title: Occ1_scTHS-Seq

description: scTHS-seq data

data_processing:
Basecalls performed using bcl2fastq v2.17.1.14
Sequencing data from the same samples was concatenated together and then as input to deindexder (https://github.com/ws6/deindexer) with 0 mismatch barcode demultiplexing.
Barcode combinations associated with each read were appended to each reads header with in house perl scripts and all fastq’s were combined and mapped to a hg38 no alternative loci plus decoy reference genome (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set) and mm10 no alternative loci reference genome (GCA_000001635.5_GRCm38.p3_no_alt_analysis_set) using BWA 0.7.12-r1039. Mapped sam outputs were redemultiplexed by barcodes, converted to bam files and clonal reads removed with samtools 1.3.1
multimapping reads MAPQ<5 were removed from each single cell dataset to remove reads in repeat regions
Joint peak calling was performed on pooled bam files using SPP (v1.13; https://github.com/hms-dbmi/spp). Reads mapping within 100bps of known repeat regions according to annotations from Repeat Masker (http://www.repeatmasker.org) were removed. A smoothed density of pooled reads was generated using window tag counts with a window size of 500bps and a window step of 100bps. DNA accessible regions (peaks) were called based on the smoothed density with a minimum threshold of 5 reads and minimum span of 5 steps between each peak. Peaks were filtered using a permutation based FDR of 10e-8 and filtered for presence in at least 40 cells from the visual cortex. Called peaks were then assessed for reads in each individual cell to generate a matrix of peaks versus cells for downstream clustering and analysis.
Genome_build: GENCODE GRCh38, GENCODE GRCm38
Supplementary_files_format_and_content: tab-delimited text files including accessibilty peak files, and differential accessibility peak files, and count matrices

extract_protocol:
Cryofrozen post-mortem brain tissue was treated with nuclear extraction buffer, isolated nuclei was stained with DAPI and FACS purified.
To the 384 well plate of freshly generated uniquely barcoded Tn5059 r5 transposome complexes, 4 µL of human/mouse mixed cell sample was added for a total of ~960 nuclei/well and final concentration of 0.7 µM Tn5059 r5 transposome complex. Each sample was mixed gently 5X by the electronic pipettor. Optimally ~2000 nuclei/well are wanted, however nuclei yields were low. The 384 well plate was then incubated at 37ºC for 30 minutes. To stop the reaction, 4.0 µL of 50 mM EDTA was added to each well and mixed gently 5X by the electronic pipettor for a final concentration of 20 mM EDTA in 10 uL, followed by incubating the 384 well plate at 37ºC for 15 minutes. The 384 well plate of samples was then frozen at -20ºC overnight. The next day, the 384 well plate of samples was thawed, and one volume of cold 2X FACS buffer (1X FACS buffer: 2 mM EDTA, 1% BSA in PBS) was added to each well. Samples are then mixed gently 3X by the electronic pipettor and pooled into one tube on ice, which was spun down at 500xg for 5 minutes at 4ºC. Supernatant was removed, and tagmented nuclei resuspended in 1.5 mL cold 1X FACS buffer. Next, 75 µL eBioscience Propidium Iodide (PI) was added to the tube, and gently mixed. Nuclei were then sorted by flow cytometry into 96 well plates containing 10 µL PBS/well at 100 nuclei/well, and put on ice. Doublets were removed based on forward and side scatter plots, and PI stained events selected. Nuclei were now ready for RNA amplification and processing.
Each 96 well plate of nuclei was processed individually. First, 11 µL guanidine hydrochloride was added to each well and mixed by lightly vortexing. Reactions were purified by addition of 40 µL (1.8X) AMPure SPRI beads and lightly vortexed, then bead pelleting and 80% ethanol washes were performed with the “flick and blot” method and magnetic plate from V&P Scientific. After 80% ethanol washes were complete the plate was quickly spun down at 500xg and leftover 80% ethanol removed by pipetting. 10 µL 1X NEB Taq polymerase was added to each reaction and the plate was lightly vortexed to resuspend the beads (SPRI beads left in reaction), followed by running the reactions at 72ºC for 3 minutes for end fill in and put on ice. For in vitro transcription (IVT) amplification the NEB HiScribe T7 high yield synthesis kit was used. To each reaction a mastermix of 2 µL of 10X transcription buffer, 2 µL ATP, 2 µL CTP, 2 µL GTP, 2 µL UTP was directly added to the end fill in reactions, lightly vortexed, and incubated at 37ºC for 19 hours. To check IVT amplification, two full reactions were purified with SPRI binding buffer, run on a 6% Tris-Borate-Urea (TBU) gel for 20 minutes at 250 volts followed by SYBR gold staining and visualization on a UV-transilluminator. Next, reactions were purified by addition of 44 µL (2.0X) SPRI binding buffer (20% PEG 8000, 2.5 M NaCl, 10 mM Tris–HCl, 1 mM EDTA) to each reaction and the plate vortexed thoroughly. 80% ethanol washes and leftover 80% ethanol removal were performed as describe above, and SPRI beads were resuspended in 9 µL nuclease free water. For reverse transcription, first 2.5 µL of 20 µM random hexamers was added to each reaction, the plate vortexed lightly and then heated to 70ºC for 3 minutes, and immediately cooled on ice. Then Clontech SMART® MMLV Reverse Transcriptase kit was used with addition of 4 µL 5X first strand synthesis, 2 µL dNTP mix, 2 µL 100 mM DTT, 0.5 µL SMART MMLV RT in a mastermix to each reaction and the plate vortexed lightly. Reactions were incubated at 22ºC for 10 minutes, then 42ºC for 60 minutes, and terminated at 70ºC for 10 minutes. To degrade RNA in cDNA-RNA hybrids 1 µL of 0.5 units Enzymatics RNase H was added to each reaction, the plate was vortexed lightly and incubated at 37ºC for 20 minutes. For second strand synthesis first 2.5 µL of 20 µM sss_scnXTv2 (Table S12) was added to each reaction and lightly vortexed, then incubated for 2 minutes at 65ºC and immediately cooled on ice. Then 5.9 µL of NEB taq5X was added to each reaction and incubated at 72ºC for 8 minutes. After cooling on ice, 60 µL (2.0X) SPRI binding buffer was added to each sample. The plate was vortexed thoroughly and 80% ethanol washes and leftover 80% ethanol removal performed as described previously, and SPRI beads resuspended by light vortexing in 7 µL of nuclease free water. Double stranded cDNA fragments then undergo simultaneous fragmentation and 3’ adaptor addition with a custom nXTv2_i7 Tn5059 transposome (Table S12). To 7 µL of sample, 2 µL of 5X tagmentation buffer was added to each sample, followed by addition of 2 µL of prepared 0.7 µM custom nXTv2_i7 Tn5059 transposomes (final transposome concentration of 0.14 µM), vortexed lightly, then incubated at 55ºC for 6 minutes, and cooled briefly on ice. Immediately after cooling, 19 µL of 6.32M guanidine hydrochloride, for a final guanidine hydrochloride concentration of 4M was added to each reaction and briefly vortexed. Then 60 µL (2.0X) SPRI binding buffer was added to each sample. The plate was vortexed thoroughly and 80% ethanol washes and leftover 80% ethanol removal was performed as described previously. However, for this purification SPRI beads were resuspended in 16 µL nuclease free water and the plate was placed back onto the magnetic plate. Sample was eluted off SPRI beads held by the magnetic plate, and transferred to a qPCR plate. Standard Illumina Nextera XT v2 barcoding in an 8x12 (i5xi7) format was performed with qPCR, using custom scTHS-seq i5 indexes and standard Illumina i7 indexes (Table S12). In total, 20 µL of KAPA SYBR Fast, 2 µL of 10 µM scT7_S5XX index primer and 2 µL of 10 µM nXTv2_i7XX index primer were added to each reaction for a total volume of 40 µL, and mixed well. qPCR was run at 72ºC for 3 minutes, 95ºC for 30 seconds, followed by cycling for (95ºC for 10 seconds, 63ºC for 30 seconds, 72ºC for 1 minute) until curves reach saturation, typically 9-12 cycles. Plates were stored at -20ºC.
scTHS-seq and Nextera

value: Occipital Lobe

value: Coronal sample, Section 31

value: 23 years

value: Male

value: African American

value: Maryland Brain Bank


title: 35S:RPS4, T0, rep3

status: Public on Dec 11 2017

type: SRA

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

description: polyA-enriched and rRNA-depleted RNA

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Sequenced reads were mapped to the genome of Arabidopsis thaliana (TAIR10) using tophat v2.0.10 with parameters -a 10  -g 10 - r 160  --mate-std-dev 160 --library-type fr-unstranded
Read counts per gene per sample were obtained using the htseq-count script in the HTSeq Python package with options -s reverse -t exon
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis leaves

growth_protocol: Plants were grown for 3,5 weeks at 28°C

extract_protocol:
Total RNA were extracted using the Qiagen Rneasy kit. RNA were DNaseI-treated and a purification was done using the Qiagen Rneasy MinElute kit. Ribosomal RNAs were depleted from 2.5 µg RNA using the RiboMinus Plant Kit for RNA-seq (Life Technologies).
For library preparation, oligodT-primed cDNA synthesis was done using the TruSeq RNA preparation kit (Life Technologies).  All proceadures were performed according to the manufacturer's instructions.
paired-end RNA-seq

treatment_protocol: Plants were shifted from 28°C to 19°C for 4 and 8h before collecting and freezing the samples. T0 samples were not shifted.

tag: tissue

value: leaves

tag: genotype

value: Col-0 35S:RPS4-HS

tag: time

value: 0 h


title: 35S:RPS4, T0, rep2

description: polyA-enriched and rRNA-depleted RNA


title: PC-3M_luc2 cells RNAi Control, biological replicate 2

city: Freiburg

first: Judith

middle: M

last: Müller

address: Breisacherstr. 66

department: Uniklinik Urologie/ZKF

institute: University Freiburg

data_processing:
We aligned these reads to the hg19 build of the human genome using TopHat
The aligned reads were counted with the homer software (analyzeRNA) and DEG’s were identified using EdgeR and DESeq
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file are text files that include the overall read count for a specific transcript (indicated by the NM accession number)

molecule: total RNA

organism: Homo sapiens

growth_protocol: cells were maintained in RPMI medium supplemented with 10 % FBS and glutamine.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files).

treatment_protocol: Knockdown was performed using transfection Dharmafect 2 (Thermo Scientific, T-2002-01)

tag: cell line

value: PC-3M androgen-independent prostate cancer cell line

tag: treatment

value: RNAi Control


title: PC-3M_luc2 cells RNAi PRK1, biological replicate 2

value: RNAi PRK11


title: PC-3M_luc2 cells RNAi PRK1, biological replicate 1


title: somatic 1

city: Saint Louis

first: James

last: Umen

state: MO

address: 975 N Warson Rd

country: USA

institute: Donald Danforth Plant Science Center

data_processing:
bcl2fastq v1.8.4 software was used for base-calling
Low quality sequences, short sequences, and adaptor sequences were removed from sequenced reads using Trimmomatic.
An index of the Volvox version 2 genome was made using STAR, supplemented with the GFF3 file of the merged set of Volvox version 2 gene models, with parameters --runMode genomeGenerate  --sjdbGTFfile <GFF3 file> --sjdbGTFtagExonParentTranscript Parent  --sjdbOverhang 49
Trimmed reads were mapped to the genome index using STAR with parameters --outFilterMultimapNmax 10 --outFilterMismatchNoverLmax 0.06
Uniquely mapping reads were assigned to the merged set of gene models using HTSeq with parameters --stranded=no --minaqual 0
Read counts for each gene were normalized using upper quantile (UQ) normalization and differential gene expression analysis was done using DESeq2. In parallel, read counts were also normalized using RPKM (reads per kilobase per million mapped reads) normalization, but RPKM values were not used for differential expression analysis.
Genome_build: Vcarteri_199_v2 (Volvox version 2 genome available on Phytozome)
Supplementary_files_format_and_content: Tab-delimited text file containing raw read counts for each gene in each sample

organism: Volvox carteri

source_name: somatic cells

extract_protocol:
Cell types were separated into gonidial and somatic cell type fractions and fractions were resuspended in a 1:1 ratio of Buffer C (2% SDS in Tris-Buffered Saline) and Trizol and then immediately flash frozen in liquid nitrogen and stored at -80C. Lysates were thawed and sonicated using a Covaris S220 ultrasonicator after which DNA was removed and RNA purified using the RNeasy Mini Kit (Qiagen).
Biological replicate samples of gonidial and somatic total RNA were submitted to the Genome Technology Access Center (GTAC) in the Department of Genetics at Washington University School of Medicine for Illumina-based polyA library preparation and sequencing. oligo-dT selected RNA was fragmented to an average size of ~200nt and reverse transcribed to produce double stranded cDNA using random hexamers. cDNA ends were end repaired, 3’ dA-tailed, and then ligated to Illumina sequencing adapters. Adaptor-ligated fragments were amplified for 12 cycles using indexed primers and sequenced on an Illumina HiSeq-2500 with 50 bp single-end reads.

