title: ZNF341_ChIPSeq_1

city: Freiburg

first: Claudia

last: Bossen

address: Breisacher Strasse 115

department: Center for Chronic Immunodeficiency

institute: University Hospital Freiburg (D)

data_processing:
Basecalls were performed using CASAVA
Reads were aligned to hg19 using Bowtie with the parameter –m 1 (v0.12.7)
Data was analyzed using HOMER (http://homer.salk.edu/homer) (v4.9.1)
High-confidence peaks (ZNF341.peaks.txt) were identified using getDifferentialPeaksReplicates.pl (HOMER) command using the ChIP-Seq data obtained with the two antibodies as replicates and Input as control. Peak file was annotated with tag number from each experiment.
Bedgraph were generated using makeUCSCfile command (HOMER).
Genome_build: hg19
Supplementary_files_format_and_content: ZNF341.peaks.txt: ZNF341 binding sites; bedGraph files can be uploaded to UCSC Genome Browser for data visualization.

source_name: ZNF341_ChIPSeq, EBV-transformed B cells

growth_protocol: Epstein-Barr virus (EBV) transformed lymphoblastic B cell lines were generated from healthy donor PBMCs by standard methods.

extract_protocol:
Cells were fixed for 15 minutes in 1% formaldehyde in PBS with 2% FCS. Formaldehyde was quenched for 10 minutes with 0.2M glycine. Cells were washed 2 times with ice-cold PBS. 30µl Protein G Dynabeads (Life Technologies) were blocked with 0.5% BSA (w/v) in PBS. Magnetic beads were bound with 5µg of anti-ZNF341 antibody. Crosslinked cells were lysed in lysis buffer (0.5% NP-40, 10mM HEPES, 85mM KCl, 4ul EDTA). After centrifugation, nuclei were resuspended and sonicated in sonication buffer (50mM Tris-HCl pH8.0, 1% SDS, 10mM EDTA) for 5 cycles at 10 sec each on ice (20W) with 50 sec on ice between cycles. Lysates were cleared by centrifugation and Triton X-100 was added at a final concentration of 1%. Lysates were then incubated overnight at 4°C with the previously prepared magnetic beads. Beads were washed once with RIPA (50mM Tris-HCl pH8.0, 150mM NaCl, 0.1% SDS, 0.1% Na-Deoxycholate, 1% Triton X-100, 1mM EDTA), once with RIPA 500 (50mM Tris-HCl pH8.0, 500mM NaCl, 0.1% SDS, 0.1% Na-Deoxycholate, 1% Triton X-100, 1mM EDTA), once with LiCl wash (10mM Tris-HCl pH8.0, 250mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1mM EDTA) and finally twice with TE (10mM Tris pH8.0, 1mM EDTA). Bound complexes were eluted from the beads in elution buffer (10mM Tris-HCl pH8.0, 0.5% SDS, 300mM NaCl, 5mM EDTA) for 30 min at 65 °C with shaking. Crosslinks were reversed overnight at 65°C. RNA and protein were digested in the supernatant using RNase A and Proteinase K. DNA was purified using ChIP DNA clean and concentrator columns (Zymoresearch).
Libraries were prepared according to Illumina's instructions. 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 (minus exo) 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, ChIP DNA was PCR-amplified with Illumina primers with the respective indexes for 18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size- selected with AMPure XP beads (Beckman Coulter).

value: EBV-transformed B cells

tag: chip antibody

value: ZNF341 (Atlas Antibodies,HPA024607, Lot:R12522)


title: Input

status: Public on May 02 2018

type: SRA

country: Germany

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Input, EBV-transformed B cells

tag: cell type


title: Mouse_in_vitro_45h_ctrl_ATAC-seq_re1

status: Public on May 03 2018

city: Beijing

first: Wei

last: Xie

address: zhongguancun beidajie

country: China

institute: Tsinghua University

data_processing:
Basecalls performed using CASAVA version 1.8
ATAC-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
Genome_build: mm9

organism: Mus musculus

source_name: Preimplantation embryo

growth_protocol: Cultured in CZB medium

extract_protocol:
After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al. with slightly modification

tag: developmental stage


title: Mouse_TBE_45h_ATAC-seq_re2

treatment_protocol: PN3 zygotes 22h after hCG were treated with 250 ng/ul alpha amanitin (Sigma) for 45h

value: Arrest 2-cell


title: ZNF341_ChIPSeq_2

value: ZNF341 (monoclonal customized antibody)


title: RNA-seq DMSO rep1

city: Worcester

first: Lucio

last: Castilla

state: MA

address: 364 Plantation Street

department: MCCB

country: USA

institute: University of Massachusetts

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to hg19 whole genome using topht v2.0.9 with bowtie v2.1.0 with parameters --library-type fr-unstranded --b2-very-sensitive --mate-inner-dist 100 --mate-std-dev 80 --no-coverage-search
Gene expression was quantified using cufflinks v2.2.0 cuffdiff with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample, and the log2FC, p-value, FDR adjusted q-value calculated by cuffdiff

molecule: total RNA

extract_protocol:
RNA was harvested using PureLink RNA Mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ME-1 cells were treated with DMSO/ AI-10-49 (1uM) for six hours.

tag: cell line

value: Human inv(16) leukemia cell line

tag: treated with

value: DMSO


title: ATAC-seq DMSO rep2

data_processing:
the adaptors were removed using cutadapt program v 1.3
The reads were then mapped onto the human genome hg19 assembly using Bowtie2. The standard default settings were modified to allow mapped paired-end fragments up to 2 kb.
Only the reads with mapping quality greater than 20 were kept, and the duplicated reads were removed using picard tools v1.96 (https://broadinstitute.github.io/picard/). the reads from mitochondria were also removed.
The regions of nucleosome free reads enrichment were called by MACS2 v2.1.0 (Zhang et al., 2008) with default parameters with q value threshold 0.05 using the reads  with fragment size less than 100 bp.
The bigwig files were generated using deepTools2 (Ramirez et al., 2016) to visualize the mapped reads normalized by RPKM.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited narrowPeak files generated by macs2, and the bigwig files generated by the bamcoverage command of the deeptools2.

growth_protocol: ME-1 cells were treated with DMSO/ AI-10-49 (1uM) for six hours.

extract_protocol:
ATAC-seq libraries were prepared for sequencing using standard Illumina protocols
ATAC-seq

treatment_protocol: Lysates were clarified from tagmented DNA and libraries were prepared using indexing primers included in the Nextera Index kit (Illumine, FC-121-1030) and NEBNext High-Fidelity 2× PCR Master Mix (NEB, M 0541S).


title: MiaPaCa2.CTCF

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

description: Chromatin IP against CTCF

data_processing:
Reads were quality filtered according to the Illumina pipeline, then were mapped to the hg19 human reference genome using Bowtie2 v2.2.6 with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools.
Peak calling was performed using MACS2 (version 2.1.0.20150731) with the “--nomodel”, “--extsize 200” and “--qvalue 0.01” flags and arguments. Each IP was compared to input DNA.
Genome_build: hg19 (NCBI build GRCh37)
Supplementary_files_format_and_content: *.narrowPeak, list of the peaks called by MACS2

source_name: Pancreatic Ductal Adenocarcinoma (PDAC) cell line

growth_protocol: DMEM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep

extract_protocol: ChIP lysates were generated from 20-40x10^6 cells. Cells were fixed in 1% formaldehyde for 10min.  Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by QIAquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

value: original PDAC cell line (MiaPaCa2)

tag: antibody

value: Anti-CTCF (Antibody Millipore Rb Antiserum 07-729 Lot. 2275585)

tag: treatment


title: ATAC-seq DMSO rep1


title: ATAC-seq AI-10-49 rep2


title: ATAC-seq AI-10-49 rep1


title: RNA-seq DMSO rep2


title: PANC1.Input

description: Control IP DNA

value: original PDAC cell line (PANC1)


title: MiaPaCa2.WT.rep2

data_processing:
Reads were quality filtered according to the Illumina pipeline, then were aligned to the hg19 human reference genome and to the Homo Sapiens transcriptome (NCBI build 37.2) using TopHat v2.1.0 with the option “--b2-very-sensitive”. Only uniquely mapped reads were retained.
Gene expression counts were estimated using HTSeq v0.6.1, summarized across all exons as annotated in the NCBI build 37.2, with option “union” and “no strand-specific assay”.
Differentially expressed genes in biological triplicates of wild type and ZEB1-KO MiaPaCa2 clones were identified using EdgeR R-package v3.2.2.
Genome_build: hg19 (NCBI build GRCh37)
Supplementary_files_format_and_content: The file gene.counts.txt contains the raw read counts for each samples. The file edgeR_results.txt contains differentially expressed genes in biological triplicates of wild type and ZEB1-KO MiaPaCa2 clones. The file genes.normalized_TPM.txt contains Transcripts Per Million (TPM) values for each samples.

extract_protocol: 2x10^3 cells are lysed and processed according to SMART-Seq2 protocol. Briefly, after cell lysis the poly-A containing mRNA molecules are copied into first strand cDNA by reverse transcription and template-switching using oligo(dt) primers and LNA-containing template-switching oligo (TSO). cDNA is pre-amplified using limited number of cycles, purified and tagmented with Tn5 transposase. cDNA fragments generated after tagmentation are gap-repaired, enriched by PCR and purified to create the final cDNA library for HiSeq 2000 Illumina sequencing.

treatment_protocol: Isolation of clonal cell line by sorting GFP+ MiaPaCa2 cells electroporated with plasmid pSpCas9-2A-GFP (px458; Addgene #48138)

value: MiaPaCa2 clonal cell line


title: MiaPaCa2.WT.rep3


title: MiaPaCa2.ZEB1-KO.rep2

treatment_protocol: Isolation of clonal cell line by sorting GFP+ MiaPaCa2 cells electroporated with plasmid ZEB1.gRNA-pSpCas9-2A-GFP.

value: MiaPaCa2 genome-edited clonal cell line


title: MiaPaCa2.WT.rep1


title: MiaPaCa2.ZEB1-KO.rep3


title: MiaPaCa2.ZEB1-KO.rep1


title: MiaPaCa2.delta-Repeat.ZEB1

description: Chromatin IP against ZEB1

value: Anti-ZEB1 (Antibody SC-25388 Lot. K1615)

value: Isolation of clonal cell line by dilution of MiaPaca2 cells electroporated with two plasmids pX330A_D10A-1x2 driving the expression of the Cas9-nickase and different pairs of gRNAs designed to target the repeated genomic region upstream MIR200A/B locus . (Multiplex CRISPR/Cas9 Assembly System Kit).


title: MiaPaCa2.WT.ZEB1

description: Chromatin IP against ZEB1

value: Isolation of clonal cell line by dilution of MiaPaca2 cells electroporated with plasmids pX330A_D10A-1x2 containing Cas9 nickase. (Multiplex CRISPR/Cas9 Assembly System Kit; Addgene # 1000000055).


title: RKO.Input

description: Control IP DNA

source_name: Colon Carcinoma cell line

growth_protocol: Minimum Essential Medium (MEM) with Earle's Salts supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine, 1mM Sodium Pyruvate (NaP), 0.1mM Non-Essential Amino Acids (NEAA) and 1% Pen/Strep.

