title: RDES_siPool_1_split1, technical replicate, 72h

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

description:
RDES_siPool_1_split1
processed data file: Normalized_counts.txt
processed data file: RDES-siPool1_vs_RDES-Control.txt

data_processing:
Sequencing was carried out on an Illumina HiSeq2500. Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the Homo sapiens genome reference (hg19) using STAR aligner.
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Normalized_counts.txt: Tab-delimited text file includes normalized counts.
Supplementary_files_format_and_content: *txt: Tab-delimited textt files include DESEQ2 output for each comparison.

source_name: siPOOL against SOX2

growth_protocol: 300,000 cells per well/6well-plate were cultured for 72h after transfection.

extract_protocol:
RNA was extracted by using RNA isolation kit from Macherey-Nagel.
To prepare RNA-Seq libraries using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA), 100-200 ng of total RNA was used.

treatment_protocol: Cells were transfected with 5nM siPOOL.

value: RDES

value: Ewing sarcoma cell line

value: Pool of 30 siRNAs against SOX2


title: RDES_siPool_2_split2, technical replicate, 72h

status: Public on Aug 19 2019

type: SRA

description:
RDES_siPool_2_split2
processed data file: Normalized_counts.txt
processed data file: RDES-siPool2_vs_RDES-Control.txt

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment


title: C11

city: Worcester

first: Silvia

last: Corvera

address: 373 Plantation St

country: USA

institute: University of Massachusetts Medical School

description: processed data file: TPM.txt

data_processing:
The FASTQ files obtained were de-multiplexed using SMART-Seq DE3 Demultiplexing Software by Clontech.
Bowtie was used to align the reads to the human genome assembly hg19.
The aligned reads were then processed by RSEM to generate un-normalized and TPM counts.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: TPM.txt: Tab-delimited text file includes TPM values for each sample.

source_name: subcutaneous white adipose tissue

extract_protocol:
Total RNA extraction was performed using NucleoSpin RNA XS kit (Clontech Laboratories Inc. Cat. No. 740902). Briefly, cells were detached as mentioned in previous section, snap frozen in liquid nitrogen and stored at -80oC overnight. Next day, RNA was prepared from a total of 168 samples across three conditions (C, M and F) according to the manufacturer’s instructions.
cDNA library was prepared using SMART-Seq v4 3’ DE kit according to the manufacturer’s instructions (Clontech Laboratories Inc. Cat. No. 635040). For each clone, 1 ng of total RNA was used as input to synthesize cDNA which was subsequently amplified. Control RNA was provided with the kit. All samples were processed concurrently during library preparation. Prior to purification, the amplified cDNA’s were grouped in fourteen pools of twelve samples each with a unique barcode (Clonetech Oligo dT in-line indexes or IL 1-12) ligated to the 3’end during cDNA synthesis. Pooled and purified libraries were fragmented using Nextera XT DNA Sample Preparation Kit (Illumina, Cat. Nos. FC-131-1024, FC-131- 1096). Illumina sequencing indexes (provided with the SMART-Seq v4 3’ DE kit) were added to the fragmented libraries and indexed libraries were amplified. For intermittent purification steps, Agencourt AMPure XP PCR purification kit (5 ml Beckman Coulter Part No. A63880; 60 ml Beckman Coulter Part No. A63881) was used.

value: Subcutaneous adipose tissue-derived mesenchymal progenitor cells

tag: condition

value: C


title: C102

description: processed data file: TPM.txt


title: C10

description: processed data file: TPM.txt


title: C1

description: processed data file: TPM.txt


title: DOHH2-Ib

city: Lyon

first: Charles

last: Dumontet

address: 8 avenue Rockefeller

department: Immunology

country: France

institute: INSERM

data_processing:
bcl2fastq
cutadapt
tophat2
cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: tabular file with transcript expression (FPKM), output from cufflinks

molecule: polyA RNA

source_name: representative of follicular lymphoma

growth_protocol: Cell lines  used are DAUDI, representative of Burkitt lymphoma and DOHH2, representative of follicular lymphoma. Both cell lines were obtained from ATCC.

extract_protocol:
Total RNA was extracted from cell suspensions
NEXTflex Rapid Directional mRNA-Seq Kit (BiooScientific)

tag: resistance

value: Ibrutinib


title: 387_shCONT

city: San Diego

first: Jeremy

last: Rich

state: CA

address: 9500 Gilman Drive #0695

institute: University of California, San Diego

description: ELOVL2_Knockdown_Salmon_Abundance.txt (387-NT)

data_processing:
FASTQ sequencing reads were trimmed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and transcript quantification was performed using Salmon in the quasi-mapping mode
Salmon “quant” files were converted using Tximport (https://bioconductor.org/packages/release/bioc/html/tximport.html) and differential expression analysis was performed using DESeq2
Gene set enrichment analysis was performed by selecting differentially expressed genes (FDR-corrected p-value < 0.05), generating a pre-ranked list, and inputting a pre-ranked list into the GSEA desktop application (http://software.broadinstitute.org/gsea/downloads.jsp) (22,23). Pathway enrichment bubble plots were generated using the Bader Lab Enrichment Map Application (24) and Cytoscape (http://www.cytoscape.org).
Genome_build: hg38
Supplementary_files_format_and_content: Text files of Salmon Counts, Abundances, and DESeq2 Differentially expressed genes

source_name: Glioblastoma Stem Cell

growth_protocol:
GSC387 cells from a primary patient derived glioblastoma tumor were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.
All GSCs were cultured in Neurobasal media (Invitrogen) supplemented with B27 without vitamin A (Invitrogen), EGF, and bFGF (10 ng/ml each; R&D Systems), sodium pyruvate, and glutamax.

extract_protocol:
Cells were dissociated from the tumor and cultured as described in the methods
Cellular RNA was extracted using the Qiagen miRNeasy Mini Kit (catalog number 217004) according to the manufacturers instructions.

treatment_protocol: Cells were treated with a non-targeting control shRNA (shCONT) or shRNAs targeting ELOVL2

tag: transfection

value: shCONT

tag: tumor type

value: Glioblastoma


title: C13

description: processed data file: TPM.txt


title: RDES_siPool_1_split2, technical replicate, 72h

description:
RDES_siPool_1_split2
processed data file: Normalized_counts.txt
processed data file: RDES-siPool1_vs_RDES-Control.txt


title: clone_c_rep1

city: Atlanta

first: Greg

last: Gibson

state: Georgia

address: 950 Atlantic Drive

institute: Georgia Institute of Technology

description:
Raw_counts_single_cell_clone.csv
Normalized_single_cell_clone.csv

data_processing:
RNA-Seq quality control was initiated with Trim Galore, which was used to trim the 13bp Illumina standard adapter (‘AGATCGGAAGAGC’) by default.
Reads were mapped to hg38 human reference genome by STAR with defalut parameters.
Aligned sequencing reads were counted with intersection-strict mode in HTSeq.
Scale factors of each sample were computed using the trimmed mean of M-value (TMM) algorithm in edgeR.
Raw read counts were normalized by scale factors and then transformed into log2 counts per million reads (CPM). Genes were kept if expressed in at least three samples.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include raw and normalized read counts at the gene level for each sample

source_name: HL60 cell line

extract_protocol: Illumina TruSeq Stranded Sample Preparation, Low Sample (LS) Protocol was used for the samples sequenced by Illumina HiSeq 2500. And NEBNext Ultra II Directional 162 RNA Library Prep Kit for Illumina was used for samples sequenced by Illumina NextSeq 550.

tag: differentiation type

value: Parental

tag: clone


title: 387_shELOVL2.308

description: ELOVL2_Knockdown_Salmon_Abundance.txt (387-314664)


title: C12

description: processed data file: TPM.txt


title: RDES_siPool_2_split1, technical replicate, 72h

description:
RDES_siPool_2_split1
processed data file: Normalized_counts.txt
processed data file: RDES-siPool2_vs_RDES-Control.txt


title: RDES_siCTR_split2, technical replicate, 72h

description:
RDES_siCTR_split2
processed data file: Normalized_counts.txt
processed data file: RDES-siPool1_vs_RDES-Control.txt

source_name: siPOOL control

value: Pool of 30 siRNAs control


title: DOHH2-WT

value: WT


title: DOHH2-Cal

value: idelalisib


title: POE_siPool_2_split1, technical replicate, 72h

description:
POE_siPool_2_split1
processed data file: Normalized_counts.txt
processed data file: POE-siPool2_vs_POE-Control.txt

value: POE


title: DAUDI-Cal

source_name: representative of Burkitt lymphoma

value: DAUDI


title: RDES_siCTR_split1, technical replicate, 72h

description:
RDES_siCTR_split1
processed data file: Normalized_counts.txt
processed data file: RDES-siPool1_vs_RDES-Control.txt


title: POE_siPool_2_split2, technical replicate, 72h

description:
POE_siPool_2_split2
processed data file: Normalized_counts.txt
processed data file: POE-siPool2_vs_POE-Control.txt


title: POE_siPool_1_split2, technical replicate, 72h

description:
POE_siPool_1_split2
processed data file: Normalized_counts.txt
processed data file: POE-siPool1_vs_POE-Control.txt


title: DAUDI-Ib


title: DAUDI-WT


title: POE_siPool_1_split1, technical replicate, 72h

description:
POE_siPool_1_split1
processed data file: Normalized_counts.txt
processed data file: POE-siPool1_vs_POE-Control.txt


title: cde-1 rep2

city: Cambridge

first: Konrad

middle: Ludwig Moritz

last: Rudolph

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: TAIL-seq

data_processing:
Basecalling was performed using Tailseeker 2
Reads were trimmed using cutadapt 1.10 with Illumina small RNA-seq adapters to a minimum length of 5bp
5ʹ reads were mapped using STAR 2.5.2 against a combined meta-genome consisting of the C. elegans refrence genome and the Orsay virus genome using parameters “--alignEndsType EndToEnd --scoreInsOpen -10000 --scoreDelOpen -10000 --outFilterMismatchNmax 0 --outFilterMultimapNmax 1”
5ʹ reads were assigned to genes via bedtools intersect 2.26 using default parameters
3ʹ reads without poly(A) tail or with too many dark cycles were filtered out using a custom script
Genome_build: WBcel235
Supplementary_files_format_and_content: Tailseeker taginfo file: tab-delimited files containing the Tailseeker read support count, poly(A) length, tail modification, gene ID, as well as three columns identifying the library

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Approximately 200 cde-1 (tm1021) mutants or N2 animals were infected for 48 hours from the L2 stage to the adult stage with 20 µl filtrate of the Orsay virus on 50mm plate seeded with HB101 bacteria, in biological duplicates.

extract_protocol:
Animals were then washed in M9 and resuspended in 1 ml TRIsure (Bioline). Samples were freeze-thaw three times using liquid nitrogen and RNA purification was performed according to Bioline’s guidelines.
As described in Chang, et al. Moll. Cell 2014

treatment_protocol: Orsay virus infection as described above.

tag: genotype/variation

tag: strain

tag: agent

value: Orsay virus


title: POE_siCTR_split2, technical replicate, 72h

description:
POE_siCTR_split2
processed data file: Normalized_counts.txt
processed data file: POE-siPool1_vs_POE-Control.txt


title: MCF-7/FR cells_fulv-withdrawn for 4 days_replicate 3

type: RNA

city: Lebanon

first: Todd

last: Miller

state: NH

address: DHMC One Medical Center Dr, HB-7936

institute: Geisel School of Medicine at Dartmouth

hyb_protocol: 1.5 μg of cRNA was used for hybridization to beadchip arrays for 16 hours at 55°C.

scan_protocol: Arrays were washed and stained with streptavidin-Cy3. Fluorescent images were obtained with an Illumina 500GX scanner.

data_processing: Images were processed with BeadScan and GenomeStudio software (Illumina).

label: biotin

label_protocol: Reverse transcription using an oligo(dT) primer bearing a T7 promoter and the high yield ArrayScript reverse transcriptase were used to make cDNA. The cDNA was made double-stranded and purified to use as a template for in vitro transcription with T7 RNA polymerase and  biotin-NTPs. Labeled cRNA was purified.

