title: P14_1_F24


title: P14_1_G18

status: Public on Apr 22 2021

type: SRA

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

library_source: transcriptomic

data_processing:
Basecalls performed using illumina's bcl2fastq
Sequenced reads were trimmed for adaptor sequence, low complexity and low quality sequences. Then reads were aligned to Ensembl GRCm38.p5 genome assembly using STAR 2.6.1c with following parameters: '--outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif'
Counts were generated by Rsubread 1.32.4
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: count file was generated by 'featureCounts' from Rsubread package. The numbers are raw counts.

molecule: total RNA

organism: Mus musculus

source_name: Sciatic nerve

tag: biological replicate

tag: cell type

value: Schwann cells

tag: age

value: postnatal day 14


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title: P1_1_J03


title: P1_1_I23


title: P1_1_J02


title: P1_1_I22


title: P1_1_I21


title: P1_1_I20


title: P1_1_I19


title: P1_1_I17


title: P1_1_J10


title: P1_1_I18


title: P1_1_I15


title: P1_1_I13


title: P1_1_I14


title: P1_1_I12


title: P1_1_I08


title: P1_1_I10


title: P1_1_I09


title: P1_1_J05


title: P1_1_I05


title: P1_1_I06


title: P1_1_I04


title: P1_1_I03


title: P1_1_J01


title: DNase-seq from S2 (ENCLB005UWT)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR834VXA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR834VXA
assay title: DNase-seq
encode release date: 2014-03-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB005UWT

library_source: genomic

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

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Drosophila melanogaster strain Oregon-R S2 cell line

extract_protocol: not provided

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: not collected

tag: dev stage

value: unknown

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: John Stamatoyannopoulos

tag: link

value: ENCBS826KGJ at ENCODE; https://www.encodeproject.org/ENCBS826KGJ/

value: Derived from ENCODE donor ENCDO995VAO; https://www.encodeproject.org/ENCDO995VAO/


title: P1_1_I24


title: P1_1_I02


title: P1_1_I01


title: P1_1_H24


title: P1_1_H23


title: ATAC-seq from thoracic aorta (ENCLB573HMC)

description:
https://www.encodeproject.org/experiments/ENCSR344ZTM/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human thoracic aorta
experiment encode accession: ENCSR344ZTM
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-06-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB573HMC
size range: 150-250

organism: Homo sapiens

source_name: Homo sapiens male adult (54 years) thoracic aorta tissue

value: thoracic aorta

value: tissue

value: male

value: adult

value: 54 year

value: Michael Snyder, Stanford

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS532TUO at ENCODE; https://www.encodeproject.org/ENCBS532TUO/


title: P1_1_H22


title: P1_1_I16


title: P1_1_H21


title: P1_1_H20


title: ATAC-seq from thoracic aorta (ENCLB508SCY)

description:
https://www.encodeproject.org/experiments/ENCSR344ZTM/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human thoracic aorta
experiment encode accession: ENCSR344ZTM
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-06-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB508SCY
size range: 150-250


title: P1_1_H19


title: P1_1_H18


title: P1_1_I07


title: P1_1_H17


title: P1_1_H14


title: P1_1_H11


title: P1_1_H13


title: P1_1_H12


title: P1_1_H08


title: P1_1_H09


title: P1_1_H15


title: P1_1_H10


title: P1_1_I11


title: P1_1_H07


title: P1_1_H06


title: P1_1_H05


title: Th17 without IL1b 5 days donor 5

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2015_1 were also provide

source_name: CD4+ T cells isolated from Peripheral blood mononuclear cells

growth_protocol: Peripheral blood mononuclear cells were isolated by Ficoll gradient centrifugation from whole blood of healthy donors. After isolation, the cells were stained with anti-CD4 FITC (Miltenyi Biotec), anti-CD45RA BV421 (BD Biosciences), anti-CD45RO PE (BD Biosciences), anti-CD27 APC (Beckman Coulter), and then sorted by MoFlo high-speed cell sorter (Coulter) as CD4high, CD45RAhigh, CD45RO- and CD27+.

extract_protocol:
Total RNA was isolated and Dnase treated with ReliaPrep RNA Cell - Miniprep System (Promega).
Library was prepared using the TruSeq Stranded total RNA kit protocol (Illumina technology).

treatment_protocol: Th17 differentiation: CD4+ T cells were cultured in 96-well plates at a density of 50000 per well, in X-VIVO 15 serum free medium (Lonza), in presence of Dynabeads CD3/CD28 T cell expander (1 bead per cell) (Life Technologies) and cytokines: IL-1β (10 ng/ml), IL-6 (20 ng/ml), TGF-β (1ng/ml), IL- 23 (100 ng/ml) (Miltenyi Biotec). For “Regulatory-Th17” differentiation IL-1β was omitted. The cells were harvested after 48 hours or 5 days of incubation under stable conditions (temperature 37°C with 5% of CO2).

tag: differentiation condition

value: Th17 differentiated without IL-1ββ

tag: differentiation timing

value: 5 days


title: Th17 without IL1b 48h donor 5


title: Th0 5 days donor 5

value: unpolarised


title: P1_1_H04


title: Th17 48h donor 5

value: Th17 differentiated


title: P1_1_H16


title: P1_1_H01


title: Th0 48h donor 5


title: P1_1_H02


title: Th0 5 days donor 4


title: Th17 without IL1b 5 days donor 4


title: P1_1_G23


title: Th17 without IL1b 48h donor 4


title: Th17 5days donor 5


title: Th17 5days donor 4


title: P1_1_G22


title: Th17 48h donor 4


title: P1_1_G20


title: P1_1_G18


title: Th0 48h donor 4


title: P1_1_H03


title: Th17 without IL1b 5 days donor 3


title: P1_1_G19


title: P1_1_G16


title: Th17 5days donor 3


title: Th17 48h donor 3


title: Th17 without IL1b 48h donor 3


title: Th17 without IL1b 5 days donor 2


title: P1_1_G13


title: Th0 5 days donor 2


title: P1_1_G11


title: P1_1_G17


title: Th17 5days donor 2


title: P1_1_K07


title: P1_1_G15


title: P1_1_G14


title: Th17 48h donor 2


title: Th17 without IL1b 48h donor 2


title: P1_1_G21


title: Th0 48h donor 2


title: Th0 48h donor 3


title: P1_1_G12


title: P1_1_G09


title: P1_1_G07


title: Th17 without IL1b 48h donor 1


title: Th0 5 days donor 1


title: Th17 without IL1b 5 days donor 1


title: P1_1_G04


title: P1_1_G10


title: P1_1_G03


title: P1_1_F24


title: P1_1_F23


title: P1_1_G01


title: P1_1_G08


title: DIV10 SOX5

city: Pisa

first: Federico

last: Cremisi

address: Piazza dei Cavalieri, 7

department: Science

country: Italy

institute: Scuola Normale

description:
pool of 3 independent experiments
ARA_SOX_EMBRYO_RPM_counts.csv

data_processing:
FASTQ demultiplexing  (CASAVA v.1.8, Illumina)
Quality control check (FastQC algorithm)
Adapters trimming  (Cutadapt v1.2.1)
Clustering by unique hits and mapping to pre-miRNA sequences (miRExpress tool v 2.1.3 5)
Genome_build: miRBase release 21
Supplementary_files_format_and_content: .csv data files (read counts)

source_name: Neural progenitor cells

growth_protocol: Murine ESC lines E14Tg2A (passages 25-38) and 46 C (transgenic Sox1-GFP ESCs kindly provided by A. Smith, University of Cambridge, UK, passages 33–39) were differentiated in Chemically defined minimal medium (CDMM) under Wnt and BMP inhibition for 11 days in vitro (DIV), from DIV0 to DIV11, and then maintained in culture in minimal medium until the DIV of analysis. CDMM composition: DMEM/F12 (21331-046, ThermoFisher Scientific), 2mM Glutamine, 1mM sodium Pyruvate, 0.1Mm NEAA, 0.05mM β-mercaptoethanol, 100 U/ml Penicillin/Streptomycin, N-2 Supplement (175020, ThermoFisher Scientific), B-27 Supplement minus Vitamin A (125870, ThermoFisher Scientific), 2.5μM 53AH Wnt inhibitor (C5324-10, Cellagen Technology),  0.25μM BMP inhibitor (SML0559, Sigma Aldrich). Minimal medium composition: Neurobasal (ThermoFisher Scientific), 2mM Glutamine, 1mM sodium Pyruvate, 0.1Mm NEAA, 0.05mM β-mercaptoethanol, 100 U/ml Penicillin/Streptomycin, B-27 Supplement.