tag: strain

value: Eve

tag: cell type

value: somatic cells

tag: developmental stage

value: Hatched adult spheroid. Hour 42 in the 48 hour life cycle (6hrs into the second light period).


title: 35S:RPS4, T0, rep1

description: polyA-enriched and rRNA-depleted RNA


title: somatic 2


title: Oocyte_S1

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

data_processing:
Adaptor sequences and low quality bases with PHERD scores (Q) ≤ 30 were removed. And we employed Trimmomatic for removal of adapter sequences.
The read mapping into assembled transcriptome was performed using tophat2
Finally, HTSeq-count was employed for quantification.
Genome_build: We used watermelon reference genome (97103) version 1 in Curcurbit Genomics Database.
Supplementary_files_format_and_content: TSV file for each sample

organism: Gallus gallus

source_name: Embryonic cell

extract_protocol:
Total RNA was prepared from the samples and Total RNA was extracted using TRIzol reagent (MRC).
Libraries were prepared based on Illimina instruction

value: Oocyte


title: gonidia 2

source_name: gonidial cells

value: gonidial cells


title: PC-3M_luc2 cells RNAi Control, biological replicate 1


title: met18_MethylC-Seq

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: treated with bisulfite

library_source: genomic

data_processing:
Reads were mapped to TAIR10 using BRAT-BW v2.0.1 with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (converted_C / ( converted_C+ unconverted_C ) ).

molecule: genomic DNA

source_name: Seedlings

extract_protocol: Genomic DNA was extracted from 14-d-old seedlings and sent to BGI (Shenzhen, China) for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.

tag: genotype/variation

value: met18 mutant


title: gonidia 1


title: N3

status: Public on Dec 10 2017

city: shanghai

first: chun

last: luo

address: 415# fengyang road

department: neurosurgery

country: China

institute: changzheng hospital

data_processing:
Basecalls performed using CASAVA version 1.8
circRNA-seq reads were mapped to human genome by BWA-MEM software by default parameters except -T = 19
circRNAs were detected and annotated with CIRI software
Genome_build: hg19
Supplementary_files_format_and_content: Number of raw junction read

source_name: normal brain

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: normal brain

tag: tumor stage

value: normal


title: N2


title: 35S:RPS4, 4h, rep2

description: polyA-enriched and rRNA-depleted RNA

value: 4 h


title: N1


title: N5


title: T5

source_name: glioblastoma

value: glioblastoma

value: WHO IV


title: T3


title: T2


title: T1


title: C3_miRNA

city: Changchun

first: Man

last: Bai

address: Xincheng Street

department: College of animal science and technology

institute: Jilin Agricultural University

description:
small RNA
miRNA.All.Counts.txt

data_processing:
(mRNA) Reads filtering under criteria removing reads with 20% of the base quality lower than 13
(mRNA) Mapsplice v2.2.0 mapping to reference genome
(mRNA) count counting
(miRNA) We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 17bp c) adaptor sequence.
(miRNA) Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Ovis aries miRNA database and Oar_v3.1 genome.
(miRNA) count counting
Genome_build: Oar_v3.1 / miRBase 21.0
Supplementary_files_format_and_content: Counts

organism: Ovis aries

source_name: Testis

extract_protocol:
(mRNA) total  RNA was extracted using Trizol reagent. Ion Total RNA-seq Kit v2 (Life Technologies, USA) was used for the construction of sequencing libraries.
(miRNA) miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
RNA libraries were prepared for sequencing using standard protocols of Total RNA-seq Kit v2 (Life Technologies, USA). Briefly, poly(A)-containing mRNA was purified by Dynabeads (Life technologies, USA) and subsequently fractionated into short fragments using RNase III and an Ion adaptor. The short RNA fragments was ligated with a 3’ adaptor and a 5’ adaptor.  Emulsion PCR was performed using mRNA and miRNA cDNA library as the template. Then, the short mRNA fragments were reverse-transcribed and amplified to synthetize double-stranded cDNA.

treatment_protocol: Testis were collected by surgical operation and immediately frozen in liquid nitrogen

tag: age

value: testis


title: C2_miRNA

description:
small RNA
miRNA.All.Counts.txt


title: Fcx1_scTHS-Seq

city: La Jolla

first: Kun

last: Zhang

state: CA

address: 9500 Gilman Drive, MC0412, PFBH402

department: Bioengineering

institute: University of California San Diego

description: scTHS-seq data

source_name: Brain

tag: experiment

tag: patient

tag: region

value: Frontal Cortex

tag: brodmann area

tag: histology

value: Coronal sample, Section 31

value: 34 years

tag: Sex

value: Male

tag: source

value: University of Miami School of Medicine Brain Bank


title: C1_miRNA

description:
small RNA
miRNA.All.Counts.txt

tag: tissue


title: B3_miRNA

description:
small RNA
miRNA.All.Counts.txt


title: B2_miRNA

description:
small RNA
miRNA.All.Counts.txt


title: B1_miRNA

description:
small RNA
miRNA.All.Counts.txt


title: A2_miRNA

description:
small RNA
miRNA.All.Counts.txt


title: A1_miRNA

description:
small RNA
miRNA.All.Counts.txt


title: C2_mRNA

description: all.counts.txt


title: C3_mRNA

description: all.counts.txt


title: N4


title: RNA_Col-0

city: Bloomington

first: Ram

last: Podicheti

institute: Indiana University

data_processing:
NRO and RNA reads were adapter trimmed quality trimmed using Trimmomatic ver 0.33. The cutoff threshold for average base quality score over a window of 3 bases was set at 20. Reads shorter than 20 bases in length post trimming were excluded.
Trimmed NRO and RNA reads and exoChIP reads were mapped to TAIR10 Arabidopsis reference genome using Tophat ver. 2.1.0.
From NRO and RNA alignment data, the number of reads uniquely mapping to each of the annotated TAIR10 genes is computed using the software htseq-counts ver. 0.5.4p1.
From exoChIP alignment data, bedgraph files containing coverage information across the length of the reference genome are generated using custom perl scripts.
Genome_build: TAIR10
Supplementary_files_format_and_content: htcounts files contain number of uniquely mapped NRO and RNA reads for each of the TAIR10 annotated genes. These numbers are a measure of gene expression. bedgraph files contain ChIP coverage information in bedgraph format

molecule: nuclear RNA

source_name: plants

growth_protocol:
Plants were cultivated at 22°C under long-day conditions (16 h day/8 h night)
Plants were cultivated at 22°C under long-day conditions (16 h day/8 h night)

extract_protocol:
RNA was harvested using Trizol reagent. Biotinylated RNA was precipitated from total RNA with Dynabeads MyOne Streptavidin C1 (Invitrogen, Calsbad, CA) and eluted from beads by adding 50 uL of 10 uM EDTA/95% formamide and incubation at 65°C for 5 min.
Illumina TruSeq Stranded mRNA Sample Prep Kit
RNA was harvested using Trizol reagent. Biotinylated RNA was precipitated from total RNA with Dynabeads MyOne Streptavidin C1 (Invitrogen, Calsbad, CA) and eluted from beads by adding 50 uL of 10 uM EDTA/95% formamide and incubation at 65°C for 5 min.
Illumina TruSeq Stranded mRNA Sample Prep Kit

value: leaf

value: 3 week old

tag: genotype

tag: molecule type

value: nuclear RNA


title: RNA_nrpd1-3


title: T4


title: C1_mRNA

description: all.counts.txt


title: NRO_nrpe1-11

description: Biotin-UTP

value: nascent RNA


title: RNA_nrpe1-11


title: B3_mRNA

description: all.counts.txt


title: NRO_nrpd1-3

description: Biotin-UTP


title: A3_mRNA

description: all.counts.txt


title: NRO_Col-0

description: Biotin-UTP


title: exoChIP_nrpe1-11

extract_protocol:
Leaf tissue was cross-linked, lysed, and sonicated before shipping samples to Peconic LLC for chromatin immunoprecipitation (ChIP)  with RNA pol II antibody and subsequent enzymatic reactions that were performed while protein-DNA complexes were still on the beads. Subsequently, DNA was eluted from antibody beads, protein-DNA crosslinks were reversed and DNA was extracted using phenol/chloroform/isoamyl alcohol.
SOLiD Systems 5500 Series fragment library preparation
RNA was harvested using Trizol reagent. Biotinylated RNA was precipitated from total RNA with Dynabeads MyOne Streptavidin C1 (Invitrogen, Calsbad, CA) and eluted from beads by adding 50 uL of 10 uM EDTA/95% formamide and incubation at 65°C for 5 min.
Illumina TruSeq Stranded mRNA Sample Prep Kit

value: genomic DNA

tag: chip antibody

value: Rpb1 CTD (4H8) Mouse monoclonal Ab (Cell Signaling, Catalog# 2629S)


title: A2_mRNA

description: all.counts.txt


title: B1_mRNA

description: all.counts.txt


title: exoChIP_Col-0


title: B2_mRNA

description: all.counts.txt


title: mrna-seq 10

city: Nanjing

first: Shaowu

last: Yin

state: jiangsu

address: College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road,  210023, China.

institute: Nanjing Normal University

data_processing:
The library for sequencing was generated using an Illumina TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). analysis.
Transcriptome sequencing was carried out on an Illumina HiSeq 2500 platform that generated approximately 100-bp paired-end (PE) raw reads by LC Sciences (Houston, TX, USA).
After removing adaptor sequences, ambiguous ‘N’ nucleotides (with the ratio of ‘N’ greater than 5%) and low quality sequences (with quality score less than 20), the remaining clean reads were assembled using trinity software as described for de novo transcriptome assembly without a reference genome. The quality of the assembly was critically assessed by LC Sciences before subsequent
For homology annotation, non-redundant sequences were annotated based on the following databases: Swiss-Prot (a manually annotated and reviewed protein sequence database); Nr (NCBI non-redundant protein sequences); Pfam (protein family); KEGG (KEGG Ortholog database); and KOG (euKaryotic Ortholog Groups).
Genome_build: Anguilla_anguilla_cDNA.fa (Trinity)
Supplementary_files_format_and_content: The expression level of each transcript was measured as the number of clean reads mapped to its sequence. The mapped clean read number was normalized to FPKM (FPKM- Fragments Per Kilobase of transcript per Million fragments mapped). We used DESeq to determine the FDR threshold. FDR < 0.05 and fold change > 2 were considered to indicate significant expression abundance.

organism: Anguilla marmorata

source_name: gill, kidney, intestine

growth_protocol: Healthy juveniles of A. marmorata (total length: 100–120 mm, body weight: 10.0–28.0 g) were randomly transferred to three aquaria with bio-filtered water recirculation systems (equipped with cooling and heating functions and a volume of 200 L and flow rate of 5 L/min) and fed with artificial compound feed, including more than 42.0% protein (Zhenjiang Jiaji Feed Co. Ltd., China). Normal oxygen concentration was 6.8 mg/L (measured with an HQd portable meter and LDO101 probe).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s protocol. The total RNA quantity and purity were analysed with Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
For nine cDNA library constructions, approximately 5μg of total RNA per sample was used for the RNA sample preparations. The library for sequencing was generated using an Illumina TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). Transcriptome sequencing was carried out on an Illumina HiSeq 2500 platform that generated approximately 125-bp paired-end (PE) raw reads by LC Sciences (Houston, TX, USA). After removing adaptor sequences, ambiguous ‘N’ nucleotides (with the ratio of ‘N’ greater than 5%) and low quality sequences (with quality score less than 20), the remaining clean reads were assembled using trinity software

treatment_protocol: Control fish (0) were removed from three aquaria for immediate gill, kidney and intestine dissection. Next, the Juveniles in FW were exposed to a gradual increase in per two salinities every day to BW and SW. After salinity was maintained in 10 and 25 salinity, the experimental fish (10) were quickly removed for gill, kidney and intestine dissection. Samplings of control fish (0), experime. Fish were killed by dissection after mild anaesthetisation in a eugenol bath (1:10,000), after which they were frozen in liquid nitrogen and stored at -80°C.

value: juvenile

value: gill, kidney, intestine

tag: salinity


title: mrna-seq 25


title: A1_mRNA

description: all.counts.txt


title: DsRed-D1(ATAC-seq)-rep2

status: Public on Dec 09 2017

city: Guangzhou

first: dongwei

last: Li

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
ATAC-seq reads were aligned to the mm10 genome assembly using bowtie2 with options --very-sensitive
Data were filterd using samtools -q  35 and awk '!x[$0]++'
peaks were called using run_dfilter15 with options -non-zero -bs=100 -ks=20 -lpval=3 -refine -std=5
Genome_build: mm10
Supplementary_files_format_and_content: wig file were generated with genomeCoverageBed and bedGraphToBigWig. Scores represent the number of fragments overlapping each genomic position.

