title: mut_CH12+BORIS_ChIP-seq_with RAD21 Abs

description: mut_CH12+BORIS_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz


title: U1-1_cell

status: Public on Jan 01 2020

type: SRA

city: Beijing

first: Yafei

last: Yin

state: Beijing

address: Zhongguancun North Street

department: Medical School

country: China

institute: Tsinghua University

description: Normalized abundance of lncRNAs in whole cell or subcellular fractions upon AMO treatment.txt

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version
Reads obtained from RNA-seq library sequencing were aligned to the mm10 genome assembly using tophat with uniq mapping parameters.
Gene expression (FPKM) were further calculated from mapped reads through Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs

molecule: total RNA

organism: Mus musculus

source_name: 46C mES cells

growth_protocol:
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). 293T cells  were maintained in medium supplemented with 10% heat-inactivated FCS, Penicillin-Streptomycin Solution (100 × stock, Life Technologies).

extract_protocol:
Subcellular fractionation was performed as previously described with following modifications45. Cytoplasmic buffer containing 0.05% or 0.15% NP-40 was used for isolating cytoplasmic fraction of mESC or 293T cells respectively. The whole sample of each subcellular fraction was spiked and mixed thoroughly with 5 µl 0.1 ng/µl spike-in RNA [contain two in vitro transcribed RNA: lacZ and mCherry, For polyA RNA-seq or SLAM-seq, ERCC spike-in (Thermo Fisher) was used].
For total RNA-seq, ribosomal RNAs were removed through Ribo-Zero rRNA Removal Kits (Epicentre), for polyA RNA-seq, polyA RNAs were isolated through Dynabeads mRNA Purification Kit (Thermo Fisher). RNA-seq libraries were constructed through NEBNext Ultra II Directional RNA Library Prep Kit (NEB).
Subcellular fractionation was performed as previously described with following modifications45. Cytoplasmic buffer containing 0.05% or 0.15% NP-40 was used for isolating cytoplasmic fraction of mESC or 293T cells respectively. The whole sample of each subcellular fraction was spiked and mixed thoroughly with 5 µl 0.1 ng/µl spike-in RNA [contain two in vitro transcribed RNA: lacZ and mCherry, For polyA RNA-seq or SLAM-seq, ERCC spike-in (Thermo Fisher) was used].
For total RNA-seq, ribosomal RNAs were removed through Ribo-Zero rRNA Removal Kits (Epicentre), for polyA RNA-seq, polyA RNAs were isolated through Dynabeads mRNA Purification Kit (Thermo Fisher). RNA-seq libraries were constructed through NEBNext Ultra II Directional RNA Library Prep Kit (NEB).

treatment_protocol:
mESCs were transfected with 75 μM U1 AMO, and culture at 37℃ for 2 hours.
IAA, 4 hours

tag: cell type

value: embryonic stem cells

tag: treatment

value: U1 AMO nucleofection, 2 hours

tag: strain

tag: fraction

value: total RNA


title: CC043_kidney_atac

city: Chapel Hill

first: Terry

last: Furey

state: NC

address: 120 Mason Farm Road

department: Genetics

country: USA

institute: University of North Carolina, Chapel Hill

library_source: genomic

data_processing:
Sequencing reads in FASTQ files were filtered (sequence quality score ≥ 20 for ≥ 90% of bases) and adapter contamination was removed using TagDust
Reads with >5 exact duplicates were filtered to only retain 5 of the reads
Reads were aligned to the appropriate pseudo-genome using GSNAP (parameter set: -k 15, -m 1, -i 5, –sampling=1, –trim-mismatch-score=0, –genome-unk-mismatch=1, –query-unk-mismatch=1)
Uniquely mapped reads were converted to mm9 (NCBI37) mouse reference genome coordinates using the associated MOD files (Build37, http://csbio.unc.edu/CCstatus/index.py?run=Pseudo) to allow comparison across strains.
Alignments overlapping regions in the mm9 blacklist (UCSC Genome Browser) were removed
Alignments were converted to BED format and shifted by +5 base pairs and -5 base pairs for the positive and negative strand alignments respectively
Genome_build: mm9
Supplementary_files_format_and_content: BED files containing ATAC-seq read alignments to the mm9 mouse reference genome

molecule: genomic DNA

source_name: kidney tissue

growth_protocol: Adult male mice (8-12 weeks old) from 47 CC strains were acquired from the University of North Carolina Systems Genetics Core and maintained on an NTP 2000 wafer diet (Zeigler Brothers, Inc., Gardners, PA) and water ad libitum. The housing room was maintained on a 12-h light-dark cycle

extract_protocol:
Mice were euthanized by exsanguination following deep nembutal (100 mg/kg intraperitoneal injection) anesthesia. Lungs, livers, and kidneys were excised, snap-frozen in liquid nitrogen, and stored at –80°C. Flash frozen tissue samples were pulverized in liquid nitrogen using the BioPulverizer (Biospec) to break open cells and allow even exposure of intact chromatin to Tn5 transposase. Pulverized material was thawed in glycerol containing nuclear isolation buffer to stabilize nuclear structure and then filtered through Miracloth (Calbiochem) to remove large tissue debris. Nuclei were washed and directly used for treatment with Tn5 transposase
TruSeq libraries were constructed as per manufacturer's recommendations

treatment_protocol: Mice were placed in cylindrical, metal mesh exposure chambers emitting clear air for 6 hours a day, Monday-Friday, across a two week period

tag: tissue

value: kidney


title: CT-3_nuc

treatment_protocol:
mESCs were transfected with 75 μM CT (scramble) AMO, and culture at 37℃ for 2 hours.
IAA, 4 hours

value: CT (scramble) AMO nucleofection, 2 hours

value: nucleoplasmic total RNA


title: COAD.ct-72

city: La Jolla

first: Kang

last: Zhang

address: 9500 Gilman Dr

institute: UCSD

data_processing:
unique molecular identifiers were extracted from each read using custom script
reads were adaptor and quality trimmed using Trim-galore and Cutadapt 1.4.1 with parameters -e 0.1 -q 20 -O 1
BisReadMapper1.3 (D.Diep, K.Zhang) using Bowtie2 was used to align reads to in-silico bisulfite-converted genome sequence
C and Ts were extracted from reads at the targeted positions using only reads with unique identifiers using custom scripts (BamExtractor, D.Diep, K.Zhang)
methylation frequencies were calculated by binning data into 100bp regions and aggregating methylated and non-methylated cytosines within 100bp bins
Genome_build: hg19
Supplementary_files_format_and_content: text file containing beta values for all samples at all analyzed 100bp genomic regions

organism: Homo sapiens

source_name: blood serum

extract_protocol:
cfDNA extraction from 1.5 ml of serum samples was performed using QIAamp cfDNA Kit (Qiagen) according to manufacturer’s recommendations
10 ng of cfDNA was bisulfite-converted using EZ DNA Methylation-Lightning™ Kit (Zymo). Bis-DNA specific "padlock" probes (molecular inversion probes, MIPS) were used to capture genomic regions and provide adaptors for NGS library construction. Nextera-XT compatible barcoding primers were used to amplify DNA for sequencing. Library (~300bp) was purified using AMPure beads.
custom-made libraries were sequenced on HiSeq2500 using 150PE reads

tag: sample type

value: cell-free DNA


title: COAD.ct-71


title: COAD.ct-70


title: mut_CH12+BORIS_ChIP-seq_with CTCF Abs

city: Bethesda

first: Elena

last: Pugacheva

state: MD

department: NIAID

institute: NIH

description: mut_CH12+BORIS_ChIP_seq_CTCF_ABs_treat_pileup.bdg.gz

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to either the hg19 (Human) or mm9 (Mouse) genome assembly using Bowtie program (http://bowtie-bio.sourceforge.net) with default parameters
Peaks were called using Model-based Analysis for ChIP-Seq (MACS) and MACS2 (http://liulab.dfci.harvard.edu/MACS) using default parameters. After MACS, we applied Peak Splitter algorithm (MACS) to call sub-peaks, summit of peaks and improve peak resolution.
RNA-seq reads were aligned  to UCSC Human reference (build mm9) using TopHat2 with the default parameter setting of 20 alignments per read and up to 2 mismatches per alignment.
RNA-seq aligned reads (BAM files) were analyzed with Cufflinks 2.0.0 to estimate the transcripts relative abundance using the UCSC reference annotated transcripts (build mm9). The expression of each transcript was quantified as the number of reads mapped to a transcript divided by the transcript length in kilobases and the total number of mapped reads in millions (FPKM).
Genome_build: hg19 (for human), mm9 (for mouse)
Supplementary_files_format_and_content: Narrow peak (bed), bdg, and wig files were generated either by MACS or MACS2

source_name: Mouse B lymphoma cell

growth_protocol: K562 and MCF7 cell lines (obtained from ATCC) were grown in Dulbecco's modified Eagle medium (DMEM) supplemented with 10 % fetal calf serum and penicillin-streptomycin. CH12, B-cell lymphoma, cell line was maintained in RPMI 1640 supplemented with 10% FBS, 1% penicillin/streptomycin and 55 μM 2-β mercaptoethanol. CH12 wild type (wt) and mutant (mut) cells were described previously in (PMID: 29706548 ) and obtained as a gift from Dr. Rafael Casellas.

extract_protocol:
Immunoprecipitated DNA was purified with QIAquick columns (ZymaResearch). DNA concentration was assessed with a Qubit4 (ThermoFisher) and 5–10 ng was used to generate sequencing libraries using a TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA).
TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA). RNA-seq libraries were prepared using either Ion Total RNA-seq v2 kit or TruSeq Stranded RNA LT Kit (Illumina).

treatment_protocol: For ChIP-seq 60 million of asynchronously growing cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1x PBS, and resuspended in ChIP lysis buffer (150 mM NaCl, 1% Triton X‐100, 0.1% SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to an average length of 200–500 bp using a Bioruptor sonication.

tag: cell line

tag: genotype

value: mutant (mut)

tag: expressed vector

value: mut_CH12 stably expressed BORIS from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

tag: chip antibody

value: custom mouse monoclonal CTCF (characterized in PMID:15731119)

tag: mutation

value: homozygous deletion of ZF9-11 in CTCF gene


title: mut_CH12_ChIP-seq_with_RAD21_Abs_Rep4

value: RAD21 ABs Abcam (ab992)


title: CT-3_cyto

value: cytoplasmic total RNA


title: COAD.ct-69


title: CC042_lung_atac

source_name: lung tissue

value: lung


title: mut_CH12_ChIP-seq_with_RAD21_Abs_Rep3


title: CT-3_chr

value: chromatin total RNA


title: CC042_liver_atac

source_name: liver tissue

value: liver


title: CC042_kidney_atac


title: mut_CH12_ChIP-seq_with_RAD21_Abs_Rep2


title: COAD.ct-68


title: CC041_lung_atac


title: mut_CH12_ChIP-seq_with_RAD21_Abs_Rep1


title: COAD.ct-73


title: COAD.ct-66


title: mut_CH12_ChIP-seq_with_CTCF_Abs_Rep4


title: CT-3_cell


title: CT-2_nuc


title: CC041_kidney_atac


title: CC041_liver_atac


title: CT-2_cyto


title: mut_CH12_ChIP-seq_with_CTCF_Abs_Rep3


title: COAD.ct-65


title: CT-2_chr


title: COAD.ct-64


title: mut_CH12_ChIP-seq_with_CTCF_Abs_Rep2


title: CC040_liver_atac


title: CT-2_cell


title: COAD.ct-63


title: mut_CH12_ChIP-seq_with_CTCF_Abs_Rep1


title: CT-1_nuc


title: COAD.ct-67


title: COAD.ct-62


title: CC040_kidney_atac


title: wt_CH12+BORIS_ChIP-seq_with BORIS Abs_Rep2

description: wt_CH12+BORIS_ChIP_seq_BORIS_ABs_treat_pileup.bdg.gz

value: wild type (wt)

value: wt_CH12 stably expressed BORIS from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: custom mouse monoclonal BORIS  (characterized in PMID:21659515)

value: wild type


title: CC039_lung_atac


title: CT-1_chr

value: embryonic stem cells


title: CT-1_cyto

value: CT (scramble) AMO nucleofection, 2 hours


title: COAD.ct-61


title: CT-1_cell

value: total RNA


title: COAD.ct-60

value: cell-free DNA


title: wt_CH12+BORIS_ChIP-seq_with RAD21 Abs

description: wt_CH12+BORIS_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz


title: COAD.ct-59


title: wt_CH12+BORIS_ChIP-seq_with CTCF Abs

description: wt_CH12+BORIS_ChIP_seq_CTCF_ABs_treat_pileup.bdg.gz


title: CC039_kidney_atac

value: kidney


title: CC039_liver_atac


title: wt_CH12_Input_For_ChIP-seq_Rep2


title: SNRNP70AID-SLAM_+IAA-3_nuc

description: Normalized abundance of lncRNAs identified by SLAM-seq in subcellular fractions upon SNRNP70-AID depletion.txt

source_name: SNRNP70-AID mESC (constructed from 46C mES cells)

treatment_protocol:
SNRNP70-AID mESCs were treated by adding 500 μM IAA, and culture at 37℃ for 2 hours, then culture for another 3 hours with (500 μM IAA + 300 mM 4sU).
IAA, 4 hours

value: IAA, 2 hours; then (IAA + 4sU), 3 hours

value: nucleoplasmic polyA RNA


title: CC040_lung_atac


title: CC038_lung_atac


title: COAD.ct-58


title: CC038_liver_atac


title: SNRNP70AID-SLAM_+IAA-3_cyto

value: cytoplasmic polyA RNA


title: wt_CH12_Input_For_ChIP-seq_Rep1


title: SNRNP70AID-SLAM_+IAA-3_chr


title: wt_CH12+BORIS_ChIP-seq_with BORIS Abs_Rep1


title: wt_CH12_ChIP-seq_with_RAD21 Abs_Rep3

value: Abcam RAD21 ABs (ab992)


title: SNRNP70AID-SLAM_+IAA-2_nuc


title: wt_CH12_ChIP-seq_with_RAD21 Abs_Rep2


title: COAD.ct-56


title: SNRNP70AID-SLAM_+IAA-2_cyto


title: CC038_kidney_atac


title: COAD.ct-55


title: COAD.ct-54


title: CC037_liver_atac


title: CC037_lung_atac


title: SNRNP70AID-SLAM_+IAA-2_chr


title: wt_CH12_ChIP-seq_with_RAD21 Abs_Rep1


title: wt_CH12_ChIP-seq_with_CTCF_Abs_Rep3

description:
wt_CH12_CTCF_treat_pileup.bdg
5K_Lost_CTCFsites.xlsx

value: custom mouse monoclonal CTCF (characterized in PMID:15731119)


title: CC037_kidney_atac


title: CC036_lung_atac

value: lung


title: SNRNP70AID-SLAM_+IAA-1_nuc


title: wt_CH12_ChIP-seq_with_CTCF_Abs_Rep2


title: COAD.ct-52


title: COAD.ct-51


title: CC036_liver_atac


title: SNRNP70AID-SLAM_+IAA-1_cyto


title: wt_CH12_ChIP-seq_with_CTCF_Abs_Rep1


title: COAD.ct-57


title: COAD.ct-50


title: SNRNP70AID-SLAM_+IAA-1_chr

value: chromatin total RNA


title: SNRNP70AID-SLAM_no-IAA-3_nuc

treatment_protocol:
SNRNP70-AID mESCs were treated by adding 300 mM 4sU for 3 hours.
IAA, 4 hours

value: 4sU, 3 hours


title: CC035_lung_atac


title: KLRGminusNFIL3minusTreg_R4 [Bulk RNA-seq]

city: Mainz

first: Michael

last: Delacher

state: Rhineland-Palatinate

address: Langenbeckstrasse 1

department: Institute for Immunology

country: Germany

institute: University Medical Center of the Johannes Gutenberg-University Mainz

description:
ILSE 9202 Lane 3
KLRGminusNFIL3minusTreg_R4

data_processing:
For all samples, low quality bases were removed with Fastq_quality_filter from the FASTX Toolkit 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html) with 90% of the reads needing a quality phred score > 20. Homertools 4.7 were used for PolyA-tail trimming, and reads with a length < 17 were removed. PicardTools 1.78 (https://broadinstitute.github.io/picard/) were used to compute the quality metrics with CollectRNASeqMetrics. With STAR 2.3, the filtered reads were mapped against mouse genome using default parameters. Count data and RPKM tables were generated by mapping filtered reads against union transcripts (derived from Mouse Ensembl 90) using a custom pipeline. Mapping was carried out with bowtie2 version 2.2.4 against union mouse genes: every gene is represented by a union of all its transcripts (exons). The count values (RPKM and raw counts) were calculated by running CoverageBed from Bedtools v2.26.0 of the mapped reads together with the mouse annotation file (Ensembl 90) in gtf format and parsing the output with custom perl scripts. The input tables containing the replicates for groups to compare were created by a custom perl script. For DESeq2, DESeqDataSetFromMatrix was applied, followed by estimateSizeFactors, estimateDispersions, and nbinomWald testing. The result tables were annotated with gene information (gene symbol, gene type) derived from the gencode.vM16.annotation.gtf file. The results were then filtered for protein-coding genes according to the gencode.vM16.annotation.gtf file.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain counts and rpkm

source_name: Spl Klrg1negNfil3neg Treg

growth_protocol: Mice were housed at DKFZ or UKR central animal facility

extract_protocol:
For tissue digestion and flow cytometry protocol, please refer to the associated publication
cDNA was generated and amplified using equal amounts of total RNA (RNEeasy Mini Kit) and SMARTer Ultra Low Input RNA for Illumina Sequencing - HV (Clontech Laboratories, Inc.) according to the manufacturer’s protocol. Then, sequencing libraries were prepared using the NEXT ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs) according to the manufacturer's instructions with the following modifications: The adapter-ligated double-stranded cDNA (10µl) was amplified using NEBNext Multiplex Oligos for Illumina (New England Biolabs, 25 µM primers), NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs) and 15 cycles of PCR. Final libraries were validated using Agilent 2100 Bioanalyzer (Agilent Technologies) and Qubit flourometer (Invitrogen), normalized and pooled in equimolar ratios. 50bp single-read sequencing was performed on the Illumina HiSeq 2000 v4 according to the manufacturer’s protocol.

treatment_protocol: For Treg expansion and in-vitro differentiation protocol, please refer to the associated publication

value: Klrg1-negative Nfil3(GFP)-negative


title: COAD.ct-53


title: COAD.ct-47


title: CC035_kidney_atac


title: KLRGminusNFIL3minusTreg_R1 [Bulk RNA-seq]

description:
ILSE 9202 Lane 3
KLRGminusNFIL3minusTreg_R1


title: CC035_liver_atac

value: liver


title: SNRNP70AID-SLAM_no-IAA-3_cyto


title: COAD.ct-48


title: KLRGminusNFIL3minusTreg_R3 [Bulk RNA-seq]

description:
ILSE 9202 Lane 3
KLRGminusNFIL3minusTreg_R3


title: KLRGminusNFIL3plusTreg_R5 [Bulk RNA-seq]

description:
ILSE 9202 Lane 2
KLRGminusNFIL3plusTreg_R5

source_name: Spl Klrg1negNfil3pos Treg

value: Klrg1-negative Nfil3(GFP)-positive


title: SNRNP70AID-SLAM_no-IAA-2_cyto


title: KLRGminusNFIL3plusTreg_R4 [Bulk RNA-seq]

description:
ILSE 9202 Lane 2
KLRGminusNFIL3plusTreg_R4


title: SNRNP70AID-SLAM_no-IAA-2_nuc


title: CC033_lung_atac


title: CC033_liver_atac


title: CC033_kidney_atac


title: SNRNP70AID-SLAM_no-IAA-1_nuc


title: SNRNP70AID-SLAM_no-IAA-2_chr


title: COAD.ct-46


title: COAD.ct-45


title: KLRGminusNFIL3plusTreg_R3 [Bulk RNA-seq]

description:
ILSE 9202 Lane 2
KLRGminusNFIL3plusTreg_R3


title: COAD.ct-44


title: CC032_lung_atac


title: CC036_kidney_atac


title: KLRGminusNFIL3plusTreg_R1 [Bulk RNA-seq]

description:
ILSE 9202 Lane 2
KLRGminusNFIL3plusTreg_R1


title: COAD.ct-49


title: COAD.ct-43


title: SNRNP70AID-SLAM_no-IAA-3_chr


title: SNRNP70AID-SLAM_no-IAA-1_cyto


title: KLRGplusNFIL3plusTreg_R5 [Bulk RNA-seq]

description:
ILSE 9202 Lane 1
KLRGplusNFIL3plusTreg_R5

source_name: Spl Klrg1posNfil3pos Treg

value: Klrg1-positive Nfil3(GFP)-positive


title: SNRNP70AID-SLAM_no-IAA-1_chr

value: embryonic stem cells


title: KLRGplusNFIL3plusTreg_R4 [Bulk RNA-seq]

description:
ILSE 9202 Lane 1
KLRGplusNFIL3plusTreg_R4


title: CC032_liver_atac


title: CC032_kidney_atac


title: COAD.ct-42


title: CC031_lung_atac


title: KLRGplusNFIL3plusTreg_R3 [Bulk RNA-seq]

description:
ILSE 9202 Lane 1
KLRGplusNFIL3plusTreg_R3


title: COAD.ct-41


title: SNRNP70AID-4h-pA-3_chr

description: Normalized abundance of lncRNAs identified by polyA RNA-seq in whole cell or chromatin fraction upon SNRNP70AID depletion.txt

treatment_protocol:
SNRNP70-AID mESCs were treated by adding 500 μM IAA, and culture at 37℃ for 4 hours
IAA, 4 hours

value: IAA, 4 hours

value: chromatin polyA RNA


title: COAD.ct-39

value: cell-free DNA


title: SNRNP70AID-4h-pA-3_cell

value: polyA RNA


title: COAD.ct-38


title: KLRGplusNFIL3plusTreg_R1 [Bulk RNA-seq]

description:
ILSE 9202 Lane 1
KLRGplusNFIL3plusTreg_R1


title: CC031_liver_atac


title: SNRNP70AID-4h_pA-2_cell


title: CC030_lung_atac


title: Treg_IL2+IFNg_R4.fastq_35020.clean_17449.all_txt [Bulk RNA-seq]

description:
ILSE 9201 Lane 5
Treg_IL2+IFNg_R4.fastq_35020.clean_17449.all_txt

source_name: In-vitro exp Treg

value: In-vitro exp Treg


title: SNRNP70AID-4h_pA-2_chr


title: SNRNP70AID-4h_pA-1_chr


title: COAD.ct-37


title: CC031_kidney_atac

value: kidney


title: CC030_liver_atac


title: Treg_IL2+IFNg_R3.fastq_34858.clean_17407.all_txt [Bulk RNA-seq]

description:
ILSE 9201 Lane 5
Treg_IL2+IFNg_R3.fastq_34858.clean_17407.all_txt


title: SNRNP70AID-4h_pA-1_cell


title: Treg_IL2+IFNg_R2.fastq_34775.clean_17367.all_txt [Bulk RNA-seq]

description:
ILSE 9201 Lane 5
Treg_IL2+IFNg_R2.fastq_34775.clean_17367.all_txt


title: CC030_kidney_atac


title: Treg_IL2+IFNg_R1.fastq_34704.clean_17326.all_txt [Bulk RNA-seq]

description:
ILSE 9201 Lane 5
Treg_IL2+IFNg_R1.fastq_34704.clean_17326.all_txt


title: COAD.ct-35


title: CC029_lung_atac


title: COAD.ct-40


title: Treg_IL2_R3.fastq_34568.clean_17228.all_txt [Bulk RNA-seq]

description:
ILSE 9201 Lane 4
Treg_IL2_R3.fastq_34568.clean_17228.all_txt


title: Treg_IL2_R4.fastq_34620.clean_17279.all_txt [Bulk RNA-seq]

description:
ILSE 9201 Lane 4
Treg_IL2_R4.fastq_34620.clean_17279.all_txt


title: COAD.ct-33


title: CC029_liver_atac


title: COAD.ct-34


title: SNRNP70AID-4h-3_chr

description: Normalized abundance of lncRNAs in whole cell or subcellular fractions upon SNRNP70AID depletion.txt


title: COAD.ct-31


title: CC028_lung_atac


title: COAD.ct-30


title: CC029_kidney_atac


title: Treg_IL2_R2.fastq_34500.clean_17189.all_txt [Bulk RNA-seq]