extract_protocol:
miRNeasy Mini Kit (217004, QIAGEN)
Small-RNA libraries were prepared using TruSeq Small RNA Sample Preparation Kit (RS-200-0012/24/36, Illumina)

treatment_protocol: Dividing progenitors were isolated by FACS sorting 46 C cells and post-mitotic precursors were obtained by Aracytin (ARA C) treament of  E14Tg2A cells 24hr before analysis (see Bertacchi et al., 2015; DOI 10.1002/dneu.22209). E14Tg2A cell extracts were hybridized with Dig-labeled “odd” and “even” probes to Satb2 3’UTR to pull-down microRNA-mRNA complexes for enriched miRNAome analysis (miR-CATCHv2.0, Marranci et al., 2019, https://doi.org/10.1080/15476286.2019.1600934).

value: ESC-derived neural progenitor cells

tag: strain

tag: Stage

tag: treatment

value: FACS sorting


title: Th17 5days donor 1


title: P1_1_G06


title: DIV10 SOX3


title: DIV10 SOX1


title: P0 cortex

description:
pool of three animals
ARA_SOX_EMBRYO_RPM_counts.csv

source_name: Mouse cortex

value: cerebral cortex

value: untreated


title: P1_1_F18


title: E12 cortex


title: P1_1_F16


title: DIV26 ARAC

value: ARA C


title: P1_1_F15


title: P1_1_G05


title: Th17 48h donor 1


title: DIV20 ARAC


title: DIV12 cells miR-CATCH rep 3

value: MiR-CATCH even probe


title: DIV18 cells miR-CATCH rep 3

value: MiR-CATCH odd probe


title: P1_1_F10


title: P1_1_G02


title: DIV10 SOX2


title: DIV10 SOX4


title: P1_1_F07


title: P1_1_F20


title: P1_1_F21


title: P1_1_F19


title: Th0 48h donor 1


title: DIV16 ARAC


title: P1_1_F22


title: DIV10 ARAC


title: P1_1_F17


title: DIV18 cells rep3


title: DIV12 ARAC


title: DIV18 cells miR-CATCH rep 4


title: P1_1_F11


title: DKO_RNA-seq_Rep2

city: Washington

first: Samuel

last: Rivero-Hinojosa

state: District of Columbia

address: 111 Michigan Ave NW

department: Children’s Research Institute, Center for Cancer and Immunology Research

institute: Children’s National Health System

description: ribosomal depleted RNA

data_processing: RNA-seq FASTQ files were mapped to UCSC mouse reference (build mm9) using two-step alignments. First, the reads were aligned with TopHat2. Second, the unmapped reads from the first step are then extracted and aligned with Bowtie2 with –local mode and --very-sensitive-local option. The resulting aligned reads (BAM files) were then analyzed with Cufflinks 2.0.0 to estimate the transcripts relative abundance using the UCSC reference annotated transcripts (build mm9). The expression of each transcript was quantified as the number of reads mapping to a transcript divided by the transcript length in kilobases and the total number of mapped reads in millions (FPKM). Diferentyally expressed genes (DEG) were obtained with the R package DESeq2. The genes with an p-adjusted < 0.001 and Fold change > 2 were consider as significant differentially expressed genes. Chip-seq sequences generated by the Illumina genome analyzer (50bp reads) were aligned against mouse (build mm9) genome using Bowtie program (http://bowtie-bio.sourceforge.net).  The alignment was performed with default parameters except the sequence tags that mapped to more than one location in the genome were excluded from the analysis using –m1 option. Peaks were called using Model-based Analysis for ChIP-Seq (MACS) (http://liulab.dfci.harvard.edu/MACS) using default parameters. After MACS, we applied Peak Splitter algorithm (part of MACS) to call sub-peaks, summit of peaks and improve peak resolution

source_name: Mouse male germ cells

extract_protocol:
Germ cells enriched preparations were prepared as follows. Decapsulated testes were treated with collagenase to digest interstitial tissue and release single tubules in suspension. The tubules were next treatment with trypsin to generate a germ cells enriched single cells suspension. The supernatant were then filtered in PVDF 100 um filter to discard tissue debris and washed with PBS. In order to obtain a better cell representation of the phenotypes observed, we included 4 different mice in each germ cells preparation.For RNA-seq, rRNA-depleted RNA from 3 independents germ cells preparations (4 mice in each preparation) was prepared using the RiboMinus Eukaryote System v2 kit (Life Technologies) according to the manufacture recommendations.For Chip-seq, germ cells enriched preparations were obtained as described before.  60 million cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1x PBS, and resuspended in ChIP lysis buffer (150 mM NaCl, 1% Triton X‐100, 0.1% SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to an average length of 200–500 bp using a Bioruptor sonication. After overnight incubation with DiaMag magnetic beads (Diagenode, Inc.) and antibodies, precipitated chromatin was then washed, decrosslinked, and digested with proteinase K.  The resulting DNA was purified using phenol/chloroform/isoamyl alcohol. DNA concentration was assessed with Quant‐it PicoGreen dsDNA kit (Invitrogen) and 5–10 ng was used to generate sequencing libraries. For CTCF Chip-seq, we used an equimolar mix of CTCF C-terminus commercial antibody were used (anti-CTCF B-5(sc-271514) and C-20 (sc-15914)) from Santa Cruz; Anti-CTCF (D3H2) from cell signaling: anti-CTCF (07-727) from Millipore: anti-CTCF (70303) from Abcam: anti-CTCF (A300-543A) from Bethyl and anti-CTCF (NB500-177 and NB500-194) from Novus. For Pol2 Chip-seq, we used the Anti-Pol2(4H8) antibodies from Abcam (ab5408). For H3K4m3 Chip-seq, we used the  Anti-H3 (tri methyl K4) antibodies from Abcam (ab8580)
For RNA-seq Ion Torrent libraries, 500 ng of rRNA-depleted RNA was used for library preparation using the Ion Total RNA-seq v2 kit. The enriched libraries were diluted to a final concentration of 11 pM and subjected to sequencing from a single end in Ion Proton Sequencer. ChIP DNA was amplified using TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA). Briefly, the immunoprecipitated material was end-repaired, A-tailed, ligated to the sequencing adapters, amplified by 15 cycles of PCR, and size selected (200–400 bp) followed by single end sequencing on an Illumina Genome Analyzer according to the manufacturer's recommendations