organism: Mus musculus

source_name: reprogramming cells

growth_protocol: ESCs cells and iPSCs cells were cultured in N2B27+2i+LIF medium, MEF cells were cultured in 10% FBS medium

extract_protocol:
A total of 50,000 cells were washed once with cold PBS and resuspended in 50ul lysis buffer. The suspension of nuclei was then centrifuged for 10 min at 500g at 4°C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase and 22.5 μl nuclease-free H2O) of Nextera DNA library Preparation Kit (96 samples) (FC-121-1031, Illumina), and incubated at 37°C for 30min. DNA was isolated using a MinElute Kit (Qiagen).
ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR the library was assessed by quantitative PCR as described5, and the library was then PCR amplified for the appropriate number of cycles. Libraries were purified with a Qiaquick PCR (Qiagen) column. Library concentration was measured using a KAPA Library Quantification kits (KK4824) according to the manufacturers instructions. Library integrity was checked by gel electrophoresis. Finally, the ATAC library was sequenced on a NextSeq 500 using a NextSeq 500 High Output Kit v2 (150 cycles) (FC-404-2002, Illumina) according to the manufacturers instructions.

treatment_protocol: MEFs were reprogrammed as previously described2. Briefly, MEFs within 2 passages were plated at 2*104 per well (12 well plate) and then infected with retrovirus generated from PlatE cells. Infected cells were cultured in iCD1 medium or ESC medium (DMEM, 15% (v/v) FBS, penicillin/streptomycin (GIBCO), NEAA, GlutaMAX, LIF (10 ng/ml)). iPSC colonies were picked and then maintained as described above for ESCs. A step-by-step protocol describing the reprogramming procedure in this study can be found at the Nature Protocol Exchange3. shRNAs were transfected into cells by Lenti virus.

tag: cell type

value: reprogramming cells

tag: day of reprogramming


title: DsRed-D1(ATAC-seq)-rep1


title: A3_miRNA

description:
small RNA
miRNA.All.Counts.txt


title: OSK-D3-GFP-neg(ATAC-seq)-rep4


title: OSK-D3-GFP-neg(ATAC-seq)-rep3


title: mrna-seq 0


title: OSK-shSap30-D7-H3K27ac-Chipseq

description: chip antibody: H3K27ac (AB4729)

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
ChIIP-seq reads were aligned to the mm10 genome assembly using bowtie2 with options --very-sensitive
Data were filterd using samtools -q  35 and awk '!x[$0]++'
peaks were called using MACS14, using input as control
Genome_build: mm10
Supplementary_files_format_and_content: wig file were generated with genomeCoverageBed and bedGraphToBigWig. Scores represent the number of fragments overlapping each genomic position.

extract_protocol:
ChIP was performed as described previously(Liu et al., 2015), Briefly, cells were fixed in 18 ml DMEM (Hyclone) containing 1% formaldehyde for 15 min at room temperature with rotation, the reaction was quenched by the addition of 2 ml of 0.125 M glycine. And then the cells were washed with PBS 3 times. Cells were lysed in ChIP buffer A (50mM HEPES-KOH, 140 mM NaCl, 1mM EDTA (pH 8.0), 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 50 mM Tris-HCl (pH 8.0), and protease inhibitor cocktail) for 10 min at 4°C. Pellets were lysed in ChIP buffer B (1% SDS, 50 nM Tris-HCl (pH 8.0), 10mM EDTA and protease inhibitor cocktail) for 5 min at 4°C. The DNA was fragmented to 100-500 bp by sonication, and then centrifuged at 12,000g for 2 min. The supernatant was diluted with ChIP IP buffer (0.01% SDS, 1% Triton X-100, 2mM EDTA, 50mM Tris-HCl (pH 8.0), 150 mM NaCl and protease inhibitor cocktail). Immunoprecipitation was performed using 2μg of H3K27ac antibody added to protein A/G Dynabeads, and incubated overnight at 4°C. Beads were washed, eluted and reverse crosslinked. DNA was purified by using the MinElute Reaction Clean up Kit (QIAGEN).
The ChIP DNA library for NextSeq 500 sequencing was constructed with VAHTS Turbo DNA Library Prep Kit for Illumina (Vazyme Biotech) according to manufacturer’s instructions. AMPure XP beads were used for purification steps. The library was quantified with VAHTS Library Quantification Kit for Illumina (Vazyme Biotech). Libraries were sequenced on an Illumina NextSeq 500 v2 using 50bp paired-end reads.

value: day 7


title: OSK-shSap30-D3-H3K27ac-Chipseq

description: chip antibody: H3K27ac (AB4729)

value: day 3


title: OSK-scramble-D7-input-Chipseq

description: chip antibody: input


title: OSK-shSap30-D3-input-Chipseq

description: chip antibody: input


title: OSK-Sap30-D7-input-Chipseq

description: chip antibody: input


title: OSK-Sap30-D7-Chipseq

description: chip antibody: Flag ( sigma m1804)


title: OSK-scramble-D7-H3K27ac-Chipseq

description: chip antibody: H3K27ac (AB4729)


title: OSK-Sin3a-D7-Chipseq

description: chip antibody: SIN3A (AB3479)


title: OSK-shSap30-D7-input-Chipseq

description: chip antibody: input


title: OSK-Sap30-D3-Chipseq

description: chip antibody: Flag ( sigma m1804)


title: OSK-Sin3a-D3-Chipseq

description: chip antibody: SIN3A (AB3479)


title: MEF-H3K27ac-Chipseq

description: chip antibody: H3K27ac (AB4729)

source_name: mouse embryonic fibroblast

value: MEF cells

tag: passages


title: OSK-D7-input-Chipseq

description: chip antibody: input


title: OSK-D3-input-Chipseq

description: chip antibody: input


title: ESCs-input-Chipseq

description: chip antibody: input

source_name: Embryonic stem cells

value: ESCs cells

tag: strain

value: CBA/CaJ X C57BL/6J


title: ESCs-H3K27ac-Chipseq

description: chip antibody: H3K27ac (AB4729)


title: OSK-D7-H3K27ac-Chipseq

description: chip antibody: H3K27ac (AB4729)


title: OSK-Sap30-D3-input-Chipseq

description: chip antibody: input


title: exoChIP_nrpd1-3

tag: age


title: OSK-shSap30-D7(RNAseq)-rep2

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
RNAseq reads were aligned to the mm10 genome assembly using rsem with options --bowtie2 --bowtie2-sensitivity-level very_sensitive
expected_count were extract from the sample_name.genes.results and merged together to get a big table
RNAseq data was normalized by EDAseq
Genome_build: mm10
Supplementary_files_format_and_content: tsv file was generated form normalized RNAseq data, it include all samples' RNAseq data

extract_protocol:
Total RNA was prepared with TRIzol. For quantitative PCR, cDNAs were synthesized with ReverTra Ace (Toyobo) and oligo-dT (Takara), and then analyzed by qPCR with Premix Ex Taq (Takara).
For RNA-seq, TruSeq RNA Sample Prep Kit (RS-122-2001, Illumina) was used for library construction and the sequencing was done using a NextSeq 500 High Output Kit v2 (75 cycles) (FC-404-1005, Illumina), according to the manufacturers instructions.


title: OSK-shSap30-D7(RNAseq)-rep1


title: OSK-D7(RNAseq)-rep1


title: OSK-D7(RNAseq)-rep2


title: OSK-D5(RNAseq)-rep1


title: OSK-D3(RNAseq)-rep2


title: MEF-input-Chipseq

description: chip antibody: input


title: OSK-D3-H3K27ac-Chipseq

description: chip antibody: H3K27ac (AB4729)


title: OSK-D0(RNAseq)-rep1


title: OSK-D1(RNAseq)-rep1


title: OSK-D0(RNAseq)-rep2


title: OSK-cJun-D3(RNAseq)-rep1


title: OSK-cJun-D3(RNAseq)-rep2


title: OSK-cJun-D7(RNAseq)-rep2


title: OSK-D1(RNAseq)-rep2


title: OSK-cJun-D0(RNAseq)-rep1


title: MEF(RNAseq)-rep1


title: OSK-cJun-D7(RNAseq)-rep1


title: iPS(RNAseq)-rep1

source_name: induced pluripotent stem cell

value: iPSCs cells


title: ESCs(RNAseq)-rep2


title: OSK-cJun-D0(RNAseq)-rep2


title: SK-D1(ATAC-seq)-rep1


title: OSK-cJun-D1(RNAseq)-rep2


title: ESCs(RNAseq)-rep1


title: MEF(RNAseq)-rep2


title: SK-D1(ATAC-seq)-rep2


title: OSK-D3(RNAseq)-rep1


title: iPS(RNAseq)-rep2


title: S-D1(ATAC-seq)-rep2


title: S-D1(ATAC-seq)-rep1


title: OSK-D5(RNAseq)-rep2


title: OSK-shSap30#1-D7


title: OSK-scramble-D3


title: OSK-shSap30#2-D3


title: OSK-scramble-D7


title: OSK-cJun-D1(RNAseq)-rep1


title: OSK-DR-D7(ATAC-seq)-rep2


title: OSK-DR-D3(ATAC-seq)-rep1


title: OSK-shSap30#1-D3


title: OSK-DR-D0(ATAC-seq)-rep2


title: OSK-D7(ATAC-seq)-rep1


title: OSK-DR-D0(ATAC-seq)-rep1


title: OSK-DR-D1(ATAC-seq)-rep2


title: OSK-shSap30#2-D7


title: OSK-D5(ATAC-seq)-rep2


title: OSK-D7-GFP-neg(ATAC-seq)-rep1


title: OSK-D3(ATAC-seq)-rep2


title: OSK-D7-GFP-pos(ATAC-seq)-rep2


title: OSK-DR-D1(ATAC-seq)-rep1


title: OSK-DR-D3(ATAC-seq)-rep2


title: OSK-D7-GFP-pos(ATAC-seq)-rep1


title: OSK-D5(ATAC-seq)-rep1


title: OSK-D1(ATAC-seq)-rep1


title: OSK-D7(ATAC-seq)-rep2


title: OSK-D7-GFP-neg(ATAC-seq)-rep2


title: OSK-D1(ATAC-seq)-rep2


title: OSK-cJun-D7(ATAC-seq)-rep2


title: OSK-DR-D7(ATAC-seq)-rep1


title: OSK-D3-GFP-pos(ATAC-seq)-rep1


title: OSK-D3-GFP-pos(ATAC-seq)-rep2


title: OSK-D3(ATAC-seq)-rep1


title: OSK-D3-GFP-neg(ATAC-seq)-rep1


title: OSK-D0(ATAC-seq)-rep2


title: OSK-D3-GFP-neg(ATAC-seq)-rep2


title: OSK-D0(ATAC-seq)-rep1


title: OSK-cJun-D7(ATAC-seq)-rep1


title: OSK-cJun-D3(ATAC-seq)-rep2


title: OSK-cJun-D3(ATAC-seq)-rep1


title: OSK-cJun-D1(ATAC-seq)-rep2


title: OSK-cJun-D1(ATAC-seq)-rep1


title: OSK-cJun-D0(ATAC-seq)-rep1


title: OSK-cJun-D0(ATAC-seq)-rep2


title: OS-D1(ATAC-seq)-rep1


title: mES-OSK-D7(ATAC-seq)-rep1


title: MEF(ATAC-seq)-rep1


title: OS-D1(ATAC-seq)-rep2


title: OK-D1(ATAC-seq)-rep2


title: K-D1(ATAC-seq)-rep2

value: day 1


title: iPS(ATAC-seq)-rep1


title: OK-D1(ATAC-seq)-rep1


title: O-D1(ATAC-seq)-rep2


title: mES-OSK-D7(ATAC-seq)-rep2


title: O-D1(ATAC-seq)-rep1


title: iPS(ATAC-seq)-rep2


title: K-D1(ATAC-seq)-rep1


title: MEF(ATAC-seq)-rep2


title: ESCs(ATAC-seq)-rep1


title: CreERT2 Syk flox/flox +iso_3

city: Cambridge

first: Marko

last: Knoll

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

description: Biological rep 3

data_processing:
RNASeq paired-end reads, using Illumina 1.5 encoding, were aligned using TopHat (v 2.0.13)  to the mouse genome with Ensembl annotation (release 67) in gtf format.
mRNA sequencing triplicates were performed as independent experiments. Differential analysis and counts per millions (cpm) were obtained by using HTSeq Count (-m intersection-strict and --strand=reverse; Ensembl annotation release 67) and edgeR.
TMM method in edgeR was used for normalization.
The three replicates were done at different time points, batch effects were minimized by taking this into account in the design matrix and model for the comparisons in edgeR.
Genome_build: Mouse (mm9: NCBI Build 37)
Supplementary_files_format_and_content: log2 counts per million (cpm) and batch-corrected log2 cpm from edgeR

source_name: brown adipocyte

growth_protocol: Preadipocytes derived from BAT were cultured to confluence and then subsequently overgrown for 4 - 6 additional days until growth arrested. The cells were then induced to differentiate by culturing them for two days in induction medium consisting of DMEM supplemented with 10 % heat inactivated fetal bovine serum (FBS, Sigma-Aldrich F2442) and 850 nM insulin (Sigma-Aldrich # I1882), 0.5 µM dexamethasone (Sigma-Aldrich # D4902), 250 µM 3-isobutyl-1-methylxanthine (IBMX, Sigma-Aldrich # I5879), 1 µM rosiglitazone (Cayman Chemical # 71742), 1 nM 3,3,5-triiodo-L-thyronine (T3, VWR # 100567-778) and 125 nM indomethacin (Sigma-Aldrich # I7378). Subsequently, the induction medium was replaced with DMEM supplemented with 10 % FBS and 160 nM insulin and 1 nM T3 for another two days. The cells were then cultured in DMEM 10 % FBS and 1 nM T3 until day 8 of differentiation, and the medium was replaced every other day.