value: original Colon Carcinoma cell line (RKO)


title: RKO.ZEB1

description: Chromatin IP against ZEB1

value: Anti-ZEB1 (Antibody SC-25388 Lot. G2315)


title: RNA-seq AI-10-49 rep2


title: MiaPaCa2.Input.rep2

description: Control IP DNA


title: CFPAC1.Input

description: Control IP DNA

value: original PDAC cell line (CFPAC1)


title: H3K27ac: DMSO

data_processing:
Basecalls performed using CASAVA version 1.4
The first 5 bases of the ChIP-seq reads were trimmed with fastx_toolkit v0.0.14 , and aligned to the human genome (hg19) with Bowtie2 v2.1.0 with the standard default settings.
The reads with mapping quality score greater than 20 were kept (samtools v1.3), and the duplicated reads were removed using picard tools v1.96 (https://broadinstitute.github.io/picard/).
Peak calling was performed with macs2 v2.1.0 (Zhang et al., 2008) with default parameters.  Inputs were used as a control for peak-calling.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited narrowPeak files generated by macs2 with q-value threshold 0.01, and the bigwig files generated with the signal as fold enrichment by macs2 following the procedure at https://github.com/taoliu/MACS/wiki/Build-Signal-Track.

source_name: ME-1 cells

extract_protocol:
Lysates were clarified from sonicated nuclei and RUNX1-DNA and histone-DNA complexes were isolated with antibodies.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

value: Anti-Histone H3 (acetyl K27) antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: miRNA.PANC1

data_processing:
Reads were quality filtered according to the Illumina pipeline, then were filtered for low-quality reads, contaminating adapters and homopolymers using Cutadapt v1.7.1 .
The preprocessed reads were aligned to known microRNAs (obtained from GENCODE release 24, mapped to GRCh37) and to the hg19 human reference genome using Bowtie2 v2.2.6.
Quantification of the expression of each annotated miRNAs was estimated as raw read counts within its genomic coordinates using  bedtools v2.25.0. Then, differential miRNA expression between Low-grade PDACs (CAPAN1, CAPAN2 and CFPAC1) and High-grade PDACs (MiaPaCa2, PANC1 and PT45P1) was calculated using EdgeR R-package v3.2.2.
Genome_build: hg19 (NCBI build GRCh37)
Supplementary_files_format_and_content: The file miRNA.counts.txt contains the raw read counts for each annotated miRNAs across cell lines. The file miRNA.edgeR_results.txt contains differentially expressed miRNA between Low-grade PDACs and High-grade PDACs. The file miRNA.normalized_CPM.txt contains normalized Counts Per Million (CPM) values.

extract_protocol:
Total RNA was extracted using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit was used with 1 ug of total RNA to produce microRNA sequencing libraries.
RNA adapters specifically modified to target microRNAs and other small RNAs that have 3’-hydroxyl and 5’-phosphate group resulting from enzymatic cleavage by RNA processing enzymes are ligated to each end of the RNA molecules. After synthesis of the first strand cDNA using reverse transcriptase and random primers, the cDNA is PCR amplified with indexed Illumina oligos. cDNA libraries generated by mature microRNA are separated by size on acrylamide gels and gel purified before proceeding to HiSeq 2000 Illumina sequencing.


title: miRNA.CAPAN1

growth_protocol: RPMI-1640 supplemented with 20% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep


title: miRNA.PT45P1

growth_protocol: RPMI-1640 supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep


title: miRNA.CFPAC1

growth_protocol: Iscove's Modified Dulbecco Medium (IMDM) supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep


title: miRNA.CAPAN2

growth_protocol: RPMI-1640 supplemented with 15% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep


title: H3K27ac: AI-10-49


title: MiaPaCa2.ZEB1

description: Chromatin IP against ZEB1

value: Anti-ZEB1 (Antibody SC-25388 Lot. H1513)


title: input DNA: DMSO


title: miRNA.MiaPaCa2


title: KMT2A-MLLT3 + Empty-GFP Kras-G12D (MAF >0.3) [SJ046295]

city: Lund

first: Axel

last: Hyrenius Wittsten

address: Klinikgatan 28

department: Division of Clinical Genetics

country: Sweden

institute: Lund University

data_processing:
Bcl2FastQ software was used for basecalling.
Paired-end reads from RNA sequencing were aligned using BWA (0.5.10).
Fragments per kilobase of transcript per million mapped fragments (FPKM) and gene FPKM was calculated using Cuffdiff2 and log2 transformed.
FPKM cutoff of ≥0.5 was used to define “expressed” genes and genes not expressed in at least one sample were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file including a filtered log2 FPKM value matrix for all samples.

source_name: Bone marrow

extract_protocol:
AllPrep DNA/RNA Mini Kit (Cat# 80204)
llumina TruSeq RNA Sample Prep Kit v2 (Cat# RS-122-2001).

tag: strain

tag: tissue

value: Bone marrow

value: KMT2A-MLLT3 leukemia


title: KMT2A-MLLT3 + Empty-GFP Ptpn11-E69K (MAF ≤0.3) [SJ046299]


title: KMT2A-MLLT3 + Empty-GFP Ptpn11-S506W (MAF >0.3) [SJ046294]


title: KMT2A-MLLT3 + NRAS-G12D [SJ046274]


title: KMT2A-MLLT3 + Empty-GFP Braf-V637E (MAF ≤0.3) [SJ046293]


title: KMT2A-MLLT3 + Empty-GFP Ptpn11-S506W (MAF >0.3) [SJ016337]


title: KMT2A-MLLT3 + NRAS-G12D [SJ046273]


title: KMT2A-MLLT3 + Empty-GFP [SJ046285]


title: KMT2A-MLLT3 + FLT3-ITD [SJ046278]


title: KMT2A-MLLT3 + Empty-GFP [SJ046286]


title: KMT2A-MLLT3 + FLT3-ITD [SJ046277]


title: KMT2A-MLLT3 + FLT3-ITD [SJ046276]


title: KMT2A-MLLT3 + FLT3-N676K [SJ046280]


title: input DNA: AI-10-49

value: Human inv(16) leukemia cell line


title: RUNX1: AI-10-49

value: Anti-RUNX1/AML1 antibody


title: RUNX1: DMSO

value: DMSO


title: KMT2A-MLLT3 + Empty-GFP Kras-G12D (MAF ≤0.3) [SJ016338]


title: KMT2A-MLLT3 + FLT3-N676K [SJ046279]


title: KMT2A-MLLT3 + NRAS-G12D [SJ046272]


title: KMT2A-MLLT3 + Empty-GFP [SJ046283]


title: KMT2A-MLLT3 + Empty-GFP [SJ018153]


title: KMT2A-MLLT3 + NRAS-G12D [SJ046271]


title: KMT2A-MLLT3 + Empty-GFP [SJ018151]


title: KMT2A-MLLT3 + Empty-GFP [SJ018150]


title: KMT2A-MLLT3 + Empty-GFP [SJ018148]


title: KMT2A-MLLT3 + Empty-GFP Braf-V637E (MAF ≤0.3) [SJ018146]


title: KMT2A-MLLT3 + Empty-GFP [SJ018149]


title: KMT2A-MLLT3 + Empty-GFP [SJ046284]


title: KMT2A-MLLT3 + Empty-GFP Ptpn11-S506W (MAF ≤0.3) [SJ046296]


title: KMT2A-MLLT3 + Empty-GFP [SJ018147]


title: KMT2A-MLLT3 + Empty-GFP [SJ018145]


title: KMT2A-MLLT3 + Empty-GFP [SJ018143]


title: KMT2A-MLLT3 + Empty-GFP [SJ018152]


title: KMT2A-MLLT3 + NRAS-G12D [SJ017001]


title: KMT2A-MLLT3 + FLT3-N676K [SJ017011]


title: KMT2A-MLLT3 + Empty-GFP [SJ018144]


title: KMT2A-MLLT3 + FLT3-N676K [SJ017012]


title: KMT2A-MLLT3 + FLT3-N676K [SJ017009]


title: KMT2A-MLLT3 + FLT3-N676K [SJ017010]


title: KMT2A-MLLT3 + FLT3-ITD [SJ017008]


title: KMT2A-MLLT3 + FLT3-ITD [SJ017006]


title: KMT2A-MLLT3 + FLT3-ITD [SJ017007]


title: KMT2A-MLLT3 + FLT3-ITD [SJ017005]


title: KMT2A-MLLT3 + FLT3-N676K [SJ046281]


title: KMT2A-MLLT3 + FLT3-N676K [SJ046282]


title: KMT2A-MLLT3 + NRAS-G12D [SJ017004]


title: KMT2A-MLLT3 + NRAS-G12D [SJ017003]


title: B6_young_rep5

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

description: Animal tissue

data_processing:
Raw sequence reads were pseudo aligned to the mouse transcriptome mm10 (Ensembl Build 84) using Kallisto (Version 0.43.0, Bray et al. Nat. Biotechnology 2016) runing 30 bootstrap rounds.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files per sample include effectice read counts and transcript per million (TPM) values for each transcript

source_name: Liver obtained from C57BL/6J mouse

extract_protocol:
Total RNAs were extracted from liver samples obtained from conplastic mouse strains (C57BL/6J and C57BL/6J-mtAKR/J), using innuPREP RNA Mini Kit (Analytik Jena) according to the manufacturer’s protocol. RNAs quality was checked using a Bioanalyzer system (Agilent Genomics).
RNA sequencing of primary samples was carried out employing the TruSeq  stranded Total RNA kit (Illumina Inc.), starting from 0.6µg total RNA of  each sample and sequenced on an Illumina HiSeq4000 (75-nucleotide  paired-end  reads). Aiming for high transcriptome coverage, sequencing runs were  performed out combining 4 samples per lane (corresponding to approximately  50 million reads per sample).

value: Liver

tag: knockdown

value: lower 12A heteroplasmy in OriL

tag: age

value: 4 months

tag: replicate


title: Sox2-GFP+ve alone 2

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3300 Hospital Dr NW

country: Canada

institute: University of Calgary - Faculty of Veterinary Medicine

data_processing:
Reads were processed using the 10X Genomics Cell Ranger Single Cell 2.0.0 pipeline with default and recommended parameters, as previously described (Zheng et al., 2017). FASTQs generated from Illumina sequencing output were aligned to the mouse GRCm38.p5 (primary assembly) reference genome using the STAR algorithm. Next, Gene-Barcode matrices were generated for each individual sample by counting unique molecular identifiers (UMIs) and filtering non-cell associated barcodes. Finally, all three samples were aggregated, with intermediary depth normalization, to generate a gene-barcode matrix containing 1700 barcoded cells and gene expression counts. This output was then imported into the Seurat (v1.4.0.15) R toolkit for quality control and downstream analysis of our single cell RNAseq experiment. All functions were run with default parameters, unless specified otherwise. Low quality cells (<400 genes/cell and <3 cells/gene) were discluded from the overall experiment. Gene expression was log normalized to a scale factor of 10 000.
Genome_build: mm10 (GRCm38.p5)
Supplementary_files_format_and_content: Tab-delimited table of Seurat processed and scaled single cell barcoded mRNA counts

molecule: polyA RNA

source_name: subventricular zone

extract_protocol:
The lateral wall of lateral ventricles (SVZ) from adult mice (n = 5) were microdissected and enzymatically dissociated with Papain (Worthington, 30 U/mL with 330µg/mL L-Cysteine in HBSS) at 37 °C for 30 mins with trituration every 10 minutes. Cell suspensions were then filtered through a 40µm Nylon cell strainer to obtain a single cell suspension. Liberated cells were re-suspended in 0.5% BSA in HBSS before FACS purification. For FACS purification/sorting, a stringent initial gate was used to exclude debris, and cell doublets. Wildtype cells were used as negative control to determine gates for detection of GFP and tdTOMATO-fluorescence, then cells from αSMACreERT2::tdTomato/Sox2::GFP mice were purified according to these gates. Cortical tissue (devoid of ependymal cells) was dissociated and sorted as above in order to determine gates distinguishing two subpopulations of αSMACreERT2::tdTomato+ve cells from SVZ tissue. All cells were processed according to 10x Genomics ChromiumTM Single Cell 3’ Reagent Guidelines (v2 Chemistry; https://support.10xgenomics.com/single-cell-gene-expression). Briefly, cells were partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology.
Primers containing (i) an Illumina R1 sequence, (ii) a 16 bp 10x barcode, (iii) a 10 bp Unique Molecular Identifier (UMI) and (iv) a poly-dT primer sequence were incubated with partitioned cells resulting in barcoded, full-length cDNA from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents/primers, then cNDA was amplified by PCR. Enzymatic Fragmentation and Size Selection was used to optimize cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) were added during GEM incubation, whereas P5, P7, a sample index (i7), and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation and PCR. Quality control and quantification was performed using a Kapa Library Quantification qPCR kit.