description:
ILSE 9201 Lane 4
Treg_IL2_R2.fastq_34500.clean_17189.all_txt


title: SNRNP70AID-4h-2_cyto

value: cytoplasmic total RNA


title: Treg_IL2_R1.fastq_34451.clean_17145.all_txt [Bulk RNA-seq]

description:
ILSE 9201 Lane 4
Treg_IL2_R1.fastq_34451.clean_17145.all_txt


title: CC028_liver_atac


title: SNRNP70AID-4h-3_cell

value: total RNA


title: COAD.ct-29


title: SNRNP70AID-4h-2_nuc

value: nucleoplasmic total RNA


title: COAD.ct-36


title: Treg_IL2+4+33_R4.fastq_34372.clean_16881.all_txt [Bulk RNA-seq]

description:
ILSE 9201 Lane 3
Treg_IL2+4+33_R4.fastq_34372.clean_16881.all_txt


title: Treg_IL2+4+33_R3.fastq_34109.clean_16841.all_txt [Bulk RNA-seq]

description:
ILSE 9201 Lane 3
Treg_IL2+4+33_R3.fastq_34109.clean_16841.all_txt


title: CC028_kidney_atac


title: SNRNP70AID-4h-3_nuc


title: CC027_lung_atac

value: lung


title: SNRNP70AID-4h-3_cyto


title: SNRNP70AID-4h-2_chr

value: chromatin total RNA


title: Treg_IL2+4+33_R2.fastq_33873.clean_16800.all_txt [Bulk RNA-seq]

description:
ILSE 9201 Lane 3
Treg_IL2+4+33_R2.fastq_33873.clean_16800.all_txt


title: COAD.ct-32


title: CC027_kidney_atac


title: tisTregST2_Liver_R4 [Bulk RNA-seq]

description:
ILSE 6965 Lane 6
tisTregST2_Liver_R4

source_name: Liver

value: Klrg1-positive ST2-positive

value: Liver


title: SNRNP70AID-4h-1_nuc


title: SNRNP70AID-4h-1_cyto


title: COAD.ct-26


title: COAD.ct-25


title: COAD.ct-24


title: CC025_liver_atac

value: liver


title: CC025_kidney_atac


title: CC025_lung_atac


title: SNRNP70AID-4h-1_chr


title: COAD.ct-23


title: COAD.ct-28


title: CC024_lung_atac


title: COAD.ct-22


title: SNRNP70AID-0h-pA-3_cell

treatment_protocol:
none
IAA, 4 hours


title: SNRNP70AID-4h-1_cell


title: SNRNP70AID-0h-pA-3_chr


title: Treg_IL2+4+33_R1.fastq_33644.clean_16757.all_txt [Bulk RNA-seq]

description:
ILSE 9201 Lane 3
Treg_IL2+4+33_R1.fastq_33644.clean_16757.all_txt


title: CC024_liver_atac


title: COAD.ct-27


title: tisTregST2_Liver_R1 [Bulk RNA-seq]

description:
ILSE 6965 Lane 6
tisTregST2_Liver_R1


title: tisTregST2_Lung_R4 [Bulk RNA-seq]

description:
ILSE 6965 Lane 5
tisTregST2_Lung_R4

source_name: Lung

value: Lung


title: tisTregST2_Liver_R2 [Bulk RNA-seq]

description:
ILSE 6965 Lane 6
tisTregST2_Liver_R2


title: CC024_kidney_atac


title: CC027_liver_atac


title: SNRNP70AID-0h_pA-2_chr


title: COAD.ct-21


title: tisTregST2_Liver_R3 [Bulk RNA-seq]

description:
ILSE 6965 Lane 6
tisTregST2_Liver_R3


title: tisTregST2_Lung_R2 [Bulk RNA-seq]

description:
ILSE 6965 Lane 5
tisTregST2_Lung_R2


title: CC023_lung_atac


title: tisTregST2_Lung_R1 [Bulk RNA-seq]

description:
ILSE 6965 Lane 5
tisTregST2_Lung_R1


title: CC023_liver_atac


title: COAD.ct-19


title: COAD.ct-18


title: SNRNP70AID-0h-3_nuc


title: tisTregST2_Lung_R3 [Bulk RNA-seq]

description:
ILSE 6965 Lane 5
tisTregST2_Lung_R3


title: tisTregST2_Skin_R4 [Bulk RNA-seq]

description:
ILSE 6965 Lane 4
tisTregST2_Skin_R4

source_name: Skin

value: Skin


title: CC023_kidney_atac


title: SNRNP70AID-0h_pA-1_cell

value: embryonic stem cells


title: tisTregST2_Skin_R3 [Bulk RNA-seq]

description:
ILSE 6965 Lane 4
tisTregST2_Skin_R3


title: CC021_lung_atac


title: COAD.ct-16


title: SNRNP70AID-4h-2_cell

value: IAA, 4 hours


title: CC021_liver_atac


title: COAD.ct-17


title: tisTregST2_Skin_R1 [Bulk RNA-seq]

description:
ILSE 6965 Lane 4
tisTregST2_Skin_R1


title: SNRNP70AID-0h-3_cyto


title: COAD.ct-20


title: COAD.ct-14


title: SNRNP70AID-0h_pA-2_cell


title: COAD.ct-15


title: tisTregST2_Fat_R4 [Bulk RNA-seq]

description:
ILSE 6964 Lane 8
tisTregST2_Fat_R4

source_name: Gonadal fat

value: Gonadal fat


title: CC021_kidney_atac


title: SNRNP70AID-0h_pA-1_chr

value: chromatin polyA RNA


title: tisTregST2_Skin_R2 [Bulk RNA-seq]

description:
ILSE 6965 Lane 4
tisTregST2_Skin_R2


title: SNRNP70AID-0h-3_cell


title: COAD.ct-13

value: cell-free DNA


title: SNRNP70AID-0h-2_nuc


title: SNRNP70AID-0h-2_cyto


title: CC020_kidney_atac


title: COAD.ct-12


title: SNRNP70AID-0h-3_chr


title: CC019_lung_atac


title: KLRGminusNFIL3minusTreg_R5 [Bulk RNA-seq]

description:
ILSE 9202 Lane 3
KLRGminusNFIL3minusTreg_R5

value: Klrg1-negative Nfil3(GFP)-negative


title: CC020_lung_atac


title: tisTregST2_Fat_R1 [Bulk RNA-seq]

description:
ILSE 6964 Lane 8
tisTregST2_Fat_R1


title: SNRNP70AID-0h-2_chr


title: Klrg1-Il1rl1-Treg_BM_R3 [Bulk RNA-seq]

description:
ILSE 6964 Lane 7
Klrg1-Il1rl1-Treg_BM_R3

source_name: Bone marrow

value: Klrg1-negative ST2-negative

value: Bone marrow


title: COAD.ct-10


title: CC019_liver_atac


title: tisTregST2_Fat_R2 [Bulk RNA-seq]

description:
ILSE 6964 Lane 8
tisTregST2_Fat_R2


title: COAD.ct-9


title: SNRNP70AID-0h-1_nuc


title: SNRNP70AID-0h-2_cell

value: total RNA


title: Klrg1-Il1rl1-Treg_BM_R4 [Bulk RNA-seq]

description:
ILSE 6964 Lane 7
Klrg1-Il1rl1-Treg_BM_R4


title: SNRNP70AID-0h-1_cyto

value: cytoplasmic total RNA


title: COAD.ct-7


title: COAD.ct-8


title: CC019_kidney_atac

value: kidney


title: Klrg1-Il1rl1-Treg_BM_R1 [Bulk RNA-seq]

description:
ILSE 6964 Lane 7
Klrg1-Il1rl1-Treg_BM_R1


title: Klrg1-Il1rl1-Treg_BM_R2 [Bulk RNA-seq]

description:
ILSE 6964 Lane 7
Klrg1-Il1rl1-Treg_BM_R2


title: CC017_lung_atac

value: lung


title: SNRNP70AID-0h-1_chr

value: chromatin total RNA


title: CC020_liver_atac


title: tisTregST2_Fat_R3 [Bulk RNA-seq]

description:
ILSE 6964 Lane 8
tisTregST2_Fat_R3

value: Klrg1-positive ST2-positive


title: CC017_liver_atac

value: liver


title: tisTregST2_BM_R4 [Bulk RNA-seq]

description:
ILSE 6964 Lane 6
tisTregST2_BM_R4


title: COAD.ct-6


title: COAD.ct-11


title: CC017_kidney_atac


title: COAD.ct-5


title: CC016_lung_atac


title: tisTregST2_BM_R3 [Bulk RNA-seq]

description:
ILSE 6964 Lane 6
tisTregST2_BM_R3


title: tisTregST2_BM_R2 [Bulk RNA-seq]

description:
ILSE 6964 Lane 6
tisTregST2_BM_R2


title: 70AID-4h-TT-seq

description: RNA of TT-seq library

data_processing:
Library strategy: TT-Seq
Basecalls performed using CASAVA version
Reads obtained from ChIP-seq and ChIRP-seq library sequencing were aligned to the mm9 genome assembly using Bowtie2 with uniq mapping parameters.
Reads from TT-seq were aligned to the mm9 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
macs1.4 were used for peak calling with default parameters
bedtools were used for generating bigwig files.
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing peaks called from Pol2 ChIP-seq, bigwig (bw) files containing the sequencing signals of TT-seq and ChIRP-seq

extract_protocol:
TT-seq was modified from previous reports (Schwalb, 2016). Auxin treated or untreated SNRNP70AID mESCs were incorporated with 4-sU (300 mM final) for 10 minutes, cells were harvested and RNAs were extracted by TRIzol. Labeled RNAs were further biotinylated as described70 and fragmented by 0.1×NaOH on ice for 10 minutes. The fragmented RNAs were subjected to purification as previously described70. RNA-seq library construction, deep sequencing, and data analysis were further performed as described above.
RNA-seq libraries for TT-seq were constructed through NEBNext Ultra II Directional RNA Library Prep Kit (NEB) according to manufacturer's instructions.
ChIP was done following previously protocol (Shen, 2008). Briefly, cells were crosslinked on plate with 1% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 2 μg antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for  4 hours at  4℃. After thoroughly washing, the targeted DNA was eluted by elution buffer with protease K at 65℃.
DNA Libraries were prepared by NEBNext Ultra II DNA library preparation kit according to the standard protocols provided by the manufacturer. RNA-seq libraries for TT-seq were constructed through NEBNext Ultra II Directional RNA Library Prep Kit (NEB) according to manufacturer's instructions.

treatment_protocol:
SNRNP70-AID mESCs were treated by adding 500 μM IAA, and culture at 37℃ for 4 hours, and then pulse-labeled with 300 mM 4-thiol-Uridine (4sU) in the existence of 500 μM IAA for 10 minute at 37℃
IAA, 4 hours

value: IAA, 4 hours, 4sU, 10 min


title: COAD.ct-4


title: Klrg1-Il1rl1-Treg_Spleen_R4 [Bulk RNA-seq]

description:
ILSE 6964 Lane 5
Klrg1-Il1rl1-Treg_Spleen_R4

source_name: Spleen

value: Spleen


title: DMSO_Malat1-ChIRP

description: DNA of ChIRP-seq

data_processing:
Library strategy: ChIRP-seq
Basecalls performed using CASAVA version
Reads obtained from ChIP-seq and ChIRP-seq library sequencing were aligned to the mm9 genome assembly using Bowtie2 with uniq mapping parameters.
Reads from TT-seq were aligned to the mm9 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
macs1.4 were used for peak calling with default parameters
bedtools were used for generating bigwig files.
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing peaks called from Pol2 ChIP-seq, bigwig (bw) files containing the sequencing signals of TT-seq and ChIRP-seq

source_name: 46C mES cells

extract_protocol:
Auxin treated or untreated SNRNP70AID cells were crosslinked by 2 mM DSP for 30 minutes, followed by 15-minute 3.7% formaldehyde crosslinking. The crosslinked cells were first partial digested by 12 U/ml DNase I at 37℃ for 10 minutes, then sonicated at 25% amplitude for 30 seconds. The following procedures were performed as previously described60. The probes used for Malat1 ChIRP were listed in Supplementary Table 9. For ChIRP RNA, auxin untreated or treated SNRNP70AID mESCs were crosslinked by 2% formaldehyde for 10 minutes, the following procedures were performed as previously described (Yin, 2015)
Libraries were prepared by NEBNext Ultra II DNA library preparation kit according to the standard protocols provided by the manufacturer.
ChIP was done following previously protocol (Shen, 2008). Briefly, cells were crosslinked on plate with 1% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 2 μg antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for  4 hours at  4℃. After thoroughly washing, the targeted DNA was eluted by elution buffer with protease K at 65℃.
DNA Libraries were prepared by NEBNext Ultra II DNA library preparation kit according to the standard protocols provided by the manufacturer. RNA-seq libraries for TT-seq were constructed through NEBNext Ultra II Directional RNA Library Prep Kit (NEB) according to manufacturer's instructions.