extract_protocol:
Total RNA was extracted using Trizol following product manual
10ug poly A+ mRNA for each sample was used to prepare mRNA-seq libraries according to manufacturer's instruction (Illumina). These libraries were sequenced to produce 100bp pairend end reads

treatment_protocol: Poly A+ RNA sequencing (TrueSeqStrandedPolyA) was performed on RNA samples from in vitro tamoxifen treated day 8 brown adipocytes derived from UBC-CreERT2 Sykflox/flox and Sykflox/flox mice 6 h following stimulation with 0.1 μM isoproterenol in serum free medium and from unstimulated controls using a HiSeq genome sequencer (Illumina).

tag: agent

value: isoproterenol

tag: genotype/variation

value: CreERT2 Syk flox/flox

value: in vitro differentiated brown fat

value: primary cells

tag: differentiation stage

value: 8 days after induction


title: CreERT2 Syk flox/flox -iso_3

description: Biological rep 3

value: unstimulated


title: CreERT2 Syk flox/flox -iso_2

description: Biological rep 2


title: CreERT2 Syk flox/flox +iso_2

description: Biological rep 2


title: Syk flox/flox -iso_3

description: Biological rep 3

value: Syk flox/flox


title: Syk flox/flox -iso_2

description: Biological rep 2


title: Syk flox/flox +iso_2

description: Biological rep 2


title: ESCs(ATAC-seq)-rep2


title: CreERT2 Syk flox/flox +iso_1

description: Biological rep1


title: CreERT2 Syk flox/flox -iso_1

description: Biological rep1


title: Syk flox/flox +iso_3

description: Biological rep 3


title: Syk flox/flox +iso_1

description: Biological rep1


title: Syk flox/flox -iso_1

description: Biological rep1


title: TAµ_P10 [Sample_20_1]

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

description: TAµ

data_processing:
Alignment with STAR (STAR_2.3.0_r291)
Count reads with HT-Seq 0.5.3 with Ensembl72 gtf annotation
Differential Expression analysis with limma/voom
Genome_build: UCSC mm10 (Jun 2012)
Supplementary_files_format_and_content: xlsx file were generated after reformatting the txt output from limma write.fit function

source_name: TAµ

extract_protocol:
RNeasy Plus Micro kit (Qiagen) was used to extract RNA from the sorted myeloid brain populations. In particular we retrieved different myeloid brain subpopulation sorted from: P10 (TAµ cells), 5 month old C57bl6/j mice (ADULT µ cells) and BU-treated mice(BU_TX) at 3 months from GFP Lin- transplantation (µ and TAµ cells). RNeasy Plus Micro kit (Qiagen) was used to extract RNA from the sorted myeloid brain populations
Briefly, amplification of cDNA from total RNA (starting amount =100 ng per sample) was performed using the Ovation RNA-Seq System V2 (Nugen), cDNA was then fragmented and ligated into a sequencing library using NuGEN's Ovation Ultralow Library Systems
After barcoding, the RNA libraries were pooled, denatured and diluted to an 8 pM final concentration. Cluster formation was performed on cBot (Illumina) (single-end) using flow cells v.3. The SBS (sequencing by synthesis) was performed according to TruSeq SR protocol (Illumina) for the HiSeq 2500 (Illumina) set to 50 cycles, yielding an average of 30x106 clusters for each sample

value: brain

tag: condition

tag: cell population

value: TAu


title: TAµ_P10 [Sample_19_1]

description: TAµ


title: TAµ_P10 [Sample_17_1]

description: TAµ


title: µ_ADULT_CT [Sample_o]

description: µ

source_name: µ

value: ADULT

value: u


title: TAµ_P10 [Sample_18_1]

description: TAµ


title: TAµ_P10 [Sample_14_1]

description: TAµ


title: TAµ_P10 [Sample_13_1]

description: TAµ


title: TAµ_BU_TX [Sample_c2]

description: TAµ


title: µ_ADULT_CT [Sample_q]

description: µ


title: TAµ_P10 [Sample_15_1]

description: TAµ


title: µ_ADULT_CT [Sample_p]

description: µ


title: µ_BU_TX [Sample_a1]

description: µ


title: Rorβ-CRISPR (KO) Cell Line - Replicate 2

city: Rochester

first: David

last: Monroe

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing software (version 3) and SCS data collection software (version 1.4.8)
Base calling was performed using Illumina RTA (version 1.12.4.2)
Paired-end reads from the raw RNAseq data were aligned using TopHat (version 2.0.6)
Quality control assessments were made using RSeQC software
Gene counts were generated using HTSeq software and gene annotation files were obtained from Illumina
Genome_build: mm9

source_name: MC3T3-E1 osteoblastic cell line

growth_protocol: Upon confluence, all cells were differentiated in standard osteoblastic medium for 2 days

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared according to the manufacturer’s instructions for the Encore NGS Library Systems (San Carlos, CA).

tag: cell line

value: osteoblast


title: µ_BU_TX [Sample_c1]

description: µ


title: TAµ_P10 [Sample_16_1]

description: TAµ


title: TAµ_BU_TX [Sample_a2]

description: TAµ


title: dcp2-N245-198Q-rep3

city: Worcester

first: Feng

last: He

address: 368 Plantation Street

department: Microbiology and Physiological Systems

institute: University of Massachusetts Medical School

data_processing:
RSEM program (Li and Dewey 2011) was used to map the sequence reads to the transcriptome and to quantify individual transcript levels with settings --bowtie-m 30 --no-bam-output --forward-prob 0.
The expected read counts for individual transcripts from RSEM were considered as the number of reads mapped to each transcript and were then imported into Bioconductor DESeq package (Anders and Huber 2010) for differential expression analysis.
Genome_build: R64-2-1 S288C sacCer3 genome assembly
Supplementary_files_format_and_content: Tab-delimited text files include the estimated read counts (normalized abundance estimates) of individual transcripts in wild-type cells and in each of the mutant strains

organism: Saccharomyces cerevisiae

growth_protocol: Cells were all grown in YEPD media at 30°C. In each case, cells (15 ml) were grown to an OD600 of 0.7 and harvested by centrifugation. Cell pellets were frozen on dry ice and then stored at -80°C until RNA isolation.

extract_protocol:
Total RNA was extracted from yeast cells using hot phenol.
Total RNA was treated with Baseline-zero DNase (Epicenter, cat# DB0711K) to remove any genomic DNA contamination. Five micrograms of DNase-treated total RNA was then depleted of rRNAs using the Illumina yeast RiboZero Removal Kit (cat# MRZY1306) and the resulting RNA was used for RNA-Seq library preparation. Multiplex strand-specific cDNA libraries were constructed using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (cat# RS-122-2101).

tag: background

tag: time

value: experiment at time period II


title: Rorβ-CRISPR (KO) Cell Line - Replicate 1


title: TAµ_BU_TX [Sample_b2]

description: TAµ

tag: tissue


title: µ_BU_TX [Sample_b1]

description: µ


title: MC3T3-Control Cell Line - Replicate 1


title: Rorβ-CRISPR (KO) Cell Line - Replicate 3


title: dcp2-N245-198Q-rep2

tag: genotype


title: MC3T3-Control Cell Line - Replicate 2


title: MC3T3-Control Cell Line - Replicate 3


title: dcp2-N245-198Q-rep1


title: dcp2-N245-E153Q-rep2


title: dcp2-N245-E153Q-rep1


title: dcp2-N245-rep3


title: dcp2-N245-rep2


title: dhh1∆-rep3

value: experiment at time period I


title: WT2-rep3

value: Wild-type


title: lsm1∆-rep3


title: WT2-rep1


title: WT2-rep2


title: dhh1∆-rep2


title: pat1∆-rep3


title: lsm1∆-rep1


title: dhh1∆-rep1


title: RA72Q-C-2

status: Public on Dec 08 2017

first: Jungmin

last: Choi

address: 73, Goryeodae-ro, Seongbuk-gu

institute: Korea University College of Medicine

description: Biological replicate 2

data_processing:
Sequencing reads were trimmed for bases with base quality score less than 20
Trimmed sequencing reads were aligned to human transcriptome hg19 using TopHat2 (2.0.12)
Transcript abundances were estimated and differentially expressed transcripts were detected by cuffdiff2 (2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for all samples

source_name: H295R cells_RA72Q-C-2

growth_protocol: H295R cells were cultured in DMEM/F12 + HEPES (Gibco) + 2.5 % Ultroser G (Pall, Port Washington, NY, USA) + 1% Insulin-Transferrin-Selenium+ (ITS+; Corning, Corning, NY, USA) + 1 % Penicillin/Streptomycin (Gibco) at 37°C and 5% CO2 in humidified atmosphere. 24h after transfection, H295R cells were starved in DMEM/F12 + HEPES + 0.1 % Ultroser G + 1 % Penicillin/Streptomycin for additional 24h.

extract_protocol:
RNA was isolated using Trizol (Thermo Fisher Scientific), followed by DNase digest and column purification (RNeasy, Qiagen).
Libraries were prepared after Poly A selection.

treatment_protocol: Cells were transfected using an Amaxa Nucleofector I (Lonza).

value: adrenocortical carcinoma cell line

tag: transfection method

value: electroporation

tag: vector

tag: construct

value: p.Arg172Gln CLCN2


title: WT-rep2


title: EVC-B-2

description: Biological replicate 2

source_name: H295R cells_EVC-B-2

tag: cell type

value: empty vector


title: WT-1-1

description: Biological replicate 1

source_name: H295R cells_WT-1-1

value: WT CLCN2


title: WT-rep3


title: WT-rep1


title: pat1∆-rep1


title: RA72Q-A-3

description: Biological replicate 1

source_name: H295R cells_RA72Q-A-3


title: WT-2-2

description: Biological replicate 2

source_name: H295R cells_WT-2-2


title: pat1∆-rep2


title: dcp2-N245-E-153Q-rep3


title: EVC-A-1

description: Biological replicate 1

source_name: H295R cells_EVC-A-1


title: R9881_CA1_Y

city: Phoenix

first: Matthew

last: Huentelman

state: AZ

address: 445 N 5th St

department: Neurogenomics

institute: TGen

data_processing:
Bcl files were converted to FASTQ and demultiplexed with Illumina's Bcl2Fastq version 2.17
Reads were trimmed of adapter sequences with CutAdapt version 1.8.3
Reads were aligned to the Rattus norvegicus reference genome rn5 with STAR version 2.5
Aligned reads were summarized as gene-level counts with featureCounts version 1.4.4
Gene-level counts were normalized with DESeq2 1.16.1
Genome_build: rn5
Supplementary_files_format_and_content: Plain-text, tab-seperated table of gene-level read counts.