tag: transgenic line

tag: facs strategy

value: tdTomato-negative/GFP-positive

tag: # facs sorted cells

tag: library preparation

value: 10X Genomics Single Cell RNAseq v2

tag: strain background


title: Sox2-GFP+ve alone 1


title: aSMA::tdTomato/Sox2-GFP+ve

value: tdTomato-positive/GFP-positive


title: Normal_wt4

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

data_processing:
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and  employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC mm10 assembly using Tophat2 and counted for gene associations against the UCSC genes database with HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

source_name: tissue

extract_protocol:
RNA was extracted from cell cultures every two weeks during the exponential growth phase; RNA was isolated from 0.5-1.0×106 cells. Total RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: supratentorial ependymoma


title: PDGFA_INK4ARF3


title: TYPE1_INK4ARF1


title: Normal_wt3


title: TYPE1_wt3


title: TYPE1_INK4ARF3


title: NORMAL_INK4ARF3


title: PDGFA_INK4ARF1


title: TYPE1_wt4


title: NORMAL_INK4ARF2


title: PDGFA_INK4ARF2


title: Normal_wt1


title: Normal_wt2


title: TYPE1_INK4ARF2


title: TYPE1_wt2


title: NORMAL_INK4ARF4


title: TYPE1_wt1


title: PDGFA_INK4ARF4


title: CREE replicate 1

description: CREE replicate 1


title: GFP replicate 1

description: GFP replicate 1


title: CRS486E replicate 2

description: CRS486E replicate 2


title: GFP replicate 2

description: GFP replicate 2


title: NORMAL_INK4ARF1


title: CREE replicate 2

description: CREE replicate 2


title: TYPE1_INK4ARF4


title: CRS486E replicate 1

description: CRS486E replicate 1


title: RELA-S276E replicate 2

description: RELA-S276E replicate 2


title: KMT2A-MLLT3 + NRAS-G12D [SJ017002]

tag: cell type


title: RELA-S276E replicate 1

description: RELA-S276E replicate 1


title: CRKR replicate 2

description: CRKR replicate 2


title: CRKR replicate 1

description: CRKR replicate 1


title: CR1 replicate 2

description: CR1 replicate 2


title: CRS746E replicate 2

description: CRS746E replicate 2


title: RELA-S536E replicate 2

description: RELA-S536E replicate 2


title: CRS746E replicate 1

description: CRS746E replicate 1


title: RELA-S536E replicate 1

description: RELA-S536E replicate 1


title: CR1 replicate 1

description: CR1 replicate 1


title: Rela replicate 1

description: Rela replicate 1


title: ChIPseq_male_6w_cortex_WT_H4K20me3_rep1

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq mapping and peak calling. The ChIP-seq FASTQ files were mapped to the mouse mm10 genome by bowtie using “-v 2 -m 1”. Only uniquely mapped reads were included for further analysis. The Homer findPeaks function was used to call peaks from the H3K4me3 data sets using the parameters of “-style histone -minDist 2500”.
ATAC-seq mapping. The mate1 and mate2 files of the paired-end sequencing were mapped separately to the mm10 genome by bowti2 using “-v 2 -m 1”. If both mates of a read pair were mapped to the opposite strands of the same chromosome and the distance in-between was less than 2 kb, the read pair was included for further analysis.
TAB-seq and WGBS mapping and analysis. Trim Galore was used to remove the adaptor contamination from the raw sequencing reads using “-stringency 2 --length 36”. The trimmed reads were mapped to mm10 genome by Bismark using parameters  “-n 2 -l 40”. Clonal reads were excluded to avoid PCR artifacts. Methylation calling was performed by Binomial distribution followed by the Benjamini-Hochberg procedure to identify cytosine whose methylation level was significantly higher than the non-conversion rate, which is set to 0.02 for TAB-seq and 0.001 for WGBS. The cutoff was FDR < 0.0001. The hmC level for a cytosine was calculated as the number of methylated TAB-seq reads covered this cytosine divided by the total number of TAB-seq reads covered this cytosine. The mC level for a cytosine was calculated as the number of methylated WGBS reads covered this cytosine divided by the total number of WGBS reads covered this cytosine, then subtract the hmC level in this cytosine. The minimum mC level was set to zero.
Genome browser track files. Samtools was used to convert sam files into bam files and sorted the bam files. For GRO-seq, Bedtools genomecov was used to convert the bam files into bedGraph files using “-bga -split -strand”, and then bedGraphToBigWig was used to convert the bedGraph files into BigWig files. For ATAC-seq, IGVtools was used to generate the TDF files using “count -z 5 -w 25 --pairs”. For ChIP-seq, IGVTools was used to generate the TDF files using “count -z 5 -w 25 -e 250”.
Genome_build: mm10
Supplementary_files_format_and_content: Samtools was used to convert sam files into bam files and sorted the bam files. For ATAC-seq, IGVtools was used to generate the TDF files using “count -z 5 -w 25 --pairs”. For ChIP-seq, IGVTools was used to generate the TDF files using “count -z 5 -w 25 -e 250”. For TABseq and WGBS, bedGraph files include the methylation levels.

source_name: Cortex

growth_protocol: All the mice used were in the C57BL/6 background, were housed in a 12h light/12h dark cycle, and were given enough amounts of food and water. All experiments were conducted in accordance with the ethical guidelines of the US National Institutes of Health and with the approval of the Institutional Animal Care and Use Committee of the University of Pennsylvania.

extract_protocol:
For ChIP-seq, chromatin of whole cortex from two 6-week-old C57BL/6 mice were used. For TAB-seq and WGBS, the genomic DNA was isolated from the nuclei of the cortical excitatory neurons. For ATAC-seq, the chromatin was isolated from the nuclei of the cortical excitatory neurons.
Libraries were prepared for sequencing using standard Illumina protocols

value: Cortical cells

value: 6 week old

tag: chip antibody

value: Abcam ab9053

tag: gender

value: male


title: ChIPseq_male_6w_cortex_WT_Input_rep2


title: WGBS_male_6w_Excitatory_WT

value: Cortical excitatory neurons


title: TABseq_male_6w_Excitatory_WT

data_processing:
Library strategy: TAB-seq
Illumina Casava1.7 software used for basecalling.
ChIP-seq mapping and peak calling. The ChIP-seq FASTQ files were mapped to the mouse mm10 genome by bowtie using “-v 2 -m 1”. Only uniquely mapped reads were included for further analysis. The Homer findPeaks function was used to call peaks from the H3K4me3 data sets using the parameters of “-style histone -minDist 2500”.
ATAC-seq mapping. The mate1 and mate2 files of the paired-end sequencing were mapped separately to the mm10 genome by bowti2 using “-v 2 -m 1”. If both mates of a read pair were mapped to the opposite strands of the same chromosome and the distance in-between was less than 2 kb, the read pair was included for further analysis.
TAB-seq and WGBS mapping and analysis. Trim Galore was used to remove the adaptor contamination from the raw sequencing reads using “-stringency 2 --length 36”. The trimmed reads were mapped to mm10 genome by Bismark using parameters  “-n 2 -l 40”. Clonal reads were excluded to avoid PCR artifacts. Methylation calling was performed by Binomial distribution followed by the Benjamini-Hochberg procedure to identify cytosine whose methylation level was significantly higher than the non-conversion rate, which is set to 0.02 for TAB-seq and 0.001 for WGBS. The cutoff was FDR < 0.0001. The hmC level for a cytosine was calculated as the number of methylated TAB-seq reads covered this cytosine divided by the total number of TAB-seq reads covered this cytosine. The mC level for a cytosine was calculated as the number of methylated WGBS reads covered this cytosine divided by the total number of WGBS reads covered this cytosine, then subtract the hmC level in this cytosine. The minimum mC level was set to zero.
Genome browser track files. Samtools was used to convert sam files into bam files and sorted the bam files. For GRO-seq, Bedtools genomecov was used to convert the bam files into bedGraph files using “-bga -split -strand”, and then bedGraphToBigWig was used to convert the bedGraph files into BigWig files. For ATAC-seq, IGVtools was used to generate the TDF files using “count -z 5 -w 25 --pairs”. For ChIP-seq, IGVTools was used to generate the TDF files using “count -z 5 -w 25 -e 250”.
Genome_build: mm10
Supplementary_files_format_and_content: Samtools was used to convert sam files into bam files and sorted the bam files. For ATAC-seq, IGVtools was used to generate the TDF files using “count -z 5 -w 25 --pairs”. For ChIP-seq, IGVTools was used to generate the TDF files using “count -z 5 -w 25 -e 250”. For TABseq and WGBS, bedGraph files include the methylation levels.


title: ChIPseq_male_6w_cortex_WT_H3K9me3_rep2

value: Abcam ab8898


title: ATACseq_male_6w_Excitatory_WT_PE_rep1


title: ATACseq_male_6w_Excitatory_WT_PE_rep2


title: ChIPseq_male_6w_cortex_WT_H3K79me2_rep1

value: Abcam ab3594


title: ChIPseq_male_6w_cortex_WT_H3K9me3_rep1


title: ChIPseq_male_6w_cortex_WT_H3K4me3_rep2

value: Millipore 07-473


title: ChIPseq_male_6w_cortex_WT_H3K79me2_rep2


title: ChIPseq_male_6w_cortex_WT_H3K4me3_rep1


title: ChIPseq_male_6w_cortex_WT_H3K36me3_rep2

value: Abcam ab9050


title: ChIPseq_male_6w_cortex_WT_H3K36me3_rep1


title: 129297_WT_CL_TR

city: Rozzano

first: Alberto

last: Termanini

state: MI

address: Via Manzoni, 113

institute: Istituto Clinico Humanitas

description: total RNA extracted from liver tissue of Mdr2-WT mice treated with clodronate liposomes

data_processing:
Reads were quality filtered according to the Illumina pipeline.
Reads were mapped to the mouse mm9 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches and with a mean distance between pairs (-r) of 120bp.
Transcripts abundance and differentially expressed genes were obtained using Cufflinks 2.2.1 (PMID: 20436464).
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus Ensembl Build 67 (GRCh37.p7).
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression (FPKM), *.diff list the statistics for differential expression between sample groups (refer to http://cole-trapnell-lab.github.io/cufflinks/manual/ for details).

growth_protocol: Liver tissue from Mdr2-WT mice or Mdr2-KO mice HCC nodules was collected at 14 to 19 months of age. Liver tissue from Mdr2-KO mice at the "inflamed" stage was collected at 7 to 8 months of age.

extract_protocol: Total RNA was extracted using Maxwell 16 total RNA purification kit (Promega). Libraries were prepared from 4 µg of RNA, after treatment with Ribo-Zero rRNA removal kit (Illumina), using the TruSeq RNA sample preparation kit (Illumina).

treatment_protocol: 48 hours treatment with clodronate liposomes via tail injection (50ug/g body weight), followed by sample collection.

