title: ChIP-seq from H1-hESC (ENCLB261FLT)

description:
https://www.encodeproject.org/experiments/ENCSR000AMI/
***************
biological replicate number: 3
technical replicate number: 1
description: Control ChIP-seq on human H1-hESC
experiment encode accession: ENCSR000AMI
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB261FLT
size range: 200-600

value: Control

value: stem cell

value: embryonic

value: ENCBS849HZG at ENCODE; https://www.encodeproject.org/ENCBS849HZG/


title: ChIP-seq-WCE

status: Public on Mar 09 2017

type: SRA

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

country: Japan

institute: Nagoya University

library_source: genomic

data_processing:
ChIP-seq samples were analyzed by Illumina HiSeq 2000 for 40 bases in single end read mode.
Reads were aligned to the mouse genome build mm9 using bowtie 1.0.1 (Langmead et al., 2009). The following parameters were used: -n 2, -e 70, -m 1, -k 1, and -l 40.
ChIP-seq peaks were called using MACS version 1.4.2. (model-based analysis of ChIP-seq) (Zhang et al., 2008) with a p value threshold of enrichment of 1 x 10–6.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were produced by MACS 1.4 with --space=100, and then converted to bw files in a rpm scale.

molecule: genomic DNA

organism: Mus musculus

source_name: V6.5 embryonic stem cells

growth_protocol: V6.5 mESCs were cultured in mES media.

extract_protocol:
Cells were crosslinked for 10 min at room temperature by the addition of one-sixth of the volume of 6 % formaldehyde solution (diluted from methanol-free formaldehyde (Thermo Scientific)) to the growth media followed by 5 min quenching with 250 mM glycine. Cells were washed twice with cold PBS, then the supernatant was aspirated and the cell pellet was flash frozen in liquid nitrogen. Frozen crosslinked cells were stored at -80 ºC. Cell pellets were resuspended in ChIP Lysis buffer and ChIP Dilution buffer, treated with MNase for 30 min at -37 ºC followed by quenching with EDTA and EGTA, and further sonicated for 10 cycles at 30 s each with BioRupter. MNase-digested and sonicated lysates were cleared and incubated overnight at 4 ºC with 10 μg DGCR8 or Drosha antibody, and further incubated with pre-washed Dynabeads Protein G (Thermo Scientific) for 2 hrs. Beads were washed two times with sonication buffer, one time with sonication buffer with 500 mM NaCl, one time with LiCl wash buffer and one time with TE with 50 mM NaCl. After resuspension in elution buffer and reversal of crosslink at 65 ºC overnight, RNA and protein were digested using RNase A and Proteinase K, respectively, and DNA was purified with phenol chloroform extraction and ethanol precipitation.
After end-repair and A-tailing, ChIP DNA or whole cell extract DNA (50 ng) were ligated to diluted Illumina Adaptor Oligos and size-selected by two step AMPure bead selection (0.9x and 1.8x). After 16 cycle amplification with Phusion HF DNA polymerase, libraries were size-selected with 1.8x AMPure beads.

treatment_protocol: Cells were treated with DMSO or JQ1 (500 nM) for 12 hrs before ChIP-seq analysis.

tag: cell type

value: Embryonic stem cells

tag: antibody

value: WCE

tag: treatment


title: ChIP-seq-Drosha-JQ1

value: Drosha


title: Actin KO1

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Mus musculus GRCm38.p4 genome using tophat2 v2.1.0 with the parameters “–no-novel-junctions” and “–G” when specifying the genome file
Cufflinks v2.2.1 was used to derive FPKM (Fragments Per Kilobase of transcript per Million mapped reads)
Differential gene expression was analyzed by Cuffdiff
Genome_build: Mus musculus GRCm38.p4 genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, tab-delimited text files include fold change and p-values of each comparison

molecule: total RNA

source_name: connective tissue

growth_protocol: Dulbecco’s modified Eagle medium (DMEM) with high glucose (Sigma), 10% fetal bovine serum (Sigma) and 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma), in a humidified incubator with 5% CO2 at 37 Deg.

extract_protocol:
Total RNA was extracted from 70% confluent cells using TRI Reagent according to the manufacturer protocol (Sigma-Aldrich).
Library construction according to the SciLife lab guideline using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer protocol

tag: tissue

value: embryonic fibroblasts

tag: strain

value: BALB/c

tag: developmental stage

value: 10.5 day old embryos

tag: genotype

value: Actb -/-


title: H3K9K14AC_ESNTPA_replicate1

city: London

first: Francesco

last: Gualdrini

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Francis Crick Institute

description: Chip-Seq

data_processing:
ChipSeq: Wig files are those generated by MACS at 1bp resolution and a set normalised to 30 million mapped reads and to the assessed scaling factors are additionally provided.
Genome_build: MM9
Supplementary_files_format_and_content: wig files

source_name: Cultured MEFs (Mouse Embryonic fibroblasts)

growth_protocol: The different types of MEFs were cultured in Dulbecco modified Eagles medium (DMEM) supplemented with 10% fetal calf serum (FCS), 100 IU/ml penicillin, and 100 μ/ml streptomycin.

extract_protocol: Chip-Seq: DNA samples were end repaired, poly-A tailed and Illumina single end adapters were ligated following the standard Illumina protocol with minor adjustments. Agencourt AMPure XP beads at 0.8x ratio were used to size select out adapter dimers after adapter ligation.  The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix. Post PCR, AMPure XP beads were used at a 1:1 ratio to maintain size integrity and to allow size select on 2%Agarose gel.  Samples were finally purified with QAIquick gel extraction kit and quality controlled on the DNA 1000 BioAnalyser 2100 chip.

treatment_protocol: Cells were  starved for 48h in 0.3%FCS. Where indicated, cells were stimulated for 30 minutes with 12-O-tetradecanoyl phorbol-13-acetate (Sigma TPA, 50 ng/ml).

value: TCF KO (TKO)

tag: chip antibody

value: H3K9acK14ac ( Millipore Cat# 06-599 Lot# 1969119)

tag: scaling factor used (reads*scaling factor)


title: ChIP-seq-DGCR8-JQ1


title: ChIP-seq from H1-hESC (ENCLB038EWS)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR000AMI/
***************
biological replicate number: 3
technical replicate number: 2
description: Control ChIP-seq on human H1-hESC
experiment encode accession: ENCSR000AMI
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB038EWS
size range: 200-600

data_processing: See GSM*_README.txt supplementary file linked below

organism: Homo sapiens

source_name: Homo sapiens H1-hESC stem cell male embryo

extract_protocol: not provided

tag: biosample encode accession

tag: dev stage

tag: Sex

value: male

tag: age

value: unknown

tag: health state

value: healthy

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: H3K9K14AC_ESN_03_replicate2

description: Chip-Seq


title: ChIP-seq from H1-hESC (ENCLB839IKQ)

description:
https://www.encodeproject.org/experiments/ENCSR000AMI/
***************
biological replicate number: 4
technical replicate number: 1
description: Control ChIP-seq on human H1-hESC
experiment encode accession: ENCSR000AMI
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB839IKQ
size range: 200-600

value: Control

value: stem cell

value: ENCBS952IPA at ENCODE; https://www.encodeproject.org/ENCBS952IPA/


title: ChIP-seq-Drosha-Control

value: Embryonic stem cells


title: ChIP-seq from H1-hESC (ENCLB967KMI)

description:
https://www.encodeproject.org/experiments/ENCSR000AMI/
***************
biological replicate number: 2
technical replicate number: 2
description: Control ChIP-seq on human H1-hESC
experiment encode accession: ENCSR000AMI
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB967KMI
size range: 300-600

value: embryonic

value: ENCBS011NFB at ENCODE; https://www.encodeproject.org/ENCBS011NFB/

value: ENCODE dbxrefs Cellosaurus CVCL_9771; http://web.expasy.org/cellosaurus/CVCL_9771


title: H3K9K14AC_ESN_03_replicate1

description: Chip-Seq


title: ChIP-seq-DGCR8-Control


title: H3K9K14AC_MEFTPA_replicate2

description: Chip-Seq

value: normal


title: ChIP-seq from H1-hESC (ENCLB082PCW)

description:
https://www.encodeproject.org/experiments/ENCSR000AMI/
***************
biological replicate number: 2
technical replicate number: 6
description: Control ChIP-seq on human H1-hESC
experiment encode accession: ENCSR000AMI
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB082PCW
size range: 300-600


title: Gfi1cre/+ replicate3

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

data_processing:
Reads were aligned to the mouse genome (mm10) using tophat
Gene expression levels were calculated using Htseq-count based on Genecode gene annotations
Gene expression levels were next normalized across samples using quantile normalization
Only genes with at least 40 reads in at least one sample were included in the analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each sample.

molecule: polyA RNA

source_name: Cochlear duct

growth_protocol: Mouse inner ear tissue

extract_protocol:
Direct-zol RNA Mini-prep kit (Zymo Research)
TruSeq RNA Sample Prep kit (Illumina)

treatment_protocol: Dissected cochlea from two genotypes

value: Cochlear duct


title: H3K9K14AC_EMPTY_TPA

description: Chip-Seq

value: TKO recon pMY Empty


title: ChIP-seq from K562 (ENCLB971INW)

description:
https://www.encodeproject.org/experiments/ENCSR000AKY/
***************
biological replicate number: 2
technical replicate number: 2
description: Control ChIP-seq on human K562
experiment encode accession: ENCSR000AKY
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB971INW
size range: 200-600

source_name: Homo sapiens K562 immortalized cell line

tag: line

value: immortalized cell line

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS979ZKW at ENCODE; https://www.encodeproject.org/ENCBS979ZKW/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: H3K9K14AC_MEF_03_replicate2

description: Chip-Seq

value: H3K9acK14ac ( Millipore Cat# 06-599 Lot# 1969119)


title: Gfi1cre/+ replicate1


title: Gfi1cre/+ replicate2


title: H3K9K14AC_MEF_03_replicate1

description: Chip-Seq


title: H3K9K14AC_MEFTPA_replicate1

description: Chip-Seq


title: Gfi1+/+ replicate3


title: H3K27AC_NONA_TPA

description: Chip-Seq

value: TKO recon pMY Elk-1 nonA mutant

value: H3K27ac ( Abcam Cat# Ab4729 Lot# GR144577-2)


title: Gfi1+/+ replicate1


title: H3K27AC_NONA_03

description: Chip-Seq


title: Gfi1+/+ replicate2


title: 1FV31

city: Xinxiang

first: Changbo

last: Ou

state: Henan

address: No.90 Hualan Road

country: China

institute: Henan Institute of Science and Technology

description: Processed data file: All_sample_gene_expression_information.txt

data_processing:
The raw reads were cleaned by a short-reads pre-processing tool (FASTX-Toolkit, version 0.0.13).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to galGal4 whole genome using TopHat2 (version: 2.0.9).
Genome_build: galGal4 (Gallus_gallus-4.0)
Supplementary_files_format_and_content: All_sample_gene_expression_information.txt: Tab-delimited text file includes FPKM values for each Sample.

organism: Gallus gallus

source_name: bursae, IBDV, 1 dpi

extract_protocol:
Total RNA was separately extracted from each bursa using RNAiso Plus Total RNA extraction reagent (TAKARA, China) following the manufacturer's instructions and checked for RNA integrity number (RIN) to inspect RNA integrity by an Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Chickens from the infection group were inoculated with 0.1 mL of 103 EID50 IBDV CJ801 stock through eye-nose drops. The chickens from the mock group were kept in a separate isolator and mock challenged with PBS.