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
Rats were anesthetized with isoflurane, decapitated and the brain was rapidly removed. The hippocampus was isolated, and the CA1, CA3 and dentate gyrus (DG) regions were dissected. The collected tissue was immediately frozen in liquid nitrogen and stored in -80ºC.
Total RNA was isolated using the miRNeasy Mini kit (Qiagen, cat #: 217004).
Sequencing libraries were prepared with the Truseq Stranded mRNA Sample Preparation Kit (Illumina Inc) following the manufacturer’s protocol. Final PCR-enriched fragments were validated on a 2200 Tapestation Instrument using the D1000 ScreenTape (Agilent Technologies) and quantified by qPCR using a Universal Library Quantificiation Kit (Kapa Biosystems) on the QuantStudio 6 Flex (ThermoFisher Scientific).

value: hippocampus

tag: brain tissue

value: Young

tag: age impairment

tag: gender

value: male

value: Fisher 344


title: dcp2-N245-rep1


title: R9879_DG_Y

value: DG

tag: age

tag: strain


title: R9879_CA3_Y


title: R9879_CA1_Y


title: lsm1∆-rep2


title: R9877_DG_Y


title: R9877_CA3_Y


title: R9877_CA1_Y


title: R9876_CA3_Y


title: R9875_DG_OB

value: Old

value: Impaired


title: R9876_CA1_Y


title: R9881_DG_Y


title: R9874_DG_OB


title: R9874_CA3_OB


title: R9875_CA3_OB


title: R9875_CA1_OB


title: R9872_CA1_OB


title: R9872_CA3_OB


title: R9870_CA3_OB


title: R9874_CA1_OB


title: R9872_DG_OB


title: R9870_CA1_OB


title: R9869_DG_OG

value: Unimpaired


title: R9869_CA3_OG


title: R9870_DG_OB


title: R9867_DG_OG


title: R9865_DG_OG


title: R9867_CA3_OG


title: R9867_CA1_OG


title: R9869_CA1_OG


title: R9865_CA1_OG


title: R9862_DG_OG


title: R9876_DG_Y


title: R9860_DG_OG


title: R9860_CA3_OG


title: R9862_CA3_OG


title: R9782_CA1_OG


title: R9782_DG_OG


title: R9860_CA1_OG


title: R9782_CA3_OG


title: R9865_CA3_OG


title: R2233_CA3_OB


title: R2233_CA1_OB


title: R9780_DG_Y


title: R9781_CA3_OB


title: R2235_CA1_OB


title: R9862_CA1_OG


title: R2237_CA3_OG


title: R2238_CA1_OB


title: R9881_CA3_Y


title: R2235_DG_OB


title: R2237_CA1_OG


title: R9781_CA1_OB


title: R9780_CA1_Y


title: R2238_DG_OB


title: R2237_DG_OG


title: R9781_DG_OB


title: R2238_CA3_OB


title: R2235_CA3_OB


title: R9780_CA3_Y


title: R2233_DG_OB


title: R2232_DG_OG


title: R2231_DG_OB


title: R2232_CA3_OG


title: R2231_CA3_OB


title: R2230_DG_OG


title: R2230_CA1_OG


title: R2230_CA3_OG


title: R2221_DG_Y


title: R2221_CA3_Y


title: R2189_DG_OB


title: R2221_CA1_Y


title: R2231_CA1_OB


title: R2184_CA3_OG


title: R2175_DG_Y


title: R2189_CA3_OB


title: R1931_CA1_OB


title: R2189_CA1_OB


title: R2232_CA1_OG


title: R2185_CA1_OG


title: R2182_CA3_OB


title: R2184_DG_OG


title: R2185_DG_OG


title: R2182_DG_OB


title: R2185_CA3_OG


title: R2175_CA3_Y


title: R2184_CA1_OG


title: R1931_DG_OB


title: R1931_CA3_OB


title: R2175_CA1_Y


title: R1923_DG_Y


title: R1930_DG_OG


title: R1930_CA1_OG


title: R1923_CA3_Y


title: R2176_CA1_Y


title: R2182_CA1_OB


title: R2176_DG_Y


title: R1923_CA1_Y


title: R2176_CA3_Y


title: R1930_CA3_OG


title: R1922_CA3_Y


title: R1922_DG_Y


title: R9881.CA1.Y

city: Gainesville

first: Thomas

middle: C

last: Foster

state: Florida

address: 1149 Newell Drive Bldg 59

department: Neuroscience

institute: University of Florida-McKnight Brain Institute

description:
PolyA RNA
Processed data file: UF_mRNA_normalizedCounts.csv

data_processing:
Ion Proton: Low quality reads were removed from FASTQ files and the data was aligned to the rn5 genome using the two step alignment method for Ion Proton transcriptome data with TopHat2 and Bowtie2 in the Partek Flow servers (Partek Inc.). Two step alignment parameters included tophat --b2-sensitive -p 8 -N 4 -a 8 -m 0 -i 50. Bowtie 2 parameters: --very-sensitive-local.
Illumina: Illumina BCL files were converted and demultiplexed (bcl2fastq 2.17). FASTQ files were trimmed of adapter sequences (CutAdapt 1.8.3) and aligned to the rat reference genome rn5 (STAR 2.5).
For both sequencing systems, aligned reads were summarized as gene-level counts (featureCounts 1.4.4) and count normalization followed by differential expression was performed with the R package, DeSeq2 (1.10.1).
Genome_build: rn5 (Rnor_5.0)
Supplementary_files_format_and_content: UF_mRNA_normalizedCounts.csv: Comma-separated values file contains the normalized gene-level counts for each biological sample.

extract_protocol:
Rats were anesthetized with isoflurane, decapitated and the brain was rapidly removed. The hippocampus was isolated, and the CA1, CA3 and dentate gyrus (DG) regions were dissected. The collected tissue was immediately frozen in liquid nitrogen and stored in -80ºC. Total RNA was isolated using the miRNeasy Mini kit (Qiagen, cat #: 217004).
For the Ion Proton library construction, 250ng of total RNA was used for polyA selection with the Dynabeads mRNA DIRECT Micro kit (Thermo Fisher, cat #: 61021). Transcriptome libraries were made with the Ion Total RNA-seq Kit v2 (Thermo Fisher, cat#: 4475936) with the addition of the Ion Xpress barcodes for multiplex sequencing (Thermo Fisher, cat#: 4475485). All libraries were quantified in an Agilent 220 Tapestation system.

tag: strain/background

value: Fischer 344

tag: hippocampal subregion

tag: rat identifier


title: R9881.DG.Y

value: dentate gyrus (DG)


title: R9881.CA3.Y


title: R1922_CA1_Y


title: R9879.DG.Y


title: R9877.CA1.Y


title: R9876.DG.Y


title: R9879.CA1.Y


title: R9877.CA3.Y


title: R9876.CA3.Y


title: R9877.DG.Y


title: R9876.CA1.Y


title: R9875.DG.OB

value: Aged


title: R9875.CA1.OB


title: R9874.CA3.OB


title: R9874.DG.OB


title: R9872.CA3.OB


title: R9872.CA1.OB


title: R9870.CA3.OB


title: R9870.DG.OB


title: R9870.CA1.OB


title: R9869.DG.OG


title: R9879.CA3.Y


title: R9869.CA3.OG


title: R9875.CA3.OB


title: R9874.CA1.OB


title: R9869.CA1.OG


title: mes-2_FedL1 PGC transcriptome mes-2_FedL1_Slee41

city: Baltimore

first: Geraldine

last: Seydoux

state: MD

address: 725 N. wolfe St. PCTB 706

department: MBG

institute: Johns Hopkins University

description: Truseq  RNA library Prep Kit v2

data_processing:
Base calling and demultiplexing was performed at UC reverside IIGB Genomics Core facility with CASAVA 1.8.
Differential expression analysis was done using Tophat (V.2.0.8) and Cufflink (V 2.0.2). The command lines for Tuxedo suit are listed as below:
$ tophat2 -p 12 -g 1 --output-dir <output> --segment-length 20 --min-intron-length 10 --max-intron-length 25000 -G <gene.gtf> --transcriptome-index <Name.fastq>
$ cuffdiff -p 12 -o <output> --compatible-hits-norm --upper-quartile-norm -b <genome.fa> <genes.gtf>  <tophat output1> <tophat output2>
Genome_build: ce10
Supplementary_files_format_and_content: Output file for Pair-wise analysis are NAME_exp.diff

organism: Caenorhabditis elegans

source_name: sorted mes-2(RNAi) L1 PGCs

growth_protocol: For embryonic PGCs: Embryos were collected from adult worms and used for PGC isolation; For L1 PGCs: Embryos were collected from adult worms and cultured for overnight in M9 solution. Synchronized L1 were collected and used for PGC isolation.

extract_protocol:
Worm were dissociated with pronase solution. Cell suspensions were subjected to FACS to isolated PGL-1::GFP marked primordial germ cells (PGCs). Total RNAs were extracted using Trizol reagent and RNA purifiaction was done using RNA clean and concentrator-5 (Zymo researh).
Three different RNA-seq library preparation methods were used for this study.SMART-seq libraries: libraries were made from 2ng of total RNA isolated from sorted PGCs from worms grown at 25oC using SMART-seq v4 Ultra Low input RNA kit (Clontech, Cat. No. 634888 ) followed by Low Input Library Prep Kit (Clontech, Cat. No. 634947). The cDNAs were then fragmented using Covaris AFA system at the Johns Hopkins University microarray core and cloned using the Low Input library prep Kit. Nugen Ovation libraries: libraries were made from 3ng of total RNA isolated from sorted cells from worms grown at 25oC using Nugen Ovation system V2 (# 7102-08) followed by Nugen Ultralow library system. TruSeq libraries: 50ng of total RNA isolated from sorted PGCs from L1 worms grown at 20oC were subjected to Ribozero kit (illumina, MRZE706) to remove rRNA. Libraries were constructed using Truseq Library Prep Kit V2.

treatment_protocol: All worms were grown on HT115 bacteria containing either empty vector(L4440) or nos-2(RNAi) plasmid. For Fed condition, synchronized L1 were transfer to RNAi bacteria containing plates for additional 5 hours.

tag: developmental stage

tag: temperature for culturing

tag: feeding condition

value: Fed for 5 hours


title: nanos;lin-15B L1 PGC transcriptome nanos.lin-15B_L1_Slee53

description: Truseq  RNA library Prep Kit v2

source_name: sorted nos-1(gv5)nos-2(RNAi);lin-15B(RNAi) L1 PGCs

value: Starved L1


title: R9867.CA3.OG

tag: tissue


title: mes-2_Fed L1 PGC transcriptome mes-2_FedL1_Slee40

description:
Truseq  RNA library Prep Kit v2
FedWTL1_vs_Fedmes-2L1_Truseq_exp.diff


title: mes-4_Fed L1 PGC transcriptome mes-4_FedL1_Slee43

description: Truseq  RNA library Prep Kit v2

source_name: sorted mes-4(RNAi) L1 PGCs


title: R9862.DG.OG


title: R9865.CA1.OG


title: R9862.CA3.OG


title: R9872.DG.OB


title: R9867.DG.OG


title: nanos Fed L1 PGC transcriptome nanos_FedL1_Slee39

description: Truseq  RNA library Prep Kit v2

source_name: sorted nos-1(gv5)nos-2(RNAi)  L1 PGCs


title: R9867.CA1.OG


title: R9865.DG.OG


title: R9865.CA3.OG


title: mes-4_Fed L1 PGC transcriptome mes-4_FedL1_Slee42

description:
Truseq  RNA library Prep Kit v2
FedWTL1_vs_Fedmes-4L1_Truseq_exp.diff


title: R9860.DG.OG


title: 16week_fetal_cartilage_RNAseq

city: Los Angeles

first: Daniel

last: Cohn

address: 615 Charles E Young Dr. South

department: Molecular, Cell, and Developmental Biology

institute: University of California, Los Angeles

data_processing:
Reads were mapped to the human genome (hg19) using TopHat (v2.0.9).
The mapped reads were analyzed using Cufflinks (v2.2.1) package. Transcript abundance in each sample was quantified with Cuffquant.
The Cuffquant output for all samples were then joined and normalized with Cuffnorm. Gene expression level is represented as FPKM (fragments per kilobase of exon per million fragments mapped) value.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file with FPKM value

source_name: Chondrocytes

extract_protocol:
RNA was isolated and purified from five independent 14-18 week distal human femur growth plate cartilage samples. The fetal cartilage was digested in 0.3% bacterial collagenase, the chondrocytes were collected by centrifugation and total RNA was isolated with TRIZol (Thermo Fisher Scientific). Genomic DNA contamination was removed by DNase I (Thermo Fisher Scientific) digestion and the RNA was further purified with the RNeasy Mini Kit (Qiagen).
PolyA-tailed mRNA was isolated from total RNA and used as the input for sequencing library construction with the TruSeq RNA Preparation Kit (Illumina).