tag: genotype/variation

tag: treatment

value: clodronate liposomes (50ug/g body weight) for 48hrs


title: 133626_WT_CL_UT

description:
total RNA extracted from liver tissue of Mdr2-WT mice
genes2.fpkm_tracking.gz
gene_exp2.diff.gz

source_name: Liver tissue

value: Liver

value: Untreated


title: 130747_WT_CL_TR


title: 132948_WT_CL_UT


title: 130748_WT_CL_TR


title: Rela replicate 2

description: Rela replicate 2


title: ChIPseq_male_6w_cortex_WT_Input_rep1


title: 129296_WT_CL_TR


title: ChIPseq_male_6w_cortex_WT_H4K20me3_rep2


title: 149199_inflamed_CL_TR

description: total RNA extracted from liver tissue of Mdr2-KO mice treated with clodronate liposomes


title: 149198_inflamed_CL_TR


title: 134501_WT_CL_TR


title: 148997_inflamed_CL_TR


title: 148990_inflamed_CL_TR


title: 123390_nodule_CL_TR

description: total RNA extracted from HCC nodules of Mdr2-KO mice treated with clodronate liposomes

source_name: Mdr2-KO_hepatocarcinoma nodules


title: 125279_nodule_CL_TR


title: 125278_nodule_CL_TR


title: Mdr2-WT_liver Input

description: Chromatin IP against IgG

data_processing:
Reads pooled: Sample 19 and Sample 20; Sample 21 and Sample 22; Sample 24 and Sample 25; Sample 26 and Sample 27; Sample 28 and Sample 29.
Reads quality filtered according to the Illumina pipeline.
Reads were mapped to the mouse mm9 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID 18798982) with default parameters and --gsize=2.72e9, --tsize=36. Each IP was compared to input DNA.
Genome_build: mm9 (NCBI Build 37).
Supplementary_files_format_and_content: *_input_peaks.bed: list of the peaks vs input called by MACS having -10*log10(pvalue) >= 50.

extract_protocol: Tissues were chopped and fixed in 1% formaldehyde for 15min. Lysates were immunoprecipitated with 5ug of antibody. Antibodies were pre-bound overnight to 50ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (after an overnight preclearing step) and the mix was incubated overnight at 4°C. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by overnight incubation at 65ºC. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters and PCR with index primers. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

tag: treated with

value: Liver tissue

tag: antibody

value: IgG (Santa Cruz, sc-2027)


title: 123206_nodule_CL_TR_H3K27Ac

description: Chromatin IP against H3K27Ac

tag: strain

value: Hepatocarcinoma tissue

value: H3K27Ac (Abcam, ab4729)


title: 125279_nodule_CL_TR_H3K27Ac

description: Chromatin IP against H3K27Ac

tag: tissue


title: 123390_nodule_CL_TR_H3K27Ac

description: Chromatin IP against H3K27Ac


title: 149199_inflamed_CL_TR_H3K27Ac

description: Chromatin IP against H3K27Ac


title: 148990_inflamed_CL_TR_H3K27Ac

description: Chromatin IP against H3K27Ac


title: 125278_nodule_CL_TR_H3K27Ac

description: Chromatin IP against H3K27Ac


title: 124711_nodule_CL_TR_H3K27Ac

description: Chromatin IP against H3K27Ac


title: 148997_inflamed_CL_TR_H3K27Ac

description: Chromatin IP against H3K27Ac


title: 130748_WT_CL_TR_H3K27Ac

description: Chromatin IP against H3K27Ac


title: 149198_inflamed_CL_TR_H3K27Ac

description: Chromatin IP against H3K27Ac


title: 129297_WT_CL_TR_H3K27Ac

description: Chromatin IP against H3K27Ac


title: 129296_WT_CL_TR_H3K27Ac

description: Chromatin IP against H3K27Ac


title: 130747_WT_CL_TR_H3K27Ac

description: Chromatin IP against H3K27Ac


title: 148998_inflamed_CL_TR


title: 148998_inflamed_CL_TR_H3K27Ac

description: Chromatin IP against H3K27Ac


title: 134501_WT_CL_TR_H3K27Ac

description: Chromatin IP against H3K27Ac


title: YY-1-c

city: Tianjin

first: Jingen

last: Li

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Monascus purpureus YY-1 genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p2).
Genome_build: Monascus purpureus YY-1
Supplementary_files_format_and_content: tab-delimited text file including Reads count for each sample.

organism: Monascus purpureus

source_name: Monascus purpureus YY-1

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mycelia


title: Winter_b

source_name: Monascus purpureus Winter

value: Winter


title: YY-1-b


title: Winter_c


title: Winter_a


title: 124711_nodule_CL_TR


title: WT rep2

status: Public on May 01 2018

city: 2215 Garland Ave

first: Michael

last: Litt

state: TN

address: 702 Light Hall

department: MPB

institute: Vanderbilt University

data_processing:
Illumina HiSeq300 reads were converted to FASTQ files using the Bcl2fastq2 conversion software.
Read quality was checked using FastQCv0.11.5. TopHat v2.1.0 was then used for read allignment  Tool Parameters  Is this single-end or paired-end data? paired_collection   RNA-Seq FASTQ paired reads No dataset collection.   Mean Inner Distance between Mate Pairs 300   Std. Dev for Distance between Mate Pairs 20   Report discordant pair alignments? Yes   Use a built in reference genome or own from your history indexed   Select a reference genome mm10   TopHat settings to use full   Max realign edit distance 1000   Max edit distance 2   Library Type FR First Strand   Final read mismatches 2   Use bowtie -n mode No   Anchor length (at least 3) 8   Maximum number of mismatches that can appear in the anchor region of spliced alignment 0   The minimum intron length 70   The maximum intron length 500000   Allow indel search Yes   Max insertion length. 3   Max deletion length. 3   Maximum number of alignments to be allowed 20   Minimum intron length that may be found during split-segment (default) search 50   Maximum intron length that may be found during split-segment (default) search 500000   Number of mismatches allowed in each segment alignment for reads mapped independently 2   Minimum length of read segments 25   Output unmapped reads False   Do you want to supply your own junction data Yes   Use Gene Annotation Model Yes   Gene Model Annotations 220: UCSC Main on Mouse: refGene (genome)   Use Raw Junctions No   Only look for supplied junctions No   Use coverage-based search for junctions auto   Use Microexon Search No   Do Fusion Search No   Set Bowtie2 settings No   Specify read group? no   Job Resource Parameters no
Aligned reads were then assembled into transcripts with Cufflinks v2.2.1 Tool Parameters:  SAM or BAM file of aligned RNA-Seq reads 240: TopHat on data 220, data 33, and data 22: accepted_hits   Max Intron Length 300000   Min Isoform Fraction 0.1   Pre MRNA Fraction 0.15   Use Reference Annotation Use reference annotation   Reference Annotation 220: UCSC Main on Mouse: refGene (genome)   Count hits compatible with reference RNAs only No   Perform Bias Correction Yes   Reference sequence data cached   Using reference genome mm10   Use multi-read correct No   Apply length correction Cufflinks Effective Length Correction   Global model (for use in Trackster) No dataset.   Set advanced Cufflinks options Yes   Library prep used for input reads fr-firststrand   Mask File    Inner mean distance 300   Inner distance standard deviation 20   Max MLE iterations 5000   Alpha value for the binomial test used during false positive spliced alignment filtration 0.001   percent read overhang taken as suspiciously small 0.09   Intronic overhang tolerance 8   Maximum genomic length of a given bundle 3500000   Maximum number of fragments per locus 1000000   Minimal allowed intron size 50   Minimum average coverage required to attempt 3prime trimming. 10   The fraction of average coverage below which to trim the 3prime end of an assembled transcript. 0.1   Job Resource Parameters no
Files were then merged using Cuffmerge v2.2.1 and RMPK values were quantified using CuffQuant v2.2.1:Tool Parameters  Transcripts 341: Cuffmerge on data 220, data 333, and others: merged transcripts   Add replicate 225: TopHat on data 220, data 39, and data 38: accepted_hits   Use multi-read correct False   Perform Bias Correction Yes   Reference sequence data cached   Using reference genome mm10   apply length correction cufflinks effective length correction   Set Additional Parameters for single end reads? (not recommended for paired-end reads) No   Set Advanced Cuffquant parameters? Yes   Library prep used for input reads fr-firststrand   Mask File    Max MLE iterations 5000   Maximum number of fragments per locus 500000   Job Resource Parameters no
Cuffnorm v2.2.1.1 was then used to normalize for transcript length: Tool Parameters  Transcripts 341: Cuffmerge on data 220, data 333, and others: merged transcripts   Input data type CXB   Name WT   Replicates 442: Cuffquant on data 225 and data 341: Abundances.cxb , 443: Cuffquant on data 230 and data 341: Abundances.cxb , 444: Cuffquant on data 235 and data 341: Abundances.cxb , 445: Cuffquant on data 240 and data 341: Abundances.cxb   Name KO   Replicates 447: Cuffquant on data 250 and data 341: Abundances.cxb , 448: Cuffquant on data 255 and data 341: Abundances.cxb , 449: Cuffquant on data 260 and data 341: Abundances.cxb , 450: Cuffquant on data 265 and data 341: Abundances.cxb , 451: Cuffquant on data 270 and data 341: Abundances.cxb , 452: Cuffquant on data 275 and data 341: Abundances.cxb   Library normalization method geometric   Include Read_Group/Attribute Datasets Yes   output_format Simple Table   Set Advanced Cuffnorm parameters? Yes   Library prep used for input reads fr-firststrand   Hits included in normalization Compatible Hits   Job Resource Parameters no
Differnetial gene trasncription testing was then conducted using Cuffdiff v2.2.1.3: Tool Parameters   Library normalization method geometric   Dispersion estimation method pooled   False Discovery Rate 0.05   Min Alignment Count 10   Use multi-read correct False   Perform Bias Correction No   Include Read Group Datasets No   Include Count Based output files No   apply length correction cufflinks effective length correction   Set Additional Parameters for single end reads? (not recommended for paired-end reads) No   Set Advanced Cuffdiff parameters? No   Job Resource Parameters no
Genome_build: mm10
Supplementary_files_format_and_content: cuffnorm_allsamples.txt: Tab-delimited text file with a matrix of all RPKM values. Cuffdiff_q_0.05.txt: Tab-delimited text file of log fold change RPKM values with q<0.05

source_name: Left ventricle posterior wall

growth_protocol: Mice were generated using a het-het breeding strategy and housed at 24degC for 30 weeks.

extract_protocol:
Mice were anethetized with TBE and then hearts were flash frozen in liquid nitogen. Total RNA was extracted usign trizol with a quiagen column cleanup with on column DNAse.
200ng of DNase-treated total RNA with a RNA integrity number greater than 7 was used to generate polyA-enriched mRNA libraries using KAPA Stranded mRNA sample kits with indexed adaptors (Roche; Basel, Switzerland).

