3 010

description: DRG 3 weeks after sham operation


title: RD_40-30767164

value: male


title: RD_4-30749822

value: hippocampus


title: RD_48-30780091

value: cortex


title: RD_42-30782123


title: DRG Sham week 3 011

description: DRG 3 weeks after sham operation


title: DRG Sham week 3 008

description: DRG 3 weeks after sham operation


title: 9h-B37Htn1-1

source_name: B37Htn1, leaf, 9 hours post inoculation

value: 9 hours post inoculation


title: DRG Sham week 3 007

description: DRG 3 weeks after sham operation


title: DRG SNL week 3 012

description: DRG 3 weeks after spinal nerve ligation

value: 3 weeks after spinal nerve ligation


title: DRG SNL week 3 011

description: DRG 3 weeks after spinal nerve ligation


title: 9h-B37Htn1-4


title: 9h-B37Htn1-3


title: RD_4-31000000


title: 3d-w22Htn1-3

value: 3 days post inoculation


title: 9h-B37-3

source_name: B37, leaf, 9 hours post inoculation


title: RD_39-31003095


title: DRG SNL week 3 010

description: DRG 3 weeks after spinal nerve ligation


title: RD_37-31000153


title: RD_38-30769101


title: 9h-B37-2


title: 9h-w22Htn1-4

source_name: w22Htn1, leaf, 9 hours post inoculation

value: Near isogenic lines with Htn1 gene


title: DRG SNL week 3 008

description: DRG 3 weeks after spinal nerve ligation


title: DRG SNL week 3 007

description: DRG 3 weeks after spinal nerve ligation


title: 9h-w22Htn1-1

value: E. turcium


title: RD_36-30999153


title: RD_37-30770172


title: 9h-w22-4

source_name: w22, leaf, 9 hours post inoculation


title: RD_39-30782122


title: DRG Sham day 3 005

description: DRG 3 days after sham operation

value: 3 days after sham operation


title: DRG Sham day 3 006

description: DRG 3 days after sham operation


title: RD_35-31009050


title: RD_36-30767163


title: DRG SNL day 3 006

description: DRG 3 days after spinal nerve ligation

value: 3 days after spinal nerve ligation


title: DRG Sham day 3 004

description: DRG 3 days after sham operation


title: 9h-B37-4

value: Leaves


title: 9h-w22-1


title: 9h-w22Htn1-3


title: RD_38-31008059


title: RD_35-30770171


title: 9h-w22-3


title: RD_34-30778131


title: DRG SNL week 3 009

description: DRG 3 weeks after spinal nerve ligation

value: dorsal root ganglion


title: RD_33-31015047


title: RD_34-31014060


title: DRG SNL day 3 005

description: DRG 3 days after spinal nerve ligation

value: Sprague-Dawley


title: 0-B37Htn1-4

source_name: B37Htn1, uninfected leaf

value: uninfected

value: control


title: RD_33-30783905

value: WT


title: Cellophane infectious hyphae rep1

city: Yangling

first: bo

last: wang

state: Shaanxi

address: No. 3 Taicheng Road

country: China

institute: Northwest A&F University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to 1104-7 whole genome (GenBank accession no. MVNS00000000) using TopHat v. 2.1.0 with parameters --bowtie1 -p 8 -g 1
A gene expression profile was created using a combination of DESeq2 and edgeR packages.
Genes with a significant P-value (< 0.05) and a greater than threefold change (log2) in transcript level were considered to be differently expressed, and the different expression needs to be supported by both DESeq2 and edgeR. All P-values were corrected for false discoveries resulting from multiple hypothesis testing using the Benjamini-Hochberg procedure.
Genome_build: reference genome deposited at DDBJ/EMBL/GenBank under the accession MVNS00000000
Supplementary_files_format_and_content: tab-delimited text files include read counts and expression profiles with annotations.
Supplementary_files_format_and_content: 1104_genes-exp-annot.txt: Differently expressed genes with log2 fold changes and annotations.
Supplementary_files_format_and_content: 1104_genes.count.txt: Reads counts per gene.
Supplementary_files_format_and_content: 1104.transcripts.fasta: Transcript FASTA sequences.

organism: Colletotrichum fructicola

source_name: Cellophane infectious hyphae

extract_protocol:
Total RNA was extracted according to the instruction manual of the Trizol Reagent (Life technologies, California, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Cellophane infectious hyphae


title: DRG Sham day 3 001

description: DRG 3 days after sham operation

value: adult


title: Cellophane infectious hyphae rep3


title: DRG Sham day 3 003

description: DRG 3 days after sham operation


title: DRG Sham day 3 002

description: DRG 3 days after sham operation


title: Infected apple (c.v. Gala) leaf rep2

source_name: Infected apple leaf

value: Infected apple leaf


title: Cellophane infectious hyphae rep2


title: 0-B37-1

source_name: B37, uninfected leaf

value: Recurrent parental line


title: Infected apple (c.v. Gala) leaf rep1


title: 0-B37Htn1-3


title: 0-B37Htn1-1


title: RD_2-30999000

source_name: hippocampus, WT, 4m

value: male

value: hippocampus


title: RD_2-30767762


title: 0-w22Htn1-3

source_name: w22Htn1, uninfected leaf


title: RD_3-30996000


title: Infected apple (c.v. Gala) leaf rep3


title: RD_3-30766751


title: DRG Sham week 3 003

description: DRG 3 weeks after sham operation

value: 3 weeks after sham operation


title: DRG SNL day 3 002

description: DRG 3 days after spinal nerve ligation


title: Appressoria rep2

source_name: Appressoria on cellophane

value: Appressoria on cellophane


title: DRG SNL day 3 003

description: DRG 3 days after spinal nerve ligation


title: DRG SNL day 3 001

description: DRG 3 days after spinal nerve ligation


title: 0-w22Htn1-4

value: Near isogenic lines with Htn1 gene


title: 0-w22Htn1-1


title: DRG SNL day 3 004

description: DRG 3 days after spinal nerve ligation


title: RD_16-30996993

source_name: hippocampus, TREM2KO, 4m


title: Appressoria rep3


title: RD_15-30766750


title: Conidia rep3

source_name: Conidia

value: Conidia


title: RD_15-30974040


title: 0-w22-3

source_name: w22, uninfected leaf


title: Conidia rep2


title: DRG SNL week 3 002

description: DRG 3 weeks after spinal nerve ligation

value: 3 weeks after spinal nerve ligation


title: 0-B37-3

value: Leaves


title: RD_16-30749821


title: DRG Sham week 3 002

description: DRG 3 weeks after sham operation

value: dorsal root ganglion


title: DRG SNL week 3 003

description: DRG 3 weeks after spinal nerve ligation

value: Sprague-Dawley


title: Conidia rep1


title: 0-w22-4

value: uninfected


title: Appressoria rep1


title: 0-B37-4

value: control


title: RD_14-30770753


title: 0-w22-1


title: DRG SNL week 3 001

description: DRG 3 weeks after spinal nerve ligation


title: RD_13-30754835


title: RD_12-30977063


title: RD_14-30916087


title: RD_12-30769752


title: RD_13-30978067


title: RD_112-30900070

source_name: cortex, TREM2KO, 8m

value: cortex


title: RD_111-31371487


title: DRG Sham week 3 001

description: DRG 3 weeks after sham operation

source_name: DRG


title: RD_110-30909943


title: RD_11-30974039


title: RD_112-31384402


title: RD_110-31388424


title: RD_108-31394364


title: RD_111-30888013


title: RD_108-30893061


title: RD_109-31388423


title: RD_11-30754834


title: RD_109-30900008


title: RD_106-31379405


title: RD_105-31392369


title: RD_107-31388422


title: RD_105-30887042


title: RD_106-30893060


title: RD_107-30905952


title: RD_102-31391417

source_name: cortex, WT, 8m

value: WT


title: RD_104-31395369


title: RD_103-31384404


title: RD_104-30903952


title: RD_102-30890999


title: RD_101-30908994


title: RD_10-30996001


title: RD_100-30892002


title: RD_101-31391416


title: RD_1-30974037


title: RD_10-30747819


title: RD_1-30772751


title: RD_100-31394365


title: Luminal Wt 3

status: Public on Jun 28 2018

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by RSubread 1.24.2.
Read counts were summarized by Entrez Gene ID using featureCounts and NCBI annotation in Rsubread.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: organoid

growth_protocol: Organoids were cultured in Advanced DMEM/F12 supplemented with growth factors excluding Wtn3a or FGF2.