tag: breed

value: White Leghorn

value: bursa of Fabricius

value: infection with infectious bursal disease virus (IBDV)

tag: time point

value: 1 dpi


title: 1FV21

tag: treatment


title: 3FV3

source_name: bursae, IBDV, 3 dpi

tag: tissue

value: 3 dpi


title: H3K27AC_FW_03

description: Chip-Seq

value: TKO recon pMY Elk-1 FW mutant


title: H3K27AC_FW_TPA

description: Chip-Seq


title: 1FH31

source_name: bursae, mock

value: mock infection


title: 1FH21


title: H3K27AC_WT_TPA

description: Chip-Seq

value: TKO recon pMY Elk-1 wt


title: H3K27AC_WT_03

description: Chip-Seq


title: 1FH11


title: H3K27AC_EMPTY_03

description: Chip-Seq

value: TKO recon pMY Empty


title: 1FV11


title: 3FV4


title: H3K27AC_ESNTPA_replicate1

description: Chip-Seq

value: TCF KO (TKO)


title: H3K27AC_ESN_03_replicate2

description: Chip-Seq


title: H3K27AC_ESN_03_replicate1

description: Chip-Seq


title: H3K27AC_MEFTPA_replicate1

description: Chip-Seq

value: normal


title: H4K16AC_NONA_TPA

description: Chip-Seq

value: H4K16ac ( Abcam Cat# Ab61240, Lot# GR284-15)


title: BisPCR2_6dpfF25AC5

city: Olso

first: Jorke

last: Kamstra

address: Ullevålsveien 72

department: Basic Sciences and Aquatic Medicine

country: Norway

institute: Norwegian University of Life Sciences

description: processed data file: 6dpfF2.xlsx

data_processing:
Trimming was performed with trim_galore (v0.4.0) with the following parameters:  RRBS: trim_galore --quality 20 --phred64 --paired --three_prime_clip_R1 10 --clip_R2 5 --three_prime_clip_R2 10 --fastqc –rrbs  BisPCR2:  trim_galore –fastqc --paired --clip_R1 20 --clip_R2 20
Bismark (0.14.5) mapping was performed with the following parameters:   bismark –bowtie2 -N 0 -L 30 --score_min L,0,-0,6
Sorted bismark.sam files were imported in MethylKit (v 0.9.2) with the read.bismark function, only allowing sequence reads with a phred score higher than 20 and minimum 5 reads per CpG. Next, samples were filtered by excluding reads above the 99.9 percentile, since these reads are either mapped against repeat elements or have very high PCR bias. Two strategies were taken to assess differential methylation. First, differentially methylated regions (DMRs) were found by dividing the genome in regions of 300 bp, with at least 4 Cs analyzed with at least 5 reads. With this analysis, DMRs were detected using a FDR cut off of 1% and a methylation difference of at least 10%. These probes were used for downstream analysis pathway analysis (see supplemental excel files CvsMEHP.xlsx and Cvs5AC.xlsx).
Data from Bismark methylation extractor loaded into Seqmonk (v0.33) genome browser. (used to feature enrichment)
BisPCR2:Data from Bismark methylation extractor loaded into Seqmonk (v0.33) genome browser. Used the logistic regression filter in R to assess differential methylation
Genome_build: GRCz10
Supplementary_files_format_and_content: Processed data files are in excel format. They represent differential methylated sites or regions, as analyzed by Seqmonk or MethylKit.

organism: Danio rerio

source_name: 6 dpf whole zebrafish embryos

extract_protocol:
Precipitation and purification of genomic DNA was performed with the Gentra puregene tissue DNA extraction kit (Qiagen, Germany). Pools of zebrafish (10 and 2 embryos, for 6 and 15 dpf, respectively) and tissues were snap frozen in liquid nitrogen. Prior to DNA extraction the pools of zebrafish embryos and tissues were disrupted in 300 µL lysis buffer with a 20G needle, followed by an overnight incubation at 65°C with 1.5 µL of proteinase K (Qiagen, Germany) and 1.5 µL of RNAse A (20 mg/mL) (Life Technologies, Germany). After the incubation an extra 1.5 µL of RNAse was added and samples were incubated at room temperature for 1 hour. Proteins were precipitated with protein precipitation buffer (Qiagen, Germany) and DNA was precipitated by adding 0.5 mL isopropanol and 90 µL 3M NaAc (pH 5.3). After centrifugation (1 min, 13000 rpm), the pellet was washed twice with 70% ethanol, followed by rehydration in TE buffer. Samples were stored at -20°C until further analysis. Quality of DNA was assessed by gel electroforeses for fragmentation and RNA contamination, and quantity and purity by nanodrop (ND-1000, Thermo Scientific, Germany).
Genomic DNA was measured with the Quant-it Picogreen dsDNA assay (Thermo Fischer) and 1 µg total genomic DNA was digested overnight with MSP1 at 37°C. Digestions were terminated by adding 0.5M EDTA and digested DNA was purified on a GeneJET PCR purification column (Thermo Fischer). Libraries were made using the NEBNext Ultra DNA library preparation kit for Illumina, including methylated index adapters. Adapter ligated fragments were bisulfite converted using the zymo EZ DNA Methylation Gold kit (Zymo Research, US), followed by 14 cycles of PCR. PCR products were purified suing AMPure XP beads and quality was assessed on a Bioanalyzer (Agilent, Belgium), using a High sensitivity DNA chip (Agilent, Belgium). Concentrations of the library were measured by QPCR. Samples were pooled in equal concentrations and sequencing was performed on an Illumina HiSeq2500 in paired end (2x100pb)
We developed primers for a random subset of DMCs. We used the recently developed bisPCR2 method which uses two rounds of PCR [1]. One round is used for amplifying PCR products with primers with illumina adapter overhangs. In a second PCR all amplicons of one sample are pooled in equal amounts (gel electrophoresis intensity bands) and are subjected to PCR with specific indices and standard illumina library primers. Bernstein et al reported 48 primer indices in their method, which we all used. We followed the method with slight deviations. First we developed primers using bisearch (http://bisearch.enzim.hu/), added the overhangs and optimized and checked the products with the type-it HRM kit (Qiagen, Germany). We checked the right product size, the Cq value of the product and the efficiency of the PCR with unmethylated to methylated control material. To produce unmethylated DNA, we subjected 50 ng of 6 dpf zebrafish genomic DNA to a whole genome amplification reaction with the repli-G kit (Qiagen, Germany) according to the manufacturer’s recommendations. Furthermore we subjected 1 µg of the same DNA sample to an M.SssI CpG methylase reaction (New England Biolabs, USA) to produce fully methylated DNA using 2 µl of NEB2 buffer, 0.5 µL of 32 mM SAM, 4 U of M.SssI in a 20 µL reaction. After 2 hr incubation at 37 ºC another 0.5 µL of SAM and 4 U of M.SssI was added to the sample and the mixture was incubated for another 4 hrs. Samples were bisulfite converted with the epitect bisulfite kit according to the manufacturer (Qiagen, Germany) and measured on nanodrop (ND-1000, Thermo Scientific) in ssDNA mode for an estimation of the concentration. Samples were diluted to 5 ng/µL and mixed in different ratios (0, 25, 50, 75 and 100%). Type-IT HRM reactions, which is the same family of TAQ as the pyromark kit (used in the  bisPCR2 method), were performed in 10 µL buffer, 700 nM primer mix and 10 ng template in 20 µL reactions. All PCR reactions were performed with a 5 min hot start and cycling condition of 95ºC 30 s, Ta 30 s, 63, 2 min (45 cycles). The optimized Ta is shown in supplementary table $$. Following PCR#1 optimization, the protocol of Bernstein et al [1] was followed using the pyromark PCR kit (Qiagen, Germany), using optimized annealing temperatures and an extension temperature of 63 ºC, which greatly enhanced Cq values and unbiased the PCR reactions with regard to methylated or unmethylated DNA. PCR#1 reactions were performed with the pyromark PCR kit (Qiagen, Germany) in 20 µL reactions (10 µL buffer, 700 nM primer mix, 20 ng DNA template) with a 15 min hot start, followed by 45 cycles of 95 ºC 30s, TaºC 30s and 63ºC for 1 min and a final extension of 10 min. After all PCR reactions were performed, amplicons were pooled. PCR#1 pools were purified using the Qiagen PCR purification kit (Qiagen, Germany) and concentrations were measured on nanodrop (ND-1000, Thermo Scientific). PCR#2 reactions were performed with index specific primers in 20 µL reactions consisting of 10 µL pyromark buffer, 700 nM index primer, 700 nM library primer and 1 ng of pooled PCR#1 product, with 15 min hot start, followed by 10 cycles of 95 ºC 30 s, 56 ºC 30 s and 63 ºC for 2 min followed by a final extension of 10 min. PCR#2 samples were purified with AMPure XP beads (Beckman Coulter, USA) according to manufacturer. Concentrations were measured using the Qubit fluorimeter (Life technologies, Norway) and calculated to nM using the formula:   c (nM) =(Qubit conc (ng/µL)*1000000)/(660*average length)  A subset of PCR#2 samples was analyzed on agilent 2100 bioanalyzer and highly comparable profiles were observed between analyzed samples (data not shown). PCR#2 samples were diluted in equimolar portions to 2 nM and next generation sequencing was performed as described earlier by Bernstein et al. After sequencing the samples were analyzed as described above. Differential methylation was calculated using logistic regression with BH FDR multiple comparisons and sites with a difference of more than 10% methylation were considered biologically relevant differences.    1. Bernstein DL, Kameswaran V, Le Lay JE, Sheaffer KL, Kaestner KH. The BisPCR2 method for targeted bisulfite sequencing. Epigenetics Chromatin. 2015;8:27.

value: whole embryos

tag: strain

value: AB strain

tag: Stage

value: 6 dpf

tag: generation


title: H3K27AC_MEFTPA_replicate2

description: Chip-Seq

tag: genotype

tag: chip antibody


title: H3K27AC_MEF_03_replicate2

description: Chip-Seq

tag: scaling factor used (reads*scaling factor)


title: H3K27AC_MEF_03_replicate1

description: Chip-Seq


title: H4K16AC_NONA_03

description: Chip-Seq

value: TKO recon pMY Elk-1 nonA mutant


title: H4K16AC_FW_03

description: Chip-Seq


title: H4K16AC_FW_TPA

description: Chip-Seq


title: BisPCR2_6dpfF25AC4

description: processed data file: 6dpfF2.xlsx


title: BisPCR2_6dpfF25AC3

description: processed data file: 6dpfF2.xlsx


title: BisPCR2_6dpfF25AC2

description: processed data file: 6dpfF2.xlsx


title: H3K27AC_EMPTY_TPA

description: Chip-Seq

value: H3K27ac ( Abcam Cat# Ab4729 Lot# GR144577-2)


title: BisPCR2_6dpfF25AC1

description: processed data file: 6dpfF2.xlsx


title: H4K16AC_EMPTY_TPA

description: Chip-Seq


title: H4K16AC_WT_TPA

description: Chip-Seq


title: H4K16AC_ESNTPA_replicate2

description: Chip-Seq


title: BisPCR2_6dpfF2MEHP5

description: processed data file: 6dpfF2.xlsx

value: MEHP (30 µM)


title: BisPCR2_6dpfF2MEHP3

description: processed data file: 6dpfF2.xlsx


title: H4K16AC_WT_03

description: Chip-Seq


title: H4K16AC_EMPTY_03

description: Chip-Seq


title: H3K27AC_ESNTPA_replicate2

description: Chip-Seq


title: H4K16AC_ESN_03_replicate1

description: Chip-Seq


title: BisPCR2_6dpfF2MEHP4

description: processed data file: 6dpfF2.xlsx


title: BisPCR2_6dpfF2MEHP1

description: processed data file: 6dpfF2.xlsx


title: BisPCR2_6dpfF2MEHP2

description: processed data file: 6dpfF2.xlsx


title: BisPCR2_6dpfF2C4

description: processed data file: 6dpfF2.xlsx

value: Control (0.01% DMSO)


title: SmallRNA-seq-DcrKO-JQ1-12hr

data_processing:
Small RNA-seq samples were analyzed by Illumina HiSeq 2000
Sequences from the Illumina HiSeq 2000 Sequencing system were processed for adaptor removal and size exclusion of sequences < 15 nt with Cutadapt.
Filtered reads were mapped to mm9 assembly with bowtie 1.0.1 (Langmead et al., 2009), allowing two mismatches.
Pre-miRNA expression levels were computed as the number of reads that mapped to pre-miRNA in miRBase v18..
Genome_build: mm9
Supplementary_files_format_and_content: Bw files were produced in a rpm scale.