tag: tissue

value: Testis

tag: genotype

value: DKO

value: 3 months


title: DKO_RNA-seq_Rep1

description: ribosomal depleted RNA


title: DIV18 cells rep1

tag: cell type


title: BORIS-ko_RNA-seq_Rep3

description: ribosomal depleted RNA

value: BORIS KO

tag: age


title: DIV12 cells miR-CATCH rep 2


title: DIV12 cells miR-CATCH rep 1


title: P1_1_F09

tag: technical run


title: P1_1_F08


title: DIV18 cells miR-CATCH rep 2


title: P1_1_F04


title: BORIS-ko_RNA-seq_Rep2

description: ribosomal depleted RNA


title: DIV18 cells miR-CATCH rep 1


title: DIV12 cells rep3


title: P1_1_F13


title: P1_1_F06


title: BORIS-ko_RNA-seq_Rep1

description: ribosomal depleted RNA


title: CTCF_het_RNA-seq_Rep2

description: ribosomal depleted RNA

value: CTCF het


title: P1_1_F14


title: P1_1_F01


title: WT_RNA-seq_Rep3

description: ribosomal depleted RNA

value: WT


title: DIV18 cells rep2


title: DKO_RNA-seq_Rep3

description: ribosomal depleted RNA


title: P1_1_F05


title: P1_1_E23


title: P1_1_E22


title: P1_1_E21


title: rrf3_mutant_dt7_R2_sRNA-seq

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 4eme Etage

department: Development and stem cell biology

institute: Institut Pasteur

description:
ego-1 RNAi in WT N2 and rrf-3 mutant experiment
total sRNA

data_processing:
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) was trimmed from the raw reads using cutadapt (version 1.18)
The trimmed reads were sorted by sequence using fastq-sort (from fastq-tools version 0.8) with option -s and deduplicated using a custom haskell program, keeping the highest quality among duplicates, at any given position
The 5' and 3' 4 nt UMIs were removed from the deduplicated reads using cutadapt (version 1.18) with options -u 4 and -u -4
After removing UMIs, the reads from 18 to 24 nt were selected using bioawk version 20110810 (git commit fd40150b7c557da45e781a999d372abbc634cc21)
The size-selected reads were mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with options -L 6 -i S,1,0.8 -N 0
The reads that failed to map were inspected using grep -E -B 1 -A 2 "^G[ACGTN]{20,25}T+$" to detect possible reads starting with G with 20 to 25 nt followed by a poly-U tail that might have prevented the mapping, and this tail was removed from such reads using a custom haskell program before re-mapping them.
Mapped and remapped reads were used to estimate the abundance of small RNAs derived from structural RNAs using featureCounts (version 1.6.3) with options -O -s 1 --fracOverlap 1 and annotations corresponding to tRNA, snRNA, snoRNA, rRNA or RNA (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The abundance of non-structural RNAs was estimated by subtracting the above counts from the number of mapped and remapped reads.
Initially mapped reads were classified using a custom python program according to their length, composition and on the annotations on which they mapped. Reads that didn't match miRNA and piRNA annotations were considered as potential endo-siRNAs.
The potential endo-siRNAs of size 21 to 23 nt that started with G were classified as “si_22G” if they mapped antisense to annotation belonging to the following categories: DNA transposons, RNA transposons, satellites, simple repeats (as annotated in http://hgdownload.cse.ucsc.edu/goldenPath/ce11/database/rmsk.txt.gz) or pseudogene or protein-coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The “si_22G” reads were re-mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with options -L 6 -i S,1,0.8 -N 0
The resulting alignment was used to generate the normalized bigwig file using millions of non-structural RNAs as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.35) and bedGraphToBigWig (version 4)
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of “si_22G” RNAs along the genome

organism: Caenorhabditis elegans

source_name: nematodes

growth_protocol: Strains were maintained at 20°C, using standard methods (Brenner, 1974).

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food or otherwise described in treatment protocol , at a density of maximum 40,000 animals per 15 cm Petri dish. Worms were carefully monitored using a stereomicroscope and sorted using COPAS bio sorter at 44 h to enrich for late L4 stage larval population. Sorted worms were frozen in dry ice with Trizol reagent (Ambion). After five repetitions of freeze and thaw in dry ice, total RNA was isolated according to the Trizol Reagent protocol. Agilent 2200 TapeStation System was used to evaluate the RIN indexes of all the RNA preps, and only samples with RIN > 8 was used for downstream applications. 6 µg of total RNAs with RIN > 8 was size selected from 15% UREA PAGE gel and used to generate small RNA libraries.
The library preparation was performed as essentially described by Jayaprakash et al., 2011, except that a 5’ polyphosphatase (Lucigen RP8092H) treatment was performed to be able to clone tri-phosphate small RNAs, and that the PAGE gel extraction after each ligation was substitute with purification by 1.8 volumes of Agencourt RNAClean XP Beads (Beckman Coulter, NC0068576) and 3 volumes of isopropanol. The multiplexed amplified libraries were further purified using PippinPrep DNA size selection with 3% gel cassettes and the following parameters for the selection: BP start (115) and the BP end (165). The purified libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced either on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005).

treatment_protocol: For experiment "ego-1 RNAi in WT N2 and rrf-3 mutant", synchronised worms were grown on NGM plates containing IPTG and seeded with bacteria either containing control RNAi vector or ego-1 RNAi clone from Ahringer library from L1 to 44 h.

value: whole worm

tag: developmental stage

value: Late L4 larval stage

value: control RNAi from L1 to 44h


title: CTCF_het_RNA-seq_Rep3

description: ribosomal depleted RNA


title: P1_1_F02


title: CTCF_het_RNA-seq_Rep1

description: ribosomal depleted RNA


title: P1_1_F03


title: KO,Control

type: RNA

city: kobe

first: Yu

last: Hirata

address: chuo-ku, kusunoki-chou, 7-5-2

country: Japan

institute: Kobe University

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

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

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

label: biotin

source_name: Gastrocnemius muscle at 3 days after control treatment of skeletal muscle specific KLF15 knockout mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Gastrocnemius muscle collections of mice at 3 days after control or immobilization treatment.

extract_protocol: Total RNA was extracted from mouse skeletal muscle with the use of the RNeasy Mini Kit (Qiagen, Venlo, the Netherlands).

treatment_protocol: The anesthetized mice were subjected to hindlimb cast-immobilization with plastic tube and adhesive tape for 3 days.

value: Gastrocnemius muscle

value: KLF15 knockout


title: P1_1_E20


title: rrf3_mutant_ego1_RNAi_R1_sRNA-seq

value: ego-1 RNAi from L1 to 44h


title: DIV12 cells rep1

value: ESC-derived neural progenitor cells


title: KO,IM

source_name: Gastrocnemius muscle at 3 days after immobilization treatment of skeletal muscle specific KLF15 knockout mice


title: rrf3_mutant_ego1_RNAi_R2_sRNA-seq


title: DIV12 cells rep2

value: untreated


title: P1_1_E19


title: WT_RNA-seq_Rep2

description: ribosomal depleted RNA


title: WT_RNA-seq_Rep1

description: ribosomal depleted RNA


title: rrf3_mutant_dt7_R1_sRNA-seq


title: P1_1_E18


title: p00wild_080

city: Santa Cruz

first: Bin

last: Chen

address: 1156 High St.

department: MCD Biology

institute: University of California Santa Cruz

data_processing:
paired-end map to mouse RepeatMasker elements with bowtie. Use remaining (not mapped to repeat elements) reads in next steps
paired-end map (repeat-filtered reads) to mm9 with STAR
convert mappings to coverage of mm9 UCSC Known Genes
differential expression analysis with DESeq on per-gene, per-sample read counts, 3 replicates per condition
use DESeq sizeFactors to report per-sample normalized read counts for significant genes
Genome_build: mm9
Supplementary_files_format_and_content: for each gene, the read counts, normalized by DESeq sizeFactors, are shown for all replicates.

source_name: cortex

growth_protocol: Fezf2+/- mice were bred with each other. P0 Fezf2+/+ and Fezf2-/- pups were used for the study.

extract_protocol:
Qiagen RNAeasy protocol was followed to isolate total RNAs from the dissected cortices.
Illumina TruSeq RNA sample preparation protocol

treatment_protocol: Cerebral cortex was dissected out from 3 P0 Fezf2+/+ and 3 Fezf2-/- mice. Total RNAs from each brain were isolated using Qiagen RNAeasy kit. The sequencing libraries were generated following Illumina RNA TruSeq protocol. The libraries were sequenced on an Illumina Genome Analyzer II platform. DESeq was used to identify genes differentially expressed in Fezf2-/- cortices.

value: cortex

value: post-natal day 0

value: wild type

tag: litter


title: p00wild_099


title: N2_ego1_RNAi_R1_sRNA-seq


title: N2_dt7_R2_sRNA-seq


title: EGO-1_KO_late_L4_R1_sRNA-seq

description:
sRNA-seq in WT N2, CSR-1 KO and EGO-1 KO experiment
total sRNA


title: N2_dt7_R1_sRNA-seq


title: EGO-1_KO_late_L4_R2_sRNA-seq


title: p00wild_085


title: CSR-1_KO_late_L4_R1_sRNA-seq


title: CSR-1_KO_late_L4_R2_sRNA-seq


title: WT,IM

source_name: Gastrocnemius muscle at 3 days after immobilization treatment of wild type


title: N2_ego1_RNAi_R2_sRNA-seq


title: P1_1_E17


title: p00fezf_098

value: Fezf2 KO


title: WT,Control

source_name: Gastrocnemius muscle at 3 days after control treatment of wild type


title: p00fezf_086


title: P1_1_E16


title: p00fezf_076


title: klp-7_co_heterozygote_lateL4_sRNA-seq

description: klp-7 WT and codon optimised sRNA-seq in heterozygote worms

growth_protocol: Strains were maintained at 20°C, using standard methods (Brenner, 1974) with the exception for "P-grnaule RNAi  experimet"which was performed at 25 °C.