value: Left ventricle posterior wall

value: 30 weeks


title: MC4R-/- rep2


title: WT rep4


title: MC4R-/- rep4


title: MC4R-/- rep1


title: MC4R-/- rep6


title: MC4R-/- rep3


title: WT rep1


title: MC4R-/- rep5


title: WT rep3


title: Final_Total_Lib3

city: Nottingham

first: Stephan

last: Heeb

state: Nottinghamshire

address: Centre for Biomolecular Sciences, University Park, University of Nottingham

country: United Kingdom

institute: University of Nottingham

description: total RNA

data_processing:
Raw reads were assessed using the FastQC tool version 0.11.5 and then adapter trimmed using Scythe with -q (quality type)  as sanger and -n (minimum match) as 10 and the quality trimmed using Sickle using -t  (quality values) as sanger, SE and PE settings were used according to the documentation. Reads quality was then reassessed using FastQC.
To filter out tRNAs and rRNAs reads that were still present despite the ribodepletion, a reference was made of annotated rRNAs and tRNAs in the gtf file. Reads were then aligned to the filter reference using TopHat v2.1.1 with default parameters except --library-type fr-firststrand --no-gtf-juncs –no-novel-juncs. Reads were then extracted from the unmapped.bam file with standard proceedures for bedtools bamtofastq. A subset of reads for each paired end data set was extracted and aligned to the reference using Bowtie2 version 2.2.9 with default parameters, Picard Tools CollectInsertSizemetrics (version 2.7.1) was then used to ascertain the insert size information for alignment. Alignment to the reference was performed using Bowtie2 2.2.9, as the insert sizes fell within default settings, default parameters were used for the alignment. Bams were filtered for scores of MAPQ20 or greater.
Wig files were created for each sample using the default settings of bedtools genomecov (bedtools v2.25.0).  For the preliminary experiment in which strandedness had been lost (Prelim_RsmN_Lib1, Prelim_RsmN_Lib2, Prelim_Total_Lib1, Prelim_Total_Lib2), corresponding count pairs were combined in single wig files.  For the final experiment containing strand information (Total_Lib1, Total_Lib2, Total_Lib3, RsmN_Lib1, RsmN_Lib2, RsmN_Lib3) counts for bases on each strand were separated in wig files according to the strand to which they mapped (positive or negative).
Inspection of raw wig files revealed that they still contained strong rRNA signals.  A further filtering step ("riboskipping") was performed by zeroing all the values between 21775-727262, 4788574-4793732, 5276152-5281666 and 6051627-6057275 in each wig file.  Then data from corresponding duplicate (preliminary experiment) and triplicate (final experiment) wig files were added and average read per base for each sum was calculated to normalise each value by dividing it by this average.  Finally, for each base the ratio between RsmN-bound to Total-RNA was calculated as log(100 x (RsmN-bound/Total-RNA)).  When Total-RNA values were zero (undefined ratio), the resulting ratios were set to zero.  This resulted in the three *.ribosk.norm.logratio100.wig files.
Genome_build: NC_002516.inverted.RGP42insertion : see supplementary files
Supplementary_files_format_and_content: Wig files were generates using Bedtools genomecov and default settings. Counts are shown for each bp of the genome.

organism: Pseudomonas aeruginosa

source_name: cultured cells

growth_protocol: Hexahistidine-tagged RsmN was expressed from plasmid pMR4 in P. aeruginosa PAO1-L growing in LB at 37°C with shaking.  Cells were induced with 1 mM IPTG at OD600 0.6, and samples collected 5h later (early stationary phase).

extract_protocol:
RNA from the Total RNA and from the 6xHisRsmN-RNA samples were extracted using RNeasy Mini Kit (Qiagen), with treatment with Turbo DNAse (Ambion) to eliminate any genomic DNA.
For the preliminary experiment (Prelim_*, duplicates), RNA quality was assessed using the Agilent RNA 6000 Nano Kit (Agilent Tecnologies, 5067-1511) on the Agilent 2100 Bioanalyzer, and concentration was measured using Qubit RNA BR assay kit (Life technologies, Q10210). RNA was ribodepleted using Ribo-Zero rRNA Removal Kit (Illumina, MRZGP126). Illumina stranded whole transcriptome sequencing libraries were prepared using NEBNext Ultra Directional RNA library prep kit for Illumina (NEB, E7420S).  The following steps were carried out with parts of the Illumina TruSeq ChIP Seq kit (Part#15023092Rev.B): due to library yields that were considered suboptimal in this preliminary experiment, Sample Preparation Kit was used to amplify the libraries, which caused loss of strand information.  Library QC was performed using bioanalyser HS kit (Agilent biotechnologies, 5067-4626). The Illumina TruSeq ChIP Seq protocol was then followed according to the manufacturer's instructions and the size selection of ligated products were performed using BluePippin. The sequencing was performed using Illumina MiSeq on 150 cycles cartridge, using v3 chemistry to generate 75-bp paired end reads.  For the final experiment (Final_*, triplicates), samples were processed as for the preliminary experiment, excepted that the TruSeq ChIP Sample Preparation Protocol was skipped to the Enrich DNA Fragments step to conserve strand information.  Libraries were sequenced as for the preliminary experiment obtaining an average read length of 51 sequenced via single-read approach.

treatment_protocol: Samples were collected for the simultaneous extraction of (i) total RNA, and (ii) for the native purification of 6xHisRsmN-RNA using the Ni-NTA Fast Start Kit (Qiagen) followed by further clean-up and concentration using 3 kDa Amicon Ultra-4 centrifugal filters (Millipore).


title: Final_Total_Lib2

description: total RNA

value: Hexahistidine-tagged RsmN was expressed from plasmid pMR4


title: Prelim_RsmN_Lib2

description: HisRsmN-bound RNA


title: Final_RsmN_Lib1

description: HisRsmN-bound RNA


title: Final_Total_Lib1

description: total RNA


title: YY-1-a


title: Final_RsmN_Lib2

description: HisRsmN-bound RNA


title: Prelim_Total_Lib1

description: total RNA


title: Prelim_Total_Lib2

description: total RNA


title: Final_RsmN_Lib3

description: HisRsmN-bound RNA


title: TRAIL-treated, repeat 1

city: Boston

first: Rui

last: Fu

address: 200 Longwood Ave

department: PCMM

institute: boston children's hospital

data_processing:
alignment by TopHat2
read counting by HTSeq
differential expression analysis by DESeq2
Genome_build: GENCODE GRCh38
Supplementary_files_format_and_content: csv, normalized abundance measurements from DESeq2

extract_protocol:
TRIzol
NEBNext Ultra RNA Library Prep Kit

tag: cel line

value: 100ng/ml TRAIL for 2 hrs


title: untreated, repeat 2

value: none (untreated)


title: TRAIL-treated, repeat 2


title: co-culture LEC +Bowes elute2 III (S6_R4)

city: Helsinki

first: Paivi

middle: Marjut

last: Ojala

address: Haartmaninkatu 8 (P.O.Box 63)

department: Research Programs Unit

country: Finland

institute: University of Helsinki

description:
S6_R4
Bowes_geneMatrix_countArray_sort.txt

data_processing:
Conventional basecalls with Sanger / Illumina 1.9
PRINSEQ poly A/T tails trimming, Created with operation: Preprocessing / Trim reads for several criteria with PRINSEQ, Parameter Input file format: FASTQ, Parameter Base quality encoding: Sanger, Parameter Trim 5-prime end by quality: 0, Parameter Trim 3-prime end by quality: 5, Parameter Quality score calculation method: minimum quality value, Parameter Quality score comparison condition: less than, Parameter Window size for quality calculation: 1, Parameter Step size used to move the quality window: 1, Parameter Trim left A/T tails: 10, Parameter Trim right A/T tails: 10, Parameter Trim left poly-N tails: 10, Parameter Trim right poly-N tails: 10, Parameter Minimum length: 20, Parameter Write a log file: yes
Created with operation: Alignment / TopHat2 for single end reads, Parameter Genome: Homo_sapiens.GRCh38, Parameter Use annotation GTF: yes, Parameter When GTF file is used, ignore novel junctions: no, Parameter Base quality encoding used: Sanger - Phred+33, Parameter How many hits is a read allowed to have: 20, Parameter Number of mismatches allowed in final alignment: 2, Parameter Minimum anchor length: 8, Parameter Maximum number of mismatches allowed in the anchor: 0, Parameter Minimum intron length: 70, Parameter Maximum intron length: 500000, Parameter Library type: fr-unstranded
HTSeq for counting reads: Dataset name: htseq-counts.tsv, Created with operation: RNA-seq / Count aligned reads per genes with HTSeq, Parameter Reference organism: Homo_sapiens.GRCh38.78, Parameter Chromosome names in the BAM file look like: 1, Parameter Does the BAM file contain paired-end data: no, Parameter Was the data produced with a strand-specific protocol: no, Parameter Mode to handle reads overlapping more than one feature: union, Parameter Minimum alignment quality: 10, Parameter Feature type to count: exon,   Parameter Feature ID to use: gene_id, Parameter Add chromosomal coordinates to the count table: no
Genome_build: GRCh38.76 reference genome
Supplementary_files_format_and_content: metadata and raw counts separately for each cell line

source_name: co-culture LEC +Bowes elute2 III

extract_protocol:
Extract protocol according to Illumina standards
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Bowes

value: melanoma cell line

tag: cell source

value: metastasis and primary tumor


title: co-culture LEC +Bowes elute2 III (S6_R3)

description:
S6_R3
Bowes_geneMatrix_countArray_sort.txt


title: untreated, repeat 1


title: co-culture LEC +Bowes elute2 III (S6_R1)

description:
S6_R1
Bowes_geneMatrix_countArray_sort.txt


title: Prelim_RsmN_Lib1

description: HisRsmN-bound RNA


title: co-culture LEC +Bowes elute2 III (S6_R2)

description:
S6_R2
Bowes_geneMatrix_countArray_sort.txt


title: co-culture LEC +Bowes elute2 II (S4_R2)

description:
S4_R2
Bowes_geneMatrix_countArray_sort.txt

source_name: co-culture LEC +Bowes elute2 II


title: co-culture LEC +Bowes elute2 II (S4_R3)

description:
S4_R3
Bowes_geneMatrix_countArray_sort.txt


title: co-culture LEC +Bowes elute2 II (S4_R4)

description:
S4_R4
Bowes_geneMatrix_countArray_sort.txt


title: Bowes III (S5_R3)

description:
S5_R3
Bowes_geneMatrix_countArray_sort.txt

source_name: Bowes III


title: Bowes III (S5_R1)

description:
S5_R1
Bowes_geneMatrix_countArray_sort.txt


title: co-culture LEC +Bowes elute2 II (S4_R1)

description:
S4_R1
Bowes_geneMatrix_countArray_sort.txt


title: Bowes II (S3_R4)

description:
S3_R4
Bowes_geneMatrix_countArray_sort.txt

source_name: Bowes II


title: Bowes III (S5_R2)

description:
S5_R2
Bowes_geneMatrix_countArray_sort.txt


title: Bowes I (S1_R3)

description:
S1_R3
Bowes_geneMatrix_countArray_sort.txt

source_name: Bowes I


title: Bowes I (S1_R4)

description:
S1_R4
Bowes_geneMatrix_countArray_sort.txt


title: co-culture LEC +Bowes elute2 I (S2_R1)

description:
S2_R1
Bowes_geneMatrix_countArray_sort.txt

source_name: co-culture LEC +Bowes elute2 I


title: co-culture LEC +Bowes elute2 I (S2_R3)

description:
S2_R3
Bowes_geneMatrix_countArray_sort.txt


title: co-culture LEC +Bowes elute2 I (S2_R2)

description:
S2_R2
Bowes_geneMatrix_countArray_sort.txt


title: Bowes I (S1_R1)

description:
S1_R1
Bowes_geneMatrix_countArray_sort.txt


title: co-culture LEC +WM852 beads elute2 III (S6_L4)

description:
S6_L4
WM852_geneMatrix_countArray_sort.txt

source_name: co-culture LEC +WM852 beads elute2 (III)


title: co-culture LEC +WM852 beads elute2 III (S6_L3)

description:
S6_L3
WM852_geneMatrix_countArray_sort.txt


title: co-culture LEC +WM852 beads elute2 III (S6_L2)

description:
S6_L2
WM852_geneMatrix_countArray_sort.txt


title: Bowes I (S1_R2)

description:
S1_R2
Bowes_geneMatrix_countArray_sort.txt


title: 123206_nodule_CL_TR

description: total RNA extracted from HCC nodules of Mdr2-KO mice treated with clodronate liposomes