growth_protocol: Cells were maintained in DMEM + 10% FBS + 1 uM fulvestrant

extract_protocol: RNA was extracted using Qiagen Rneasy kit.

treatment_protocol: Cells were treated with DMEM + 10% FBS (without fulvestrant) for 0-14 days, and RNA was extracted in 2-day intervals in triplicate.

value: MCF-7/FR cells

value: fulvestrant-withdrawn

tag: time

value: 4 days


title: MCF-7/FR cells_fulv-withdrawn for 8 days_replicate 1

value: 8 days


title: MCF-7/FR cells_fulv-withdrawn for 10 days_replicate 1

value: 10 days


title: cde-1 rep1

description: TAIL-seq


title: MCF-7/FR cells_fulv-withdrawn for 6 days_replicate 2

value: 6 days


title: Cerebellum, EOD.R_Input_rep1 (ChIP-seq)

city: Singapore

first: Gavin

last: Ng

address: Block MD9, Level 4  2 Medical Drive  117597

department: Physiology

country: Singapore

institute: National University of Singapore

library_source: genomic

data_processing:
RNA samples from the cerebellum was isolated using EZ-10 DNAaway RNA Mini-Preps Kit (Bio Basic, Canada) according to the manufacturers’ protocol. Briefly, frozen cerebellum samples were homogenized and lysed in the provided lysis buffer. Prevention of genomic DNA contamination was achieved using the provided gDNA eliminator column. The RNA’s purity was determined by using the Nanodrop ND-1000 (Thermo Fisher Scientific, USA), whereas the RNA’s integrity was assessed via agarose gel electrophoresis as well as from the Agilent 2100 Bioanalyzer (Agilent, USA). Enrichment of high-quality RNA samples should demonstrate an OD260/OD280 ratio of 1.9-2.0 from Nanodrop readings, two distinct bands indicating 28S and 18S following agarose gel electrophoresis, as well as showing ≥ 6.8 RNA integrity number with a smooth base line using the Agilent 2100 Bioanalyzer.
Following the isolation of these high-quality and pure total RNA samples from the cerebellum tissues, cDNA library construction was mediated using the NEBNext® UltraTM RNA library preparation kit as per the manufacturers’ protocol (New England BioLabs, USA). mRNA was first purified via the addition of poly-T-oligo-attached magnetic beads, before subjecting them to random fragmentation mediated by the usage of a fragmentation buffer. The initial strand of the cDNA is first synthesized through the utilisation of a random hexamer primer and RNase H- (M-MuLV reverse transcriptase). The second strand of cDNA is then synthesized using DNA polymerase I and RNase H, and the resulting double stranded cDNA is then purified using AMPure XP beads. The overhangs of these purified double-stranded cDNA were then processed by exonuclease and polymerase to become blunt ends, before subjecting the 3’ ends of these DNA fragments to adenylation and subsequent ligation of NEBNext hairpin loop structure adaptor on both ends for hybridisation. For optimal isolation of cDNA fragments of approximately 150-200 base pairs in length, DNA fragments were then purified using the AMPure XP system (Beckman Coulter, USA), before utilising both PCR amplification and purification by AMPure XP beads to obtain the completed library DNA fragments. The resultant libraries were then sequenced using HiSeqTM 2500 Illumina platforms to obtain 12GB of raw data per sample (Illumina, USA).
The reference genome for Mus musculus (mm10) and gene model annotation files were downloaded from the National Center for Biotechnology Information (NCBI) genome website browser. Following which, indexes of the reference genome was constructed before the paired-end clean reads were then mapped to the reference genome using STAR (v2.5) [12] for the cerebellum transcriptome.
To count the number of reads mapped onto each gene, HTSeq (v0.6.1) [13] was used to compute such quantification. From there, the Reads Per Kilobase of exon model per Million mapped reads (FPKM) of each gene was then computed using the length of the gene and reads count mapped to this particular gene. The FPKM value was then used for estimation of gene expression levels. 35,275 unique RNA transcripts each were quantified in total for cerebellum datasets.
Differential gene expression analysis between five biological replicates per condition were performed using the DESeq2 R Package (v2_1.6.3). A negative binomial distribution was used to model a statistical analysis for differential gene expression as achieved in DESeq2. The resultant p-values were then adjusted using Benjamini and Hochberg’s test to control false discovery rate (FDR). Genes with adjusted p < 0.05 were assigned as differentially expressed [14]. Principal component plots, venn diagrams and volcano plots in this study were prepared using the ggplot2 R package (v3.0.0) [15].
To allow logarithm adjustment, genes showing FPKM values of zero were assigned a corresponding value of 0.01. Correlation was then determined using the “cor.test” function in R with options set alternative= “greater” and method= “Spearman”. All experiments were performed using at least five biological replicates per condition, and Pearson correlation coefficients obtained of at least 0.9 value demonstrated high coverage and reproducibility. After which, to establish relationship between the different samples, clustering was performed using the FPKM expression level by utilising the hierarchical clustering distance method with the aid of heatmap, self-organisation mapping (SOM) and k-means via silhouette coefficient in order to adapt optimal classification with R’s default parameters imbued. Heatmap illustrated in this manuscript was prepared using pheatmap R package (v1.0.10).
To understand the gene ontology (GO) as well as the pathway association for these differentially expressed genes, gprofile R package (v0.6.7) [17] and clusterProfiler R package (v3.8) [18] were utilised for this function.  After correction of gene length biasness, GO terms with adjusted p-value < 0.05 were assigned as significantly enriched among the pool of differentially expressed genes. Diagrams demonstrating enrichment analysis was plotted using ggplot2 R package (v3.0.0) and Sigmaplot (v1.3).
Frozen organ was crushed into a fine powder with liquid nitrogen using a pestle and mortar. Tissue was then crosslinked with 1% formaldehyde (Merck, New Jersey, United States) for 10 min at room temperature and the reaction was stopped by adding glycine (Abcam, Cambridge, United Kingdom) to a final concentration of 0.125M for five minutes at room temperature. Fixed cells were rinsed twice with PBS with protease (Thermo Scientific, Massachusetts, USA) inhibitor in 1:1000 ratios and resuspended in 10 ml of lysis buffer (10mM Tris-HCl pH 8, 0.25% Triton X-100, 10mM EDTA, 0.1M NaCl). The lysates were then subjected to further lysis using a Dounce tissue grinder (Sigma-Aldrich, Missouri, United States) for 14-16 strokes. After which, the lysates were suspended in 1% SDS lysis buffer (50mM HEPES-KOH pH 7.5, 150mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1% SDS) before undergoing ultracentrifuge at 18000rpm for 30 minutes. The subsequent chromatin jelly was then resuspended in 0.1% SDS lysis buffer (50mM HEPES-KOH pH 7.5, 150mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS) and underwent another round of ultracentrifuge at 18000rpm for 30 minutes. After which, the lysate was resuspended in 0.1% SDS buffer and sonicated for 30 sec on / 30 sec off for 15 cycles in a sonicator (Diagenode, New Jersey, USA) and centrifuged at 14000 rpm for 10 min. Approximately 500 ng of sonicated chromatin was stored at -80°C as an input DNA control.     The remaining sonicated chromatin was incubated with 30 ul of Protein G Dynabeads (Invitrogen, California, United States) conjugated overnight previously to 4 ug of ChIP-grade H3K9me3 antibody (Abcam, Cambridge, United Kingdom). The beads were then washed for 5 minutes once, in Low Salt 0.1% SDS FA Lysis Buffer (50mM HEPES-KOH pH 7.5, 150mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), then High Salt 0.1% SDS FA Lysis Buffer (50mM HEPES-KOH pH 7.5, 350mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), followed by LiCl buffer wash (10mM Tris-HCl pH8, 0.25mM LiCl, 1mM EDTA, 0.5% NP40, 0.5% sodium deoxycholate). Lastly, the ChIPed material was washed twice with TE buffer (10mM Tris-HCl pH8, 1mM EDTA), before eluted by ChIP Elution buffer (50mM Tris-HCl pH8, 10mM EDTA, 1% SDS) incubation for two hours at 68°C for both input and immunoprecipitated DNA. Finally, chromatin was treated with one-hour incubation with RNase at 37°C, before subjected to 10 ul 5mM NaCl and 5 ul of Proteinase K digestion overnight at 68°C. DNA was then extracted using phenol-chloroform and eluted in nuclease-free water.     Extracted DNA was quantified using Quantifluor double-stranded DNA kit (Promega Corporation, Australia) as per manufacturer instruction. 20X TE buffer is first dilu

molecule: genomic DNA

organism: Mus musculus

source_name: Cerebellum

extract_protocol:
The cerebellum was harvested, immediately flash frozen and stored at -80°C.
ChIP & RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Cerebellum

tag: age

value: 3M before expt, 8M after expt

tag: chip antibody


title: MCF-7/FR cells_fulv-withdrawn for 10 days_replicate 3


title: MCF-7/FR cells_fulv-withdrawn for 6 days_replicate 3


title: MCF-7/FR cells_fulv-withdrawn for 10 days_replicate 2


title: MCF-7/FR cells_fulv-withdrawn for 14 days_replicate 2

value: 14 days


title: MCF-7/FR cells_fulv-withdrawn for 12 days_replicate 1

value: 12 days


title: MCF-7/FR cells_fulv-withdrawn for 2 days_replicate 1

value: 2 days


title: POE_siCTR_split1, technical replicate, 72h

description:
POE_siCTR_split1
processed data file: Normalized_counts.txt
processed data file: POE-siPool1_vs_POE-Control.txt

value: Ewing sarcoma cell line

value: Pool of 30 siRNAs control


title: WT rep2

description: TAIL-seq

value: wildtype


title: MCF-7/FR cells_fulv-withdrawn for 4 days_replicate 2


title: MCF-7/FR cells_fulv-withdrawn for 6 days_replicate 1


title: MCF-7/FR cells_with fulvestrant_replicate 2

source_name: MCF-7/FR cells_with fulvestrant

value: with fulvestrant

value: 0 days


title: MCF-7/FR cells_fulv-withdrawn for 8 days_replicate 2


title: MCF-7/FR cells_fulv-withdrawn for 8 days_replicate 3


title: MCF-7/FR cells_fulv-withdrawn for 4 days_replicate 1


title: MCF-7/FR cells_fulv-withdrawn for 2 days_replicate 2


title: Cerebellum, IF16.R_Input_rep1 (ChIP-seq)


title: WT rep1

description: TAIL-seq

value: Orsay virus


title: MCF-7/FR cells_fulv-withdrawn for 2 days_replicate 3

value: MCF-7/FR cells


title: MCF-7/FR cells_fulv-withdrawn for 12 days_replicate 3

value: fulvestrant-withdrawn


title: EW1_siPool_2_split2, technical replicate, 72h

description:
EW1_siPool_2_split2
processed data file: Normalized_counts.txt
processed data file: EW1-siPool2_vs_EW1-Control.txt

value: Pool of 30 siRNAs against SOX2


title: EW1_siPool_2_split1, technical replicate, 72h

description:
EW1_siPool_2_split1
processed data file: Normalized_counts.txt
processed data file: EW1-siPool2_vs_EW1-Control.txt


title: MCF-7/FR cells_fulv-withdrawn for 12 days_replicate 2


title: Cerebellum, EOD.R_rep1 (ChIP-seq)

value: Anti-histone H3 (tri methyl K9) antibody- ChIP grade ab8898, abcam


title: MCF-7/FR cells_fulv-withdrawn for 14 days_replicate 1


title: RMB407

first: Jinmiao

last: Chen

address: 8A Biomedical Grove, #04-06 Immunos

institute: Singapore Immunology Network

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB407_GTAGAGGA-AGAGTAGA_L005

data_processing:
Raw reads were aligned to the mouse reference genome GRCm38 from GENCODE using RSEM program version 1.2.19 with default parameters. Gene expression values in transcripts per million (TPM) were calculated using the same RSEM program and the mouse GENCODE annotation version 4.
Genome_build: GRCm38
Supplementary_files_format_and_content: transcripts per million (TPM)

growth_protocol: primary cells

extract_protocol:
bones were removed, bone marrow was flushed out, red blood cells were lysed prior antibody staining, progenitor cells were enriched using magnetic beads prior FACS sorting, IFC capture, on-chip lysis & rt-pcr Nextera_XT Kit (Illumina, PN FC-131-1096) with dual indices (Illumina, PN FC-131-1002) was used to prepare single-cell multiplexed libraries
Cells were loaded onto C1 integrated fluidic circuits IFC (5- to 10-μm chip) for cell lysis, reverse transcription with oligo (dT) primers and amplification of cDNA on a C1 Single Cell Auto Prep System according to the mRNA-seq protocol of the manufacturer (Fluidigm). Only cells with high-quality cDNA were processed for subsequent library preparation. A Nextera_XT Kit (PN FC-131-1096; Illumina) with dual indices (PN FC-131-1002; Illumina) was used for the preparation of single-cell multiplexed libraries.