source_name: Dicer knockout embryonic stem cells

growth_protocol: mESCs were cultured in mES media.

extract_protocol:
Small RNA fraction from Dicer KO mESCs was extracted by miRNeasy Mini Kit (Qiagen).
Small RNA fraction was subjected to library preparation using the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs), and analyzed by Illumina HiSeq 2000.

treatment_protocol: Cells were treated with DMSO or JQ1 (500 nM) for 6 or 12 hrs.

tag: cell type

value: Embryonic stem cells

value: Dicer KO


title: BisPCR2_6dpfF2C5

description: processed data file: 6dpfF2.xlsx


title: H4K16AC_MEFTPA_replicate1

description: Chip-Seq


title: BisPCR2_6dpfF2C2

description: processed data file: 6dpfF2.xlsx


title: H4K16AC_MEFTPA_replicate2

description: Chip-Seq


title: H4K16AC_MEF_03_replicate2

description: Chip-Seq


title: BisPCR2_6dpfF2C1

description: processed data file: 6dpfF2.xlsx


title: BisPCR2_6dpfF15AC5

description: processed data file: 6dpfF1.xlsx


title: BisPCR2_6dpfF15AC4

description: processed data file: 6dpfF1.xlsx


title: H3K9S10_NONA_TPA

description: Chip-Seq


title: BisPCR2_6dpfF15AC3

description: processed data file: 6dpfF1.xlsx


title: H4K16AC_ESNTPA_replicate1

description: Chip-Seq


title: H4K16AC_ESN_03_replicate2

description: Chip-Seq


title: H3K9S10_FW_TPA

description: Chip-Seq


title: BisPCR2_6dpfF15AC2

description: processed data file: 6dpfF1.xlsx


title: H3K9S10_FW_03

description: Chip-Seq


title: BisPCR2_6dpfF1MEHP4

description: processed data file: 6dpfF1.xlsx


title: H3K9S10_NONA_03

description: Chip-Seq


title: BisPCR2_6dpfF1MEHP5

description: processed data file: 6dpfF1.xlsx


title: H3K9S10_WT_03

description: Chip-Seq


title: BisPCR2_6dpfF1MEHP3

description: processed data file: 6dpfF1.xlsx


title: H3K9S10_EMPTY_TPA

description: Chip-Seq


title: BisPCR2_6dpfF1MEHP2

description: processed data file: 6dpfF1.xlsx


title: BisPCR2_6dpfF15AC1

description: processed data file: 6dpfF1.xlsx


title: BisPCR2_6dpfF2C3

description: processed data file: 6dpfF2.xlsx


title: H3K9S10_EMPTY_03

description: Chip-Seq


title: H3K9S10_ESN_TPA_replicate2

description: Chip-Seq


title: BisPCR2_6dpfF1C4

description: processed data file: 6dpfF1.xlsx


title: H4K16AC_MEF_03_replicate1

description: Chip-Seq


title: BisPCR2_6dpfF1C3

description: processed data file: 6dpfF1.xlsx


title: H3K9S10_ESN_03_replicate1

description: Chip-Seq


title: BisPCR2_6dpfF1C5

description: processed data file: 6dpfF1.xlsx


title: H3K9S10_MEF_TPA_replicate2

description: Chip-Seq


title: BisPCR2_6dpfF1C2

description: processed data file: 6dpfF1.xlsx


title: BisPCR2_6dpfF1C1

description: processed data file: 6dpfF1.xlsx


title: H3K9S10_WT_TPA

description: Chip-Seq


title: BisPCR2_F0Sperm5AC6

description: processed data file: SpermF0.xlsx

source_name: Sperm

value: Sperm

value: adult


title: H3K9S10_MEF_TPA_replicate1

description: Chip-Seq


title: BisPCR2_F0Sperm5AC5

description: processed data file: SpermF0.xlsx


title: H3K9S10_MEF_03_replicate1

description: Chip-Seq


title: H3K9S10_MEF_03_replicate2

description: Chip-Seq


title: Whole embryo

city: Guangzhou

first: Jingchen

last: Chen

address: International Bioisland

institute: Maijing Gene Diagnostics

description:
3ss
PolyA RNA
Processed data files: Count.txt, RPKM.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Alignment was performed with Tophat2 with following parameters: -N 4 --read-edit-dist 6 -m 1 --max-insertion-length 5 --max-deletion-length 5 --no-discordant --no-mixed --microexon-search --library-type fr-unstranded
Normalized RPKM for each gene was generated with cuffdiff2 with following parameters: -u -N --library-type fr-unstranded --library-norm-method geometric --dispersion-method blind
easyRNAseq (R package) was used to get the raw count.
Genome_build: Gallus_gallus-4.0 (galGal4.71)
Supplementary_files_format_and_content: Raw counts and normalized RPKMs are provided in tab-delimited text files (GSE69185_Count.txt, GSE69185_RPKM.txt).
Supplementary_files_format_and_content: The sequences of the transcripts are provided in a FASTA file (GSE69185_genes.fa).

source_name: whole embryo, 3 somite stage

extract_protocol:
Tissue was dissected from the embryo, lysed in lysis buffer (Ambion AM1931) and snap-frozen in liquid nitrogen. RNA was isolated using the RNAqueous-Micro Kit (Ambion AM1931).
Libraries were prepared with TrueSeq RNA Sample Preparation V2 kit (Illumina).

value: Bovans Brown

value: whole embryo

tag: developmental stage

value: 3 somite stage


title: BisPCR2_F0Sperm5AC4

description: processed data file: SpermF0.xlsx


title: Thickened otic placode

description:
8-9ss
PolyA RNA
Processed data files: Count.txt, RPKM.txt

source_name: otic placode, 8-9 somite stage

value: thickened otic placode

value: 8-9 somite stage


title: Posterior pre-placodal region

description:
HH6
PolyA RNA
Processed data files: Count.txt, RPKM.txt

source_name: otic placode, HH6

value: posterior pre-placodal region


title: Otic-epibranchial progenitors

description:
5-6ss
PolyA RNA
Processed data files: Count.txt, RPKM.txt

source_name: otic placode, 5-6 somite stage

value: otic-epibranchial progenitors

value: 5-6 somite stage


title: BisPCR2_F0Sperm5AC3

description: processed data file: SpermF0.xlsx

value: AB strain


title: BisPCR2_F0Sperm5AC2

description: processed data file: SpermF0.xlsx


title: BisPCR2_F0SpermMEHP6

description: processed data file: SpermF0.xlsx


title: BisPCR2_6dpfF1MEHP1

description: processed data file: 6dpfF1.xlsx

value: whole embryos

value: 6 dpf


title: BisPCR2_F0Sperm5AC1

description: processed data file: SpermF0.xlsx


title: Invaginating otic placode

description:
11-12ss
PolyA RNA
Processed data files: Count.txt, RPKM.txt

source_name: otic placode, 11-12 somite stage

value: invaginating otic placode

value: 11-12 somite stage


title: H3K9S10_ESN_TPA_replicate1

description: Chip-Seq

value: TCF KO (TKO)


title: H3K9S10_ESN_03_replicate2

description: Chip-Seq


title: BisPCR2_F0SpermMEHP5

description: processed data file: SpermF0.xlsx

value: MEHP (30 µM)


title: BisPCR2_F0SpermMEHP4

description: processed data file: SpermF0.xlsx

value: Sperm


title: BisPCR2_F0SpermMEHP3

description: processed data file: SpermF0.xlsx

value: adult


title: BisPCR2_F0SpermMEHP1

description: processed data file: SpermF0.xlsx


title: BisPCR2_F0SpermC1

description: processed data file: SpermF0.xlsx

value: Control (0.01% DMSO)


title: BisPCR2_F0SpermC3

description: processed data file: SpermF0.xlsx


title: BisPCR2_F0SpermC5

description: processed data file: SpermF0.xlsx


title: BisPCR2_F0SpermC2

description: processed data file: SpermF0.xlsx


title: LXD_LE_2

first: andyslee

last: Li

address: Wushan 483

institute: South China Agricultural University

data_processing:
The raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and then the dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18-25 nt were mapped to rice precursors in miRBase 20.0 (ftp://mirbase.org/pub/mirbase/CURRENT/) by BLAST search to identify known miRNAs
The unmapped sequences were BLASTed against the rice genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi).
We used PhaseTank to systemically characterize the 21 and 24nt phasiRNAs (Guo et al. 2015). Then the confidence phasiRNAs with phasing scores higher than or equal to 25 were selected (Zhai et al. 2015), and filtered the phasiRNAs that were triggered by miR2118 and miR2275 families. Finally, it yielded 1117 loci generating 21nt-phasiRNAs and 190 loci generating 24nt-phasiRNAs. PhasiRNAs with P-value (Fisher exact test) < 0.05 and log2 (fold change ratio) >1 were considered as differentially expressed phasiRNAs.
To find out the siRNAs associated with the transposable elements, we followed the method described by Zhang et al. (2015). Firstly, we filtered the reads that did not match miRNA, rRNA, tRNA, snRNA, or snoRNA, and then selected the reads which mapped to the transposable elements of rice reference genome. These subsequent of siRNAs were considered as TEs-siRNAs, and used for further analysis. The classifications of TEs-siRNAs were done by Li et al. (2016). The differentially expressed TEs-siRNAs were identified by the conditions of P-value (Fisher exact test) < 0.05 and log2 (fold change ratio) >1.
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each Sample

organism: Oryza sativa Japonica Group

source_name: rice ovary

extract_protocol: Total RNA was extracted from the anthers using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 1 μg of total RNA were used to prepare small RNA library according to the protocol of TruSeq small RNA sample preparation Kits (Illumina, San Diego, USA). Then we performed the single-end sequencing (36 bp) on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China) according to the manufacturer’s protocol. After the Illumina sequencing, the raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and then the dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to detected the known and novel miRNA.

treatment_protocol: Autotetraploid rice, 02428-4x, and its diploid rice, 02428-2x, were used in this study. 02428-4x was developed from the chromosome doubling of 02428-2x by colchicine and was self-crossed for more than 25 generations in our lab. They were planted at the experimental farm of South China Agricultural University (SCAU) under field conditions. Anthers with four pollen development stages, including pre-meiotic interphase (PMA), meiosis (MA), single microspore stage (SCP) and bi-cellular pollen stage (BCP), were collected from 02428-4x and 02428-2x based on the floret length and DAPI fluorescence (Additional file 2: Table S23). The ovary tissues were collected with their corresponding embryo sac development stages (i.e. megasporocyte formation stage (MF), megasporocyte meiosis stage (MM), functional megaspore formation stage (FMF) and eight-nucleate embryo sac developing-stage (EES)). All the samples were stored at 4 °C for cytological observation and -80 °C for RNA isolation.