value: clodronate liposomes (50ug/g body weight) for 48hrs


title: WM852 beads III (S5_L4)

description:
S5_L4
WM852_geneMatrix_countArray_sort.txt

source_name: WM852 beads (III)


title: co-culture LEC +WM852 beads elute2 III (S6_L1)

description:
S6_L1
WM852_geneMatrix_countArray_sort.txt


title: WM852 beads III (S5_L3)

description:
S5_L3
WM852_geneMatrix_countArray_sort.txt


title: WM852 beads III (S5_L1)

description:
S5_L1
WM852_geneMatrix_countArray_sort.txt


title: WM852 beads III (S5_L2)

description:
S5_L2
WM852_geneMatrix_countArray_sort.txt


title: Bowes III (S5_R4)

description:
S5_R4
Bowes_geneMatrix_countArray_sort.txt


title: Bowes II (S3_R3)

description:
S3_R3
Bowes_geneMatrix_countArray_sort.txt


title: co-culture LEC +WM852 beads elute2 II (S4_L4)

description:
S4_L4
WM852_geneMatrix_countArray_sort.txt

source_name: co-culture LEC +WM852 beads elute2 (II)


title: co-culture LEC +WM852 beads elute2 II (S4_L3)

description:
S4_L3
WM852_geneMatrix_countArray_sort.txt


title: co-culture LEC +WM852 beads elute2 II (S4_L1)

description:
S4_L1
WM852_geneMatrix_countArray_sort.txt


title: WM852 beads II (S3_L2)

description:
S3_L2
WM852_geneMatrix_countArray_sort.txt

source_name: WM852 beads (II)


title: WM852 beads II (S3_L1)

description:
S3_L1
WM852_geneMatrix_countArray_sort.txt


title: WM852 beads II (S3_L4)

description:
S3_L4
WM852_geneMatrix_countArray_sort.txt


title: co-culture LEC +WM852 beads elute2 II (S4_L2)

description:
S4_L2
WM852_geneMatrix_countArray_sort.txt


title: co-culture LEC +Bowes elute2 I (S2_R4)

description:
S2_R4
Bowes_geneMatrix_countArray_sort.txt


title: Bowes II (S3_R2)

description:
S3_R2
Bowes_geneMatrix_countArray_sort.txt


title: Bowes II (S3_R1)

description:
S3_R1
Bowes_geneMatrix_countArray_sort.txt


title: co-culture LEC +WM852 beads elute2 I (S2_L1)

description:
S2_L1
WM852_geneMatrix_countArray_sort.txt

source_name: co-culture LEC +WM852 beads elute2 (I)


title: co-culture LEC +WM852 beads elute2 I (S2_L4)

description:
S2_L4
WM852_geneMatrix_countArray_sort.txt


title: WM852 beads I (S1_L3)

description:
S1_L3
WM852_geneMatrix_countArray_sort.txt

source_name: WM852 beads (I)


title: WM852 beads I (S1_L2)

description:
S1_L2
WM852_geneMatrix_countArray_sort.txt


title: WM852 beads I (S1_L4)

description:
S1_L4
WM852_geneMatrix_countArray_sort.txt


title: co-culture LEC +WM852 beads elute2 I (S2_L3)

description:
S2_L3
WM852_geneMatrix_countArray_sort.txt


title: WM852 beads II (S3_L3)

description:
S3_L3
WM852_geneMatrix_countArray_sort.txt


title: co-culture LEC +WM852 beads elute2 I (S2_L2)

description:
S2_L2
WM852_geneMatrix_countArray_sort.txt


title: WM852 beads I (S1_L1)

description:
S1_L1
WM852_geneMatrix_countArray_sort.txt


title: G33pos CEL-Seq bulk

first: Alan

middle: G

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

description:
Donor G33, CD127+ cells.
PolyA RNA.
Processed data file: ESAT_4samp_out.gene.txt

data_processing:
ILC SC analysis: step 1 - select reads with valid or correctable cell barcodes and UMIs with no Ns from R1 reads. Concatenate ":<cell barcode>:<UMI>" to the corresponding R2 read name and save into a modified version of the R2 reads file containing only reads with valid barcodes and UMIs. (Custom Python script. Also produces barcode counts file containing the number of reads from each barcode.)
ILC SC analysis step 1 detail: The cell and transcript barcoding methodology is described in detail in Supplemental information of "Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells", Klein, et al., Cell 161, 1187–1201 (2015), Table S5. Briefly, the custom Python script processes the R1 and R2 fastq files in parallel, one read at a time. It first locates the two 8-base barcode segments (bc1 and bc2) in the R1 read, and applies error-correction if necessary to determine if the barcodes are valid. If they are valid (or correctable) they are concatenated into a single BC. The unique molecular identifier (UMI) is then located and checked to ensure that it doesn't contain any Ns. If the barcode is not valid (or correctable) or the UMI contains Ns, the read pair is discarded. Otherwise, the barcode and UMI are appended to the corresponding R2 read name with the colon-separated format ":<BC>:<UMI>". Only reads with valid barcodes and UMIs are saved, and the resulting R2 (sequence) file is treated as single-ended, carrying the cell barcode an UMI with the read name for the remainder of the analysis. The script also keeps a count of the number of reads from each cell barcode and writes a 'barcode counts' file after processing all reads.
ILC SC analysis: step 2 - process step 1 output with Tophat v2.0.14, hg19, single-ended, default parameters to produce genome alignment file.
ILC SC analysis: step 3 - filter alignments from step 2 to remove any reads from barcodes with too few reads (fewer than 10,000 reads for this analysis) using barcode counts file generated in step 1 (custom Python script). This step reduces both the memory requirements and processing time for ESAT.
ILC SC analysis: step 4 - ESAT analysis parameters: wExt=1000, multimap=ignore, task=score3p, scPrep, umiMin=1, geneMapping:(hg19, only NM annotations).
ILC SC analysis: step 5 - For this analysis, we used an experimental version of ESAT that produces a file containing the total number of observations of each cell/transcript/UMI combination. A custom python script processes this file to produce a quantification file with reduces the noise in 'singletons' - UMIs for a transcripts with a single observation. We check to see if that UMI for the singleton has a Hamming distance of one from any non-singleton UMI for that transcript. If so, the singleton is combined with the counts for the non-singleton. If not, it is left as a singleton. The final output of this step are genes x cells quantification files (*_uClean.gene.txt files).
ILC bulk analysis: step1 - The raw pooled CEL-Seq reads are demultiplexed using the sample barcode encoded in the R1 read sequence. The sample index is the last 6 of the first 12 bases in R1. Sample index sequences are: G27pos=CATGAG, G27neg=AGACTC, G33pos=TCACAG, G33neg=CAGATC. Reads without one of those index sequences are discarded.
ILC bulk analysis: step 2 - process step 1 output with Tophat v2.0.14, hg19, single-ended, default parameters to produce genome alignment file.
ILC bulk analysis: step 3 - ESAT analysis parameters: wExt=1000, multimap=ignore, task=score3p, geneMapping:(hg19, only NM annotations). The gene x sample quantification file output by ESAT is ESAT_4samp_out.gene.txt.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ESAT files are tab-delimited text files containing gene/transcript ID, [genomic location for bulk analysis, ] and ESAT-quantified read counts for each gene/transcript, one data column per experiment or cell.
Supplementary_files_format_and_content: *uClean.gene.txt: ESAT single-cell text; Raw UMI counts, rows=genes, columns=cell (cell barcode).
Supplementary_files_format_and_content: ESAT_4samp_out.gene.txt: ESAT gene-level text; Raw transcript counts, rows=genes, columns=chr, strand, then one sample per column.

source_name: ILC

extract_protocol:
ThermoFisher TRIzol.
CEL-Seq

value: innate lymphocyte cell (ILC)

tag: cell population

value: Lin-CD56+CD94+ (NK)

tag: donor

tag: sample type

value: bulk


title: G27neg CEL-Seq bulk

description:
Donor G27, CD127- cells.
PolyA RNA.
Processed data file: ESAT_4samp_out.gene.txt


title: G27pos inDrop single-cell

description:
Donor G27, CD127+ cells.
PolyA RNA.

extract_protocol:
Cells lysed in droplets.
Modified CEL-Seq.

value: single cell


title: G27pos CEL-Seq bulk

description:
Donor G27, CD127+ cells.
PolyA RNA.
Processed data file: ESAT_4samp_out.gene.txt


title: G33neg CEL-Seq bulk

description:
Donor G33, CD127- cells.
PolyA RNA.
Processed data file: ESAT_4samp_out.gene.txt


title: G33pos inDrop single-cell

description:
Donor G33, CD127+ cells.
PolyA RNA.


title: G27neg inDrop single-cell

description:
Donor G27, CD127- cells.
PolyA RNA.


title: ChIPSeq_siRAM_2

city: Dundee

first: Dhaval

last: Varshney

address: Dow Street

department: Centre for Gene Regulation and Expression

institute: University of Dundee

description:
36 hours post treatment
ChIPSeq_siRAM.bigWig

data_processing:
Base calling performed using the BCL2Fastq2
CLIP data was preprocessed by CIMS pipeline as in Moore et at, Nat. Protocols, 2014. Briefly, 3' adapter (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC) was trimmed and PCR duplicates collapsed. 5nt barcode at the 5' end was stripped and appended to the tag name
CLIP data was aligned using novoaligm with 85 as the maximum alignment score acceptable for the best alignment, step size of 1 and read length of 20. RNASeq and ChIPSeq reads were aligned using STAR 2.5.1b.
Number of CLIP aligned per transcript were counted using htseq-count with Gencode v24 annotation. RNASeq reads were quantified using -quantmode GeneCounts for genome indexed with Gencode v24 annotation. Number of ChIP aligned per gene locus were counted using htseq-count with Gencode v24 annotation.
Differential expression analysis performed using edgeR Bioconductor package. ChIPSeq pileups were obtained from pooled alignment files using macs2 pileup utility.
Genome_build: hg38
Supplementary_files_format_and_content: CLIP processed data contains raw counts from htseq-count. RNASeq processed data contains raw counts output from STAR 2.5.1b -quantmode GeneCounts per ensembl gene id. ChIP processed data contains macs2 pileup output from pooled alignment files.

source_name: HeLa Cells

growth_protocol: HeLa cells grown in DMEM 10% FCS at 37 degree celsius and 5% CO2

extract_protocol:
RNA extracted using Trizol. ChIP-Seq performed as in Varshney et al, Nat. Comms, 2015
CLIP libraries prepared as in Huppertz et al, Methods, 2014 with a modified 3' RNA linker (3'-UGGAAUUCUCGGGUGCCAAGG-5'). RNASeq libraries were prepared according to Illumina's TruSeq Stranded Total RNA with Ribo-Zero Gold for Human/Mouse/Rat (RS-122-2303). ChIP-Seq libraries prepared as in Wiechens et al, PLoS genetics, 2016.

treatment_protocol: siRNA transfections performed using Lipofectamine RNAimax (Thermo Fisher).

value: HeLa

tag: replicate

value: Replicate 2

value: siRNA against RAM


title: ChIPSeq_scsiRNA_2

description:
36 hours post treatment
ChIPSeq_scsiRNA.bigWig

value: scrambled siRNA


title: ChIPSeq_scsiRNA_3

value: Replicate 3


title: RNASeq_siRAM_4

description:
36 hours post treatment
RNASeq-counts.csv

value: Replicate 4


title: ChIPSeq_siRAM_1

value: Replicate 1


title: RNASeq_siRAM_5

value: Replicate 5


title: RNASeq_siRAM_2


title: RNASeq_siRAM_3


title: ChIPSeq_siRAM_3


title: ChIPSeq_scsiRNA_1


title: RNASeq_siRAM_1


title: RNASeq_scsiRNA_5


title: RNASeq_scsiRNA_4


title: CLIP_Input

description: CLIP-counts.csv

value: Untreated


title: RNASeq_scsiRNA_1


title: RNASeq_scsiRNA_3


title: G33neg inDrop single-cell

description:
Donor G33, CD127- cells.
PolyA RNA.