treatment_protocol: untreated

tag: markers


title: RMB403

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB403_AAGAGGCA-CTAAGCCT_L005


title: RMB405

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB405_GTAGAGGA-CTCTCTAT_L005


title: EW1_siPool_1_split2, technical replicate, 72h

description:
EW1_siPool_1_split2
processed data file: Normalized_counts.txt
processed data file: EW1-siPool1_vs_EW1-Control.txt

tag: cell line


title: Cerebellum, IF16.R_rep1 (ChIP-seq)


title: RMB404

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB404_GTAGAGGA-TAGATCGC_L005

tag: cell type


title: RMB408

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB408_GTAGAGGA-GTAAGGAG_L005


title: RMB402

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB402_AAGAGGCA-AAGGAGTA_L005


title: Cerebellum, AL.R_Input_rep1 (ChIP-seq)

tag: treatment


title: RMB400

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB400_AAGAGGCA-GTAAGGAG_L005


title: EW1_siPool_1_split1, technical replicate, 72h

description:
EW1_siPool_1_split1
processed data file: Normalized_counts.txt
processed data file: EW1-siPool1_vs_EW1-Control.txt


title: RMB399

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB399_AAGAGGCA-AGAGTAGA_L005


title: RMB398

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB398_AAGAGGCA-TATCCTCT_L005


title: RMB397

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB397_AAGAGGCA-CTCTCTAT_L005


title: EW1_siCTR_split2, technical replicate, 72h

description:
EW1_siCTRsplit2
processed data file: Normalized_counts.txt
processed data file: EW1-siPool1_vs_EW1-Control.txt


title: Cerebellum, AL.R_rep1 (ChIP-seq)


title: Cerebellum, EOD_Input_rep1 (ChIP-seq)

value: EOD

value: 3M before expt, 6M after expt


title: RMB396

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB396_AAGAGGCA-TAGATCGC_L005


title: EW1_siCTR_split1, technical replicate, 72h

description:
EW1_siCTR_split1
processed data file: Normalized_counts.txt
processed data file: EW1-siPool1_vs_EW1-Control.txt


title: RMB393

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB393_CGAGGCTG-ACTGCATA_L005


title: MCF-7/FR cells_with fulvestrant_replicate 3


title: Cerebellum, IF16_Input_rep1 (ChIP-seq)

value: Cerebellum


title: RMB391

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB391_CGAGGCTG-AGAGTAGA_L005


title: MCF-7/FR cells_fulv-withdrawn for 14 days_replicate 3


title: RMB390

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB390_CGAGGCTG-TATCCTCT_L005


title: Cerebellum, AL_Input_rep1 (ChIP-seq)

value: AL


title: MCF-7/FR cells_with fulvestrant_replicate 1


title: RMB389

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB389_CGAGGCTG-CTCTCTAT_L005


title: Cerebellum, EOD_rep1 (ChIP-seq)


title: RMB383

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB383_GCTACGCT-AGAGTAGA_L005


title: RMB378

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB378_CAGAGAGG-AAGGAGTA_L005


title: Cerebellum, IF16_rep1 (ChIP-seq)


title: Cerebellum, EOD.R_rep5 (RNA-Seq)

description:
EOD_R5
fpkm_genename_Refeed_RNA.txt
fpkm_group_Refeed_RNA.txt
fpkm_sample_Refeed_RNA.txt
readcount_Refeed_RNA.txt
readcount_genename_Refeed_RNA.txt

value: 3M before expt, 8M after expt


title: Cerebellum, AL_rep1 (ChIP-seq)


title: RMB376

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB376_CAGAGAGG-GTAAGGAG_L005


title: RMB375

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB375_CAGAGAGG-AGAGTAGA_L005


title: Cerebellum, EOD.R_rep4 (RNA-Seq)

description:
EOD_R4
fpkm_genename_Refeed_RNA.txt
fpkm_group_Refeed_RNA.txt
fpkm_sample_Refeed_RNA.txt
readcount_Refeed_RNA.txt
readcount_genename_Refeed_RNA.txt


title: RMB365

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB365_CTCTCTAC-CTCTCTAT_L005


title: Cerebellum, EOD.R_rep2 (RNA-Seq)

description:
EOD_R2
fpkm_genename_Refeed_RNA.txt
fpkm_group_Refeed_RNA.txt
fpkm_sample_Refeed_RNA.txt
readcount_Refeed_RNA.txt
readcount_genename_Refeed_RNA.txt


title: RMB370

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB370_CTCTCTAC-AAGGAGTA_L005


title: RMB366

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB366_CTCTCTAC-TATCCTCT_L005


title: RMB373

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB373_CAGAGAGG-CTCTCTAT_L005


title: RMB364

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB364_CTCTCTAC-TAGATCGC_L005


title: RMB386

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB386_GCTACGCT-AAGGAGTA_L005


title: RMB384

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB384_GCTACGCT-GTAAGGAG_L005


title: Cerebellum, IF16.R_rep5 (RNA-Seq)

description:
IF_R5
fpkm_genename_Refeed_RNA.txt
fpkm_group_Refeed_RNA.txt
fpkm_sample_Refeed_RNA.txt
readcount_Refeed_RNA.txt
readcount_genename_Refeed_RNA.txt


title: RMB380

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB380_GCTACGCT-TAGATCGC_L005


title: Cerebellum, EOD.R_rep1 (RNA-Seq)

description:
EOD_R1
fpkm_genename_Refeed_RNA.txt
fpkm_group_Refeed_RNA.txt
fpkm_sample_Refeed_RNA.txt
readcount_Refeed_RNA.txt
readcount_genename_Refeed_RNA.txt


title: RMB361

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB361_TAGGCATG-ACTGCATA_L005


title: Cerebellum, IF16.R_rep4 (RNA-Seq)

description:
IF_R4
fpkm_genename_Refeed_RNA.txt
fpkm_group_Refeed_RNA.txt
fpkm_sample_Refeed_RNA.txt
readcount_Refeed_RNA.txt
readcount_genename_Refeed_RNA.txt


title: RMB360

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB360_TAGGCATG-GTAAGGAG_L005


title: RMB353

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB353_TCCTGAGC-ACTGCATA_L005


title: RMB359

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB359_TAGGCATG-AGAGTAGA_L005


title: RMB374

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB374_CAGAGAGG-TATCCTCT_L005


title: RMB356

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB356_TAGGCATG-TAGATCGC_L005


title: RMB350

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB350_GGACTCCT-TATCCTCT_L005


title: RMB349

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB349_GGACTCCT-CTCTCTAT_L005


title: RMB367

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB367_CTCTCTAC-AGAGTAGA_L005


title: Cerebellum, EOD.R_rep3 (RNA-Seq)

description:
EOD_R3
fpkm_genename_Refeed_RNA.txt
fpkm_group_Refeed_RNA.txt
fpkm_sample_Refeed_RNA.txt
readcount_Refeed_RNA.txt
readcount_genename_Refeed_RNA.txt


title: RMB344

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB344_TCCTGAGC-GTAAGGAG_L005


title: Cerebellum, IF16.R_rep2 (RNA-Seq)

description:
IF_R2
fpkm_genename_Refeed_RNA.txt
fpkm_group_Refeed_RNA.txt
fpkm_sample_Refeed_RNA.txt
readcount_Refeed_RNA.txt
readcount_genename_Refeed_RNA.txt


title: RMB347

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB347_TCCTGAGC-CTAAGCCT_L005


title: Cerebellum, IF16.R_rep1 (RNA-Seq)

description:
IF_R1
fpkm_genename_Refeed_RNA.txt
fpkm_group_Refeed_RNA.txt
fpkm_sample_Refeed_RNA.txt
readcount_Refeed_RNA.txt
readcount_genename_Refeed_RNA.txt


title: cattle_low_spleen3

city: Chengdu

first: Yao

last: Ma

state: Sichuan

address: Huiming road #211

country: China

institute: Sichuan Agricultural University

data_processing:
Small RNA libraries were constructed using the Illumina TruSeq Small RNA Sample Prep kit. Libraries were assessed using the Agilent 2200 TapeStation and sequenced on the Illumina HiSeq 2500 platforms. Initial bioinformatics analysis (base calling) was performed with CASAVA 1.8 (Illumina) to generate raw reads(in FASTQ form). Next, raw reads were subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and processed sequences were then mapped to corresponding reference genome (i.e.,chicken (Galgal4), pig (Suscrofa 10.2), cattle (UMD3.1), goat (CHIR 1.0), and sheep (Oar v3.1)) for each species with stringent criteria (less than 1 mismatch along the whole sequence) using Bowtie software. Thereafter, mappable reads were submitted to miRDeep2.0 to detect miRNAs for each species with default parameters. Notably, mature miRNA sequence of chicken and all annotated mammalian species in miRbase21 were selected as reference. miRNAs with greater than or equal to 4 reads across > 40% samples were remained for further analysis.
Genome_build: chicken (Galgal4), pig (Suscrofa 10.2), cattle (UMD3.1), goat (CHIR 1.0), and sheep (Oar v3.1); miRbase 21.0
Supplementary_files_format_and_content: Identified miRNAs in each library with reads

organism: Bos taurus

source_name: spleen

extract_protocol:
Three adult females for each population of the five species from distinct altitudes (600 m, 2000 m, and 3000 m) were used (Table 1). Animals were humanely killed to ameliorate suffering. Upon excised from the corpse, a piece of tissue fragments from six organs including heart, liver, spleen, lung, kidney and skeletal muscle(longissimus muscle for pig, cattle, yak and sheep, and pectoral muscle for chicken) were placed immediately frozen in liquid nitrogen, and then stored at −80 °C until use. Of note, the skeletal muscle for pig, cattle, yak sheep were longissimus muscle, and the pectoral muscle for chicken. Total RNA were extracted using a standard TRIzol (Takara, Japan) protocol.
Small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: altitude

value: low

value: spleen

value: > 4 year

tag: group

value: Luxi cattle


title: RMB343

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB343_TCCTGAGC-AGAGTAGA_L005


title: RMB342

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB342_TCCTGAGC-TATCCTCT_L005


title: RMB340

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB340_TCCTGAGC-TAGATCGC_L005


title: Cerebellum, AL.R_rep4 (RNA-Seq)

description:
AL_R4
fpkm_genename_Refeed_RNA.txt
fpkm_group_Refeed_RNA.txt
fpkm_sample_Refeed_RNA.txt
readcount_Refeed_RNA.txt
readcount_genename_Refeed_RNA.txt


title: RMB338

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB338_AGGCAGAA-AAGGAGTA_L005


title: cattle_low_kidney2

source_name: kidney

value: kidney


title: RMB336

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB336_AGGCAGAA-GTAAGGAG_L005


title: Cerebellum, AL.R_rep5 (RNA-Seq)

description:
AL_R5
fpkm_genename_Refeed_RNA.txt
fpkm_group_Refeed_RNA.txt
fpkm_sample_Refeed_RNA.txt
readcount_Refeed_RNA.txt
readcount_genename_Refeed_RNA.txt