extract_protocol:
RNA was isolated from freshly sorted cells with the RNeasyPlus Mini kit (Qiagen).
mRNA reverse transcription cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: To induce R26creERT2-mediated deletion of Suz12, 0.1 micromolar 4-hydroxytamoxifen was added to culture medium on day 4 of culture.

value: Mammary epithelium

tag: background strain

tag: cell type from which organoid was derived

value: Luminal

tag: phenotype

value: Wild-type

value: female


title: Luminal Suz12-deleted 2

tag: tissue


title: Luminal Suz12-deleted 3


title: Basal Wt 4

value: Basal


title: Basal Suz12-deleted 4


title: Luminal Wt 2


title: Luminal Wt 1


title: Basal Wt 1


title: Basal Suz12-deleted 1


title: Luminal Suz12-deleted 1


title: RD_103-30894000

tag: age

value: male


title: Flp8_NoDox_exp1_S186

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

data_processing:
Read Preprocessing: Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.7.1. Using FastX 0.0.14 and ShortRead 1.24.0, we filtered subsequently small reads (length < 35 bp), polyA-reads (more than 90% of the bases equal A), ambiguous reads (containing N) and low quality reads (more than 50% of the bases < Q25). With Bowtie2 v2.2.4 we identified and removed reads that mapped to the spiked-in PhiX. The number of processed reads per sample then varied between 16,086,947 and 20,042,939.
Alignment: Processed reads were aligned with STAR v2.4.1d to the reference genome of Homo sapiens (GRCh38), as downloaded from the Genome Reference Consortium. Default STAR parameter settings were used, except for ‘outSAMprimaryFlag=OneBestScore’, ‘twopassMode=Basic’, ‘alignIntronMin=50’, ‘alignIntronMax=500000’, ‘outSAMtype=BAM’, SortedByCoordinate. Using Samtools 1.1, reads with a mapping quality smaller than 20 were removed from the alignments.
Counting: Transcript coordinates were extracted from the GRC reference annotation with Gffread from the Cufflinks v2.1.1 suite and merged to gene coordinates with mergeBed from the Bedtools v2.17.0 toolkit. GC content and gene length were derived from the gene coordinates. The numbers of aligned reads per gene were summarized using featureCounts 1.4.6 with parameters ‘Q=0’, ‘s=2’, ’t=exon’ and ‘g=gene_id’. We removed 41,248 genes for which all samples had less than 1 count-per-million. As such, we continued with raw counts for 16,985 genes. Raw counts were further corrected within samples for GC-content and between samples using full quantile-normalization, as implemented in the EDASeq package from Bioconductor.
Identifying differential gene expression: With the EdgeR 3.16.5 package, a negative binomial generalized linear model (GLM) was fitted against the normalized counts. We did not use the normalized counts directly, but worked with offsets. Differential expression was tested for with a GLM likelihood ratio test, also implemented in the EdgeR package. The resulting p-values were corrected for multiple testing with Benjamini-Hochberg to control the false discovery rate.
Genome_build: GRCh38
Supplementary_files_format_and_content: One tab-delimited text file with raw read counts per gene and per sample. Gene IDs are Ensembl IDs.

organism: Homo sapiens

source_name: Flp-In™ T-Rex Hela cells with doxycycline-inducible EGFP transgene

growth_protocol: Cells were grown in low glucose-DMEM medium supplemented with 10% fetal bovine serum and penicilline/streptomycin

extract_protocol:
RNA was extracted with the Mammalian Total RNA Miniprep kit (GenElute from SIGMA)
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyzer 2100 (Agilent). Per sample, an amount of 1 microgram of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single ‘A’ base to the 3’ ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Sequence-libraries of each sample were equimolarly pooled and sequenced on an Illumina NextSeq 500 instrument (High Output, 75 bp, Single Reads, v2) at the VIB Nucleomics core (www.nucleomics.be).

treatment_protocol: Cells were synchronized with a double thymidine arrest (18 hours 2mM thymidine, 9 hours release, 16 hours 2mM thymidine) and after 1 hour release harvested for mRNA isolation. The expression of PP1-NIPP1 wild-type or mutants was induced by the addition of 10 ng/ml Doxycycline to the medium of the cells for the last 13 hours before the cells were harvested.

value: Flp-In T-Rex Hela cells

value: doxycycline-inducible EGFP transgene

tag: passage

tag: experiment


title: Flp8_Dox_exp3_S203

tag: cell line

tag: treatment

value: doxycycline


title: Flp8_NoDox_exp3_S202

tag: genotype/variation


title: Flp8_Dox_exp2_S195


title: Flp8_Dox_exp1_S187


title: Flp7_NoDox_exp3_S206

source_name: Flp-In™ T-Rex Hela cells with doxycycline-inducible EGFP-PP1m-NIPP1 transgene (PP1 is mutated at Aa 64, i.e. D64A)


title: Flp7_NoDox_exp2_S198


title: Flp7_Dox_exp3_S207


title: Flp7_NoDox_exp1_S190


title: Flp7_Dox_exp1_S191


title: Flp6_NoDox_exp3_S204

source_name: Flp-In™ T-Rex Hela cells with doxycycline-inducible EGFP-PP1-NIPP1 transgene


title: Flp6_NoDox_exp2_S196


title: Flp6_Dox_exp1_S189


title: Flp7_Dox_exp2_S199


title: Flp6_NoDox_exp1_S188


title: Flp6_Dox_exp2_S197


title: Flp2_NoDox_exp3_S208

source_name: Flp-In™ T-Rex Hela cells with doxycycline-inducible EGFP-PP1-NIPP1m transgene (NIPP1 is mutated at the position AA 68-71, i.e. alanine mutation of NIPP1 residues 68-71)


title: Flp8_NoDox_exp2_S194


title: Flp2_NoDox_exp2_S200


title: Flp2_NoDox_exp1_S192


title: Flp2_Dox_exp2_S201


title: Flp2_Dox_exp3_S209


title: Flp2_Dox_exp1_S193


title: Empty Vector_3_pool

description: Empty vector pooled cells 3

data_processing:
Library strategy: DREAM
Illumina HiSeq 2500 paired ends sequencing.
Raw sequencing data were converted to fastq.gz files.
Bowtie2 --sensitive alignment of the reads in fastq files to hg19 and generating SAM files.
Generating sorted bam files from the sam files with samtools.
Counting methylated CCGGG signatures and unmethylated GGG at the reads aligned to CCCGGG sites with a Python script.
Adjusting methylation values based on the spiked in standards. At each SmaI/XmaI site, let Xma be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and Sma be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*(Xma)/(c*(Xma)+Sma)), where c was the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_hg19 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), meth_reads (observed number of reads corresponding to methylated CpG, Xma),  unmeth_reads (observed number of reads corresponding to unmethylated CpG, Sma), total_reads, raw_methylation (unadjusted methylation value), adjusted_methylation (methylation value adjusted based on the spiked in standards). Summary table lists methylation percent values supported by more than 19 equencing reads at individual CCCGGG sites.