treatment_protocol: No treatment

value: Chondrocytes isolated from growth plate

value: fetal 16 weeks

value: Female


title: 18week_fetal_cartilage_RNAseq

value: fetal 18 weeks

value: Male


title: 15week_fetal_cartilage_RNAseq

value: fetal 15 weeks


title: nanos Fed L1 PGC transcriptome nanos_FedL1_Slee38

description:
Truseq  RNA library Prep Kit v2
FedWTL1_vs_FednosL1_Truseq_exp.diff


title: R9860.CA3.OG

value: male

value: hippocampus


title: R9860.CA1.OG


title: R9862.CA1.OG


title: nanos;lin-15B L1 PGC transcriptome nanos.lin-15B_L1_Slee52

description:
Truseq  RNA library Prep Kit v2
nosL1_vs_noslin15BL1_exp.diff


title: R9782.DG.OG


title: 14week_fetal_cartilage_rep2_RNAseq

value: fetal 14 weeks


title: 14week_fetal_cartilage_rep1_RNAseq


title: Wild-type Fed L1 PGC transcriptome WT_FedL1_Slee37

description: Truseq  RNA library Prep Kit v2

source_name: sorted L1 PGCs


title: R9782.CA3.OG


title: R9782.CA1.OG


title: R9781.DG.OB


title: Wild-type Fed L1 PGC transcriptome WT_FedL1_Slee36

description: Truseq  RNA library Prep Kit v2


title: R9781.CA3.OB


title: Wild-type Fed L1 PGC transcriptome WT_FedL1_Slee35

description: Truseq  RNA library Prep Kit v2


title: IgG_rep2

city: Cardiff

middle: James

last: Hill

address: Maindy Road

country: United Kingdom

institute: Cardiff University

data_processing:
Reads were aligned to the human reference genome (hg19) with BWA (version 0.7.5a)
Peaks were called according to the ENCODE IDR analysis pipeline (https://sites.google.com/site/anshulkundaje/projects/idr). Briefly, peaks were called using MACS 2.0  in each replicate against a pooled IgG negative control sample using a P-value cut-off of 0.05. The replicates were then randomly split into pseudo replicates and peaks called in those using the same parameters. Finally peaks were called in the pooled replicates and in random pseudo replicates of the pooled data. IDR analysis suggested the optimum number of peaks from the pooled replicates was 10,604
The HOMER ChIP-seq analysis package was used to annotate peaks, link them to nearest transcription start site and for motif analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing alignments of processed reads

source_name: neuroblastoma cell line (SH-SY5Y)

growth_protocol: SH-SY5Y cells were cultured in Dulbecco’s modified Eagle medium (DMEM, Invitrogen) supplemented with 10% (v/v) foetal calf serum (FCS, PAA laboratories) without antibiotics

extract_protocol:
Confluent cells were fixed with 1% (v/v) formaldehyde for 5min at room temperature and then quenched with 125mM glycine. Cells were then washed twice with cold phosphate buffered saline (PBS) and collected by scraping into cold PBS. Cells were pelleted by centrifugation (2000g, 5min, 4°C) and then washed in PBS and collected by centrifugation as before. 1 x 107 pelleted cells were lysed in 1ml ChIP buffer (150mM NaCl, 50mM Tris-HCl (pH 7.5), 5mM EDTA, NP-40 (0.5% v/v), Triton X-100 (1.0% v/v) for 30 min on ice. Nuclei were released by passing the lysate through a 23-gauge needle. Nuclei were collected by centrifugation (2000g, 5 min, 4°C), the supernatant was discarded and remaining pellet resuspended in 1ml of shearing buffer (50mM Tris pH 8.0, 5mM EDTA, 150mM NaCl, 0.1% (v/v) SDS). The lysate was then clarified by centrifugation (13,000rpm for 10min at 4°C) and the supernatant transferred to a new tube. Chromatin was fragmented by sonication using a Covaris S2 at recommended settings. Following sonication, SDS was sequestered by addition of Triton-X-100 to a final concentration of 1% (v/v). Sonicated chromatin was then pre-cleared for 1h at 4°C using bovine serum albumin (BSA) blocked beads.     For each ChIP reaction, chromatin prepared from approximately 1 x 107 cells was incubated with 5µg anti-TCF4 or anti-IgG antibody, overnight at 4°C with rotation. The chromatin was then centrifuged (13,000rpm for 10min at 4°C) and the supernatant transferred to a tube containing BSA-blocked beads. Protein-antibody complexes were then captured for 30 min at 4°C with rotation. Beads were then washed twice with ChIP buffer containing 0.5M NaCl, followed by five washed with LiCl wash buffer (50mM Tris pH 8.0, 5mM EDTA, 0.5% (v/v) NP-40, 1.0% (v/v) Triton X-100, 500mM LiCl and then twice with rinse buffer (50mM Tris pH 8.0, 5mM EDTA). Beads were then resuspended in 100µl elution buffer (10mM Tris pH 8.0, 1mM EDTA, 0.1% (w/v) SDS) and incubated with RNase for 30 min at 37°C). Proteinase K was added and incubated over night at 60°C. The eluate was then cleaned up using the QIAgen PCR clean up Kit (Qiagen).
Enriched chromatin was processed and sequenced by Source BioScience (Nottingham, UK). using the Illumina TruSeq ChIP Sample Preparation Kit (San Diego CA, USA). Barcode info: TCF4_rep1 = GTGAAA, TCF4_rep2 = CAGATC, IgG_rep1 = ACAGTG, IgG_rep2 = GCCAAT

tag: cell line

value: neuroblastoma cell line (SH-SY5Y)

tag: antibody

value: IgG


title: nanos L1 PGC transcriptome nanos_L1_Slee57

description: Truseq  RNA library Prep Kit v2


title: R9781.CA1.OB

value: Impaired


title: Wild-type L1 PGC transcriptome WT_L1_Slee50

description: Truseq  RNA library Prep Kit v2


title: R2238.CA3.OB

value: Fischer 344


title: R9780.CA3.Y

value: Young


title: R9780.CA1.Y


title: nanos L1 PGC transcriptome nanos_L1_Slee51

description: Truseq  RNA library Prep Kit v2


title: IgG_rep1


title: R9780.DG.Y

value: dentate gyrus (DG)


title: TCF4_ChIP_rep2


title: TCF4_ChIP_rep1


title: R2237.DG.OG

value: Aged

value: Unimpaired


title: R2238.DG.OB


title: Wild-type L1 PGC transcriptome WT_L1_Slee34

description: Truseq  RNA library Prep Kit v2

value: Starved L1


title: R2237.CA3.OG


title: Qki5_CLIP1-3

city: Niigata

first: Masato

last: Yano

address: 757, Ichibancho, Asahimachidori, Chuo-ku, Niigata-shi,

department: Division of Neurobiology and Anatomy

country: Japan

institute: Niigata University

description: Qki5_CLIP1, Qki5_CLIP2, Qki5_CLIP3

data_processing:
Library strategy: HITS-CLIP
Collapsing of exact sequences.
Stripping of degenerate linker (barcode:First 5nt; ends with a C and next 9nt degenerate linker ends with a C) .
Alignment with Bowtie
to have Bed and wiggle file.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Bed file, bedGraph file

source_name: mouse embryonic brain

extract_protocol:
Qki5 bound fragments were ligated to a degenerate 3' linker to discriminate derivative tags from 3 different brains.
HITS-CLIP

treatment_protocol:
Brain tissue was UV irradiated and subjected to Qki5-CLIP.
Partial RNase digestion, RNA linker ligation and PCR amplification.

tag: genotype/variation

value: wild-type

value: brain


title: R2237.CA1.OG


title: osteoblast_ctrl_rep3

city: Richard B. Simches Research Center

first: Mikael

last: Pittet

state: 185 Cambridge Street

address: Center for Systems Biology, Massachusetts General Hospital

institute: CSB

data_processing:
quality filtering: fastx 0.0.13: fastq_quality_filter -v -Q 33 -q 20 -p 80 -i bcumiR1.fastq -o bcumiR1.filtered.fastq
mapping: tophat 2.0.10 with mm10 transcriptome: tophat -p 2 --library-type fr-firststrand --read-mismatches 5 --read-gap-length 5 --read-edit-dist 5 --no-coverage-search --segment-length 15
multiple mapping reads removed with samtools flag 256
duplicated reads removed using unique molecular identifiers
gene counts: hte-seq
Genome_build: mm10
Supplementary_files_format_and_content: count file (unnormalized)

source_name: osteoblast_KP-Ocn-GFP control

growth_protocol: Ex vivo examination of lung weight as proxy for tumor burden

extract_protocol:
Trizol; 2000 cells were sorted per mouse into Trizol and frozen at -80oC
3' digital gene expression, custom CelSeq protocol, with unique molecular identifier and multiplexing

treatment_protocol: Tumors were induced in lungs of KP-Ocn-GFP mice with AdCre intratracheally and mice were euthanized 14 weeks after AdCre infection. All bones were harvested, digested with collagenase and bone marrow fraction was depleted of lineage positive cells using the EasySep lineage depletion kit (Stem cell technologies) and pooled with the digested bone fraction. Ocn expressing cells were Facs-sorted based on GFP expression.

value: osteoblasts

tag: genetic background

tag: Sex

value: M

value: 23 week-old

tag: tumor

value: no


title: R2235.CA3.OB

value: male

value: hippocampus

tag: age impairment


title: Wild-type L1 PGC transcriptome WT_L1_Slee33

description: Truseq  RNA library Prep Kit v2


title: R2235.DG.OB

tag: gender


title: Wild-type L1 PGC transcriptome WT_L1_Slee32

description:
Truseq  RNA library Prep Kit v2
WTL1_vs_nosL1_Truseq_exp.diff


title: osteoblast_tumor_rep4

source_name: osteoblast_KP-Ocn-GFP tumor

tag: age

value: yes


title: R2235.CA1.OB


title: osteoblast_tumor_rep3

value: 31 week-old


title: R2233.DG.OB

value: Impaired


title: nanos L1 PGC transcriptome nanos_L1_25_Slee86

description:
SMART-seq V4 RNA-seq system
nosEMB_vs_nosL1_exp.diff

source_name: sorted nos-1(gv5)nos-2(RNAi) L1 PGCs


title: R2238.CA1.OB

value: Fischer 344


title: R2233.CA3.OB


title: R2233.CA1.OB


title: nanos L1 PGC transcriptome nanos_L1_25_Slee85

description:
SMART-seq V4 RNA-seq system
WTL1_vs_nosL1_smartseq_exp.diff


title: R2232.DG.OG


title: R2232.CA3.OG


title: osteoblast_ctrl_rep2


title: osteoblast_tumor_rep2


title: Wild-type L1 PGC transcriptome WT_L1_25_Slee84

description: SMART-seq V4 RNA-seq system


title: R2232.CA1.OG


title: R2231.CA1.OB


title: Wild-type L1 PGC transcriptome WT_L1_25_Slee83

description:
SMART-seq V4 RNA-seq system
WTEMB_vs_WTL1_gene_exp.diff


title: Wild-type embryonic soma transcriptome WT_embsoma_25_Slee12

description: Ovation RNA-seq V2 system

source_name: sorted wild-typeembryonic somatic cells

value: embryonic


title: R2230.DG.OG

value: dentate gyrus (DG)


title: osteoblast_tumor_rep1


title: Wild-type embryonic soma transcriptome WT_embsoma_25_Slee3

description: Ovation RNA-seq V2 system

source_name: sorted wild-type embryonic somatic cells


title: shQk_NSC_3

description: mRNA-seq

data_processing:
Alignment with Tophat
to have BAM and Bed file.
Transcript level and alternative splicing events with Quantas.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: .txt: Tab-delimited text files; gene_id, gene_symbol, tag_number, RPKM, start and end position, strand and isoform tag_number.

source_name: mouse neural stem cells, Qk knockdown

growth_protocol: Neural stem cells were isolated from the E14.5 mouse cortex and cultured with KBM neural stem cell medium (KOHJIN BIO, Japan) supplemented with 10 ng/ml bFGF.

extract_protocol:
Six days after infection, the cells were collected and subjected to mRNA-library generation.
TruSeq RNA Sample Prep Kit v2.

treatment_protocol: Lentiviruses encoding sh-control or sh-Qk, which targeted all Qki proteins for knock-down (KD), were produced and infected into cultured neural stem.

tag: cell type

value: Neural stem cells

tag: lentivirus

value: sh-Qk


title: R2230.CA1.OG

tag: strain/background

tag: hippocampal subregion

value: Aged

value: Unimpaired


title: shQk_NSC_2

description: mRNA-seq

tag: developmental stage


title: R2230.CA3.OG

tag: rat identifier


title: R2221.CA3.Y

value: Young


title: Wild-type embryonic soma transcriptome WT_embsoma_25_Slee1

description: Ovation RNA-seq V2 system

tag: temperature for culturing

tag: feeding condition


title: R2221.CA1.Y

tag: tissue


title: Wild-type embryonic PGC transcriptome WT_emb_25_Slee11

description: Ovation RNA-seq V2 system

source_name: sorted wild-type embryonic PGCs


title: R2221.DG.Y


title: osteoblast_ctrl_rep1

value: osteoblasts


title: R2231.CA3.OB


title: R2231.DG.OB


title: R2189.CA3.OB


title: Wild-type embryonic PGC transcriptome WT_emb_25_Slee4

description: Ovation RNA-seq V2 system


title: shQk_NSC_1

description: mRNA-seq


title: R2185.CA3.OG


title: R2189.CA1.OB


title: R2189.DG.OB


title: shCont_NSC_2

description: mRNA-seq

source_name: mouse neural stem cells, control

value: sh-control


title: shCont_NSC_3

description: mRNA-seq


title: nanos embryonic PGC transcriptome nanos_emb_25_Slee82

description: SMART-seq V4 RNA-seq system

source_name: sorted nos-1(gv5)nos-2(RNAi)  embryonic PGCs


title: R2184.DG.OG

source_name: Brain


title: shCont_NSC_1

description: mRNA-seq


title: R2184.CA3.OG


title: Wild-type embryonic PGC transcriptome WT_emb_25_Slee2

description: Ovation RNA-seq V2 system


title: PriMBs_Input (ChIP-seq)

city: Freiburg

first: Holger

last: Greschik

address: Breisacher Strasse 66

department: ZKF

institute: University Medical Center Freiburg

data_processing:
Paired-end reads were mapped to the mouse reference genome (mm10) using bowtie 2.
Data were further analyzed using the peak finding algorithm of MACS 1.4.2 using input as control.
Genome_build: mm10
Supplementary_files_format_and_content: bed, wig

source_name: skeletal muscle

extract_protocol:
Primary myoblasts (PriMBs) were isolated from limb muscle of 10-day old mice using the preplating technique and cultivated to about 70% confluency. Chromatin was prepared and ChIP performed according to Arrigoni, L. et al. (2016) Nucleic Acids Res. 55, e67.
Libraries were prepared using the NEBNext Ultra DNA library preparation kit (NEB, E7370S). Adapter-ligated fragments were amplified with 12 PCR cycles and sequenced on the Illumina HiSeq 2500 platform.