title: Axenic replicate 3, 13:11 day:night cycle -> extended darkness, Time 96

city: Cambridge

first: Steven

last: Biller

address: 15 Vassar St, MIT 48-424

department: Civil and Environmental Engineering

institute: MIT

description:
A96D_3
Processed data file: extended_darkness_counts.txt

data_processing:
Low-quality sequence removed using quality_trim (CLCbio) using default parameters.
Alignment of paired-end reads to references using the Burrows-Wheeler Aligner V0.7.12.
Number of aligned read pairs mapping in the sense orientation to each ORF determined using HTSeq (Anders, S., Pyl, P. T., & Huber, W. (2014). HTSeq–A Python framework to work with high-throughput sequencing data. Bioinformatics (Oxford, England)).
Genome_build: NCBI accessions CP000095.2 (Prochlorococcus marinus) and JXRW01000000.1 (Alteromonas macleodii).
Supplementary_files_format_and_content: extended_darkness_counts.txt: Tab-delimited text file with the number of reads mapping to each ORF for all timepoints and replicates, as well as associated annotation data.

organism: Prochlorococcus marinus str. NATL2A

source_name: Bacterial culture, extended darkness, 96hr

growth_protocol: Cultures were grown in natural seawater-based PRO99 media under a 13:11 day:night light cycle.

extract_protocol:
Culture samples added to cold RNAlater at each timepoint, cells collected onto a 0.2µm filter, and total RNA extracted with the mirVana kit (Ambion).
Strand-specific RNA-seq library construction starting with 100ng of total RNA using the dUTP second-strand approach; duplex-specific normalization was performed to reduce ribosomal RNA content in each sample.

treatment_protocol: Cultures were split after 24 hours of sampling under the day:night light cycle; at 'sundown', half experienced the normal light regime, the other half stayed in the dark.

tag: p. marinus strain/background

tag: condition

value: 13:11 light:dark light cycle -> extended darkness

tag: timepoint

value: 96 hours


title: Axenic replicate 3, 13:11 day:night cycle -> extended darkness, Time 144

description:
A144D_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, extended darkness, 144hr

value: 144 hours


title: Axenic replicate 2, 13:11 day:night cycle -> extended darkness, Time 144

description:
A144D_2
Processed data file: extended_darkness_counts.txt


title: Axenic replicate 2, 13:11 day:night cycle -> extended darkness, Time 96

description:
A96D_2
Processed data file: extended_darkness_counts.txt


title: Axenic replicate 1, 13:11 day:night cycle -> extended darkness, Time 144

description:
A144D_1
Processed data file: extended_darkness_counts.txt


title: ch12_SAd_localhic_b1

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Gro-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50 --trim5 2
Gro-Seq_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
Gro-Seq_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
HiC-Seq: alignment: bwa-sw with default parameter (map each read separately)
HiC-Seq: filter: remove duplicates and near duplicates, removes reads that map to the same fragemnt and low quality reads (MAPQ <30)
HiC-Seq: generate contact matrix: juicer runnning with default parameter
4C-Seq: filtering: each read pair was tested for the presence of a perfect match to the respective bait primer as well as the bait spacer  between the  end of the primer and the restriction sites  used  in  the  corresponding  experiment.
4C-Seq: mapping: bowtie-1.1.1/bowite -X 500 -p 3 -v2 -k2 -m1 --phred64-quals -sam
4C-Seq: frequency: assign to DPNII/CSP6i fragment to calculate fraction of restriction fragments for which 4C reads were found
ChIAPET: followed the process described in Li et al.,2010
ChIAPET: interaction call by chiapettool v2 program with default parameter
ChIA-PET: Chia-PET processing pipeline is described in greater detail in Li et al., 2010 (PMCID: PMC2872882)
local HiC: preprocess & normalization: juicer.sh using default parameter
local HiC: 5kb resolution matrices extraction: juicebox dump obsevered NONE .hic BP 5000
local HiC: R & custom script: generate genome wide contact matrix as in Sanborn et al. PNAS 2015
local HiC: estimation of number of in silico spike-ins: median of the genome-wide per-bin coverage of the local HiC matrix at the targeted region
local HiC: reconstruct HiC matrix: combine the targeted region local HiC with the global CH12 wt matrix which matched to spike-ins
local HiC: re-normalization: Knight-Ruiz balancing algorithm with the juicebox pre -r 5000
ChromRNA_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChromRNA_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
ChromRNA_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content:
ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Gro-Seq: .wig files tag density divided by library size in millions to obtain normalized read density (rpkm)
HiC-Seq: .hic format including contact matrix, normalization information generated by juicer.sh
ChIAPET: bed12 format by editting the result of chiapettool by restricting to show only interactions having more than or equal to 3 PETs
4C-Seq: bed file showing read frequency in 100K window normalized by the number of fragments in each window
mRNA-Seq:.wig files tag density divided by library size in millions to obtain normalized read density (rpkm)
ChromRNA: strand-specific density tracks are generated by using bedtools genomecov program divided by library size in millions to obtain normalized read density (rpm)

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at 37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. MNase-Seq: 4x107 resting and activated B cells were digested with 24 different concentrations of MnaseI. After an initial RT-qPCR analysis and curve-fitting, the MnaseI concentrations for the most representative nucleosomal fraction was determined. The lowest three nucleosomal fractions (which corresponded to MnaseI concentrations of 0U, 0U, and 0.0026U) were pooled together and used as input control. Nucleosomal fractions 16-18 (which corresponded to enzyme concentrations of 0.068U, 0.045U, and 0.03U) were also pooled for further processing. Input samples were sonicated to obtain similar fragment sizes as the MnaseI-digested samples. DNA was then concentrated and each sample was spiked with 0.055mg of l DNA (also sonicated to match the sample size as was input DNA).
HiC-Seq: we used the same protocol for in situ HiC libraries at Rao et al., (Cell, 2014 Dec; 159:1-16)
Gro-seq: Nuclei was extracted from 8-12 million cells grown on 10 cm plates and after run-on reaction the RNA was extracted with Trizol LS Reagent (Invitrogen, Carlsbad, CA, USA). RNA was treated with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and purified by running through P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was dephosphorylated with PNK (New England Biolabs, Ipswich, MA, USA) followed by heatinactivation. Dephosphorylation reactions were purified using anti-BrdU beads (SantaCruz Biotech, Santa Cruz, CA, USA) and precipitated overnight. Poly(A)-tailing and cDNA synthesis was performed the next day as described in (Wang et al., 2011). However, for reverse transcription oligos with custom barcodes (underlined) were used : 5’-Phos CA/TG/AC/GT GATCGTCGGACTGTAGAACTCT /idSp/CAAGCAGAAGACGGCATACGA TTTTTTTTTTTTTTTTTTTTVN-3'. After cDNA synthesis, Exonuclease I (New England Biolabs; 30 min) was used to catalyze the removal of excess oligo. Enzyme was inactivated and RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA fragments of were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel (Invitrogen). The recovered cDNA was circularized, linearized, amplified for 10-14 cycles. The final product was ran on Novex 10%TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit (Zymo Research Corporation, Irvine, CA, USA).
4C-seq: The 4C assay was performed as previously described van de Werken et al. (2012) with minor modifications. Ten million of CH12 B cell line were crosslinked in 2% formaldehyde at 37°C for 10 min. The reaction was quenched by the addition of glycine (final concentration of 0.125 M). Cells were then washed with cold PBS and lysed (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40, 1× complete protease inhibitors [Roche]) at 4°C for 1 hr. Nuclei were incubated at 65°C for 30 min, 37°C for 30 min in 500 μl of restriction buffer (New England BioLabs DpnII buffer) containing 0.3% SDS. To sequester SDS, Triton X-100 was then added to a final concentration of 1.8%. DNA digestion was performed with 400 U of DpnII (New England Biolabs) at 37°C overnight. After heat inactivation (65°C for 30 min), the reaction was diluted to a final volume of 7 ml with ligation buffer containing 100 U T4 DNA Ligase (Roche) and incubated at 16°C overnight. Samples were then treated with 500 μg Proteinase K (Ambion) and incubated overnight at 65°C to reverse formaldehyde crosslinking. DNA was then purified by phenol extraction and ethanol precipitation. For circularization, the ligation junctions were digested with Csp6I (Fermentas) at 37°C overnight. After enzyme inactivation and phenol extraction, the DNA  was  religated  in  a  7 ml  volume  (1,000 U  T4  DNA  Ligase,  Roche).  Three micrograms of 4C library DNA was amplified with Expand Long template PCR System (Roche). Thermal cycle conditions were DNA denaturing for 2 min at 94°C, followed by 30 cycles of 15 s at 94°C, 1 min at 58°C, 3 min at 68°C, and a final step of 7 min at 68°C.  Bait was amplified with inverse PCR primers as follows: 3RR with DpnII:_4C 5'-GCTTATCTGTAAAGAATGGGTC-3', 3RR_Csp6i 5'-GGCCTTAGAAGGCTCTGTAC-3'. 4C-amplified DNA was microsequenced with the Illumina platform.
mRNA-seq: Total RNA from 106 of WT or ZF9-11 CH12 cells was isolated by Trizol extraction. mRNA was then isolated .
local Hi-C: 500ng of Hi-C library (8 cycles of amplification) was mixed with 2.5 µg of mouse Cot-1 DNA and 10µg of salomon sperm DNA in a total volume of 25µl. The sample was heated to 95℃ for 5 minutes. Next the temperature was diminished to 65℃ and the samples incubated for at least 5 minutes at 65℃. In the meantime 6µl of a RNA probe mixture (500ng of RNA probes, 20U of supreRNAseIn) and 33µl of hybridization buffer (10xSSPE, 10xDenhardt buffer, 10mM EDTA, 0.2% SDS) were incubated at 65℃. Next, the hybridization buffer and the RNA probe mixture were added to the sample. The final mix was incubated at 65℃ for 24 hours. Following the hybridization, 50 µl of MyOne Streptavidin T1 beads were washed 3 times with Bind-and-Wash buffer (1M NaCl, 10 mM Tris-HCl, pH=7.5, 1mM EDTA) and then resuspended in 134 µl of Bind-and-Wash buffer and added to the sample. The mixture was incubated for 30 minutes at room temperature with occasional swirling. Next, beads were separated using a magnet and the supernatant discarded. Beads were then washed once with 200µl of low-stringency buffer (1xSSC, 0.1%SDS) and incubated for 15 minutes at RT. Beads were separated and washed 3 times with high stringency.
ChromRNA-seq: chromatin RNA fraction was prepared from 3*10^6 cells following the method previously described (Pandya-Jones & Black, RNA, 2009) with some modifications. The pellet was lysed in a cytoplasm lysis buffer (20mM Hepes-KOH pH 7.6, 2mM MgCl2, 10% glycerol, 0.1% NP40, 0.5mM DTT with protease inhibitor, phosphatase inhibitor and RNase inhibitor). The lysate was then layered on top of a sucrose buffer in order to isolate the nuclei fraction from the cytoplasmic one (10mM Hepes-KOH pH7.6, 10mM NaCl, 1.5mM MgCl2, 10% glycerol, 0.5mM EDTA, 0.5mM DTT, 34% sucrose w/v with protease inhibitor, phosphatase inhibitor and RNase inhibitor).
ChromRNA-seq: The nuclei fraction was resuspended and lysed in a nuclear lysis buffer (10mM Hepes-KOH pH 7.6, 100mM NaCl, 0.5mM EDTA, 50% glycerol, 0.5mM DTT with protease inhibitor, phosphatase inhibitor and RNase inhibitor). Chromatin was precipitated by adding a Urea c