treatment_protocol:
wild-type mESCs were teated by adding 1/10000 volume of DMSO, and culture at 37℃ for 1 hour
IAA, 4 hours

value: embryonic stem cells

value: DMSO, 1 hour


title: CC016_liver_atac


title: tisTregST2_BM_R1 [Bulk RNA-seq]

description:
ILSE 6964 Lane 6
tisTregST2_BM_R1


title: CC016_kidney_atac

source_name: kidney tissue


title: COAD.ct-2

source_name: blood serum


title: 70AID-4h_Pol2S5P

description: DNA of ChIP-seq

data_processing:
Basecalls performed using CASAVA version
Reads obtained from ChIP-seq and ChIRP-seq library sequencing were aligned to the mm9 genome assembly using Bowtie2 with uniq mapping parameters.
Reads from TT-seq were aligned to the mm9 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
macs1.4 were used for peak calling with default parameters
bedtools were used for generating bigwig files.
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing peaks called from Pol2 ChIP-seq, bigwig (bw) files containing the sequencing signals of TT-seq and ChIRP-seq

extract_protocol:
ChIP was done following previously protocol (Shen, 2008). Briefly, cells were crosslinked on plate with 1% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 2 μg antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for  4 hours at  4℃. After thoroughly washing, the targeted DNA was eluted by elution buffer with protease K at 65℃.
Libraries were prepared by NEBNext Ultra II DNA library preparation kit according to the standard protocols provided by the manufacturer.
ChIP was done following previously protocol (Shen, 2008). Briefly, cells were crosslinked on plate with 1% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 2 μg antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for  4 hours at  4℃. After thoroughly washing, the targeted DNA was eluted by elution buffer with protease K at 65℃.
DNA Libraries were prepared by NEBNext Ultra II DNA library preparation kit according to the standard protocols provided by the manufacturer. RNA-seq libraries for TT-seq were constructed through NEBNext Ultra II Directional RNA Library Prep Kit (NEB) according to manufacturer's instructions.

value: IAA, 4 hours

value: RNAPII Ser5P (Cell Signaling Technology, 13523)


title: 70AID-4h_Pol2S2P

description: DNA of ChIP-seq

value: RNAPII Ser2P (Cell Signaling Technology, 13499)


title: Klrg1-Il1rl1-Treg_Spleen_R2 [Bulk RNA-seq]

description:
ILSE 6964 Lane 5
Klrg1-Il1rl1-Treg_Spleen_R2


title: CC015_lung_atac


title: CC015_liver_atac


title: Klrg1-Il1rl1-Treg_Spleen_R3 [Bulk RNA-seq]

description:
ILSE 6964 Lane 5
Klrg1-Il1rl1-Treg_Spleen_R3


title: COAD.ct-1

value: cell-free DNA


title: CC015_kidney_atac


title: 70AID-4h_Malat1-ChIRP

description: DNA of ChIRP-seq


title: 70AID-0h-TT-seq

description: RNA of TT-seq library

treatment_protocol:
SNRNP70-AID mESCs were pulse-labeled by 300 mM 4-thiol-Uridine (4sU) for 10 minute at 37℃
IAA, 4 hours

value: 4sU, 10 min


title: COAD.ct-3


title: CC013_lung_atac


title: tisTregST2_Spleen_R4 [Bulk RNA-seq]

description:
ILSE 6964 Lane 4
tisTregST2_Spleen_R4


title: tisTregST2_Spleen_R3 [Bulk RNA-seq]

description:
ILSE 6964 Lane 4
tisTregST2_Spleen_R3


title: TPL_Malat1-ChIRP

description: DNA of ChIRP-seq

treatment_protocol:
wild-type mESCs were teated by adding 1 μM Triptolide, and culture at 37℃ for 1 hour
IAA, 4 hours

value: Triptolide, 1 hour


title: 70AID-0h-Pol2S5P

description: DNA of ChIP-seq


title: CC013_liver_atac


title: tisTregST2_Spleen_R2 [Bulk RNA-seq]

description:
ILSE 6964 Lane 4
tisTregST2_Spleen_R2


title: tisTregST2_Spleen_R1 [Bulk RNA-seq]

description:
ILSE 6964 Lane 4
tisTregST2_Spleen_R1


title: 70AID-0h_Malat1-ChIRP

description: DNA of ChIRP-seq


title: CC013_kidney_atac


title: 70AID-0h_Pol2S2P

description: DNA of ChIP-seq


title: CC012_lung_atac


title: Klrg1-Il1rl1-Treg_Spleen_R1 [Bulk RNA-seq]

description:
ILSE 6964 Lane 5
Klrg1-Il1rl1-Treg_Spleen_R1

value: Klrg1-negative ST2-negative


title: 3T3-L1_Palmitate Treated_Rep2

city: London

first: Eugene

last: Schuster

address: 123 Old Brompton Road

department: Breast Cancer Research

country: United Kingdom

institute: Institute of Cancer Research

description:
Palmitate Treated R2
tr_pal_r2

data_processing:
alignment to genome with tophat-2.0.11.OSX_x86_64
htseq_deseq2_api
Genome_build: Mus_musGRCm38
Supplementary_files_format_and_content: raw counts

source_name: 3T3-L1_Palmitate Treated

growth_protocol: 3T3-L1 pre-adipocytes, cultured in DMEM (4 g/L glucose) supplemented with 10% fetal bovine serum in 6-well plates, were induced to differentiate by addition of insulin (1uM), dexamethasone (1uM), isobutylmethylxanthine (0.5 mM) and rosiglitazone (1uM).

extract_protocol:
Total RNA was extracted using Trizol reagent followed by further purification with Qiagen RNeasy easy kit.
Illumina TruSeq Stranded mRNA Sample Prep with oligo dT selection

treatment_protocol: On day 8 after induction of differentiation, cells were treated with A66 (2 uM) or palmitate (0.5 mM, conjugated to BSA at 3:1 molar ratio) or a combination of palmitate and A66 or were left untreated for 24 h.

value: adipocytes

value: palmitate plus A66


title: CC012_liver_atac


title: ISC_input

city: xiamen

first: hongda

last: li

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District, Xiamen, Fujian Province, China

institute: Xiamen University

data_processing:
The image analysis and base calling were performed by using Illumina’s Genome Analysis pipeline.
clean reads were aligned to the mouse genome (GRCm38/mm10) using Bowtie2 (version 2.2.8).
Enriched peaks of H3K9me3 were identified by HOMER v4.10.1 with histone style (http://homer.ucsd.edu/homer).
Aligned H3K9me3 bam file was converted into the bigWig file and processed to plot the H3K9me3 density on the interesting ERVs by using deepTools2.0
Genome_build: mm10

source_name: intestines

extract_protocol:
GFP high CD24low ISCs were obtained from Lgr5-EGFP-IRES-creERT2;setdb1fl/fl mice (n=12) by FACS. The protocol of ChIP-seq was performed as previously described with slight emendations. Briefly, approximately 5 x 10^6 cells were cross-linked with 1% formaldehyde for 10min at room temperature, followed by quenching in 125nm glycine. Cell nuclei were obtained by lysing while cells in lysing buffer(50mM HEPES/KOH ph7.6, 1mM EDTA，140nM NaCL, 10%v/v Glycerol, 0.5% NP-40, 0.25% v/v Triton X-100) supplemented with protease inhibitor. Nuclei were subjected to sonication to acquire DNA fragments of 200-350 bp. The sonicated chromatin was applied to immunoprecipitation by incubation with H3K9me3 antibody(2ug) overnight at 4℃, followed with collected using 50ul protein A/G plus agarose beads(Millipore). Subsequent process were implement by following the protocol.
The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 7962347001)

value: intestinal stem cell

tag: antibody

value: IgG

tag: age

value: post natal 8 weeks


title: ISC_ChIP_H3K9me3


title: 3T3-L1_Palmitate Treated_Rep1

description:
Palmitate Treated R1
tr_pal_r1


title: CC012_kidney_atac

value: kidney


title: ISC_MUT

description: rRNA-depleted RNA

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute using BGISEQ-500 sequencer or illumina X-TEN sequencer.
Clean reads were mapped onto the mouse genome (GRCm38/mm10) using hisat2 to obtain the aligned bam files.
The mouse ERVs annotation file was generated by RepeatMasker v4.0.7 comparing with Repbase consensus sequences (Edition-20181026)
The overlap reads for ERVs were summarized by featureCounts  and then quantified by EdgeR  with the Benjamini-Hochberg corrected p-value <0.05.
Genome_build: mm10

extract_protocol:
Crypts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries(WT, VEDM2, VEMD3, VEMD4, VEMD6, VEMD8) were prepared for sequencing using standard BGI-500 protocols. Besides this, purified total RNA from ISC cells isolated from Lgr5–EGFP–ires–CreERT2-mice was quantified by Qubit(invitrogen) and analyzed by an Agilent Bioanalyzer to evaluate RNA quality. rRNA-depleted was used to generate the cDNA library. cDNA library construction and sequencing were prepared for using illumina Hiseq X-TEN protocol.

treatment_protocol: For activation of CreERT2 mediated recombination, 8-10 weeks old Villin-CreERT2 mice and WT littermates were received one dose of tamoxifen (800 mg/kg) by gavage and harvested sacrificed as indicated in each figure. 8-10 weeks old Lgr5-EGFP-IRES-CreERT2;Setdb1fl/fl mice were received 200mg/kg tamoxifen every day for consecutive 3 days.


title: CC011_lung_atac

source_name: lung tissue

value: lung


title: 3T3-L1_Palmitate Untreated_Rep2

description:
Palmitate Untreated R2
cntl_pal_r2

source_name: 3T3-L1_Palmitate Untreated

value: palmitate


title: CC011_liver_atac

source_name: liver tissue

value: liver


title: ISC_WT

description: rRNA-depleted RNA


title: 3T3-L1_Control Treated_Rep2

description:
Control Treated R2
tr_r2

source_name: 3T3-L1_Control Treated

value: p110alpha inhibitor (A66)


title: CC011_kidney_atac


title: WBJPE171125800

city: Hangzhou

first: Yixiao

last: Liu

state: 浙江

address: Yuhangtang road

institute: Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Single-cell RNA sequence reads were evaluated by FastQC
Bad reads were detected automatically and removed. Bases at 3' end of the read were further timmed by NGSQCToolkit if their PHRED quality score were less than 20.
The reads were mapped to the mm9 using bowtie2.
The mapped reads for genes were counted via Htseq.

source_name: skeleton muscle

extract_protocol:
Cells were isolated by preplating mehods (Nat. Protocols 3, 1501-1509 (2008)).
single cell were captured, lysated, preamplified and library prepared according to "Using the C1 High-Throughput IFC to Generate Single-Cell cDNA Libraries for mRNA Sequencing"

treatment_protocol: 563 mice skeletal muscle derived single cells were form  6~8 weeks old male C57BL/6 mice.

value: mice skeletal muscle

tag: gender

value: male


title: WBJPE171125799


title: CC010_lung_atac


title: WBJPE171125798


title: 3T3-L1_Control Treated_Rep1

description:
Control Treated R1
tr_r1


title: 3T3-L1_Control Untreated_Rep2

description:
Control Untreated R2
cntl_r2

source_name: 3T3-L1_Control Untreated

value: untreated


title: jaz10phyb MeJA R2

type: RNA

city: Buenos Aires

first: Carlos

middle: Daniel

last: Crocco

state: Buenos Aires

address: Av. San Martín 4453

country: Argentina

institute: University of Buenos Aires - IFEVA - CONICET

hyb_protocol: Samples were hybridized to the arrays in accordance with the manufacturer’s instructions for the GeneChip Arabidopsis Gene 1.0 ST Array (Affymetrix). Raw

scan_protocol: Scan protocol in accordance with the manufacturer’s instructions for the GeneChip Arabidopsis Gene 1.0 ST Array (Affymetrix). Raw

data_processing:
Raw microarray data were processed and analyzed using Affymetrix Expression Console® software. Genes with ‘absent’ calls and a signal of <50 units in all replicate experiments were filtered out.
Significantly differentially expressed genes were identified by performing profile analysis using Significance Analysis of Microarrays (Tusher et al., 2001) with a p-value <0.05. A test filter was performed to work only with those genes for which the ratio of expression showed at least a 2‐fold change between “col mock” vs “col MeJA”

label: biotin

organism: Arabidopsis thaliana

source_name: jaz10phyb MeJA

label_protocol: RNA was prepared and labelled in accordance with the manufacturer’s instructions for the GeneChip Arabidopsis Gene 1.0 ST Array (Affymetrix). Raw

growth_protocol: 4 weeks‐day‐old plants were grown under short day conditions (8 hours light – 16 hours dark) at 22°C. For the experiments we used wild-type (Col-0), phyB-9, jaz10 and jaz10phyB-9 mutant plants.