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food or otherwise described in treatment protocol ,  at a density of maximum 40,000 animals per 15 cm Petri dish. Worms were carefully monitored using a stereomicroscope and sorted using COPAS bio sorter at 44 h to enrich for late L4 stage larval population.  Sorted worms were frozen in dry ice with Trizol reagent (Ambion). After five repetitions of freeze and thaw in dry ice, total RNA was isolated according to the Trizol Reagent protocol. Agilent 2200 TapeStation System was used to evaluate the RIN indexes of all the RNA preps, and only samples with RIN > 8 was used for downstream applications. 6 µg of total RNAs with RIN > 8 was size selected from 15% UREA PAGE gel and used to generate small RNA libraries.
The library preparation was performed as essentially described by Jayaprakash et al., 2011, except that a 5’ polyphosphatase (Lucigen RP8092H) treatment was performed to be able to clone tri-phosphate small RNAs, and that the PAGE gel extraction after each ligation was substitute with purification by 1.8 volumes of Agencourt RNAClean XP Beads (Beckman Coulter, NC0068576) and 3 volumes of isopropanol. The multiplexed amplified libraries were further purified using PippinPrep DNA size selection with 3% gel cassettes and the following parameters for the selection: BP start (115) and the BP end (165). The purified libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced either on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005).

treatment_protocol: Auxin treatment were performed by placing worms on plates containing 500 µM Auxin dissolved in Ethanol (at a final concentration of 0.5% ) from L1 to 38 H, worms were then transferred to NGM plates for CSR-1 expression recovery for 5 or 10 h for "CSR-1 expression recovery experiment". For experiment "CSR-1 degron and ego-1 RNAi experiment", synchronised worms were grown on NGM plates containing IPTG and seeded with bacteria either containing control RNAi vector or ego-1 RNAi clone from Ahringer library from L1 to 38 h, at 38 hours worms were transfered to plates containing either 500 µM Auxin or only 0.5 % Ethanol (control) and were grown for further 6 hours to deplete CSR-1. For "P-granule RNAi experiment", N2 worms were grown  on IPTG NGM plates seeded with bacteria either expressing control RNAi vector or pDU49vector containing quadruple RNAi for glh-1, glh-4, pgl-1 and pgl-3 for two generations at 25 °C.

value: klp-7(gc047[klp-7_codon_optimised])/hT2 [bli-4(e937) let-?(q782) qIs48]) (I;III).


title: N2_WTklp-7_lateL4_rep2_sRNA-seq

description: klp-7 WT and codon optimised sRNA-seq experiment


title: N2_late_L4_R2_sRNA-seq


title: P1_1_E15


title: N2_late_L4_R1_sRNA-seq


title: N2_RNAi_P-granule_rep2_sRNA-seq

description: P-granule RNAi experiment

value: P-granule RNAi for 2 generations at 25degreeC (quadruple Rnai - pDU49 for glh-1, glh-4, pgl-1, pgl-3)


title: klp-7_co_lateL4_rep2_sRNA-seq

value: klp-7(gc047[klp-7_codon_optimised]) III


title: N2_WTklp-7_lateL4_rep1_sRNA-seq


title: klp-7_co_lateL4_rep1_sRNA-seq


title: P1_1_E11


title: N2_RNAi_control_rep2_sRNA-seq

description: P-granule RNAi experiment

value: Control RNAi for 2 generetions grown at 25degreeC


title: N2_RNAi_P-granule_rep1_sRNA-seq

description: P-granule RNAi experiment


title: N2_RNAi_control_rep1_sRNA-seq

description: P-granule RNAi experiment


title: CSR-1_degron_control_RNAi_ego-1_rep2_sRNA-seq

description: CSR-1 degron and ego-1 RNAi experiment

value: ieSi64 [gld-1p::TIR1::mRuby::gld-1 3'UTR + Cbr-unc-119(+)] II; csr-1(gc029[degron::mCherry::3xflag::ha::csr-1])

value: ego-1 RNAi from L1 to 38 h, 0.5 % Ethanol (Auxin control) 38 h to 44 h


title: P1_1_E10


title: P1_1_E09


title: CSR-1_degron_control_RNAi_ego-1_rep1_sRNA-seq

description: CSR-1 degron and ego-1 RNAi experiment

value: whole worm

value: Late L4 larval stage


title: P1_1_E08


title: CSR-1_degron_auxin_RNAi_ego-1_rep2_sRNA-seq

description: CSR-1 degron and ego-1 RNAi experiment

value: ego-1 RNAi from L1 to 38 h, Auxin (500µM) 38 h to 44 h


title: CSR-1_degron_auxin_RNAi_ego-1_rep1_sRNA-seq

description: CSR-1 degron and ego-1 RNAi experiment


title: CSR-1_degron_auxin_RNAi_control_rep2_sRNA-seq

description: CSR-1 degron and ego-1 RNAi experiment

value: Contorl RNAi from L1 to 38 h, Auxin (500µM) 38 h to 44 h


title: P1_1_E14


title: CSR-1_degron_control_RNAi_control_rep1_sRNA-seq

description: CSR-1 degron and ego-1 RNAi experiment

value: Contorl RNAi from L1 to 38 h, 0.5 % Ethanol (Auxin control) 38 h to 44 h


title: WT_BORIS_ChIP-seq_Rep2

description:
Chip-seq
WT_BORIS_ChIP-seq_peaks.bed
WT_BORIS_ChIP-seq.wig.gz

value: Testis

value: WT

value: 3 months

tag: chip-seq antibody

value: custom rabbit polyclonal BORIS Abs


title: P1_1_E13


title: P1_1_E07


title: DKO_H3K4me3_ChIP-seq

value: DKO

value: Anti-H3(tri methyl K4) Abcam-ab8580


title: WT_BORIS_ChIP-seq_Rep1


title: CSR-1_degron_10h_recovery_rep2_sRNA-seq

description: CSR-1 expression recovery experiment

value: Auxin (500µM) from L1 for 38 h followed by 10 h recovery on plates without Auxin


title: WT_H3K4me3_ChIP-seq

value: Anti-H3 (tri methyl K4) Abcam-ab8580


title: P1_1_E06


title: CSR-1_degron_0h_recovery_rep2_sRNA-seq

description: CSR-1 expression recovery experiment

value: Early L4 larval stage

value: Auxin (500µM) from L1 for 38 h


title: CSR-1_degron_5h_recovery_rep2_sRNA-seq

description: CSR-1 expression recovery experiment

value: ieSi64 [gld-1p::TIR1::mRuby::gld-1 3'UTR + Cbr-unc-119(+)] II; csr-1(gc029[degron::mCherry::3xflag::ha::csr-1])

value: Mid L4 larval stage

value: Auxin (500µM) from L1 for 38 h followed by 5 h recovery on plates without Auxin


title: P1_1_E05


title: CSR-1_degron_control_RNAi_control_rep2_sRNA-seq

description: CSR-1 degron and ego-1 RNAi experiment

value: whole worm

value: Late L4 larval stage


title: CSR-1_degron_5h_recovery_rep1_sRNA-seq

description: CSR-1 expression recovery experiment


title: DKO_Pol2_ChIP-seq_Rep1

value: Anti-Pol2(4H8) Abcam-ab5408


title: CSR-1_degron_10h_recovery_rep1_sRNA-seq

description: CSR-1 expression recovery experiment


title: CSR-1_degron_0h_recovery_rep1_sRNA-seq

description: CSR-1 expression recovery experiment


title: DKO_Pol2_ChIP-seq_Rep2


title: P1_1_E04


title: GFP_HRDE-1_csr-1_KO_lateL4_input_rep2_sRNA-seq

description: GFP HRDE-1 IP in WT or CSR-1 knockout background experiment

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food at a density of maximum 40,000 animals per 15 cm Petri dish. Worms were carefully monitored using a stereomicroscope and sorted using COPAS bio sorter at 44 h to enrich for late L4 stage larval population. Harvested worms were suspended in the IP buffer (50 mM Tris, 500 mM NaCl, 5mM MgCl2 10 % glycerol, 1% NP40, protease inhibitor cocktails (Thermo Scientific, 1860932), 40U/mL RNase inhibitor) followed by 30 strokes using a metal dounce on ice. Crude protein extracts were centrifuged at 18,000 rpm at 4°C for 10 minutes. Protein concentration was quantified by the Bradford assay, and 500 µg of protein extract was incubated with 15 μl of packed Anti-FLAG M2 Magnetic Agarose Beads (Sigma M8823) for 2 hour at 4°C. After four washes with IP buffer, the beads were resuspended in 750 µL of TRIzol LS reagent (Ambion) to extract the immunoprecipitated RNAs. 750 µL of TRIzol LS reagent (Ambion) was also added to 10% of protein extract before the immunoprecipitation (Input). RNA extracted from IPs and Inputs were size selected from 15% UREA PAGE gel.
The library preparation was performed as essentially described by Jayaprakash et al., 2011, except that a 5’ polyphosphatase (lucigen RP8092H) treatment was performed to be able to clone tri-phosphate small RNAs, and that the PAGE gel extraction after each ligation was substitute with purification by 1.8 volumes of Agencourt RNAClean XP Beads (Beckman Coulter, NC0068576) and 3 volumes of isopropanol. The multiplexed amplified libraries were further purified using PippinPrep DNA size selection with 3% gel cassettes and the following parameters for the selection: BP start (115) and the BP end (165). The purified libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced either on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005).