value: CH12 B

value: SA deletion

tag: cell type

value: lymphoma cell line


title: Axenic replicate 1, 13:11 day:night cycle -> extended darkness, Time 96

description:
A96D_1
Processed data file: extended_darkness_counts.txt


title: Axenic replicate 3, 13:11 day:night cycle -> extended darkness, Time 72

description:
A72D_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, extended darkness, 72hr

value: 72 hours


title: Axenic replicate 1, 13:11 day:night cycle -> extended darkness, Time 72

description:
A72D_1
Processed data file: extended_darkness_counts.txt


title: ch12_SAd_localhic_b2

tag: genotype/variation


title: Axenic replicate 3, 13:11 day:night cycle -> extended darkness, Time 48

description:
A48D_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, extended darkness, 48hr

value: 48 hours


title: Axenic replicate 3, 13:11 day:night cycle -> extended darkness, Time 40

description:
A40D_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, extended darkness, 40hr

value: 40 hours


title: RNASeq_scsiRNA_2

value: HeLa

value: Replicate 2

tag: treatment


title: Axenic replicate 1, 13:11 day:night cycle -> extended darkness, Time 48

description:
A48D_1
Processed data file: extended_darkness_counts.txt


title: Axenic replicate 1, 13:11 day:night cycle -> extended darkness, Time 36

description:
A36D_1
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, extended darkness, 36hr

value: 36 hours


title: Axenic replicate 3, 13:11 day:night cycle -> extended darkness, Time 32

description:
A32D_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, extended darkness, 32hr

value: 32 hours


title: Axenic replicate 2, 13:11 day:night cycle -> extended darkness, Time 32

description:
A32D_2
Processed data file: extended_darkness_counts.txt


title: Axenic replicate 3, 13:11 day:night cycle -> extended darkness, Time 36

description:
A36D_3
Processed data file: extended_darkness_counts.txt


title: Axenic replicate 1, 13:11 day:night cycle -> extended darkness, Time 40

description:
A40D_1
Processed data file: extended_darkness_counts.txt


title: Axenic replicate 2, 13:11 day:night cycle -> extended darkness, Time 40

description:
A40D_2
Processed data file: extended_darkness_counts.txt


title: Axenic replicate 2, 13:11 day:night cycle -> extended darkness, Time 36

description:
A36D_2
Processed data file: extended_darkness_counts.txt


title: Axenic replicate 3, 13:11 day:night cycle -> extended darkness, Time 28

description:
A28D_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, extended darkness, 28hr

value: 28 hours


title: Axenic replicate 1, 13:11 day:night cycle -> extended darkness, Time 32

description:
A32D_1
Processed data file: extended_darkness_counts.txt


title: Axenic replicate 2, 13:11 day:night cycle -> extended darkness, Time 28

description:
A28D_2
Processed data file: extended_darkness_counts.txt


title: Epidermis Adam17 KO rep2

city: Bethesda

first: Tetsuro

last: Kobayashi

address: 9000 Rockville Pike, Bldg 10, Rm12N256

institute: NIAMS/NIH

data_processing:
Illumina Bcl2fastq v2.17 software  was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR version 2.5.1  with parameters -genomeDir $star_genome -readFilesIn R1_trimmed.fastq  R2_trimmed.fastq -outTmpDir /logs/star -outSAMunmapped Within -  outFilterType BySJout -outFilterMultimapNmax 20 -  outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.04 -  alignIntronMin 20 -alignIntronMax 1000000 --alignMatesGapMax  1000000 -alignSJoverhangMin 8 -alignSJDBoverhangMin 1 -  sjdbScore 1 -runThreadN 8 - -genomeLoad NoSharedMemory
Reads Per Kilobase of exon per Megabase of library size (RPKM) or Transcripts Per Kilobase Million (TPM) were calculated using a RSEM software tool to quantifiy the transcript abundance.
Please add additional steps for differential analysis
Genome_build: mm10
Supplementary_files_format_and_content: Rsem gene quantification file

source_name: Epidermis Adam17 KO

extract_protocol:
TruSeq Stranded mRNA Sample Prep Kit (Cat#RS-122-2101, RS-122-2102 and RS-122-2103) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: ADAM17 cKO

tag: age

value: 10 weeks

value: epidermis


title: Epidermis Adam17 KO rep3


title: Epidermis Adam17 KO rep1


title: Axenic replicate 2, 13:11 day:night cycle -> extended darkness, Time 72

description:
A72D_2
Processed data file: extended_darkness_counts.txt

value: 13:11 light:dark light cycle -> extended darkness


title: ch12_HSAd_localhic

value: half SA deletion


title: Epidermis WT rep1

source_name: Epidermis WT

value: wild type


title: Epidermis WT rep2


title: Epidermis WT rep3


title: Axenic replicate 1, 13:11 day:night cycle -> extended darkness, Time 28

description:
A28D_1
Processed data file: extended_darkness_counts.txt


title: Axenic replicate 3, 13:11 day:night cycle, Time 48

description:
A48L_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, normal light regime, 48hr

value: 13:11 light:dark light cycle


title: Skin Adam17 KO rep3

source_name: Skin Adam17 KO

value: Skin


title: Skin Adam17 KO rep1


title: Axenic replicate 2, 13:11 day:night cycle, Time 48

description:
A48L_2
Processed data file: extended_darkness_counts.txt


title: Skin WT rep3

source_name: Skin WT


title: Axenic replicate 2, 13:11 day:night cycle -> extended darkness, Time 48

description:
A48D_2
Processed data file: extended_darkness_counts.txt


title: Skin WT rep2


title: Axenic replicate 1, 13:11 day:night cycle, Time 48

description:
A48L_1
Processed data file: extended_darkness_counts.txt


title: Axenic replicate 3, 13:11 day:night cycle, Time 40

description:
A40L_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, normal light regime, 40hr


title: Skin WT rep1


title: Axenic replicate 1, 13:11 day:night cycle, Time 40

description:
A40L_1
Processed data file: extended_darkness_counts.txt


title: M2

city: Beijing

first: Wei

last: Chen

state: Beijing

address: No. 95 Yong’an road, Xicheng District

department: Beijing Friendship Hospital

institute: Capital Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
For all generated raw reads, adaptor sequences, low-quality reads, contaminant reads, and reads that were shorter than 18 nt or larger than 30 nt were eliminated and trimmed with the Fastx-Toolkit software.
The resulting set of trimmed reads were then mapped against the Homo sapiens or Mus musculus genome of Ensembl (Release 80, http://www.ensembl.org/) using the program SOAP . Subsequently, by the same approach, the perfectly matched reads were screened against miRBase (Release 21, http://www.mirbase.org/)  and human or mouse non-coding RNA sequence of Ensembl (Release 80, http://www.ensembl.org/) to obtain the annotation of known mature miRNAs and other small non-coding RNAs (allowing two mismatches)
To correct for the difference in tag counts between samples, the tag counts were scaled to the copy number of transcripts per million (TPM) based on the total number of tags aligned to known human or mouse mature miRNAs in miRBase 21.
Genome_build: hg38 and mm8
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: Hippocampus

extract_protocol:
Total RNA from the frozen hippocampus was purified using Trizol (Invitrogen, USA) protocol with no modifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: race/strain

value: Hippocampus

value: 8~9 month

tag: gender

value: male


title: Axenic replicate 3, 13:11 day:night cycle, Time 36

description:
A36L_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, normal light regime, 36hr


title: M7

tag: tissue


title: M3


title: M4


title: Axenic replicate 2, 13:11 day:night cycle, Time 40

description:
A40L_2
Processed data file: extended_darkness_counts.txt

value: 40 hours


title: Axenic replicate 2, 13:11 day:night cycle, Time 36

description:
A36L_2
Processed data file: extended_darkness_counts.txt


title: M6


title: Axenic replicate 1, 13:11 day:night cycle, Time 36

description:
A36L_1
Processed data file: extended_darkness_counts.txt


title: M1


title: Skin Adam17 KO rep2


title: MUT rep2 (21-6)

city: Davis

first: Nadean

last: Brown

state: CA

address: 4407 Tupper Hall

department: Dept of Cell Biology and Human Anatomy

institute: University of California, Davis

data_processing:
Sequenced reads were trimmed and aligned to mm10 genome with Bowtie2
Transcripts were assembled and abundances estimated by Cufflinks (usegalaxy.org) using mm10 reference annotation; bias correction, multi-read correct; Cufflinks effective length correction
Assembled transcripts were analyzed for differential expression with CuffDiff (usegalaxy.org); geometric library normalization; pooled dispersion method; multi-read correct, Cufflinks effective length correction
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include RPKM values, p-values and adjusted p-values (q-values) for each genotype

source_name: Retina

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Zymo Research Quick miniprep kit (Cat#:R1055). Total RNA samples were sent to the Cincinnati Children's Hospital Medical Center DNA Sequencing Core for library preparation and high throughput and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols by CCHMC DNA sequencing Core

tag: strain

value: retina

tag: genotype


title: MUT rep3 (23-1)


title: MUT rep5 (23-12)


title: MUT rep4 (23-9)


title: MUT rep1 (7-13)


title: HET rep4 (23-3)


title: HET rep5 (23-10)


title: Axenic replicate 3, 13:11 day:night cycle, Time 32

description:
A32L_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, normal light regime, 32hr


title: HET rep2 (7-5)


title: Axenic replicate 1, 13:11 day:night cycle, Time 32

description:
A32L_1
Processed data file: extended_darkness_counts.txt


title: Axenic replicate 3, 13:11 day:night cycle, Time 28

description:
A28L_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, normal light regime, 28hr


title: HET rep3 (21-10)


title: WT rep5 (23-11)


title: HET rep1 (7-4)


title: M5


title: Axenic replicate 2, 13:11 day:night cycle, Time 28

description:
A28L_2
Processed data file: extended_darkness_counts.txt


title: WT rep4 (23-4)


title: WT rep2 (21-4)


title: WT rep3 (23-2)


title: Axenic replicate 1, 13:11 day:night cycle, Time 28

description:
A28L_1
Processed data file: extended_darkness_counts.txt


title: WT rep1 (7-8)


title: Axenic replicate 2, 13:11 day:night cycle, Time 24

description:
A24L_2
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, normal light regime, 24hr

value: 24 hours


title: Axenic replicate 3, 13:11 day:night cycle, Time 24

description:
A24L_3
Processed data file: extended_darkness_counts.txt


title: 360min D310N 2

city: London

first: Steve

last: Ley

address: Pond Street

department: Institute of Immunity & Inflammation

institute: University College London

data_processing:
The RSEM package (version 1.2.31) in conjunction with the STAR alignment algorithm (version 2.5.2a)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to mm10 Refseq genes downloaded from the UCSC Table Browser on 19th Feb 2016
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.2.3)
Genome_build: mm10 Refseq
Supplementary_files_format_and_content: Tab delimited text files containing TMM normalised data from DESEQ2 output. Rows represent Refseq mouse genes and columns represent individual samples.

growth_protocol: Bone marrow cells were cultured for 7 days on non-adherent plates in RPMI containing 10% FCS and 10% L929 supernantant

extract_protocol:
RNA was extracted using the Rneasy kit (Qiagen) following the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs were treated with 100ng/ml LPS for the times indicated

tag: cell line

value: BMDM

value: LPS (100ng/ml)


title: 360min D310N 1


title: 240min D310N 3