title: RMB339

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB339_AGGCAGAA-CTAAGCCT_L005


title: Cerebellum, AL.R_rep3 (RNA-Seq)

description:
AL_R3
fpkm_genename_Refeed_RNA.txt
fpkm_group_Refeed_RNA.txt
fpkm_sample_Refeed_RNA.txt
readcount_Refeed_RNA.txt
readcount_genename_Refeed_RNA.txt


title: cattle_low_spleen2


title: Cerebellum, IF16.R_rep3 (RNA-Seq)

description:
IF_R3
fpkm_genename_Refeed_RNA.txt
fpkm_group_Refeed_RNA.txt
fpkm_sample_Refeed_RNA.txt
readcount_Refeed_RNA.txt
readcount_genename_Refeed_RNA.txt


title: cattle_low_liver2

source_name: liver

value: liver


title: RMB332

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB332_AGGCAGAA-TAGATCGC_L005


title: RMB352

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB352_GGACTCCT-GTAAGGAG_L005


title: Cerebellum, AL.R_rep2 (RNA-Seq)

description:
AL_R2
fpkm_genename_Refeed_RNA.txt
fpkm_group_Refeed_RNA.txt
fpkm_sample_Refeed_RNA.txt
readcount_Refeed_RNA.txt
readcount_genename_Refeed_RNA.txt


title: RMB331

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB331_CGTACTAG-CTAAGCCT_L005


title: RMB328

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB328_CGTACTAG-GTAAGGAG_L005


title: RMB326

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB326_CGTACTAG-TATCCTCT_L005


title: Cerebellum, EOD_rep4 (RNA-Seq)

description:
EOD_3M4
fpkm_genename_IF_RNA.txt
fpkm_group_IF_RNA.txt
fpkm_sample_IF_RNA.txt
readcount_IF_RNA.txt
readcount_genename_IF_RNA.txt


title: cattle_low_muscle1

source_name: muscle

value: muscle


title: Cerebellum, AL.R_rep1 (RNA-Seq)

description:
AL_R1
fpkm_genename_Refeed_RNA.txt
fpkm_group_Refeed_RNA.txt
fpkm_sample_Refeed_RNA.txt
readcount_Refeed_RNA.txt
readcount_genename_Refeed_RNA.txt


title: RMB324

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB324_CGTACTAG-TAGATCGC_L005


title: Cerebellum, EOD_rep5 (RNA-Seq)

description:
EOD_3M5
fpkm_genename_IF_RNA.txt
fpkm_group_IF_RNA.txt
fpkm_sample_IF_RNA.txt
readcount_IF_RNA.txt
readcount_genename_IF_RNA.txt


title: RMB335

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB335_AGGCAGAA-AGAGTAGA_L005


title: cattle_low_liver3


title: cattle_low_spleen1


title: cattle_low_kidney1


title: RMB319

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB319_TAAGGCGA-AGAGTAGA_L005


title: RMS322

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS322_GTAGAGGA-TATCCTCT_L002


title: RMB321

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB321_TAAGGCGA-ACTGCATA_L005


title: RMB320

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB320_TAAGGCGA-GTAAGGAG_L005


title: Cerebellum, IF16_rep5 (RNA-Seq)

description:
IF_3M5
fpkm_genename_IF_RNA.txt
fpkm_group_IF_RNA.txt
fpkm_sample_IF_RNA.txt
readcount_IF_RNA.txt
readcount_genename_IF_RNA.txt


title: RMS327

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS327_GTAGAGGA-CTAAGCCT_L002


title: RMS317

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS317_AAGAGGCA-ACTGCATA_L002


title: RMB317

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB317_TAAGGCGA-CTCTCTAT_L005


title: Cerebellum, EOD_rep3 (RNA-Seq)

description:
EOD_3M3
fpkm_genename_IF_RNA.txt
fpkm_group_IF_RNA.txt
fpkm_sample_IF_RNA.txt
readcount_IF_RNA.txt
readcount_genename_IF_RNA.txt


title: RMS324

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS324_GTAGAGGA-GTAAGGAG_L002


title: Cerebellum, IF16_rep4 (RNA-Seq)

description:
IF_3M4
fpkm_genename_IF_RNA.txt
fpkm_group_IF_RNA.txt
fpkm_sample_IF_RNA.txt
readcount_IF_RNA.txt
readcount_genename_IF_RNA.txt


title: Cerebellum, EOD_rep2 (RNA-Seq)

description:
EOD_3M2
fpkm_genename_IF_RNA.txt
fpkm_group_IF_RNA.txt
fpkm_sample_IF_RNA.txt
readcount_IF_RNA.txt
readcount_genename_IF_RNA.txt


title: Cerebellum, EOD_rep1 (RNA-Seq)

description:
EOD_3M1
fpkm_genename_IF_RNA.txt
fpkm_group_IF_RNA.txt
fpkm_sample_IF_RNA.txt
readcount_IF_RNA.txt
readcount_genename_IF_RNA.txt


title: RMB323

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB323_TAAGGCGA-CTAAGCCT_L005


title: RMB322

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB322_TAAGGCGA-AAGGAGTA_L005


title: RMS316

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS316_AAGAGGCA-GTAAGGAG_L002


title: RMS320

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS320_GTAGAGGA-GCGTAAGA_L002


title: RMS315

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS315_AAGAGGCA-AGAGTAGA_L002


title: RMS314

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS314_AAGAGGCA-TATCCTCT_L002


title: Cerebellum, IF16_rep3 (RNA-Seq)

description:
IF_3M3
fpkm_genename_IF_RNA.txt
fpkm_group_IF_RNA.txt
fpkm_sample_IF_RNA.txt
readcount_IF_RNA.txt
readcount_genename_IF_RNA.txt


title: RMS313

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS313_AAGAGGCA-CTCTCTAT_L002


title: Cerebellum, IF16_rep2 (RNA-Seq)

description:
IF_3M2
fpkm_genename_IF_RNA.txt
fpkm_group_IF_RNA.txt
fpkm_sample_IF_RNA.txt
readcount_IF_RNA.txt
readcount_genename_IF_RNA.txt


title: Cerebellum, IF16_rep1 (RNA-Seq)

description:
IF_3M1
fpkm_genename_IF_RNA.txt
fpkm_group_IF_RNA.txt
fpkm_sample_IF_RNA.txt
readcount_IF_RNA.txt
readcount_genename_IF_RNA.txt


title: RMS310

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS310_CGAGGCTG-AAGGAGTA_L002


title: RMS308

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS308_CGAGGCTG-GTAAGGAG_L002


title: RMS306

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS306_CGAGGCTG-TATCCTCT_L002


title: RMS311

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS311_CGAGGCTG-CTAAGCCT_L002


title: Cerebellum, AL_rep5 (RNA-Seq)

description:
AL_3M5
fpkm_genename_IF_RNA.txt
fpkm_group_IF_RNA.txt
fpkm_sample_IF_RNA.txt
readcount_IF_RNA.txt
readcount_genename_IF_RNA.txt


title: RMS319

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS319_AAGAGGCA-CTAAGCCT_L002


title: RMS305

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS305_CGAGGCTG-CTCTCTAT_L002


title: RMS304

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS304_CGAGGCTG-GCGTAAGA_L002


title: Cerebellum, AL_rep4 (RNA-Seq)

description:
AL_3M4
fpkm_genename_IF_RNA.txt
fpkm_group_IF_RNA.txt
fpkm_sample_IF_RNA.txt
readcount_IF_RNA.txt
readcount_genename_IF_RNA.txt


title: RMS303

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS303_GCTACGCT-CTAAGCCT_L002


title: RMS301

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS301_GCTACGCT-ACTGCATA_L002


title: RMS300

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS300_GCTACGCT-GTAAGGAG_L002


title: Cerebellum, AL_rep3 (RNA-Seq)

description:
AL_3M3
fpkm_genename_IF_RNA.txt
fpkm_group_IF_RNA.txt
fpkm_sample_IF_RNA.txt
readcount_IF_RNA.txt
readcount_genename_IF_RNA.txt


title: RMS299

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS299_GCTACGCT-AGAGTAGA_L002


title: RMS294

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS294_CAGAGAGG-AAGGAGTA_L002


title: Cerebellum, AL_rep1 (RNA-Seq)

description:
AL_3M1
fpkm_genename_IF_RNA.txt
fpkm_group_IF_RNA.txt
fpkm_sample_IF_RNA.txt
readcount_IF_RNA.txt
readcount_genename_IF_RNA.txt


title: RMS293

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS293_CAGAGAGG-ACTGCATA_L002


title: RMS298

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS298_GCTACGCT-TATCCTCT_L002


title: RMS290

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS290_CAGAGAGG-TATCCTCT_L002


title: Cerebellum, AL_rep2 (RNA-Seq)

description:
AL_3M2
fpkm_genename_IF_RNA.txt
fpkm_group_IF_RNA.txt
fpkm_sample_IF_RNA.txt
readcount_IF_RNA.txt
readcount_genename_IF_RNA.txt


title: RMS292

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS292_CAGAGAGG-GTAAGGAG_L002


title: RMS288

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS288_CAGAGAGG-GCGTAAGA_L002


title: mature CD4SP, wt_msp_atac_r2

city: Shanghai

first: Yi

last: Zhong

address: 227 South Chongqing Rd.

institute: SJTU

data_processing:
Align ATAC-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ATAC-seq duplicates: Picard v1.141
Call ATAC-seq peaks: MACS2 v2.1.1
Count ATAC-seq reads: GenomicAlignments v1.2.2
Genome_build: GRCm38
Supplementary_files_format_and_content: A text file showing read counts for ATAC-seq peaks

source_name: Sorted thymocytes

growth_protocol: Thymuses were mechanically disrupted and cells were purified by FACS sorting

extract_protocol:
Nuclei were isolated by lysing cells with 0.1% NP-40.
ATAC-seq libraries were generated as published (Buenorostro et al. 2015). Briefly, nuclei were treated with tagmentation enzyme from Nextera Library Prep Kit, and DNA was purified on a Qiagen MinElute column. Libraries were amplified and sequencing adaptors were added by PCR.
HiSeq 2500 in Rapid Mode

value: CNS4-fl Foxp3-GFP

value: mature CD4SP

value: thymus


title: mature CD4SP, wt_msp_atac_r1


title: semi-mature CD4SP, wt_imsp_atac_r2

value: semi-mature CD4SP


title: RMS289

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS289_CAGAGAGG-CTCTCTAT_L002


title: RMS287

description:
Single_cell
RMS287.fastq.gz


title: RMS286

description:
Single_cell
RMS286.fastq.gz


title: semi-mature CD4SP, wt_imsp_atac_r1


title: RMS285

description:
Single_cell
RMS285.fastq.gz


title: HDF_iPS_NC_2

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

institute: Tongji Hospital, Tongji University

data_processing:
Reads of RNA-seq were aligned to human reference genome (hg19) by the spliced read aligner Hisat2(vision 2.1.0) (Kim et al., 2015). The gene abundances were estimated and normalized to fragments per kilobase per million (fpkm) using stringtie (version 2.2.1) (Pertea et al., 2015) with default settings, and read counts of genes were summarized by HTSeq (vision 0.7.2) (Anders et al., 2015).
The ultrafast, memory-efficient read aligner bowtie2 (vision 2.2.6) (Langmead et al., 2009) was used to align the reads of ChIP-seq to human reference genome (hg19). The output of bowtie2 was sorted and index by SAMtools (Li et al., 2009). Peak calling was performed by MACS2 (version 2.1.1.20160309). DeepTools (Ramírez et al., 2014) was used for alignment of reads as input and normalized to RPKM (reads per kilobase and million mapped reads).
Genome_build: hg19

growth_protocol: Human pluripotent stem cells (hPSCs) were cultured feeder free on Matrigel (BD Biosciences) in TeSR-E8 medium (Stem Cell Technologies), and their medium was changed daily. The hPSCs were passaged with Versene (Gibco) every 5-7 days. Culture conditions of stable CCDC144NL-AS1-KD and NC hPSCs were the same as that of hPSCs. Rock inhibitor Y27632 (Merck Millipore) was suggested to be added into the culture medium for 1 day at the final concentration of 10 μM during the first few passages of CCDC144NL-AS1-KD hPSCs.