tag: material

value: diploid rice

tag: floret length/mm

tag: pollen/embryo sac stage

value: megasporocyte meiosis stage (MM)


title: LXD_4LE_1

value: autotetraploid rice

value: megasporocyte formation stage (MF)


title: LXD_4LE_2


title: LXD_4LE_4

value: eight-nucleate embryo sac developing-stage (EES)


title: LXD_4L_4

source_name: rice anther

value: bi-cellular pollen stage (BCP)


title: BisPCR2_ControlDNA100%

description: processed data file: ControlDNA.xlsx

value: ControlDNA


title: LXD_4L_3

value: single microspore stage (SCP)


title: BisPCR2_ControlDNA75%

description: processed data file: ControlDNA.xlsx

value: whole embryos

value: AB strain


title: LXD_LE_3

value: functional megaspore formation stage (FMF)


title: BisPCR2_ControlDNA25%

description: processed data file: ControlDNA.xlsx

value: 6 dpf


title: LXD_4L_2

value: meiosis (MA)


title: BisPCR2_15dpfF05AC3

description: processed data file: 15dpfF0.xlsx

source_name: 15 dpf whole zebrafish embryos

value: 15 dpf


title: BisPCR2_F0SpermMEHP2

description: processed data file: SpermF0.xlsx

value: Sperm

value: MEHP (30 µM)


title: BisPCR2_ControlDNA50%

description: processed data file: ControlDNA.xlsx


title: BisPCR2_15dpfF05AC4

description: processed data file: 15dpfF0.xlsx


title: LXD_LE_1


title: LXD_4L_1

value: pre-meiotic interphase (PMA)


title: LXD_4LE_3


title: BisPCR2_15dpfF05AC2

description: processed data file: 15dpfF0.xlsx


title: BisPCR2_15dpfF05AC1

description: processed data file: 15dpfF0.xlsx


title: LXD_L_4_2

value: diploid rice


title: BisPCR2_F0SpermC4

description: processed data file: SpermF0.xlsx

value: adult

value: Control (0.01% DMSO)


title: BisPCR2_F0SpermC6

description: processed data file: SpermF0.xlsx


title: LXD_LE_4_2


title: BisPCR2_ControlDNA0%

description: processed data file: ControlDNA.xlsx


title: BisPCR2_15dpfF0MEHPC5

description: processed data file: 15dpfF0.xlsx


title: BisPCR2_15dpfF05AC5

description: processed data file: 15dpfF0.xlsx


title: LXD_L_3


title: BisPCR2_15dpfF0MEHPC4

description: processed data file: 15dpfF0.xlsx


title: BisPCR2_15dpfF0MEHPC3

description: processed data file: 15dpfF0.xlsx


title: ChrRNA-seq-DGCR8KO - replicate 1

description: chromatin-associated RNA

data_processing:
Library strategy: ChrRNA-seq
ChrRNA-seq samples were analyzed by NextSeq.
Reads were mapped to mm9 assembly and ChrRNA abundance at gene level was estimated using TopHat (version 2.0.12.) and Cufflinks (version 2.2.0.) (Trapnell et al., 2012).
For quantification of pri-miRNAs, reads were mapped to mm9 assembly with bowtie 1.0.1 (Langmead et al., 2009), allowing two mismatches, and quantitated as the numbers of reads that mapped to pre-miRNA and flanking 100 base pair regions in a reads per million scale.
Genome_build: mm9
Supplementary_files_format_and_content: Bw files were produced in a rpm scale.

source_name: DGCR8 knockout embryonic stem cells

extract_protocol:
Cells were trypsinized, washed with cold PBS and resuspended in cold lysis buffer (10 mM Tris pH 7.4; 150 mM NaCl; 0.15% NP-40; RNase inhibitor). After 5 min incubation on ice, the suspension was layered over 1 ml sucrose buffer (10 mM Tris pH 7.4; 150 mM NaCl; 24% sucrose) and centrifuged (5 min, 3500 g). After removal of supernatant, nuclei pellet was briefly rinsed with cold PBS, resuspended in 250 μl Glycerol buffer (20 mM Tris pH 7.4; 75 mM NaCl; 0.5 mM EDTA; 50% Glycerol) and mixed with 250 μl nuclear lysis buffer (10 mM Tris pH 7.4, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M Urea, 1% NP-40) by vortexing for 4 sec. After 2 min incubation on ice, samples were centrifuged for 2 min at full speed. The remaining chromatin pellet was rinsed with cold PBS and resuspended in QIAzol lysis agent. RNA was extracted using QIAshredder and miRNeasy Mini Kit (Qiagen).
After removal of rRNA by Ribo-Zero rRNA removal kit (Illumina), DNA libraries were generated using TruSeq Stranded Total RNA LT Sample Prep Kit and analyzed by NextSeq.

treatment_protocol: Cells were treated with DMSO or JQ1 (500 nM) for 12 hrs before fractionation.

value: Embryonic stem cells


title: LXD_L_2


title: BisPCR2_15dpfF0MEHPC2

description: processed data file: 15dpfF0.xlsx


title: LXD_L-1


title: BisPCR2_15dpfF0MEHPC1

description: processed data file: 15dpfF0.xlsx


title: ChrRNA-seq-WT-Control - replicate 1

description: chromatin-associated RNA

source_name: V6.5 WT embryonic stem cells

value: WT

value: control


title: ChrRNA-seq-WT-JQ1 - replicate 2

description: chromatin-associated RNA


title: ChrRNA-seq-DGCR8KO - replicate 2

description: chromatin-associated RNA


title: BisPCR2_15dpfF0C4

description: processed data file: 15dpfF0.xlsx


title: ChrRNA-seq-WT-JQ1 - replicate 1

description: chromatin-associated RNA


title: BisPCR2_15dpfF0C5

description: processed data file: 15dpfF0.xlsx


title: BisPCR2_15dpfF0C2

description: processed data file: 15dpfF0.xlsx


title: ChrRNA-seq-WT-Control - replicate 2

description: chromatin-associated RNA


title: edn1-fli1a-sox10_1

city: Los Angeles

first: Gage

middle: DeKoeyer

last: Crump

state: California

address: 1425 San Pablo St, BCC403

department: Broad CIRM Center for Regenerative Medicine and Stem Cell Research

institute: University of Southern California

data_processing:
Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification.
Pre-alignment QC showed that the reads from all samples had generally high quality, with the average Phred quality score for each sample being above 30.
Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25.
The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly (Ensembl_v80).
Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values.
Genome_build: GRCz10
Supplementary_files_format_and_content: csv text files include TPM values for each gene in each sample

source_name: Pharyngeal arches

extract_protocol:
GFP/DsRed double-positive, double-negative, and single-positive populations were collected directly into RLT lysis buffer (Qiagen). Total RNA was immediately extracted using the RNeasy Micro kit (Qiagen) following the manufacturer’s protocol.
The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip (Agilent, Santa Clara, CA). cDNA was then made from the extracted RNA using the SMARTer kit (Clontech, Mountain View, CA), according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator (Covaris, Woburn, MA) according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit (Kapa Biosystems, Wilmington, MA) and NextFlex adapters (Bioo Scientific, Austin, TX). Libraries were visualized by Bioanalyzer analysis and quantified by qPCR (Kapa library quantification kit). Sequencing was performed on Illumina HiSeq 2000 (50-bp paired end reads) and NextSeq 500 (75-bp paired end reads) machines (Illumina, San Diego, CA). DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.

value: 36 hpf

value: Genotyped


title: BisPCR2_15dpfF0C3

description: processed data file: 15dpfF0.xlsx

value: whole embryos


title: HEK293T-DXO-KO NAD-Capture 2

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description: repFpkmMatrix-isoforms.csv.gz

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to hg19 whole genome using TopHat v2.1.1 (with Bowtie 2.2.8.0) using default settings.
All samples were modeled using cuffdiff with options -p 6  --no-update-check and the UCSC hg19 genes.gtf file from the Illumina iGenomes site
Raw cuffdiff output files were loaded into the R package cummeRbund
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by cuffdiff and output by cummeRbund
Genome_build: hg19
Supplementary_files_format_and_content: Gzipped, comma-separated-values (CSV) file containing isoform_ID row labels and sample replicate column labels.  The values are FPKM.

source_name: Cell culture

growth_protocol: HEK293T cells were cultured under standard conditions with no modifications

extract_protocol:
Total RNA was isolated by TRIzol extraction, following the manufacturers recommended protocol
enrichment protocol: RiboMinus enrichment for non-ribosomal RNAs was performed as recommended by the kit manufacturer
enrichment protocol: NAD-Capture enrichment was performed using the NAD-RNA Capture protocol (Cahova et al., 2015) with minor modification.  NAD-Capture was carried out with 100µg total RNAs treated with 10µl 4-pentyn-1-ol (Sigma-Aldrich) and 1.5U Adenosine diphosphate-ribosylcyclase (ADPRC) in 100µl reaction containing 50mM HEPES, 5mM MgCl2 (pH 7) and 40U RNasin® Ribonuclease Inhibitor (Promega) at 37oC 60 minutes. The reaction minus ADPRC was used as background control. The reaction was stopped with phenol/chloroform extraction and RNAs were precipitated with ethanol. The precipitated RNAs were subjected to copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction by incubating with 250µM biotin-PEG3-azide, freshly mixed 1mM CuSO4, 0.5mM THPTA, 2mM Sodium Ascorbate in 100µl reaction with 50mM HEPES, 5mM MgCl2 (pH7) and 40U RNasin® Ribonuclease Inhibitor (Promega) at 30oC for 30 minutes. Following extraction with phenol/chloroform and RNA precipitation, the NAD clicked RNAs were captures by binding to 20µl streptavidin magnet beads at room temperature with gentle rocking for 1 hour in 100µl binding buffer (1M NaCl, 10mM HEPES (pH7) and 5mM EDTA). The beads were washed three time with wash buffer (8mM Urea, 50mM Tris-HCl (pH7.4), 0.25% Triton-X100) and three washes with nuclease free H2O.
RiboMinus-selected RNAs were reverse transcribed and converted to libraries using the Illumina TruSeq RNA Sample Preparation Kit v2.
For NAD-Capture RNAs, samples were reverse transcribed into cDNA and synthesized into dsDNA with the SMARTer® Universal Low Input RNA Kit for Sequencing (Clontech Laboratories, Inc.) following the manufacturer’s protocol.