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium with 10% fetal bovine serum

extract_protocol:
Genomic DNA was extracted using Puregene Gentra DNA extraction protocol.
Genomic DNA extracted from tissue samples was spiked with methylation standards and sequentially digested with two restriction endonucleases recognizing CCCGGG sites in DNA. SmaI cleaved only unmethylated sites resulting in blunt ended fragments starting with 5’-GGG. Next, XmaI cleaved the remaining methylated sites creating 5’-CmeCGG overhang sequences. Exonuclease-deficient Klenow fragment DNA polymerase was then used to fill in the 3’ recesses left by XmaI and add 3’-dA overhangs to the ends of all fragments. Thus, specific signatures 5’-GGG and 5’-CCGGG were created at unmethylated and methylated CpG sites, respectively. Illumina sequencing adapters were then ligated to the enzyme-treated DNA; sequencing libraries were generated according to Illumina protocols and run on an Illumina HiSeq 2500 instrument at Fox Chase Cancer Center Genomics facility. Sequencing data were aligned to the rat genome (rn4), and the reads with unmethylated and methylated signatures were counted at individual CCCGGG sites. Methylation levels were calculated as the ratio of reads with the methylated signature to all reads mapping to each respective site. DNA methylation values at individual CpG sites were adjusted based on spiked in standards and filtered for the minimum sequencing depth of 100 reads.

treatment_protocol: gRNAs targeting 3 different TET1 exons were cloned into the Lenti CRISPR V2 plasmid.  gRNAs targeted exon 6 (KO-1), exon 3 (KO-2) and exon 11 (KO-3).  Lentiviruses were generated using HEK293T cells by transfecting with packaging plasmid (psPAX2, Addgene 12260), envelope plasmid (pMD2.G, Addgene 12259) and lenti-CRISPR V2 plasmid (Addgene 52961).  Cells were transfected using Lipofectamine 2000.  Viral supernatant was collected at 48 and 72 hours, filtered with 0.45µm membrane and incubated on MDA-MB-231 cells for 7 hours in the presence of polybrene (6µg/mL, Millipore).  We puromycin selected (1µg/mL) the cells for three days, followed by single cell cloning using serial dilution in 96 well plates.  After selection, cells were maintained in normal media supplemented with 0.25 µg/mL puromycin.

tag: cell type

value: Triple negative breast cancer cell line

value: adult

value: Empty vector pooled cells 3


title: RNA-seq_Caki-1-shTGFBR3_B_TGF-b2

city: Wakayama

first: Shogo

last: Ehata

state: Wakayama

address: Kimiidera 811-1

department: School of Medicine

country: Japan

institute: Wakayama Medical University

description: Caki-1-shTGFBR3 #B cells treated with TGF-b2

data_processing:
Ion Proton
Reads per kilobase of exon permMegabase of library size (RPKM) were calculated by CLC Genomics Workbench (Qiagen).
Genome_build: hg19
Supplementary_files_format_and_content: Expression data of the four samples were summarized into three processed files.

molecule: polyA RNA

source_name: Caki-1-shTGFBR3 #B

growth_protocol: Caki-1 cells (Cell Resource Center for Biomedical Research, Tohoku University, Miyagi, Japan) were cultured as recommended by ATCC.

extract_protocol:
Total RNA was isolated with RNeasy (Qiagen).
cDNA libraries were prepared using Dynabeads mRNA DIRECT Purification Kit (Life Technologies) and Ion Total RNA-Seq Kit v.2 (Life Technologies).

treatment_protocol: Cells were seeded in 6-well plates. On the following day, cells were cultured with or without 0.3 ng/ml of TGF-b2 for 24 hour.

tag: agent

value: TGF-b2 (0.3 ng/ml)

tag: histology

value: clear cell renal cell carcinoma


title: RNA-seq_Caki-1-shNTC_TGF-b2

description: Caki-1-shNTC cells treated with TGF-b2


title: Empty Vector_2_pool

description: Empty vector pooled cells 2

value: Empty vector pooled cells 2


title: RNA-seq_Caki-1-shNTC_no_treatment

description: untreated Caki-1-shNTC cells

value: no treatment


title: TET1_KO_3_2

description: TET1 KO_3 single clone (gRNA targeting exon 11)


title: TET1_KO_2_2

description: TET1 KO_2 single clone (gRNA targeting exon 3)


title: TET1_KO_3_1

value: TET1 KO_3 single clone (gRNA targeting exon 11)


title: Empty Vector_1_pool

description: Empty vector pooled cells 1

value: Empty vector pooled cells 1


title: TET1_KO_2_1

value: TET1 KO_2 single clone (gRNA targeting exon 3)


title: TET1_KO_1_3

description: TET1 KO_1 single clone (gRNA targeting exon 6)


title: Flp6_Dox_exp3_S205


title: TET1_KO_1_1

value: TET1 KO_1 single clone (gRNA targeting exon 6)


title: TET1_KO_1_2


title: Empty Vector_3

description: Empty vector single clone 3

value: Empty vector single clone 3


title: Empty Vector_1

description: Empty vector single clone 1

value: Empty vector single clone 1


title: Empty Vector_2

description: Empty vector single clone 2

value: Empty vector single clone 2


title: anti-luciferase shRNA [261-1]

city: Cincinnati

first: H. Leighton

last: Grimes

state: OH

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

institute: Cincinnati Childrens Hospital Medical Center

data_processing:
FASTQ sequence files were aligned to the mouse genome version 9 using TopHat2 with de novo junction discovery.
The fastq files were aligned to mouse genome Mm9 using BowTie 2 and TopHat 2 (Kim et al., 2013; Trapnell et al., 2009). Gene level FPKM (Fragments Per Kilobase of transcript per Million mapped reads) were obtained using Cufflinks 2 (Trapnell et al., 2010) and further processed in AltAnalyze 2.0.9 (Emig et al., 2010; Salomonis et al., 2009; Salomonis et al., 2010). To identify differentially expressed genes using default parameters moderated t-test with Benjamini-Hochberg multiple testing correction, raw p-value cut-off of 0.05, and an expression cut-off of 2-fold.
For all RNAseq experiments pathways and ontology enrichment analyses were performed with ToppGene (Chen et al., 2009) and GO-Elite (Zambon et al., 2012). All heatmaps from AltAnalyze were created using the HOPACH package via a connection to R (Salomonis et al., 2005). All gene set enrichment analyses were performed using GSEA v.2.2.0 (Mootha et al., 2003; Subramanian et al., 2005).
Genome_build: mouse genome version 9
Supplementary_files_format_and_content: tab-delimited text files

source_name: anti-luciferase shRNA control MLL-AF9 primary AML

growth_protocol: MLL-AF9 leukemic splenocytes were transduced as indicated in treatment protocol with the individually purchased shRNA lentiviruses (Broad Institute) for the indicated gene or control hairpins. A total of 5x10^4 puromycin selected MLL-AF9 cells were transplanted into 4 sublethally irradiated (500 Rads) recipient mice each.

extract_protocol:
Leukemic splenocytes were harvested from independent mice each transplanted with MLL-AF9 leukemia transduced with either Cdkn1b shRNA, Phc2 shRNA or control shRNA. Red blood cells were lysed, and 5x10^6 leukemia cells were lysed with Trizol. RNA was extracted according to Meyer et al., 2009. RNA quality and quantity were measured by Agilant Bioanalyzer. Then samples with a RIN>8.0 were processed by poly-A selection, stranded True-seq, paired-end 75 base pair (bp), 20 million reads.
RNAs were detected by RNAseq analysis using paired-end 75 nucleotide (nt) sequencing and 20 million reads for all samples. RNA Seq libraries were generated with Illumina TruSeq Stranded mRNA HT kits.

treatment_protocol: MLL-AF9 leukemic splenocytes were thawed from liquid nitrogen and allowed to recover for 48 hours in standard growth medium RPMI 1640 (Thermo Fisher Scientific) containing 20% FBS (HyClone) supplemented with mouse recombinant SCF (60ng/ml), IL6 (20ng/ml), and IL3 (20ng/ml) (Miltenyi Biotech). 1x10^6 MLL-AF9 leukemia cells in 400ul standard growth medium containing FBS were mixed with 100ul lentiviral supernatant. Cytokines (60ng/ml SCF, 20ng/ml IL6 and IL3) and polybrene (10mg/ml, Sigma) were added to the final volume. Cells were incubated with virus for 6 hours at 37°C with 5% CO2, then virus supernatant was replaced with standard growth medium containing FBS and cytokines. Cells were incubated for 48 hours, then for an additional 48 hours with 1ug/ml puromycin in fresh growth medium. Cell were tranplanted as described in the growth protocol.

value: MLL-AF9 primary AML (acute myeloid leukemia)

tag: transduced with

value: anti-luciferase shRNA

tag: host strain

tag: transplanted with

tag: murine cell type

value: leukemic splenocytes


title: empty vector shRNA [001-2]

source_name: empty vector shRNA control MLL-AF9 primary AML

value: empty vector shRNA

value: sublethally irradiated (500 Rads) recipient


title: Phc2 shRNA [969-4]

source_name: Phc2 specific shRNA expressing MLL-AF9 primary AML

value: Phc2 specific shRNA


title: anti-luciferase shRNA [261-2]

value: anti-luciferase shRNA control MLL-AF9 primary AML


title: Phc2 shRNA [967-3]

value: Phc2 specific shRNA expressing MLL-AF9 primary AML


title: RNA-seq_Caki-1-shTGFBR3_B_no_treatment

description: untreated Caki-1-shTGFBR3 #B cells

value: DMSO

value: clear cell renal cell carcinoma


title: Cdkn1b shRNA [SH67-3]

source_name: Cdkn1b specific shRNA expressing MLL-AF9 primary AML

value: Cdkn1b specific shRNA


title: Cdkn1b shRNA [SH67-2]

value: Cdkn1b specific shRNA expressing MLL-AF9 primary AML


title: NT shRNA [NTSH-3]

source_name: non-targeting scramble shRNA control MLL-AF9 primary AML

value: non-targeting scramble shRNA


title: NT shRNA [NTSH-2]

value: non-targeting scramble shRNA control MLL-AF9 primary AML


title: TET1_KO_3_3

value: Triple negative breast cancer cell line

value: adult

value: TET1 KO_3 single clone (gRNA targeting exon 11)


title: TET1_KO_2_3

value: TET1 KO_2 single clone (gRNA targeting exon 3)


title: Phc2 shRNA [969-3]

value: MLL-AF9 primary AML (acute myeloid leukemia)


title: wild type larval type I neuroblasts; age:5h - replicate2

status: Public on Jun 27 2018

city: Vienna

first: Sebastian

last: Wissel

address: Dr. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology (IMBA)

data_processing:
Bascalling performed using RTA 1.18.61.0
The unstranded reads were screened for ribosomal RNA by aligning with BWA (v0.7.12) against known rRNA sequences (RefSeq).
The rRNA subtracted reads were aligned with TopHat (v2.1.1) against the Drosophila melanogaster genome (FlyBase r6.12). Introns between 20-150000 bp are allowed which is based on FlyBase statistics. Microexon-search was enabled. Additionally, a gene model was provided as GTF (FlyBase r6.12).
Reads arising from duplication events are marked as such in the alignment (SAM/BAM files) as follows. The different tags are counted at each genomic position. Thereafter, the diversity of tags at each position is examined. First, tags are sorted descending by their count. If several tags have the same occurrence, they are further sorted alphanumerically. Reads sharing the same tag, are sorted by the average PHRED quality. Again if several reads have the same quality, they are further sorted alphanumerically. Now the tags are cycled through by their counts. Within one tag, the read with the highest average PHRED quality is the unique correct read and all subsequent reads with the same tag are marked as duplicates. Furthermore, all reads which have tags with one mismatch difference compared the pool of valid read tags are also marked as duplicates.
snRNA, rRNA, tRNA, snoRNA and pseudogenes are masked from the GTF (FlyBase r6.12) with subtractBed from bedtools (v2.26.0).
The aligned reads were counted with HTSeq (v0.6.1; intersection-nonempty).
The genes were subjected to differential expression analysis with DESeq2 (v1.12.4).
Genome_build: FlyBase r6.12
Supplementary_files_format_and_content: Excel files (xlsx) containing the differential expression analysis (standard DESeq2 output); text file of counts (HTSeq count output)

organism: Drosophila melanogaster

source_name: larval brain

growth_protocol: Flies expressing UAS-dcr2; ase-GAL4, UAS-stinger::GFP;; were raised at 25C. Wandering L3 larval brains were collected and prepared for FACS-sorting. We cultured sorted type I NBs for 1.5h, 3h or 5h, where they continued to divide asymmetrically. We subjected the cell suspension containing NBs and newly formed GMCs to a second FACS sort to collect pure populations of both daughter cells.

extract_protocol: Type I neuroblasts and GMCs of different ages were FACS sorted and total RNA was isolated using TRIzol LS reagent. Total RNA was converted to first strand (using oligo-(dT)20 primers) and second strand cDNA. Library preparation was done using Illumina's protocol with Nextera DNA Library Preparation Kit using a modified Index primer 1 (i7), which included random octamere sequences for molecular barcoding.

value: Type I neuroblasts

tag: developmental stage

value: third instar larva

tag: marker

value: cells express nuclear GFP marker (UAS-stinger::GFP)


title: wild type larval GMC; age:5h - replicate2

value: GMC


title: wild type larval type I neuroblasts; age:5h - replicate3


title: wild type larval type I neuroblasts; age:3h - replicate3


title: wild type larval type I neuroblasts; age:3h - replicate1


title: wild type larval GMC; age:3h - replicate2


title: OR3

city: Cambridge

first: Nina

middle: Evgenjevna

last: Gubina

state: MA

address: 77 Massachusetts Ave, 56-670

department: CEHS

institute: MIT

data_processing:
Illumina bcl2fastq software was used for basecalling.
The quality of reads was checked using FastQC tool.
Reads were aligned to Drosophila melanogaster reference genome assembly BDGP5.25 (Ensembl) using Tophat2 (version 2.0.7) with default parameters
The raw expression values were determined by counting the number of reads mapping to each gene. Normalization of the raw gene expressions across all genotype groups and differential gene expression analysis between two genotypes were done using DESeq2 package. Dahomey was treated as an "experimental" and Oregon R was treated as a "control" strain.
Genome_build: BDGP5.25 (Ensembl)
Supplementary_files_format_and_content: Excel .xls file with DESeq2 results

source_name: Head and thorax

growth_protocol: Flies were crossed and maintained at +25C on standard oatmeal-molasses diet in a controlled 12:12 hour light:dark cycle. Mated females were collected 1-2 days after eclosion under CO2 anaesthesia and transferred to fresh vials. In all experiments flies were kept at a density of 20 flies per  20ml vial with 4.5 ml of food  and food was replaced every two-three days. Flies were aged to 10 days, flash frozen in liquid nitrogen and kept at -80 prior to RNA preparation

extract_protocol:
Heads and thoraxes of frozen flies were separated on dry ice, mixed and immediately used for RNA isolation. Total RNA was isolated using RNeasy Microarray Tissue Mini Kit (Qiagen) according to the manufacturer’s instructions. Eluted RNA was treated with DNAse I (Thermo Scientific) and concentrated by ethanol precipitation. All RNA samples of OR and DAH were prepared simultaneously
Library preparation and indexing were performed from 1 ug of total RNA using the TruSeq RNA sample prep v2 kit (Illumina) according to the manufacturer's instructions

tag: strain

value: Oregon R

value: head and thorax

tag: Sex

value: female

value: 10 days old

tag: temperature of breeding and maintenance


title: OR2

tag: tissue

tag: age


title: OR1


title: DAH3

value: Dahomey


title: wild type larval GMC; age:5h - replicate1


title: CTRL sample 2

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description: RNA from cardiac stromal cells derived from an explanted heart of a (male) individual without any cardiac disease.

data_processing:
Read filtering and trimming:
Alignment: GSNAP (version 2014-12-16) using a splice-site-file generated with gene models from Ensembl 81. Settings: -m 6 -t 8 --batch=5 --filter-chastity=either
Feature quantification: summarizeOverlaps method from Bioconductor's GenomicAlignments package (version: 1.7.20. settings: mode="IntersectionStrict", ignore.strand=TRUE, inter.feature=TRUE, singleEnd=FALSE, fragments=TRUE ; only reads with an alignment quality > 30 were considered).
Prefiltering: remove genes with a normalized read count < 10 in any of the two sample groups.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file containing read counts per feature (gene), each column contains values for one sample, column gene_id contains the Ensembl gene Ids (Ensembl version 81). Feature counting was performed with Bioconductor's GenomicAlignments package (version: 1.7.20. settings: mode="IntersectionStrict", ignore.strand=TRUE, inter.feature=TRUE, singleEnd=FALSE, fragments=TRUE ; only reads with an alignment quality > 30 were considered).

source_name: Healthy control individual 2

growth_protocol: Cardiac stromal cells were cultured instandard cell culture conditions.

extract_protocol:
RNA was extracted using TRIzol reagent, according to manufacturer's protocol, and quantified with a NanoDrop ND-1000 Spectrophotometer.
Illumina TruSeq RNA Sample Prep Kit v2-Set A starting from 1 µg of total RNA, according to manufacturer’s instructions.

tag: disease

value: Healthy control

tag: passage

value: male


title: DAH2


title: DAH1


title: CTRL sample 3

source_name: Healthy control individual 3


title: CTRL sample 1

source_name: Healthy control individual 1


title: ACM sample 1

description: RNA from cardiac stromal cells derived from a diagnostic heart biopsy (right ventricle) from a male patient suffering from Arrhythmogenic cardiomyopathy (ACM).

source_name: ACM patient 1

value: Arrhythmogenic cardiomyopathy (ACM)


title: wild type larval type I neuroblasts; age:3h - replicate2


title: wild type larval GMC; age:3h - replicate1


title: ACM sample 3

source_name: ACM patient 3


title: OR4


title: ACM sample 2

source_name: ACM patient 2


title: GBM9sh3

first: Biplab

last: Dasgupta

address: 3333 Burnet ave

institute: CCHMC

description:
collected soon after surgery
run0182_lane5_index12=9sh3~human_align

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19  whole genome using bowtie v0.12.2
Post Binary Alignment/Map (BAM) aligned files of RNASeq data were analyzed using Avadis® NGS software, Version 1.3.0. Reads were filtered to remove 1) duplicate reads, 2) non-primary-matched reads and 3) reads with alignment scores <95. Quantification was performed on the filtered reads against the RefSeq annotation.
Data normalization was performed with DESeq. The sequencing depth is estimated by the read count of the gene with the median read count ratio across all genes. The method is based on the negative binomial distribution, which allows for less restrictive variance parameter assumptions than does the Poisson distribution. The false discovery rate (FDR) was calculated according to the Benjamini and Hochberg algorithm.  1.5 FC with an FDR of 0.05 was used as selection criteria
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include DESeq normalised values values for each Sample

source_name: Glioblastoma

growth_protocol: GBM cells were grown in DMEM/F12 supplemented with 10% Fetal Bovine Serum

extract_protocol:
Total RNA was extracted from GBM cells using Rneasy Mini kit from Qiagen.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GBM cells were treated with equal titer of scramble or PRKAB1 shRNA expressing lentiviral particles. Cells were washed and fresh media was added after 24h. Cells were collected for RNA extraction after 72h of lentiviral infection.

tag: race

value: caucasian

value: Brain

tag: gbm grade

value: IV

tag: shRNA

value: PRKAB1 shRNA


title: GBM10sh3

description:
collected soon after surgery
run0182_lane5_index19=10sh3~human_align


title: GBM10scr3

description:
collected soon after surgery
run0182_lane5_index15=10scr3~human_align

value: scramble


title: GBM9sh2

description:
collected soon after surgery
run0182_lane5_index7=9sh2~human_align


title: GBM10sh2

description:
collected soon after surgery
run0182_lane5_index18=10sh2~human_align


title: GBM10scr2

description:
collected soon after surgery
run0182_lane5_index14=10scr2~human_align


title: GBM10scr1

description:
collected soon after surgery
run0182_lane5_index13=10scr1~human_align


title: GBM9scr1

description:
collected soon after surgery
run0182_lane5_index2=9scr1~human_align


title: wild type larval GMC; age:1.5h - replicate2

tag: cell type


title: wild type larval GMC; age:1.5h - replicate3


title: wild type larval type I neuroblasts; age:1.5h - replicate2

value: Type I neuroblasts


title: wild type larval type I neuroblasts; age:1.5h - replicate3

value: third instar larva


title: GBM10sh1

description:
collected soon after surgery
run0182_lane5_index16=10sh1~human_align


title: EpCAM+_organoids_R2

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

description: cells cultured in matrigel in organoid medium for 6 days

data_processing:
Reads mapped to GRCm38, counts were generated and Differential Expression was calculated  using edgeR with an FDR≤0.05
Genome_build: GRCm38
Supplementary_files_format_and_content: RPKMs

source_name: FACS sorted cells from adult liver

extract_protocol:
Total RNA extracted using RNAeasy micro kit (Qiagen) according to manifacture's instructions
SmartSeq2 followed by NexteraXT tagmentation (according to protocols published in PMID 24385147)

value: Adult healthy liver

tag: gender

value: Male

tag: time point

value: 6 days


title: EpCAM+_48h

description: cells cultured in matrigel in organoid medium for 24hrs


title: EpCAM+_organoids_R1

value: cells cultured in matrigel in organoid medium


title: EpCAM+_24h


title: GBM9sh1

description:
collected soon after surgery
run0182_lane5_index6=9sh1~human_align


title: GBM9scr3

description:
collected soon after surgery
run0182_lane5_index5=9scr3~human_align


title: EpCAM+_12h_R2

description: cells cultured in matrigel in organoid medium for 12hrs


title: 14 GW cortical plate after 16 hours of FFT culture subjected to HLC-treatment

city: Dresden

first: Holger

last: Brandl

state: Choose One...

address: Pfotenhauerstrasse 108

department: Bioinformatics Service

country: Germany

institute: Max Planck Institute of Molecular Cell Biology and Genetics

description:
hsap_tpms_matrix.txt
hsap_counts_matrix.txt

data_processing:
Basecalls performed using bcl2fastq
Reads were mapped using STAR 2.5.2b (--outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --sjdbGTFfile ${gtfFile} --outFilterIntronMotifs   RemoveNoncanonicalUnannotated --outFilterType BySJout --quantMode GeneCounts --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3)
Abundance estimation was performed with STAR (--quantMode GeneCounts)
Genome_build: GRCh38, Ensembl v88
Supplementary_files_format_and_content: Raw counts and TPM normalized expression scores

source_name: 14 GW cortical plate HLC-treatment

growth_protocol: FFT culture for 16 hours

extract_protocol:
Total RNA was extracted using the RNAeasy Mini kit (Qiagen) according to the manufacturer's instructions.
Polyadenylated mRNA was enriched with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) according to the manufacturer's instructions. The cDNA and second strand synthesis as well as the library preparation (consisting of cDNA fragmentation, end repair, A-tailing, ligation of sequencing adapters, indexing by PCR amplification for 15 cycles) were performed using the NEBNext Ultra II Directional RNA Library Prep Kit Illumina (New England Biolabs). Libraries were purified using XP beads (Beckman Coulter), quantified by Fragment Analyzer (AATI) and subjected to Illumina 75-bp single end sequencing on the Illumina Nextseq500 platform providing a minimum of 21 Mio reads per sample.

treatment_protocol: Control or addition of recombinant HAPLN1, lumican and collagen I (HLC-treatment).

value: 14 GW

tag: treatment

value: 16 hours of HLC-treatment


title: EpCAM+ 0h_R2

description: freshly isolated cells

value: freshly isolated cells


title: EpCAM+ 0h_R1

description: freshly isolated cells


title: EpCAM+_12h_R1


title: 14 GW cortical plate after 16 hours of FFT culture subjected to control

source_name: 14 GW cortical plate control

value: control


title: 12 GW cortical plate after 16 hours of FFT culture subjected to HLC-treatment

source_name: 12 GW cortical plate HLC-treatment

value: 12 GW


title: 12 GW cortical plate after 16 hours of FFT culture subjected to control

source_name: 12 GW cortical plate control


title: 13 GW cortical plate after 16 hours of FFT culture subjected to HLC-treatment

source_name: 13 GW cortical plate HLC-treatment

value: 13 GW


title: wild type larval type I neuroblasts; age:5h - replicate1

value: cells express nuclear GFP marker (UAS-stinger::GFP)


title: low-one

city: Bronx

first: Chunliang

last: Xu

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

description: EC RNAseq

data_processing:
single-end sequencing reads were aligned to the mouse genome using Spliced Transcripts Alignment to a Reference (STAR). We next used htseq-count to assign aligned reads to genes. Reads per kilobase of transcript per million (RPKM) was used as the expression quantification method. The RPKM matrix was log2-transformed.
We first filtered out genes that had a CPM < 0.1 in at least 7 of the 9 samples. 17,232 genes remained after filtering. Next, we normalised for RNA composition by calculating scaling factors for each sample using calcNormFactors in edgeR (version 3.12.0). The default method for computing scaling factors in calcNormFactors, trimmed mean of M-values (TMM) between each pair of samples, was used. The original library size, before normalising, was calculated as the sum of the counts in each sample. The effective library size of each sample is the product of the original library size and the scaling factor for a given sample. Next, the estimate Disp function in edgeR was used to calculate the dispersions of the negative binomial model using the quantile-adjusted conditional maximum likelihood (qCML) method.
Genome_build: mm9
Supplementary_files_format_and_content: RPKM in Excel

source_name: Nestin-GFP mice

extract_protocol:
Total RNA from sorted Nestin-GFPbright AECs, Nestin-GFPdim AECs and SECs was extracted using the RNAeasy Plus Micro kit (Qiagen). The integrity and purity of total RNA were assessed using an Aligent 2100 Bioanalyzer (Agilent Technologies).
Complementary DNA was generated using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories) from total RNA. The Nextera XT DNA Sample Preparation Kit (Illumina) was used for the preparation of DNA libraries.
The libraries were then submitted for Illumina HiSeq2500 sequencing (Illumina) according to standard operation procedures for RNAseq.

value: Bone marrow

value: AEC

tag: cell type (sorted)

value: CD45-CD31+PDPN-Sca-1high Nestin-GFPlow


title: wild type larval GMC; age:1.5h - replicate1

value: GMC

tag: developmental stage


title: high-three

description: EC RNAseq

value: CD45-CD31+PDPN-Sca-1high Nestin-GFPhigh


title: 13 GW cortical plate after 16 hours of FFT culture subjected to control

source_name: 13 GW cortical plate control


title: H9 miR-146a-Mut Diff 3

city: Paris

first: Lam Son

last: Nguyen

state: IDF

address: 24 Bld du Montparnasse

department: Institute Imagine

country: France

institute: INSERM U1163

description: H9 Processed File.txt

data_processing:
Sequence reads were aligned to the human HG19 or mouse mm9 reference genome using the Burrows-Wheeler Alignment version 0.6.2.13.
Gene expression was analyzed by three different tools: limma, Deseq and EdgeR. Differentially expressed genes were determined by threshold P<0,05 and fold change >1,5 for H9 cells and 1,2 for mouse brains.
Genome_build: HG19 or mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample as analyzed by EdgeR for reference.

source_name: Human neural stem cell

growth_protocol: GIBCO® human neural stem cells (H9 hESC-Derived) was purchased commercially (N7800100, ThermoFisher Scientific). Cells were cultured in flasks or plates previously coated for at least 1H with GelTrex™ LDEV-Free, hESC-qualified, reduced growth factor basement membrane matrix (A1413302, ThermoFisher Scientific). Cells were maintained in Complete StemPro® NSC SFM medium (growth media) consisting of KnockOut™ D-MEM/F-12 (12660012, ThermoFisher Scientific) supplemented with 2% StemPro® Neural Supplement (A1050901, ThermoFisher Scientific), 20 ng/mL EGF (PHG0315, ThermoFisher Scientific), 20 ng/mL bFGF (GF003, ThermoFisher Scientific), 2 mM GlutaMax™-I (35050038, ThermoFisher Scientific) and 10 μg/mL Penicillin-Streptomycin (15140122, ThermoFisher Scientific). For passaging, cells were washed once with DPBS (14190169, ThermoFisher Scientific) and detached from the surface by StemPro™ Accutase (A1110501, ThermoFisher Scientific), centrifuged at 1500 RPM for 5 minutes, and replated in fresh growth media. To initiate spontaneous differentiation, H9 cells were plated at a density of 20-25000 cells/cm2 in growth media for 24H, after which media was replaced with differentiating media (growth media without growth factors). Differentiating media was changed every 2-3 days during the course of the differentiation process.

extract_protocol:
Total RNA was extracted using TRizol reagent (15596026, ThermoFisher Scientific) and RNeasy Mini Kit (74104, QIAGEN) with DNase I treatment step (79254, QIAGEN) following the manufacturer’s protocol. The integrity of RNA was determined by RNA ScreenTape (5067-5576, Agilent Technologies) on the Agilent 4200 TapeStation (Agilent Technologies).
RNAseq libraries were prepared starting from 600 ng of total RNA using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) as recommended by the manufacturer. Half of the oriented cDNA produced from the poly-A+ fraction were PCR amplified (11 cycles). The RNAseq libraries were sequenced on an Illumina HiSeq2500 (Paired-End sequencing 130x130 bases, High Throughput Mode). A minimum of 10 million of paired-end reads was produced per library sample.


title: GBM9scr2

description:
collected soon after surgery
run0182_lane5_index4=9scr2~human_align

value: caucasian

value: Brain

value: IV

value: scramble


title: H9 miR-146a-Mut Diff 1

description: H9 Processed File.txt


title: wild type larval type I neuroblasts; age:1.5h - replicate1

source_name: larval brain

value: Type I neuroblasts

value: third instar larva

tag: marker


title: H9 miR-146a Diff 3

description: H9 Processed File.txt


title: low-four

description: EC RNAseq


title: high-one

description: EC RNAseq


title: SEC-three

description: EC RNAseq

value: SEC


title: H9 miR-146a Diff 2

description: H9 Processed File.txt


title: high-four

description: EC RNAseq


title: low-three

description: EC RNAseq


title: H9 miR-146a-Mut Undiff 3

description: H9 Processed File.txt


title: SEC-four

description: EC RNAseq


title: H9 miR-146a-Mut Undiff 1

description: H9 Processed File.txt


title: cKO 4h

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: Spic–/– BMDMΦ pretreated with 40 mM hemin for 18 h were stimulated with 100 ng/ml LPS for 4 h.

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: text file with FPKM values.

source_name: Spic–/– BMDMΦ pretreated with hemin and stimulated with LPS

extract_protocol:
The total RNAs were extracted from these cells using RNeasy Mini Kit (Qiagen)
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Control and Spic–/– BMDMΦ pretreated with 40 μM hemin for 18 h were stimulated with (designated ‘CNT_4’ and ‘cKO_4’, respectively) or without (designated ‘CNT_0’ and ‘cKO_0’, respectively) 100 ng/ml LPS for 4 h.

tag: genotype

value: Spic-/-

value: with 100 ng/ml LPS for 4 h

value: bone marrow

value: macrophage


title: H9 miR-146a-Mut Diff 2

description: H9 Processed File.txt


title: ctrl 4h

description: Control BMDMΦ pretreated with 40 mM hemin for 18 h were stimulated with 100 ng/ml LPS for 4 h.

source_name: Control BMDMΦ pretreated with hemin and stimulated with LPS

value: Spic+/+


title: H9 miR-146a Undiff 3

description: H9 Processed File.txt


title: H9 miR-146a Undiff 1

description: H9 Processed File.txt


title: H9 miR-146a Undiff 2

description: H9 Processed File.txt


title: cKO 0h

description: Spic–/– BMDMΦ pretreated with 40 mM hemin for 18 h were stimulated without 100 ng/ml LPS for 4 h.

source_name: Spic–/– BMDMΦ pretreated with hemin and stimulated without LPS

value: without 100 ng/ml LPS for 4 h


title: ctrl 0h

description: Control BMDMΦ pretreated with 40 mM hemin for 18 h were stimulated without 100 ng/ml LPS for 4 h.

source_name: Control BMDMΦ pretreated with hemin and stimulated without LPS


title: 386R

first: Alberto

last: Rosello-Diez

address: Physiology building. Downing St.

department: Physiology, Development and Neuroscience

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 transcriptome and quantified using Kallisto
rlog normalized counts were calculated using DESeq2 in R
Genome_build: mm10
Supplementary_files_format_and_content: tsv file with abundance measurements (estimated counts and tpm)

source_name: growth plate from right distal femur and proximal tibia

growth_protocol: Doxycycline was provided to the pregnant female from E12.5 to E17.5 to activate transgene expression

extract_protocol:
Trizol extraction of RNA from frozen cartilage
Illumina TruSeq Stranded mRNA

treatment_protocol: Enzymatic digestion to remove perichondrium

value: growth plate chondrocytes

value: Pitx2-Cre; Col2a1-rtTA;Igs7TRE-LtSL-p21

tag: side

value: right

tag: embryo id


title: 386L

source_name: growth plate from left distal femur and proximal tibia

tag: tissue

value: left


title: 388L


title: 387R


title: 387L


title: H9 miR-146a Diff 1

description: H9 Processed File.txt


title: GA RNA-seq repeat 1

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

description: high-throughput profiling of transcriptome in GA repeat1

data_processing:
The paired-end reads were aligned to the moso bamboo genome using tophat-2.0.11 with anchor length more than 8nt for spliced alignments (Kim et al. 2013).
Genome_build: P.heterocycla-v1.0
Supplementary_files_format_and_content: bigwig files were generated using wig2bw program

organism: Phyllostachys edulis

source_name: One-month-old seedlings

growth_protocol: For materials used for RNA-Seq analysis, seeds were sterilized with chlorine gas for 3-5 hours, and then were put on MS agar for germination and growth vertically over a 1-month period.

extract_protocol:
Total RNA from bamboo root was extracted using the RNAprep Pure Plant Kit (QIAGEN, China) according to the manufacturer’s instructions.
In total, there were 6 strand-specific RNA-Seq libraries that were sequenced in this study using dUTP method (Parkhomchuk et al. 2009).

treatment_protocol: One-month-old seedlings were sprayed with 100μM GA for 4 hours with 1-hour interval, and the root part were dissected for RNA extraction.

value: One-month-old seedlings

value: seedlings

value: Gibberellin


title: Mock RNA-seq repeat 2

description: high-throughput profiling of transcriptome in Mock repeat2

value: mock


title: 388R


title: GA RNA-seq repeat 2

description: high-throughput profiling of transcriptome in GA repeat2


title: H9 miR-146a-Mut Undiff 2

description: H9 Processed File.txt


title: GA RNA-seq repeat 3

description: high-throughput profiling of transcriptome in GA repeat3


title: Mock RNA-seq repeat 3

description: high-throughput profiling of transcriptome in Mock repeat3


title: Col-0_R2_LL

status: Public on Jun 26 2018

first: haifeng

last: WANG

institute: Gregor Mendel Institute of Molecular Plant Biology

data_processing:
The gene counts were estimated using Kallisto v 0.42 [kallisto] with the parameters -l 180 -s 20 -b 100 (fragment length=180 bp, fragment standard deviation =20 and bootstrap =100)
Using DESeq2 the normalisation and dispersion estimation were done using the default settings.
The counts per gene were modelled as a function of the genotype (wt or ko) and the growth condition (normal light (130 μMol s-1 m-2 μA) or low light (30 μMol s-1 m-2 μA) )
Genes with a significant up or down regulation in the ko compared to the wt were identified using a FDR cutoff of 0.1.
Genome_build: Tair10
Supplementary_files_format_and_content: .tsv file format with gene id, length, effective length, estimated counts and tpm

organism: Arabidopsis thaliana

growth_protocol: Plants were grown in the green house under long day (LD) condition (16h light/8h dark) at 21°C with normal light (130 μMol s-1 m-2 μA) or low light (30 μMol s-1 m-2 μA) condition.

extract_protocol:
Total RNA from 10-day old seedlings was extracted using RNeasy plus mini kit (Qiagen). Reverse transcription was performed with RevertAid first strand synthesis kit (Thermo Scientific).
RNA libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs) and the samples were sequenced as 50bp single reads in one flow cell on Illumina HiSeq2000

tag: age

value: 10 days old

value: whole seedling

value: wildtype

tag: light level

value: Under Low Light (LL):30 μMol s-1 m-2 μA


title: atrx-2_R1_LL

source_name: atrx-2 mutant_low_light


title: atrx-2_R2_LL


title: atrx-2_R3_NL

source_name: atrx-2 mutant_normal_light

value: Under Normal Light (NL):130 μMol s-1 m-2 μA


title: atrx-2_R3_LL


title: SEC-one

description: EC RNAseq

value: Bone marrow

value: SEC


title: Col-0_R3_NL


title: Col-0_R3_LL


title: MRE_KO1_3T9_sample3

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

institute: Istituto Italiano di Tecnologia

description: RNA sequencing Illumina

data_processing:
FASTQ data of the total RNA sequencing experiment were aligned using TopHat 2.0.6 with default parameters
Differentially expressed genes (DEGs) were identified using the Bioconductor package DESeq2 based on read counts, considering genes whose q value relative to the control is lower than 0.05 and whose maximum expression is higher than RPKM of 1
Genome_build: mm9
Supplementary_files_format_and_content: Excel Spreadsheet containing FPKM counts each gene and the output of the analysis with DESeq2 package to identify regulated genes

source_name: 3T9 FIBROBLAST

growth_protocol: cells were grown in complete medium (10% FBS)

extract_protocol:
Total RNA  was isolated through the miRNeasy mini kit (Qiagen).
1000 nanograms of total RNA were used to prepare RNA libraries following the Illumina TruSeq Library Preparation Kit instructions

value: 3T9 FIBROBLAST


title: MRE_KO2_3T9_sample2

description: RNA sequencing Illumina


title: atrx-2_R2_NL


title: MRE_KO1_3T9_sample2

description: RNA sequencing Illumina


title: Col-0_R1_LL


title: Parental_3T9_sample3

description: RNA sequencing Illumina


title: Mock RNA-seq repeat 1

description: high-throughput profiling of transcriptome in Mock repeat1


title: Col-0_R2_NL


title: atrx-2_R1_NL


title: Parental_3T9_sample2

description: RNA sequencing Illumina


title: Col-0_R1_NL


title: MRE_KO2_3T9_sample3

description: RNA sequencing Illumina


title: Parental cells_3

description: small RNA sequecing Illumina

data_processing:
FASTQ data were trimmed using cutadapt-1.9.1; then trimmed data was aligned to custom sequence libraries listing all isoforms of small RNA molecules by using Bowtie with --best and -v 0 switches and saved in .map output format.
Isomirage software was used to count the number of occurrences in the .map file of each isoform listed in the .genome file
Raw counts were finally normalized using CPM (copies-per-million)
Genome_build: mm9
Supplementary_files_format_and_content: Excel Spreadsheet containing the raw counts of miRNA, including miRNA isoforms

extract_protocol:
Total RNA, including small species, was isolated through the miRNeasy mini kit (Qiagen).
1000 nanograms of total RNA were used to prepare Small RNA libraries following the Illumina TruSeqTM Small RNA kit instructions

tag: genotype/variation

tag: cell line

value: fibroblast


title: MRE_KO1_3

description: small RNA sequecing Illumina


title: Parental cells_2

description: small RNA sequecing Illumina


title: Parental cells_4

description: small RNA sequecing Illumina


title: MRE_KO2_3T9_sample1

description: RNA sequencing Illumina


title: MRE_KO1_1

description: small RNA sequecing Illumina


title: MRE_KO1_2

description: small RNA sequecing Illumina


title: MRE_KO1_3T9_sample1

description: RNA sequencing Illumina


title: SCA+_34a -1

description: CommaDb

data_processing:
FASTQ data of the total RNA sequencing experiment were aligned using TopHat 2.0.6 with default parameters
Differentially expressed genes (DEGs) were identified using the Bioconductor package DESeq2 based on read counts, considering genes whose q value relative to the control is lower than 0.05 and whose maximum expression is higher than RPKM of 1
Genome_build: mm9
Supplementary_files_format_and_content: Excel Spreadsheet containing the raw counts of each gene and the output of the analysis with DESeq2 package to identify regulated genes

source_name: FACS sorted Sca-1 positive cells infected with a lentiviral inducible vector expressing miR-34a and induced with doxycycline for 24 hours

value: normal mammary epithelial cells

value: FACS sorted Sca-1 positive cells

value: control


title: Parental cells_1

description: small RNA sequecing Illumina


title: Parental_3T9_sample1

description: RNA sequencing Illumina


title: MRE_KO2_1

description: small RNA sequecing Illumina


title: MRE_KO2_3

description: small RNA sequecing Illumina


title: SCA- -2

description: CommaDb

source_name: FACS sorted Stem Cell antigen-1 (Sca-1) negative cells representing differentiated/luminal cells


title: MRE_KO2_2

description: small RNA sequecing Illumina


title: SCA+_34a -2

description: CommaDb


title: SCA- -1

description: CommaDb

value: FACS sorted Stem Cell antigen-1 (Sca-1) negative cells


title: SCA+_NI -3

description: CommaDb

source_name: FACS sorted Sca-1 positive cells infected with a lentiviral inducible vector expressing miR-34a; NI=not induced with doxycycline

value: expressing miR-34a


title: SCA+-3

description: CommaDb

source_name: FACS sorted Stem Cell antigen-1 (Sca-1) positive cells, representing undifferentiated/basal cells with properties of mammary stem/progenitor cells


title: Littermate control 8h LPS 80U DNase

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

data_processing:
Base-calling with Illumina run time analysis software 1.12.4.2
Alignment to mm9 using Casava Eland extended
Areas of enrichment were identified using DNase2Hotspots software(http://sorceforge.net/proujects/dnase2hotspots/) software with FDR 0%.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Values for tag densities were normalized to 10 million reads to adjust for differences in the sequencing depth between samples.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph, CSV

source_name: Bone marrow derived macrophages

extract_protocol:
After treatment with 10 ng/ml LPS for the indicated times, cells were pelleted at 500 g for 5 min at 4°C followed by nuclei isolation with ice-cold buffer A (15 mM Tris-Cl (pH 8), 15 mM NaCl, 60 mM KCl, 1 mM EDTA (pH 8), 0.5 mM EGTA (pH 8), 0.04% NP-40, 0.5 mM Spermidine), and the nuclei were centrifuged at 500 g for 5 min at 4°C. The isolated nuclei were washed with fresh-cold buffer A and chromatin from 5 million cells were digested with 80 U/ml DNase I (Sigma) for 3 min at 37ºC followed by termination of the reaction with an equal volume of Stop buffer (50 mM Tris-Cl, pH 8, 100 mM NaCl, 0.1% SDS, 100 mM EDTA, pH 8). The DNase I digested nuclei were deproteinized at 55ºC overnight with 10 μg/ml of RNaseA (Invitrogen) and Proteinase K (Ambion). Digested DNA fragments were purified using phenol-chloroform and enriched by size selection over a sucrose gradient. DNA fragments between 100 bp and 500 bp were precipitated and dissolved in nuclease free water (Ambion).
Sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 51 bp single-end sequencing on Illumina HiSeq2000.

treatment_protocol: Primary macrophages derived from bone marrow were stimulated with lipopolysaccharide for the indicated number of hours.

tag: strain

value: Bone marrow derived macrophages

value: Littermate control

tag: stimulated with

value: 10 ng/ml LPS for 8h


title: Littermate control 3h LPS 80U DNase

tag: cell type

value: 10 ng/ml LPS for 3h


title: KO 3h LPS rep1 80U DNase

value: Ikzf KO


title: KO 0h LPS rep1 80U DNase

value: 10 ng/ml LPS for 0h


title: SCA+_NI -2

description: CommaDb


title: SCA- -3

description: CommaDb


title: WT 0h LPS 100U DNase rep2

value: wild type


title: WT 3h LPS 100U DNase rep2


title: SCA+-2

description: CommaDb

value: FACS sorted Stem Cell antigen-1 (Sca-1) positive cells


title: SCA+-1

description: CommaDb


title: DAH4

source_name: Head and thorax

value: Dahomey

value: head and thorax

tag: Sex

value: female

value: 10 days old

tag: temperature of breeding and maintenance


title: KO 8h LPS rep2 80U DNase


title: KO 0h LPS rep2 80U DNase


title: SCA+_34a -3

description: CommaDb

value: normal mammary epithelial cells


title: KO untreated input genomic DNA

extract_protocol:
For the RelA and Ikaros ChIP, BMDMs were cross-linked with 1% formaldehyde for 10 min at room temperature. After cross-linking, chromatin was isolated from approximately 2 × 107 cells and processed as follows. The lysis buffer to shear the chromatin contained 0.5% SDS, 10 mM EDTA (pH 8), 50 mM tris-HCl (pH 8), and proteinase inhibitor cocktail. Sonication was performed with a Bioruptor Plus (Diagenode) at medium setting for a total time of 17 min for Ikaros ChIP, 20 min for RelA ChIP, using a 30 sec ON, 30 sec OFF cycle to shear the chromatin to generate DNA fragments with a size range of 200 to 600 base pairs. The sonicated mixture was centrifuged at 14,000 rpm for 10 min. The sheared chromatin samples were diluted 1:5 in dilution buffer [0.01% SDS, 1.1% Triton-X, 1.2 mM EDTA (pH 8), 20 mM tris-HCl (pH 8), 167 mM NaCl, and proteinase inhibitor cocktail]. For the RelA ChIP, 10 ml of a rabbit polyclonal anti-RelA antibody (ab7970, Abcam) was diluted in 1 ml immune complex buffer with Dynabeads protein A (Invitrogen). For the Ikaros ChIP, 10 ul of a goat polyclonal Ikaros antibody ((M-20), Santa Cruz)) was diluted in 1 ml immune complex buffer with Dynabeads protein G (Invitrogen). 200 mg chromatin DNA was immunoprecipitated with antibody-bead complexes at 4oC overnight. The chromatin-DNA complexes were washed with immune complex buffers (Low salt, High salt, LiCl and TE) and were eluted followed by reverse cross-linking (10 mM Tris-HCl, 300 mM NaCl, 55 mM EDTA, 0.5% SDS).
Sequencing libraries were generated using Illumina TruSeq V3 protocol and subjected to 51 bp single-end sequencing on an Illumina HiSeq2000.

tag: strain background

value: none (untreated)


title: Littermate control 0h LPS RelA ChIP-seq

value: LPS for 0h

tag: chip antibody

value: RelA (ab7970, Abcam)


title: Littermate control 3h LPS RelA ChIP-seq

value: LPS for 3h


title: WT 8h LPS 100U DNase rep2

value: Bone marrow derived macrophages


title: SCA+_NI -1

description: CommaDb

value: FACS sorted Sca-1 positive cells

value: expressing miR-34a


title: WT 3h LPS Ikaros ChIP-seq

value: Ikaros (M-20, Santa Cruz)


title: WT 8h LPS 80U DNase rep1

value: 10 ng/ml LPS for 8h


title: WT 3h LPS 80U DNase rep1

value: 10 ng/ml LPS for 3h


title: WT 0h LPS 80U DNase rep1

value: wild type

value: 10 ng/ml LPS for 0h


title: Littermate control untreated input genomic DNA

value: Littermate control


title: WT untreated input genomic DNA


title: KO 3h LPS rep2 80U DNase

value: Ikzf KO


title: Littermate control 0h LPS 80U DNase


title: Littermate control 8h LPS RelA ChIP-seq

value: LPS for 8h


title: KO 8h LPS rep1 80U DNase


title: KO 10h LPS rep2

data_processing:
The Illumina basecalling and read generation algorithm versions were RTA 1.12.4.2 and CASAVA-1.8.2.
Samples were demultiplexed allowing one mismatch on the barcode and each sample was separated in by the given six bait primers. Reads are filtered and trimmed based on the bait sequences
Samples were aligned to the reference human genome hg19 using TopHat v2.0.8 with -r 10 –mate-std-dev 200 options.
Gene model annotation for hg19 from Ensembl was provided to the aligner with the -G parameter.
Cufflinks v2.1.1 with hg19 UCSC genes from iGenomes was used to generate gene-level abundance estimates.
Genome_build: hg19
Supplementary_files_format_and_content: fpkm_tracking files contain Cufflinks output for gene expression

source_name: Bone marrow derived macrophages_KO 10h LPS

extract_protocol: Extraction and library construction methods are described in the accompanying publication.

value: 10 ng/ml LPS for 10h


title: KO 0h LPS rep2

source_name: Bone marrow derived macrophages_KO 0h LPS


title: WT 4h LPS rep2

source_name: Bone marrow derived macrophages_WT 4h LPS

value: 10 ng/ml LPS for 4h


title: WT 0h LPS Ikaros ChIP-seq


title: WT 0h LPS rep2

source_name: Bone marrow derived macrophages_WT 0h LPS


title: KO 0h LPS rep1