extract_protocol:
For RNA-seq, total RNA of cells was extracted by RNAiso Plus (Takara), according to the manufactures’ instructions. For ChIP-seq, lysates were clarified from sonicated nuclei and histone-DNA complexes isolated with antibody
RNA libraries were prepared for sequencing using standard Illumina protocols. ChIP-seq libraries were prepared for sequencing using TruSeq Nano DNA Sample Prep Kit (Illumina), according to the manufacter's instructions.

treatment_protocol: Single cells of human pluripotent stem cell (hPSCs) were obtained through Accutase (Gibco) digestion, and Y27632 (10 μM) was added to the medium for 1 day after plating cells.Single cells of hPSCs were seeded at 50,000 cells per well on a 24-well plate the day before infection. Cells were infected with shCCDC144NL-AS1 or shNC viruses in TeSR-E8 medium supplemented with 2 μg/ml polybrene (Sigma-Aldrich), and the medium was renewed 6 hours after virus infection. Positively infected cells were isolated by adding 2 μg/ml puromycin (Life Technologies) into the culture medium 48 hours after virus infection. The concentrations and time of antibiotics utilized should be adjusted according to different cell viability.

value: human induced pluripotent stem cells

tag: condition

value: negative control

tag: passages


title: RMS283

description:
Single_cell
RMS283.fastq.gz


title: HDF_iPS_NC_3


title: RMS281

description:
Single_cell
RMS281.fastq.gz


title: HDF_iPS_NC_1


title: RMS279

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS279_TAGGCATG-CTAAGCCT_L002


title: thymic Treg, wt_foxp3_atac_r1

value: thymic Treg


title: RMS277

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS277_TAGGCATG-ACTGCATA_L002


title: cattle_low_muscle3


title: Treg precursor, wt_cd25_atac_r2

value: Treg precursor


title: RMS274

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS274_TAGGCATG-TATCCTCT_L002


title: RMS273

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS273_TAGGCATG-CTCTCTAT_L002


title: RMS270

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS270_GGACTCCT-AAGGAGTA_L002


title: HDF_iPS_CCDC144NL_AS1_KD_1

value: CCDC144NL-AS1 KD


title: RMS272

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS272_TAGGCATG-GCGTAAGA_L002


title: RRBS DKO+3bCD

city: Gainesville

first: Rene

last: Opavsky

state: FL

address: 2033 Mowry rd, CGRC r..265

department: Anatomy and cell biology

institute: University of FLORIDA

data_processing:
The input sequences were trimmed using trimmomatic. Quality control was performed before and after trimming using FastQC. The input reads were aligned to the reference genome (mm10) using bsmap. Methylation calling was performed using Methyldackel (v 0.3.0.1). Differentially methylated regions (DMRs) were determined by Metilene. DMRs were determined based on average DMC methylation change of 30 percent or greater, p-values (MWU) < 0.05, with a minimum of three DMCs represented in a maximum distance of 200bp.
For RNA-seq, trimmed sequencing data were first aligned to mm10 reference genome using STAR aligner. RNA-seq data with minimum mapped quality 50 were quantitated using the RNA-seq quantitation pipeline in SeqMonk software. Genome version used was Mus musculus GRCm38 (08/06/2012). DeSeq2 was used to calculate differential expression. For differentially expressed genes, only genes with a fold change ≥ 2 and a p-value < 0.05 were considered to be significant.
Genome_build: mm10

source_name: lymphoma cell line

extract_protocol:
For RRBS, genomic DNA was isolated from two independent Dnmt3b+/+, Dnmt3b-/- and Dnmt3bCI/CI embryos and tumor cell line using phenol/chloroform. For RNA-seq, total RNA was isolated by trizol from three independent  Dnmt3b+/+; Dnmt3b-/- and Dnmt3bCI/CI embryos.
The RRBS libraries were prepared and sequenced on an Illumina HiSeq2500 sequencer. RNA-seq was performed  on NovaSeq 6000 platform using paired-end 150bp runs.

value: FVB


title: Treg precursor, wt_cd25_atac_r1


title: HDF_iPS_CCDC144NL_AS1_KD_2


title: RMS264

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS264_GGACTCCT-GCGTAAGA_L002


title: RMS265

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS265_GGACTCCT-CTCTCTAT_L002


title: thymic Treg, wt_foxp3_atac_r2


title: RMS269

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS269_GGACTCCT-ACTGCATA_L002


title: H14_NC_3

value: human embryonic stem cells


title: H14_NC_2


title: RRBS DKO+empty vector


title: RMS261

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS261_TCCTGAGC-ACTGCATA_L002


title: H14_NC_1


title: RMS259

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS259_TCCTGAGC-AGAGTAGA_L002


title: RMS258

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS258_TCCTGAGC-TATCCTCT_L002


title: HDF_iPS_CCDC144NL_AS1_KD_3


title: RRBS 3bKI 2

source_name: whole embryo

tag: embryo stage

tag: genotype

value: Dnmt3b CI/CI


title: RMS262

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS262_TCCTGAGC-AAGGAGTA_L002


title: H14_CCDC144NL_AS1_KD_3


title: RRBS 3bKI 1


title: RMS254

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS254_AGGCAGAA-AAGGAGTA_L002


title: RMS252

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS252_AGGCAGAA-GTAAGGAG_L002


title: RMS257

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS257_TCCTGAGC-CTCTCTAT_L002


title: RRBS 3bKO 2

value: Dnmt3b -/-


title: RMS251

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS251_AGGCAGAA-AGAGTAGA_L002


title: H14_CCDC144NL_AS1_KD_2


title: H14_CCDC144NL_AS1_KD_1


title: RRBS DKO+3bWT


title: RRBS 3bKO 1


title: RMS250

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS250_AGGCAGAA-TATCCTCT_L002


title: RMS249

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS249_AGGCAGAA-CTCTCTAT_L002


title: H9_NC_3

data_processing:
Reads of RNA-seq were aligned to human reference genome (hg19) by the spliced read aligner Hisat2(vision 2.1.0) (Kim et al., 2015). The gene abundances were estimated and normalized to fragments per kilobase per million (fpkm) using stringtie (version 2.2.1) (Pertea et al., 2015) with default settings, and read counts of genes were summarized by HTSeq (vision 0.7.2) (Anders et al., 2015).
The ultrafast, memory-efficient read aligner bowtie2 (vision 2.2.6) (Langmead et al., 2009) was used to align the reads of ChIP-seq to human reference genome (hg19). The output of bowtie2 was sorted and index by SAMtools (Li et al., 2009). Peak calling was performed by MACS2 (version 2.1.1.20160309). DeepTools (Ramírez et al., 2014) was used for alignment of reads as input and normalized to RPKM (reads per kilobase and million mapped reads).
Genome_build: hg 19

growth_protocol: Human embryonic stem cells (hESCs) were cultured feeder free on Matrigel (BD Biosciences) in TeSR-E8 medium (Stem Cell Technologies), and their medium was changed daily. The hESCs were passaged with Versene (Gibco) every 5-7 days. Culture conditions of stable CCDC144NL-AS1-KD and NC hESCs were the same as that of hESCs. Rock inhibitor Y27632 (Merck Millipore) was suggested to be added into the culture medium for 1 day at the final concentration of 10 μM during the first few passages of CCDC144NL-AS1-KD hESCs.

treatment_protocol: Single cells of human embryonic stem cell (hESCs) were obtained through Accutase (Gibco) digestion, and Y27632 (10 μM) was added to the medium for 1 day after plating cells.Single cells of hESCs were seeded at 50,000 cells per well on a 24-well plate the day before infection. Cells were infected with shCCDC144NL-AS1 or shNC viruses in TeSR-E8 medium supplemented with 2 μg/ml polybrene (Sigma-Aldrich), and the medium was renewed 6 hours after virus infection. Positively infected cells were isolated by adding 2 μg/ml puromycin (Life Technologies) into the culture medium 48 hours after virus infection. The concentrations and time of antibiotics utilized should be adjusted according to different cell viability.


title: RMS246

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS246_CGTACTAG-AAGGAGTA_L002


title: RMS247

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS247_CGTACTAG-CTAAGCCT_L002


title: RRBS WT 2

value: Dnmt3b +/+


title: H9_NC_2


title: RMS245

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS245_CGTACTAG-ACTGCATA_L002


title: RRBS WT 1


title: RMS240

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS240_CGTACTAG-GCGTAAGA_L002


title: RMS242

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS242_CGTACTAG-TATCCTCT_L002


title: H9_CCDC144NL_AS1_KD_6


title: H9_NC_1


title: RMS243

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS243_CGTACTAG-AGAGTAGA_L002


title: DFL16.1JH4inv_RAG2del_GROSeq_rep3

city: Boston

first: Frederick

middle: W

last: Alt

state: MA

address: 1 Blackfan Circle

department: PCMM

institute: Boston Children's Hospital

description: aligned to modified mm9 genome with DH-JH region replaced by DFL16.1JH4 join sequence

data_processing:
Library strategy: GRO-Seq
Reads were aligned to mm9_DFL16.1JH4 genome using bowtie 2.2.8 with --non-deterministic flag
Aligned reads were separated into positive and negative strand using samtools 1.8
wig files were produced using RSeQC tool 2.6.3 and normalized to a coverage of 10 million 100nt reads for display
Genome_build: mm9_DFL16.1JH4
Supplementary_files_format_and_content: wig files contain peak information for samples

molecule: nuclear RNA

source_name: v-Abl transformed pro-B cell line

extract_protocol:
Briefly, 10 million cells were permeabilized with permeabilization buffer (10 mM Tris-HCl, pH 7.4, 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40 substitute, 0.5 mM DTT, one tablet of protease inhibitors per 50 ml and 4 units Rnase inhibitor per ml) and resuspended in 100 ul storage buffer (10 mM Tris-HCl, pHHH 8.0, 25% (vol/vol) glycerol, 5 mM MgCl2, 0.1 mM EDTA and 5 mM DTT). Permeabilized cells were subjected to nuclear run-on (2xRun-on mix: 5 mM Tris-Cl, PH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.5 mM BrUTP, 10 units of RNase inhibitor, 1% sarkosyl) at 37o for 5 min, followed by Trizol-based RNA extraction.
Illumina adapters were ligated to RNA followed by cDNA generation with reverse transcriptase.  Libraries were PCR-amplified with Illumina primers and subjected to sequencing.