treatment_protocol: No treatment

tag: cell line

tag: modification

value: DXO-KO

tag: enrichment

value: NAD-Capture


title: HEK293T-DXO-KO NAD-Capture 1

description: repFpkmMatrix-isoforms.csv.gz


title: BisPCR2_6dpfF0105AC62

description: processed data file: 5AC6 duplicate analysis.xls

value: AB strain

value: 6 dpf


title: BisPCR2_6dpfF0105AC52

description: processed data file: 5AC5 duplicate analysis.xls


title: BisPCR2_6dpfF0255AC6

description: processed data file: 6dpfF0.xlsx


title: BisPCR2_15dpfF0C1

description: processed data file: 15dpfF0.xlsx

value: 15 dpf


title: WT-sox10_1

source_name: Mixed/Ear

value: 20 hpf


title: HEK293T-Wt NAD-Capture 3

description: repFpkmMatrix-isoforms.csv.gz

value: Wt


title: WT-fli1a_1

source_name: Mixed/Vaculature


title: WT-hand2-sox10_1


title: BisPCR2_6dpfF0255AC5

description: processed data file: 6dpfF0.xlsx

source_name: 6 dpf whole zebrafish embryos


title: HEK293T-Wt NAD-Capture 2

description: repFpkmMatrix-isoforms.csv.gz


title: BisPCR2_6dpfF0255AC4

description: processed data file: 6dpfF0.xlsx


title: HEK293T-DXO-KO NAD-Capture 3

description: repFpkmMatrix-isoforms.csv.gz


title: WT-fli1a-sox10_1


title: BisPCR2_6dpfF0255AC3

description: processed data file: 6dpfF0.xlsx


title: HEK293T-Wt NAD-Capture 1

description: repFpkmMatrix-isoforms.csv.gz


title: HEK293T Control 2

description: repFpkmMatrix-isoforms.csv.gz

value: RiboMinus


title: BisPCR2_6dpfF0255AC2

description: processed data file: 6dpfF0.xlsx


title: BisPCR2_6dpfF0255AC1

description: processed data file: 6dpfF0.xlsx


title: BisPCR2_6dpfF0105AC6

description: processed data file: 6dpfF0.xlsx


title: MCF7_input_ShCtrl

city: Boston

first: Koen

last: Dreijerink

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using Bowtie.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline at the DFCI

source_name: MCF-7 breast cancer cells

growth_protocol: Cells were maintained at 37oC and 5% CO2 in DMEM + 10% FBS and Pen-Strep.

extract_protocol:
Cells were crosslinked, lysed in a buffer containing SDS and sonicated.
ThruPLEX-FD Prep kit, Rubicon Genomics

treatment_protocol: MCF-7 cells that had been lentivirally infected with constructs for inducible expression of small hairpin RNA's directed against the MEN1 mRNA (ShMEN1#1) or a control sequnece were synchronized for 72 hrs in phenol red-free medium (DMEM) containing 10% charcoal dextran-treated fetal bovine serum (CDT medium). Expression of small hairpin RNA's was induced by adding 100 ng/ml for 72 hrs.

tag: induced

value: ShCtrl


title: MCF7_input_ShMEN1


title: MCF7_DMSO_2

data_processing:
Basecalls were performed with FastQC version 0.10.0.
RNA-seq reads were aligned to the hg19 genome assembly using Tophat
Genome_build: hg19

extract_protocol:
RNA was extracted using RNeasy
Libraries were made from total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Samples 1-8. MCF-7 cells that had been lentivirally infected with constructs for inducible expression of small hairpin RNA's directed against the MEN1 mRNA (ShMEN1#1) or a control sequence (ShCtrl) were synchronized for 72 hrs in phenol red-free medium (DMEM) containing 10% charcoal dextran-treated fetal bovine serum (CDT medium). Expression of small hairpin RNA's was induced by adding 100 ng/ml doxycycline for 72 hrs. 10nM estradiol or vehicle was added to the cells for 45 mins. Samples 9-12. MCF-7 cells were treated with 1mM of the menin inhibitor MI-2 or DMSO for 4 days.

tag: treatment

value: DMSO


title: MCF7_MI2_1

value: 1mM of the menin inhibitor MI-2


title: BisPCR2_6dpfF0105AC5

description: processed data file: 6dpfF0.xlsx

tag: tissue


title: 42 DAF_1

city: Muan

first: Yong-Hwa

last: Lee

address: 199 Muanro

country: South Korea

institute: Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration

data_processing:
The cDNA library was sequenced and analyzed by Macrogen (Seoul, Korea) using the HiSeqTM 2000 platform (Illumina, USA).
Sequence quality was verified using FastQC ver. 0.10.0 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
We used normalized values of RPKM (reads per kilobase per million mapped reads) as expression level in RNA-Seq.
To remove the feature-length and library size effects, we calculated RPKM as a within-sample normalization method. Afterward, RPKM values for transcripts are ranked in quantiles containing identical numbers to facilitate the further statistical analysis with a balanced distribution using quantile normalization
For each contig, we calculated the fold change between the case and control. The differences in fold change were calculated between two time points (28, 35, and 42 DAF relative to 21 DAF).
Genome_build: Sequences were aligned to the cDNA of B. napus (Brassica napus Gene Index Release 5.0, March 18, 2011, using Bowtie (Langmead et al., 2009).
Supplementary_files_format_and_content: data.xlsx includes RPKM values for each Sample.  Columns are:
Test/21 DAF.fc : fold change value was calculated as the difference of the value of the expression between two groups(using normalized signal ) (ex) If the value of Test/21 DAF is "2" , it means that Test is 2 fold more expressed (up) compared with 21 DAF. If the value is "-2", it means that Test is 2 fold less expressed (down) compared with 21 DAF. Fc >=2 marked in red, FC<=2 marked in green.
Test/21 DAF.fc.sd : standard deviation of values of fc
Test/21 DAF.volume : squared root(Normalized value of 21 DAF * Normalized value of Test)
T-test test statistic, T-test p-value (raw.pval), FDR correction p-value (bh.pval)
*.mean, *.sd : Average and standard deviation  of normalized value
N_[sample name] :  normalized value for raw signal value via logarithm and normalization
[sample name]_RPKM : raw signal value
Fold change calculation : Step 1. log2fc = Normalized value of Test - Normalized value of 21 DAF. Step 2. fc = 2^(log2fc). Step 3. If fc value has between 0 and 1, fc is calculated by a minus reciprocal(= -1/fc).

organism: Brassica rapa

source_name: Seed

growth_protocol: The plants were soil-grown in a controlled greenhouse environment (16 h light/8 h dark) under a 2800-lx light. The temperature was maintained at 21 ± 1C. Plants were bagged during bolting and allowed to self-pollinate. The developing seeds of ‘Sarsyun’ (VI032716) were harvested 14, 21, 28, 35, 42, and 49 days after flowering (DAF)

extract_protocol:
Total RNA was extracted from the developing seeds collected 21, 28, 35, and 42 DAF using an RNeasy plant mini kit (Qiagen, Valencia, CA, USA).
We constructed Illumina-compatible libraries using a TruSeq RNA library preparation kit (Illumina, San Diego, CA, USA) following manufacturer protocol. The RNA libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (Illumina, CA, USA) and qualified using the Agilent 2100 Bioanalyzer.

treatment_protocol: The developing seeds of ‘Sarsyun’ (VI032716) were harvested 21, 28, 35, and 42 days after flowering (DAF)

value: 42 days after flowering

value: Seed

tag: silique type

value: tetralocular type

value: wild type


title: 42 DAF_2


title: BisPCR2_6dpfF0105AC3

description: processed data file: 6dpfF0.xlsx

tag: strain

tag: Stage


title: MCF7_MI2_2


title: 35 DAF_2

value: 35 days after flowering

tag: genotype


title: MCF7_Veh_input

extract_protocol:
Cells were crosslinked, lysed in a buffer containing sarkosyl and sonicated.
ThruPLEX-FD Prep kit, Rubicon Genomics

treatment_protocol: MCF-7 cells were synchronized for 72 hrs in phenol red-free medium (DMEM) containing 10% charcoal dextran-treated fetal bovine serum (CDT medium). Cells were treated with 10 nM estradiol or vehicle for 45 min.

tag: chip antibody

tag: cell  line


title: 28 DAF_2

value: 28 days after flowering


title: MCF7_DMSO_1


title: BisPCR2_6dpfF0105AC4

description: processed data file: 6dpfF0.xlsx

value: whole embryos

tag: generation


title: BisPCR2_6dpfF0105AC2

description: processed data file: 6dpfF0.xlsx


title: MCF7_MLL2_Veh

description: MLL2 ChIP-seq in MCF-7 cells in the absence of E2

value: anti-MLL2/TRX2 (A300-113A, Bethyl)

value: vehicle


title: 28 DAF_1

tag: developmental stage


title: BisPCR2_6dpfF0105AC1

description: processed data file: 6dpfF0.xlsx

value: AB strain

value: 6 dpf


title: 21 DAF_2

value: 21 days after flowering


title: MCF7_MLL1_Veh

description: MLL1 ChIP-seq in MCF-7 cells in the absence of E2

value: anti-MLL1 (A300-086A, Bethyl)


title: HEK293T Control 1

description: repFpkmMatrix-isoforms.csv.gz

value: Wt

value: RiboMinus


title: BisPCR2_6dpfF0MEHP6

description: processed data file: 6dpfF0.xlsx

value: MEHP (30 µM)


title: MCF7_input_E2

value: 10 nM estradiol (E2)


title: 21 DAF_1


title: BisPCR2_6dpfF0MEHP5

description: processed data file: 6dpfF0.xlsx


title: 35 DAF_1


title: BisPCR2_6dpfF0MEHP4

description: processed data file: 6dpfF0.xlsx


title: MCF7_input_Veh


title: BisPCR2_6dpfF0MEHP3

description: processed data file: 6dpfF0.xlsx


title: D0368

city: Gießen

first: Gerrit

last: Joop

address: Heinrich-Buff-Ring 26-32

department: Institute for Phytopathology and Applied Zoology

country: Germany

institute: University of Gießen

description:
Diluted by methanol
BI5Q96

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then pooled as input for de novo transcript assembly by Trinity (r20140413p1) using the following parameters: --trimmomatic --normalize_reads --normalize_max_read_cov 50 --normalize_by_read_set --jaccard_clip. Then reads were aligned to the assembly transcripts by RSEM v1.2.15.
Fragments Per Kilobase per Megabase of library size (FPKM) and expected counts (expected_counts) were called by RSEM v1.2.15
Genome_build: The transcript assembly fasta file is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include gene ID, transcript ID, real gene length and effective length, expected read counts, TPM and FPKM values for each Sample.

organism: Beauveria bassiana

source_name: whole body

extract_protocol:
RNA was harvested using Macherey and Nagel Plant RNA extraction kit, using β-mercapto-ethanol as the reducing agent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Beauveria bassiana (Ancestral and evolved isolates) were exposed to Quinone or control (methanol). The Quinone were diluted at 0.11µg per ml diluted in methanol.