value: ggSi1[hrde-1p::3xflag::gfp::hrde-1] II ; csr-1(tm892)/nT1 [unc-?(n754) let-? qIs51] (IV;V)

tag: antibody


title: GFP_HRDE-1_csr-1_KO_lateL4_input_rep1_sRNA-seq


title: P1_1_E03


title: P1_1_E02


title: CSR-1_degron_auxin_RNAi_control_rep1_sRNA-seq

description: CSR-1 degron and ego-1 RNAi experiment

value: Contorl RNAi from L1 to 38 h, Auxin (500µM) 38 h to 44 h


title: WT_Pol2_ChIP-seq_Rep2

value: Testis

value: WT


title: WT_Pol2_ChIP-seq_Rep1

value: 3 months


title: P1_1_D24


title: P1_1_E01


title: GFP_HRDE-1_csr-1_KO_lateL4_IP_rep2_sRNA-seq

value: FLAG


title: GFP_HRDE-1_WT_lateL4_IP_rep2_sRNA-seq

value: ggSi1[hrde-1p::3xflag::gfp::hrde-1] II


title: GFP_HRDE-1_WT_lateL4_input_rep2_sRNA-seq


title: GFP_HRDE-1_WT_lateL4_IP_rep1_sRNA-seq


title: GFP_HRDE-1_WT_lateL4_input_rep1_sRNA-seq


title: P1_1_D23


title: DKO_CTCF_ChIP-seq_Rep1

value: DKO

value: Equimolar mix of CTCF C-terminus commercial antibody were used (anti-CTCF B-5(sc-271514) and C-20 (sc-15914)) from Santa Cruz; Anti-CTCF (D3H2) from cell signaling:anti-CTCF (07-727) from Millipore:anti-CTCF (70303) from Abcam:anti-CTCF (A300-543A) from Bethyl and anti-CTCF (NB500-177 and NB500-194) from Novus.


title: FLAG_CSR-1_ADH_lateL4_input_rep2_sRNA-seq

description: FLAG CSR-1 WT IP or FLAG CSR-1 catalytic mutant IP  experiment


title: FLAG_CSR-1_ADH_lateL4_input_rep1_sRNA-seq


title: P1_1_D22


title: WT_CTCF_ChIP-seq_Rep1

value: Equimolar mix of CTCF C-terminus commercial antibody were used (anti-CTCF B-5(sc-271514) and C-20 (sc-15914)) from Santa Cruz; Anti-CTCF (D3H2) from Cell signaling:anti-CTCF (07-727) from Millipore:anti-CTCF (70303) from Abcam:anti-CTCF (A300-543A) from Bethyl and anti-CTCF (NB500-177 and NB500-194) from Novus.


title: WT_CTCF_ChIP-seq_Rep2


title: P1_1_D21


title: FLAG_CSR-1_WT_lateL4_input_rep1_sRNA-seq


title: GFP_HRDE-1_csr-1_KO_lateL4_IP_rep1_sRNA-seq


title: FLAG_CSR-1_ADH_lateL4_IP_rep1_sRNA-seq


title: Input_DKO_ChIP-seq

value: none (input)


title: P1_1_D20


title: FLAG_CSR-1_ADH_lateL4_IP_rep2_sRNA-seq


title: FLAG_CSR-1_WT_lateL4_IP_rep2_sRNA-seq


title: klp-7_co_heterozygote_lateL4_RNA-seq

description: klp-7 WT and codon optimised RNA-seq in heterozygote worms

data_processing:
Reads were mapped on the C. elegans genome (WBcel235) using hisat2 (version 2.1.0) with default parameters
Mapped reads were used to estimate the abundance of protein coding genes using featureCounts (version 1.6.3) with options -O -M --primary -s 2 --fracOverlap 0 and annotations corresponding to protein coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The alignment was used to generate the normalized bigwig file using millions of summed forward reads per kilobase in protein coding genes as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.35) and bedGraphToBigWig (version 4)
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of RNAs along the genome

growth_protocol: Strains were maintained at 20°C, using standard methods (Brenner, 1974). Bristol N2 was the wild-type strain used.

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food  at a density of maximum 40,000 animals per 15 cm Petri dish. Worms were carefully monitored using a stereomicroscope and sorted using COPAS bio sorter at 44 h to enrich for late L4 stage larval population. Sorted worms were frozen in dry ice with Trizol reagent (Ambion). After five repetitions of freeze and thaw in dry ice, total RNA was isolated according to the Trizol Reagent protocol. Ten micrograms of RNA were treated with 2 U of Turbo DNase (Ambion) at 37°C for 30 minutes followed by phenol-extraction and isopropanol precipitation. Agilent 2200 TapeStation System was used to evaluate the RIN indices of all the RNA preps, and only samples with RIN > 8 was used for downstream applications.
DNase-treated total RNA with RIN > 8 was used to prepare strand-specific RNA libraries. We developed an RNase H based method to degrade C. elegans and mitochondrial ribosomal RNAs (rRNAs) using 50nt oligos complementary to rRNA and mtRNA C. elegans sequences. 100 ng of DNase-treated total RNA was mixed with 1.5 µg of oligos at equimolar concentration and 1X probe hybridization buffer (200 mM NaCl, 10 mM Tris pH 7.5) and incubated in a thermocycler using the following parameters: 2 minutes at 95°C followed by 0.1°C/sec at 95-45°C, and 2 minutes hold at 45°C. Next 2 µl of Thermostable RNase H (epicentre) was added to the reactions together with 1X RNase H reaction buffer 50 mM Tris pH 7.5, 100 mM NaCl, 10 mM MgCl2) and incubated for 30 minutes at 45°C. Next, digested RNAs were treated with 2 U of Turbo DNase (Ambion) at 37°C for 30 minutes followed by purification using 2.2 volumes of Agencourt RNAClean XP Beads (Beckman Coulter, NC0068576) following the manufacturer’s instructions. 100 ng of Ribosomal-depleted RNAs were then used to generate strand-specific RNA libraries using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (E7760S). Multiplexed RNA libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005).

value: klp-7(gc047[klp-7_codon_optimised])/hT2 [bli-4(e937) let-?(q782) qIs48]) (I;III).


title: DKO_CTCF_ChIP-seq_Rep2


title: klp-7_co_lateL4_rep2_RNA-seq

description: klp-7 WT and codon optimised RNA-seq experiment

value: klp-7(gc047[klp-7_codon_optimised]) III


title: P1_1_D19


title: P1_1_D18


title: klp-7_co_lateL4_rep1_RNA-seq


title: P1_1_D17


title: Sciatic nerve 10X_P60_3

description: 10x raw data contains cell barcode and UMI, cell barcode and UMI, cDNA reads

data_processing:
Chromium data was demultiplexed with cellranger mkfastq v2.0.2.
Gene-cell count matrix was generated by cellranger count v2.0.2 against Ensembl GRCm38.p5 reference genome.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Filtered count matrix from cellranger count is stored in three files: barcodes.tsv, genes.tsv and matrix.mtx.

extract_protocol: Library construction was performed according to the 10x Chromium Single Cell 3' Reagent Kit v2.