extract_protocol: RNA was extracted using The Spectrum Plant Total RNA Kit (Sygma)

treatment_protocol: Plants were sprayed with 250uM of MeJA or water-mock (control). Plant samples were harvested at 3 hours after MeJA treatment. Each sample consist in at least 4 pooled plants.

value: MeJA

value: 4 week-old plants

value: whole plant


title: CC010_liver_atac


title: jaz10phyb MeJA R1


title: 3T3-L1_Control Untreated_Rep1

description:
Control Untreated R1
cntl_r1


title: 3T3-L1_Palmitate Untreated_Rep1

description:
Palmitate Untreated R1
cntl_pal_r1


title: CC010_kidney_atac


title: jaz10 MeJA R1

source_name: jaz10 MeJA


title: jaz10 Control R2

source_name: jaz10 Control

value: Control


title: WBJPE171125797


title: WBJPE171125796


title: jaz10phyb Control R2

source_name: jaz10phyb Control


title: CTX rep3

city: Changchun

first: Qi

last: Li

address: No 71 Xinmin street

institute: First Hospital, Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: ovary

extract_protocol:
Ovary was removed, snap frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. The Illumina TruSeq RNA Sample Preparation Kit was used with 1 μg of total RNA to construct a sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

value: cyclophosphamide

value: 8-9 weeks old


title: CC007_liver_atac


title: jaz10 MeJA R2


title: WBJPE171125795


title: jaz10phyb Control R1


title: jaz10 Control R1


title: phyb Control R2

source_name: phyb Control

value: phyb


title: phyb MeJA R2

source_name: phyb MeJA


title: CTX rep2


title: phyb MeJA R3


title: WBJPE171125794


title: phyb MeJA R1


title: phyb Control R1


title: phyb Control R3


title: CC007_kidney_atac

source_name: kidney tissue


title: CTX rep1


title: WBJPE171125793


title: CC006_lung_atac


title: control rep3

value: control


title: CC006_liver_atac


title: control rep2


title: CC007_lung_atac


title: Col MeJA R2

source_name: Col MeJA

value: wild-type


title: SNRNP70AID-0h-1_cell

source_name: SNRNP70-AID mESC (constructed from 46C mES cells)

value: embryonic stem cells

value: total RNA


title: WBJPE171125790


title: WBJPE171125788


title: 7KO

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to Ensembl BDGP6 whole genome using TopHat v2.0.13
Count data are prepared with HTSeq v.0.6.1
Normalization and differential expression analysis performed with R/Bioconductor edgeR package v.3.10.5
Genome_build: Ensembl BDGP6
Supplementary_files_format_and_content: tab-delimited text files include normalized count for each sample

organism: Drosophila melanogaster

source_name: rfx KO_GFP-positive_neuron

extract_protocol:
Cells from dissociated larval Drosophila brains were sorted by FACS. RNA was extracted using NucleoSpin RNA XS (Macherey Nagel). 4ng of total RNAs were used for constructing libraries.
Clontech Smarter Ultra low + Illumina Nextera library protocols

tag: genotype/variation

value: rfx knock-out

tag: gfp

value: positive

value: third early instar larval brain

value: neuron


title: 8KO

source_name: rfx KO_GFP-negative_neuron

value: negative


title: Col Control R2

source_name: Col Control


title: CC006_kidney_atac

value: kidney


title: CC005_lung_atac

source_name: lung tissue

value: lung


title: Col MeJA R1

value: MeJA

value: 4 week-old plants

value: whole plant


title: Heart_wtTg-4_mRNA

city: San Diego, California

first: Kathia

last: Zaleta-Rivera

state: CA

address: 9500 Gilman Drive, MC 0412

description:
processed data file: genes.fpkm_table
Heart_wtTg-4_Aliquot_2_CTCAGA

data_processing:
Quality control (FASTQC v0.11.2 ), leading and trailing bases with quality less than 5 were trimmed and reads with a windowed-average (window of size 5) quality of less than 20 were filtered out.
Alignment (STAR v2.40)
Quantification (Cufflinks v2.2.1 standard pipeline using Cuffquant then Cuffdiff)
Genome_build: mm9
Supplementary_files_format_and_content: the fpkm table is derived from cufflinks, containing counts and fragments per kilobase values of all genes in mm9 (rows) and samples (columns)

extract_protocol:
Total RNA was isolated using Trizol
Small RNA library was prepared
Two illumina RNA libraries were prepared: one Small RNA library ran in MiSeq Rapid Mode 50 nt-single end and an Poly A library in HiSeq Rapid mode 100 nt -pair end

treatment_protocol:
Virus preparation protocol: Cells AAV-293 cells (Stratagene) were cultured in DMEM containing 10% fetal bovine serum (Invitrogen) in T-225 cm2 for growth and expansion. After cells reached 80% confluency, HEPES was added to buffer pH (0.4 ml 1.0 M HEPES to 36 ml media to result in 10 mM HEPES). Mix A=Plasmid DNA (27g of each plasmid) of adenovirus helper, pladeno5; AAV helper, pAA-2/9-731 and AAV vector, pAAV shRNA RSV cerulean were mixed in a 0.3 M CaCl2 solution. Mix B= In a 50 ml falcon tube 4 ml of 2X HBS (280 mM NaCl, 1.5mM Na2HPO4, 50mM HEPES, pH 7.05). A and B were mix by gently pipetting and immediately added to the cell media. Media was mixed by cross swirling and incubated during 18 h. Media was changed after incubation to remove CaPO4/DNA precipitate and continue incubation for 72 h for virus production. Media was removed from T-225 flask and 5 ml of PBS containing 10mM EDTA was used to remove the cells. Flasks were bang gently to dislodge the cells and washed with PBS to collect the rest of the cells. Cells were centrifuged at 2700 rpm for 15 min at 4C. Supernatant was removed and the cell pellet was resuspended in 1 ml freezing buffer (150mM NaCl, 20mM TRIS pH 8.0, 2mM MgCl2) and transferred to 1.5 ml Eppedorf tube. The tube was incubated at -80oC for 15 min. Samples were thaw at 42oC in a water bath for a total of 3 freeze-thaw cycles. After cell lysis, DNA digestion was carried out with benzonase (250 unit/l) to a final concentration of 50 units / ml crude lysate and incubated at 37oC for 30 minutes. Cell debris was removed by centrifugation at 13,500 xg (11,100 rpm in Sorvall legend centrifuge) for 30 min at 4oC. Virus purification was carried out with different iodixanol gradients. Gradients were prepared in a 5.5 ml thick-walled polycarbonate tubes as follows: 1.5 ml of 60%, 1.0 of 40%, 1.0 ml of 25%, and 1.0 ml of 15% iodixanol solution (heaviest layer in the tube first). To the top of each iodixanol gradient 1.0 ml crude lysate was added. Ultracentrifugation was carried out at 66,100 rpm (400,000 x g) at 10 oC for 2 hrs in T-1270 rotor in Thermo WX Ultra centrifuge. The top 3 layers (0, 15, 25%) were collected avoiding the clear 40% layer (AAV is in the 40% iodixanol). Iodixanol was removed by ultracentrifugation using 100 kDak molecular weight cut off filters (Millipore). Centrifugation was repeat at 4000 rpm at 4oC until the sample reached a volume of ~ 200 l. Ultracentrifugation was repeat one more time at 13500 x g (12000 rpm in Eppendorf 5424 centrifuge) at 20 oC until volume was ~20-100 l and transfer to a 1.5 ml Eppendorf tube. Genomic titer and infectious titer was determined using standard protocols.
Neonatal transgenic mice were injected via intrajugular vein with AAV9 H1-M7.8L shRNA RSVp Cerulean at threed days old age. Tretament end at 4 months of age. Heart tissue was isolated from treated, untreated and control mice for total RNA extraction for RNA library prep

tag: strain background

value: RLC-47K L6

value: control virus treatment

value: heart


title: 6co

tag: cell type


title: WBJPE171125787

value: mice skeletal muscle

value: male


title: 5co

value: wild-type


title: CC005_liver_atac

source_name: liver tissue

treatment_protocol: Mice were placed in cylindrical, metal mesh exposure chambers emitting clear air for 6 hours a day, Monday-Friday, across a two week period

value: liver


title: CC005_kidney_atac


title: Col Control R1

tag: treatment

value: Control


title: WBJPE171125785

source_name: skeleton muscle

tag: strain


title: 4KO

value: rfx knock-out


title: WBJPE171125786


title: WBJPE171125792


title: Heart_wtTg-3_mRNA

description:
processed data file: genes.fpkm_table
Heart_wtTg-3_ATTCCT


title: Heart_wtTg-3_smallRNA

description:
processed data file: smallRNA_genes.fpkm_table
Heart-wtTg-3_S16


title: CC004_lung_atac


title: Heart_wtTg-2_smallRNA

description:
processed data file: smallRNA_genes.fpkm_table
Heart-wtTg-2_S15


title: CC004_liver_atac


title: WBJPE171125782


title: 3KO

value: positive

value: third early instar larval brain


title: Heart_wtTg-2_mRNA

description:
processed data file: genes.fpkm_table
Heart_wtTg-2_TGACCA


title: control rep1

value: ovary

value: control

value: 8-9 weeks old


title: CC004_kidney_atac

value: kidney


title: 1co

value: neuron


title: Heart_mutTg-11_mRNA

description:
processed data file: genes.fpkm_table
Heart_mutTg-11_GGCTAC

value: Untreated


title: 2co

value: negative


title: WBJPE171125779


title: CC003_lung_atac

value: lung


title: 16KO


title: Heart_mutTg-11_smallRNA

description:
processed data file: smallRNA_genes.fpkm_table
Heart-mutTg-11_S10

value: RLC-47K L6

value: heart


title: CC003_kidney_atac


title: WBJPE171125777

value: mice skeletal muscle

value: male


title: CC003_liver_atac

value: liver


title: 15KO


title: Heart_mutTg-10_mRNA

description:
processed data file: genes.fpkm_table
Heart_mutTg-10_CATTTT


title: WBJPE171125773


title: Heart_mutTg-9_smallRNA

description:
processed data file: smallRNA_genes.fpkm_table
Heart-mutTg-9_S8


title: WBJPE171125771


title: Heart_mutTg-9_mRNA

description:
processed data file: genes.fpkm_table
Heart_mutTg-9_CGGAAT


title: CC002_liver_atac


title: 13co

value: wild-type


title: 14co


title: WBJPE171125768


title: WBJPE171125770


title: CC002_kidney_atac


title: WBJPE171125780


title: WBJPE171125765


title: CC001_lung_atac


title: Heart_mutTg-7_mRNA

description:
processed data file: genes.fpkm_table
Heart_mutTg-7_CTTGTA

value: shRNA treatment


title: Heart_mutTg-8_smallRNA

description:
processed data file: smallRNA_genes.fpkm_table
Heart-mutTg-8_S7


title: CC001_liver_atac


title: Wild strain_36h_2

city: Nanjing

first: Huanqing

last: Niu

state: Jiangsu

address: No.30, Puzhu South Road

institute: Nanjing Tech University

description: Gene expression in 36h-grown wild strain

hyb_protocol: each Slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US). After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Arthrobacter sp. CGMCC 3584

source_name: Wild strain, 36h, replicate 2

label_protocol: Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany). Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: The seed culture medium contained in grams per liter: glucose 10, peptone 10, beef extract 10, and NaCl 3. The fermentation medium contained in grams per liter: glucose 50, urea 8, K2HPO4 18, KH2PO4 5, MgSO4 0.1, biotin 0.01, hypoxanthine 8, NaF 0.4 and CoCl2 0.005. The initial pH was adjusted to 7.0 by NaOH and the medium was autoclaved for 20 min at 115 ◦C. The seed cultures were incubated at 30 ◦C and 300 rpm for 18 h. Then the seed medium was transferred into a 500mL flask containing 50mL of fermentation medium at an inoculum dose of 10% (v/v). The fermentation parameters were controlled by a digital measurement and control system. The medium was incubated at 30°C, 260r/min for 72 h.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: The cells were pelleted by centrifugation at 5000 × g for 10 min at 4 °C and rinsed twice with ice-cold PBS buffer (137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 2 mMKH2PO4, pH 7.40). All the cells were frozen immediately using liquid nitrogen and then stored at -80 °C.