value: Quinone

tag: timepoint

tag: medium

value: potato dextrose broth (PDB)


title: D0367

description:
Diluted by methanol
BI5Q96


title: MCF7_Menin_Veh

description: Menin ChIP-seq in MCF-7 cells in the absence of E2

value: anti-Menin(MEN1) (A300-115A,Bethyl)


title: BisPCR2_6dpfF0MEHP1

description: processed data file: 6dpfF0.xlsx


title: D0365

value: Control (methanol)


title: D0366

description:
Diluted by methanol
BI5Q96


title: MCF7_H3K4me3_ShMEN1_2

description: ChIP-seq of H3K4me3 in ShMEN1 treated cells, sample 2

value: H3K4me3 antibody Abcam (Ab8580)


title: BisPCR2_6dpfF0C6

description: processed data file: 6dpfF0.xlsx

value: Control (0.01% DMSO)


title: MCF7_H3K4me3_ShMEN1_1

description: ChIP-seq of H3K4me3 in ShMEN1 treated cells, sample 1


title: D0364


title: BisPCR2_6dpfF0MEHP2

description: processed data file: 6dpfF0.xlsx

value: whole embryos


title: BisPCR2_6dpfF0C5

description: processed data file: 6dpfF0.xlsx


title: MCF7_H3K4me3_ShCtrl_2

description: ChIP-seq of H3K4me3 in ShCtrl treated cells, sample 2

value: ShCtrl


title: D0363


title: MCF7_H3K4me3_ShCtrl_1

description: ChIP-seq of H3K4me3 in ShCtrl treated cells, sample 1


title: D0362

description:
Diluted by methanol
BI3Q96


title: BisPCR2_6dpfF0C4

description: processed data file: 6dpfF0.xlsx


title: BisPCR2_6dpfF0C3

description: processed data file: 6dpfF0.xlsx


title: D0361

description:
Diluted by methanol
BI3Q96


title: MCF7_Menin_E2

description: Menin ChIP-seq in MCF-7 cells after treatment with E2


title: Sal_Low Mg2+_mRNA

city: Chicago

first: Hyunwoo

state: IL

address: 900 S. Ashland Ave., MBRB #3020

department: Center for Biomolecular Sciences

institute: University of Illinois at Chicago

description:
mRNA
RNA-seq in N-minimal medium at low Mg2+ concentration (10 μM)

data_processing:
Data were processed as described by Oh et al. [Oh et al., Cell (2011) 147:1295]. Sequenced reads were trimmed using Cutadapt v 1.3.
Trimmed reads were aligned using Bowtie v 1.0.0 to Salmonella enterica rRNA and tRNA allowing two mismatches. Reads aligning to rRNA and tRNA were discarded.
The remaining reads were aligned using Bowtie v 1.0.0 against Salmonella genome (CP001363.1) allowing two mismatches. Bowtie alignments to the Salmonella genome were converted to wiggle files.
Ribosome density was calculated using center-weighted scoring as described by Oh et al. [Cell (2011) 147:1295]. Both ribosome density and mRNA coverage were normalized to reads per million (rpm) to adjust for differences in library size or sequencing depth.
Genome_build: CP001363.1
Supplementary_files_format_and_content: wig files with two columns: first column contains chromosome coordinates and second column contains ribosome or mRNA density values (read per million).

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

growth_protocol: The overnight culture of Salmonella enterica cells grown in LB, MOPS rich defined medium, N-minimal medium at low Mg2+ (10 µM), or N-minimal medium at pH 5.8 were diluted 100 fold into 200 ml of the same medium and grown to OD600 of 0.3~0.4.

extract_protocol:
Cells were harvested by rapid filtration, frozen in liquid nitrogen, and processed for ribosome profiling and mRNA seq as described [Oh et al., Cell 147, 1295 (2011)].
RNA libraries for Illumina sequencing were prepared with RNA fragments in size between 28 and 42 nt as described [Oh et al., Cell 147, 1295 (2011)].

tag: genotype/variation

value: Wild type


title: D0360

description:
Diluted by methanol
BI3Q96


title: Sal_Low pH_mRNA

description:
mRNA
RNA-seq in N-minimal medium at low pH (pH 5.8)

source_name: N-minimal medium at low pH (pH 5.8)


title: Sal_MOPS_mRNA

description:
mRNA
RNA-seq in MOPS rich defined medium

source_name: MOPS rich defined medium


title: D0359


title: BisPCR2_6dpfF0C1

description: processed data file: 6dpfF0.xlsx

value: AB strain


title: D0358


title: D0356

description:
Diluted by methanol
AQ96

value: Ancestral


title: Sal_Low pH_Ribo

description:
Ribosomal footprint
Ribosome profiling in N-minimal medium at low pH (pH 5.8)

data_processing:
Library strategy: Ribosome profiling
Data were processed as described by Oh et al. [Oh et al., Cell (2011) 147:1295]. Sequenced reads were trimmed using Cutadapt v 1.3.
Trimmed reads were aligned using Bowtie v 1.0.0 to Salmonella enterica rRNA and tRNA allowing two mismatches. Reads aligning to rRNA and tRNA were discarded.
The remaining reads were aligned using Bowtie v 1.0.0 against Salmonella genome (CP001363.1) allowing two mismatches. Bowtie alignments to the Salmonella genome were converted to wiggle files.
Ribosome density was calculated using center-weighted scoring as described by Oh et al. [Cell (2011) 147:1295]. Both ribosome density and mRNA coverage were normalized to reads per million (rpm) to adjust for differences in library size or sequencing depth.
Genome_build: CP001363.1
Supplementary_files_format_and_content: wig files with two columns: first column contains chromosome coordinates and second column contains ribosome or mRNA density values (read per million).


title: D0357


title: Sal_MOPS_Ribo

description:
Ribosomal footprint
Ribosome profiling in MOPS rich defined medium


title: Sal_Low Mg2+_Ribo

description:
Ribosomal footprint
Ribosome profiling in N-minimal medium at low Mg2+ concentration (10 μM)


title: D0355

description:
Diluted by methanol
AQ96


title: hspEdn1-fli1a-sox10

value: 36 hpf

value: hspGal4 ; UASEdn1

value: Heat shocked


title: D0354

description:
Diluted by methanol
AQ96


title: Sal_LB_Ribo

description:
Ribosomal footprint
Ribosome profiling in LB medium

source_name: LB medium


title: hspGal4-fli1a-sox10


title: D0353


title: hspNICD-fli1a-sox10

value: hspGal4 ; UASNICD


title: D0350

description:
Diluted by methanol
BI5Q72


title: D0351


title: D0352


title: jag1b-fli1a-sox10

value: Genotyped


title: D0347


title: WT-sox10_2

value: 28 hpf

value: WT


title: BisPCR2_6dpfF0C2

description: processed data file: 6dpfF0.xlsx

value: 6 dpf


title: D0348

description:
Diluted by methanol
BI5Q72

value: Quinone

value: potato dextrose broth (PDB)


title: WT-sox10_3


title: edn1-fli1a-sox10_2


title: D0346

value: Control (methanol)


title: Sal_LB_mRNA

description:
mRNA
RNA-seq in LB medium


title: WT-fli1a_2


title: D0345


title: jag1b++-fli1a-sox10


title: WT-dlx5a-sox10


title: D0334


title: WT-hand2-sox10_2


title: D0335


title: WT-fli1a-sox10_3


title: WT-fli1a-sox10_2


title: D0349

description:
Diluted by methanol
BI5Q72


title: muscle_pooled 6 pigs_enriched diet (H)

status: Public on Mar 08 2017

city: Magdalenka

first: Magdalena

last: Ogłuszka

address: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

department: Genomics

country: Poland

data_processing:
Illumina pipeline was used for image acquisition and basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Sus scrofa v.10.2 whole genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Alignment and filtering were performed using ArrayStar application from DNASTAR Lasergene Genomics Suite software.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values and counts for each Sample.

organism: Sus scrofa

source_name: muscle, diet enriched with PUFA

extract_protocol:
Total RNA was extracted from the muscle samples using RNeasy Fibrous Tissue Mini Kit (Qiagen).
Illumina TruSeq RNA Sample Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Pigs were fed either a control diet or a diet supplemented with linseed and rapeseed oil to increase polyunsaturated fatty acid (omega-6 and omega-3) content.

tag: breed

value: Polish Landrace

value: gluteus medius muscle

value: diet enriched with polyunsaturated fatty acids (PUFA)


title: muscle_pooled 6 pigs_control diet (L)

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

source_name: muscle, standard diet

value: standard diet (control)


title: wt_S_6

city: Cambridge

first: Katarzyna

middle: Kinga

last: Modrzynska

address: Genome Campus

department: Malaria program

institute: Wellcome Trust Sanger Institute

data_processing:
The raw *cram files were generated using standard NGS data analysis pipelines of the Wellcome Trust Sanger Institute (the details of the pre-processing included in the header of each file).
The raw *cram files were transformed into *bam files (supplied here as raw data) using samtools suite v. 0.1.18.
The *fastq files containing raw, unaligned reads were generated using from *bam files using picard-tools-1.117.
*fastq giles were mapped against the P. berghei transcriptome (PlasmoDB ver. 9.3) using Tophat aligner v2.0.9  set to “fr-firststrand” for library type and a maximum intron size of 15 kb.
The re-aligned *.bam files were sorted and indexed using samtools suite v. 0.1.18 and used to generate read count tables for all annotated P. berghei transcripts with HTSeq Python package v. 0.6.1
Genome_build: PlasmoDB release 9.3;
ftp://ftp.sanger.ac.uk/pub/project/pathogens/Plasmodium/berghei/March_2012/
Supplementary_files_format_and_content: A table with uncorrected read counts for each feature (predicted transcript) as described by http://www-huber.embl.de/HTSeq/doc/count.html.

organism: Plasmodium berghei

source_name: wt_P.berghei schizont culture

growth_protocol: To synchronize parasites at the schizont stage, phenylhydrazine-treated TO mice were injected intraperitoneally with ~1×107 infected red blood cells. On day 3 post infection the presence of parasitaemia (5-15%) was confirmed using Giemsa stained thin blood smears and blood was harvested by cardiac puncture. White blood cells were removed using Plasmodipur filters (Europroxima). The parasites were cultured for 22h and red blood cells harbouring schizonts or gametocytes were purified using 55% Nycodenz/culture medium cushion, as described previously (Janse et al., 2006). The resulting pellet was washed in ice cold erythrocyte lysis buffer (0.15 M NH4Cl, 0.01 M KHCO3, 0.001 M EDTA) till the supernatant was clear, in order to remove host cell RNA, and parasites were resuspended in TRIzol reagent (Invitrogen).  To obtain highly enriched gametocytes, phenylhydrazine-treated mice were infected with ~1×107 parasites, and treated with sulfadiazine by intraperitoneal injection (100 μl of 40 μg/ml solution in PBS) from day 2 post infection as well as by addition of drug to the drinking water (20mg/l). On day 4, after verifying the absence of asexual stages, the blood was harvested by cardiac puncture and transferred into suspended animation (SA) medium (RPMI1640 with L-glutamine, 25 mM HEPES, 4 mM NaHCO3, 5% FCS, pH = 7.2), which prevents gametocyte activation. White blood cells were removed using Plasmodipur filters and the blood was layered on a cushion of 48% Nycodenz/SA buffer and spun for 15 min at 500 g (no breaks) to separate the gametocytes from the other blood cells. The gametocyte layer was harvested, pelleted and resuspended in TRIzol reagent.  For ookinete samples animals were infected and drug treated as for gametocyte preparations. To initiated gamete formation and fertilization, gametocyte infected blood from 1 mouse was added to 30 ml of the ookinete medium (RPMI1640 containing 25 mM HEPES, 10% FCS, 100 µM xanthurenic acid, pH 7.5) and cultured at 19 °C . After 22 h parasites were purified using MACS CS magnetic separation columns (Miltenyi Biotec) according to manufactures instructions, with ookinete medium used for column conditioning, washes and elution. The ookinetes were spun down at 500g and resuspended in TRIzol reagent. TRIzol samples from all parasite stages were left at room temperature for 10 min and then either frozen at -80 °C or used directly for RNA extraction.

extract_protocol:
Total RNA was extracted from the Trizol lysate using standard chloroform extraction and isopropanol precipitation (Chomczynski, 1993).
1-2 μg of total RNA from each sample was used for mRNA extraction (Magnetic mRNA Isolation Kit, NEB). First strand cDNA synthesis was done using the SuperScript III First-Strand Synthesis System and a 1:1 mix of Oligo(dT) and random primers (Invitrogen). The DNA/RNA hybrids were purified using Agencourt RNAClean XP beads (Beckman Coulter) and the second cDNA strand was synthetized using dUTP nucleotide mix, DNA Polymerase I (Invitrogen) and RNAseH (NEB) during  2.5 h at 16 °C. CDNA was purified and fragmented using a Covaris S220 system (Duty Cycle = 20, Intensity = 5, Cycles/burst =200, time= 30 s). The ~200 bp long fragments were end-repaired, TA-tailed and ligated to Illumina adapters with index tags using NEBNext kits according to the manufacturer’s instructions. Excess adapters were removed by two rounds of clean-up with 1x of Agencourt AMPure XP beads. Final libraries were eluted in 30 μl water, quality-controlled using Agilent High Sensitivity DNA chip, digested with USER enzyme and and submitted for sequencing.

