title: WT614M_idx12*

city: Rancagua

first: Mauricio

middle: Alejandro

last: Latorre

state: VI

address: Av. Libertador Bernardo OHiggins 611

department: ICI

country: Chile

institute: Universidad de OHiggins

description:
Sample 1
PE reads
all_samples_counts.txt
DEgenesKOvsWT.txt

data_processing:
Reads from each sample were mapped to mus musculus genome assembly GRCm38 using STAR v 2.4 with default parameters. STAR was provided with both fasta and GTF files for the reference genome downloaded from Ensembl.
Genes and exons read counts were calculated using featureCounts from the R package Rsubread version 1.16
Gene differential expression of KO vs WT samples was calculated using the R package edgeR version 3.8. To do this edgeR quasi-likelihood pipeline was used. First; only genes with a count-per-million above 1 in at least  three samples were retained. Then TMM normalization was performed. A Negative Binomial model extended with quasi-likelihood  was considered to take into account the different sequencing techniques used as well as samples type (KO or WT). Differentially expressed genes (DE) were determined through the QL F-test and multiple testing correction was carried out using the Benjamini-Hochberg method. Genes with adjusted p-values < 0.05 were considered DE.
Genome_build: mus musculus GRCm38
Supplementary_files_format_and_content: all_samples_counts.txt: text file with all samples read counts (tab separated) ; differential_expression_results.xlsx: excel file with the list of differentially expressed genes between KO and WT samples;

source_name: Liver

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent and cleanup with the Qiagen RNeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

value: male


title: 19606M1

status: Public on Dec 01 2017

type: SRA

city: Oxford

first: Luis

middle: A

last: Actis

state: OH

address: 700 E. High St.

department: Microbiology

country: USA

institute: Miami University

description:
rRNA-depleted total RNA.
19606M1_S4_L001
Processed data file: 19606vs19606M1.txt

library_source: transcriptomic

data_processing:
Illumina MiSeq Generate FastQ 1.0.
edgeR values generated using CLC Genomics Workbench 7.0.4.
Genome_build: NC_009085.1, NC_009084.1, NC_009083.1
Supplementary_files_format_and_content: 19606vs19606M1.txt: Tab-delimited text file includes edgeR values for each Sample.

molecule: total RNA

organism: Acinetobacter baumannii

source_name: monoculture with mucin

growth_protocol: Twenty-five ml of SB or SB+M were inoculated with 0.25 ml of overnight SB cultures in 125-ml flasks, which were incubated at 37°C with shaking at 200 rpm for 4 h or until an OD600 of approximately 0.5 was reached. Triplicates of three different biological replicates of bacteria cultured in SB in the absence or presence of 0.5% mucin were used to isolate total RNA as described below.

extract_protocol:
Briefly, 10 ml of culture were directly added to an equal volume of acid phenol (pH 4.3 ± 0.2) and 0.1% SDS followed by immediate incubation at 90°C for 10 min. The aqueous fraction was then extracted with acid phenol:chloroform (5:1, pH 4.5 ± 0.2) followed by chloroform. Total RNA was precipitated overnight at -20°C with 2.5 volumes of absolute ethanol. RNeasy on-column DNase I treatment was performed as per the manufacturer’s instructions (Qiagen). DNA removal was confirmed using QuantiTect SYBER Green PCR kit (Qiagen) with primers 3968 and 3969 (Table S4) for the recA gene with amplification on a Bio-Rad CFX Connect real-time PCR detection system.
RNA quantity was routinely estimated using a NanoDrop ND-2000 spectrophotometer and quality was assessed with an Agilent Bioanalyzer 2100 using the RNA 6000 Pico LabChip Kit (Agilent). DNA-free total RNA was rRNA depleted by treatment with the Ribo-Zero Magnetic Kit (Epicentre). Depletion was assessed using the RNA 6000 Pico LabChip Kit and the Bioanalyzer 2100. Cognate rRNA-depleted technical triplicates isolated from each of the three independent biological samples cultured in SB or SB+M were combined to prepare six (three for each culture condition) Illumina-compatible libraries using the NEBNext Ultra Directional RNA Library preparation kit (New England Biolabs Inc.) according to the manufacturer’s instructions. All purifications were performed with Agencourt AMPure XP Beads (Beckman Coulter, Inc.) as described in the NEBNext protocol. After purification, the size of the DNA amplicons was assessed with the Agilent High Sensitivity DNA Kit on a Bioanalyzer 2100. The KAPA Library Quantification kit (Kapa Biosystems Inc.) was used to quantify libraries on a BioRad CFX Connect real-time PCR detection system.

tag: strain/background

value: ATCC 19606T

tag: growth media

value: SB + mucin


title: 19606m2

description:
rRNA-depleted total RNA.
19606m2_S1_L001
Processed data file: 19606vs19606M1.txt


title: 196063

description:
rRNA-depleted total RNA.
196063_S3_L001
Processed data file: 19606vs19606M1.txt

source_name: monoculture without mucin

value: SB


title: 19606m3

description:
rRNA-depleted total RNA.
19606m3_S2_L001
Processed data file: 19606vs19606M1.txt


title: KO620F_idx12*

description:
Sample 6
PE reads
all_samples_counts.txt
DEgenesKOvsWT.txt

organism: Mus musculus

tag: strain

tag: tissue

value: liver

tag: genotype

tag: Sex

value: female


title: 196062

description:
rRNA-depleted total RNA.
196062_S2_L001
Processed data file: 19606vs19606M1.txt


title: 196061

description:
rRNA-depleted total RNA.
196061_S1_L001
Processed data file: 19606vs19606M1.txt


title: CD24Neg_45-U-Neg_8

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

data_processing:
100BP reads were trimmed to 50BP and aligned to the NCBIM37.67 transcriptome using Bowtie version 0.12.8 using parameters as recommended by MMSeq guidelines
Gene expression estimates were calculated using the MMSeq workflow
Genome_build: NCBIM37.67 (transcriptome)
Supplementary_files_format_and_content: MMSeq gene expression estimates (FPKM)

source_name: Small intestine epithelium

growth_protocol: not applicable

extract_protocol:
Total RNA (miRNeasy kit, Qiagen) from the flow sorted cells was used to prepare libraries using the TruSeq RNA sample preparation kit (Illumina).
as per instructions from the TruSeq RNA sample preparation kit

treatment_protocol: not applicable

tag: cell type

tag: antibodies

value: Anti-CD24 (Biolegend), anti-CD45 D Pharmingen Cat. No. 553080, Ulex europaeus agglutinin I (UEA)(custom conjugation)


title: CD24Neg_45-U-Neg_4


title: CD24Mid_45-U-Neg_3


title: CD24Neg_45-U-Neg_2


title: MycER_MEFs + OHT rep2

city: milano

first: stefano

last: campaner

address: via adamello 16

department: Center for Genomic Science

country: Italy

institute: fondazione Istituto italiano di tecnologia

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts (RPKMs) over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Genome_build: mm9
Supplementary_files_format_and_content: excel file containing expression quantification (reads per kilobase per million exonic mapped reads: eRPKM) of genes in MEF cells (WT and YAP2s) not treated and treated with Y27, OHT or both

source_name: MycER_MEFs + OHT rep2

growth_protocol: murine fibroblast were grown in DMEM medium supplemented with 10% tetracyclin-free serum, penicillin/streptomycin and 2mM L-Gln

extract_protocol:
RNA was extracted with the RNeasy MinElute Spin columns from Qiagen according to the manufacturer and eluted in 14µl of RNase free water
Libraries for RNA-Seq were prepared with the TruSeq RNA Sample Preparation Kits v2 (Illumina) following manufacturer instruction (except for skipping the first step of mRNA purification with poly-T oligo-attached magnetic beads)

treatment_protocol: ROCK inhibitor Y27632 (used 50µM), MycER was activated by OHT (400nM).

value: mouse embryonic fibroblasts

value: MycER


title: T02_Y

city: Zhenjiang

first: Xiangfeng

last: Zheng

state: Jiangsu

address: 301, Xuefu Road

department: Food school

country: China

institute: Jiangsu university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Pyrus x bretschneideri whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase Million was the value of expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced.
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000315295.1/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values  for each Sample

organism: Pyrus x bretschneideri

source_name: Meyerozyma guilliermondii

growth_protocol: Pears treated with sterile distilled water or Meyerozyma guilliermondii， at 20℃，95% for 3 days.

extract_protocol:
The around tissues of wounds in pears were collected and ground to powder, and RNA was extracted using the PrimeScript RT reagent kit . Illumina TruSeq RNA Sample  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The sample of CK was the control, pears treated with distilled water, and Y were pears treated with Meyerozyma guilliermondii.

value: fruit; pears

tag: treated with

value: Meyerozyma guilliermondii

tag: incubation time

value: 3 days

tag: incubation conditions


title: CD24Mid_45-U-Neg_1


title: 334

city: Palo Alto

first: Liana

middle: Nicole

last: Bonanno

state: California

address: 3801 Miranda Ave, Bldg 100 Rm D3-111

department: Neurology

institute: Stanford University

description: NormalizedCounts.csv

data_processing:
The quality of fastq files was assessed using FASTQC (v 0.11.4)
Reads were trimmed to 75bp using fastX toolkit (v 0.0.14)
Trimmed reads were mapped to mouse mm9 reference genome using STAR (v 2.5.1b). Raw read counts were generated with STAR using the GeneCounts function.
Differential expression in RNA-Seq was analyzed using the R DESeq2 package
Differential expression in RNA-Seq was analyzed using the R DESeq2 package. Read counts were used as input and normalized using built-in algorithms in DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: comma separated value file of normalized read counts from DESeq2 software

source_name: Microglia

extract_protocol:
All procedures were carried out at 4°C. Mice were perfused, cerebella were chopped and homogenized using a Dounce homogenizer in 2ml cold Medium A (HBSS+ 15mM HEPES+0.05% glucose+ 1:500 DnaseI), filtered through 100µm cell strainer, rinsed with 5ml Medium A and centrifuged at 340g for 5 mins. For myelin removal, the precipitate was resuspended in 25% standard isotonic percoll (25% Percoll in PBS, diluted with Medium A) and centrifuged at 950g for 20 mins. CD11b+Tmem119+ microglia (~20,000 per sample) were FACS sorted into 500µl RLT buffer (Qiagen) and stored on -80°C.
RNA was extracted from isolated microglia using RNeasy Plus Micro kit (Qiagen) and the quality assessed by Agilent 2100 Bioanalyzer (Stanford PAN facility). About 1ng RNA was converted to cDNA and amplified for 12 cycles using SMART-seq v4 Ultra Low input RNA kit for sequencing (Takara Bio USA, Inc.) according to manufacturer’s instructions. Amplified cDNA was then purified by immobilization on AMPure XP beads. Purified cDNA was normalized and tagmented for 5 mins using Nextera XT DNA library prep kit (Illumina). Unique indexes were then added to each sample, which were then amplified for 12 cycles. cDNA was purified using AMPure XP beads and quality assessed by Advanced Analytical Fragment Analyzer (Stanford PAN facility). Samples were then normalized and pooled together and sequenced on Illumina Novaseq 6000 (Novogene Corporation Inc.) to obtain 150bp paired-end reads.

value: Brain>Cerebellum

value: STINGgt/gt

tag: treatment

value: GCV


title: 340

description: NormalizedCounts.csv


title: 358

description: NormalizedCounts.csv


title: MycER_MEFs_YAP2S + OHT rep1

source_name: MycER_MEFs_YAP2S + OHT rep1


title: 208

description: NormalizedCounts.csv

value: Wild Type

value: PBS


title: 209

description: NormalizedCounts.csv


title: 356

description: NormalizedCounts.csv


title: 336

description: NormalizedCounts.csv


title: 215

description: NormalizedCounts.csv


title: 220

description: NormalizedCounts.csv


title: 203

description: NormalizedCounts.csv


title: CD24Mid_45-U-Neg_7


title: 211

description: NormalizedCounts.csv


title: CD24Neg_45-U-Neg_6


title: CD24Mid_45-U-Neg_5


title: 42

description: NormalizedCounts.csv


title: 76

description: NormalizedCounts.csv


title: Nitrogen-Starvation 2

city: Verona

first: Massimo

last: Delledonne

address: Strada le Grazie 15

institute: Universita' degli Studi di Verona

data_processing:
Bad quality read are removed, then the Scythe software removed adapters and the Sickle software the bad quality end from the reads.
For each condition assemblies are built with the filtered reads of the 3 replicates independently with Velvet. For Velvet different k-value are used (21; 25; 27; 29) and are merged using k=27 as starting point. Trinity and velvet are used with a minimun contig length of 200 and for velvet insert sizes of respectively 415, 400, 373, 392, 432 and 403 are used. The version of velvet used is 1.2.10. And the version of Oases is 0.2.08. For trinity it is 1.8.26.
The assemblies are merged with CD-HIT (0.95 of cut-off)
The RSEM software is used to perform the data analysis and the aligner provided to RSEM is Bowtie
Differential expression analysis is performed using DESeq and edgeR packages.
Supplementary_files_format_and_content: tab delimited file with raw counts, FPKM, log2 Fold Change, p-value and padj

organism: Amphidinium carterae

source_name: Microalgal cells

growth_protocol: The microalgae was cultured in Keller medium. Experimental culturing (control and nitrogen starvation conditions) were performed in two-liter polycarbonate bottles (each experiment was performed in triplicate) constantly bubbled with air filtered through 0.2 µm membrane filters. Cultures were kept in a climate chamber at 19°C on a 12:12 h light:dark cycle at 100 µmol photons m-2 s-1.