tag: growth phase

value: stable phase

value: wildtype

tag: timepoint


title: Heart_mutTg-7_smallRNA

description:
processed data file: smallRNA_genes.fpkm_table
Heart-mutTg-7_S6

tag: tissue


title: WBJPE171125764


title: WBJPE171125762


title: Heart_mutTg-6_mRNA

description:
processed data file: genes.fpkm_table
Heart_mutTg-6_GATCAG


title: CC001_kidney_atac


title: CC002_lung_atac


title: Heart_mutTg-8_mRNA

description:
processed data file: genes.fpkm_table
Heart_mutTg-8_TAATCG


title: MBD-calvarial-OB rep3-input

city: stanford

first: Hui

last: Zhu

address: 1651 Page Mill Road

institute: Stanford Universtiy

description: DNA methylation analysis

data_processing:
For RNA-seq, paired end sequencing reads (100bp) were generated and aligned to mouse reference sequence NCBI Build 37/mm9 with the STAR (v2.4.2a) algorithm. For MBD-seq,pPaired-end reads were mapped to mouse reference sequence NCBI Build 37/mm9 using BOWTIE 2.
For RNA-seq, normalization of RefSeq annotated genes, expression level and differential expression analysis were performed using the Bioconductor package DESeq2 in R (Version 3.2.2) ; For MBD-seq, genome wide methylation signal and differential methylation regions were calculated by using Bioconductor package MEDIPS under R environment.
Genes with False Discovery Rate (FDR) <0.05 were defined as differentially expressed genes.
Genome_build: mm9

source_name: calvarial progeniter cell

growth_protocol: Col2.3GFP fibroblasts were derived from mous tail tip, expanded for two passages and frozen for future use. For direct reprogramming, Col2.3GFP fibroblast cells were seeded on gelatin-coated 6 well plates in fibroblast growing medium. The following day, the cells were transducted with lentivirus containing transription factor gene. After 24 hours, the viruses were washed out and cells recovered in fresh fibroblast growing medium.  On day 3, the cells were trypsinized and split (1:2) to new gelatin-coated dishes. On day 5, the fibroblast growing medium was replaced by osteogenic medium.

extract_protocol:
RNA was extracted by using PureLink® RNA Mini Kit. Poly-A mRNA was purified using Dynabeads® mRNA Purification Kit according to the manufacturer’s instructions. Genomic DNA was extracted by NucleoSpin Tissu kit
RNA sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.  Genomic DNA was sonicated to generate 100-350 bp fragments. 100ng of fragmented DNA were subjected to MethylCollector Ultra (MBD2b and MBD3L1) kit.

value: osteoblast differentiation


title: WBJPE171125758


title: Wild strain_36h_1

source_name: Wild strain, 36h, replicate 1


title: Heart_mutTg-6_smallRNA

description:
processed data file: smallRNA_genes.fpkm_table
Heart-mutTg-6_S5


title: Heart_mutTg-5_mRNA

description:
processed data file: genes.fpkm_table
Heart_mutTg-5_CGATGT


title: WBJPE171125756


title: MBD-calvarial-OB rep2-input

description: DNA methylation analysis


title: WBJPE171125759


title: MBD-calvarial-OB rep3

description: DNA methylation analysis


title: MBD-calvarial-OB rep1-input

description: DNA methylation analysis


title: WBJPE171125755


title: Wild strain_18h_1

description: Gene expression in 18h-grown wild strain

source_name: Wild strain, 18h, replicate 1

value: logarithmic phase


title: Wild strain_18h_2

source_name: Wild strain, 18h, replicate 2


title: WBJPE171125754


title: WBJPE171125750


title: dPDE_36h_2

description: Gene expression in 36h-grown arpde knockout mutant

source_name: arpde knockout mutant, 36h, replicate 2

value: arpde knockout mutant


title: MBD-calvarial-OB rep2

description: DNA methylation analysis


title: Heart_mutTg-3_smallRNA

description:
processed data file: smallRNA_genes.fpkm_table
Heart-mutTg-3_S3

value: control virus treatment


title: dPDE_18h_2

description: Gene expression in 18h-grown arpde knockout mutant

source_name: arpde knockout mutant, 18h, replicate 2


title: dPDE_18h_1

source_name: arpde knockout mutant, 18h, replicate 1


title: MBD-iOB-rep3-input

description: DNA methylation analysis

source_name: induced osteoblast

value: osteoblast


title: dPDE_36h_1

source_name: arpde knockout mutant, 36h, replicate 1


title: Heart_mutTg-2_mRNA

description:
processed data file: genes.fpkm_table
Heart_mutTg-2_ATCACG


title: Heart_mutTg-5_smallRNA

description:
processed data file: smallRNA_genes.fpkm_table
Heart-mutTg-5_S4


title: WBJPE171125749


title: MBD-iOB-rep2-input

description: DNA methylation analysis


title: WBJPE171125743


title: Heart_mutTg-2_smallRNA

description:
processed data file: smallRNA_genes.fpkm_table
Heart-mutTg-2_S2


title: Heart_mutTg-1_mRNA

description:
processed data file: genes.fpkm_table
Heart_mutTg-1_CAGATC


title: WBJPE171125742


title: Heart_mutTg-1_smallRNA

description:
processed data file: smallRNA_genes.fpkm_table
Heart-mutTg-1_S1


title: Heart_mutTg-3_mRNA

description:
processed data file: genes.fpkm_table
Heart_mutTg-3_TCGGCA


title: MBD-iOB-rep1-input

description: DNA methylation analysis


title: WBJPE171125741


title: MBD-iOB-rep3

description: DNA methylation analysis


title: MBD-calvarial-OB rep1

description: DNA methylation analysis


title: MBD-iOB-rep2

description: DNA methylation analysis


title: WBJPE171125738


title: KO-GT cortex2

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
FASTQ reads were quality checked and adaptor trimmed with FastQC (Andrews, S.. FastQC A Quality Control tool for High Throughput Sequence Data).
High quality trimmed reads were mapped to the mm10/GRCm38.p6 reference genome with Bowtie2 v2.3.4.3 (Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359).
Gene counts were calculated with featureCount using latest GENCODE main annotation file (Liao, Y., Smyth, G. K., & Shi, W. (2014). FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923–930).
Differential gene expression was calculated with DESeq2 (Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550).
Genome_build: mm10/GRCm38.p6
Supplementary_files_format_and_content: featureCount read counts

source_name: KO-GT cortex

extract_protocol:
RNA was isolated with Trizol (Thermo Fisher), and treated with DNase I (NEB) according to manufacturer's instructions.
Library preparation was done with TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer's instructions.

treatment_protocol: 3 WT and 3 KO mice were treated with the PHP.eB-iMeCP2 AAV9 vector; 3 WT and 3 KO mice were treated with the PHP.eB-GFP AAV9 vector

value: MECP2 KO

value: Gene therapy-treated

value: Cerebral cortex


title: WBJPE171125737


title: ILC2_Myc KO_rep3

city: Albany

last: Yang

address: 43 New Scotland Avenue

institute: Albany Medical College

hyb_protocol: Standard Affymetrix protocol. Performed at Boston University Microarray and Sequencing Resource Core Facility, Boston, MA, USA

data_processing: CDF: mogene20st_Mm_ENTREZG_17.1.0. Mouse Gene 2.0 ST CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the affymetrix package (version 1.36.1). Differential expression was assessed using the moderated (empirical Bayesian) t test implemented in the limma package (version 3.14.4).

source_name: ILC2, Myc CRISPR, 6 days post-transduction

growth_protocol: C57BL/6J mice ILC2 lines were cultured with 10ng/ml of IL-2 and IL-33

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: gRNAs targeting Myc or Non-target control were inserted into LentiV2CRISPRGFP constructs to generate CRISPR knockout constructs. Lentivirus were prepared and transduced into ILC2 line cells.  GFP+ cells were sorted at 6 days post-transduction.

tag: cell line

value: Myc knock out


title: ILC2_Myc KO_rep2

scan_protocol: Standard Affymetrix protocol. Performed at Boston University Microarray and Sequencing Resource Core Facility, Boston, MA, USA

tag: genotype


title: ILC2_Myc KO_rep1

label_protocol: Standard Affymetrix protocol. Performed at Boston University Microarray and Sequencing Resource Core Facility, Boston, MA, USA


title: ILC2_control_rep3

source_name: ILC2, NTC CRISPR, 6 days post-transduction

value: Non-target Control


title: KO-GT cortex1


title: MBD-fibroblast-rep2-input

description: DNA methylation analysis

source_name: tail-tip derived fibroblast

value: fibroblast


title: Bull2_WGBS

first: Shengli

address: 2rd, Yuanmingyuan West Road

department: Colledge of Animal Science and Techonology

institute: China Agricultural University

description: Sperm whole genome bisulfite sequencing for Bull2

data_processing:
Raw data in FastQ format were first preprocessed to remove low quality reads using FastQC (0.11.2) and Trim Galore (0.4.0). After filtering, the clean reads were aligned to a reference genome (UMD3.1) with the default parameters using Bismark bowtie2 (version 0.14.5). Deduplicated reads were used to calculate sequencing depth and coverage of CG sites. The sodium bisulfite non-conversion rate was calculated as the percentage of cytosines sequenced at cytosine reference positions in the lambda genome.
The methylcytosine information was extracted using the bismark_methylation_extractor after deduplicating the duplication reads.
Genome_build: UMD3.1
Supplementary_files_format_and_content: The data files contain the methylatin information for the CG detected. The column names are: chrmosome, position, position (same as the second column), methylation level, coverage for methylated cytosine, coverage for unmethylated cytosine, total coverage

organism: Bos taurus

source_name: Sperm

extract_protocol:
Sperm DNA was extracted using a proteinase K lysising protocol.  Breifly, frosen semen samples were liquefied at 37°C and were analyzed for concentration, motility and vitality. The semen was centrifuged at 3400 rpm for 5 min to remove supernatant. Then the pellets were washed twice with 1000  µL sterile phosphate buffered saline (PBS, 0.5 M). Then the remaining spermatozoa were incubated overnight in lysis buffer containing dithiothreitol (DDT)and protein K. After lysis, samples were centrifuged to separate the cell debris in the pellet. The supernatant was carefully removed and the sperm DNA was precipitated using ethanol. After that the pellet was dried,  the DNA was redissolved in TE buffer or ddH2O for further use.
A total of 5.2 μg of genomic DNA spiked with 26 ng of lambda DNA was fragmented into 200–300 bp, followed by end repair and adenylation. Cytosine-methylated adapters provided by Illumina were ligated to the sonicated DNA. Then, these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-Gold™ kit (Zymo Research), as per the manufacturer’s instructions. The resulting DNA fragments were amplified by two cycles of PCR using KAPA HiFi HotStart Uracil + ReadyMix. The libraries were sequenced on an Illumina Hiseq 2500 platform and 125-bp paired-end reads were generated.

tag: species

value: Holstein


title: Bull1_WGBS

description: Sperm whole genome bisulfite sequencing for Bull1


title: MBD-iOB-rep1

description: DNA methylation analysis


title: ILC2_control_rep2


title: WBJPE171125736

value: mice skeletal muscle

value: male


title: MBD-fibroblast-rep3-input

description: DNA methylation analysis


title: KO cortex3

source_name: KO cortex

value: Untreated


title: PromHet5

city: Ann Arbor

first: Adam

last: Helms

address: 7220 MSRB3, 1150 W. Medical Center Dr., SPC 5644

department: Internal Medicine

institute: University of Michigan

data_processing:
Illumina HiSeq 4000 reads
Reads aligned to genome using STAR (gene level)
Read counts per gene exported from STAR
Reads normalized to library size for each sample using DESeq2
Read counts controlled for technical and batch variability using RUVseq and housekeeping control gene set
Differential expression quantified using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data file containing read counts per gene from STAR

source_name: iPSC-derived cardiomyocytes

growth_protocol: iPSCs were differentiated using standard wnt signaling protocols. Cardiomyocytes were purified using magnetic bead sorting for the SIRPA cell surface marker.