tag: life stage

value: schizont

value: wt

tag: culture type

value: P.berghei schizont culture


title: ap2-o4_S_3

source_name: ap2-o4 ko_P.berghei schizont culture

value: ap2-o4 ko


title: ap2-sp2_S_3

source_name: ap2-sp2 ko_P.berghei schizont culture

value: ap2-sp2 ko


title: 131970_S_3

source_name: PBANKA_131970 ko_P.berghei schizont culture

value: PBANKA_131970 ko


title: ap2-sp_S_3

source_name: ap2-sp ko_P.berghei schizont culture

value: ap2-sp ko


title: ap2-l_S_3

source_name: ap2-l ko_P.berghei schizont culture

value: ap2-l ko


title: WT-fli1a_3

value: 36 hpf

value: WT


title: wt_S_5


title: ap2-sp2_S_2


title: ap2-sp3_S_3

source_name: ap2-sp3 ko_P.berghei schizont culture

value: ap2-sp3 ko


title: 131970_S_2


title: ap2-sp_S_2


title: D0337

description:
Diluted by methanol
AQ72

value: Ancestral

value: Quinone

value: potato dextrose broth (PDB)


title: ap2-sp3_S_2


title: ap2-l_S_2


title: ap2-sp2_S_1


title: D0333

value: Control (methanol)


title: wt_S_4


title: ap2-sp_S_1


title: 131970_S_1


title: ap2-l_S_1


title: ap2-o4_S_1


title: ap2-o3_G_3

source_name: ap2-o3 ko_purified P.berghei gametocytes

value: gametocyte

value: ap2-o3 ko

value: purified P.berghei gametocytes


title: ap2-o3_O_3

source_name: ap2-o3 ko_purified P.berghei ookinetes

value: ookinete

value: purified P.berghei ookinetes


title: ap2-o_G_3

source_name: ap2-o ko_purified P.berghei gametocytes

value: ap2-o ko


title: ap2-sp3_S_1

value: schizont

value: P.berghei schizont culture


title: ap2-o_O_3

source_name: ap2-o ko_purified P.berghei ookinetes


title: ap2-o2_O_3

source_name: ap2-o2 ko_purified P.berghei ookinetes

value: ap2-o2 ko


title: wt_G_3

source_name: wt_purified P.berghei gametocytes

value: wt


title: ap2-o2_G_3

source_name: ap2-o2 ko_purified P.berghei gametocytes


title: ap2-o4_S_2

value: ap2-o4 ko


title: ap2-o_G_2


title: ap2-o2_G_2


title: ap2-o3_O_2


title: ap2-o_O_2


title: wt_G_2


title: ap2-o3_O_1


title: ap2-o_G_1


title: wt_O_2

source_name: wt_purified P.berghei ookinetes


title: ap2-o2_G_1


title: wt_O_3


title: ap2-o3_G_1


title: ap2-o_O_1


title: wt_G_1


title: ap2-o3_S_3

source_name: ap2-o3 ko_P.berghei schizont culture


title: wt_O_1


title: ap2-o2_S_3

source_name: ap2-o2 ko_P.berghei schizont culture


title: ap2-g2_S_3

source_name: ap2-g2 ko_P.berghei schizont culture

value: ap2-g2 ko


title: ap2-g_S_3

source_name: ap2-g ko_P.berghei schizont culture

value: ap2-g ko


title: ap2-o3_S_2


title: ap2-o_S_2

source_name: ap2-o ko_P.berghei schizont culture


title: wt_S_3

source_name: wt_P.berghei schizont culture


title: ap2-g2_S_2


title: ap2-o3_G_2


title: ap2-g_S_2


title: wt_S_2


title: ap2-o2_S_2


title: ap2-g2_S_1


title: ap2-g_S_1


title: ap2-o_S_1


title: ap2-o3_S_1


title: ap2-o2_S_1


title: wt_S_1


title: L8 [RNA-seq]

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

data_processing:
All the reads were demultiplexed according to their index sequences using CASAVA version 1.8 (Illumina)
Paired end fastq files were mapped to refenrence genome by using Tophat 2.0.10 with default parameters.
The output mapping files from the TopHat2 alignment, along with the GTF file from ENSEMBL (http://uswest.ensembl.org/) rat gene annotation v75.30, were used in the htseq-count (http://www-huber.embl.de/users/anders/HTSeq/) to count the total number of reads mapped to each gene.
The expression level of mRNAs in each library was obtained by normalizing reads number to counts per million reads (CPM): CPM = (gene reads number / total mapped reads number per library) × 1,000,000.
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: Tab-delimited text files include CPM values (Abundance of mRNAs) for each Sample

organism: Ovis aries

source_name: 10% decrease in body mass_Testes

extract_protocol:
Testes tissues were frozen on dry ice, and RNA was extracted using Trizol reagent. Illumina TruSeq Stranded mRNA Library Prep Kit (Cat#RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: male

tag: fed for

value: 10% decrease in body mass over 65 days

value: testes


title: L7 [RNA-seq]

tag: tissue


title: L5 [RNA-seq]


title: H8 [RNA-seq]

source_name: 10% increase in body mass_Testes

value: 10% increase in body mass over 65 days


title: L1 [RNA-seq]


title: L3 [RNA-seq]


title: L2 [RNA-seq]


title: L6 [RNA-seq]


title: L4 [RNA-seq]


title: ap2-o_S_3


title: H3 [RNA-seq]


title: H6 [RNA-seq]


title: H4 [RNA-seq]


title: H5 [RNA-seq]


title: H7 [RNA-seq]


title: H1 [RNA-seq]


title: NA12892exosome.reseq

first: Emiy

middle: K

last: Tsang

department: Pathology

institute: Stanford University

description: Resequencing of the NA12892exosome library

data_processing:
Sequencing adapters were trimmed with Trimmomatic (v0.27) and were also provided to Novoalign (v3.00.02), which handled incomplete adapter trimming while mapping. The reads were mapped in two steps where they were first mapped to miRBase (release 20) and piRNABank then unmapped reads were aligned to the human reference genome (hg19).
The reads that mapped to the reference genome were assigned to transcripts annotated in Gencode (version 17), miRBase or piRNABank using HTSeq (v0.5.4p3).
The read counts from the first mapping step were added to those generated by HTSeq to get a single read count per transcript.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including counts for each Sample

source_name: lymphoblastoid cell line exosomes

growth_protocol: CEPH/UTAH family EBV-transformed peripheral blood B lymphoblastoid cell lines (LCLs) (Cat# XC01463) were purchased from Coriell Institute for Medical Research and were grown in RPMI 1640 supplemented with 10% fetal calf serum (Gibco, Life Technologies) and 1x penicillin/streptomycin (Life Technologies) in humidified 5% CO2 to 150 x 106 cells while maintaining a maximum density of 2\times 106 cells/ml.  Fetal calf serum was depleted of bovine exosomes prior to use by overnight centrifugation at 120,000 x g.

extract_protocol:
Small RNA from Trizol-lysed LCLs and exosomes was isolated from 1 µg total RNA using the TruSeq Small RNA Sample Prep Kit (Illumina, San Diego) with minor modifications.
Small RNA libraries were constructed following standard Illumina protocols. PCR-amplified small RNA libraries were gel purified with 3% NuSieve GTG low-melt agarose (Lonza, Rockland) and target bands of 147–157 nt, containing adapter sequence of 125 nt, were excised and column purified (Qiagen, Germantown).

treatment_protocol: Exosomes were isolated by differential centrifugation and filtration through a 200 nm Acrodisc (PAL Corp, Ann Arbor).

tag: cell line

tag: cell type

value: EBV transformed peripheral blood B lymphocytes

tag: compartment

value: exosome


title: NA12893exosome.reseq

description: Resequencing of the NA12893exosome library


title: NA12891exosome.reseq

description: Resequencing of the NA12891exosome library


title: NA12890exosome.reseq

description: Resequencing of the NA12890exosome library


title: NA12888exosome.reseq

description: Resequencing of the NA12888exosome library


title: NA12887exosome.reseq

description: Resequencing of the NA12887exosome library


title: NA12884exosome.reseq

description: Resequencing of the NA12884exosome library


title: NA12886exosome.reseq

description: Resequencing of the NA12886exosome library


title: NA12885exosome.reseq

description: Resequencing of the NA12885exosome library


title: NA12883exosome.reseq

description: Resequencing of the NA12883exosome library


title: NA12882exosome.reseq

description: Resequencing of the NA12882exosome library


title: NA12893cell.reseq

description: Resequencing of the NA12893cell library

source_name: lymphoblastoid cell line

value: cell


title: NA12878exosome.reseq

description: Resequencing of the NA12878exosome library


title: NA12879exosome.reseq

description: Resequencing of the NA12879exosome library


title: NA12889cell.reseq

description: Resequencing of the NA12889cell library


title: NA12881exosome.reseq

description: Resequencing of the NA12881exosome library


title: H2 [RNA-seq]


title: NA12892cell.reseq

description: Resequencing of the NA12892cell library


title: NA12880exosome.reseq

description: Resequencing of the NA12880exosome library


title: NA12891cell.reseq

description: Resequencing of the NA12891cell library


title: NA12890cell.reseq

description: Resequencing of the NA12890cell library


title: NA12887cell.reseq

description: Resequencing of the NA12887cell library


title: NA12888cell.reseq

description: Resequencing of the NA12888cell library


title: NA12885cell.reseq

description: Resequencing of the NA12885cell library


title: NA12886cell.reseq

description: Resequencing of the NA12886cell library


title: NA12884cell.reseq

description: Resequencing of the NA12884cell library


title: NA12883cell.reseq

description: Resequencing of the NA12883cell library


title: NA12889exosome.reseq

description: Resequencing of the NA12889exosome library


title: NA12880cell.reseq

description: Resequencing of the NA12880cell library


title: NA12878cell.reseq

description: Resequencing of the NA12878cell library


title: NA12879cell.reseq

description: Resequencing of the NA12879cell library


title: NA12877cell.reseq

description: Resequencing of the NA12877cell library


title: Sham 4 batch2

first: Xia

last: Yang

address: 2000 Terasaki Life Sciences Bldg, 610 Charles E. Young Drive East

department: IBP

institute: UCLA

description: replicate 1

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.  Bisulfite-converted reads were aligned to aligned to rat genome (UCSC assembly 5.0) using using the bisulfite aligner BS Seeker2, which utilizes the short read aligner Bowtie. As bisulfite treatment converted unmethylated cytosines (Cs) to thymines (Ts), we estimated the methylation level at each covered cytosine by methylation percentage which was calculated as NC/(NC + NT), where NC is the number of methylated reads and NT is the number of unmethylated reads
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files including the methylation level of cytosines in CpG, CHH and CHG context. The 8 fields in the files are (1) chromosome, (2) nucleotide on Watson (+) strand, (3) position, (4) context (CG/CHG/CHH), (5) dinucleotide-context (CA/CC/CG/CT), (6) methylation-level = #_of_C / (#_of_C + #_of_T)., (7) #_of_C (methylated C, the count of reads showing C here), (8) = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here)

organism: Rattus norvegicus

source_name: rat WBC

extract_protocol:
Geome DNA was extracted with Qiagen AllPrep DNA/RNA Mini Kit. Quantity and quality of DNA were checked using Nanodrop (Thermo Fisher Scientific, MA, USA), Qubit RNA assay (Life Technologies, NY, USA) and gel electrophoresis
Reduced representation bisulfite sequencing (RRBS) libraries were constructed as described previously with some modifications (Chen, P.Y. et al. Physiol Genomics 45, 565-576). Briefly, about 1,000 ng genomic DNA was digested with the MspI enzyme. Digested DNA was then purified, end-repaired, and adenylated, followed by ligation to Illumina TruSeq barcode adapters (Illumina Inc, CA, USA). Fragments of 150-300 bp in size were selected, bisulfite-treated, and sequenced using an Illumina Hiseq 2500 System (Illumina Inc, CA, USA).