tag: strain

value: primary myoblasts

value: isolated from 10-day-old mice

tag: chip antibody


title: R2184.CA1.OG

value: male


title: nanos embryonic PGC transcriptome nanos_emb_25_Slee80

description:
SMART-seq V4 RNA-seq system
WTEMB_vs_nosEMB_gene_exp.diff

source_name: sorted nos-1(gv5)nos-2(RNAi) embryonic PGCs


title: nanos embryonic PGC transcriptome nanos_emb_25_Slee81

description: SMART-seq V4 RNA-seq system


title: R2182.DG.OB

value: hippocampus


title: R2182.CA3.OB


title: PriMBs_H3K4me3 (ChIP-seq)

value: anti-H3K4me antibody (Diagenode, catalog# C15410003, lot# A5051-001P)


title: PriMBs_SPIN1-5867 (ChIP-seq)

value: anti-SPIN1 antibody (custom SPIN1-5867)


title: Wild-type embryonic PGC transcriptome WT_emb_25_Slee79

description: SMART-seq V4 RNA-seq system


title: R2182.CA1.OB

value: Impaired


title: R2185.DG.OG

value: Fischer 344


title: R2176.CA3.Y


title: H2_Clone_DoxB

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

data_processing:
library strategy: 4sU-RNA-seq
The libraries were sequenced by Illumina NextSeq 500.
The raw reads were filtered by removing the reads mapping to rRNA bulid.
Filtered and adptor-removed reads were aligned to N-masked mm10 genome by STAR
Unique alignment were split by SNPsplit.
Allelic expression value and repression score were calculated by custom scripts.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

growth_protocol: ES cells were grown in ES cell medium, which consisted of Dulbecco’s Modified Eagle Medium (DMEM, from Life Technologies) supplemented with 9% foetal calf serum (FCS, from Seralab), 2mM L-glutamine, 1x non-essential amino acids, 50 μM β-mercaptoethanol, 50g/mL penicillin/streptomycin (all from Invitrogen) and LIF- conditioned medium, made in house, at a concentration equivalent to 1000U/mL. Non-differentiating ES cells were grown on tissue culture dishes coated with PBS+1% gelatine. EC10 medium consisted of DMEM, supplemented with 9% FCS, 2mM L-glutamine, 1x non-essential amino acids, 50 μM β-mercaptoethanol and 50 g/mL penicillin/streptomycin. Cells were grown at 37ºC in a humid atmosphere with 5% CO2. Cells were passaged using 0.05% trypsin-EDTA (Life Technologies) with 2% Chicken Serum (Life Technologies) and frozen in FCS + 10% DMSO.

extract_protocol:
Total RNAs were extracted according to TRIzol manuals, followed by DNaseI treatment.For each μg of total RNA, 2μL of Biotin-HPDP (Pierce, 50mg EZ-Link Biotin-HPDP), previously dissolved in DMF at a concentration of 1mg/mL, and 1μL of 10xBiotinylation buffer (100mM Tris HCl pH 7.4, 10mM EDTA), were added. The reaction was incubated with rotation for 15 min at 25ºC. Biotinylated 4sU-RNA was recovered using the μMacs Streptavidin Kit.
Illumina TruSeq Stranded Total RNA Library Prep Kit

treatment_protocol: Xist expression driven by TetO promoter was induced by adding doxycycline (1.5μg/mL) to the culture medium for 3 days. To achieve differentiation, ES cells were plated at a low density (0.6·10^6 cells) in 14 cm non-gelatineised tissue culture dishes in EC10 medium, and grown in LIF-depleted conditions for 72 hours. 4sU was thawed just before use and added to the cells in the growing media at a concentration of 500μM. Cells were incubated with the 4sU-implemented medium for 12 minutes.

tag: strain background

value: 129S1 x Cast

tag: cell line

value: Cell line integrating with XistDelXR-PID-bgl randomly and hnRNPK-bglG

value: mouse embryonic stem cells

tag: treated with

value: doxycycline (1.5μg/mL) for 72hrs

tag: molecule subtype


title: Wild-type embryonic PGC transcriptome WT_emb_25_Slee78

description: SMART-seq V4 RNA-seq system

value: embryonic


title: R2176.CA1.Y

tag: gender

tag: age impairment


title: H2_Clone_DoxA

tag: cell type


title: R2175.CA3.Y

tag: age


title: R2175.DG.Y

tag: strain/background

value: dentate gyrus (DG)


title: R2185.CA1.OG

tag: hippocampal subregion

value: Aged

value: Unimpaired


title: F1_Clone_DoxB


title: R1931.DG.OB


title: R2175.CA1.Y

value: Young


title: R1931.CA1.OB


title: R1930.CA3.OG


title: R1931.CA3.OB


title: H2_Clone_NoDox


title: F1_Clone_DoxA


title: R1930.DG.OG


title: R1930.CA1.OG


title: P4D7C2(XistDelXR-PID)_Dox_Rep2

description:
DelB-2C-Dox-Rep5
processed data file
DelB-2C_Rep5_Dox_NoDox.diff.bedGraph.gz

data_processing:
The raw paired-end reads were mapped to ‘N_masked’ mm10 genome with STAR (2.4.2a) using the parameters “--alignIntronMax 10 --outFilterMultimapNmax 1 --outFilterMismatchNmax 2 --alignEndsType EndToEnd”.
The unique alignment were reserved and split allelically with SNPSplit.
The bedGraph files containing the library-size normalised differences between G1 (Cast.) and G2 (129S1) for each biological replicate were generated by Bedtools. The differences between Dox and NoDox treatment were further defined.
Genome_build: mm10

growth_protocol: ES cells were grown in ES cell medium, which consisted of Dulbecco’s Modified Eagle Medium (DMEM, from Life Technologies) supplemented with 9% foetal calf serum (FCS, from Seralab), 2mM L-glutamine, 1x non-essential amino acids, 50 uM β-mercaptoethanol, 50g/mL penicillin/streptomycin (all from Invitrogen) and LIF- conditioned medium, made in house, at a concentration equivalent to 1000U/mL. Non-differentiating ES cells were grown on tissue culture dishes coated with PBS+1% gelatine. EC10 medium consisted of DMEM, supplemented with 9% FCS, 2mM L-glutamine, 1x non-essential amino acids, 50 uM β-mercaptoethanol and 50g/mL penicillin/streptomycin. Cells were grown at 37ºC in a humid atmosphere with 5% CO2. Cells were passaged using 0.05% trypsin-EDTA (Life Technologies) with 2% Chicken Serum (Life Technologies) and frozen in FCS + 10% DMSO.

extract_protocol:
genomic DNA
ATAC-Seq libraries were prepared using methods developed by Buenrostro et al.

treatment_protocol: Xist expression driven by TetO promoter was induced by adding doxycycline (1.5μg/mL) to the culture medium for 24 hours.

tag: genotype/variation

value: integrating with XistDelXR-PID randomly (pre-characterized on Chr2)

value: 1.5μg/mL doxycycline for 24h


title: R1923.CA3.Y

value: male

tag: rat identifier


title: R1923.DG.Y

value: hippocampus


title: R1923.CA1.Y


title: R1922.DG.Y


title: H2644-log2

city: London

first: Finn

last: Werner

address: Gower Street

department: Institute of Structural and Molecular Biology

institute: University College London

data_processing:
Sequencing reads were trimmed to remove the adaptor parts using Trimmomatic
For differential expression analysis, reads were mapped to the Haloferax volcanii DS2 genome using TopHat using parameters --no-novel-juncs --no-mixed --library-type fr-first strand with filtering out reads mapping to tRNA and rRNA genes as well as reads that do not map uniquely
RPKM values (reads per kb per million) were calculated using HTseq-count.
Data were analysed using DESeq2 to identify significant differentially expressed genes (p  adj < 0.01)
In order to estimate expression levels of genes we used RSEM in paired end mode and forward-prob 0 for libraries prepared with the dUTP method. As no transcript map of Hvo is available, we calculated transcript abundance for the region from the TSS to the stop codon of the first cistron.
Genome_build: Haloferax volcanii DS2 (NCBI genome ID 1149)
Supplementary_files_format_and_content: xls file with gene coordinates, deSeq results and TPM estimates for WT strain H53 replicates

organism: Haloferax volcanii

source_name: Hvo ∆tfeB H2644

growth_protocol: 50 ml of cells grown in Hv-YPC broth to early log phase (OD 650 = 0.2)

extract_protocol:
Total RNA was isolated from H. volcanii using the TRIzol method. Cells were resuspended in 250 µl of unbuffered spheroplast solution (1M NaCl, 27 mM KCl, 15% sucrose, pH 7.5) (29). 750 µl of TRIzol (Invitrogen) was added and mixed by pipetting. 200 µl of chloroform (Sigma) was added and vortexed for 15 s, then centrifuged at 20,000 x g for 15 min. The upper phase was transferred to a fresh tube, 500 µl of isopropanol was added and incubated for 10 min at room temperature. RNA was pelleted by centrifugation at 20,000 x g for 10 min, washed with 75% ethanol, air-dried and resuspended in 50 μl of RNase-free dH2O. 1 µg of total RNA was used for rRNA depletion using Ribo-Zero rRNA Removal Kit (Illumina).
Libraries were prepared using the dUTP method with NEBNext Ultra Directional RNA Library Prep kit for Illumina (New England Biolabs)

value: {delta}tfeB H2644

tag: genotype

value: markerless deletion of tfeB (Hvo_1090) in strain H53


title: R2176.DG.Y


title: P4D7C2(XistDelXR-PID)_NoDox_Rep2

description:
DelB-2C-NoDox-Rep5
processed data file
DelB-2C_Rep5_Dox_NoDox.diff.bedGraph.gz


title: R1922.CA3.Y


title: P4D7F4(FLXist)_Dox_Rep2

description:
P4D7F4-Dox-Rep5
processed data file
P4D7F4_Rep5_Dox_NoDox.diff.bedGraph.gz

value: integrating with FLXist randomly (pre-characterized on Chr3)


title: H2644-log


title: SC3

city: Yangzhou

first: Yifan

last: Liu

address: No.58 Cangjie road

institute: Institute of Poultry Science, Chinese Academy of Agricultural Science

data_processing:
mapped to chicken genome galgal5 using Tophat2
htseq was used to calculate gene expression level in each sample
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: galgal5.0
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: chicken comb

extract_protocol:
Total comb RNA was extracted from each comb sample using TRIzol reagent (Invitrogen, USA) according to the manufacturer's instructions.
TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina, CA, USA) was used to establish strand-specific RNA-seq libraries following the manufacturer's recommendations.

tag: comb size

value: small

value: chicken comb


title: R1922.CA1.Y

value: Fischer 344

tag: tissue


title: P4D7F4(FLXist)_NoDox_Rep2

description:
P4D7F4-NoDox-Rep5
processed data file
P4D7F4_Rep5_Dox_NoDox.diff.bedGraph.gz

value: 129S1 x Cast

value: mouse embryonic stem cells


title: H26log2

source_name: parental H53 strain

tag: strain

value: DS2 derrivative with genomic integration of pHV2


title: SC2


title: P4D7C2(XistDelXR-PID)_Dox_Rep1

description:
DelB-2C-Dox-Rep6
processed data file
DelB-2C_Rep6_Dox_NoDox.diff.bedGraph.gz


title: BC3

value: big


title: F1_Clone_NoDox

value: Cell line integrating with XistDelXR-PID-bgl randomly and hnRNPK-bglG


title: BC2


title: H26log


title: BC1


title: P4D7F4(FLXist)_Dox_Rep1

description:
P4D7F4-Dox-Rep6
processed data file
P4D7F4_Rep6_Dox_NoDox.diff.bedGraph.gz


title: Shp2 CKO_Rep1

city: New york

first: Xin

last: Zhang

state: New york

department: Ophthalmology

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat [1] (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [2] (version 2.0.2) with default settings.
We test for differentially expressed genes under various conditions using DEseq [3]. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: Mouse: UCSC/mm9

source_name: lacrimal gland mesenchyme

extract_protocol:
RNA extraction was performed by Nugen's Ovation RNA-seq System V2
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.