extract_protocol:
Cells were lysed using half a spatula of glass beads (about 200 mg; Sigma-Aldrich, Milan, Italy) for each 2 mL tube, incubating and mixing tubes for 10 min at 60°C and maximum speed in the Thermo Shaker BS100 (Biosan). RNA was then extracted using using the Direct-zolTM RNA MiniPrep (Zymo Research), following the manufacturer’s instructions. RNA quantity and purity were assessed by Nano-Drop (ND-1000 UV-Vis spectrophotometer; NanoDrop Technologies) monitoring the absorbance at 260 nm and the 260/280 nm and 260/230 nm ratios (Both ratios were about 2.0). RNA quality was evaluated by gel electrophoresis that showed intact RNA, with sharp ribosomal bands. Total RNA quality was evaluated by measuring the RNA Integrity Number (RIN) with Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.); high quality (RIN >8) RNA was used for the RNAseq.
RNA-Seq libraries were constructed from 2.5 µg of total RNAusing the Illumina TruSeq® Stranded mRNA kit (Illumina Inc., San Diego, CA, USA) according to manufacturer instructions. The libraries were size selected using the Pippin Prep automated gel electrophoresis system (Sage Science, Beverly, MA, USA) for 350 to 550 bp. Paired-end sequencing (100 bp × 2) was performed with the HiSeq 1000 Illumina platformusing the TruSeq SBS v3-HS kit (200 cycles) and TruSeq PE Cluster v3-cBot-HS kit (Illumina).

treatment_protocol: In the nitrogen-starvation condition a reduced concentration of nitrogen was used in the medium preparation (30 µmol L-1 of NO3-).

tag: strain code

tag: growth phase

value: Late stationary phase

tag: culturing condition

value: Starved medium


title: Control condition 2

value: Complete medium


title: Nitrogen-Starvation 1


title: Nitrogen-Starvation 3


title: 217

description: NormalizedCounts.csv


title: Control condition 1


title: 202

description: NormalizedCounts.csv


title: T01_CK

source_name: sterile distilled water

value: sterile distilled water


title: liver28 [tilapia]

status: Public on Nov 30 2017

city: Shanghai

first: Peng

last: Hu

address: Huchenghuan Road 999

institute: Shanghai Ocean University

data_processing:
Illumina’s base-caller Bustard used for basecalling.
The raw reads were trimmed for their quality. A quality score of 10 is required on a sliding window of 35 bases, and a minimum length of 35 bases after trimming in enforced.
Before reads mapping, the id and quality score of each reads were formmatted to be suitable for Tophat software by the custom perl scripts
Bowtie was used to map the reads to the reference genome. Then HTSeq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html), which is a python based script, was then applied to count the number of reads mapped to the genes.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: tilapia genome sequence and gtf files were downloaded from the Ensembl release 72
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Oreochromis niloticus

source_name: liver

extract_protocol:
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: fish were maintained 12h to adapt low temperatures and then killed by pithing

value: liver

tag: temperature

tag: age

value: Six months old


title: kidney10 [tilapia]

source_name: kidney

value: kidney


title: muscle28 [tilapia]

source_name: muscle

value: muscle


title: liver10 [tilapia]


title: kidney28 [tilapia]


title: spleen10 [tilapia]

source_name: spleen

value: spleen


title: kidney18 [tilapia]


title: heart28 [tilapia]

source_name: heart

value: heart


title: gill28 [tilapia]

source_name: gill

value: gill


title: gill10 [tilapia]


title: heart10 [tilapia]


title: brain10 [tilapia]

source_name: brain

value: brain


title: Mouse distal colon crypt 2

city: Fremont

first: Matthew

last: Siegel

state: CA

address: 34175 Ardenwood Blvd

institute: Ardelyx

data_processing:
Basecalls performed using RTA2.0
RNAseq reads were aligned to the mm10 genome assembly using STAR alignment in Illumina basespace RNAexpress application
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Genome_build: mm10

source_name: Distal Colon

growth_protocol: The process of isolating mouse intestinal crypts from the colon and small intestine was based on modifications of a published protocol (Gracz et al., 2012). Three-dimensional human intestinal organoid cultures were grown from biopsies and cultured for 7–12 days before being used to plate monolayer cultures (used up to passage 15) (Sato et al., 2011). Growth media and growth factors for mouse and human intestinal cultures were based on modifications of published protocols (Sato et al., 2011; Sato et al., 2009), and optimized growth conditions for monolayer cultures on Transwells are described in the Results section (Table 1) and Supplemental Information.

extract_protocol:
RNA was isolated from monolayer cultures and from tissue using RNeasy kits (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina Truseq mRNA stranded library prep protocol.

tag: tissue or tissue-derived primary cell culture

value: Distal Colon


title: Mouse distal colon crypt 1


title: Mouse proximal colon crypt 2

source_name: Proximal Colon

value: Proximal Colon


title: Mouse proximal colon crypt 1


title: Control condition 3


title: Mouse proximal colon APECCS at differentiated state 2

value: Proximal Colon-derived APECCS


title: Mouse proximal colon APECCS at undifferentiated state 1


title: Mouse proximal colon APECCS at differentiated state 1


title: Mouse distal colon APECCS at differentiated state 2

value: Distal Colon-derived APECCS


title: Mouse distal colon APECCS at differentiated state 1


title: liver18 [tilapia]


title: Mouse proximal colon APECCS at undifferentiated state 2


title: Mouse distal colon APECCS at undifferentiated state 2


title: muscle18 [tilapia]


title: Mouse distal colon APECCS at undifferentiated state 1


title: Mouse Ileum Crypt 2

source_name: Ileum

value: Ileum


title: Mouse Jejnum Villi 2

source_name: Jejunum

value: Jejunum


title: Mouse Jejnum Crypt 1


title: Mouse Jejnum Villi 1


title: Mouse Jejnum Crypt 2


title: Mouse Ileum Villi 2


title: Mouse Ileum Crypt 1


title: Mouse Ileum Villi 1


title: Mouse Duodenum Villi 2

source_name: Duodenum

value: Duodenum


title: Mouse Duodenum Crypt 2


title: Mouse Duodenum Crypt 1


title: Mouse Duodenum Villi 1


title: Mouse Ileum APECCS with ET

value: Ileum-derived APECCS


title: Mouse Ileum APECCS with ET, BMP4


title: Mouse Ileum APECCS with ET, BMP2


title: Mouse Ileum APECCS with ET, BMP2, BMP4 and BMP7


title: Mouse Jejunum APECCS with ET

value: Jejunum-derived APECCS


title: Mouse Jejunum APECCS with ET, BMP2


title: Mouse Jejunum APECCS with ET, BMP2, BMP4 and BMP7


title: Mouse Duodenum APECCS with ET

value: Duodenum-derived APECCS


title: Mouse Jejunum APECCS with ET, BMP2 and BMP4


title: Mouse Duodenum APECCS with ET, BMP2 and BMP4


title: Mouse Duodenum APECCS with ET, BMP4


title: Mouse Ileum APECCS with 10ng/ml BMP4 collected on D8


title: Mouse Ileum APECCS with ET collected on D8


title: Mouse Duodenum APECCS with ET, BMP2


title: Mouse Ileum APECCS with 10ng/ml BMP2 collected on D8


title: Mouse Ileum APECCS with ET, BMP2 and BMP4


title: Mouse Ileum APECCS with 30ng/ml BMP7 collected on D8


title: Mouse Ileum APECCS with 30ng/ml BMP4 collected on D8


title: Mouse Ileum APECCS with 100ng/ml BMP4 collected on D8


title: Mouse Ileum APECCS with 30ng/ml BMP2 collected on D8


title: Mouse Ileum APECCS with 100ng/ml BMP2 collected on D8


title: Mouse Ileum APECCS with 300ng/ml BMP4 collected on D8


title: Mouse Ileum APECCS with 300ng/ml BMP2 collected on D8


title: Mouse Ileum APECCS with 300ng/ml BMP7 collected on D8


title: Mouse Jejunum APECCS with 10ng/ml BMP4 collected on D8


title: Mouse Jejunum APECCS with 30ng/ml BMP4 collected on D8


title: Mouse Jejunum APECCS with 10ng/ml BMP2 collected on D8


title: Mouse Jejunum APECCS with 30ng/ml BMP7 collected on D8


title: Mouse Jejunum APECCS with 30ng/ml BMP2 collected on D8


title: Mouse Jejunum APECCS with ET collected on D8


title: Mouse Jejunum APECCS with ET, BMP4


title: Mouse Jejunum APECCS with 100ng/ml BMP4 collected on D8


title: Mouse Jejunum APECCS with 100ng/ml BMP7 collected on D8


title: Mouse Jejunum APECCS with 300ng/ml BMP7 collected on D8


title: Mouse Jejunum APECCS with 100ng/ml BMP2 collected on D8


title: Mouse Jejunum APECCS with 300ng/ml BMP4 collected on D8


title: S24

city: Brno

first: Jiri

last: Baloun

address: Kamenice 5

country: Czech Republic

institute: CEITEC - Masaryk University

description: miRNA

data_processing:
Count-based miRNA expression data were generated by the Chimira (Vitsios et al, Bioinformatics, 2015) tool from FASTQ files.
All sequences were adapter trimmed and mapped against miRBase v21 allowing up to two mismatches per sequence.
Raw reads were analysed by DESeq2 method
Genome_build: miRBase v21
Supplementary_files_format_and_content: tab-delimited text file containing miRNAs mapped in ech sample and its read count

organism: Homo sapiens

source_name: Hippocampal tissue

extract_protocol:
Total RNA was isolated from FFPE tissue sections using the High Pure miRNA Isolation Kit (Roche) according to the manufacturer`s protocol. Libraries for sequencing were prepared from 1.1 µg of total RNA using a NEXTflex Small RNA-Seq Kit v2 (Bioo Scientific) according to the manufacturer`s protocol.
small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject

value: control


title: S22

description: miRNA


title: S21

description: miRNA


title: S20

description: miRNA


title: S19

description: miRNA


title: S23

description: miRNA


title: Mouse Ileum APECCS with 100ng/ml BMP7 collected on D8

tag: strain


title: S18

description: miRNA


title: S13

description: miRNA

value: mTLE+HS patient


title: S17

description: miRNA


title: S16

description: miRNA


title: S12

description: miRNA


title: S9

description: miRNA


title: S10

description: miRNA


title: S14

description: miRNA


title: S11

description: miRNA


title: S15

description: miRNA


title: S5

description: miRNA


title: S8

description: miRNA


title: S1

description: miRNA


title: S3

description: miRNA


title: S7

description: miRNA


title: spleen18 [tilapia]

tag: tissue

value: Six months old


title: S2

description: miRNA


title: muscle10 [tilapia]

value: muscle


title: S6

description: miRNA


title: brain18 [tilapia]


title: spleen28 [tilapia]

value: spleen


title: gill18 [tilapia]

value: gill


title: heart18 [tilapia]

value: heart


title: Pat_15-03_tumor

city: Liege

first: Stephane

last: Wenric

address: Avenue de l'Hopital 1

department: Unit of Human Genetics

country: Belgium

institute: University of Liege

description: sample paired with Pat_15-03_normal

data_processing:
Basecalling was performed on the Illumina HiSeq 2000
Read quality was checked for each sample using FastQC v0.11.2
Sequencing reads were mapped using the Star 2.4.1c software
Mapping quality was assessed with the Picard RnaSeqMetrics tool of the Picard software suite (v. 1.1)
Read counts assignment was performed with the htseq-count tool of the HTSeq software suite (v. 0.6.1)
Data quality assessment was performed by computing the strand-specificity of all samples with htseq-count, leading to the removal of one patient with aberrant strand specificity.
Genome_build: hg19 GRCh37.75
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each sample
Supplementary_files_format_and_content: read counts (output of htseq-count)

source_name: mammary tissue

extract_protocol:
Total RNA were simultaneously extracted with DNA and miRNA using All Prep DNA/RNA/miRNA Universal kit (Qiagen) according to the manufacturer protocol.
RNA-Sequencing libraries for 22 breast tumors and paired adjacent tissues were constructed from 500 ng of total RNA, using the TruSeq® Stranded Total RNA kit and Ribo-Zero rRNA Removal kit (Illumina). A step of chemical fragmentation generated RNA fragment of 180 pb.

tag: tissue nature

value: primary invasive breast carcinoma

tag: tumor receptors

tag: bloom

tag: er subtype

value: A

tag: tnm


title: Pat_15-02_tumor

description: sample paired with Pat_15-02_normal


title: brain28 [tilapia]

value: brain


title: Pat_15-04_tumor

description: sample paired with Pat_15-04_normal

value: B


title: Pat_15-01_tumor

description: sample paired with Pat_15-01_normal


title: Pat_14-41_tumor

description: sample paired with Pat_14-41_normal


title: Pat_14-38_tumor

description: sample paired with Pat_14-38_normal


title: S4

description: miRNA


title: Pat_14-31_tumor

description: sample paired with Pat_14-31_normal


title: Pat_14-36_tumor

description: sample paired with Pat_14-36_normal


title: Pat_13-17_tumor

description: sample paired with Pat_13-17_normal


title: Pat_13-13_tumor

description: sample paired with Pat_13-13_normal


title: Pat_14-33_tumor

description: sample paired with Pat_14-33_normal


title: Pat_14-34_tumor

description: sample paired with Pat_14-34_normal


title: Pat_13-10_tumor

description: sample paired with Pat_13-10_normal


title: Pat_13-02_tumor

description: sample paired with Pat_13-02_normal


title: Pat_13-05_tumor

description: sample paired with Pat_13-05_normal


title: Pat_13-03_tumor

description: sample paired with Pat_13-03_normal


title: Pat_12-03_tumor

description: sample paired with Pat_12-03_normal


title: Pat_13-07_tumor

description: sample paired with Pat_13-07_normal


title: Pat_15-04_normal

description: sample paired with Pat_15-04_tumor

value: normal


title: Pat_12-02_tumor

description: sample paired with Pat_12-02_normal


title: Pat_15-02_normal

description: sample paired with Pat_15-02_tumor


title: Pat_15-03_normal

description: sample paired with Pat_15-03_tumor


title: Pat_14-36_normal

description: sample paired with Pat_14-36_tumor


title: Pat_15-01_normal

description: sample paired with Pat_15-01_tumor


title: Pat_14-38_normal

description: sample paired with Pat_14-38_tumor


title: Pat_14-41_normal

description: sample paired with Pat_14-41_tumor


title: Pat_14-35_normal

description: sample paired with Pat_14-35_tumor


title: Pat_14-35_tumor

description: sample paired with Pat_14-35_normal


title: Pat_14-31_normal

description: sample paired with Pat_14-31_tumor


title: Pat_14-33_normal

description: sample paired with Pat_14-33_tumor


title: Pat_13-11_tumor

description: sample paired with Pat_13-11_normal


title: Pat_14-25_tumor

description: sample paired with Pat_14-25_normal


title: Pat_14-25_normal

description: sample paired with Pat_14-25_tumor


title: Pat_14-34_normal

description: sample paired with Pat_14-34_tumor


title: Pat_13-17_normal

description: sample paired with Pat_13-17_tumor


title: Pat_13-10_normal

description: sample paired with Pat_13-10_tumor


title: Pat_13-05_normal

description: sample paired with Pat_13-05_tumor


title: Pat_12-03_normal

description: sample paired with Pat_12-03_tumor


title: Pat_13-02_normal

description: sample paired with Pat_13-02_tumor


title: Pat_13-03_normal

description: sample paired with Pat_13-03_tumor


title: WR Dv-1 cells control rep1

city: Ann Arbor

first: Yang

last: Lyu

state: Michigan

address: 109 Zina Pitcher Place

institute: University of Michigan

data_processing:
Pipeline from Beijing Genomics of Institute (Shenzhen) was used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the conspecific Drosophila whole genome using TopHat (v.1.3.1) with the parameter -r 20
Gene expression was estimated as FPKM (Fragments Per Kilobase Million) using Cufflink (v.2.1.1) with default parameters. Differentially expressed genes were estimated using Cuffdiff (v.2.1.1) with default parameters.
Genome_build: D. melanogaster BDGP5.19, D. simulans WUGSC1.19 and D. virilis caf1.19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Drosophila virilis

source_name: WR Dv-1 cell

extract_protocol:
Total RNAs were extracted from cells using TRIzol (Thermo Fisher Scientific, catalog no. 15596026)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected in 48-well plates with 100 ng of ub-GAL4 and 200 ng of conspecific pUAST-mir-975 or empty vectors (pUAST only) using Lipofectamine 2000 (Thermo Fisher Scientific, catalog no.12566014), and were harvested 48 hours after transfection.

tag: cell type

value: First instar larval derived cells

tag: transfecting vector

value: pUAST-only


title: Pat_12-02_normal

description: sample paired with Pat_12-02_tumor


title: WR Dv-1 cells control rep2


title: WR Dv-1 cells overexpressing dvi-miR-975 rep1


title: WR Dv-1 cells overexpressing dvi-miR-975 rep2


title: ML82-19a cells control rep1

organism: Drosophila simulans

source_name: ML82-19a cell

value: Embryo derived cells


title: ML82-19a cells overexpressing dsi-miR-975 rep2


title: ML82-19a cells overexpressing dsi-miR-975 rep1


title: ML82-19a cells control rep2


title: S2 cells control rep2

organism: Drosophila melanogaster

source_name: S2 cell


title: S2 cells control rep1


title: S2 cells overexpressing dme-miR-975 rep1


title: Pat_13-13_normal

description: sample paired with Pat_13-13_tumor


title: Pat_13-07_normal

description: sample paired with Pat_13-07_tumor


title: KO_High Cholesterol Diet_Rep2

city: Boston

first: Scott

last: Widenmaier

state: MA

address: 665 Huntington Avenue

department: Genetics and Complex Diseases

institute: Harvard TH Chan School of Public Health

description: mRNA was enriched from total RNA for library prep

data_processing:
Using the Illumina HiSeq 2500, Real Time Analysis provided basecalling.
Sequenced reads were mapped to mm10 whole genome using TopHat version 8.7.
Accepted read Bam files were sorted using Picard SortSam.
Sorted Bam files were input for transcript assembly using Cufflinks version 7 for individual samples, and the complete transcript assembly for differential analysis was done generated using Cuffmerge version 3.
CuffDiff version 7 was used for differential expression analysis. Transcript abundance was reported as Fragment reads Per Kilobase of exon per Megabase of library size (FPKM).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include average FPKM values, relative differences, and statistical signficance, reported as p-value and false discovery rate (q)

source_name: KO_High Cholesterol Diet

extract_protocol:
Livers were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. mRNA enriched libraries were prepared using Directional RNA-Seq Wafergen.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and Nrf1 KO mice were fed regular diet (RD) or 1 week with high cholesterol diet (CholD).

tag: genotype/variation

value: Nrf1 KO

tag: treatment

value: High cholesterol diet

value: Liver

tag: replicate


title: KO_High Cholesterol Diet_Rep3


title: Day15_NKX2-1_2 NKX2-1_ChIP Seq

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

library_source: genomic

data_processing:
RNA-seq reads were aligned to the human genome (assembly hg38) with STAR version 2.4.2a . Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount , version 1.4.6, with GENCODE gene annotation (V23)
All gene-level transcript counts were then imported into the R/Bioconductor package EdgeR  and TMM normalized to adjust for differences in library size.
ChIP-seq reads were aligned to human genome (assembly hg38) with bwa 0.7.12-r1039, bam files were further processed by methylQA 0.1.6 (r039) in Density mode. MACS2 was used to call peaks with default parameter and q-value cut-off 0.01.
Genome_build: hg38
Supplementary_files_format_and_content: narrow peak bed; gene-level reads counts

molecule: genomic DNA

source_name: hESC derived cIN

growth_protocol: Human embryonic stem cell (hESC) lines WA-09 (H9) and were grown under feeder free conditions on Matrigel (Corning) in mTeSR1 (Stem Cell Technologies). For differentiation , hESCs were dissociated with Accutase (Life technologies) to single cells and ~30,000 cells per well were seeded on V- Bottom 96 well nonadherent plates (Corning). To generate embryoid bodies (EBs) with ventral tencephalic regional characteristics, plates were spun at 200g for 5 minutes and incubated in 5% CO2 at 37°C in ventral neural progenitor (VNPM) medium. This medium consists of Neurobasal–A (Life Technologies), 1XB27 supplement without vitamin A (Life Technologies), SB431542 (10µM, Tocris Biosciences), plus purmorphamine  (1.5 µM, Calbiochem), LDN193189 (100nM, Stemgent) and XAV939 (2 µM, Stemgent). After 15 days of EB culture, we induced MGE-like progenitors to undergo cIN differentiation and maturation by removal of the small molecules listed above from the VNPC medium and addition of the gamma secretase inhibitor DAPT (10µM, Tocris), to inhibit Notch signaling, along with cyclic AMP (200 µM, Sigma), Ascorbic acid (200 µM, Sigma), and BDNF (20ng;Peprotech).

extract_protocol:
For RNA sequencing, total RNA was collected from H9 hESCs and H9-derived neural derivatives, differentiated, at day 0, 4, 15, 25 and 35, using the Nucleospin RNA II (Takara) kit. This involves an on column DNA digestion to remove DNA contamination. RNA was quantified by NanoDrop ND-1000 (Thermo Scientific) and the quality of total RNA was further confirmed using the Agilent Bioanalyzer 2100. For ChIP sequencing, H9 hESC-derived MGE-like progenitor cells at day15 were dissociated with Accutase and the cell suspension was fixed with 1% formaldehyde and washed with ice cold PBS with protease inhibitors (Complete mini, Roche) . Pellet was lysed first with cell lysis buffer (5mM PIPES pH8, 85mM KCl, 0.5% NP-40) and then with nuclear lysis buffer (50mM Tris-HCl pH8.1, 10mM EDTA, 1% SDS). The lysed cell pellet was sonicated using the Sonifier 250 (Branson), the supernatant was collected after centrifugation at 14,000g, and the size of the sheared chromatin was confirmed to be between 300-500bp by agarose gel electrophoresis.
For RNA-seq, library preparations and Illumina sequencing were performed by the Genome Technology Access Center (GTAC) at Washington University. For ChIP sequencing library preparation, 1ng of immunoprecipitated chromatin was used for Illumina sequencing-compatible library preparation with the DNA Smart ChIP-Seq kit (Takara) as recommended in the manufacturer’s protocol.

treatment_protocol: To define the CHD2-dependent gene expression programs during cIN specification, we used CHD2 knockdown (KD) to conduct RNA-seq analysis in d15 CHD2 KD MGE-like cells

value: hESC derived cIN

tag: days of differentiation


title: Day15_NKX2-1_3 NKX2-1_ChIP Seq


title: Day15_NKX2-1_1 NKX2-1_ChIP Seq


title: KO_High Cholesterol Diet_Rep1


title: Day15_IgG_2 NKX2-1_ChIP Seq

description: IgG


title: WT_High Cholesterol Diet_Rep3

source_name: WT_High Cholesterol Diet

value: WT


title: WT_High Cholesterol Diet_Rep1


title: Day15_IgG_1 NKX2-1_ChIP Seq

description: IgG


title: Day15_Input NKX2-1_ChIP Seq

description: input


title: WT_High Cholesterol Diet_Rep2


title: KO_Regular Diet_Rep3

source_name: KO_Regular Diet

value: Regular diet


title: Day15_CHD2KD_1 CHD2KD_RNA Seq


title: Day15_CHD2KD_2 CHD2KD_RNA Seq


title: KO_Regular Diet_Rep2


title: Pat_13-11_normal

description: sample paired with Pat_13-11_tumor


title: S2 cells overexprssing dme-miR-975 rep2


title: KO_Regular Diet_Rep1


title: Day15_NKX2-1_4 NKX2-1_ChIP Seq


title: Day35_3 cIN_RNA Seq


title: Day35_2 cIN_RNA Seq


title: KO_High Cholesterol Diet_Rep4


title: WT_Regular Diet_Rep3

source_name: WT_Regular Diet


title: Day35_1 cIN_RNA Seq


title: WT_Regular Diet_Rep4


title: Day25_4 cIN_RNA Seq


title: Day25_3 cIN_RNA Seq


title: WT_Regular Diet_Rep1


title: WT_Regular Diet_Rep2


title: Day25_2 cIN_RNA Seq


title: Day25_1 cIN_RNA Seq


title: 14228X7_EV-3

city: Salt Lake City

first: Dean

last: Tantin

state: UT

address: 15 North Medical Drive East

department: Department of Pathology

institute: University of Utah

description:
"GFP-EV" are cells productively infected with a lentivirus expressing a control gRNA
Vazquez-Arreguin_et_al_SuppTable2_diffGeneExp.xlsx

data_processing:
Align to mouse mm10 chromosomes plus splice junctions, see http://useq.sourceforge.net/usageRNASeq.html for details. The Useq 9.0.8 package was used for these analysis, see https://github.com/HuntsmanCancerInstitute/Useq  .
Convert junction alignments to genomic coordinates and remove alignments that map equally well to multiple locations.
Count the number of alignments that intersect each Ensembl gene.  The later were created by downloading the ensGene mm10 transcripts from UCSC (last updated: 2014-03-11) and collapsing gene associated transcripts to maximize exonic and minimize intronic regions.
Perform differential gene expression analysis using DESeq2 (Bioconductor release 3.5)
Export a spreadsheet containing DESeq2's AdjPVal, Log2Ratio, and normalized gene count rLog values for each of the 8 samples
Genome_build: mm10
Supplementary_files_format_and_content: .xlsx file includes FPKM and rLog corrected gene count values for each sample, log2 fold change across replicates, and adjusted p-values for differential expression from DESeq2

molecule: polyA RNA

source_name: Immortalized cell line

growth_protocol: DMEM with 10% calf serum, supplemental glutamine. Cells were subconfluent when infected, sorted, replated and collected for RNAseq

extract_protocol:
Total RNA was prepared using Trizol reagent. Illumina TruSeq mRNA library preparation kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Following infection, cells were allowed to grow for 2 d before sorting GFP+ cells to perform RNAseq.

tag: experiment

value: Control

value: immortalized MEFs (BRCA1-I26A mutant)


title: Day15_4 cIN_RNA Seq


title: 14228X6_EV-2


title: 14228X5_EV-1


title: 14228X8_EV-4


title: 14228X3_Oct1-KO-3

description:
"KO" indicates cells productively infected with a lentivirus expressing an Oct1-specific gRNA
Vazquez-Arreguin_et_al_SuppTable2_diffGeneExp.xlsx

value: Oct1 Mutant


title: 14228X4_Oct1-KO-4


title: 14228X2_Oct1-KO-2


title: Day15_3 cIN_RNA Seq


title: Day15_1 cIN_RNA Seq


title: Day4_4 cIN_RNA Seq


title: Day4_3 cIN_RNA Seq


title: Day4_2 cIN_RNA Seq


title: 14228X1_Oct1-KO-1


title: hESC_4 cIN_RNA Seq

source_name: Human ESC

value: Human ESC


title: hESC_1 cIN_RNA Seq


title: hESC_3 cIN_RNA Seq


title: Day4_1 cIN_RNA Seq


title: hESC_2 cIN_RNA Seq


title: ES ZNF589-C Input

first: Ayush

middle: T

last: Raman

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

data_processing:
For ChIP-Seq dataset, the libraries were sequenced using Illumina HiSeq Sequencer using 36bp reads. FastQC was used for quality control analysis.
The raw reads were then aligned to Bowtie (version 1.1.1)  using following commandline arguments: bowtie -n 1 -m 1 -S --best --strata -p 4 --chunkmbs 320.
The peaks were called with MACS v1.4 using input files as a background and p-value=1e-08 as a threshold. The peaks were subjected to functional analysis with GREAT tool, motif discovery with MEME-SUITE and genomic distribution analysis.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq peak files

source_name: embryonic cell line

growth_protocol: Human embryonic stem cells (hESCs) BG01V (ATCC) and induced pluripotent stem cells (iPSCs) were routinely cultured on Matrigel (BD) and γ-irradiated mouse embryonic fibroblast feeders (MEFs) (Merck-Millipore) in DMEM/F12 medium (Merck-Millipore) supplemented with 20% KSR (Gibco), 1% non-essential amino acids (Merck-Millipore), 0.1mM β-mercoptoethanol (Merck-Millipore), 10 ng/ml bFGF (Life Technologies) and 50U/ml penicillin and 50µg/ml streptomycin (Sigma Aldrich).

extract_protocol:
DNA extraction: After selection, hESCs (10cm plate, ~80% confluence) were cross-linked in 1% formaldehyde for 10min, followed with 5min incubation with 125mM glycine. Next, the cells were washed 3x with ice cold PBS and scraped in PBS/0.2mM PMSF. The cell pellet was lysed in 500μl SDS ChIP Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl pH 8.1, 150mM NaCl, freshly supplemented with protease inhibitor cocktail from Sigma). After 10min incubation on ice, the chromatin was sonicated with 60 cycles (30s on + 30s off) in Bioruptor (Diagenode). The sonicated chromatin was centrifuged (10min, 4˚C, 12000rpm) and pre-purified on 50μl pre-washed Protein A Dynabeads (Life Technologies) (1h, 4˚C, 40rpm). Pre-purified chromatin was transferred on 50μl BSA-blocked (200μg/ul BSA in ChIP SDS Buffer for 3h followed by one wash in ChIP SDS Buffer) Streptavidin Dynabeads (Life Technologies) and incubated overnight (4˚C, 40rpm). Next, the beads were collected on a magnet and washed 2x with Buffer A (2% SDS), 1x Buffer B (0.1% deoxycholate sodium, 1% Triton X-100, 1mM EDTA, 50mM Hepes pH 7.5, 500mM NaCl), followed by 1x Buffer C (250mM LiCl, 0.5% NP40, 0.5% deoxycholate sodium, 1mM EDTA, 10mM Tris-HCl pH 8.1) and 2x TE (10mM Tris-HCl pH 7.5, 1mM EDTA). All washing steps were carried out in room temperature (8min, 40rpm) and in the presence of protease inhibitor cocktail (apart from the last washing in TE). After washing, the beads were resuspended in ChIP Elution Buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.1) and the chromatin was de-cross-linked (overnight,  65˚C). Next day, the eluted chromatin was separated from the beads and subjected to digestion with 5ng/µl RNase (30min at 37˚C) and 0.2µg/µl Proteinase K  (2h at 55˚C)  followed by column purification using ChIP DNA Clean and Concetrator kit (Zymo Research). DNA quantity was assessed with the picogreen dye using Qubit dsDNA HS Assay kit (Life Technologies) according to manufacturer’s protocol. RNA for RNA-seq analysis was isolated using TRIzol reagent solution according to manufacturer’s protocol. The RNA quantity and integrity number (RIN) was assessed using an Agilent BioAnalyzer 2000 (Agilent Technologies).
The libraries for ChIP-seq were prepared with relevant library construction kits (NEB, Illumina, respectively) according to the manufacturer’s protocols.

treatment_protocol: For ChIP-seq experiments HESCs were co-transduced with two vectors: one containing biotin ligase sequence and the other with the sequence of selected KRAB-ZNF tagged with the biotinylation peptide. The cells were collected for ChIP-seq analysis after antibiotic selection. For RNA-seq analysis, TRIM28 was knockdown was achieved with a lentiviral vector carrying shRNA sequence against TRIM28 (AATTCCCGCACTAGCTGTGAGGATAATTCAAGAGATTATCCTCACAGCTAGTGCTTTTTG). Induced pluripotent stem cells were generated using a polycistronic lentiviral vector carrying the plasmid pHAGE2-hSTEMCCA-EF1α-loxp, which was a kind gift from Professor Gustavo Mostoslavsky from Boston University School of Medicine. A week after transduction the cells were transfered into pluripotent stem cells culture conditions. IPS colonies were collected 3 weeks post transduction for further expansion and analysis. To induce differentiation, hESCs and iPSCs were cultured without FGF.

tag: cell line

value: BG01V - ATCC SCRC-2002

tag: modifications or treatment

value: Transduced with a vector with biotin ligase sequence and a vector with the sequence of selected ZNF589 tagged with the biotinylation peptide

tag: sample type

value: Input


title: Aedes_aegypti_RE

city: Heidelberg

first: Cassandra

last: Falckenhayn

address: Im Neuenheimer Feld 580

department: Epigenetics

country: Germany

institute: German Cancer Research Center (DKFZ)

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
BS-mapping: bsmap 2.0
computation of methylation ratios: methratio.py (part of bsmap package)
Genome_build: AaegL3
Supplementary_files_format_and_content: bedGraph-format containing the genomic methylation ratios and coverage of the sample

organism: Aedes aegypti

source_name: whole mosquitoes

extract_protocol:
Genomic DNA was prepared using the DNeasy Blood & Tissue Kit (Qiagen) following the manufacturer's instructions
5 µg (8 % spike-in control DNA of human blood & 1 % spike-in control unmethylated bacteriophage lambda DNA) of high molecular weight DNA were used for fragmentation using the Covaris S2 AFA System in a total volume of 100 µl. Fragmentation-run parameters: Duty cycle 10%; Intensity: 5; Cycles/burst: 200; Time: 3 min; number of cycles: 3, resulting in a total fragmentation-time of 180 s. Fragmentation was confirmed with a 2100 Bioanalyzer (Agilent Technologies) using a DNA1000 chip. The fragmented DNAs were concentrated to a final volume of 75 µl using a DNA Speed Vac. End repair of fragmented DNA was carried out in a total volume of 100 µl using the Paired End DNA Sample Prep Kit (Illumina) as recommended by the manufacturer. For the ligation of the adaptors, the Illumina Early Access Methylation Adaptor Oligo Kit and the Paired End DNA Sample Prep Kit (Illumina) were used, as recommended by the manufacturer. For the size selection of the adaptor-ligated fragments, we used the E-Gel Electrophoresis System (Invitrogen) and a Size Select 2% precast agarose gel (Invitrogen). Each fragmented DNA was loaded on two lanes of the E-gel. Electrophoresis was carried out using the “Size Select” program for 16 min. According to the standard loaded (50 bp DNA Ladder, Invitrogen), 240 bp fragments were extracted from the gel, pooled, and directly transferred to bisulfite treatment without further purification. For the bisulfite treatment we used the EZ-DNA Methylation Kit (Zymo) as recommended by the manufacturer with the exception of a modified thermal profile for the bisulfite conversion reaction. The conversion was carried out in a thermal cycler using the following thermal profile: 95°C for 15 s, 50°C for 1 h, repeat from step 1, 15×, 4°C for at least 10 min. The libraries were subsequently amplified, using the Fast Start High Fidelity PCR System (Roche) with buffer 2, and Illuminas PE1.1 and PE2.1 amplification primers. PCR thermal profile: 95°C for 2 min, 95°C for 30 s, 65°C for 20 s, 72°C for 30 s, then repeat from step 2, 11×, 72°C for 7min, hold at 4°C. PCR reactions were purified on PCR purification columns (MinElute, Qiagen) and eluted in 20 µl elution buffer (Qiagen).

value: Wild type

tag: strain

value: red eye strain


title: ES ZNF114-C Input

value: Transduced with a vector with biotin ligase sequence and a vector with the sequence of selected ZNF114 tagged with the biotinylation peptide


title: ES ZNF57-C Input

value: Transduced with a vector with biotin ligase sequence and a vector with the sequence of selected ZFP57 tagged with the biotinylation peptide


title: ES PB-C Input

value: Transduced with a vector with biotin ligase sequence and a control vector with the sequence of the biotinylation peptide


title: ES ZNF589-B Input


title: ES ZNF483-B Input

value: Transduced with a vector with biotin ligase sequence and a vector with the sequence of selected ZNF483 tagged with the biotinylation peptide


title: ES ZNF57-B Input


title: Day15_2 cIN_RNA Seq


title: ES ZNF483-A Input

value: Transduced with a vector with biotin ligase sequence and a vector with the sequence of selected ZNF4783 tagged with the biotinylation peptide


title: ES ZNF114-A Input


title: ES ZNF57-A Input


title: ES ZNF589-C Streptavidin ChIP

value: streptavidin ChIP


title: ES ZNF114-C Streptavidin ChIP


title: ES ZNF589-A Streptavidin ChIP


title: ES ZNF589-B Streptavidin ChIP


title: ES PB-C Streptavidin ChIP


title: ES ZNF114-B Streptavidin ChIP


title: 15917_B-ALSK-non-2

status: Public on Nov 29 2017

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
Sample 4
LSK-non-2
Processed data file: miRNA.txt

data_processing:
Adapter was trimmed using cutadapt.
Reads were aligned to mm9 genome using Bowtie.
Expression value of miRNAs in miRBase v18 was counted using customized R script.
Count data were normalized by TMM method using "edgeR" package.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: miRNA.txt: Tabular file containing raw counts.

source_name: Lin-Sca-1+c-kit+ (LSK) cells

extract_protocol:
LSK cells from non-induced and induced CML mice were sorted and total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Valencia, CA).
Illumina small RNA-seq protocol (TruSeq Small RNA Sample Prep kit) with some modifications.