treatment_protocol: 3 uM STI-571 treated for 4 days

value: v-Abl transformed pro-B cell line

value: DFL16.1JH4-inv, Emu-Bcl2, RAG2 deficient


title: RMS239

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS239_TAAGGCGA-CTAAGCCT_L002


title: DFL16.1JH4inv_RAG2del_GROSeq_rep2


title: RMS237

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS237_TAAGGCGA-ACTGCATA_L002


title: RMS238

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS238_TAAGGCGA-AAGGAGTA_L002


title: H9_CCDC144NL_AS1_KD_5


title: RMS235

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS235_TAAGGCGA-AGAGTAGA_L002


title: H9_CCDC144NL_AS1_KD_4


title: DFL16.1JH4inv_RAG2del_GROSeq_rep1

data_processing:
Library strategy: GRO-Seq
Reads were aligned to mm9_DFL16.1JH4 genome using bowtie 2.2.8 with --non-deterministic flag
Aligned reads were separated into positive and negative strand using samtools 1.8
wig files were produced using RSeQC tool 2.6.3 and normalized to a coverage of 10 million 100nt reads for display
Genome_build:mm9_DFL16.1JH4
Supplementary_files_format_and_content: wig files contain peak information for samples


title: RMS280

description:
Single_cell
RMS280.fastq.gz


title: JHdel_GROSeq_rep3

description: aligned to mm9 genome

data_processing:
Library strategy: GRO-Seq
Reads were aligned to mm9 genome using bowtie 2.2.8 with --non-deterministic flag
Aligned reads were separated into positive and negative strand using samtools 1.8
wig files were produced using RSeQC tool 2.6.3 and normalized to a coverage of 10 million 100nt reads for display
Genome_build: mm9
Supplementary_files_format_and_content: wig files contain peak information for samples

value: JH-del, Emu-Bcl2, RAG2 deficient


title: RMS234

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS234_TAAGGCGA-TATCCTCT_L002


title: RMS236

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS236_TAAGGCGA-GTAAGGAG_L002


title: RMS232

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS232_TAAGGCGA-GCGTAAGA_L002


title: JHdel_GROSeq_rep2

description: aligned to mm9 genome


title: RMS233

description:
Single_cell
HS003-SR-R00186_BC6D96ACXX.RMS233_TAAGGCGA-CTCTCTAT_L002


title: H9_CCDC144NL_AS1_KD_2


title: RMB409

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB409_GTAGAGGA-ACTGCATA_L005

source_name: Blood


title: RMB410

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB410_GTAGAGGA-AAGGAGTA_L005


title: JHdel_GROSeq_rep1

description: aligned to mm9 genome


title: H9_CCDC144NL_AS1_KD_1


title: RMB406

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB406_GTAGAGGA-TATCCTCT_L005


title: RMB401

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB401_AAGAGGCA-ACTGCATA_L005


title: RMB395

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB395_CGAGGCTG-CTAAGCCT_L005


title: Ig2bdel_DpnII_iEmubait_rep2

description: DpnII digestion, aligned to mm9 genome

data_processing:
Library strategy: 3C-HTGTS
Sequencing reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files

extract_protocol:
Briefly, 10 million cells were cross-linked with 2% formaldehyde at room temperature for 10 minutes, quenched by glycine (final 0.125M), and then lysed with cold cell lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, one tablet of protease inhibitor in 50 ml) on ice for 10 min. Nuclei were subjected to 0.3% SDS treatment (37oC, 1 hour) and 1.8% Triton X-100 treatment (37 oC, 1 hour) successively, followed by overnight digestion with indicated restriction enzyme (700 units) at 37oC. Restriction enzyme was inactivated at 65oC for 20 min and samples were subjected to ligation under diluted condition with T4 DNA ligase (100 units, NEB, M0202L). Ligated chromatin was de-crosslinked with Proteinase K (56oC, O/N) and treated with RNaseA (37oC, 1 hour). DNA was purified via phenol/chloroform extraction and resuspended in 200 ul 1XT.E. buffer. DNA templates were then subjected to 3C-HTGTS library preparation.
3C-HTGTS libraries were prepared using linear-amplification PCR-mediated HTGTS.

value: JH-del, dCas9 expressing, Ig2b-del/del, Emu-Bcl2, RAG2 deficient


title: Ig2bdel_DpnII_iEmubait_rep3

description: DpnII digestion, aligned to mm9 genome


title: Rad21_dCas9Block_rep1

description: aligned to mm9 genome

data_processing:
Library strategy: ChIP-Seq
Reads were aligned to mm9 genome using bowtie 2.2.8 with --non-deterministic flag
Unmapped reads were filtered using samtools 1.8
wig files were produced using RSeQC tool 2.6.3 and normalized to a coverage of 10 million 100nt reads for display
Peak calling was performed using MACS2 with the following commands:
macs2 callpeak -t IP.bam -c Input.bam -n Result_directory --nomodel --extsize 51 --nolambda -B --SPMR -g mm --verbose 0 --broad
Genome_build: mm9
Supplementary_files_format_and_content: wig files contain peak information for samples, bed files contain peak calling information.

extract_protocol: Briefly, 20 million cells were crosslinked in 37oC prewarmed culture medium with 1% formaldehyde for 10 min at RT.  Cells were then treated with cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% NP-40) for 10 min on ice, followed by treatment with nuclei lysis buffer (50 mM TrisCl pH 8.1, 10 mM EDTA, 1% SDS) for 10 min at RT. Chromatin was subjected to sonication with Diagenode Bioruptor at 4oC to achieve an average size of 200-300 bp (30 sec on, 30 sec off, 20 cycles with high energy input). Chromatin was then precleared with Dynabeads Protein A at 4oC for 2 hours. 1/30 lysates were kept as input and the rest were incubated with 5 ug RAD21 antibody (Abcam, ab992) overnight at 4oC.  IP samples were then captured by Dynabeads Protein A at 4oC for at least 2 hours, followed by bead washing and elution. IP and Input DNA were de-crosslinked at 65oC overnight and purified via Qiagen PCR purification columns. Purified DNA was subjected to ChIP-Seq library preparation with Illumina Truseq ChIP Sample Preparation Kit (Illumina, IP-202-1012).

value: JH-del, dCas9 expressing, Sg1-sgRNA expressing, Emu-Bcl2, RAG2 deficient


title: RMB394

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB394_CGAGGCTG-AAGGAGTA_L005


title: Ig2bdel_DpnII_iEmubait_rep1

description: DpnII digestion, aligned to mm9 genome

data_processing:
Library strategy: 3C-HTGTS
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files

extract_protocol:
Briefly, 10 million cells were cross-linked with 2% formaldehyde at room temperature for 10 minutes, quenched by glycine (final 0.125M), and then lysed with cold cell lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, one tablet of protease inhibitor in 50 ml) on ice for 10 min. Nuclei were subjected to 0.3% SDS treatment (37oC, 1 hour) and 1.8% Triton X-100 treatment (37 oC, 1 hour) successively, followed by overnight indicated restriction enzyme (700 units) digestion at 37oC. Restriction enzyme was inactivated at 65oC for 20 min and samples were subjected to ligation under diluted condition with T4 DNA ligase (100 units, NEB, M0202L). Ligated chromatin was de-crosslinked with Proteinase K (56oC, O/N) and treated with RNaseA (37oC, 1 hour). DNA was purified via phenol/chloroform extraction and resuspended in 200 ul 1XT.E. buffer. DNA templates were then subjected to 3C-HTGTS library preparation via linear amplification-mediated PCR.
3C-HTGTS libraries were prepared using linear-amplification PCR-mediated HTGTS.


title: RMB387

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB387_GCTACGCT-CTAAGCCT_L005


title: RMB392

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB392_CGAGGCTG-GTAAGGAG_L005


title: Rad21_dCas9Control_rep1

description: aligned to mm9 genome

value: JH-del, dCas9 expressing, Emu-Bcl2, RAG2 deficient


title: RMB388

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB388_CGAGGCTG-TAGATCGC_L005


title: Rad21_dCas9Control_rep2

description: aligned to mm9 genome


title: Rad21_dCas9Block_Input

description: aligned to mm9 genome

data_processing:
Library strategy: ChIP-Seq
Reads were aligned to mm9 genome using bowtie 2.2.8 with --non-deterministic flag
Unmapped reads were filtered using samtools 1.8
wig files were produced using RSeQC tool 2.6.3 and normalized to a coverage of 10 million 100nt reads for display
Genome_build: mm9
Supplementary_files_format_and_content: wig files contain peak information for samples.


title: RMB381

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB381_GCTACGCT-CTCTCTAT_L005


title: H9_CCDC144NL_AS1_KD_3


title: RMB385

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB385_GCTACGCT-ACTGCATA_L005


title: Ig2bwt_DpnII_iEmubait_rep2

description: DpnII digestion, aligned to mm9 genome


title: RMB379

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB379_CAGAGAGG-CTAAGCCT_L005


title: Rad21_dCas9Control_Input

description: aligned to mm9 genome


title: Ig2bwt_DpnII_iEmubait_rep3

description: DpnII digestion, aligned to mm9 genome


title: RMB377

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB377_CAGAGAGG-ACTGCATA_L005


title: RMB372

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB372_CAGAGAGG-TAGATCGC_L005


title: Ig2bwt_DpnII_iEmubait_rep1

description: DpnII digestion, aligned to mm9 genome


title: HL60/S4_bulk_N_rep2

description:
Raw_counts_differentiation.csv
Normalized_differentiation.csv

data_processing:
RNA-Seq quality control was initiated with Trim Galore, which was used to trim the 13bp Illumina standard adapter (‘AGATCGGAAGAGC’) by default.
Reads were mapped to hg38 human reference genome by STAR with defalut parameters.
Aligned sequencing reads were counted with intersection-strict mode in HTSeq.
Scale factors of each sample were computed using the trimmed mean of M-value (TMM) algorithm in edgeR.
Raw read counts were normalized by scale factors and then transformed into log2 counts per million reads (CPM). Genes were kept if expressed in at least three samples.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include raw and normalized read counts at the gene level for each sample

source_name: HL60/S4 cell line

tag: differentiation type

value: Neutrophil

tag: clone


title: Rad21_dCas9Block_rep2

description: aligned to mm9 genome


title: RMB371

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB371_CTCTCTAC-CTAAGCCT_L005

tag: strain


title: RMB369

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB369_CTCTCTAC-ACTGCATA_L005


title: HL60/S4_bulk_N_rep1


title: RMB368

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB368_CTCTCTAC-GTAAGGAG_L005


title: dCas9Block_DpnII_iEmubait_rep3

description: DpnII digestion, aligned to mm9 genome


title: HL60/S4_bulk_CN_rep2

value: Parental


title: RMB362

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB362_TAGGCATG-AAGGAGTA_L005


title: dCas9Block_DpnII_iEmubait_rep2

description: DpnII digestion, aligned to mm9 genome


title: RMB382

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB382_GCTACGCT-TATCCTCT_L005


title: HL60/S4_bulk_CN_rep1


title: RMB358

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB358_TAGGCATG-TATCCTCT_L005


title: RMB357

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB357_TAGGCATG-CTCTCTAT_L005


title: clone_d_N


title: clone_d_CN_rep2


title: dCas9Control_DpnII_iEmubait_rep4

description: DpnII digestion, aligned to mm9 genome


title: RMB348

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB348_GGACTCCT-TAGATCGC_L005


title: dCas9Control_DpnII_iEmubait_rep3

description: DpnII digestion, aligned to mm9 genome

extract_protocol:
Briefly, 10 million cells were cross-linked with 2% formaldehyde at room temperature for 10 minutes, quenched by glycine (final 0.125M), and then lysed with cold cell lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, one tablet of protease inhibitor in 50 ml) on ice for 10 min. Nuclei were subjected to 0.3% SDS treatment (37oC, 1 hour) and 1.8% Triton X-100 treatment (37 oC, 1 hour) successively, followed by overnight digestion with indicated restriction enzyme (700 units) at 37oC. Restriction enzyme was inactivated at 65oC for 20 min and samples were subjected to ligation under diluted condition with T4 DNA ligase (100 units, NEB, M0202L). Ligated chromatin was de-crosslinked with Proteinase K (56oC, O/N) and treated with RNaseA (37oC, 1 hour). DNA was purified via phenol/chloroform extraction and resuspended in 200 ul 1XT.E. buffer. DNA templates were then subjected to 3C-HTGTS library preparation via linear amplification-mediated PCR.
3C-HTGTS libraries were prepared using linear-amplification PCR-mediated HTGTS.


title: RMB345

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB345_GGACTCCT-ACTGCATA_L005


title: RMB346

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB346_TCCTGAGC-AAGGAGTA_L005


title: RMB351

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB351_GGACTCCT-AGAGTAGA_L005


title: RMB354

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB354_GGACTCCT-AAGGAGTA_L005


title: clone_d_CN_rep1


title: dCas9Control_DpnII_iEmubait_rep2

description: DpnII digestion, aligned to mm9 genome


title: RMB341

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB341_TCCTGAGC-CTCTCTAT_L005


title: RMB363

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB363_TAGGCATG-CTAAGCCT_L005


title: RMB337

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB337_AGGCAGAA-ACTGCATA_L005


title: RMB334

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB334_AGGCAGAA-TATCCTCT_L005


title: dCas9Control_DpnII_iEmubait_rep1

description: DpnII digestion, aligned to mm9 genome


title: clone_c_CM_rep2

description:
Raw_counts_differentiation.csv
Normalized_differentiation.csv


title: clone_c_CM_rep1


title: RMB333

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB333_AGGCAGAA-CTCTCTAT_L005


title: dCas9Block_DpnII_iEmubait_rep4

description: DpnII digestion, aligned to mm9 genome


title: clone_c_M_rep2

value: Monocyte


title: dCas9Block

description: aligned to mm9 genome

data_processing:
The paired end reads were aligned separately using BWA against the mm9 genome, PCR duplicates, low mapping quality and unligated reads were filtered, contact matrices and loops were annotated using the Juicer pipeline (Durand N.C. et al., 2016).
Genome_build: mm9
Supplementary_files_format_and_content: hic and bedpe files

extract_protocol:
Hi-C libraries were generated using the in situ Hi-C protocol based on Rao and Huntley et al. Cell 2014. Approximately 1 million cells were crosslinked to create each library. Cells were then then lysed with nuclei permeabilized while keeping them intact. DNA was then restricted  using the restriction enzyme MboI, and the overhangs filled in incorporating the biotinylated base bioU. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads. Small modifications in reagent volumes and incubation times were incorporated to optimize library quality for these cell types.