treatment_protocol: Embryos were flash frozen in OCT

value: Wnt-1 Cre, Shp2fl/fl

value: mixed background

value: lacrimal gland mesenchyme


title: P4D7F4(FLXist)_NoDox_Rep1

description:
P4D7F4-NoDox-Rep6
processed data file
P4D7F4_Rep6_Dox_NoDox.diff.bedGraph.gz


title: BisPCR2_ControlDNA_75%

city: Olso

first: Jorke

last: Kamstra

address: Ullevålsveien 72

department: Basic Sciences and Aquatic Medicine

country: Norway

institute: Norwegian University of Life Sciences

description:
BisPCR2
processed data file:
Results_Standard_Curve.xlsx

data_processing:
Trimming was performed with trim_galore (v0.4.1) with the following parameters: BisPCR2:  trim_galore –fastqc --paired --clip_R1 20 --clip_R2 20
Bismark (0.15) mapping was performed with the following parameters:   bismark –bowtie2 -N 0 -L 30 --score_min L,0,-0,4
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
processed data 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 larvae

extract_protocol:
DNA was purified with the Gentra puregene tissue DNA extraction kit (Qiagen, Germany), with modifications. Embryos were lysed in 300 µL lysis buffer and disrupted with the use of a 20G needle. To remove RNA, 5 µL of 20 mg/mL RNAse A (Qiagen, Germany) was added, followed by an overnight proteinase K incubation (20 µL of 20 mg/mL) (Qiagen, Germany) at 65 °C, under continuous shaking at 300 rpm. Following incubation, an extra 5 µL RNAse A was added and incubated at room temperature for 1 hr to ensure complete removal of RNAs. Protein precipitation buffer (supplied by kit) was added (100 µL) and after vigorously shaking, the precipitate was centrifuged at 13000 rpm for 3 min. Supernatant was added to a 1.5 mL reaction tube containing 300 µL isopropanol, supplemented with 90 µL of 3M sodium acetate (pH 5.3). The mixture was mixed by inverting 50 times and centrifuged for 1 min at 13000 rpm. Supernatant was discarded and the pellet was rinsed twice with 70 % freshly prepared ethanol (300 µL) by gentle shaking and centrifugation at 13000 rpm for 1 min. The pellet was air dried for 5 minutes and resuspended in hydration buffer, supplied with the kit. DNA was assessed for RNA contamination and length with gel electrophoreses and measured for concentration and quality by Nanodrop (ND-1000; Thermo Scientific). DNA was stored at -20 °C until further analysis.
We used the BisPCR2 method (Bernstein et al. 2015), which was adapted at our lab and is extensively described (Kamstra et al. 2017). In short, the method uses specific developed primers for bisulfite converted DNA (Epitect kit, Qiagen, Germany), with an Illumina adapter overhang (Supplemental material, Table 1). Primers were developed using the online Bisearch tool (http://bisearch.enzim.hu/), and validated for specificity and amplicon size by gel electrophoresis, as described previously (Kamstra et al. 2017). From every bisulfite converted DNA sample, PCRs for each of the 20 targets were performed, these were pooled in equal volumes, purified (PCR purification kit, Qiagen, Germany) and subjected to a second PCR with Illumina specific barcoded primers (sequences described previously (Bernstein et al. 2015)). Following the second PCR, products were purified with AMPure XP beads (Beckman Coulter, USA), and measured using Qubit. Random samples were analyzed on the Agilent 2100 bioanalyzer for library quality, which showed high quality libraries (data not shown). Concentrations were converted to nM with c (nM) = (Qubit conc (ng/µL) * 1000000) / (660 * average length). All second PCR products were pooled in equimolar portions to a final concentration of 2 nM, followed by 150 base paired end sequencing analysis on Miseq (Illumina, US) as described previously (Bernstein et al. 2015).
DNA was purified with the Gentra puregene tissue DNA extraction kit (Qiagen, Germany), with modifications. Embryos were lysed in 300 µL lysis buffer and disrupted with the use of a 20G needle. To remove RNA, 5 µL of 20 mg/mL RNAse A (Qiagen, Germany) was added, followed by an overnight proteinase K incubation (20 µL of 20 mg/mL) (Qiagen, Germany) at 65 °C, under continuous shaking at 300 rpm. Following incubation, an extra 5 µL RNAse A was added and incubated at room temperature for 1 hr to ensure complete removal of RNAs. Protein precipitation buffer (supplied by kit) was added (100 µL) and after vigorously shaking, the precipitate was centrifuged at 13000 rpm for 3 min. Supernatant was added to a 1.5 mL reaction tube containing 300 µL isopropanol, supplemented with 90 µL of 3M sodium acetate (pH 5.3). The mixture was mixed by inverting 50 times and centrifuged for 1 min at 13000 rpm. Supernatant was discarded and the pellet was rinsed twice with 70 % freshly prepared ethanol (300 µL) by gentle shaking and centrifugation at 13000 rpm for 1 min. The pellet was air dried for 5 minutes and resuspended in hydration buffer, supplied with the kit. DNA was assessed for RNA contamination and length with gel electrophoreses and measured for concentration and quality by Nanodrop (ND-1000; Thermo Scientific). DNA was stored at -20 °C until further analysis.

value: whole embryos

value: AB

value: 6 dpf

tag: treatment

value: ControlDNA


title: BisPCR2_ControlDNA_100%


title: BisPCR2_ControlDNA_50%


title: BisPCR2_ControlDNA_25%


title: EvXist△XR-PID_Dox_R1

data_processing:
The libraries were sequenced by Illumina HiSeq 2000 or NextSeq 500.
The raw reads were filtered by removing the reads mapping to rRNA bulid.
Filtered and adptor-removed reads were aligned to N-masked mm10 genome by STAR
Unique alignment were split by SNPsplit.
Allelic expression value and repression score were calculated by custom scripts.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig
Not all the samples have processed data. The bigwig files are generated for the samples which has been performed deep analysis on our studies.

source_name: mouse embryonic stem cells

treatment_protocol: Xist expression driven by TetO promoter was induced by adding doxycycline (1.5μg/mL) to the culture medium for 24 hours to 3 days. To achieve differentiation, ES cells were plated at a low density (0.6·10^6 cells) in 14cm non-gelatineised tissue culture dishes in EC10 medium, and grown in LIF-depleted conditions for 72 hours. 4sU was thawed just before use and added to the cells in the growing media at a concentration of 500μM. Cells were incubated with the 4sU-implemented medium for 12 minutes.

tag: strain background

value: male

value: EvXistdeltaXR-PID was CRISPR into Chr11 Locus

tag: agent

value: Dox

tag: time point


title: EvXist△XR-PID_Dox_R2

tag: cell line


title: EvXist△XR-PID_NoDox

tag: gender


title: P4D7G9(EvXist△XR-PID)_Dox_R2

value: Cell lines Integating with EvXistdeltaXR-PID randomly


title: EvXist_Dox_R1

value: EvXist RNA was CRISPR into Chr11 Locus


title: EvXist_NoDox

value: 129S1 x Cast


title: EvXist_Dox_R2


title: BisPCR2_ControlDNA_0%


title: P4D7G9(EvXist△XR-PID)_NoDox


title: SC1

value: small

value: chicken comb


title: P4D7C2(XistDelXR-PID)_NoDox_Rep1

description:
DelB-2C-NoDox-Rep6
processed data file
DelB-2C_Rep6_Dox_NoDox.diff.bedGraph.gz

value: mouse embryonic stem cells

value: integrating with XistDelXR-PID randomly (pre-characterized on Chr2)

tag: treated with


title: P4D7D9(EvXist)_Dox_R1

value: Cell lines Integating with EvXist randomly


title: P4D7D9(EvXist)_NoDox


title: BisPCR2_F3_exposed_5

description:
BisPCR2
processed data file:
Results_BisPCR2.xlsx

source_name: 5.5 hpf zebrafish embryos

value: 5.5 hpf

tag: parental treatment

value: 8.7 mGy/h

tag: generation


title: P4D7D9(EvXist)_Dox_R2


title: BisPCR2_F3_exposed_4

value: whole embryos

tag: age


title: P4D7H8(EvXist△XR-PID)_Dox_R2


title: P4D7A12(EvXist)_Dox_R2


title: P4D7A12(EvXist)_NoDox


title: P4D7A12(EvXist)_Dox_R1


title: WT_Rep1

value: Wild type

value: mixed background

value: lacrimal gland mesenchyme


title: P4D7H8(EvXist△XR-PID)_NoDox

value: male


title: P4D7D12(DelSX)_Dox_R4

value: Cell line integrating with XistDelSX randomly


title: P4D7G9(EvXist△XR-PID)_Dox_R1

value: Dox


title: P4D7D12(DelSX)_Dox_R3


title: P4D7A2(XistDelXR-PID)_Dox_R2

value: Cell line integrating with XistDelXR-PID randomly


title: BisPCR2_F3_exposed_2

value: AB


title: P4D7D12(DelSX)_Dox_R2

value: 129S1 x Cast


title: BisPCR2_F3_exposed_1


title: P4D7D12(DelSX)_NoDox


title: P4D7D12(DelSX)_Dox_R1


title: P4D7A2(XistDelXR-PID)_NoDox


title: P4D7A2(XistDelXR-PID)_Dox_R1


title: BisPCR2_F3_control_5

value: control


title: P4D7B11(DelXN)_Dox_R2

value: Cell line integrating with XistDelXN randomly


title: P4D7H8(EvXist△XR-PID)_Dox_R1

value: Cell lines Integating with EvXistdeltaXR-PID randomly


title: P4D7B11(DelXN)_Dox_R1


title: BisPCR2_F3_exposed_3


title: P4D7C2(XistDelXR-PID)_Dox_R2


title: P4D7C2(XistDelXR-PID)_Dox_R1


title: P4D7B11(DelXN)_NoDox


title: P4D7C5(FLXist)_48hDox_R2

value: Cell line integrating with FLXist randomly


title: P4D7C5(FLXist)_72hDox_R2


title: BisPCR2_F3_control_4


title: BisPCR2_F3_control_3


title: BisPCR2_F3_control_2


title: P4D7C5(FLXist)_72hDox_R1


title: P4D7D12(DelSX)_NoDox_2


title: P4D7C5(FLXist)_NoDox_R2


title: BisPCR2_F3_control_1


title: BisPCR2_F2_exposed_5


title: P4D7C5(FLXist)_NoDox_R1


title: P4D7C5(FLXist)_24hDox_R1


title: P4D7D1(DelXN)_Dox_R2


title: P4D7D1(DelXN)_Dox_R1


title: P21_Ctrl_rep4 (RNA-seq)

data_processing:
Reads were aligned to the mm10 build of the mouse genome using TopHat version 2.
Aligned reads were counted with the Homer software (analyzeRepeats) and differentially expressed genes identified using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Excel tables containing normalized read counts obtained from edgeR

source_name: tibialis anterior

extract_protocol:
Trizol extraction of total RNA (according to the manufacturer's instructions) from skeletal muscle of front and hind limb of fetuses at E15.5 and E16.5, and from tibialis anterior of mice at three weeks of age (P21).
RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq).

value: tibialis anterior

value: P21 (three weeks)


title: P4D7C5(FLXist)_48hDox_R1


title: P21_Ctrl_rep3 (RNA-seq)


title: BisPCR2_F2_exposed_3

value: 5.5 hpf

value: 8.7 mGy/h


title: P4D7F4(FLXist)_Dox_R2

value: Cell line integrating with FLXist randomly (P4D7F4)


title: BisPCR2_F2_exposed_4

value: whole embryos


title: BisPCR2_F2_exposed_2


title: P21_KO_rep3 (RNA-seq)


title: P21_Ctrl_rep1 (RNA-seq)


title: P21_KO_rep4 (RNA-seq)


title: P4D7C2(XistDelXR-PID)_NoDox


title: P21_KO_rep1 (RNA-seq)


title: P21_KO_rep2 (RNA-seq)


title: P4D7F4(FLXist)_NoDox


title: P4D7F4(FLXist)_Dox_R1


title: BisPCR2_F2_exposed_1


title: E16.5_Ctrl_rep4 (RNA-seq)

value: skeletal muscle


title: BisPCR2_F2_control_5


title: E16.5_Ctrl_rep3 (RNA-seq)


title: BisPCR2_F2_control_4


title: P21_Ctrl_rep2 (RNA-seq)


title: E16.5_KO_rep3 (RNA-seq)


title: BisPCR2_F2_control_3


title: E16.5_KO_rep2 (RNA-seq)