tag: strain/background

value: BCR-ABL negative

value: LSK

tag: tissue origination

value: bone marrow


title: ES ZNF483-A Streptavidin ChIP


title: ES ZNF57-B Streptavidin ChIP


title: ES ZNF57-A Streptavidin ChIP


title: 15916_B-ALSK-non-1

description:
Sample 3
LSK-non-1
Processed data file: miRNA.txt


title: 15915_B-A-LSK-indu-2

description:
Sample 2
LSK-induced-2
Processed data file: miRNA.txt

value: BCR-ABL positive


title: 15914_B-A-LSK-indu-1

description:
Sample 1
LSK-induced-1
Processed data file: miRNA.txt


title: ES ZNF114-B Input


title: Fyn-D0_2

first: Jing-Dong

middle: Jackie

last: Han

address: 320 Yueyang Road

institute: CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: RNAseqValidation.genes.fpkm.txt

data_processing:
The reads for all samples are mapped to the mm10 using Tophat v2.0.8b
The mapped reads were used to estimate alignment rates, and as input in Cufflinks v2.1.1 (Trapnell et al., 2013) to quantify gene expression levels (fragment per kilobase per million, FPKM) with the default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for cell population samples

source_name: Mouse embryonic stem cell

growth_protocol: Mouse E14 ES cells were propagated as described previously (Fei et al., 2010)

extract_protocol: Libraries were constructed using illumina Nextera XT DNA sample preparation kit

treatment_protocol: For monolayer differentiation, ES cells were dissociated with TrypLE (Invitrogen) and resuspended in N2B27 medium. After that, ES cells were plated onto gelatin-coated dishes at a density of 5×104/ml and the medium was changed every other day. On day 6, cells were replated onto PDL/laminin/fibronectin coated dishes at a density of 0.5~1.5×104/cm2 2. For SFEB differentiation, ES cells were dissociated and resuspended in GKSR medium at a density of 5×104/ml. Then the cells were seeded into petri-dishes (10ml). On day 6, cells were dissociated and resuspended in GMEM-N2 medium. Then the cells were replated onto PDL/laminin/fibronectin coated dishes at a density of 0.5~1.5×104/cm2

tag: neural induction time (day)

tag: genotype

value: Fyn-KO


title: Fyn-D0_3

description: RNAseqValidation.genes.fpkm.txt


title: ES ZNF589-A Input


title: Fyn-D4_3

description: RNAseqValidation.genes.fpkm.txt


title: Fyn-D0_1

description: RNAseqValidation.genes.fpkm.txt


title: Fyn-D4_1

description: RNAseqValidation.genes.fpkm.txt


title: Fyn-D4_2

description: RNAseqValidation.genes.fpkm.txt


title: E14-D4_3

description: RNAseqValidation.genes.fpkm.txt


title: E14-D4_2

description: RNAseqValidation.genes.fpkm.txt


title: ES ZNF57-C Streptavidin ChIP


title: ES ZNF483-B Streptavidin ChIP


title: E14-D0_3

description: RNAseqValidation.genes.fpkm.txt


title: E14-D0_2

description: RNAseqValidation.genes.fpkm.txt


title: E14-D4_1

description: RNAseqValidation.genes.fpkm.txt


title: ES ZNF114-A Streptavidin ChIP


title: E14-D0_1

description: RNAseqValidation.genes.fpkm.txt


title: AdherentMonoculture_101-5h

description: AdherentMonoculture.genes.fpkm.txt

data_processing:
The reads for all samples are mapped to the mm9 using Tophat v2.0.8b with parameter: -p 20 -g 1 -N 4 --read-edit-dist 4 --microexon-search
The mapped reads were used to estimate alignment rates, and as input in Cufflinks v2.1.1 (Trapnell et al., 2013) to quantify gene expression levels (fragment per kilobase per million, FPKM) with the default parameters
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for cell population samples and log10 transformed FPKM values for single cells

growth_protocol: Mouse R1 ES cells were propagated as described previously (Fei et al., 2010)

tag: neural induction time (hour)

value: Adherent monoculture


title: AdherentMonoculture_140-5h

description: AdherentMonoculture.genes.fpkm.txt


title: AdherentMonoculture_125-5h

description: AdherentMonoculture.genes.fpkm.txt


title: AdherentMonoculture_92-5h

description: AdherentMonoculture.genes.fpkm.txt


title: AdherentMonoculture_216h

description: AdherentMonoculture.genes.fpkm.txt


title: AdherentMonoculture_68-5h

description: AdherentMonoculture.genes.fpkm.txt


title: AdherentMonoculture_144h

description: AdherentMonoculture.genes.fpkm.txt


title: AdherentMonoculture_41-5h

description: AdherentMonoculture.genes.fpkm.txt


title: AdherentMonoculture_35-5h

description: AdherentMonoculture.genes.fpkm.txt


title: AdherentMonoculture_20-5h

description: AdherentMonoculture.genes.fpkm.txt


title: AdherentMonoculture_53-5h

description: AdherentMonoculture.genes.fpkm.txt


title: AdherentMonoculture_0h

description: AdherentMonoculture.genes.fpkm.txt


title: AdherentMonoculture_8-5h

description: AdherentMonoculture.genes.fpkm.txt


title: SFEB_SC_216h06

value: Single cells


title: SFEB_SC_216h07


title: SFEB_SC_216h02


title: SFEB_SC_216h01


title: AdherentMonoculture_2-5h

description: AdherentMonoculture.genes.fpkm.txt


title: SFEB_SC_216h16


title: SFEB_SC_144h16


title: SFEB_SC_216h12


title: SFEB_SC_144h17


title: AdherentMonoculture_80-5h

description: AdherentMonoculture.genes.fpkm.txt


title: SFEB_SC_144h10


title: SFEB_SC_144h11


title: SFEB_SC_144h08


title: SFEB_SC_144h02


title: SFEB_SC_144h04


title: SFEB_SC_216h13


title: SFEB_SC_216h04


title: SFEB_SC_106h05


title: SFEB_SC_106h03


title: SFEB_SC_84h08


title: SFEB_SC_106h04


title: SFEB_SC_106h01


title: SFEB_SC_106h09


title: SFEB_SC_106h11


title: SFEB_SC_84h09


title: SFEB_SC_84h06


title: SFEB_SC_144h14


title: SFEB_SC_84h04


title: SFEB_SC_84h03


title: SFEB_SC_84h02


title: SFEB_SC_84h01


title: SFEB_SC_60h09


title: SFEB_SC_60h08


title: SFEB_SC_60h06


title: SFEB_SC_60h04


title: SFEB_SC_106h12


title: SFEB_SC_106h08


title: SFEB_SC_60h01


title: SFEB_SC_38h09


title: SFEB_SC_38h13


title: SFEB_SC_84h05


title: SFEB_SC_38h08


title: SFEB_SC_38h07


title: SFEB_SC_38h04


title: SFEB_SC_38h01


title: SFEB_SC_38h06


title: SFEB_SC_9h08


title: SFEB_SC_9h13


title: SFEB_SC_60h10


title: SFEB_SC_9h09


title: SFEB_SC_9h06


title: SFEB_SC_38h02


title: SFEB_SC_9h03


title: SFEB_SC_9h04


title: SFEB_SC_9h02


title: SFEB_SC_9h05


title: SFEB_SC_60h05


title: SFEB_SC_0h07


title: SFEB_SC_0h12


title: SFEB_SC_0h06


title: SFEB_SC_0h05


title: SFEB_SC_0h03


title: SFEB_SC_0h04


title: SFEB_SC_60h02


title: SFEB_SC_0h02


title: SFEB_SC_0h01


title: SFEB_CP_144h

description: SFEB.CellPopulation.genes.fpkm.ComBat.txt

value: Cell Population


title: SFEB_CP_216h


title: SFEB_CP_106h


title: SFEB_CP_60h


title: SFEB_CP_38h


title: SFEB_CP_9h


title: SFEB_CP_84h


title: SFEB_CP_0h


title: SFEB_42-5h


title: SFEB_68h


title: SFEB_54-5h


title: SFEB_80h


title: SFEB_126h


title: SFEB_142h


title: SFEB_103h


title: SFEB_1h


title: SFEB_0h


title: SFEB_8h


title: SFEB_22h


title: SFEB_92h


title: SFEB_2h


title: SFEB_34h


title: RNASeq_largazole_300nM

city: Boulder

first: Xuedong

last: Liu

state: CO

address: 3415 Colorado Avenue C318

department: Chemistry and Biochemistry

institute: University of Colorado Boulder

data_processing:
Reads were filtered by Illumina CASAVA 1.8.2 software
RNA-seq reads were trimmed to a final length 43bp and mapped to human genome 18 (RefSeq hg18) using Bowtie version 2.0.2.0 and TopHat version 2.0.6, a short read aligner that is capable of predicting exon-exon splice junctions. After mapping, alignment files were processed using SAMtools version 0.1.18.0. Using Cufflinks version 2.1.1 we counted the total number of sequencing reads that aligned to each putative gene model in the human genome and generated FPKM values. To determine which genes were differentially expressed, we used the R package DESEq.
ChIP-seq datasets were aligned using Bowtie mapping software version 0.12.7. To maintain the same read length across all experiments, H3K4me1 and H3K4me2 ChIP-seq raw datasets (fastq files) were trimmed to 50bp using FASTX-toolkit version 0.0.13.2. All reads were mapped to the hg18 reference human genome with a number of base pairs mismatch not greater than 2 (96% sequence match). We used SAMtools version 0.1.19 to generate a sorted pileup format of the aligned reads. Reads were then extended from the 3’–end to a final length of 150bp. For each experiment, genome coverage bed graph files were generated using BEDTools2 version 2.25.0 and then normalized by multiplying the read density times 100 and dividing by the total number of mapped reads.
With the exception of H3K9ac and H3K27ac, signal analyses for all ChIP-seq datasets experiments were performed using MACS2 version 2.1.0.20150731 under default settings and a p-value cutoff of 1e-05. We used --broad -g hs --keep-dup=auto -p 1e-5 -m 10 200 --bw 200 and selected broad peak calls. FStitch algorithm was used to identify genomic regions enriched with H3K9ac and H3K27ac signal from ChIP-seq experiments. In order to acquire uniform FStitch signal calls across experiments targeting the same acetylated lysine, we determined the minimal number of unique reads found in datasets for H3K9ac as well as in those for H3K27ac. Based on these numbers, we randomly subsample 12,844,004 unique reads from all H3K9ac ChIP-seq experiments and 9,122,018 unique reads from all nine H3K27ac ChIP-seq datasets.  For H3K9ac ChIP-seq data analyses, we used 20 genomic regions from untreated HCT116 H3K9ac ChIP-seq data as FStitch-training genomic locations. In a similar manner, we used 19 genomic regions from H3K27ac under basal experimental conditions as FStitch training parameters. Segmentation analysis for all ChIP-seq experiments targeting the same lysine on histone H3 were conducted using the output parameters gathered from the training sessions. The same analysis was performed on the input experiment and any resulting signal was subtracted from all ChIP-seqs.
Genome_build: hg18
Supplementary_files_format_and_content: Data matrix contains the normalized abundance counts (FPKM values)

growth_protocol: Cells were cultured in Dulbecco modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (Sigma), 1% penicillin streptomycin, and 1% GlutaMAX (Invitrogen) and maintained at 37°C and 5% CO2. Prior to treatment, HCT116 cells were grown in complete media and passaged for 3 consecutive days.

extract_protocol:
Total RNA was extracted from 16 hours treated HCT116 cells using TRIzol reagent (Life Technologies) according to the manufacturer’s protocol.
The Illumina TruSeq RNA Sample Prepartaion kit (Illumina) was used to generate the RNA sequencing libraries. Briefly, mRNA was purified from 2.5 ug total RNA from each sample, fragmented, and converted to double-stranded cDNA with the use of modified oligo(dT) primers. Sequencing barcodes were ligated to the cDNA fragments, and the resulting fragments were amplified using PCR. The final lengths of oligos from each library were validated on an Agilent Bioanalyzer 2100.
Libraries were prepared according to Illumina's protocol. Barcodes were assigned as follows: Input.fastq.gz;TAGCTT, ChIPSeq_DMSO_H3K27ac.fastq.gz;GATCAG, ChIPSeq_largazole_4.68nM_H3K27ac.fastq.gz;ACTTGA, ChIPSeq_largazole_9.37nM_H3K27ac.fastq.gz;CAGATC, ChIPSeq_largazole_18.75nM_H3K27ac.fastq.gz;GCCAAT, ChIPSeq_largazole_30nM_H3K27ac.fastq.gz;ACAGTG, ChIPSeq_largazole_37.5nM_H3K27ac.fastq.gz;TGACCA, ChIPSeq_largazole_75nM_H3K27ac.fastq.gz;TTAGGC, ChIPSeq_largazole_150nM_H3K27ac.fastq.gz;CGATGT, ChIPSeq_largazole_300nM_H3K27ac.fastq.gz;ATCACG, ChIPSeq_DMSO_H3K9ac.fastq.gz;ATCACG, ChIPSeq_largazole_4.68nM_H3K9ac.fastq.gz;CGATGT, ChIPSeq_largazole_9.37nM_H3K9ac.fastq.gz;TTAGGC, ChIPSeq_largazole_18.75nM_H3K9ac.fastq.gz;TGACCA, ChIPSeq_largazole_30nM_H3K9ac.fastq.gz;ACAGTG, ChIPSeq_largazole_37.5nM_H3K9ac.fastq.gz;GCCAAT, ChIPSeq_largazole_75nM_H3K9ac.fastq.gz;CAGATC, ChIPSeq_largazole_150nM_H3K9ac.fastq.gz;ACTTGA, ChIPSeq_largazole_300nM_H3K9ac.fastq.gz;GATCAG, ChIPSeq_DMSO_H3K4me1.fastq.gz;GCACTA, ChIPSeq_largazole_75nM_H3K4me1.fastq.gz;ACCTCA, ChIPSeq_largazole_300nM_H3K4me1.fastq.gz;GTGCTT, ChIPSeq_DMSO_H3K4me2.fastq.gz;AAGCCT, ChIPSeq_largazole_75nM_H3K4me2.fastq.gz;GTCGTA, ChIPSeq_largazole_300nM_H3K4me2.fastq.gz;AAGAGG, ChIPSeq_DMSO_RNAPII.fastq.gz;GATCAG, ChIPSeq_largazole_75nM_RNAPII.fastq.gz;TAGCTT, ChIPSeq_largazole_300nM_RNAPII.fastq.gz;GGCTAC, RNASeq_DMSO.fastq.gz;GCCAAT, RNASeq_largazole_4.68nM.fastq.gz;CGATTT, RNASeq_largazole_9.37nM.fastq.gz;CAGATC, RNASeq_largazole_18.75nM.fastq.gz;CTTGTA, RNASeq_largazole_30nM.fastq.gz;AGTCAA, RNASeq_largazole_37.5nM.fastq.gz;AGTTCC, RNASeq_largazole_75nM.fastq.gz;GTCCGC, RNASeq_largazole_150nM.fastq.gz;GTGAAA, RNASeq_largazole_300nM.fastq.gz;ACAGTG.

treatment_protocol: Cells were treated with the indicated largazole concentration or equivalent amount of vehicle (DMSO) at 70% confluency and harvested after 16 hours for all ChIP-seq and RNA-seq experiments.

value: largazole 300nM

tag: disease

value: colorectal carcinoma


title: RNASeq_largazole_75nM

value: largazole 75nM


title: RNASeq_largazole_37.5nM

value: largazole 37.5nM


title: RNASeq_largazole_150nM

value: largazole 150nM


title: RNASeq_largazole_18.75nM

value: largazole 18.75nM


title: RNASeq_largazole_30nM

value: largazole 30nM


title: RNASeq_DMSO

value: DMSO


title: RNASeq_largazole_4.68nM

value: largazole 4.68nM


title: ChIPSeq_largazole_75nM_RNA_pol_II

extract_protocol:
HCT116 cells were treated with largazole or vehicle for 16 hours and cross-linked with 1% formaldehyde for 15 minutes at room temperature (25°C). Cells were washed two times with PBS and membranes ruptured in hypotonic buffer (50 mM NaCl, 1% NP-40 alternative, 2 mM EDTA, 10 mM Tris, 1 mM DTT, 2 mM EDTA, 1X protease inhibitor cocktail (Roche # 04693124001).  The cell nuclei were recovered by centrifugation and resuspended in lysate buffer (150 mM NaCl, 0.5% Triton X-100, 2 mM EDTA, 0.1% SDS, 20 mM Tris, 1 mM DTT, 1X protease inhibitor cocktail). Resuspended samples were sonicated for 25 cycles (30s ‘on’ at high level and 30s ‘off’ per cycle) using a Bioruptor (Diagenode; Denville, NJ, USA) and spun for 10 minutes at 16,000x g in a microcentrifuge. Samples were incubated for 5 hours at 4°C with 5 to 20 μg of antibodies and 20 μl of 50% slurry with protein A beads (Millipore; Billerica, MA, USA). The immunoprecipitated chromatin was then recovered and DNA purified using phenol chloroform extraction.
ChIP sequencing libraries were prepared using an Illumina ChIP-Seq DNA Sample Prep Kit (cat. # IP-102-1001), with a starting sample varying from 2 to 20 ng of DNA isolated from the immunoprecipitation step.
Libraries were prepared according to Illumina's protocol. Barcodes were assigned as follows: Input.fastq.gz;TAGCTT, ChIPSeq_DMSO_H3K27ac.fastq.gz;GATCAG, ChIPSeq_largazole_4.68nM_H3K27ac.fastq.gz;ACTTGA, ChIPSeq_largazole_9.37nM_H3K27ac.fastq.gz;CAGATC, ChIPSeq_largazole_18.75nM_H3K27ac.fastq.gz;GCCAAT, ChIPSeq_largazole_30nM_H3K27ac.fastq.gz;ACAGTG, ChIPSeq_largazole_37.5nM_H3K27ac.fastq.gz;TGACCA, ChIPSeq_largazole_75nM_H3K27ac.fastq.gz;TTAGGC, ChIPSeq_largazole_150nM_H3K27ac.fastq.gz;CGATGT, ChIPSeq_largazole_300nM_H3K27ac.fastq.gz;ATCACG, ChIPSeq_DMSO_H3K9ac.fastq.gz;ATCACG, ChIPSeq_largazole_4.68nM_H3K9ac.fastq.gz;CGATGT, ChIPSeq_largazole_9.37nM_H3K9ac.fastq.gz;TTAGGC, ChIPSeq_largazole_18.75nM_H3K9ac.fastq.gz;TGACCA, ChIPSeq_largazole_30nM_H3K9ac.fastq.gz;ACAGTG, ChIPSeq_largazole_37.5nM_H3K9ac.fastq.gz;GCCAAT, ChIPSeq_largazole_75nM_H3K9ac.fastq.gz;CAGATC, ChIPSeq_largazole_150nM_H3K9ac.fastq.gz;ACTTGA, ChIPSeq_largazole_300nM_H3K9ac.fastq.gz;GATCAG, ChIPSeq_DMSO_H3K4me1.fastq.gz;GCACTA, ChIPSeq_largazole_75nM_H3K4me1.fastq.gz;ACCTCA, ChIPSeq_largazole_300nM_H3K4me1.fastq.gz;GTGCTT, ChIPSeq_DMSO_H3K4me2.fastq.gz;AAGCCT, ChIPSeq_largazole_75nM_H3K4me2.fastq.gz;GTCGTA, ChIPSeq_largazole_300nM_H3K4me2.fastq.gz;AAGAGG, ChIPSeq_DMSO_RNAPII.fastq.gz;GATCAG, ChIPSeq_largazole_75nM_RNAPII.fastq.gz;TAGCTT, ChIPSeq_largazole_300nM_RNAPII.fastq.gz;GGCTAC, RNASeq_DMSO.fastq.gz;GCCAAT, RNASeq_largazole_4.68nM.fastq.gz;CGATTT, RNASeq_largazole_9.37nM.fastq.gz;CAGATC, RNASeq_largazole_18.75nM.fastq.gz;CTTGTA, RNASeq_largazole_30nM.fastq.gz;AGTCAA, RNASeq_largazole_37.5nM.fastq.gz;AGTTCC, RNASeq_largazole_75nM.fastq.gz;GTCCGC, RNASeq_largazole_150nM.fastq.gz;GTGAAA, RNASeq_largazole_300nM.fastq.gz;ACAGTG.

tag: chip antibody

value: RNAPII (Santa Cruz, sc-899, lot K0111)


title: ChIPSeq_largazole_75nM_H3K4me2

value: H3K4me2 (Abcam, ab7766)


title: ChIPSeq_DMSO_RNA_pol_II


title: ChIPSeq_DMSO_H3K4me2


title: ChIPSeq_largazole_4.68nM_H3K9ac

value: H3K9ac (Abcam, ab4441)


title: ChIPSeq_largazole_150nM_H3K9ac


title: ChIPSeq_largazole_300nM_H3K9ac


title: ChIPSeq_largazole_75nM_H3K4me1

value: H3K4me1 (Abcam, ab8895)


title: ChIPSeq_DMSO_H3K4me1


title: ChIPSeq_largazole_30nM_H3K9ac


title: ChIPSeq_largazole_37.5nM_H3K9ac


title: ChIPSeq_largazole_18.75nM_H3K9ac


title: ChIPSeq_largazole_75nM_H3K9ac


title: ChIPSeq_largazole_9.37nM_H3K9ac

value: largazole 9.37nM


title: ChIPSeq_DMSO_H3K9ac


title: ChIPSeq_largazole_300nM_H3K27ac

value: H3K27ac (Abcam, ab4729)


title: ChIPSeq_largazole_150nM_H3K27ac


title: ChIPSeq_largazole_300nM_RNA_pol_II


title: RNASeq_largazole_9.37nM


title: ChIPSeq_largazole_75nM_H3K27ac


title: ChIPSeq_largazole_30nM_H3K27ac


title: ChIPSeq_largazole_37.5nM_H3K27ac


title: ChIPSeq_largazole_18.75nM_H3K27ac


title: ChIPSeq_largazole_9.37nM_H3K27ac


title: ChIPSeq_largazole_4.68nM_H3K27ac


title: ChIPSeq_DMSO_H3K27ac


title: ChIPSeq_largazole_300nM_H3K4me2


title: Input sequencing from shBrg1 Replicate 4

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

data_processing:
Align bowtie2 --sensitive
picard MarkDuplicates
samtools merge
bamCoverage --binSize 30 --extendReads 150 --normalizeUsingRPKM --centerReads
macs2 callpeak -q 0.01 -keep-dup all --nomodel --extsize 150 -g hs
peaks were filtered against blacklist (ENCODE) using bedtools
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files = Reads per million
Supplementary_files_format_and_content: peaks are annotated against gencode v24 for nearest gene and annotated using ChromHMM states from ENCODE HepG2 data

growth_protocol: HepG2 cellls were purchased from ATCC and grown in DMEM + 10%FCS + penicillin and streptomycin

extract_protocol:
Cells were fixed in 0.3% formaldehyde for 30 minutes at 4 degrees prior to processing for ChIP using protocol from Raab et al 2015.
Kapa DNA hyperpep kit

treatment_protocol: cells were transfected with shRNA targeting BRG1 or BRM in the presence of 8ug/mL polybrene, and grown in 2ug/mL puromycin and harvested 7 days after transduction.

tag: antibody

tag: supplier

tag: lot


title: Input sequencing from shBrg1 Replicate 3


title: Input Sequencing from shNS Replicate 3


title: BRM ChIP-seq in shBRM Replicate 3

value: Cell Signaling

value: Lot 2


title: BRM ChIP-seq in shBRM Replicate 4


title: BRM ChIP-seq in shBRM Replicate 1


title: Input sequencing from shNS Replicate 4


title: RPE_ChIPSeq_largazole_300nM_RNA_pol_II

data_processing:
Reads were filtered by Illumina CASAVA 1.8.2 software
ChIP-seq datasets were aligned using Bowtie mapping software version 0.12.7. To maintain the same read length across all experiments, 1X150 bp ChIP-seq raw datasets (fastq files) were trimmed to 50bp using FASTX-toolkit version 0.0.13.2 or Trimmomatic version 0.36. All reads were mapped to the hg18 reference human genome with a number of base pairs mismatch not greater than 2 (96% sequence match). We used SAMtools version 0.1.19 to generate a sorted pileup format of the aligned reads. Reads were then extended from the 3’–end to a final length of 150bp. For each experiment, genome coverage bed graph files were generated using BEDTools2 version 2.25.0 and then normalized by multiplying the read density times 100 and dividing by the total number of mapped reads.
Genome_build: hg18
Supplementary_files_format_and_content: bigwig

source_name: RPE

growth_protocol: Cells were cultured in Dulbecco modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (Sigma), 1% penicillin streptomycin, and 1% GlutaMAX (Invitrogen) and maintained at 37°C and 5% CO2. Prior to treatment, HCT116 and RPE cells were grown in complete media and passaged for 3 consecutive days.

extract_protocol:
RPE cells were treated with largazole or vehicle for 16 hours and cross-linked with 1% formaldehyde for 15 minutes at room temperature (25°C). Cells were washed two times with PBS and membranes ruptured in hypotonic buffer (50 mM NaCl, 1% NP-40 alternative, 2 mM EDTA, 10 mM Tris, 1 mM DTT, 2 mM EDTA, 1X protease inhibitor cocktail (Roche # 04693124001).  The cell nuclei were recovered by centrifugation and resuspended in lysate buffer (150 mM NaCl, 0.5% Triton X-100, 2 mM EDTA, 0.1% SDS, 20 mM Tris, 1 mM DTT, 1X protease inhibitor cocktail). Resuspended samples were sonicated for 25 cycles (30s ‘on’ at high level and 30s ‘off’ per cycle) using a Bioruptor (Diagenode; Denville, NJ, USA) and spun for 10 minutes at 16,000x g in a microcentrifuge. Samples were incubated for 5 hours at 4°C with 5 to 20 μg of antibodies and 20 μl of 50% slurry with protein A beads (Millipore; Billerica, MA, USA). The immunoprecipitated chromatin was then recovered and DNA purified using phenol chloroform extraction.
ChIP sequencing libraries were prepared using an Illumina ChIP-Seq DNA Sample Prep Kit (cat. # IP-102-1001), with a starting sample varying from 2 to 20 ng of DNA isolated from the immunoprecipitation step.
Libraries were prepared according to Illumina's protocol. Barcodes were assigned as follows: RPE_Input.fastq.gz;CCAACACT, RPE_ChIPSeq_DMSO_H3K27ac.fastq.gz;TCTTCGAC,RPE_ChIPSeq_largazole_37.5nM_H3K27ac.fastq.gz;CTTCCTTC,RPE_ChIPSeq_largazole_75nM_H3K27ac.fastq.gz;AACTTGCC,RPE_ChIPSeq_largazole_300nM_H3K27ac.fastq.gz;CGACCTAA, RPE_ChIPSeq_DMSO_H3K4me1.fastq.gz;GACTACGA,RPE_ChIPSeq_largazole_37.5nM_H3K4me1.fastq.gz;ACCATCCT, RPE_ChIPSeq_largazole_75nM_H3K4me1.fastq.gz;GTACACCT,RPE_ChIPSeq_largazole_300nM_H3K4me1.fastq.gz;TACATCGG, RPE_ChIPSeq_DMSO_RNAPII.fastq.gz;ACTCCTAC,RPE_ChIPSeq_largazole_75nM_RNAPII.fastq.gz;ACGAGAAC, RPE_ChIPSeq_largazole_300nM_RNAPII.fastq.gz;ATCGTCTC.

treatment_protocol: Cells were treated with the indicated largazole concentration or equivalent amount of vehicle (DMSO) at 70% confluency and harvested after 16 hours for all ChIP-seq or RNA-seq experiments.

tag: tisue

value: retina

value: normal

tag: agent


title: BRM ChIP-seq in shBRM Replicate 2


title: BRM ChIP-seq in shNS Replicate 4


title: BRG1 ChIP-seq in shBRM Replicate 3

value: Abcam


title: BRG1 ChIP-seq in shBRM Replicate 2


title: BRG1 ChIP-seq in shBRM Replicate 4


title: RPE_ChIPSeq_largazole_75nM_RNA_pol_II


title: BRG1 ChIP-seq in shBrg1 Replicate 5


title: BRM ChIP-seq in shBrg1 Replicate 4


title: BRM ChIP-seq in shBrg1 Replicate 3


title: BRM ChIP-seq in shBrg1 Replicate 5


title: RPE_ChIPSeq_largazole_75nM_H3K4me1


title: BRG1 ChiP-seq in shBrg1 Replicate 3


title: RPE_ChIPSeq_largazole_37.5nM_H3K4me1


title: BRG1 ChIP-seq in shBrg1 Replicate 4


title: BRG1 ChIP-seq in shBRM Replicate 1


title: Input_DNA

tag: treatment

value: colorectal carcinoma


title: RPE_ChIPSeq_largazole_300nM_H3K4me1


title: RPE_ChIPSeq_DMSO_H3K4me1


title: BRM ChIP-seq in shNS Replicate 3


title: BRG1 ChiP-seq in shNS Replicate 3


title: RPE_ChIPSeq_largazole_37.5nM_H3K27ac


title: RPE_ChIPSeq_largazole_75nM_H3K27ac


title: RPE_ChIPSeq_largazole_300nM_H3K27ac


title: RPE_Input_DNA


title: RPE_ChIPSeq_DMSO_H3K27ac


title: B cells post therapy single cell RNA seq

city: New Haven

first: Kavita

last: Dhodapkar

address: 333 Cedar Street

institute: Yale

data_processing:
Reads were aligned, filtered, de-duplicated, and converted into a digital count matrix using Cell Ranger 1.2 (10X Genomics)
Additional quality control (QC) was performed by visual inspection of QC plots using Seurat [Satija et al. Nat Biotech 33, 495-502 (2015)]. Outlier cells were identified and filtered based on (1) anomalously high/low mitochondrial gene expression (cells with >10% or <1% mitochondrial content were removed) and (2) potential doublets/multiplets, as identified by comparing the number of expressed genes detected by per cell versus the number of unique molecular identifiers (UMIs) detected per cell (cells with greater than 2,250 expressed genes were removed). In addition, we removed 20 potential myeloid cells, identified by the expression of CD14 and/or FCN1.
To co-analyse both data-sets, an aggregate digital expression matrix was produced using cell-ranger, and above steps were carried out.
Genome_build: hg38
Supplementary_files_format_and_content: The processed files are combined digital expression matrix divided in three files.  The matrix.mtx file contains the values, barcodes.tsv contains the cell barcodes detected, and genes.tsv contains the list of genes detected.  This folder was read-in using the Seurat package.

source_name: CD19+ live cells

growth_protocol: PBMCs obtained from a patient receiving CCB therapy were thawed and sorted to obtain living CD19+ B cells using flow associated cell sorter.

extract_protocol: To prepare the libraries for sequencing, the Chromium Gel Bead and Library Kit (10X Genomics) and Chromium instrument (10X Genomics) were used following manufacturer’s protocol. Further, the barcoded libraries were sequenced using HiSeq2500.

treatment_protocol: Combination checkpoint blockade therapy (Ipilimumab and Nivolumab).

value: Post-CCB

tag: cell type

value: PBMCs

tag: cell subtype

value: Sorted live B-cells


title: B cells pre therapy single cell RNA seq

value: Pre-CCB


title: pH7_CCG rep3

city: Seoul

first: kucsbl

last: submitter

state: Seoul

address: Anamdong 5-ga, Seongbuk-gu

department: Department of Biotechnology

country: South Korea

institute: Korea University

data_processing:
Read data were aligned on the reference genome sequence.
DESeq and edgeR package in the Bioconductor/R packages were used for making RPKM values.
Base-calling by the MiSeq platform
Alignment by Bowtie software
Using R packages for DEG analysis
Genome_build: Lactobacillus rhamnosus GG (ATCC 53103, RefSeq ID: NC_013198.1)
Supplementary_files_format_and_content: CSV file of normalized RPKM value from edgeR for every samples.

organism: Lacticaseibacillus rhamnosus GG

source_name: whole transcriptome

extract_protocol:
TruSeq RNA Sample Preparation Kit (Illumina) was used.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ph


title: pH7_CCG rep2


title: pH4_24h rep3


title: ChIPSeq_largazole_300nM_H3K4me1

tag: cell line

value: largazole 300nM


title: pH4_24h rep1


title: pH4_24h rep2


title: pH4_1h rep3


title: BRG1 ChiP-seq in shNS Replicate 4


title: pH4_1h rep1


title: ZnF2 rep1

status: Public on Nov 28 2017

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

description: ZLD-ZnF2 mutant RNA-seq rep 1

data_processing:
Basecalls performed using CASAVA1.8.2
All analyses were done on the Galaxy online platform
Raw RNA-seq in FASTQ format were trimmed of adapter sequences and quality by sliding window, with a minimum score of 20
Trimmed reads were further filtered until 90% of each read had a minimum score >20
Trimmed, filtered reads were aligned to the dm6 genome assembly using the RNA-star mapper using default settings
Cufflinks was used to assemble transcripts and estimate FPKM for TopHat-aligned data
Cuffmerge was used to merge together resultant Cufflinks files (as GTF files)
Transcript expression values were pre-computed with Cuffquant using the files produced by Cufflinks and Cuffmerge
Fold change between experimental conditions was calculated using Cuffdiff, with the Cuffquant and Cuffmerge
Genome_build: dm6
Supplementary_files_format_and_content: CSV file produced by CuffDiff software for assessing RNA-seq data. Fold change, p-value, and q-values are given for each gene or locus that describes the change in gene expression between experiment conditions.

source_name: embryo

growth_protocol: Flies were raised on molasses food at 25 degrees celsius.

extract_protocol:
Stage 5 embryos were hand sorted under a microscope and harvested in trizol. RNA was isolated by phenol-chloroform extractions followed by RNeasy Mini Kit (Qiagen Cat#74104) clean-up collumn.  Illumina TruSeq RNA Sample Prep Kit v2 (Cat#FC-122-2001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina Truseq RNA sample prep kit according to manufacterer’s instructions.

tag: tissue

value: embryo

tag: developmental stage

value: stage 5

value: ZLD-ZnF2 mutant


title: ZnF2 rep2

description: ZLD-ZnF2 mutant RNA-seq rep 2


title: w1118 rep3

description: Wild Type RNA-seq rep 3

value: Wild Type


title: ZnF2 rep3

description: ZLD-ZnF2 mutant RNA-seq rep 3


title: w1118 rep2

description: Wild Type RNA-seq rep 2


title: w1118 rep1

description: Wild Type RNA-seq rep 1


title: Input Rep2

city: Portsmouth

first: Samuel

last: Robson

address: St Michael's Building

department: School of Pharmacy & Biomedical Science

institute: University of Portsmouth

data_processing:
ChIP seq: Reads were trimmed to remove the TRUseq adapter using trim_galore with parameters '-q 0 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --phred33 --fastqc'. Read quality was assessed using FastQC. Ribosomal contamination was removed by first mapping the reads to hg38 rDNA sequences using bwa (default parameters), and removing all reads that map. Trimmed non-ribosomal reads were mapped to the hg38 genome using bwa with parameters '-n 3 -k 2 -R 300 -t 4'. Multiple reads mapping to a single genomic locus were treated as PCR duplicates, and were removed using samtools rmdup. Mapped reads were filtered to remove reads mapping to more than one unique genomic locus (multihits) by keeping only reads with flag XT:A:U in the output bam file from bwa. Reads were further filtered to remove reads with mapping quality less than 20 using samtools. Genome coverage bedgraph files were generated using genomeCoverageBed from the bedtools suite of tools. Coverage files were converted to bigwig format using bedGraphToBigWig. Peaks were called against input sample using MACS2 using default parameters. Peaks from all replicates were merged to give a master list of potential binding loci per condition, and read count (normalised by overall read depth of the library) for each replicate was calculated using the GenomicRanges package in R. Peaks were treated as potential binding loci if all replicates showed normalised score greater than 1 and did not overlap a peak called in the IgG.
m6A meRIP seq: Reads were trimmed to remove the TRUseq adapter using trim_galore with parameters '-q 0 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --phred33 --fastqc'. Read quality was assessed using FastQC. Ribosomal contamination was removed by first mapping the reads to hg38 rDNA sequences using bwa (default parameters), and removing all reads that map. Trimmed non-ribosomal reads were mapped to the hg38 genome using Tophat2 with parameters '--no-coverage-search --max-multihits 300 --report-secondary-alignments --read-mismatches 2'. Gene annotations from Ensembl v86 were used to direct transcript alignment. Mapped reads were filtered to remove reads mapping to more than one unique genomic locus (multihits) by keeping only reads with flag NH:i:1 in the output bam file from Tophat. Reads were further filtered to remove reads with mapping quality less than 20 using samtools. Genome coverage bedgraph files were generated for forward and reverse strand reads using genomeCoverageBed from the bedtools suite of tools. Coverage files were converted to bigwig format using bedGraphToBigWig. Transcript assembly was performed using cufflinks2 and a single transcript database was generated using cuffmerge.
Riboprofiling: Reads were trimmed to remove the TRUseq adapter using trim_galore with parameters '-q 0 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --phred33 --fastqc'. Read quality was assessed using FastQC. Ribosomal contamination was removed by first mapping the reads to hg38 rDNA sequences using bwa (default parameters), and removing all reads that map. Trimmed non-ribosomal reads were mapped to the hg38 genome using Tophat2 with parameters '--no-coverage-search --max-multihits 300 --report-secondary-alignments --read-mismatches 2'. Gene annotations from Ensembl v86 were used to direct transcript alignment. Mapped reads were filtered to remove reads mapping to more than one unique genomic locus (multihits) by keeping only reads with flag NH:i:1 in the output bam file from Tophat. Reads were further filtered to remove reads with mapping quality less than 20 using samtools. Genome coverage bedgraph files were generated for forward and reverse strand reads using genomeCoverageBed from the bedtools suite of tools. Coverage files were converted to bigwig format using bedGraphToBigWig. Transcript assembly was performed using cufflinks and a single transcript database was generated using cuffmerge.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files give coverage scores across the whole hg38 genome at each base position for the mapped reads. Normalized (read count normalized to total library read depth) and non-normalized coverage files are provided for each sample.

source_name: Whole cell

growth_protocol: MOLM13 cells  were cultured in RPMI1640 (Invitrogen) supplemented with 10% FBS (PAA) and 1% penicillin/streptomycin/glutamine. 5*10^5 MOLM13 cells were infected using PLKO-TETon-Puro lentiviral vectors expressing shRNAs against the coding sequence of human METTL3 or a scramble control.

extract_protocol:
Chromatin immunoprecipitation was performed as previously described (Dawson et al., 2009). Firstly MOLM13 cells were cross-linked with 1% formaldehyde for 10 minutes.  20*10^6 cells were used for each immunoprecipitation with 3ug of specific antibodies or IgG. Immunoprecipitated DNA was purified using the ChIP DNA purification kit (Zymo).
Single end 50 bp libraries were prepared using the Bioo Scientific NEXTflex ChIP seq kit following manufacturer's recommendations. Reads were sequenced using HiSeq 1500 and multiplexed reads were split based on their barcodes using Illumina Basespace.

value: leukemia cell line MOLM13

tag: truseq barcode

value: GATCAG

tag: genotype/variation

value: WT

tag: ip antibody


title: Input Rep3

value: TTAGGC


title: IgG Rep3

value: ATCACG

value: IgG

tag: antibody vendor

tag: antibody catalog num

tag: antibody lot num


title: Input Rep1

value: CAGATC


title: IgG Rep2

value: ACTTGA

value: Abcam


title: pH7_CCG rep1


title: IgG Rep1

value: GCCAAT


title: H3K4me3 Rep1

value: ACAGTG


title: METTL14 Rep5

value: CTTGTA


title: RNAseq.patski.2-4.rep2

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

description:
RNA-seq experiment in subclone of Patski WT cells (Patski2-4).
RNAseq.patski.2-4.rep2.HMGHYBGX2.TGACCA
Processed data file: RNAseq.geneCounts.tsv.gz

data_processing:
RNA-seq single-end reads were mapped to the UCSC mm10 (NCBI build v38) refSeq transcriptome as downloaded and packaged in the iGenomes reference sequences and annotation files on July 17, 2015 (https://support.illumina.com/sequencing/sequencing_software/igenome.html). Tophat2 (v 2.0.12) (calling bowtie2 (v2.2.3)) was used to perform single-end mapping allowing 6 mismatches but otherwise default parameters.
To determine biallelic expression levels, mapped reads were assigned to refSeq genes using HT-seq and counts were converted into TPMs using custom R scripts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RNAseq.geneCounts.tsv: Tab-delimited text file includes gene expression measured by read counts per gene.

organism: Mus musculus x Mus spretus

source_name: Patski cells

extract_protocol:
RNA were extracted from Patski cells by the Qiagen RNeasy kit with on-column DNaseI digestion.
RNA-seq indexed libraries were prepared using Illumina TruSeq RNA sample preparation kit with standard Illumina protocols.

value: Patski

value: Fibroblasts derived from hybrid embryonic kidney

tag: strain/background

value: wild-type


title: RNAseq.patski.2-4.rep1

description:
RNA-seq experiment in subclone of Patski WT cells (Patski2-4).
RNAseq.patski.2-4.rep1.HMGHYBGX2.CGATGT
Processed data file: RNAseq.geneCounts.tsv.gz


title: METTL14 Rep3


title: pH4_1h rep2


title: METTL14 Rep2


title: METTL14 Rep4


title: METTL3 Rep4

value: TGACCA

value: Bethyl Laboratories


title: METTL3 Rep5

value: leukemia cell line MOLM13


title: RNAseq.patski.Inv-Dxz4.rep1

description:
RNA-seq experiment in CRISPR/cas9-modified Patski cells (Inv-Dxz4, clone a).
RNAseq.patski.Inv-Dxz4.rep1.HMGHYBGX2.CAGATC
Processed data file: RNAseq.geneCounts.tsv.gz


title: METTL3 Rep1

value: CGATGT


title: METTL3 Rep2

value: WT


title: METTL3 Rep3


title: RNAseq.patski.Del-Ds-TR.rep1

description:
RNA-seq experiment in CRISPR/cas9-modified Patski cells (Del-Ds-TR).
RNAseq.patski.Del-Ds-TR.rep1.H57VKBGXY.CTTGTA
Processed data file: RNAseq.geneCounts.tsv.gz

value: Del-Ds-TR


title: RNAseq.patski.Del-Dxz4.rep1

description:
RNA-seq experiment in CRISPR/cas9-modified Patski cells (Del-Dxz4).
RNAseq.patski.Del-Dxz4.rep1.H57VKBGXY.GTGAAA
Processed data file: RNAseq.geneCounts.tsv.gz


title: Ribosome Profiling METTL3 KD2 Day 8

description: Total RNA (ribodepleted)

data_processing:
Library strategy: Riboprofiling
ChIP seq: Reads were trimmed to remove the TRUseq adapter using trim_galore with parameters '-q 0 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --phred33 --fastqc'. Read quality was assessed using FastQC. Ribosomal contamination was removed by first mapping the reads to hg38 rDNA sequences using bwa (default parameters), and removing all reads that map. Trimmed non-ribosomal reads were mapped to the hg38 genome using bwa with parameters '-n 3 -k 2 -R 300 -t 4'. Multiple reads mapping to a single genomic locus were treated as PCR duplicates, and were removed using samtools rmdup. Mapped reads were filtered to remove reads mapping to more than one unique genomic locus (multihits) by keeping only reads with flag XT:A:U in the output bam file from bwa. Reads were further filtered to remove reads with mapping quality less than 20 using samtools. Genome coverage bedgraph files were generated using genomeCoverageBed from the bedtools suite of tools. Coverage files were converted to bigwig format using bedGraphToBigWig. Peaks were called against input sample using MACS2 using default parameters. Peaks from all replicates were merged to give a master list of potential binding loci per condition, and read count (normalised by overall read depth of the library) for each replicate was calculated using the GenomicRanges package in R. Peaks were treated as potential binding loci if all replicates showed normalised score greater than 1 and did not overlap a peak called in the IgG.
m6A meRIP seq: Reads were trimmed to remove the TRUseq adapter using trim_galore with parameters '-q 0 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --phred33 --fastqc'. Read quality was assessed using FastQC. Ribosomal contamination was removed by first mapping the reads to hg38 rDNA sequences using bwa (default parameters), and removing all reads that map. Trimmed non-ribosomal reads were mapped to the hg38 genome using Tophat2 with parameters '--no-coverage-search --max-multihits 300 --report-secondary-alignments --read-mismatches 2'. Gene annotations from Ensembl v86 were used to direct transcript alignment. Mapped reads were filtered to remove reads mapping to more than one unique genomic locus (multihits) by keeping only reads with flag NH:i:1 in the output bam file from Tophat. Reads were further filtered to remove reads with mapping quality less than 20 using samtools. Genome coverage bedgraph files were generated for forward and reverse strand reads using genomeCoverageBed from the bedtools suite of tools. Coverage files were converted to bigwig format using bedGraphToBigWig. Transcript assembly was performed using cufflinks2 and a single transcript database was generated using cuffmerge.
Riboprofiling: Reads were trimmed to remove the TRUseq adapter using trim_galore with parameters '-q 0 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --phred33 --fastqc'. Read quality was assessed using FastQC. Ribosomal contamination was removed by first mapping the reads to hg38 rDNA sequences using bwa (default parameters), and removing all reads that map. Trimmed non-ribosomal reads were mapped to the hg38 genome using Tophat2 with parameters '--no-coverage-search --max-multihits 300 --report-secondary-alignments --read-mismatches 2'. Gene annotations from Ensembl v86 were used to direct transcript alignment. Mapped reads were filtered to remove reads mapping to more than one unique genomic locus (multihits) by keeping only reads with flag NH:i:1 in the output bam file from Tophat. Reads were further filtered to remove reads with mapping quality less than 20 using samtools. Genome coverage bedgraph files were generated for forward and reverse strand reads using genomeCoverageBed from the bedtools suite of tools. Coverage files were converted to bigwig format using bedGraphToBigWig. Transcript assembly was performed using cufflinks and a single transcript database was generated using cuffmerge.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files give coverage scores across the whole hg38 genome at each base position for the mapped reads. Normalized (read count normalized to total library read depth) and non-normalized coverage files are provided for each sample.

extract_protocol:
5*10^7 MOLM13 CTRL or METTL3 KD cells at day 5 or day 8 after doxycycline induction were treated with 0.1 mg/ml of cycloheximide for 1 minute and the ribosome protected fragment (RPF) fraction of mRNA or total input control mRNA was isolated using the RNeasy Mini Kit (Quiagen) following the manufacturer instruction. Ribosomal RNA was removed using the Illumina Ribozero Kit.
Single end 50 bp stranded libraries were prepared using the Illumina TRUseq Ribo Profile kit following manufacturer's recommendations. Reads were sequenced using HiSeq 1500 and multiplexed reads were split based on their barcodes using Illumina Basespace.

treatment_protocol: shRNA was induced by 200 ng/ml doxycycline treatment for the indicated times (5 days or 8 days).

value: GATCAG

value: METTL3 KD2 shRNA

tag: time

value: Day 8


title: H3K4me3 Rep2

value: TTAGGC


title: Ribosome Profiling METTL3 KD2 Day 5

description: Total RNA (ribodepleted)

value: Day 5


title: Ribosome Profiling Ctrl Day 8

description: Total RNA (ribodepleted)

value: CAGATC

value: Scramble shRNA


title: RNAseq.patski.Del-hinge.4u5aza.rep1

description:
RNA-seq experiment in CRISPR/cas9-modified Patski cells (Del-hinge, clone a) with 4uM 5-aza treatment.
RNAseq.patski.Del-hinge.4u5aza.rep1.HF5MJBGXY.CTTGTA
Processed data file: RNAseq.geneCounts.tsv.gz

value: Del-hinge


title: Ribosome Profiling METTL3 KD1 Day 8

description: Total RNA (ribodepleted)

value: ACTTGA

value: METTL3 KD1 shRNA


title: RNAseq.patski.Del-hinge.4u5aza.rep2

description:
RNA-seq experiment in CRISPR/cas9-modified Patski cells (Del-hinge, clone a) with 4uM 5-aza treatment.
RNAseq.patski.Del-hinge.4u5aza.rep2.HF5MJBGXY.GTGAAA
Processed data file: RNAseq.geneCounts.tsv.gz

value: Patski

value: Fibroblasts derived from hybrid embryonic kidney


title: RNAseq.patski.Del-hinge.0u5aza.rep2

description:
RNA-seq experiment in CRISPR/cas9-modified Patski cells (Del-hinge, clone a) with mock treatment.
RNAseq.patski.Del-hinge.0u5aza.rep2.HF5MJBGXY.GCCAAT
Processed data file: RNAseq.geneCounts.tsv.gz


title: RNAseq.patski.Inv-Dxz4.rep2

description:
RNA-seq experiment in CRISPR/cas9-modified Patski cells (Inv-Dxz4, clone b).
RNAseq.patski.Inv-Dxz4.rep2.HMGHYBGX2.CCGTCC
Processed data file: RNAseq.geneCounts.tsv.gz


title: Input METTL3 KD1 Day 5

description: Total RNA (ribodepleted)

value: ACAGTG


title: RNAseq.patski.Del-hinge.0u5aza.rep1

description:
RNA-seq experiment in CRISPR/cas9-modified Patski cells (Del-hinge, clone a) with mock treatment.
RNAseq.patski.Del-hinge.0u5aza.rep1.HF5MJBGXY.ACAGTG
Processed data file: RNAseq.geneCounts.tsv.gz


title: Input METTL3 KD2 Day 8

description: Total RNA (ribodepleted)

value: leukemia cell line MOLM13

value: CTTGTA


title: Input METTL3 KD1 Day 8

description: Total RNA (ribodepleted)

value: GGCTAC


title: METTL14 Rep1

value: TGACCA

value: WT

value: Abcam


title: Input METTL3 KD2 Day 5

description: Total RNA (ribodepleted)

value: GCCAAT

value: METTL3 KD2 shRNA


title: Input Ctrl Day 8

description: Total RNA (ribodepleted)

value: TAGCTT

value: Day 8


title: RNAseq.patski.Del-hinge.rep2

description:
RNA-seq experiment in CRISPR/cas9-modified Patski cells (Del-hinge, clone b).
RNAseq.patski.Del-hinge.rep2.H53J7BGX2.ACAGTG
Processed data file: RNAseq.geneCounts.tsv.gz


title: RNAseq.patski.WT.4u5aza.rep2

description:
RNA-seq experiment in wild-type Patski cells with 4uM 5-aza treatment.
RNAseq.patski.WT.4u5aza.rep2.HF5TFBGXY.GTGAAA
Processed data file: RNAseq.geneCounts.tsv.gz

value: wild-type


title: Input Ctrl Day 5

description: Total RNA (ribodepleted)

value: Scramble shRNA

value: Day 5


title: RNAseq.patski.WT.4u5aza.rep1

description:
RNA-seq experiment in wild-type Patski cells with 4uM 5-aza treatment.
RNAseq.patski.WT.4u5aza.rep1.HF5TFBGXY.CTTGTA
Processed data file: RNAseq.geneCounts.tsv.gz


title: RNAseq.patski.Del-hinge.rep1

description:
RNA-seq experiment in CRISPR/cas9-modified Patski cells (Del-hinge, clone a).
RNAseq.patski.Del-hinge.rep1.H57VKBGXY.GCCAAT
Processed data file: RNAseq.geneCounts.tsv.gz

value: Del-hinge


title: RNAseq.patski.WT.0u5aza.rep2

description:
RNA-seq experiment in wild-type Patski cells with mock treatment.
RNAseq.patski.WT.0u5aza.rep2.HF5TFBGXY.GCCAAT
Processed data file: RNAseq.geneCounts.tsv.gz

value: Patski


title: Ribosome Profiling METTL3 KD1 Day 5

description: Total RNA (ribodepleted)

value: CGATGT

value: METTL3 KD1 shRNA