The standard Illumina library construction protocol was utilized. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina sequencing platform following the manufacturer's protocols. We sequenced 2.3B Hi-C read pairs in the control JH-del-dCas9 line, yielding 1.3B Hi-C contacts; we also sequenced 2.2B Hi-C read pairs in JH-del-dCas9-Sg1-sgRNA cells with the dCas9 impediment, yielding 1.2B Hi-C contacts.


title: RMB330

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB330_CGTACTAG-AAGGAGTA_L005


title: dCas9Block_DpnII_iEmubait_rep1

description: DpnII digestion, aligned to mm9 genome


title: RMB329

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB329_CGTACTAG-ACTGCATA_L005


title: RMB355

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB355_GGACTCCT-CTAAGCCT_L005


title: RMB327

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB327_CGTACTAG-AGAGTAGA_L005


title: clone_c_M_rep1


title: dCas9Control_HiC

description: aligned to mm9 genome


title: clone_b_CM_rep2


title: Ig2bdel_GROSeq_rep3

description: aligned to mm9 genome


title: Ig2bdel_GROSeq_rep2

description: aligned to mm9 genome


title: RMB316

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB316_TAAGGCGA-TAGATCGC_L005


title: clone_b_CM_rep1


title: Ig2bdel_GROSeq_rep1

description: aligned to mm9 genome


title: clone_b_N_rep2


title: chicken_high_heart3

organism: Gallus gallus

source_name: heart

value: high

value: heart

value: Tibetan chicken


title: chicken_high_muscle3

value: muscle


title: clone_b_CN_rep2

source_name: HL60 cell line


title: Ig2bwt_GROSeq_rep3

description: aligned to mm9 genome


title: Ig2bwt_GROSeq_rep2

description: aligned to mm9 genome


title: clone_b_N_rep1


title: chicken_high_spleen3

value: spleen


title: MKRN1 iCLIP 3

city: Mainz

first: Petra

last: Beli

address: Ackermannweg 4

institute: Institute of Molecular Biology (IMB)

description: bigwig from Illumina MiSeq

data_processing:
Library strategy: in vivo iCLIP
Basic sequencing quality checks were applied to all reads using FastQC (version 0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Afterwards, reads were filtered based on sequencing qualities (Phred score) of the barcode region. Only reads with at most one position with a sequencing quality < 20 in the experimental barcode (positions 4 to 7) and without any position with a sequencing quality < 17 in the random barcode (positions 1 to 3 and 8 to 9) were kept for further analysis. Remaining reads were de-multiplexed based on the experimental barcode on positions 4 to 7 using Flexbar (version 3.0.0) (Dodt et al., 2012) without allowing mismatches. All following steps of the analysis were performed on all individual samples after de-multiplexing. Remaining adapter sequences were trimmed from the right end of the reads using Flexbar (version 3.0.0) allowing up to one mismatch in 10 nt, requiring a minimal overlap of 1 nt of read and adapter. After trimming off the adapter, the barcode is trimmed off of the left end of the reads (first 9 nt) and added to the header of the read, such that the information is kept available for downstream analysis. Reads shorter than 15 nt were removed from further analysis. Trimmed and filtered reads were mapped to the human genome (assembly version GRCh38) and its annotation based on GENCODE release 25 (Harrow et al., 2012) using STAR (version 2.5.4b) (Dobin et al., 2013). When running STAR, up to two mismatches were allowed, soft-clipping was prohibited and only uniquely mapping reads were kept for further analysis. Following mapping, duplicate reads were marked using the dedup function of bamUtil (version 1.0.13), which defines duplicates as reads whose 5' ends map to the same position in the genome (https://github.com/statgen/bamUtil). Subsequently, marked duplicates with identical random barcodes were removed since they are considered technical duplicates, while biological duplicates showing unequal random barcodes were kept.  Resulting bam files were sorted and indexed using SAMtools (version 1.5) (Li et al., 2009). Based on the bam files, bedgraph files were created using bamToBed of the BEDTools suite (version 2.25.0) (Quinlan et al., 2010), considering only the position upstream of the 5' mapping position of the read, since this nucleotide is considered as the crosslinked nucleotide. bedgraph files were then transformed to bigWig file format using bedGraphToBigWig of the UCSC tool suite (Kent et al., 2010).
Genome_build: Genome_build: GRCh38

source_name: GFP-MKRN1 overexpression

growth_protocol: GFP-MKRN1 was transiently overexpressed in HEK293T cells for 48h.

extract_protocol:
HEK293T cells overexpressing GFP-MKRN1 were lysed in 1ml lysis buffer followed by immunoprecipitation as described on previously published protocol (Huppertz et al., 2014; Sutandy et al., 2016)
in vivo iCLIP libraries were prepared from HEK293Tcells overexpressing GFP-MKRN1 according to the previously published protocol (Huppertz et al., 2014; Sutandy et al., 2016). For immunoprecipitation, we used 20 µl slurry of GFPtrap magnetic agarose bease (Chromotek, GFP-Trap_MA) per sample. The libraries were sequenced as single-end reads on an Illumina MiSeq sequencing system.

tag: barcode

value: TACG

tag: cross-linking

tag: iped-protein


title: chicken_high_liver3

tag: tissue

value: liver

tag: age


title: chicken_high_kidney3

value: kidney


title: chicken_high_lung3

source_name: lung

value: lung


title: MKRN1 iCLIP 2

description: bigwig from Illumina MiSeq

tag: cell line

value: TATT


title: RMB325

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB325_CGTACTAG-CTCTCTAT_L005

tag: cell type

tag: markers


title: dCas9Block_GROSeq_rep3

description: aligned to mm9 genome

value: v-Abl transformed pro-B cell line


title: Ig2bwt_GROSeq_rep1

description: aligned to mm9 genome


title: clone_b_M_rep2


title: RMB318

description:
Single_cell
HS002-SR-R00152_AC5WYGACXX.RMB318_TAAGGCGA-TATCCTCT_L005


title: cattle_high_lung1a

organism: Bos grunniens

tag: altitude

value: > 4 year

value: Maiwa yak


title: chicken_high_muscle2

tag: group


title: MKRN1 iCLIP 1

description: bigwig from Illumina MiSeq

value: CGCC


title: dCas9Block_GROSeq_rep2

description: aligned to mm9 genome

value: JH-del, dCas9 expressing, Sg1-sgRNA expressing, Emu-Bcl2, RAG2 deficient


title: clone_b_M_rep1


title: chicken_high_kidney2


title: chicken_high_spleen2


title: dCas9Block_GROSeq_rep1

description: aligned to mm9 genome


title: chicken_high_liver2


title: chicken_high_lung2


title: dCas9Control_GROSeq_rep3

description: aligned to mm9 genome

value: JH-del, dCas9 expressing, Emu-Bcl2, RAG2 deficient


title: clone3_N_rep1

value: Neutrophil


title: clone_b_CN_rep1

value: Parental


title: clone3_CN_rep2


title: chicken_high_kidney1

value: high


title: chicken_high_muscle1

value: Tibetan chicken


title: dCas9Control_GROSeq_rep2

description: aligned to mm9 genome


title: chicken_high_lung1


title: chicken_high_heart1

value: heart


title: Nipbl_dCas9Block_rep2

description: aligned to mm9 genome

extract_protocol: Briefly, 20 million cells were crosslinked in 37oC prewarmed culture medium with 1% formaldehyde for 10 min at RT.  Cells were then treated with cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% NP-40) for 10 min on ice, followed by treatment with nuclei lysis buffer (50 mM TrisCl pH 8.1, 10 mM EDTA, 1% SDS) for 10 min at RT. Chromatin was subjected to sonication with Diagenode Bioruptor at 4oC to achieve an average size of 200-300 bp (30 sec on, 30 sec off, 20 cycles with high energy input). Chromatin was then precleared with Dynabeads Protein A at 4oC for 2 hours. 1/30 lysates were kept as input and the rest were incubated with 5 ug NIPBL antibody (Bethyl Laboratories, A301-779A) overnight at 4oC.  IP samples were then captured by Dynabeads Protein A at 4oC for at least 2 hours, followed by bead washing and elution. IP and Input DNA were de-crosslinked at 65oC overnight and purified via Qiagen PCR purification columns. Purified DNA was subjected to ChIP-Seq library preparation with Illumina Truseq ChIP Sample Preparation Kit (Illumina, IP-202-1012).


title: chicken_low_muscle3

value: low

value: muscle

value: Qingyuan Partridge chicken


title: chicken_high_liver1

value: liver


title: clone3_CN_rep1

extract_protocol: Illumina TruSeq Stranded Sample Preparation, Low Sample (LS) Protocol was used for the samples sequenced by Illumina HiSeq 2500. And NEBNext Ultra II Directional 162 RNA Library Prep Kit for Illumina was used for samples sequenced by Illumina NextSeq 550.


title: Nipbl_dCas9Block_rep1

description: aligned to mm9 genome


title: dCas9Control_GROSeq_rep1

description: aligned to mm9 genome


title: chicken_high_spleen1

value: spleen


title: clone2_N_rep1


title: Nipbl_dCas9Control_rep2

description: aligned to mm9 genome


title: chicken_low_heart3


title: clone3_N_rep2


title: chicken_high_heart2


title: chicken_low_kidney3

value: kidney


title: chicken_low_spleen3


title: Nipbl_dCas9Control_rep1

description: aligned to mm9 genome

value: v-Abl transformed pro-B cell line


title: clone2_N_rep2


title: clone2_CN_rep1


title: Nipbl_dCas9Block_Input

description: aligned to mm9 genome

value: JH-del, dCas9 expressing, Sg1-sgRNA, Emu-Bcl2, RAG2 deficient


title: clone1_N_rep2


title: clone2_CN_rep2


title: Nipbl_dCas9Control_Input

description: aligned to mm9 genome


title: chicken_low_muscle2


title: Rad21_Ig2bdel_rep3

description: aligned to mm9 genome

data_processing:
Library strategy: ChIP-Seq
Reads were aligned to mm9 genome using bowtie 2.2.8 with --non-deterministic flag
Unmapped reads were filtered using samtools 1.8
wig files were produced using RSeQC tool 2.6.3 and normalized to a coverage of 10 million 100nt reads for display
Peak calling was performed using MACS2 with the following commands:
macs2 callpeak -t IP.bam -n Result_directory --nomodel --extsize 51 --nolambda -B --SPMR -g mm --verbose 0 –broad
Genome_build: mm9
Supplementary_files_format_and_content: wig files contain peak information for samples, bed files contain peak calling information.