extract_protocol:
Cells were collected in RLT buffer and RNA was extracted using the RNAeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols (stranded, polyA library).

treatment_protocol: All cell lines were treated in the same way.

value: iPSC-derived cardiomyocytes

value: MYBPC3 promoter deletion


title: PromHet4


title: KO cortex1


title: KO cortex2


title: WBJPE171125730

source_name: skeleton muscle


title: WBJPE171125733


title: PromHet3


title: MBD-fibroblast-rep1-input

description: DNA methylation analysis


title: PromHet2


title: KO-GT cortex3


title: WBJPE171125727


title: WBJPE171125729


title: MBD-fibroblast-rep2

description: DNA methylation analysis


title: MBD-fibroblast-rep3

description: DNA methylation analysis


title: Ex27Hom5

value: MYBPC3 exon 27 homozygous frameshift


title: WT-GT cortex2

source_name: WT-GT cortex

value: wild type


title: WT-GT cortex3


title: WBJPE171125723


title: WT-GT cortex1


title: WBJPE171125722


title: Ex27Hom3


title: WBJPE171125720


title: Bone chip GFP+-rep3

description: gene expression profiling

source_name: GFP sorted from bone chip


title: ILC2_control_rep1


title: Bone chip GFP+-rep2

description: gene expression profiling


title: WT cortex3

source_name: WT cortex


title: MBD-fibroblast-rep1

description: DNA methylation analysis


title: WT cortex2


title: Bone chip GFP+-rep1

description: gene expression profiling


title: WT cortex1


title: WBJPE171125717


title: WBJPE171125719


title: Ex27Hom1


title: PromHet1


title: CtlB5

value: control (crispr-edited negative)


title: mTert_reactivated_Generation4_unsorted_2

city: Houston

first: Deepavali

last: Chakravarti

state: TX

address: 1881East Rd

institute: MD Anderson Cancer Center

data_processing:
Raw fastq reads for all RNA-seq experiments were aligned to the mm10 reference genome using STAR 2.3.0e
Genome_build: mm10
Supplementary_files_format_and_content: RPKM table, the 1st column is gene and the follow columns are RPKM;  one sample per column

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit and quantified using a Bioanalyzer 1000.
Libraries for Illumina sequencing were generated from 1ug of RNA using the TruSeq RNA Library Prep Kit according to manufacturers instructions.

value: 3 months

value: large intestinal crypt

value: epithelial cells


title: mTert_reactivated_Generation4_unsorted_1


title: Ex27Hom4


title: WBJPE171125716


title: CtlB4


title: mTert_NULL_Generation4_unsorted_2


title: iOB GFP+ -rep2

description: gene expression profiling

source_name: GFP sorted from induced osteoblast

value: osteoblast


title: iOB GFP+ -rep1

description: gene expression profiling

source_name: GFP  sorted from induced osteoblast


title: calvarial-OB (dataset 2) rep3

description: gene expression profiling

source_name: calvarial progeniter cell

value: osteoblast differentiation


title: CtlB3


title: WBJPE171125715


title: WBJPE171125713


title: Ex27Hom2


title: CtlB1


title: calvarial-OB (dataset 2) rep1

description: gene expression profiling


title: calvarial-OB (dataset 2) rep2

description: gene expression profiling


title: mTert_HET_unsorted_2


title: WBJPE171125712


title: mTert_NULL_Generation4_unsorted_1


title: mTert_HET_unsorted_1


title: Ex27Het5

value: MYBPC3 exon 27 frameshift


title: WBJPE171125710


title: WBJPE171125709


title: iOB GFP+ -rep3

description: gene expression profiling


title: iOB-rep3

description: gene expression profiling


title: mTert_NULL_Generation3_sorted_3

value: large intestinal sorted

value: stem/progenitor cells


title: Ex27Het4


title: mTert_NULL_Generation3_sorted_2


title: iOB-rep2

description: gene expression profiling


title: WBJPE171125714


title: mTert_NULL_Generation3_sorted_1


title: WBJPE171125707


title: iOB-rep1

description: gene expression profiling


title: CtlB2


title: Ex27Het1


title: WBJPE171125704


title: WBJPE171125703


title: WBJPE171125700


title: mTert_HET_sorted_3


title: mTert_HET_sorted_1


title: fibroblast-rep2

description: gene expression profiling

value: fibroblast


title: Ex1Het5

value: MYBPC3 start site deletion


title: fibroblast-rep1

description: gene expression profiling


title: mTert_HET_sorted_2


title: WBJPE171125699

value: mice skeletal muscle

value: male


title: miR1_TotalUninducedRPF

city: Berkeley

first: Timothy

middle: J

last: Eisen

state: CALIFORNIA

address: Stanley Hall

institute: UC Berkeley

description:
cytoplasmically-enriched RNA
continuous labeling time course

data_processing:
Library strategy: RPF
RPF and RNA-seq reads were mapped to ORFs of representative transcript models as described, which excluded the first 50 nt of each ORF to eliminate signal from ribosomes that initiated after adding cycloheximide (Eichhorn et al., 2014). PAL-seq tags were mapped to 3' UTRs of representative transcript models, and PAL-seq fluorescence intensities were converted to tail lengths according to the pipeline available on github (https://github.com/kslin/PAL-seq/tree/tailSeqPipeline); transcript models available for download (Eichhorn et al., 2014)
Illumina 1.5; Conventional base calls
filtered for only thosed that passed the chastity filter; removed first 8 nt of the read (randomized 5p adapter)
reads aligned with STAR v2.4.2: --alignIntronMax 1 --clip3pAdapterSeq TCGTATGCCGTCTTCTGCTTG --runThreadN 30 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSJfilterReads Unique
assigned to features with intersectBed: -wb -s
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM and RPKM values for each sample. PAL-seq processed files include tab-delimited files of reads.

molecule: cytoplasmic RNA

growth_protocol: Each 3T3 sample was grown or maintained according to standard protocols

extract_protocol:
RNA-seq and RPF libraries were constructed exactly as described in Subtelny et al., 2014 (GSE52809)
PAL-seq libraries were constructed and processed according to the methods.
For RNA-seq or RPF libraries, detailed protocols are available (Subtelny et al., 2014 and Bartel lab website. NEXTflex libraries were prepared according to the manufacturer's instructions. PAL-seq library construction is as follows: Tail-length standard mixes (1 ng of set 1 and 2 ng of set 2 for each 5-EU-selected sample, and twice these amounts for the steady-state sample), and trace 5′-radoiolabeled marker RNAs (Table S2) were added to each sample to assess tail-length measurements and ligation outcomes, respectively. Polyadenylated ends including those with a terminal uridine were ligated to a 3′-biotinylated adapter DNA oligonucleotide (1.8µM) in the presence of two splint DNA oligonucleotides (1.25µM and 0.25µM for the U and A-containing splint oligos, respectively, Table S2) using T4 Rnl2 (NEB) in an overnight reaction at 18 °C. Following 3′-adapter ligation the RNA was extracted with phenol-chloroform (pH 8.0), precipitated, resuspended in 1X RNA T1 sequence buffer (ThemoFisher), heated to 50°C for 5 min and then put on ice. RNA was subsequently captured on streptavidin beads, 5′ phosphorylated, and ligated to a 5′ adapter as described (Subtelny et al., 2014) but using a modified 5′ adapter sequence (Table S2). Following reverse transcription using SuperScript III (Invitrogen) with a barcode-containing DNA primer, cDNA was purified as described (Subtelny et al., 2014), except a 160–810 nt size range was selected. Libraries were amplified by PCR for 8 cycles using Titanium Taq polymerase according to the manufacturer’s protocol with a 1.5 min combined annealing/extension step at 57°C. PCR-amplified libraries were purified using AMPure beads (Agencourt, 40 µL beads per 50 µL PCR, two rounds of purification) according to the manufacturer’s instructions.

treatment_protocol: Cytoplasmically-enriched RNA was extracted, poly(A)-selected, randomly fragmented by partial alkaline hydrolysis and then size-selected RNA fragments were used for library preparation.

tag: cell line background

tag: microrna-inducible cell line

tag: time

value: Ss

tag: micrornainduction

value: FALSE

tag: libraryprepmethod

value: RPF


title: Ex1Het2

value: iPSC-derived cardiomyocytes


title: Ex27Het3


title: miR1_TotalUninducedRNA

data_processing:
RPF and RNA-seq reads were mapped to ORFs of representative transcript models as described, which excluded the first 50 nt of each ORF to eliminate signal from ribosomes that initiated after adding cycloheximide (Eichhorn et al., 2014). PAL-seq tags were mapped to 3' UTRs of representative transcript models, and PAL-seq fluorescence intensities were converted to tail lengths according to the pipeline available on github (https://github.com/kslin/PAL-seq/tree/tailSeqPipeline); transcript models available for download (Eichhorn et al., 2014)
Illumina 1.5; Conventional base calls
filtered for only thosed that passed the chastity filter; removed first 8 nt of the read (randomized 5p adapter)
reads aligned with STAR v2.4.2: --alignIntronMax 1 --clip3pAdapterSeq TCGTATGCCGTCTTCTGCTTG --runThreadN 30 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSJfilterReads Unique
assigned to features with intersectBed: -wb -s
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM and RPKM values for each sample. PAL-seq processed files include tab-delimited files of reads.

value: RNAseq matched to RPF


title: WBJPE171125696

tag: gender


title: DroshaKO1d5_A

city: Zurich

first: Constance

last: Ciaudo

email: cciaudo@ethz.ch, ciaudobeyer@gmail.com

address: Otto-Stern-Weg 7

department: D-BIOL

institute: ETH

description: reverse-stranded protocol

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using STAR v2.4.2a allowing up to 2 mismatches
FeatureCounts V1.4.5-p1 was used to summarize reads for each gene, using -s 2 (reversely stranded) and ignoring multiple-hit reads
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read count

molecule: polyA RNA

growth_protocol: serum plus LIF

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: Drosha knockout

value: Blastocyste

value: embryonic stem cells

tag: age

value: Passage 7


title: Ex27Het2


title: Input-ChIP-seq

city: Taipei

first: Kuo-Hsuan

last: Hung

address: 128 Academia Road, Section 2

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

data_processing:
The sequencing quality of ChIP-Seq libraries was evaluated and assessed by FastQC.
Bowtie ( 0.12.7, Langmead et al., Genome Biol 10, R25 (2009)) was used to align the sequencing reads to the mouse genome. Mouse mm9 (UCSC Genome Browser) were used for gene annotation.
For determining the regulatory landscape and overall number of peaks, we used the Model-based Analysis of ChIP-seq (MACS) program version 1.4.2 (4). Jmjd2a- and Jmjd2c-bound genomic regions were mapped with default parameters, the effective genome size of 2,654,911,517 bp (mm9), and mixed with an anti-rabbit IgG input control sample. Peaks were filtered for p < 10-5. Finally, the Jmjd2a and Jmjd2c arenpmalized to input.
Genome_build: mm9
Supplementary_files_format_and_content: BED file

source_name: B222+ B cells

growth_protocol: Mouse splenic B220+ B cells from mouse splenocytes were isolated by magnetic sorting with CD45R (B220) microbeads (Miltenyi Biotec).

extract_protocol:
Lysates were be prepared by the EZ-ChIP kit (EMD Millipore, Cat. #: 17-371), sequentially sonicated to obtain fragmanted DNA,  then complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions by using the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: The purified B220+ B cells were stimulated with anti-mouse CD40 , IL-21 , and HEL.