tag: strain

value: Sprague Dawley

tag: Sex

value: WBC

tag: treatment

value: sham surgery


title: Sham 3 batch2

description: replicate 1


title: FPI 4 batch2

description: replicate 1

value: fluid percussion injury


title: NA12877exosome.reseq

description: Resequencing of the NA12877exosome library


title: FPI 3 batch2

description: replicate 1


title: Sham 2 batch2

description: replicate 1


title: NA12882cell.reseq

description: Resequencing of the NA12882cell library


title: FPI 1 batch2

description: replicate 1


title: Con 4 batch2

description: replicate 1

value: non-procedure control


title: Sham 1 batch2

description: replicate 1


title: NA12881cell.reseq

description: Resequencing of the NA12881cell library


title: Con 3 batch2

description: replicate 1


title: Sham 4

description: replicate 1

tag: protocol


title: Con 1 batch2

description: replicate 1


title: Con 2 batch2

description: replicate 1


title: Con 3

description: replicate 1


title: Sham 3

description: replicate 1


title: FPI 4

description: replicate 1

value: fluid percussion injury (FPI)


title: FPI 2

description: replicate 1


title: FPI 1

description: replicate 1


title: Sham 1

description: replicate 1


title: FPI 3

description: replicate 1


title: Con 2

description: replicate 1


title: WBC_tbi4

description: replicate 1

data_processing:
Paired-end RNA-Seq reads were analyzed using the Tuxedo tool package comprised of Tophat/Bowtie, Cufflinks, and Cuffdiff. Specifically, we used TopHat2/Bowtie2 which allows alignment across splice junctions to map reads to the rat genome (UCSC assembly 5.0) and to discover transcript splice sites. Cufflinks were then used to assemble the aligned reads onto transcripts, and Cuffdiff was used to compare the aligned reads between different treatment groups to identify genes and gene transcripts that are differentially expressed. Multiple hypothesis testing was corrected using the Benjamini-Hochberg method to estimate false discover rate (FDR).
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and status ("FAIL","HIGHDATA","LOWDATA","OK",etc.) for each sample

extract_protocol:
Total RNA was extracted with Qiagen AllPrep DNA/RNA Mini Kit. Quantity and quality of RNA were checked using Nanodrop (Thermo Fisher Scientific, MA, USA), Bioanalyzer (Agilent Technologies, CA, USA) and Qubit RNA assay (Life Technologies, NY, USA).
The RNA-Seq libraries were prepared followed the standard Illumina protocol (http://support.illumina.com/sequencing/documentation.ilmn). Briefly, about 1,000 ng total RNA was first enriched for mRNA by poly-A selection, then fragmented, and reverse transcribed using random hexamer-primers to generate first-strand cDNA. Second-strand cDNA was then generated using RNase H and DNA polymerase. Fragments of 200-400 bp in size were next enriched through PCR and multiplex barcodes were also added. Sequencing was performed on HiSeq 2500 (Illumina Inc, CA, USA). Data quality check was done on Sequencing Analysis Viewer and demultiplexing was performed with CASAVA 1.8.2 (Illumina Inc, CA, USA).

value: white blood cells

value: traumatic brain injury


title: WBC_tbi1

description: replicate 1


title: WBC_tbi3

description: replicate 1


title: FPI 2 batch2

description: replicate 1


title: WBC_sham4

description: replicate 1

value: sham


title: WBC_tbi2

description: replicate 1


title: WBC_sham3

description: replicate 1


title: ap2-o2_O_2

value: ookinete

value: ap2-o2 ko

value: purified P.berghei ookinetes


title: CA1_tbi4

description: replicate 1

source_name: rat CA1

value: Region I of hippocampus


title: Con 4

description: replicate 1

value: male


title: CA1_tbi1

description: replicate 1


title: CA1_sham4

description: replicate 1


title: CA1_tbi2

description: replicate 1


title: Sham 2

description: replicate 1


title: CA1_tbi3

description: replicate 1


title: WBC_sham1

description: replicate 1


title: CA1_sham2

description: replicate 1


title: CA1_sham1

description: replicate 1


title: CA1_sham3

description: replicate 1


title: Con 1

description: replicate 1


title: tbi1 (RRBS)

description: replicate 1

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Bisulfite-converted reads were aligned to aligned to rat genome (UCSC assembly 5.0) using using the bisulfite aligner BS Seeker2, which utilizes the short read aligner Bowtie. As bisulfite treatment converted unmethylated cytosines (Cs) to thymines (Ts), we estimated the methylation level at each covered cytosine by methylation percentage which was calculated as NC/(NC + NT), where NC is the number of methylated reads and NT is the number of unmethylated reads
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files including the methylation level of cytosines in CpG, CHH and CHG context. The 8 fields in the files are (1) chromosome, (2) nucleotide on Watson (+) strand, (3) position, (4) context (CG/CHG/CHH), (5) dinucleotide-context (CA/CC/CG/CT), (6) methylation-level = #_of_C / (#_of_C + #_of_T)., (7) #_of_C (methylated C, the count of reads showing C here), (8) = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here)

source_name: rat hippocampus

value: hippocampus

value: TBI by fluid percussion injury (FPI)


title: tbi4 (RRBS)

description: replicate 1


title: tbi2 (RRBS)

description: replicate 1


title: sham3 (RRBS)

description: replicate 1


title: sham2 (RRBS)

description: replicate 1


title: tbi3 (RRBS)

description: replicate 1


title: WBC_sham2

description: replicate 1


title: sham1 (RRBS)

description: replicate 1


title: tbi2 (RNA-seq)

description: replicate 1


title: tbi3 (RNA-seq)

description: replicate 1


title: tbi4 (RNA-seq)

description: replicate 1


title: tbi5 (RNA-seq)

description: replicate 1


title: sham3 (RNA-seq)

description: replicate 1


title: tbi1 (RNA-seq)

description: replicate 1


title: sham2 (RNA-seq)

description: replicate 1


title: sham1 (RNA-seq)

description: replicate 1


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell223

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

data_processing:
Map read-pairs to the Mouse genome (Grcm38) with TopHat2
Quantify gene expression with HTSeq v0.6.1
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated values with read cunt for each gene and each cell. The first column contain the Ensembl gene identifier, the first row contains the cell identifier.

source_name: Whole cortex

extract_protocol:
Single cell were captured and RNA extracted on a C1 system, Fluidigm on a 5-10um chip, following manufacturer protocol. Lysis, reverse transcription and PCR were then performed directly on the chip using SMARTer Ultra Low RNA Kit for the C1 System (#634833,Takara® Clontech®). about 0.8 ng / ml per cell.
Illumina Nextera XT kit

tag: age


title: DNA methylation in iAsT cells_Replicate 2

city: Grand Rapids

first: Yvonne

middle: Nsokika

last: Fondufe-Mittendorf

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

description: Methyl-miniseq

data_processing:
Raw data files had their adapters removed using trim_galore, quality trimming was also done, reads shorter than 20 bp were discarded
Pre-processed fastq files were aligned to human hg19 using bismark
Methylation calling was done on the bamfiles to create browser tracks for CpG, CHG, and CHH sites for each sample, these are in bigbed format
Genome_build: hg19
Supplementary_files_format_and_content: bigbed, browser tracks that contain methylation count and total count of reads per site

source_name: Lung Epithelial

growth_protocol: Cell cultures were incubated at 37 degree with humidified air and 5% CO2. Cells were harvested after each treatment. Cells were grown ensuring that 95% of the cells were viable. Harvested cells were centrifuged for five minutes at 200 X g.

extract_protocol: Genomic DNA was extracted using Qiagen Dneasykit according to manusfacturers instructions.

treatment_protocol: Cells were treated with 0.5 uM Sodium Arsenite for 36 days until transformation

value: iAs-transformed lung epithelial cells


title: sham4 (RRBS)

description: replicate 1

value: Sprague Dawley


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell221


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell220


title: PEG group

city: Zhengzhou

first: Ming

address: Wenhua Road No.95

institute: Henan Agricultural University

data_processing:
Basecalls performed using illumina RTA2
circRNA-seq reads were mapped to wheat genome by BWA-MEM software by default parameters except -T = 19
circRNAs were detected and annotated with CIRI software
the junction reads of each circRNA are normalized by total reads of each library and log-transformed.
Genome_build: IWGSC1+popseq
Supplementary_files_format_and_content: an excel file including the junction reads and normalized intensity of each circRNA.

organism: Triticum aestivum

source_name: wheat

growth_protocol: Seeds of wheat cultivars (Triticum aestivum L. cv. Aikang 58) were surface-sterilized with 1% NaClO for 10 min, and rinsed 3 times in distilled water for 2 min each. After soaking in tap water for 12 h, the seeds were allowed to germinate for 4 days in a dark incubator at 25°C. Five germinating seeds were placed into each plastic pot containing half strength Hoagland’s nutrient solution in a phytotron. The environment was controlled at 25°C/22°C (day/night) under a 12 h photoperiod, a 300 μmol m-2 s-1 of photosynthetic photon flux density (PPFD), and a relative humidity of 75% to 85%

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Total RNA from each sample was used to prepare the circRNA sequencing library, which included the following steps: 1) 5 μg total RNA were pretreated to enrich circRNA using CircRNA Enrichment Kit (Cloud-seq Inc, USA). RNA libraries were constructed by using pretreated RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

treatment_protocol: The artificial dehydration stress group was induced by applying a final 20% polyethylene glycol (PEG) 6000 solution to achieve an osmotic potential of −0.975 MPa

value: leaf

tag: stress type

value: dehydration

tag: Stage

value: two-leaf

tag: cultivar

value: Aikang 58


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell218


title: DNA methylation in NT cells_Replicate 2

description: Methyl-miniseq

value: non-treated lung epithelial cells


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell217


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell219


title: sham5 (RNA-seq)

description: replicate 1


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell215


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell214


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell213


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell212


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell210


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell211


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell208


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell207


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell205


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell209


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell206


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell203


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell204


title: CK group

value: normal


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell202


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell201


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell222


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell199


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell197


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell200


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell196


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell198


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell216


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell193


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell192


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell195


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell186


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell191


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell189


title: sham4 (RNA-seq)

description: replicate 1


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell188


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell187


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell190


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell185


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell180


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell184


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell182


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell183


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell177


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell181


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell178


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell174


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell175


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell176


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell179


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell172


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell194


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell173


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell168


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell166


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell167


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell170


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell160


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell169


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell164


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell159


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell165


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell162


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell158


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell163


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell156


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell161


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell153


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell152


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell150


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell157


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell171


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell145


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell154