title: cMO_st12p_polyA-RNA_rep4

city: London

first: George

middle: E.

last: Gentsch

state: Greater London

address: 1 Midland Road

department: Developmental Biology Laboratory

institute: The Francis Crick Institute

description: standard control morphant, stage 12+ (late gastrula), experiment 7

data_processing:
Bases were called using Casava version 1.8.2
RNA-Seq: Paired-end reads were aligned to the X. tropicalis genome assembly v7.1 using STAR v2.5.3a with default settings and a revised version of gene models v7.2 to improve mapping accuracy across splice junctions. The alignments were sorted by read name using the sort function of samtools v1.3.1. Exon and intron counts (-t 'exon;intron') were extracted from unstranded (-s 0) alignment files using VERSE v0.1.5 in featureCounts (default) mode (-z 0). Intron coordinates were adjusted to exclude any overlap with exon annotation. Differential expression analysis was performed with both raw exon and intron counts excluding those belonging to ribosomal and mitochondrial RNA using the R package DESeq2 v1.14.1. In an effort to find genes with consistent fold changes over time, p-values were generated according to a likelihood ratio test reflecting the probability of rejecting the reduced (~ developmental stage) over the full (~ developmental stage + condition) model. Resulting p-values were adjusted to obtain false discovery rates (FDR) according to the Benjamini-Hochburg procedure with thresholds on Cook’s distances and independent filtering being switched off. Equally, dataset without time series were subjected to likelihood ratio tests with reduced (~1) and full (~ condition) models for statistical analysis.
4sU-Seq: Paired-end reads were aligned to a revised version of X. tropicalis gene models v7.2 and known off-genome EST assemblies including ribosomal and mitochondrial RNA by running Bowtie2 v2.1.0 with the following constraints: -k 200 (up to 200 alignments per fragment) -X 800 (maximum fragment length of 800 bp) -rdg 6,5 (penalty for read gaps of length N, 6+N*5) -rfg 6,5 (penalty for reference gaps of length N, 6+N*5) -score-main L,-.6,-.4 (minimal alignment score as a linear function of the read length x, f(x) = -0.6 - 0.4*x) -no-discordant (no paired-end read alignments breaching maximum fragment length X) -no-mixed (only concordant alignment of paired-end reads). Only read pairs that uniquely align to one gene were counted. Differential expression analysis was performed with raw read counts including those belonging to ribosomal and mitochondrial RNA using the R package DESeq2 v1.14.1. In an effort to find 4sU-enriched transcript levels, their DESeq2 normalised read counts genes were divided by those of the 4sU input for both developmental stages.
Genome_build: X. tropicalis v7.1
Supplementary_files_format_and_content: Raw read count tables (gzip compressed text files)

organism: Xenopus tropicalis

source_name: whole embryo

growth_protocol: Embryos were grown to the indicated developmental stage in 5% MMR at 25ºC.

extract_protocol:
Total RNA extraction: 10-15 dejellied X. tropicalis embryos were homogenized in 800 µl TRIzol reagent by vortexing. For phase separation, the homogenate supplemented with 1/5 volume of chloroform was transferred to a 1.5-ml phase-lock gel heavy microcentrifuge tube, shaken vigorously for 15 sec, left on the bench for 2 min and centrifuged (16,000 g) for 5 min at 4ºC. The upper phase was mixed with 1 volume of absolute ethanol and centrifuged (12,000 g) through the column IIC of Zymo RNA Clean and Concentrator-25 (Zymo Research) for 30 sec at room temperature. Next, the manufacturer’s instructions were followed for the recovery of total RNA (>17 nt) with minor modifications. First, the flow-through of the first spin was re-applied to the column. Second, the RNA was treated in-column with Turbo DNase (2 U/µl, ThermoFisher Scientific). Third, the RNA was eluted twice with 25 µl molecular-grade water. The concentration was determined on the Nanodrop 1000 except for RNA samples subjected to ribosomal RNA depletion in which case more accurate fluorometry was used.
Metabolic labeling of nascent transcripts: 75 ng 4-thiouridine-5'-triphosphate (4sU) was injected into the zygote’s animal pole. Total RNA was extracted as described above from 30 embryos collected at the mid-blastula transition (stage 8+) and early gastrula stage (stage 10+). Ribosomal RNA (rRNA) was removed from ~10 µg total RNA with Ribo-Zero rRNA (human/mouse/rat) magnetic beads (Illumina) following the manufacturer’s instructions. rRNA-depleted total RNA was purified with the RNA Clean & Concentrator-5 kit (Zymo Research) according to the manufacturer’s instructions. The yield was determined on a fluorometer using high-sensitivity reagents for RNA (250 pg/µl to 100 ng/µl). The purified RNA was transferred to thin-walled PCR tubes and fragmented with 40 µl 1x NEBNext RNA fragmentation buffer (NEB) in a thermocycler for 4 min at 95ºC. The fragmentation was stopped on ice with NEBNext RNA fragmentation stop solution (NEB) before purifying the fragmented RNA with RNA Clean & Concentrator-5. The RNA was eluted twice with 15 µl molecular-grade water. Approximately 10 ng of RNA was set apart to make an input library. The remaining RNA was biotinylated in the dark with EZ-Link HPDP-Biotin for 3 h at room temperature. The RNA was purified with RNA Clean & Concentrator-5 and eluted twice with 20 µl molecular-grade water. Biotinylated RNA was separated from non-labelled RNA with M270 streptavidin magnetic beads following the manufacturer’s instructions. The biotinylated RNA was stripped off the beads twice with 100 µl 100 mM 2-mercaptoethanol (pre-heated to 80ºC) and purified with RNA Clean & Concentrator-5.
RNA-Seq: Indexed paired-end libraries were made from ~1 µg total RNA by following the low sample protocol of the TruSeq RNA sample preparation guide v2 with a few modifications. First, cDNA after second strand synthesis was quantified using a fluorometer and high-sensitivity reagents for double-stranded DNA (10 pg/µl to 100 ng/µl). Second, the number of PCR cycles was adjusted to the detected yield of cDNA to avoid products of over-amplification such as chimera fragments: 7 (~20 ng), 8 (~10 ng), 9 (~5 ng), 12 (~1 ng).
4sU-Seq: Input and biotinylated RNA were converted to indexed paired-end libraries using the ScriptSeq v2 RNA-Seq preparation kit (Epicentre). We used the manufacturer’s instructions (protocol rev. C, 8/2014) starting with appendix 4.1.A (annealing cDNA synthesis primer) and 4.1.B (cDNA synthesis) followed by main protocol section 3.C (synthesis of 3’-tagged DNA). The DNA libraries were purified using 1.8x Agencourt AMPure XP beads and amplified with 11 (input) and 15 (streptavidin pull-down) PCR cycles according to section 3.D to 3.F. The DNA from the PCR reaction was purified using 1x AMPure XP beads and eluted in 10 µl molecular-grade water.
Illumina libraries were sequenced paired-end on the HiSeq 2500 (4sU-Seq) and HiSeq 4000 (RNA-Seq).
RNA-Seq: Indexed paired-end libraries were made from ~1 µg total RNA by following the low sample protocol of the TruSeq RNA sample preparation guide v2 with a few modifications. First, cDNA after second strand synthesis was quantified using a fluorometer

treatment_protocol: Injections were carried out into the zygote's animal pole: β-catenin MO (5 ng); 4x zT-box MOs (5 ng, zVegT MO, 5 ng Eomes MO, 2.5 ng Xbra.1 MO, 2.5 ng Xbra.2 MO, 2.5 ng Xbra3.1 MO and 2.5 Xbra3.2 MO); and standard control MO (5 or 20 ng according to dose used for the loss-of-function experiment). Embryos were treated with antagonists of Nodal and/or BMP signaling at the following concentrations in 5% MMR: 100 µM SB431542 and/or 10 µM LDN19318 from the 8-cell stage onwards. Control embryos were treated accordingly with DMSO, the solvent of these antagonists.

value: wild type (out-bred Nigerian)

value: 12+ (late gastrula)

value: injection of control MO


title: cMO_st12p_polyA-RNA_rep3

status: Public on May 14 2019

type: SRA

country: United Kingdom

library_source: transcriptomic

molecule: polyA RNA

tag: strain

tag: developmental stage

tag: treatment


title: KO_naive_rep1

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

data_processing:
Around 20 million reads were generated for each replicate and aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in at least two libraries.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the voom function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.05 or less and also had at least 8 RPKMs (reads per kilo exonic bases per million mapped reads) in one or both of the two cell types being compared.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-RPKM values for each gene in each library.

molecule: total RNA

organism: Mus musculus

extract_protocol:
Total RNA was prepared from purified CD8 T cell populations using an RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain background

tag: genotype/variation

value: Tcf7 Knockout

tag: tissue

value: spleen

tag: cell type

value: CD8 T cell

tag: cell subset

value: Naïve


title: KO_mem_rep2

value: Memory


title: cMO_st12p_polyA-RNA_rep2


title: cMO_st12p_polyA-RNA_rep1


title: KO_mem_rep1


title: cMO_st11p_polyA-RNA_rep4

description: standard control morphant, stage 11+ (mid-gastrula), experiment 7

value: 11+ (mid-gastrula)


title: wt_or_n2_starved_rna2

city: St. Louis, USA

first: Abhinav

last: Diwan

address: 660 S. Euclid Ave, CSRB-NTA 827a

country: USA

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultipler written in python
Fastq files were aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl WBcel235.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text format

organism: Caenorhabditis elegans

growth_protocol: All C. elegans strains were maintained at 20°C on nematode growth media (NGM) dishes seeded with the E. coli strain, OP50.

extract_protocol:
Worms were collected in Eppendorf tubes and washed three times in M9.  We added 400µL of TRIzol (Thermoscientific, 15596026) to the worm pellet (containing ~50,000 worms/sample), and the tube was frozen immediately in liquid nitrogen and stored at -80°C.  Following three cycles of freeze-thaw, 200µL of TRIzol was added with incubation at room temperature for five minutes. Thereafter, 140µL of chloroform (Sigma, 319988) was added, the samples were shaken by hand to mix for 60 seconds and incubated at room temperature for two minutes; followed by centrifugation at 12,000 X g for 15 minutes at 4°C.  The aqueous phase and an equal volume of 70% ethanol were added to a fresh 1.7mL tube.  Nucleic acids were isolated with the RNeasy Mini Kit (Qiagen, 74104) following manufacturer’s instructions.
Illumina TruSeq

treatment_protocol: Gravid adults were bleached with alkaline hypochlorite to kill all contaminants and all worms not protected by the egg-shell, then washed and placed in M9 to starve L1 worms. Starved L1 worms were refed with C. elegans maintenance medium (CeMM) for 3 and 15 hours respectively. The transcriptional profiles of these three groups were compared with fed L1 stage worms.

value: wt

tag: protocol

value: starved


title: high density, replicate 5

type: RNA

city: BARCELONA

first: Alejandro

last: Valdivieso

state: BARCELONA

address: PASSEIG MARÍTIM DE LA BARCELONETA, 37-49

country: Spain

institute: Insituto de Ciencias del Mar

description:
7G4x_1_1
Gene expression in zebrafish ovary exposed at high density at 90 dpf.

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized to the array in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wash buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100% PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

organism: Danio rerio

source_name: Ovary, high density

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: At 6 days post fertilization (dpf), fish were placed in 2.8-liter.

extract_protocol: At 90 dpf, fish were sacrificed and gonads were dissected and flash frozen. RNA was extracted by Trizol (Sigma).

treatment_protocol: The high density effects were studied during gonadal development (6–90 dpf).

tag: strain/background

value: AB

tag: gender

value: Female

tag: age

value: 90 dpf

value: Ovary

tag: condition

value: High density


title: wt_or_n2_starved_rna1


title: Jurkat High tagBFP, biological rep3

city: Tel-Aviv

first: Michael

last: Milyavsky

state: Tel Aviv

address: Klatskin St 35

department: Pathology, Sackler School of Medicine

country: Israel

institute: Tel Aviv University

description: Gene expression data from high tagBFP Jurkat cells

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Homo sapiens

source_name: Flow sorted Jurkat High tagBFP cells

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

growth_protocol: Jurkat are grown in RPMI supplemented with FBS (10%), L-Glu (1%) and P/S (1%) in 5% CO2 and 37° temperature

extract_protocol: RNA was extracted with the Trizol reagent (Invitrogen) and reverse transcribed with SuperScript III (Invitrogen),RNA from 100,000 or more sorted cells was used for microarray analysis by Human Gene Clariom S Assay (Thermo Fisher Scientific)

treatment_protocol: Viral particles were generated by transient transfection of 293T cells using CMVDeltaR8.91 and pMD2G constructs as described elsewhere (Milyavsky et al. 2010). Jurkat leukemia cells were infected by addition of viral supernatant to obtain 10-30% infection rate. Jurkat cells were sorted using BD FACSAria™ Fusion sorter (BD Biosciences)

tag: cell line

value: Jurkat T-ALL

value: 14 year old boy


title: Jurkat Low tagBFP, biological rep2

description: Gene expression data from low tagBFP Jurkat cells

source_name: Flow sorted Jurkat Low tagBFP cells


title: high density, replicate 6

description:
8G4x_1_2
Gene expression in zebrafish ovary exposed at high density at 90 dpf.


title: Jurkat Low tagBFP, biological rep1


title: control, replicate 5

description:
6G0.5x_1_4
Gene expression in control zebrafish ovary at 90 dpf.

source_name: Ovary, control

value: Control


title: high density, replicate 4

description:
5G4x_1_4
Gene expression in zebrafish ovary exposed at high density at 90 dpf.


title: KO_eff_rep1

value: Effector


title: high density, replicate 2

description:
2G4x_1_2
Gene expression in zebrafish ovary exposed at high density at 90 dpf.


title: cMO_st11p_polyA-RNA_rep3

value: wild type (out-bred Nigerian)

value: injection of control MO


title: Test_1: SP_shade grown_replicate 1

city: Bhubaneswar

first: Madhusmita

last: Panigrahy

state: Orissa

address: Siksha O Anusandhan University

country: India

institute: Government

description: Gene expression in panicle spikelets after shade grown condition

hyb_protocol: 1650ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to Agilent designed Rice Gene expression Microarray 4x44K (AMADID No: 064815) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the percentile shift method.

organism: Oryza sativa

source_name: Swarnaprabha_Test_rep 1

label_protocol: The samples for gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasyMini kit columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Seedlings of 15-days old Swarnaprabha rice line (obtained from National Rice Research Institute, Cuttack, India) were transferred to pooled pots and grown for 1 months, after which they were transferred to single plant per pot.  Plants were grown in 12 inch pots containing 8L soil from rice fields. The study was done during Apr 2017- Oct 2017 (season 1) and Oct 2017 to Apr 2018 (season 2). The geographic location of NISER is at an altitude of 38 meters above the sea level with latitude/longitude: 20°09′35″N85°42′26″E.The temperature, humidity (RH) and rainfall (RF) as recorded by The Metrological Department situated at Jatni station was average 43°C max, 34°C min, 82.7% RH, 177.2 mm RF respectively in the season 1and that in season 2 was average 41°C max, 30°C min, 71.5% RH, 23 mm RF respectively.

extract_protocol: Panicles on the final day of energence were sampled in the same light condition, spikeletes were separated from rachis and frozen in liquid nitrogen immediately

treatment_protocol: Plants were kept in sun or under continuous shade 55 days after sowing . Shade was obtained by covering the net house with 75% quantified cutoff agro net

value: panicle spikelets


title: Jurkat Low tagBFP, biological rep3


title: wt_or_n2_fed_rna2

description: control

value: fed


title: cMO_st11p_polyA-RNA_rep2


title: Jurkat High tagBFP, biological rep1


title: Jurkat High tagBFP, biological rep2


title: control, replicate 3

description:
3G0.5x_1_4
Gene expression in control zebrafish ovary at 90 dpf.


title: control, replicate 1

description:
1G0.5x_1_3
Gene expression in control zebrafish ovary at 90 dpf.


title: control, replicate 6

description:
7G0.5x_1_3
Gene expression in control zebrafish ovary at 90 dpf.


title: high density, replicate 1

description:
1G4x_1_1
Gene expression in zebrafish ovary exposed at high density at 90 dpf.


title: control, replicate 2

description:
2G0.5x_1_1
Gene expression in control zebrafish ovary at 90 dpf.


title: control, replicate 4

description:
5G0.5x_1_2
Gene expression in control zebrafish ovary at 90 dpf.


title: KO_CD25_rep2

value: Tcf7 Knockout

value: spleen

value: CD8 T cell


title: high density, replicate 3

description:
3G4x_1_3
Gene expression in zebrafish ovary exposed at high density at 90 dpf.


title: Test_2: SP_shade grown_replicate 2

source_name: Swarnaprabha_Test_rep 2


title: Control_2: SP_Normal day night grown_replicate 2

description: Gene expression in panicle spikelets after normal day night grown condition

source_name: Swarnaprabha_control_rep 2


title: Control_1: SP_Normal day night grown_replicate 1

source_name: Swarnaprabha_control_rep 1


title: KO_CD25_rep1


title: wt_or_n2_cemm_3h_rna2

value: wt

value: refed with C. elegans maintenance medium (CeMM) 3hr


title: wt_or_n2_fed_rna1

description: control


title: cMO_st11p_polyA-RNA_rep1

description: standard control morphant, stage 11+ (mid-gastrula), experiment 7

value: 11+ (mid-gastrula)


title: Sample_11_BY-B_1_gal

city: Amsterdam

first: Tineke

last: Lenstra

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

description: BY4741 replicate B

library_source: genomic

data_processing:
Basecalling with RTA 2.4.11 Illuminate instrument run time analysis software
Barcode demultiplexing with Bcl2fastq 2.17 allowing 1 mismatch
Adapter and quality trimming with Trimmomatic 0.30: PE -threads 16 -phred33 –trimlog sample.log read1.fastq.gz (read2.fastq.gz) read1_trimmed.fastq.gz (read2_trimmed.fastq.gz) ILLUMINACLIP:adapters.fa:2:36:10 LEADING:10 TRAILING:10 MAXINFO:50:0.97 MINLEN:50 CROP:50
Alignment with Bowtie2 2.1.0: Bowtie2 -p 8 -x reference -1 read1.fq -2 read2.fq
Duplication statistics with Picard 1.84: MarkDuplicates.jar INPUT=sample.bam OUTPUT=sample.MKDUP.bam METRICS_FILE=sample.bam.metric ASSUME_SORTED=true MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 VALIDATION_STRINGENCY=LENIENT
Center and smooth reads: samtools view -h reads.bam | center+smooth.pl --type paired --smooth 31 --minlen 95 --maxlen 225 | samtools sort -@16 -T tmp -O BAM > centered_reads.bam
Genome_build: S288C_reference_genome_R64-2-1_20150113
Supplementary_files_format_and_content: Bam file containing centered reads of nucleosome midpoints, smoothed with a 31bp running average

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae BY4741

growth_protocol: SC + 2% raffinose or SC + 2% galactose

extract_protocol:
spheroplasting of yeast cells with zymolyase, MNase digestion, phenol/chlorofom extraction, RNaseA treatment
TrueSeq v4.0 chemistry paired end sequencing

treatment_protocol: growth to midlog from OD 0.3 to OD1

value: galactose mid-log

tag: mnase digestion


title: wt_or_n2_cemm_3h_rna1


title: cMO_st10p_polyA-RNA_rep3

description: standard control morphant, stage 10+ (early gastrula), experiment 7

value: 10+ (early gastrula)


title: wt_or_n2_cemm_15h_rna2

value: refed with C. elegans maintenance medium (CeMM) 15hr


title: cMO_st10p_polyA-RNA_rep2


title: Sample_12_BY-B_3_gal

description: BY4741 replicate B


title: Sample_4_BY-B_3_raf

description: BY4741 replicate B

value: raffinose mid-log


title: Sample_9_BY-A_1_gal

description: BY4741 replicate A


title: cMO_st10p_polyA-RNA_rep1


title: MB09 RT3; Kidney LG Pool 1

city: Madrid

first: Alicia

last: Gibello

state: Madrid

address: Facultad de Veterinaria, Avda. Puerta de Hierro s/n

department: Animal Health

institute: Universidad Complutense de Madrid (UCM)

hyb_protocol: 1.5 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 60K Microarray (028004) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565C) using one color (Cy3) scan setting for expression array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Salmo trutta

source_name: Kidney

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the TRI Reagent® Protocol (Sigma), following the manufacturer's recommendations

value: Kidney

value: L. garvieae-infected


title: MB10 RT3; Kidney LG Pool 2


title: mutant_starved_rna2

value: mutant

value: starved


title: Sample_10_BY-A_3_gal

description: BY4741 replicate A


title: 4x-zT-LOF_st12p_polyA-RNA_rep4

description: 4x zT-box (zVegT, Eomes, Xbra + Xbra3) loss-of-function, stage 12+ (late gastrula), experiment 7

value: wild type (out-bred Nigerian)

value: 12+ (late gastrula)

value: injection of 4x zT-box MOs


title: MB11 RT3; Kidney LG Pool 3


title: 4x-zT-LOF_st12p_polyA-RNA_rep3


title: mutant_starved_rna1


title: MB08 RT3; Kidney Control Pool 2

value: control


title: Sample_3_BY-B_1_raf

description: BY4741 replicate B


title: cMO_st10p_polyA-RNA_rep4

value: injection of control MO


title: mutant_fed_rna2

value: fed


title: 4x-zT-LOF_st12p_polyA-RNA_rep2


title: MB08 RT2; Kidney Control Pool 2


title: mutant_fed_rna1


title: wt_or_n2_cemm_15h_rna1

value: wt


title: MB10 RT2; Kidney LG Pool 2


title: MB09 RT2; Kidney LG Pool 1


title: 4x-zT-LOF_st12p_polyA-RNA_rep1


title: Sample_2_BY-A_3_raf

description: BY4741 replicate A


title: Sample_1_BY-A_1_raf

description: BY4741 replicate A


title: MB11 RT2; Kidney LG Pool 3


title: mutant_cemm_3h_rna2

value: refed with C. elegans maintenance medium (CeMM) 3hr


title: mutant_cemm_3h_rna1


title: 4x-zT-LOF_st11p_polyA-RNA_rep4

description: 4x zT-box (zVegT, Eomes, Xbra + Xbra3) loss-of-function, stage 11+ (mid-gastrula), experiment 7

value: 11+ (mid-gastrula)


title: prp40c mutant rep 2

city: Buenos Aires

first: Mariano

last: Garcia-Hourquet

address: Av Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

description:
H.40c
RNA was extracted from whole seedlings
prp40c_vs_wt_counts.tab
prp40c_vs_wt_as_discovery.tab

data_processing:
Base-calling by default setting of Illumina HiSeq 1500
Aligment to to Arabidopsis thaliana TAIR10 genome using TopHat v2.1.1
Generation of BAM files with SAMtools V1.3
Data analysis with ASpli R-package 1.6.0
genome build: Arabidopsis thaliana TAIR10
processed data files format and content: All processed data files are .txt count tables containing the number of raw counts in each sample for all the sequenced gene trasncripts of Arabidopsis thaliana genome. Those extra data columns are outputs of ASspli package (http://www.bioconductor.org/packages/release/bioc/html/ASpli.html) and contain data of the reads mapped to exon-intron junctions. For further reference, you can check ASpli reference manual.

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Seeds were sown onto Murashige and Skoog medium containing 0.8% agarose, stratified for 4 d in the dark at 4°C, and then grown at 22°C in continuous light (50 μmol·m−2·s−1 of white light). Whole plants were harvested after 10-14 days.

extract_protocol:
In the transcriptional profiling assay total RNA was extracted with RNeasy Plant Mini Kit (Qiagen) following the manufacturer’s protocols.
Libraries were prepared following the TruSeq RNA Sample Preparation Guide (Illumina). Briefly, 3 μg of total RNA was polyA-purified and fragmented, first-strand cDNA synthesized by reverse transcriptase (SuperScript III; Invitrogen) using random hexamers. This was followed by RNA degradation and second-strand cDNA synthesis. End repair process and addition of a single A nucleotide to the 3′ ends allowed ligation of multiple indexing adapters. Then, an enrichment step of 12 cycles of PCR was performed. Library validation included size and purity assessment with the Agilent 2100 Bioanalyzer and the Agilent DNA1000 kit (Agilent Technologies). Samples were pooled to create 12 multiplexed DNA libraries, which were pair-end sequenced with an Illumina HiSeq1500.

value: 2 weeks old seedlings

tag: genotype

tag: ecotype

tag: growth conditions

value: Continuous white light 22degreeC


title: 4x-zT-LOF_st11p_polyA-RNA_rep3

tag: strain

tag: developmental stage


title: mutant_cemm_15h_rna2

value: refed with C. elegans maintenance medium (CeMM) 15hr


title: prp40c mutant rep 3

description:
I.40c
RNA was extracted from whole seedlings
prp40c_vs_wt_counts.tab
prp40c_vs_wt_as_discovery.tab


title: MB11 RT1; Kidney LG Pool 3

tag: treatment


title: mutant_cemm_15h_rna1

tag: genotype/variation


title: prp40c mutant rep 1

description:
G.40c
RNA was extracted from whole seedlings
prp40c_vs_wt_counts.tab
prp40c_vs_wt_as_discovery.tab


title: 4x-zT-LOF_st11p_polyA-RNA_rep1


title: MB07 RT2; Kidney Control Pool 1

tag: tissue


title: MB06 RT3; Spleen LG Pool 3

source_name: Spleen

value: Spleen


title: wt Col-0 rep 3

description:
C.Col
RNA was extracted from whole seedlings
prp40c_vs_wt_counts.tab
prp40c_vs_wt_as_discovery.tab


title: MB05 RT3; Spleen LG Pool 2


title: MB04 RT3; Spleen LG Pool 1


title: wt Col-0 rep 2

description:
B.Col
RNA was extracted from whole seedlings
prp40c_vs_wt_counts.tab
prp40c_vs_wt_as_discovery.tab


title: 4x-zT-LOF_st10p_polyA-RNA_rep4

description: 4x zT-box (zVegT, Eomes, Xbra + Xbra3) loss-of-function, stage 10+ (early gastrula), experiment 7

value: 10+ (early gastrula)


title: 4x-zT-LOF_st10p_polyA-RNA_rep3


title: SG3MHT

city: Norwich

first: Tracey

last: Chapman

address: Norwich Research Park

department: School of Biological Sciences

institute: University of East Anglia

description:
mRNA-seq
The Toliman wild type strain was sourced from the Guatemalan Mass rearing facility and was raised under laboratory conditions since 1990 (as detailed in Nash & Chapman 2014).

data_processing:
Reads were filtered and only those which did not contain Ns were included in further analysis (over 99% of total number of reads for each sample).
Reads mapped to the C. capitata genome (v1.0) using PatMan (Prueffer et al. 2008), full length, one mismatch allowed.
For comparison purposes, the reads in every sample were resampled to a fixed total (the method is called subsampling normalization).
The expression levels were obtained as indicated in Mortazavi et al. 2008.
The differential expression was determined using confidence intervals on replicates. The DE amplitude was calculated using offset fold change, with offset=20.
Genome_build: C. capitata v1.0 (Ccap_v1.0)
Supplementary_files_format_and_content: *csv: Comma-separated text files include RefSeq accession numbers and gene expression levels.

organism: Ceratitis capitata

source_name: Head-thorax, male, S food

growth_protocol: Fly eggs were taken from the 60th generation of a selection experiment, which used different larval diets to create divergent selection between replicated populations of C. capitata. These eggs were reared on a glucose-based common garden diet until third instar larvae were visible. At this point the food bottles were laid onto sand, and the emerging larvae allowed to pupate in the sand. Pupae were sieved from the sand and isolated in daily cohorts. Adults emerging from these pupae were sexed upon eclosion to ensure virginity, and placed in single sex cages at low density (40 individuals per 11x11x10cm cage). Adult flies were given access to dry food (3:1 Sugar: Yeast Hydrolysate) and water ad libitum.

extract_protocol:
Total RNA was extracted from 7 day post eclosion male C. capitata in pools of between 17-22 individuals. Total RNA was extracted using the mirVana miRNA isolation kit protocol.
Libraries were constructed by BaseClear (Netherlands).

treatment_protocol: The treatment which was used to create divergent selection between the replicated populations of C. capitata was based on two larval diets. The first, 'ASG' (A), was sucrose based, and provided ~684kcal/L. The second, 'Starch' (S), was based on starch as a primary carbohydrate source, and provided ~291kcal/L. Eggs from a wildtype base population were divided between the two diets, creating 3 replicate populations to be reared on each diet.

value: Toliman

value: Wild-type

value: Head-thorax

tag: Sex

value: Male

tag: larval diet

value: starch-based (Starch 'S')

value: Adult, 7 days post eclosion


title: SG3MAb

source_name: Abdomen, male, S food

value: Abdomen


title: MB02 RT3; Spleen control Pool 2

value: control


title: SG2MHT


title: 4x-zT-LOF_st10p_polyA-RNA_rep2

value: wild type (out-bred Nigerian)

value: injection of 4x zT-box MOs


title: 4x-zT-LOF_st11p_polyA-RNA_rep2


title: zr1699_4 mutant1 Treated

city: Valencia

first: Pablo

last: Vera

state: Valencia

address: Ingeniero Fausto Elío s/n

institute: Instituto de Biología Molecular y Celular de Plantas (IBMCP); Consejo Superior de Investigaciones Científicas (CSIC)

description: Data from two sequencing run (s1 and s2) for methylation analysis

data_processing:
Sequence reads from bisulfite-treated EpiQuest libraries were identified using standard Illumina base-calling software.
Then were analyzed using a Zymo Research proprietary analysis pipeline written in Python and using Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) as the alignment software for analysis.
Index files were constructed by bismark_genome_preparation command using the entire reference genome. The non_directional parameter was applied while running Bismark. All other parameters were set to default.
The methylation level of each sampled cytosine (methylation ratio) was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. Each analyzed cystosine had a minimum coverage of five aligned sequence reads.
Promoter, gene body and CpG island annotations were added where available.
Genome_build: TAIR10
Supplementary_files_format_and_content: Gzipped tab-separated text files with the following analyzed information for the included Arabidopsis thaliana genome positions: DNA strand, methylated reads count, total reads count, corresponding promoter, and corresponding gene. Three text files corresponding for the three different methylation contexts (CHG, CHH and CpG) are available for each sample.

source_name: 4-weeks-old plant leaves

growth_protocol: Arabidopsis thaliana plants were grown in jiffys in growth chambers (19-22ºC, 10000 luxes fluorescent illumination) on a 10h-light and 14h-dark cycle for a month. Seeds were previously stratified for 3 days. Each biological replicate for each condition were 4 plants.

extract_protocol:
DNA was extracted from 100 mg of leaves powder from 3 biological replicates using CTAB extraction protocol. We applied 500 µl CTAB and 2 µl/ml β-mercaptoethanol, and samples were incubated 1h at 60 ºC. Phases separation was done with 1 vol. of chloroform isoamyl (24:1; v:v) and for the precipitation was applied 1 vol. of isopropyl. DNA was resuspended in H2O DEPC. LiCl 2M was used for a first step of DNA purification, to remove RNA. DNA was precipitated with 0.1 vol. of AcNa 3M and 2 vol. of etanol, and resuspended in H2O DEPC. 1 μg of DNA of each sample was resuspended in 50 μl of TE buffer to send them to Zymo Research (Irvine, CA) for the next steps in DNA methylation analysis (library construction protocol, sequencing run, data processing and data analysis). There, samples were treated with RNAse (RNA removal) followed by clean-up using their genomic DNA Clean & Concentrator kit (Cat. No. D4010). Then, DNA from each sample was quantified and applied a QC check using the Qubit instrument according to the manufacturer’s guidelines (Qubit 3.0 Fluorometer; Life Technologies – Carlsbad, CA, USA).
Methyl-MaxiSeq® libraries were prepared from 80 ng of genomic DNA digested with 2 units of Zymo Research’s (ZR) dsDNA Shearase™ Plus (Cat#: E2018-50). The fragments produced were end-blunted and 3’-terminal-A extended, then purified using the Zymo Research (ZR) DNA Clean & Concentrator™ – 5 kit (Cat#: D4003). The A-tailed fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine and adapter-ligated fragments were filled-in. Bisulfite treatment of the fragments was carried out using the EZ DNA Methylation – Lightning kit (ZR, Cat#: D5030). PCR was performed with Illumina TruSeq indices and the size and concentration of the fragments (library insert size) were confirmed using the D1000 screen tape on the Agilent 2200 TapeStation (according to manufacturer’s instructions (Santa Clara, CA, USA)), then sequenced on an Illumina HiSeq instrument.

value: Pseudomonas syringae DC3000 infiltrated (OD:2x10^-4)

value: leaves

value: 4 weeks


title: SG2MAb


title: SG1MHT


title: Nodal-BMP-LOF_st9p_polyA-RNA_rep3

description: Nodal/BMP loss-of-function, stage 9+ (late blastula), experiment 4

value: 9+ (late blastula)

value: treatment with SB431542 and LDN193191


title: SG1MAb


title: zr1699_3 mutant1 Control

description: Data from one sequencing run (s1) for methylation analysis

value: Mock (10mM MgSO4) infiltrated


title: zr1699_6 mutant2 Treated


title: zr1699_2 Col-0 Treated

value: wild type


title: 4x-zT-LOF_st10p_polyA-RNA_rep1

value: 10+ (early gastrula)


title: wt Col-0 rep 1

description:
A.Col
RNA was extracted from whole seedlings
prp40c_vs_wt_counts.tab
prp40c_vs_wt_as_discovery.tab

value: 2 weeks old seedlings

value: wt

value: Continuous white light 22degreeC


title: AG3MHT

source_name: Head-thorax, male, A food

value: Toliman

value: Wild-type

value: Head-thorax

value: Male

value: sucrose-based (ASG 'A')


title: zr1699_1 Col-0 Control


title: MB03 RT3; Spleen control Pool 3

value: Spleen

value: control


title: MB09 RT1; Kidney LG Pool 1

value: Kidney

value: L. garvieae-infected


title: AG2MHT

value: Adult, 7 days post eclosion


title: Nodal-BMP-LOF_st9p_polyA-RNA_rep1

source_name: whole embryo

value: wild type (out-bred Nigerian)

value: 9+ (late blastula)

value: treatment with SB431542 and LDN193189


title: Nodal-BMP-LOF_st9p_polyA-RNA_rep2

value: treatment with SB431542 and LDN193190


title: MB10 RT1; Kidney LG Pool 2


title: BMP-LOF_st9p_polyA-RNA_rep3

description: BMP loss-of-function, stage 9+ (late blastula), experiment 4

value: treatment with LDN193189 (BMP inhibition)


title: BMP-LOF_st9p_polyA-RNA_rep2


title: AG2MAb

source_name: Abdomen, male, A food

value: Abdomen


title: AG1MHT


title: AG1MAb


title: BMP-LOF_st9p_polyA-RNA_rep1


title: AG3MAb


title: Nodal-LOF_st9p_polyA-RNA_rep3

description: Nodal loss-of-function, stage 9+ (late blastula), experiment 4

value: treatment with SB431542 (Nodal inhibition)


title: MB01 RT3; Spleen control Pool 1


title: Sample 34_sampleS2

city: Moscow

first: Philipp

last: Khaitovich

address: Nobelya Ulitsa 3

country: Russia

institute: Skolkovo Institute of Science and Technology

data_processing:
The snail neuronal transcriptome was assembled from the measured RNA-Seq dataset by SOAPdenovo-Trans (version 1.04) using the recommended parameters, after the adapter sequence removal by cutadapt (version 1.11)
Raw reads were mapped to the transcriptome assembly using bowtie (version 1.0.0) with the specifically chosen parameters by RSEM (version 1.2.18).
We took advantage of the effective handling of ambiguously-mapping reads and the absence of reference genome implemented in RSEM to locate the expression abundance (raw count) at the contig level.
In each experiment, only contigs with total counts across all 12 samples greater than 10 were determined as expressed and used in the following analyses.
We then normalized the abundance data using trimmed mean of M-values normalization method (TMM) provided by the Bioconductor package “edgeR” in R
Genome_build: assembled snail neuronal transcriptome
Supplementary_files_format_and_content: fasta file includes the assembled snail neuronal transcriptome; tab-delimited text files include raw counts for the two experiments.

organism: Helix lucorum

source_name: control_parietal ganglia

growth_protocol: The snails were kept in a wet environment and fed their usual diet of pieces of lettuce. Prior to the experiment, the snails were kept in the active state for at least two weeks.

extract_protocol:
Cellular RNAs were prepared from samples using the guanidine thiocyanate method. 500 ng of total RNA of each sample was depleted with rRNA Removal Mix (Ribo-Zero Human/Mouse/Rat) kit
cDNA preparations from RNA samples were performed using TruSeq® Stranded Total RNA Sample Preparation kit (Illumina) following the supplier’s instruction.

treatment_protocol: Animals were cooled to 4 °C and injected with isotonic MgCl2 before the CNS isolation to minimize pain. The central ganglia complex was surgically isolated from anesthetized snails, pinned to a silicone-elastomer (Sylgard)-coated dish, and kept in high-Ca2+, high-Mg2+ Ringer saline (80 мМ NaCl, 4 мМ KCl, 28 мМ СаСl2, 25 мМ MgCl2, 10 мМ Trisma, pH 7.6) to suppress electrical activity of the nervous system. The central ganglia complex was stripped of connective tissue sheath using a ﬁne forceps and scissors, ensuring the integrity of the thin layer adherent to the neurons, kept at 4 °C for 24 (± 1) hours, and then kept at room temperature for one hour. Part of CNS which was used as a self-control was cut out, transferred to the dry-ice cooled plastic tube, and frozen at -80 °C. The remaining part was washed with 50 ml of normal Ringer saline (80 мМ NaCl, 4 мМ KCl, 8 мМ СаСl2, 5 мМ MgCl2, 10 мМ Trisma, pH 7.6) containing 20 µM of anisomycin, and kept in this solution for ten minutes, then was washed with 50 ml of normal Ringer saline containing 20 µM of anisomycin, 100 µM caffeine and 5 µM 5-HT, and kept in this solution for 20-25 minutes. Part of activated CNS symmetrical to the control part was cut out, transferred to the dry-ice cooled plastic tube, and frozen at -80 °C.

tag: individual

tag: hemisphere

value: whole

tag: tissue subtype

value: parietal ganglia


title: Sample 35_sampleS3


title: Sample 33_sampleS1


title: Sample 32_sampleK4


title: K1-CDA-ER 4sU-RNA-seq rep2

city: Woolloongabba

first: Melissa

middle: D

last: Ilsley

state: Queensland

address: 36 Kent street

institute: Mater Research

description:
KLF1-E339K-ER_LimmaVoom.txt
KLF1-ER_LimmaVoom.txt

data_processing:
ChIP-Seq
Base calling was performed with Torrent Suite v4.0.1.
TMAP (v3.0.1) with the following options: mapall, -v, -Y, -u, -o 2, stage1, map4 was used to map reads to the reference genome (mm9; ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm9/Mus_musculus_UCSC_mm9.tar.gz)
Fragments mapping to the same position on the same strand were taken to be PCR duplicates and were subsequently discarded, retaining only unique alignments with the highest MAPQ score.
ChIP-seq peaks were called with MACS and GEM using uniquely mapped ChIP and input sequence alignments.
DiffBind to analyze to examine differential enrichment between peaksets.
RNA-Seq
Base calling was performed with Torrent Suite v4.0.1.
Tophat2 (v2.0.10) was used to perform spliced alignment to the reference transcriptome and genome (mm9; ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm9/Mus_musculus_UCSC_mm9.tar.gz) using default options with the following additional parameters: -N 4, --read-gap-length 4, --read-edit-dist 4, --read-realign-edit-dist 0, -a 5, -i 50, -g 6, --coverage-search, --microexon-search, --library-type fr-firststrand.
Unaligned sequences were subsequently remapped using TMAP (v3.0.1) with the following options: mapall, -v, -Y, -u, -o 2, stage1, map4.
Successful alignments were merged back into the Tophat2 SAM file.
Alignments low mapping quality (<30) were discarded.
Significantly differentially regulated genes (DEGs) were determined using the R package: Limma-Voom
Genome_build: mm9
Supplementary_files_format_and_content: ChIP: Merged_Peakset.txt: Tab-delimited annotated merged peaks file.
Supplementary_files_format_and_content: RNA: KLF1-E339K-ER_LimmaVoom.txt, KLF1-ER_LimmaVoom.txt: Tab-delimited differential gene expression analysis.

source_name: K1-CDA-ER (CLONE 2A)

growth_protocol: Erythroid cell lines were passaged (1:5) every 2-3 days in DMEM supplemented with 10% FBS, 1% Glutamine & 1% Penicillin-Streptomycin in a standard tissue culture incubator at 37 °C with 5% CO6

extract_protocol:
Total RNA was extracted using TRIzol® Reagent (Life Technologies, #15596026) according to the manufacturer’s instructions with manually dissociated cells washed in 1 ml DPBS (Gibco™, #14190-136). Extracted RNA was subsequently treated with DNase I (New England Biolabs, #M0303L) to remove residual gDNA contamination. Isolation of 4sU-RNA was performed essentially as previously described (Rabani et al. Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol 2011) with minor modifications. Purified RNA was biotinylated with EZ-Link Biotin-HPDP (Pierce; #21341) and isolated using µMacs Streptavidin Kit (Miltenyi; #130-074-101). 4sU-enriched RNA was then purified with RNeasy MinElute Spin Columns (Qiagen; #74204).
Purified 4sU-labelled RNA was used with the Ion Total RNA-Seq Kit v2 (Life Technologies; #4479789) to prepare libraries for sequencing on the Ion Proton™ System.

treatment_protocol: Cells were induced through the addition of (Z)-4-Hydroxytamoxifen at a final concentration of 200 nM and newly transcribed RNA labeled with 500 μM 4sU for 30 minutes.

tag: cell type

value: KLF1 null immortalised erythroid cell line with inducible CDA-KLF1 (E339K) transgene.

tag: transgene

value: induced with tamoxifen


title: K1-CDA-ER 4sU-RNA-seq rep3

source_name: K1-CDA-ER (CLONE 2B)

growth_protocol: Erythroid cell lines were passaged (1:5) every 2-3 days in DMEM supplemented with 10% FBS, 1% Glutamine & 1% Penicillin-Streptomycin in a standard tissue culture incubator at 37 °C with 5% CO7


title: K1 4sU-RNA-seq rep1

source_name: K1:  KLF1 null erythroid cell line

growth_protocol: Erythroid cell lines were passaged (1:5) every 2-3 days in DMEM supplemented with 10% FBS, 1% Glutamine & 1% Penicillin-Streptomycin in a standard tissue culture incubator at 37 °C with 5% CO2

value: KLF1 null immortalised erythroid cell line

value: treated with tamoxifen


title: CDA-KLF1 input DNA

growth_protocol: Erythroid cell lines were passaged (1:5) every 2-3 days in DMEM supplemented with 10% FBS, 1% Glutamine & 1% Penicillin-Streptomycin in a standard tissue culture incubator at 37 °C with 5% CO3

extract_protocol:
ChIP was performed as described (Hodge et al. A global role for EKLF in definitive and primitive erythropoiesis. Blood 2006). Cell lines were induced with 4-OHT (or ethanol control) and incubated for 3 hours before fixation with 0.4% formaldehyde. Chromatin was fragmented to approximately 200-400bp by sonication (Diagenode Bioruptor® for 15 minutes cycling between 30 seconds ‘ON’ and 30 seconds ‘OFF’), pre-cleared and immunoprecipitated with protein G sepharose beads (GE Healthcare).
Sequencing libraries were generated from 3 pooled replicates using the Ion Xpress™ Plus gDNA Fragment Library Preparation Kit following the Ion ChIP-Seq Library Preparation protocol.

treatment_protocol: Cells were induced through the addition of (Z)-4-Hydroxytamoxifen at a final concentration of 200 nM for 3 h.


title: K1-CDA-ER 4sU-RNA-seq rep1

source_name: K1-CDA-ER (CLONE 1B)

growth_protocol: Erythroid cell lines were passaged (1:5) every 2-3 days in DMEM supplemented with 10% FBS, 1% Glutamine & 1% Penicillin-Streptomycin in a standard tissue culture incubator at 37 °C with 5% CO5


title: K1 4sU-RNA-seq rep3

growth_protocol: Erythroid cell lines were passaged (1:5) every 2-3 days in DMEM supplemented with 10% FBS, 1% Glutamine & 1% Penicillin-Streptomycin in a standard tissue culture incubator at 37 °C with 5% CO4

value: treated with ethanol (vehicle)


title: CDA-KLF1 ChIP-seq

tag: chip antibody

value: Mouse monoclonal Estrogen receptor Ab-10 (clone TE111.5D11)

tag: chip antibody reference

value: ThermoScientific cat. #MS-315-P


title: K1 4sU-RNA-seq rep2


title: KO_eff_rep2

tag: strain background

value: Tcf7 Knockout

value: spleen

value: CD8 T cell

tag: cell subset

value: Effector


title: MB02 RT2; Spleen control Pool 2

value: Spleen

value: control


title: MB03 RT2; Spleen control Pool 3


title: Sample 31_sampleK3

tag: condition


title: Sample 30_sampleK2


title: DMSO_st9p_polyA-RNA_rep3

description: control (uninjected, DMSO), stage 9+ (late blastula), experiment 4

tag: strain

value: wild type (out-bred Nigerian)

value: 9+ (late blastula)

value: treatment with DMSO


title: Wnt-Nodal-BMP-LOF_st9p_polyA-RNA_rep1

description: Wnt/Nodal/BMP loss-of-function, stage 9+ (late blastula), experiment 4

tag: developmental stage

value: injection of beta-catenin MO and treatment with SB431542 and LDN193189


title: Nodal-LOF_st9p_polyA-RNA_rep1

tag: treatment

value: treatment with SB431542 (Nodal inhibition)


title: DMSO_st9p_polyA-RNA_rep2


title: Wnt-Nodal-BMP-LOF_st9p_polyA-RNA_rep2

value: injection of beta-catenin MO and treatment with SB431542 and LDN193190


title: Nodal-LOF_st9p_polyA-RNA_rep2


title: MB04 RT2; Spleen LG Pool 1

value: L. garvieae-infected


title: CutRun-27-minus-IAA

city: Memphis

first: Chunliang

last: Li

state: TN

address: 262 Danny Thomas Place

institute: St.Jude Children's Research Hospital

data_processing:
Cut&Run ChiP-seq reads from each species were aligned using Bowtie2  2.3.4
bamCoverage (Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. DeepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016)) was used to convert apping .bam file to .bw file
Genome_build: hg19

source_name: B cell precursor leukemia

growth_protocol: SEM cells were maintained in RPMI-1640 containing 10% fetal bovine serum (FBS) (HyClone), 2 mM glutamine (Sigma), and 1% penicillin/streptomycin (Invitrogen). All cells were maintained at 37°C in a 5% CO2 atmosphere and 95% humidity.

extract_protocol:
Cut&Run ChiP-seq was performed according the the protocol in, Skene PJ, Henikoff S.  2017.  An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites on Elife. Antibodies against CTCF for a pulldown assay. CTCF antibody from (abcam, ab70303) was used for immunoprecipitation.
NEBNext Ultra II DNA Library Prep Kit from New England Biolabs (E7645S)
Cut&Run ChiP-seq

value: B cell precursor leukemia

value: SEM

tag: genotype/variation

value: Clone 27 minus IAA


title: MB03 RT1; Spleen control Pool 3

tag: tissue


title: MB02 RT1; Spleen control Pool 2


title: MB05 RT2; Spleen LG Pool 2


title: MB01 RT2; Spleen control Pool 1


title: MB06 RT1; Spleen LG Pool 3


title: input_st8p_4sU_total-RNA

description:
riboZero RNA input for 4-thiouracil tagging, stage 8+ (mid-blastula transition)
rzRNA_4sU_xt71_rawCounts.txt.gz

growth_protocol: Embryos were grown to the indicated developmental stage in 5% MMR at 25ºC.

value: 8+ (mid-blastula transition)


title: CutRun-27-plus48-IAA

value: Clone 27 plus IAA


title: MB06 RT2; Spleen LG Pool 3


title: MB08 RT1; Kidney Control Pool 2

value: Kidney


title: Sample 29_sampleK1

value: whole

value: parietal ganglia


title: MB07 RT1; Kidney Control Pool 1


title: MB01 RT1; Spleen control Pool 1

value: Spleen


title: input_st10p_4sU_total-RNA

description:
riboZero RNA input for 4-thiouracil tagging, stage 10+ (early gastrula)
rzRNA_4sU_xt71_rawCounts.txt.gz

value: 10+ (early gastrula)


title: 4sU_st10p_total-RNA

description:
4-thiouracil-enriched riboZero RNA, stage 10+ (early gastrula)
rzRNA_4sU_xt71_rawCounts.txt.gz

value: wild type (out-bred Nigerian)


title: MB04 RT1; Spleen LG Pool 1


title: CutRun-42-minus-IAA

value: Clone 42 minus IAA


title: MB05 RT1; Spleen LG Pool 2


title: Wnt-Nodal-BMP-LOF_st9p_polyA-RNA_rep3

value: 9+ (late blastula)

value: injection of beta-catenin MO and treatment with SB431542 and LDN193191


title: CutRun-42-plus48-IAA

value: Clone 42 plus IAA


title: Wnt-BMP-LOF_st9p_polyA-RNA_rep3

description: Wnt/BMP loss-of-function, stage 9+ (late blastula), experiment 4

value: injection of beta-catenin MO and treatment with LDN193191


title: Sample 27_sampleO3

value: control


title: CutRun-35-plus48-IAA

value: B cell precursor leukemia

value: Clone 35 plus IAA


title: CutRun-35-minus-IAA

value: SEM

value: Clone 35 minus IAA


title: 4sU_st8p_total-RNA

description:
4-thiouracil-enriched riboZero RNA, stage 8+ (mid-blastula transition)
rzRNA_4sU_xt71_rawCounts.txt.gz

value: 8+ (mid-blastula transition)


title: Sample 26_sampleO2


title: Wnt-BMP-LOF_st9p_polyA-RNA_rep2

value: injection of beta-catenin MO and treatment with LDN193190


title: Wnt-BMP-LOF_st9p_polyA-RNA_rep1

value: injection of beta-catenin MO and treatment with LDN193189


title: S6329

city: Shanghai

first: Xingang

last: Yu

address: 518 Ziyue Road, Minhang District,

country: China

institute: Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science,

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 33bp c) adaptor sequence.
Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Schistosoma japonicum miRNA database and Schistosoma japonicum genome. Unmapped reads to predict novelmiRNA
count counting
Genome_build: schistosoma_japonicum.PRJEA34885.WBPS9
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Schistosoma japonicum

source_name: adult Schistosoma japonicum derived from water buffalo Number S6329

growth_protocol: The water buffalo and yellow cattle were each challenged percutaneously with 1000 cercariae of S. japonicum administered at the upper back.All infected animals were sacrificed 8 weeks post infection, and the adult worms were perfused from the hepatic portal vein.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA was extracted from the S. japonicum (approximately ten pairs) with Trizol (Invitrogen, Carlsbad, CA, USA) and further purified with an RNeasy mini kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s instructions.

value: Chinese mainland strain

tag: genotype

value: Anhui isolate


title: S6335

source_name: adult Schistosoma japonicum derived from water buffalo Number S6335


title: Clone 42 wash 48

data_processing:
RNA-Seq reads from each species were aligned using Bowtie2  2.3.4
FPKM value were obtained using cufflinks v2.2.1
Genome_build: hg19

source_name: blood

growth_protocol: Human B-ALL cells SEM (DSMZ) were grown in RPMI 1640 CONTAINING 10%FETAL BOVINE SERUM (FBS) (Hyclone), 2mM glutamine (Sigma) and 1% penicillin/streptomycin (Invirtogen).  Cells were maintained at 37 °C in a 5% CO2 atmosphere and 95% humidity. Immortal human erythroid precursor cell line HUDEP-2 was expanded in StemSpan SFEM (Stem Cell Technologies) supplemented with 1 µM dexamethasone, 1 µg/mL doxycycline, 50 ng/mL human SCF, 3 units/mL EPO, and 1% penicillin/streptomycin. All cells were maintained at 37 °C in a 5% CO2 atmosphere and 95% humidity. All cells were tested negative for mycoplasma infection. Cell identity was confirmed by STR analysis.

extract_protocol:
Total RNA was extracted by Trizol (Invitrogen)
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Cat. No. RS-122-2301) was used for library construction.

treatment_protocol: Distal Enhancer was deleted by CRISPR/Cas9.

value: B-ALL cells SEM (DSMZ)

value: blood

value: Add IAA then washout IAA, SEM


title: sample24

description: processed data file: E2.count.txt

source_name: activated_two giant interneurons in parietal ganglia

tag: experiment

value: left

value: activated


title: Clone 35wash 48


title: Sample 25_sampleO1

tag: individual

value: whole

value: parietal ganglia


title: Sample 28_sampleO4

tag: hemisphere

value: control


title: Clone 27 wash 48


title: sample23

description: processed data file: E2.count.txt

source_name: control_two giant interneurons in parietal ganglia

value: right

tag: tissue subtype


title: S6328

source_name: adult Schistosoma japonicum derived from water buffalo Number S6328


title: S6242

source_name: adult Schistosoma japonicum derived from water buffalo Number S6242


title: Wnt-Nodal-LOF_st9p_polyA-RNA_rep2

description: Wnt/Nodal loss-of-function, stage 9+ (late blastula), experiment 4

extract_protocol:
Total RNA extraction: 10-15 dejellied X. tropicalis embryos were homogenized in 800 µl TRIzol reagent by vortexing. For phase separation, the homogenate supplemented with 1/5 volume of chloroform was transferred to a 1.5-ml phase-lock gel heavy microcentrifuge tube, shaken vigorously for 15 sec, left on the bench for 2 min and centrifuged (16,000 g) for 5 min at 4ºC. The upper phase was mixed with 1 volume of absolute ethanol and centrifuged (12,000 g) through the column IIC of Zymo RNA Clean and Concentrator-25 (Zymo Research) for 30 sec at room temperature. Next, the manufacturer’s instructions were followed for the recovery of total RNA (>17 nt) with minor modifications. First, the flow-through of the first spin was re-applied to the column. Second, the RNA was treated in-column with Turbo DNase (2 U/µl, ThermoFisher Scientific). Third, the RNA was eluted twice with 25 µl molecular-grade water. The concentration was determined on the Nanodrop 1000 except for RNA samples subjected to ribosomal RNA depletion in which case more accurate fluorometry was used.
Metabolic labeling of nascent transcripts: 75 ng 4-thiouridine-5'-triphosphate (4sU) was injected into the zygote’s animal pole. Total RNA was extracted as described above from 30 embryos collected at the mid-blastula transition (stage 8+) and early gastrula stage (stage 10+). Ribosomal RNA (rRNA) was removed from ~10 µg total RNA with Ribo-Zero rRNA (human/mouse/rat) magnetic beads (Illumina) following the manufacturer’s instructions. rRNA-depleted total RNA was purified with the RNA Clean & Concentrator-5 kit (Zymo Research) according to the manufacturer’s instructions. The yield was determined on a fluorometer using high-sensitivity reagents for RNA (250 pg/µl to 100 ng/µl). The purified RNA was transferred to thin-walled PCR tubes and fragmented with 40 µl 1x NEBNext RNA fragmentation buffer (NEB) in a thermocycler for 4 min at 95ºC. The fragmentation was stopped on ice with NEBNext RNA fragmentation stop solution (NEB) before purifying the fragmented RNA with RNA Clean & Concentrator-5. The RNA was eluted twice with 15 µl molecular-grade water. Approximately 10 ng of RNA was set apart to make an input library. The remaining RNA was biotinylated in the dark with EZ-Link HPDP-Biotin for 3 h at room temperature. The RNA was purified with RNA Clean & Concentrator-5 and eluted twice with 20 µl molecular-grade water. Biotinylated RNA was separated from non-labelled RNA with M270 streptavidin magnetic beads following the manufacturer’s instructions. The biotinylated RNA was stripped off the beads twice with 100 µl 100 mM 2-mercaptoethanol (pre-heated to 80ºC) and purified with RNA Clean & Concentrator-5.
RNA-Seq: Indexed paired-end libraries were made from ~1 µg total RNA by following the low sample protocol of the TruSeq RNA sample preparation guide v2 with a few modifications. First, cDNA after second strand synthesis was quantified using a fluorometer and high-sensitivity reagents for double-stranded DNA (10 pg/µl to 100 ng/µl). Second, the number of PCR cycles was adjusted to the detected yield of cDNA to avoid products of over-amplification such as chimera fragments: 7 (~20 ng), 8 (~10 ng), 9 (~5 ng), 12 (~1 ng).
4sU-Seq: Input and biotinylated RNA were converted to indexed paired-end libraries using the ScriptSeq v2 RNA-Seq preparation kit (Epicentre). We used the manufacturer’s instructions (protocol rev. C, 8/2014) starting with appendix 4.1.A (annealing cDNA synthesis primer) and 4.1.B (cDNA synthesis) followed by main protocol section 3.C (synthesis of 3’-tagged DNA). The DNA libraries were purified using 1.8x Agencourt AMPure XP beads and amplified with 11 (input) and 15 (streptavidin pull-down) PCR cycles according to section 3.D to 3.F. The DNA from the PCR reaction was purified using 1x AMPure XP beads and eluted in 10 µl molecular-grade water.
Illumina libraries were sequenced paired-end on the HiSeq 2500 (4sU-Seq) and HiSeq 4000 (RNA-Seq).
RNA-Seq: Indexed paired-end libraries were made from ~1 µg total RNA by following the low sample protocol of the TruSeq RNA sample preparation guide v2 with a few modifications. First, cDNA after second strand synthesis was quantified using a fluorometer

value: wild type (out-bred Nigerian)

value: 9+ (late blastula)

value: injection of beta-catenin MO and treatment with SB431543


title: Wnt-Nodal-LOF_st9p_polyA-RNA_rep1

value: injection of beta-catenin MO and treatment with SB431542


title: H1296

source_name: adult Schistosoma japonicum derived from yellow cattle Number H1296


title: HUDEP2 C3 differentiation +IAA 48hrs

tag: cell type

value: human erythroid precursor cell line

value: Add IAA, differentiation HUDEP-2


title: H1286

source_name: adult Schistosoma japonicum derived from yellow cattle Number H1286

value: Chinese mainland strain


title: sample22

description: processed data file: E2.count.txt

value: two giant interneurons in parietal ganglia


title: sample21

description: processed data file: E2.count.txt


title: Wnt-LOF_st9p_polyA-RNA_rep3

description: Wnt loss-of-function, stage 9+ (late blastula), experiment 4

source_name: whole embryo

value: injection of beta-catenin MO (canonical Wnt inhbition)


title: Wnt-LOF_st9p_polyA-RNA_rep2


title: sample20

description: processed data file: E2.count.txt


title: HUDEP2 C16 differentiation w/o IAA

value: blood

value: wild type differentiation HUDEP-2


title: H1284

source_name: adult Schistosoma japonicum derived from yellow cattle Number H1284

value: Anhui isolate


title: Wnt-Nodal-LOF_st9p_polyA-RNA_rep3

value: injection of beta-catenin MO and treatment with SB431544


title: Wnt-LOF_st9p_polyA-RNA_rep1


title: H1279

source_name: adult Schistosoma japonicum derived from yellow cattle Number H1279


title: MF_3

city: Beijing

first: CH

last: Dong

address: NO.3 Park 1, Beichen West Road, Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

description: The fruit body with mature perithecial and ascospores was designated as mature fruitbody (MF)

data_processing:
Sequencing libraries were generated using a NEBNext® UltraTM RNA Library Prep Kit for Illumina®
The library quality was assessed on an Agilent Bioanalyzer 2100 system
The cDNA library was sequenced on an Illumina Hiseq 2000 platform at Novogene Bioinformatics Technology Co., Ltd
Clean data (clean reads) were obtained by removing reads containing an adapter, reads containing poly_Ns and low quality reads from raw data through in_house perl scripts, on which all following of the analyses were based.
Genome_build: PRJNA382001
Genome_build: http://www.plantkingdomgdb.com/Ophiocordyceps_sinensis/
Supplementary_files_format_and_content: Ophiocordyceps_sinensis_gene_fpkm excel include FPKM values for each Sample

organism: Ophiocordyceps sinensis

source_name: Ophiocordyceps sinensis

extract_protocol:
Ten individuals were pooled as one replicate and three replicates were collected for each sample. After collection, these samples were immediately frozen in liquid nitrogen and stored at _80°C refrigerator until RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: BAKG3 [CL100090297_L01_542]

city: Ulm

first: Tamás

last: Röszer

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

country: Germany

institute: University of Ulm

data_processing:
assembled clean reads into Unigenes: using HISAT2: Version: v2.0.4 Parameters: -p 8 --phred64 --sensitive -I 1 -X 10000
map the clean reads to reference using Bowtie2: Version: v2.2.5 Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
calculate the Unigene expression levels using RSEM : Version: v1.2.12 Parameters: default
DEG Detection using DEGseq: Parameters: Fold Change >= 2 and Adjusted Pvalue <= 0.001
Supplementary_files_format_and_content: Excel files include gene expression values for each Sample

source_name: brown adipose tissue

growth_protocol: conventional in vitro culture in 10% FCS

extract_protocol:
Tri Reagent (phenolic extarction) according to Sigma-Aldrich protocol
RNA libraries were prepared for sequencing using standard BGISEQ protocols: mRNA enrichment-RNA fragmentation and reverse transcription-End repair, add A tailing and adaptor ligation-PCR amplification-Denature and cyclization-Sequencing

treatment_protocol: 18h treatment with the indicated vehicles or drugs

tag: Sex

value: male

tag: tissue/cell type

value: brown adipose tissue


title: HUDEP2 C16 wash96

value: Add IAA then washout IAA, HUDEP-2


title: MF_2


title: sample18

description: processed data file: E2.count.txt

value: right

value: control


title: HUDEP2 C16 +IAA 48hrs

value: Add IAA, HUDEP-2


title: MF_1


title: sample19

description: processed data file: E2.count.txt

value: left

value: activated


title: sample17

description: processed data file: E2.count.txt


title: BAKG1 [CL100090297_L01_540]


title: sample16

description: processed data file: E2.count.txt


title: HUDEP2 C16 differentiation+IAA 48hrs

value: human erythroid precursor cell line


title: FD_3

description: The samples of stroma length 7cm were designated as developed fruitbody (FD)


title: BAKG2 [CL100090297_L01_541]


title: FD_2

description: The samples of stroma length 6cm were designated as developed fruitbody (FD)


title: Bveh3 [CL100090297_L01_545]

source_name: white inguinal adipose tissue

value: white inguinal adipose tissue


title: HUDEP2 C3 +IAA 48hrs


title: HUDEP2 C16 w/o IAA

value: wild type HUDEP-2


title: sample14

description: processed data file: E2.count.txt

value: two giant interneurons in parietal ganglia


title: HUDEP2 C3 differentiation w/o IAA


title: FD_1

description: The samples of stroma length 5cm were designated as developed fruitbody (FD)


title: HUDEP2 C3 w/o IAA


title: Bveh1 [CL100090297_L01_543]


title: YF_3

description: The samples of stroma length 1_5cm young fruitbody (YF)


title: sample13

description: processed data file: E2.count.txt


title: 36_positive_MYCp_CapC

data_processing:
The paired-end reads were reconstructed into single reads with FLASH1.2.11
Digested in silico with the DpnII2E.pl script
aligned to the human genome using Bowtie 1.0.0 (http://bowtie-bio.sourceforge.net/index.shtml).
Interaction frequencies were determined using CCanalyser2.pl (https://github.com/telenius/captureC/releases).
Genome_build: hg19

growth_protocol: Human B-ALL cells SEM (DSMZ) were grown in RPMI 1640 CONTAINING 10%FETAL BOVINE SERUM (FBS) (Hyclone), 2mM glutamine (Sigma) and 1% penicillin/streptomycin (Invirtogen).  Cells were maintained at 37 °C in a 5% CO2 atmosphere and 95% humidity.

extract_protocol:
Suspension cells (SEM) cells were collected at 1X107 cells per reaction while adherent cells (IMR90, HCT116 and human iPS) were trypsinized before collection. Cells were fixed and lysed in 15 mL conical tubes before storage in -80°C for up to 1 month before library construction. Cells were thawed on ice and spun down for 5 minutes at 4000rpm, 4°C. The remaining lysis buffer was removed and discarded. The pellets were re-suspended in 1 mL of 1x DpnII buffer and transferred to a 2 mL tube for homogenization with a pestle. The homogenized samples were then centrifuged for 14,000 rpm at 5 mins in 4°C. The supernatant was removed and discarded. After decrosslinking, phenol-chloroform-isoamylalcohol DNA extraction, and sodium acetate precipitation, a small portion of DNA was run on a gel to check for digest and ligation efficiency. Once the 3C library was construction was complete, 5-6ug of the 3C DNA in a total volume of 130ug per covaris tube (microTUBE AFA Fiber Crimp-Cap 6X16mm, catalog). Each 2ug of 3C library generated one Capture.NEBNext Ultra II DNA library kit for Illumina (NEB 7645S) was used for end-repair, adaptor ligation, and PCR enrichment of adaptor ligated DNA. NEBNext Mulitplex Oligos (Dual Index Primers Set 1) was used for indexing for four cycles.The Nimblegen SeqCap EZ Hybridization and Wash Buffer Kit (Roche) was used for subsequent hybridization and wash steps. Constructed library was sequenced on Miseq for paired-end 150bp.
NEBNext Ultra II DNA library kit for Illumina (NEB 7645S) was used for end-repair, adaptor ligation, and PCR enrichment of adaptor ligated DNA. NEBNext Mulitplex Oligos (Dual Index Primers Set 1) was used for indexing for four cycles. Agencourt AMPure XP beads were used at 0.8x for all cleanup steps.
Capture-C

treatment_protocol: Capture-C was performed on two CTCF AID homozygous knock-in clones 27 and 35.

value: SEM

value: B-ALL cells SEM (DSMZ)

value: colon

value: MYCp promoter probe


title: HUDEP2 C3 wash96

value: blood


title: sample12

description: processed data file: E1.count.txt

source_name: activated_parietal ganglia

value: parietal ganglia


title: 3T3-L1_NPFF3 [CL100084579_L02_513]

value: 3T3-L1 preadipocytes

value: 1 nM neuropeptide FF (NPFF) for 18 h


title: YF_2

description: The samples of stroma length 1_4cm young fruitbody (YF)


title: sample11

description: processed data file: E1.count.txt

source_name: control_parietal ganglia


title: YF_1

description: The samples of stroma length 1_3cm young fruitbody (YF)


title: sample10

description: processed data file: E1.count.txt

value: right


title: 3T3-L1_NPFF2 [CL100084579_L02_512]


title: 36_negative_MYCp_CapC


title: sample15

description: processed data file: E2.count.txt


title: 3T3-L1_NPFF1 [CL100084579_L02_511]


title: PR_3

description: The samples of stroma length < 3cm were designated as primordium (PR)


title: Bveh2 [CL100090297_L01_544]

value: male


title: 3T3-L1_vehicle3 [CL100084579_L02_510]

value: water


title: PR_1

description: The samples of stroma length < 1cm were designated as primordium (PR)


title: sample8

description: processed data file: E1.count.txt


title: 3T3-L1_vehicle2 [CL100084579_L02_509]


title: 27_positive_MYCp_CapC

data_processing:
Library strategy: Capture-C
The paired-end reads were reconstructed into single reads with FLASH1.2.11
Digested in silico with the DpnII2E.pl script
aligned to the human genome using Bowtie 1.0.0 (http://bowtie-bio.sourceforge.net/index.shtml).
Interaction frequencies were determined using CCanalyser2.pl (https://github.com/telenius/captureC/releases).
Genome_build: hg19

extract_protocol:
Suspension cells (SEM) cells were collected at 1X107 cells per reaction while adherent cells (IMR90, HCT116 and human iPS) were trypsinized before collection. Cells were fixed and lysed in 15 mL conical tubes before storage in -80°C for up to 1 month before library construction. Cells were thawed on ice and spun down for 5 minutes at 4000rpm, 4°C. The remaining lysis buffer was removed and discarded. The pellets were re-suspended in 1 mL of 1x DpnII buffer and transferred to a 2 mL tube for homogenization with a pestle. The homogenized samples were then centrifuged for 14,000 rpm at 5 mins in 4°C. The supernatant was removed and discarded. After decrosslinking, phenol-chloroform-isoamylalcohol DNA extraction, and sodium acetate precipitation, a small portion of DNA was run on a gel to check for digest and ligation efficiency. Once the 3C library was construction was complete, 5-6ug of the 3C DNA in a total volume of 130ug per covaris tube (microTUBE AFA Fiber Crimp-Cap 6X16mm, catalog). Each 2ug of 3C library generated one Capture.NEBNext Ultra II DNA library kit for Illumina (NEB 7645S) was used for end-repair, adaptor ligation, and PCR enrichment of adaptor ligated DNA. NEBNext Mulitplex Oligos (Dual Index Primers Set 1) was used for indexing for four cycles.The Nimblegen SeqCap EZ Hybridization and Wash Buffer Kit (Roche) was used for subsequent hybridization and wash steps. Constructed library was sequenced on Miseq for paired-end 150bp.
NEBNext Ultra II DNA library kit for Illumina (NEB 7645S) was used for end-repair, adaptor ligation, and PCR enrichment of adaptor ligated DNA. NEBNext Mulitplex Oligos (Dual Index Primers Set 1) was used for indexing for four cycles. Agencourt AMPure XP beads were used at 0.8x for all cleanup steps.


title: 35_negative_MYCp_CapC


title: 35_positive_MYCp_CapC


title: 27_negative_MYCp_CapC


title: sample7

description: processed data file: E1.count.txt

value: left

value: control


title: 3T3-L1_vehicle1 [CL100084579_L02_508]


title: ST_3

description: The mummified larvae coated with mycelia before stroma development were designated as sclerotium (ST)


title: sample6

description: processed data file: E1.count.txt

value: activated


title: ST_2


title: ATM_AKG3 [CL100055946_L02_512]

value: adipose tissue macrophages (ATMs)

value: 100 nM alkylglycerols (AKGs) for 18h in vitro


title: CTCF42_treat

growth_protocol: Human B-ALL cells SEM (DSMZ) were grown in RPMI 1640 CONTAINING 10%FETAL BOVINE SERUM (FBS) (Hyclone), 2mM glutamine (Sigma) and 1% penicillin/streptomycin (Invirtogen).  Cells were maintained at 37 °C in a 5% CO2 atmosphere and 95% humidity.% humidity.

value: CTCF deletion


title: ST_1


title: ATM_AKG2 [CL100055946_L02_511]


title: CTCF35_treat


title: CTCF42_CK

value: wild type


title: sample9

description: processed data file: E1.count.txt


title: sample4

description: processed data file: E1.count.txt


title: sample5

description: processed data file: E1.count.txt


title: HY_3

description: The hyphae cultured in potato dextrose agar supplemented with 5% wheat bran and 0.7% peptone were designated as hyphae (HY)


title: ATM_AKG1 [CL100055946_L02_510]


title: PR_2

description: The samples of stroma length < 2cm were designated as primordium (PR)


title: CTCF35_CK

value: B-ALL cells SEM (DSMZ)


title: HY_2

description: The hyphae cultured in potato dextrose agar supplemented with 5% wheat bran and 0.6% peptone were designated as hyphae (HY)


title: CTCF27_treat


title: HY_1

description: The hyphae cultured in potato dextrose agar supplemented with 5% wheat bran and 0.5% peptone were designated as hyphae (HY)


title: ATM_vehicle1 [CL100055946_L02_507]

value: ethanol


title: CTCF27_ck


title: sample1

description: processed data file: E1.count.txt


title: het_6h_3

status: Public on May 13 2019

city: Stanford

first: Thach

last: Mai

address: 269 Campus Dr

institute: Stanford University

data_processing:
Basecalls performed using Illunima HiSeq 2000 or Nextseq 500
RNA-seq reads were mapped to a concatenated genome sequence of human GRCh38/hg38 and mouse GRCm38/mm10 annotations using STAR/2.4.2a.
Following mapping, human and mouse transcript abundance were individually quantified using rsem/1.2.21.
Expression levels were normalized by transcripts per million (TPM).
Genome_build: mm10/hg19
Supplementary_files_format_and_content: text file with expected count, TPM and FPKM.

organism:
Homo sapiens
Mus musculus

source_name: human fibroblast/mouse ES cells

extract_protocol:
RNA was obtained using Rneasy purification kit
Libraries were prepared according to Illumina's instructions accompanying the Tru-Seq V2 kit (RS-122-2001). Briefly, Poly-A+ RNA was isolated from total RNA using oligo-dT magnetic beads (Illumina TruSeq V2). Following first (Superscript III, Life Technologies) and second strand synthesis, cDNA libraries were constructed according to standard Illumina protocols. RNA and DNA integrity and quality was measured using an Agilent Bioanalyzer 2100.

value: human fibroblast/mouse ES cells


title: het_12h_2


title: het_24h_1


title: het_12h_3


title: het_24h_2


title: het_12h_1


title: het_24h_3


title: het_6h_2


title: het_2h_3


title: ATM_vehicle3 [CL100055946_L02_509]


title: het_2h_2


title: het_6h_1


title: het_30min_3


title: het_2h_1


title: sample3

description: processed data file: E1.count.txt


title: het_30min_1


title: co-cult_2


title: co-cult_1


title: het_30min_2


title: sample2

description: processed data file: E1.count.txt


title: ATM_vehicle2 [CL100055946_L02_508]


title: DMSO_st9p_polyA-RNA_rep1

city: London

first: George

last: Gentsch

address: 1 Midland Road

institute: The Francis Crick Institute

description: control (uninjected, DMSO), stage 9+ (late blastula), experiment 4

data_processing:
Bases were called using Casava version 1.8.2
RNA-Seq: Paired-end reads were aligned to the X. tropicalis genome assembly v7.1 using STAR v2.5.3a with default settings and a revised version of gene models v7.2 to improve mapping accuracy across splice junctions. The alignments were sorted by read name using the sort function of samtools v1.3.1. Exon and intron counts (-t 'exon;intron') were extracted from unstranded (-s 0) alignment files using VERSE v0.1.5 in featureCounts (default) mode (-z 0). Intron coordinates were adjusted to exclude any overlap with exon annotation. Differential expression analysis was performed with both raw exon and intron counts excluding those belonging to ribosomal and mitochondrial RNA using the R package DESeq2 v1.14.1. In an effort to find genes with consistent fold changes over time, p-values were generated according to a likelihood ratio test reflecting the probability of rejecting the reduced (~ developmental stage) over the full (~ developmental stage + condition) model. Resulting p-values were adjusted to obtain false discovery rates (FDR) according to the Benjamini-Hochburg procedure with thresholds on Cook’s distances and independent filtering being switched off. Equally, dataset without time series were subjected to likelihood ratio tests with reduced (~1) and full (~ condition) models for statistical analysis.
4sU-Seq: Paired-end reads were aligned to a revised version of X. tropicalis gene models v7.2 and known off-genome EST assemblies including ribosomal and mitochondrial RNA by running Bowtie2 v2.1.0 with the following constraints: -k 200 (up to 200 alignments per fragment) -X 800 (maximum fragment length of 800 bp) -rdg 6,5 (penalty for read gaps of length N, 6+N*5) -rfg 6,5 (penalty for reference gaps of length N, 6+N*5) -score-main L,-.6,-.4 (minimal alignment score as a linear function of the read length x, f(x) = -0.6 - 0.4*x) -no-discordant (no paired-end read alignments breaching maximum fragment length X) -no-mixed (only concordant alignment of paired-end reads). Only read pairs that uniquely align to one gene were counted. Differential expression analysis was performed with raw read counts including those belonging to ribosomal and mitochondrial RNA using the R package DESeq2 v1.14.1. In an effort to find 4sU-enriched transcript levels, their DESeq2 normalised read counts genes were divided by those of the 4sU input for both developmental stages.
Genome_build: X. tropicalis v7.1
Supplementary_files_format_and_content: Raw read count tables (gzip compressed text files)

value: wild type (out-bred Nigerian)

value: 9+ (late blastula)

value: treatment with DMSO


title: Sperm 3

city: Storrs

first: Xiuchun

last: Tian

state: CT

address: 1390 Storrs Road, ABL220D

department: Animal Science

institute: University of connecticut

data_processing:
Multiplexed sequencing reads were first trimmed to remove low-quality bases and adaptor sequences using the Trim_galore tool. The clean reads were then aligned to the bisulfite-converted reference bovine genome UMD3.1.1 (bosTau8) using Bismark alignment tools (version 0.16.3) with default parameters.Bismark Methylation Extractor was used to extract the methylation call for every single C analyzed. Cytosine in CpG context was extracted and read coverage files were generated.
The methylation levels of each sampled cytosine were estimated as the number of reported C (‘methylated’ reads) divided by the sum of reported C (‘methylated’ reads) and T (‘unmethylated’ reads) at the same positions of the reference genome.
Genome_build: UMD3.1.1
Supplementary_files_format_and_content: text file, CpG report file

organism: Bos taurus

source_name: Sperm

extract_protocol:
Individual gamtes and embryos were lysis in a single tubes to obtain DNA using protease.
We conducted DNA extraction, MspI digestion, end-repair, dA-tailing, adaptor ligation, bisulfite conversion, and PCR amplification libraries in single tubes to minimize DNA loss.
Multiplex libraries using whole genome bisulfite sequencing approach.

treatment_protocol: Frozen bovine sperm were collected from a bull with proven fertility; Germinal vesicle stage and in vitro matured oocytes were produced using slaughterhouse ovaries; For embryo collection, multiparous Holstein cows (n = 10) were synchronized and superovulated. Artificial insemination using semen from a bull with proven fertility was conducted at 12 and 24 hours post standing heat (Day 0). Donor animals were sacrificed at 30 hours, and 2-4 days after estrus to collect in vivo developed oocytes and embryos at the 2- to 8-cell stages by oviductal flushing. Early/compact morulae and blastocysts were collected by routine non-surgical uterine flushing on Days 5, 6 and 7.

tag: breed

value: Hostein cow

value: Sperm


title: in vivo MII oocyte 3b

source_name: in vivo MII oocyte

value: in vivo MII oocyte


title: Sperm 2


title: Sperm 1


title: in vivo MII oocyte 1b


title: 8-cell 4


title: 8-cell 2


title: 4-cell 2


title: 4-cell 5


title: 2-cell 2


title: 2-cell 4


title: 8-cell 1


title: 4-cell 1


title: 4-cell 4


title: 8-cell 3


title: co-cult_3


title: 2-cell 1


title: in vivo MII oocyte 2


title: 16-cell 1


title: in vivo MII oocyte 3


title: 16-cell 3


title: in vivo MII oocyte 1


title: in vivo MII oocyte 2b


title: in vitro MII oocyte 3

source_name: in vitro MII oocyte

value: in vitro MII oocyte


title: 4-cell 3


title: in vitro MII oocyte 4


title: 2-cell 3


title: in vitro MII oocyte 6


title: Immature oocyte 3

source_name: Immature oocyte

value: Immature oocyte


title: Immature oocyte 4


title: Immature oocyte 1


title: in vitro MII oocyte 1


title: in vitro MII oocyte 2


title: Immature oocyte 2


title: 16-cell 2


title: in vitro MII oocyte 5


title: IA-C110EC

city: Chicago

first: Yan

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

data_processing:
Raw sequencing QC assessement: FastQC v0.11.7
Alignment: STAR_2.6.0c
Post alignement QC assessment: RSeQC and Picard tools with version: 2.18.7-SNAPSHOT0
Gene transcripts assembly: featureCounts with Rsubread 1.28.1
Differentially expressed genes analysis: DESeq2 with R version 3.4.3
Genome_build: UCSC human genome model: GENCODE GRCh38 V28 at ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/
Supplementary_files_format_and_content: tab-delimited text files include gene features raw counts values summarized by featureCouts for each Sample.

source_name: cerebral cavernous malformation_CASH

extract_protocol:
RNAs was extracted using an RNA isolation kit (RNeasy® Micro Kit, Qiagen, Hilden, Germany).
RNA libraries were prepared for sequencing using commercially low-input strand specific RNA-Seq kits (Clontech, California, USA) for human specimens

tag: subject status

value: cerebral cavernous malformation

value: CASH

value: laser microdissected  neurovascular units (NVUs)

tag: library prepartion sequencing batch


title: IA-214

data_processing:
Raw sequencing QC assessement: FastQC v0.11.7
Adapter trimming: cutadapt 1.14
Alignment: sRNAbench version 10/14
Differentially expressed miRNA analysis: DESeq2 with R version 3.4.3
Genome_build: miRBase 21 mature microRNAs
Supplementary_files_format_and_content: tab-delimited text files include reads mapped to mature miRNA from sense strand summarized by sRNAbench for each Sample.

source_name: healthy control_Healthy

extract_protocol:
RNAs was extracted using an RNA isolation kit (miRNeasy Serum/Plasma Kit (Qiagen, Venlo, Netherlands).
RNA libraries were prepared for sequencing using commercially available Illumina small RNA-Seq kits (San Diego, California, USA),

value: healthy control

value: Healthy

value: plasma


title: IA-Autopsy4

source_name: autopsy contol_Healthy

value: autopsy contol


title: IA-212


title: IA-CCM113

source_name: cerebral cavernous malformation_Non CASH

value: Non CASH


title: IA-213


title: IA-215


title: IA-211


title: IA-RG-IA-142_489


title: IA-Autopsy3


title: IA-207


title: IA-Autopsy2


title: IA-261


title: IA-209


title: IA-505-3698A

value: Non-CASH


title: IA-208


title: IA-205


title: IA-206


title: IA-AA820-1619


title: IA-C107-A


title: IA-210


title: BT245-NKO-C1P5_input

city: Montreal

first: Nada

last: Jabado

state: Québec

address: 1001 Décarie Boulevard

department: Department of Pediatrics

country: Canada

institute: McGill University

data_processing:
Adaptor sequences and the first four nucleotides of each read were removed from the read sets using Trimmomatic (Bolger et al., 2014) (v0.32).  Reads were scanned from start to end and truncated if and when the average quality of a 4-nucleotide sliding window fell too low (phred33<30). Short reads (<30 bp) were subsequently discarded. Multiple quality control metrics were obtained using FASTQC (v0.11.2), samtools (Li et al., 2009) (v0.1.19), BEDtools (Quinlan and Hall, 2010) (v2.17.0) and custom scripts.   Reads were processed as described for RNAseq, and then aligned using the human repeat genome as reference, as previously described (Solovyov et al., Cell Reports 2018). Repbase reference genome was used (Bao et al., 2015) (v23.03) (http://www.girinst.org/repbase). Since Repbase largely consists of family consensus sequences, reads are assigned to these sequences regardless of where and how many times they are present in the genome, mitigating mapping uncertainty. We combined humrep.ref and humsub.ref into a single reference of repeat sequences for the human genome, covering a total of 1132 consensus elements, and counted the number of reads mapping into each of these elements using featureCounts (MAPQ>3). Differential enrichment of H3K27ac at the consensus sequences were then calculated using DESeq2 (Love et al., 2014). The inverse of ChIP-Rx spike-in scaling factors (i.e. 1/rx) were supplied to DESeq2 as normalization factors (i.e. size factors).
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values containing raw read counts

source_name: H3.3K27M_Tumor-derived cell-line

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at -80°C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction ~5% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing (see below). ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. 25ul Protein A beads were washed and then incubated with 6ug of H3K27ac antibody (Diagenode, C15410196), and 2 million cells of sonicated cell lysate combined with protease inhibitors for 10 hr, followed by 20 min wash cycle with provided wash buffers. Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail (Life Technologies) at 65°C for 30 min followed by 2ul Proteinase K (Thermo Fisher Scientific) at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP Illumina library preparation reagents. Briefly, 25ul of ChIP sample was incubated with 45ul end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50ul buffer enzyme mix for 30°C 30 min, followed by PEG/NaCl purification. Adaptor ligation: bead bound sample was incubated with 45ul buffer enzyme mix and 5ul of different TruSeq DNA adapters (Illumina) for each sample, for 20°C 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. Size selection was performed after PCR using a 0.6x/0.8x ratio of Ampure XP beads (double size selection) set to collect 250-450bp fragments.

tag: sample type

value: Tumor-derived cell-line

tag: chip antibody


title: BT245-KO-C2P3_input

source_name: H3.3K27M-KO_Tumor-derived cell-line


title: IA-RG-IA-139_489


title: IA-RG-IA-140_489


title: DIPGXIII-C14_input


title: IA-RG-IA-138_489


title: DIPGXIII-KO-C5P5_input


title: BT245-KO-C4P6_input


title: IA-RG-IA-141_489


title: PL637_brain_input

data_processing:
Sequence reads were aligned to the human genome (HG19) using Bowtie2 (v2.1.0) (Langmead and Salzberg, 2012) under default settings. PCR duplicates were removed using PICARD tools generating .BAM files (Li et al., 2009). Read processing and alignment for analysis of repeat elements was performed separately (see below for details). Significant peaks were identified using Model-Based Analysis for ChIP-seq (MACS 1.4) (Zhang et al., 2008)with a p value cutoff of 1e-9.  Peaks were annotated using HOMER (v3.12) (Heinz et al., 2010) with promoter regions classified as any peak within +/- 2.5 kb of a transcriptional start site (TSS), and enhancer region greater than 2.5 kb from a TSS. Peaks were also annotated using ChIP-atlas annotating distal enhancers to genes based upon public CHIA-PET datasets. Super enhancers were identified using the ROSE algorithm with exclusion of peaks within +/- 2.5 kb of a TSS and a stitch distance of 12.5 kb. For visualization of H3K27 acetylation profiles, BAM alignment files were normalized to RPKM values using DeepTools (Ramirez et al., 2014) and visualized in Integrated Genome Viewer (v2.3.40).
Genome_build: hg19

value: Tumor


title: XPS124018_xenograft_input

value: Xenograft


title: BT245-NKO-C1P5_H3K27ac

value: H3K27ac antibody (Diagenode, C15410196)


title: ML_HGG_003_Xn_input


title: ML_HGG_005_Xn_input


title: BT245-nko-c1p5-Rx_PARENTAL_cells_input


title: BT245-KO-C2P3_H3K27ac


title: DIPGXIII-ko-c5p5-Rx_R1_cells_input


title: ML_HGG_002_Xn_input


title: BT245-ko-c4p6-Rx_R2_cells_input

value: H3.3K27M-KO (DIPG-XII)


title: BT245-ko-D2p8-Rx_R1_cells_input


title: pcGBM2p18_cells_input

source_name: H3.3K27WT_Tumor-derived cell-line


title: XHSJ019-X1-1-Rx_xenograft_input


title: JN57_brain_input


title: ML_HGG_006_Xn_input


title: DIPGXIII-ko-c10p5-Rx_R2_cells_input


title: DIPGXIII-KO-C5P5_H3K27ac


title: DIPGXIII-C14-nKO-Rx_PARENTAL_cells_input


title: DIPGXIIIp11_cells_input


title: BT869p21-Rx_cells_input


title: HSJ031-C3-Rx_cells_input


title: JN14-BS1_brain_input


title: ML_HGG_004_Xn_input


title: G477p6_cells_input


title: HSJD-012-DIPG-TPC-input_trim50


title: ML_HGG_001_Xn_input


title: DIPGVI_c27_cells_input


title: JN29-BS3_brain_input


title: HSJ019-Tumor-Rx_brain_input


title: BT245p6_cells_input


title: 434_brain_input


title: BT245-X0-2-Rx_xenograft_input


title: 429_brain_input


title: 2658_brain_input


title: 2230_brain_input


title: 1840_brain_input


title: 2480_brain_input


title: 2469_brain_input


title: 2168_brain_input


title: DIPGXIII-ko-c5p5-Rx_R1_cells_h3k27ac


title: 2089_brain_input_sorted


title: DIPGXIII-C14-nKO-Rx_PARENTAL_cells_h3k27ac


title: BT245-nko-c1p5-Rx_PARENTAL_cells_h3k27ac


title: 1552-TPC-input


title: ML_HGG_002_Xn_H3K27ac


title: XPS124018_xenograft_h3k27ac


title: ML_HGG_003_Xn_H3K27ac


title: ML_HGG_005_Xn_H3K27ac


title: BT245-ko-D2p8-Rx_R1_cells_h3k27ac


title: ML_HGG_006_Xn_H3K27ac


title: HSJ031-C3-Rx_cells_h3k27ac


title: HSJD-012-DIPG-TPC-H3K27AC_trim50


title: pcGBM2p18_cells_h3k27ac


title: ML_HGG_004_Xn_H3K27ac


title: ML_HGG_001_Xn_H3K27ac


title: XHSJ019-X1-1-Rx_xenograft_h3k27ac


title: 2192_brain_input


title: AK964_brain_input


title: DIPGXIII-ko-c10p5-Rx_R2_cells_h3k27ac


title: BT245-ko-c4p6-Rx_R2_cells_h3k27ac


title: DIPGXIIIp11_cells_h3k27ac


title: DIPGVI_c27_cells_h3k27ac


title: G477p6_cells_h3k27ac


title: PL637_brain_h3k27ac


title: BT869p21-Rx_cells_H3K27ac


title: 1552-TPC-H3K27AC


title: JN57_brain_h3k27ac


title: JN14-BS1_brain_h3k27ac


title: AK964_brain_h3k27ac


title: HSJ019-Tumor-Rx_brain_h3k27ac


title: 429_brain_h3k27ac


title: 434_brain_h3k27ac


title: BT245-X0-2-Rx_xenograft_h3k27ac


title: 2480_brain_h3k27ac


title: 2658_brain_h3k27ac


title: 1840_brain_h3k27ac


title: 2089_brain_h3k27ac_sorted


title: 2168_brain_h3k27ac


title: 2192_brain_h3k27ac


title: R5.7

city: Miami

first: Alexander

last: Agoulnik

state: FL

department: Human and Molecular Genetics

institute: Florida International University Herbert Wertheim College of Medicine

data_processing:
Partek Flow
STAR aligner
Differentially expressed genes were identified using Gene Specific Analysis (GSA)
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file with ratio, fold-change and p-values

source_name: TGF-β1 + ML290 5 µM

growth_protocol: LX-2 cells were grown in 2% FBS DMEM media.

extract_protocol:
Cells were lysed using Trizol and total RNA was isolated by column purification using a GeneJET RNA purification kit following manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with recombinant human TGF-β1, with DMSO or ML290 (5 µM) for 72h in 2% FBS DMEM.

tag: cell line

value: hepatic stellate cell line


title: R5.6


title: 2230_brain_h3k27ac


title: HSJ-023

data_processing:
Data processing. Adaptor sequences and the first four nucleotides of each read were removed from the read sets using Trimmomatic (v0.32).  Reads were scanned from start to end and truncated if and when the average quality of a 4-nucleotide sliding window fell too low (phred33<30). Short reads (<30 bp) were subsequently discarded. Multiple control metrics were obtained using FASTQC (v0.11.2), samtools (v0.1.19), BEDtools (v2.17.0) and custom scripts.
Gene expression analysis. The remaining clean set of reads were then aligned to the reference genome build hg19 (GRCh37) with STAR (v2.3.0e) using the default parameters. Multimapping reads (MAPQ>3) were discarded from downstream analyses. Gene expression levels were estimated by quantifying uniquely mapped reads falling into exonic regions defined by the ensGene annotation set from Ensembl (GRCh37; N=60234 genes) using featureCounts (v1.4.4). Normalization (mean-of-ratios), variance-stabilized transformations of the data, as well as differential expression analysis, were performed using DESeq2. Unless otherwise stated, all reported p-values have been adjusted for multiple testing using the Benjamini-Hochberg procedure.
Repeat element expression analysis. The clean set of rRNA-depleted RNA-seq reads were aligned to the human repeat genome, as previously described. The reference repeat sequences were downloaded from Repbase (v23.03) (http://www.girinst.org/repbase). We then combined humrep.ref and humsub.ref into a single reference of repeat sequences for the human genome, covering a total of 1132 consensus repeat element sequences. All subsequent steps closely mirror those detailed for gene expression analysis. Normalization (library size) factors derived from canonical genes (Ensembl ensGene annotation) using mean-of-ratios as described above were used to normalize repeat elements.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values containing raw read counts

source_name: Tumor

extract_protocol:
Total RNA was extracted from cell pellets using the RNeasy mini kit (Qiagen) according to instructions from the manufacturer.
Library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts. Paired-end sequencing was performed on the Illumina HiSeq 2000, 2500 and 4000 platforms.

tag: treatment


title: R5.5


title: BT245p6_cells_h3k27ac


title: R5.4


title: R4.7

source_name: TGF-β1 + DMSO


title: JN29-BS3_brain_h3k27ac


title: R4.5