value: Sciatic nerve

tag: biological replicate


title: Sciatic nerve 10X_P60_2


title: N2_1_WTcsr-1_lateL4_rep2_RNA-seq

description: RNA-seq experiment for WT N2 for input in Ribo-seq to calculated translation efficiency

value: whole worm


title: Sciatic nerve 10X_P60_1


title: N2_WTklp-7_lateL4_rep1_RNA-seq

value: Late L4 larval stage


title: N2_WTklp-7_lateL4_rep2_RNA-seq


title: N2_1_WTcsr-1_lateL4_rep1_RNA-seq


title: P1_1_D16


title: P1_1_D15


title: csr-1_KO_lateL4_rep1_RNA-seq

description: RNA-seq experiment comparing WT, csr-1 catalytic mutant and knockout


title: FLAG_CSR-1_WT_lateL4_IP_rep1_sRNA-seq


title: Input_WT_ChIP-seq


title: csr-1_ADH_lateL4_rep2_RNA-seq


title: Sciatic nerve 10X_P1_2


title: FLAG_CSR-1_WT_lateL4_input_rep2_sRNA-seq


title: Sciatic nerve 10X_P1_1


title: csr-1_ADH_lateL4_rep1_RNA-seq


title: N2_WTcsr-1_lateL4_rep2_RNA-seq


title: csr-1_KO_lateL4_rep2_RNA-seq


title: P1_1_D13


title: klp-7_co_lateL4_rep1_Ribo-seq

description: klp-7 WT and codon optimised Ribo-seq experiment

data_processing:
Library strategy: Ribo-seq
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) was trimmed from the raw reads using cutadapt (version 1.18)
The trimmed reads were sorted by sequence using fastq-sort (from fastq-tools version 0.8) with option -s and deduplicated using a custom haskell program, keeping the highest quality among duplicates, at any given position
The 5' and 3' 4 nt UMIs were removed from the deduplicated reads using cutadapt (version 1.18) with options -u 4 and -u -4
After removing UMIs, the reads from 28 to 30 nt were selected using bioawk version 20110810 (git commit fd40150b7c557da45e781a999d372abbc634cc21)
The size-selected reads were mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with options -L 6 -i S,1,0.8 -N 0
The reads that failed to map were inspected using grep -E -B 1 -A 2 "^G[ACGTN]{20,25}T+$" to detect possible reads starting with G with 20 to 25 nt followed by a poly-U tail that might have prevented the mapping, and this tail was removed from such reads using a custom haskell program before re-mapping them.
Mapped and remapped reads were used to estimate the abundance of small RNAs derived from structural RNAs using featureCounts (version 1.6.3) with options -O -s 1 --fracOverlap 1 and annotations corresponding to tRNA, snRNA, snoRNA, rRNA or RNA (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The abundance of non-structural RNAs was estimated by subtracting the above counts from the number of mapped and remapped reads.
Initially mapped reads were classified using a custom python program according to their length, composition and on the annotations on which they mapped. Reads that didn't match miRNA and piRNA annotations were considered as potential endo-siRNAs.
The potential endo-siRNAs of size 21 to 23 nt that started with G were classified as “si_22G” if they mapped antisense to annotation belonging to the following categories: DNA transposons, RNA transposons, satellites, simple repeats (as annotated in http://hgdownload.cse.ucsc.edu/goldenPath/ce11/database/rmsk.txt.gz) or pseudogene or protein-coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The “si_22G” reads were re-mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with options -L 6 -i S,1,0.8 -N 0
The resulting alignment was used to generate the normalized bigwig file using millions of non-structural RNAs as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.35) and bedGraphToBigWig (version 4)
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of “si_22G” RNAs along the genome

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food or otherwise described in treatment protocol ,  at a density of maximum 40,000 animals per 15 cm Petri dish. Worms were carefully monitored using a stereomicroscope and sorted using COPAS bio sorter at 44 h to enrich for late L4 stage larval population. Sorted worms were lysed by freeze crushing in polysome buffer (140 mM KCl, 5 mM MgCl2, 20 mM Tris HCl pH 8, 1% Triton X-100, Halt protease inhibitor cocktail (Thermo Scientific, 1860932), RiboLock RNase Inhibitor (Thermo Scientific, EO0381), 0.1 mg/mL cycloheximide) in liquid nitrogen and the lysate was then treated with RNase I at 100 U/mg of lysate for 5 minutes at 37 °C. Lysates were then franctionated on a 10-50 % sucrose gradient by ultracentrifugation at 39000 rpm in a SW41-Ti rotor from Beckmann Coulter. RNA from monosome fraction was resolved on a on a TBE-Urea gel 15% and  fragments of 28-30 nucleotides were size.
3’ phosphate and 5’-OH of 28-30 Ribosome protected fragments were repaired using Polynucleotide kinase (New England biolabs, M0201S). RNA was ligated to 3’end adapter using T4 RNA ligase 2 Truncated KQ and to 5’ adapter using T4 RNA ligase 1 (New England biolabs, M0204S). cDNA was PCR amplified with specific primers using Q5 High-Fidelity 2X Master Mix (New England biolabs, M0492S). The purified libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced either on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005).


title: N2_WTklp-7_lateL4_rep2_Ribo-seq


title: N2_WTcsr-1_lateL4_rep1_RNA-seq


title: P1_1_D11


title: klp-7_co_lateL4_rep2_Ribo-seq


title: P1_1_D14


title: P1_1_D09


title: N2_WTklp-7_lateL4_rep1_Ribo-seq


title: P1_1_D08


title: csr-1_KO_lateL4_rep1_Ribo-seq

description: Ribo-seq experiment comparing WT and csr-1knockout


title: N2_2_WTcsr-1_lateL4_rep2_Ribo-seq


title: csr-1_KO_lateL4_rep2_Ribo-seq


title: csr-1_ADH_lateL4_rep3_Ribo-seq

description: Ribo-seq experiment comparing WT and csr-1 catalytic mutant


title: csr-1_ADH_lateL4_rep2_Ribo-seq


title: P1_1_D07


title: Sciatic nerve 10X_P1_3


title: csr-1_ADH_lateL4_rep1_Ribo-seq


title: P1_1_D06


title: N2_1_WTcsr-1_lateL4_rep2_Ribo-seq


title: N2_1_WTcsr-1_lateL4_rep1_Ribo-seq


title: csr-1_KO_lateL4_rep2_GRO-seq

description: GRO-seq experiment comparing WT, csr-1 catalytic mutant and knockout

data_processing:
Library strategy: GRO-seq
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) was trimmed from the raw reads using cutadapt (version 1.18). The reads where the adaptor was not found were nonetheless kept ("untrimmed")
The 5' and 3' 4 nt UMIs were removed from the trimmed reads using cutadapt (version 1.18) with options -u 4 and -u -4
The 5' 4 nt UMIs as well as 7 nt in 3' (to be sure to eliminate possibly unrecognized first adaptor bases, as well as preceding 3' 4 nt UMIs) were removed from the "untrimmed" reads using cutadapt (version 1.18) options -u 4 and -u -7
Both types of reads were mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with default parameters, and the resulting alignment files were merged using samtools (version 1.9)
Mapped reads were used to estimate the abundance of protein coding genes using featureCounts (version 1.6.3) with options -O -M --primary -s 1 --fracOverlap 0 and annotations corresponding to protein coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The merged alignment was used to generate the normalized bigwig file using millions of summed forward reads per kilobase in protein coding genes as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.26) and bedGraphToBigWig (version 4)
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of nascent RNAs along the genome

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food  at a density of maximum 40,000 animals per 15 cm Petri dish. Worms were carefully monitored using a stereomicroscope and sorted using COPAS bio sorter at 44 h to enrich for late L4 stage larval population. The nuclei were extracted in Nuclei extraction buffer using a metal dounce on ice. GRO-seq experiments were performed as described by Barucci et al., 2014 with minor modifications.
Biotinylated nascent RNAs were fragmented and immunoprecipitated using streptavidin conjugated beads (Invitrogen, 65001). 5’-OH of fragmented RNAs was repaired using Polynucleotide kinase (New England biolabs, M0201S). RNA was ligated to 3’end adapter using T4 RNA ligase 2 Truncated KQ and subjected to a second round of immunoprecipitation with streptavidin beads. RNA was ligated at 5’ end using T4 RNA ligase 1 (New England biolabs, M0204S) and biotinylated RNA was enriched for a third time. Purified RNA was reverse transcribed using SuperScript IV Reverse Transcriptase (Invitrogen, 18091050). cDNA was PCR amplified with specific primers using Q5 High-Fidelity 2X Master Mix (New England biolabs, M0492S). The purified libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced either on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005).


title: P1_1_D10


title: P1_1_D04


title: csr-1_KO_lateL4_rep1_GRO-seq


title: P1_1_D05


title: csr-1_ADH_lateL4_rep1_GRO-seq


title: N2_2_WTcsr-1_lateL4_rep1_Ribo-seq


title: N2_WTcsr-1_lateL4_rep2_GRO-seq


title: N2_WTcsr-1_lateL4_rep1_GRO-seq


title: csr-1_ADH_lateL4_rep2_GRO-seq


title: P1_1_D03


title: P1_1_C24


title: P1_1_C22


title: P1_1_D02


title: P1_1_C20


title: P1_1_C23


title: P1_1_C19


title: P1_1_D01


title: N2_1_WTcsr-1_lateL4_rep3_Ribo-seq


title: P1_1_C21


title: P1_1_C18


title: P1_1_C17


title: Lupus nephritis 1

city: Worcester

first: John

middle: E

last: Harris

state: MA

address: 364 Plantation St

department: Dermatology

institute: University of Massachusetts Medical School

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized with R/Bioconductor and Lumi package using a variance-stabilizing transformation and Robust Spline Normalization

source_name: human kidney

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted using Roche high pure RNA paraffin kit according to the manufacturer’s instructions

value: Lupus Nephritis


title: Lupus nephritis 3


title: Lupus nephritis 9


title: Lupus nephritis 5


title: Lupus nephritis 11


title: P1_1_C15


title: KidneyControl 6

value: Kidney Control


title: Lupus nephritis 10


title: KidneyControl 5


title: Lupus nephritis 8


title: Lupus nephritis 4


title: Lupus nephritis 14


title: KidneyControl 4


title: Lupus nephritis 7


title: Lupus nephritis 2


title: Lupus nephritis 6


title: Lupus nephritis 13


title: KidneyControl 7


title: Lupus nephritis 12


title: P1_1_C13


title: P1_1_C14


title: P1_1_C08


title: P1_1_C06


title: KidneyControl 1


title: 2-SkinControl 10

source_name: human skin

value: Skin Control


title: 2-SkinControl 7


title: 2-SkinControl 9


title: 2-SkinControl 6


title: KidneyControl 3


title: 2-SkinControl 5


title: 2-SkinControl 8


title: KidneyControl 2


title: 2-Subacute cutaneous lupus 10

value: SCLE


title: P1_1_C09


title: 2-SkinControl 2


title: 2-SkinControl 3


title: 2-SkinControl 4


title: 2-Subacute cutaneous lupus 9


title: 2-SkinControl 1


title: P1_1_C03


title: 2-Subacute cutaneous lupus 1


title: P1_1_C07


title: 2-Subacute cutaneous lupus 2


title: P1_1_B23


title: P1_1_C05


title: 2-Chronic cutaneous lupus 4

value: CCLE


title: 2-Subacute cutaneous lupus 8


title: 2-Subacute cutaneous lupus 6


title: 2-Subacute cutaneous lupus 7


title: 2-Chronic cutaneous lupus 2


title: 2-Subacute cutaneous lupus 4


title: 2-Subacute cutaneous lupus 3


title: 2-Subacute cutaneous lupus 5


title: P1_1_C10


title: P1_1_C04


title: P1_1_C02


title: EyeBank_cultured_corneal_endothelial_cells_001_with TGF-beta2_rep4

city: Québec

first: Stéphanie

last: Proulx

state: Qc

address: 1050 Chemin Ste-Foy

country: Canada

institute: Université Laval

description: Gene expression of passage 3 cells after 7 days post-confluency exposed to TGF-beta2

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Supplementary file processed_data.txt forms the basis of conclusions in the manuscript.

source_name: primary corneal endothelial cell population

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50-200 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions

growth_protocol:
[Isolation protocol]  Cells were isolated from mechanically peeled Descemet's membrane using collagenase A (1mg/ml) treatment. They were then seeded in culture dishes for expansion.
Cell populations were expanded in culture medium made of OptiMem-I, 8 % fetal bovine serum, 5 ng/mL human epidermal growth factor, 20 μg/mL ascorbic acid, 0.08 % chondroitin sulfate and a 1X mix of penicilin and streptomycin. Cells were maintained in 37°C and 8% CO2 incubators.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Cat#74104)

treatment_protocol: At confluency, culture medium was switched for OptiMem-I, fetal bovin serum and penicilin/streptomycin supplemented or not with TGF-beta2 for 7 days.

tag: disease

value: no corneal pathology associated

tag: Sex

value: F


title: EyeBank_cultured_corneal_endothelial_cells_001_with TGF-beta2_rep3

value: M

value: primary corneal endothelial cell population


title: EyeBank_cultured_corneal_endothelial_cells_001_without TGF-beta2_rep2

description: Gene expression of passage 3 cells after 7 days post-confluency

value: control


title: EyeBank_cultured_corneal_endothelial_cells_001_with TGF-beta2_rep1


title: ATAC-seq from inflammation-experienced regulatory T-cells (ENCLB567UUL)

description:
https://www.encodeproject.org/experiments/ENCSR993QKC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR993QKC
assay title: ATAC-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB567UUL

source_name: Mus musculus strain Foxp3CreERT2 x Rosa26YFP male adult (6 months) inflammation-experienced regulatory T-cells primary cell originated from bone marrow hematopoietic cell

value: primary cell

tag: biosample encode accession

value: male

tag: dev stage

value: adult

value: 6 month

tag: lab

value: Christina Leslie, MSKCC

tag: source

value: Christina Leslie

tag: link

value: ENCBS150UAG at ENCODE; https://www.encodeproject.org/ENCBS150UAG/

value: Derived from ENCODE donor ENCDO820VCL; https://www.encodeproject.org/ENCDO820VCL/


title: P1_1_C01

source_name: Sciatic nerve


title: P1_1_B22


title: P1_1_B17


title: EyeBank_cultured_corneal_endothelial_cells_001_without TGF-beta2_rep1

tag: treatment


title: P1_1_B16


title: EyeBank_cultured_corneal_endothelial_cells_001_with TGF-beta2_rep2


title: ATAC-seq from inflammation-experienced regulatory T-cells (ENCLB333KTT)

description:
https://www.encodeproject.org/experiments/ENCSR993QKC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR993QKC
assay title: ATAC-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB333KTT


title: P1_1_B21


title: 2-Chronic cutaneous lupus 6

tag: tissue


title: EyeBank_cultured_corneal_endothelial_cells_001_without TGF-beta2_rep4

tag: cell type


title: DNase-seq from liver (ENCLB244PVO)

description:
https://www.encodeproject.org/experiments/ENCSR982PCS/
***************
biological replicate number: 1
technical replicate number: 2
description: DNase-seq for liver of C57BL/6J mice after 66 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.
experiment encode accession: ENCSR982PCS
assay title: DNase-seq
assembly: mm10
encode release date: 2018-12-22
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB244PVO

source_name: Mus musculus strain C57BL/6J adult (8-10 weeks) liver tissue treated with darkness for 66 hours

value: liver

value: tissue

tag: description

value: Liver from 8-10 week mice. Circadian Time 54

value: not collected

tag: age

value: 8-10 week

value: John Stamatoyannopoulos, UW

value: John Stamatoyannopoulos

tag: treatments

value: treatment_term_name:darkness; treatment_type:exposure; duration:66; duration_units:hour;

value: ENCBS794HWX at ENCODE; https://www.encodeproject.org/ENCBS794HWX/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: DNase-seq from liver (ENCLB182AXH)

description:
https://www.encodeproject.org/experiments/ENCSR982PCS/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq for liver of C57BL/6J mice after 66 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.
experiment encode accession: ENCSR982PCS
assay title: DNase-seq
assembly: mm10
encode release date: 2018-12-22
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB182AXH


title: 2-Chronic cutaneous lupus 5

value: CCLE


title: 2-Chronic cutaneous lupus 3


title: P1_1_B20

tag: technical run


title: P1_1_B19


title: 2-Chronic cutaneous lupus 1


title: P1_1_B15


title: EyeBank_cultured_corneal_endothelial_cells_001_without TGF-beta2_rep3

value: no corneal pathology associated

value: M

value: control

value: primary corneal endothelial cell population


title: P1_1_B13


title: ATAC-seq from regulatory T cell (ENCLB661PNR)

description:
https://www.encodeproject.org/experiments/ENCSR724UJS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR724UJS
assay title: ATAC-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB661PNR

source_name: Mus musculus strain Foxp3CreERT2 x Rosa26YFP male adult (4 months) regulatory T primary cell originated from bone marrow hematopoietic cell

value: regulatory T cell

value: primary cell

value: male

value: adult

value: 4 month

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS435MTJ at ENCODE; https://www.encodeproject.org/ENCBS435MTJ/


title: P1_1_B12


title: P1_1_B10


title: DNase-seq from liver (ENCLB181CHE)

description:
https://www.encodeproject.org/experiments/ENCSR130IPN/
***************
biological replicate number: 1
technical replicate number: 2
description: DNase-seq for liver of C57BL/6J mice after 54 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.
experiment encode accession: ENCSR130IPN
assay title: DNase-seq
assembly: mm10
encode release date: 2019-01-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB181CHE

source_name: Mus musculus strain C57BL/6J adult (8-10 weeks) liver tissue treated with darkness for 54 hours

value: liver

value: tissue

value: Liver from 8-10 week mice. Circadian Time 42

value: not collected

value: 8-10 week

value: John Stamatoyannopoulos, UW

value: John Stamatoyannopoulos

value: treatment_term_name:darkness; treatment_type:exposure; duration:54; duration_units:hour;

value: ENCBS707EPH at ENCODE; https://www.encodeproject.org/ENCBS707EPH/


title: DNase-seq from liver (ENCLB289FEP)

description:
https://www.encodeproject.org/experiments/ENCSR130IPN/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq for liver of C57BL/6J mice after 54 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.
experiment encode accession: ENCSR130IPN
assay title: DNase-seq
assembly: mm10
encode release date: 2019-01-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB289FEP

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: P1_1_B09


title: ATAC-seq from activated regulatory T-cells (ENCLB480YDY)

description:
https://www.encodeproject.org/experiments/ENCSR826JKN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR826JKN
assay title: ATAC-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB480YDY

source_name: Mus musculus strain Foxp3CreERT2 x Rosa26YFP male adult (4 months) activated regulatory T-cells primary cell originated from bone marrow hematopoietic cell

value: activated regulatory T-cells

value: primary cell

value: ENCBS744QIZ at ENCODE; https://www.encodeproject.org/ENCBS744QIZ/

value: Derived from ENCODE donor ENCDO820VCL; https://www.encodeproject.org/ENCDO820VCL/


title: P1_1_B18


title: P1_1_B14


title: ATAC-seq from regulatory T cell (ENCLB346WUY)

description:
https://www.encodeproject.org/experiments/ENCSR724UJS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR724UJS
assay title: ATAC-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB346WUY

value: regulatory T cell

value: male

value: adult

value: 4 month

value: Christina Leslie, MSKCC


title: P1_1_B03


title: P1_1_B04


title: P1_1_B08


title: P1_1_B11


title: P1_1_A23


title: P1_1_B02


title: P1_1_C16


title: P1_1_B07


title: DNase-seq from R1 (ENCLB872UOM)

description:
https://www.encodeproject.org/experiments/ENCSR319PWR/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR319PWR
assay title: DNase-seq
assembly: mm10
encode release date: 2018-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB872UOM

source_name: Mus musculus strain C57BL/6J R1 cell line

tag: line

value: cell line

value: embryonic

value: unknown

value: Unknown Source

value: ENCBS398YOV at ENCODE; https://www.encodeproject.org/ENCBS398YOV/


title: DNase-seq from R1 (ENCLB029LJP)

description:
https://www.encodeproject.org/experiments/ENCSR319PWR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR319PWR
assay title: DNase-seq
assembly: mm10
encode release date: 2018-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB029LJP

value: not collected

value: John Stamatoyannopoulos, UW


title: DNase-seq from liver (ENCLB447BOJ)

description:
https://www.encodeproject.org/experiments/ENCSR498GAH/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq for liver of C57BL/6J mice after 50 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.
experiment encode accession: ENCSR498GAH
assay title: DNase-seq
assembly: mm10
encode release date: 2018-12-22
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB447BOJ

source_name: Mus musculus strain C57BL/6J adult (8-10 weeks) liver tissue treated with darkness for 50 hours

value: liver

value: tissue

value: Liver from 8-10 week mice. Circadian Time 38

value: 8-10 week

value: John Stamatoyannopoulos

value: treatment_term_name:darkness; treatment_type:exposure; duration:50; duration_units:hour;

value: ENCBS402NJW at ENCODE; https://www.encodeproject.org/ENCBS402NJW/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: DNase-seq from liver (ENCLB179QEF)

description:
https://www.encodeproject.org/experiments/ENCSR297YSC/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq for liver of C57BL/6J mice after 58 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.
experiment encode accession: ENCSR297YSC
assay title: DNase-seq
assembly: mm10
encode release date: 2019-01-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB179QEF

source_name: Mus musculus strain C57BL/6J adult (8-10 weeks) liver tissue treated with darkness for 58 hours

value: Liver from 8-10 week mice. Circadian Time 46

value: adult

value: treatment_term_name:darkness; treatment_type:exposure; duration:58; duration_units:hour;

value: ENCBS983HHL at ENCODE; https://www.encodeproject.org/ENCBS983HHL/


title: DNase-seq from liver (ENCLB304KHO)

description:
https://www.encodeproject.org/experiments/ENCSR802MKV/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq for liver of C57BL/6J mice after 70 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.
experiment encode accession: ENCSR802MKV
assay title: DNase-seq
assembly: mm10
encode release date: 2018-12-22
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB304KHO

source_name: Mus musculus strain C57BL/6J adult (8-10 weeks) liver tissue treated with darkness for 70 hours

value: Liver from 8-10 week mice. Circadian Time 58

value: treatment_term_name:darkness; treatment_type:exposure; duration:70; duration_units:hour;

value: ENCBS287VJV at ENCODE; https://www.encodeproject.org/ENCBS287VJV/


title: DNase-seq from liver (ENCLB390FAW)

description:
https://www.encodeproject.org/experiments/ENCSR802MKV/
***************
biological replicate number: 1
technical replicate number: 2
description: DNase-seq for liver of C57BL/6J mice after 70 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.
experiment encode accession: ENCSR802MKV
assay title: DNase-seq
assembly: mm10
encode release date: 2018-12-22
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB390FAW

value: not collected


title: P1_1_B06


title: DNase-seq from liver (ENCLB592XZU)

description:
https://www.encodeproject.org/experiments/ENCSR297YSC/
***************
biological replicate number: 1
technical replicate number: 2
description: DNase-seq for liver of C57BL/6J mice after 58 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.
experiment encode accession: ENCSR297YSC
assay title: DNase-seq
assembly: mm10
encode release date: 2019-01-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB592XZU

value: John Stamatoyannopoulos, UW


title: P1_1_A22


title: ATAC-seq from activated regulatory T-cells (ENCLB964EWB)

description:
https://www.encodeproject.org/experiments/ENCSR826JKN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR826JKN
assay title: ATAC-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB964EWB

value: activated regulatory T-cells

value: primary cell

value: male

value: 4 month

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS744QIZ at ENCODE; https://www.encodeproject.org/ENCBS744QIZ/

value: Derived from ENCODE donor ENCDO820VCL; https://www.encodeproject.org/ENCDO820VCL/


title: P1_1_A21


title: DNase-seq from liver (ENCLB537TKW)

description:
https://www.encodeproject.org/experiments/ENCSR498GAH/
***************
biological replicate number: 1
technical replicate number: 3
description: DNase-seq for liver of C57BL/6J mice after 50 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.
experiment encode accession: ENCSR498GAH
assay title: DNase-seq
assembly: mm10
encode release date: 2018-12-22
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB537TKW

value: liver

value: tissue

value: Liver from 8-10 week mice. Circadian Time 38

value: 8-10 week

value: John Stamatoyannopoulos

value: treatment_term_name:darkness; treatment_type:exposure; duration:50; duration_units:hour;

value: ENCBS402NJW at ENCODE; https://www.encodeproject.org/ENCBS402NJW/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: P1_1_A19


title: DNase-seq from liver (ENCLB467LRO)

description:
https://www.encodeproject.org/experiments/ENCSR765TON/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq for liver of C57BL/6J mice after 62 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.
experiment encode accession: ENCSR765TON
assay title: DNase-seq
assembly: mm10
encode release date: 2018-12-22
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB467LRO

source_name: Mus musculus strain C57BL/6J adult (8-10 weeks) liver tissue treated with darkness for 62 hours

value: Liver from 8-10 week mice. Circadian Time 50

value: not collected

value: adult

value: John Stamatoyannopoulos, UW

value: treatment_term_name:darkness; treatment_type:exposure; duration:62; duration_units:hour;

value: ENCBS925YBW at ENCODE; https://www.encodeproject.org/ENCBS925YBW/