value: JH-del, dCas9 expressing, Ig2b-del/del, Emu-Bcl2, RAG2 deficient


title: clone1_N_rep1


title: clone1_CN_rep2


title: chicken_low_heart2


title: chicken_low_kidney2


title: Rad21_Ig2bdel_rep2

description: aligned to mm9 genome


title: clone_a_N_rep2


title: Rad21_Ig2bdel_rep1

description: aligned to mm9 genome


title: chicken_low_spleen2


title: Rad21_Ig2bwt_rep3

description: aligned to mm9 genome


title: chicken_low_liver2


title: Rad21_Ig2bwt_rep2

description: aligned to mm9 genome


title: chicken_low_liver3


title: clone_a_CN_rep2


title: Rad21_Ig2bwt_rep1

description: aligned to mm9 genome


title: clone_a_CN_rep1


title: clone1_CN_rep1


title: clone_a_N_rep1


title: K21FC.4H8

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

data_processing:
Demultiplexed FASTQ files were aligned to the mouse genome (mm10 build) using STAR version 2.5.2 (Dobin et al., 2013) with default options.
Reads aligned to each gene were counted using featureCounts version 1.5.1 (Liao et al., 2014)
Filtered out cells outside the limits of median ± 4 * median absolute deviations for both reads number and genes detected; and excluded cells with more than 10% of reads aligning to mitochondrial genes
Further downstream processing was performed using Seurat (version 2.3.1 (Butler et al., 2018)) and Monocle2 (version 2.6.4 (Qiu et al., 2017a, 2017b; Trapnell et al., 2014))
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files of raw count data
Supplementary_files_format_and_content: tab-delimited text files of normalised count data (log normalised, scaled by 10000)

source_name: Cortex

growth_protocol: 3, 6 and 12 month old time points: homozygous AppNL-G-F (Saito et al., 2014) mice, backcrossed for at least 2 generations with C57Bl/6 mice in the De Strooper lab ; Wild type C57Bl/6 mice. 21 month old time point: AppNL-G-F and C57Bl/6 mice were transferred from the Saido lab to the De Strooper lab, and housed at least 1 month before being used for experiments.

extract_protocol:
The dissection and microglia isolation steps were carried out on ice or at +4°C. Cortex and hippocampus were dissected and finely chopped, and transferred to a tuve containing ice-cold Hibernate A medium without phenol red. Single cell suspension prepared using the Adult Brain Dissociation kit. Single live microglia cells (CD11b+/DAPI-) were sorted using BD FACSAria III
Single cell retrotranscription and preparation of sequencing libraries was performed using a modified SmartSeq2 protocol (Picelli et al., 2013, 2014; Trombetta et al., 2014). We used 5’-biotinylated primers throughout the protocol

tag: ngene

tag: numi

tag: percentmito

tag: Sex

value: Female

tag: plate

tag: lane

tag: set


title: chicken_low_muscle1

data_processing:
Small RNA libraries were constructed using the Illumina TruSeq Small RNA Sample Prep kit. Libraries were assessed using the Agilent 2200 TapeStation and sequenced on the Illumina HiSeq 2500 platforms. Initial bioinformatics analysis (base calling) was performed with CASAVA 1.8 (Illumina) to generate raw reads(in FASTQ form). Next, raw reads were subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and processed sequences were then mapped to corresponding reference genome (i.e.,chicken (Galgal4), pig (Suscrofa 10.2), cattle (UMD3.1), goat (CHIR 1.0), and sheep (Oar v3.1)) for each species with stringent criteria (less than 1 mismatch along the whole sequence) using Bowtie software. Thereafter, mappable reads were submitted to miRDeep2.0 to detect miRNAs for each species with default parameters. Notably, mature miRNA sequence of chicken and all annotated mammalian species in miRbase21 were selected as reference. miRNAs with greater than or equal to 4 reads across > 40% samples were remained for further analysis.
Genome_build: chicken (Galgal4), pig (Suscrofa 10.2), cattle (UMD3.1), goat (CHIR 1.0), and sheep (Oar v3.1); miRbase 21.0
Supplementary_files_format_and_content: Identified miRNAs in each library with reads


title: ein6-1 een-1_10d_seedlings_H3K27me3

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
histone modification
ein6een_seedling_K27_IgG.bw

data_processing:
base-calling using RTA 2.7.7; alignment using Bowtie2 2.1.0; bam file comparison using deepTools2.0/bamCompare
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: de-etiolated seedlings

growth_protocol: etiolated seedlings were grown on Linsmaier and Skoog medium supplemented with 1% sucrose

extract_protocol:
Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hydrocarbon-free air for three days, 4 hours of ethylene treatment when indicated

value: de-etiolated seedlings

tag: treatment

value: no

tag: genotype

value: ein6-1 een-1

tag: antibodies

value: H3K27me3 (Active Motif, 39156)


title: HL60_bulk_N_rep1

tag: differentiation type

value: Neutrophil

tag: clone


title: HL60_bulk_N_rep2


title: Nucleated cells excluding tumor cells from MPE of WT mice, biological rep3

city: Beijing

first: Xin-Yu

last: Shi

address: Gongti Nan Road

institute: Beijing Chao-yang hospital

description: Gene expression data from  MPE of WT and IL-10-/- mice

hyb_protocol: 21.5 μL biotin-labeled sample were hybridized for 16 hr at 48℃ on miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol. （Affymetrix® Command Console® User Manual (P/N 702569)）

data_processing: Use Expression Console software for data summarization, normalization, and quality control.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (FlashTag™ Biotin HSR RNA Labeling Kit, Affymetrix).

growth_protocol: Ten days after injection of MC38 cells, mice were euthanized by CO2 asphyxiation, and MPE samples were collected and then centrifuged at 400 × g for 6 minutes.

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

treatment_protocol: The cell pellets of MPE were resuspended in PBS, and mononuclear cells were isolated by Ficoll-Hypaque gradient centrifugation (Pharmacia, Uppsala, Sweden) within 1 hour. Viable cells excluding tumor cells were sorted by means of BD Aria II flow cytometry (BD Bioscience).

tag: gender

value: Male

tag: genotype/variation

value: WT


title: Nucleated cells excluding tumor cells from MPE of IL-10-/- mice, biological rep2


title: Nucleated cells excluding tumor cells from MPE of IL-10-/- mice, biological rep3


title: Ler_10d_seedlings_H3K27me3

description:
histone modification
Ler_seedling_K27_IgG.bw

tag: tissue

value: Ler


title: chicken_low_lung2

tag: altitude

value: low

value: lung

tag: age


title: chicken_low_kidney1

tag: group

value: Qingyuan Partridge chicken


title: Nucleated cells excluding tumor cells from MPE of WT mice, biological rep1


title: HL60_bulk_CN_rep2

value: Parental


title: Nucleated cells excluding tumor cells from MPE of WT mice, biological rep2


title: chicken_low_heart1

value: heart


title: EIN6_ZNF_DAP-seq

source_name: flowers

growth_protocol: flowers

extract_protocol:
Bartlett et al. 2017 DOI:10.1038/nprot.2017.055
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: flowers

value: HALO (Promega, G9211)


title: Cell: dHL60_uninfected_1h

city: Suita

first: Masaya

last: Yamaguchi

state: Osaka

address: 1-8, Yamadaoka

department: Graduate School of Dentistry

country: Japan

institute: Osaka University

hyb_protocol: We followed protocol of manual that is FlashTag™ Biotin HSR RNA Labeling Kit User Manual.

scan_protocol: We followed manufacturer's protocol, and used GeneChip® Scanner 3000 7G.

data_processing: Data acquisition and normalization (RMA+DABG) were used Affymetrix® Expression Console™ Software.

source_name: Neutrophil-like differentiated HL-60 cell, uninfected, 1 h

extract_protocol: Total RNA including micro RNA was purified with miRNeasy Mini kit.

treatment_protocol:
HL-60 cells were maintained in RPMI 1640 medium supplemented with 10% FBS, and were incubated at 37˚C in 5% CO2. HL-60 cells were differentiated into neutrophil-like cells (dHL-60) for 5 days in culture media containing 1.2% DMSO.
Bacterial cells and/or rPfbA were incubated with differentiated HL-60 cells for 1 h at 37˚C in a 5% CO2 atmosphere.

tag: cell line

tag: cell type

value: Human promyelocytic leukemia cells (HL-60)


title: T4pfbA: dHL60_T4pfbAKO_infected_1h

source_name: Neutrophil-like differentiated HL-60 cell, S. pneumoniae TIGR4 pfbA mutant strain-infected, 1 h

label_protocol: We followed protocol of manual that is FlashTag™ Biotin HSR RNA Labeling Kit User Manual.


title: HL60_bulk_CN_rep1


title: ATF4 overexpression rep 3

city: London

middle: Matthew

last: Bateman

address: Cutcombe Road

department: Basic & Clinical Neuroscience

institute: King's College London

data_processing:
Illumina NextSeq 500 RTA v2 used for base calling.
Adaptors were automatically trimmed from the reads by the NextSeq 500, but a check for residual untrimmed adaptors was performed by FastQC (Galaxy Version 0.52), accessed via the user interface software Galaxy (UseGalaxy.org). RNA reads were then aligned to the dm6 genome using Bowtie2 (Galaxy Version 2.3.4.2) with default settings.
Raw fragment counts were compiled by FeatureCounts (Galaxy Version 1.6.3+galaxy2), accessed via the user interface software Galaxy (UseGalaxy.org), with default settings.
Differential gene expression was assessed via DESeq2 (Galaxy Version 2.11.40.6), accessed via UseGalaxy.org, with default settings.
Genome_build: dm6
Supplementary_files_format_and_content: Excel spreadsheets containing base means, log2(fold change), fold changes, standard errors, Wald statistics, p-values and adjusted p-values for each pair of samples.

organism: Drosophila melanogaster

source_name: Central nervous system

growth_protocol: Larvae were grown on standard fly food at 25 degrees celsius.

extract_protocol:
For each replicate, the complete CNS from 20 wandering third instar larvae were dissected in PBS and then transferred into 100ul of lysis buffer (with β-mercaptoethanol) from the Absolutely RNA Microprep kit (Stratagene) and vortexed for 5 seconds. Total RNA was then prepared using this kit. For each genotype RNA samples were prepared in quadruplicate and stored at -80 degrees celsius.
RNA samples were couriered on dry ice to the Glasgow Polyomics facility (University of Glasgow), where polyA cDNA libraries were constructed using the TruSeq Stranded mRNA Kit (Illumina).

treatment_protocol: One control and three experimental genotypes were used: Control (nsybGal4/+), Experimental group 1: TFAM3M (nsybGal4>UAS-TFAM3M), Experimental group 2: TFAM3M, ATF4 RNAi (nsybGal4>UAS-TFAM3M, UAS-ATF4 RNAi), Experimental group 3: ATF4 overexpression (nsybGal4>UAS-ATF4-HA).

tag: developmental stage

value: Late third instar larvae


title: Nucleated cells excluding tumor cells from MPE of IL-10-/- mice, biological rep1


title: rPfbA: dHL60_rPfbA_addition_1h

source_name: Neutrophil-like differentiated HL-60 cell, rPfbA-added, 1 h


title: chicken_low_liver1

source_name: liver

extract_protocol:
Three adult females for each population of the five species from distinct altitudes (600 m, 2000 m, and 3000 m) were used (Table 1). Animals were humanely killed to ameliorate suffering. Upon excised from the corpse, a piece of tissue fragments from six organs including heart, liver, spleen, lung, kidney and skeletal muscle(longissimus muscle for pig, cattle, yak and sheep, and pectoral muscle for chicken) were placed immediately frozen in liquid nitrogen, and then stored at −80 °C until use. Of note, the skeletal muscle for pig, cattle, yak sheep were longissimus muscle, and the pectoral muscle for chicken. Total RNA were extracted using a standard TRIzol (Takara, Japan) protocol.
Small RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver


title: T4WT: dHL60_T4WT_infected_1h

source_name: Neutrophil-like differentiated HL-60 cell, S. pneumoniae TIGR4 wild type-infected, 1 h