tag: strain background

value: spleen

value: splenic B220+ B cells

tag: genotype/variation

tag: chip antibody

value: normal rabbit IgG (Bethyl, P120-101)


title: miR1_totalUninduced_PAL_read1

data_processing:
Library strategy: PAL-seq
RPF and RNA-seq reads were mapped to ORFs of representative transcript models as described, which excluded the first 50 nt of each ORF to eliminate signal from ribosomes that initiated after adding cycloheximide (Eichhorn et al., 2014). PAL-seq tags were mapped to 3' UTRs of representative transcript models, and PAL-seq fluorescence intensities were converted to tail lengths according to the pipeline available on github (https://github.com/kslin/PAL-seq/tree/tailSeqPipeline); transcript models available for download (Eichhorn et al., 2014)
Illumina 1.5; Conventional base calls
filtered for only thosed that passed the chastity filter; removed first 8 nt of the read (randomized 5p adapter)
reads aligned with STAR v2.4.2: --alignIntronMax 1 --clip3pAdapterSeq TCGTATGCCGTCTTCTGCTTG --runThreadN 30 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSJfilterReads Unique
assigned to features with intersectBed: -wb -s
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM and RPKM values for each sample. PAL-seq processed files include tab-delimited files of reads.

value: PAL-seq


title: WBJPE171125695

data_processing:
Illumina Casava1.7 software used for basecalling.
Single-cell RNA sequence reads were evaluated by FastQC
Bad reads were detected automatically and removed. Bases at 3' end of the read were further timmed by NGSQCToolkit if their PHRED quality score were less than 20.
The reads were mapped to the mm9 using bowtie2.
The mapped reads for genes were counted via Htseq.

tag: strain


title: miR1_TotalInducedRPF

value: TRUE


title: Jmjd2c-ChIP-seq

source_name: B221+ B cells

tag: cell type

value: anti-Jmjd2c (abcam, ab85454)


title: Ex1Het1

value: MYBPC3 start site deletion


title: fibroblast-rep3

description: gene expression profiling

value: fibroblast


title: WBJPE171125702

value: mice skeletal muscle

value: male


title: CtlA5

value: control


title: Ex1Het4

value: iPSC-derived cardiomyocytes


title: WBJPE171125686


title: DroshaKO2d5_B

description: reverse-stranded protocol


title: Ex1Het3


title: CtlA3


title: WBJPE171125685


title: CtlA2


title: miR1_totalInduced_PAL_read1

value: Ss


title: miR1_minus5EU_UninducedRPF

value: FALSE

value: RPF


title: 83154_ICN-p53-Vav

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

country: Canada

institute: Insititut de Recherches Cliniques

description: ICN induced T-ALL in Miz1 deltaPOZ expressing, p53 KO mouse

data_processing:
RNA-Seq reads were aligned to mm10 using Tophat v2.0.10
Reads were processed with Samtools.
For differential expression, countfiles were generated by mapping reads to Ensembl genes using HTSeq. Further analysis was carried out using the DESeq R package
Genome_build: mm10
Supplementary_files_format_and_content: txt files are tab-delimited text files containing counts on GRCm38 v77 Ensembl genes

source_name: T-ALL

extract_protocol:
RNA was extracted using a MagMax-96 Total RNA Isolation kit (Ambion) and quality-checked with a RNA 6000 Pico kit (Agilent).
RNA-Seq, libraries were prepared from RNA extracts using the TruSeq Stranded mRNA kit from Illumina according to the manufacturer’s instructions and sequenced using using the TruSeq PE Clusterkit v3-cBot-HS.

value: T cell acute lymphoblastic leukemia (T-ALL)

tag: icn induction

value: Yes

tag: miz1/p53 status

value: Miz1 deltaPOZ / p53 ko


title: CtlA1


title: 85884_ICN-p53-Lck

tag: tissue


title: miR1_minus5EU_InducedRPF


title: miR1_minus5EU_UninducedRNA

value: RNAseq matched to RPF


title: WBJPE171125671


title: WBJPE171125672


title: 85883_ICN-p53-Lck


title: miR1_TotalInducedRNA


title: WBJPE171125667


title: 83159_ICN-p53

description: ICN induced T-ALL in Miz1 WT, p53 KO mouse

value: Miz1 wt / p53 ko


title: miR1_minus5EU_InducedRNA


title: WBJPE171125684


title: 83149_ICN-p53


title: miR155_TotalUninducedRNA


title: WBJPE171125668


title: 69775_p53-Vav

description: T-ALL in Miz1 deltaPOZ expressing, p53 KO mouse

value: No


title: miR155_totalUninduced_PAL_read1

value: PAL-seq


title: 68580_p53-Vav


title: miR155_TotalInducedRPF

value: TRUE


title: WBJPE171125680


title: miR155_TotalInducedRNA


title: WBJPE171125665


title: 72128_p53

description: T-ALL in Miz1 WT, p53 KO mouse


title: WBJPE171125664


title: 62731_p53

description: T-ALL in Miz1 WT, p53 KO mouse


title: WBJPE171125659


title: miR155_totalInduced_PAL_read1


title: WBJPE171125655


title: WBJPE171125658


title: 76953_ICN-Vav

description: ICN induced T-ALL in Miz1 delatPOZ expressing mouse

value: Miz1 deltaPOZ / p53 wt


title: miR155_minus5EU_InducedRPF


title: WBJPE171125654


title: miR155_minus5EU_UninducedRNA


title: 75096_ICN-Lck


title: WBJPE171125653


title: WBJPE171125666


title: miR155_minus5EU_InducedRNA


title: WBJPE171125641


title: 75085_ICN-Lck


title: miR155_8hrUninducedRPF


title: 76962_ICN

description: ICN induced T-ALL in Miz1 WT mouse

value: Miz1 wt / p53 wt


title: miR155_minus5EU_UninducedRPF


title: SH-SY5Y transduced with dCVdCT, rep 3 [dCVdCT3]

city: Sacramento

first: Julian

last: Halmai

address: 2921 Stockton Blvd

department: Department of Neurology

institute: UC Davis

data_processing:
Sequencing reads were de-multiplexed and aligned to the Hg38 reference genome with STAR Universal Aligner version 2.5.3a using the following settings: Indexed Reference Genome: Ensembl reference genome and annotation files for Hg38 release 77 were downloaded and complied into a single file, Genome was indexed using the following arguments “STAR --runMode genomeGenerate --runThreadN 12 –genomeDir /STAR_INDEX_HG38 --genomeFastaFiles GRCh38_r77.all.fa --sjdbGTFfile Homo_sapiens.GRCh38.77.gtf --sjdbOverhang 149”; Sample Read Alignment: alignment of each sample’s reads was performed with the following arguments: “STAR --runThreadN 24 --genomeDir /STAR_INDEX_HG38 --outFileNamePrefix /STAR/SampleName_ --outSAMtype BAM SortedByCoordinate --outWigType bedGraph --quantMode TranscriptomeSAM GeneCounts --readFilesCommand zcat --readFilesIn Sample-R1.fastq.gz.gz Sample-R2.fastq.gz.gz”.
Differential Expression (DE) analysis was performed with DESeq2  in R Studio
Genome_build: hg38
Supplementary_files_format_and_content: .xlsx file containing normalized read counts per gene

source_name: SH-SY5Y transduced with dCVdCT

growth_protocol: SH-SY5Y cells were grown in DME/F12 media containing 20% FBS and 1% L-glut at 37C and 5%CO2

extract_protocol:
Cells were lysed with TriZol reagent and total RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research)
Libraries were generated using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina according to protocol using 1ug of input RNA

treatment_protocol: Cells were transduced with lentivirus by protamine sulfate mediated transduction

tag: cell line

tag: treatment

value: transduced with effector domain and sgRNAs


title: miR155_8hrUninduced_PAL_read1

tag: cell line background


title: miR155_8hrUninducedRNA

tag: microrna-inducible cell line


title: WBJPE171125640

address: Yuhangtang road

extract_protocol:
Cells were isolated by preplating mehods (Nat. Protocols 3, 1501-1509 (2008)).
single cell were captured, lysated, preamplified and library prepared according to "Using the C1 High-Throughput IFC to Generate Single-Cell cDNA Libraries for mRNA Sequencing"

value: mice skeletal muscle

value: male


title: 76952_ICN-Vav


title: SH-SY5Y transduced with dCVdCT, rep 2 [dCVdCT2]


title: miR155_TotalUninducedRPF

tag: time


title: 76971_ICN

description: ICN induced T-ALL in Miz1 WT mouse


title: WBJPE171125637


title: SH-SY5Y transduced with dCVdCT, rep 1 [dCVdCT1]


title: WBJPE171125636


title: miR155_8hrInducedRPF

tag: micrornainduction


title: miR155_8hrInducedRNA

tag: libraryprepmethod


title: WBJPE171125635

tag: gender


title: SH-SY5Y transduced with dCV, rep 3 [dCV3]

source_name: SH-SY5Y transduced with dCV


title: WBJPE171125634


title: SH-SY5Y transduced with dCV, rep 2 [dCV2]


title: SH-SY5Y transduced with dCV, rep 1 [dCV1]


title: WBJPE171125633


title: miR155_8hrInduced_PAL_read1


title: miR155_4hrUninducedRPF


title: SH-SY5Y transduced with dCT, rep 1 [dCT2]

source_name: SH-SY5Y transduced with dCT


title: WBJPE171125632


title: WBJPE171125630


title: SH-SY5Y transduced with dCT, rep 1 [dCT1]


title: SH-SY5Y transduced with dC, rep 3 [dC3]

source_name: SH-SY5Y transduced with dC


title: WBJPE171125627


title: homozygotes of let-60(n2021lf) 3

city: Medford

first: David

last: Angeles-Albores

state: MA

address: 61 Locust St

institute: Northwestern University

description: let-60(n2021lf) sample 3

data_processing:
Pseudo-alignment using Kallisto
Differential expression analysis using Sleuth
Genome_build: WBcel235
Supplementary_files_format_and_content: text files with target_id, length, eff_length, est_counts,  tpm  values

organism: Caenorhabditis elegans

source_name: homozygotes of let-60(n2021lf)

growth_protocol: Synchronized growth at 20C on ample OP50

extract_protocol:
Pick 30 worms, use Zymo RNA column to extract
RNA-Seq libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530) following manufacturer’s instructions.

tag: life stage

value: Young Adult (no eggs visible)


title: N3_Random_si

city: Tokushima

first: Toshihito

last: Tanahashi

address: Kuramotocho 3-18-5

country: Japan

institute: Tokushima University

description: mRNA expression

hyb_protocol: Cy3-labelled mRNA was hybridized to SurePrint G3 human GE 8 x 60K (Agilent).

scan_protocol: Each sample was scanned by a Microarray Scanner (G2505C; Agilent).

data_processing: Fluorescence signal was extracted using Feature Extraction Software (version 10.7.3.1).

label_protocol: Total RNA was labelled with cyanine 3-cytidine bisphosphate by T4 ligase.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: After the transfection of JMJD2A siRNA (s18635; Ambion) or Negative Control #1 (Ambion), total RNA was extracted from MKN45 cells at 24 h.

value: Stomach

tag: sirna

value: Random


title: N2_Random_si

description: mRNA expression


title: J4_JMJD2A_si

description: mRNA expression


title: miR155_4hrInducedRPF

value: RPF


title: N1_Random_si

description: mRNA expression


title: N4_Random_si

description: mRNA expression


title: J3_JMJD2A_si

description: mRNA expression


title: J1_JMJD2A_si

description: mRNA expression


title: homozygotes of let-60(n2021lf) 2

description: let-60(n2021lf) sample 2

tag: genotype/variation


title: miR155_4hrInducedRNA


title: SH-SY5Y transduced with dC, rep 2 [dC2]


title: SH-SY5Y transduced with dC, rep 1 [dC1]


title: WBJPE171125625

city: Hangzhou

first: Yixiao

last: Liu

institute: Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine


title: J2_JMJD2A_si

description: mRNA expression


title: WBJPE171125626


title: Mock-treated SH-SY5Y, rep 2 [NT2]

source_name: Mock-treated SH-SY5Y

value: non-transduced


title: miR155_4hrInduced_PAL_read1


title: WBJPE171125624


title: miR155_4hrUninduced_PAL_read1

value: FALSE


title: miR155_40minUninducedRPF


title: homozygotes of let-60(n1046gf) 3

description: let-60(n1046gf) sample 3

source_name: homozygotes of let-60(n1046gf)


title: WBJPE171125623

source_name: skeleton muscle


title: miR155_40minUninducedRNA


title: homozygotes of let-60(n1046gf) 2

description: let-60(n1046gf) sample 2


title: WBJPE171125622


title: homozygotes of let-60(n2021lf) 1

description: let-60(n2021lf) sample 1


title: WBJPE171125615


title: miR155_40minUninduced_PAL_read1


title: miR155_40minInducedRPF