title: ATACseq medaka st11 replicate 1

description:
ATAC_seq
ATAC_medaka_st11_idrpeaks.bed


title: ATACseq amphioxus 8h replicate 1

status: Public on Aug 15 2018

type: SRA

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

description:
ATAC_seq
ATAC_amphioxus_8h_idrpeaks.bed

library_source: genomic

data_processing:
Alignment: reads were aligned against reference genome using Bowtie2 software.
Filtering duplicates: duplicated pairs were removed using Samtools software.
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
Visualization: bigWig files were visualized using UCSC Browser
Genome_build: Amphioxus Bl71nemr (Genomic sequencing data was submitted to ENA under the master PRJEB13665 accession), Zebrafish September 2014 (GRCz10/danRer10), Medaka October 2005 (oryLat2)
Supplementary_files_format_and_content: BED files with peaks called using Irreproducibility Discovery Rate (IDR) framework

molecule: genomic DNA

organism: Branchiostoma lanceolatum

source_name: whole embryo

growth_protocol: Embryos were cultivated at 19°C in filtered seawater until desired developmental stage

extract_protocol:
Embryos were centrifugated at 13000 rpm for 1 min, and then seawater wasa carefully removed. Cells were lysed by gently pipetting in cold lysis buffer
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109

tag: developmental stage


title: ATACseq zebra 80% epiboly replicate 1

description:
ATAC_seq
ATAC_zebra_80epi_idrpeaks.bed

organism: Danio rerio

growth_protocol: Embryos were cultivated at 28°C in E3 medium until desired developmental stage

extract_protocol:
Wild type embryos were dechorionated, deyolked and lysed
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109

value: 80% epiboly


title: ATACseq medaka st19 replicate 1

description:
ATAC_seq
ATAC_medaka_st19_idrpeaks.bed

organism: Oryzias latipes


title: ATACseq amphioxus 60h replicate 2

description:
ATAC_seq
ATAC_amphioxus_60h_idrpeaks.bed


title: ChIPseq amphioxus H3K27ac 8h replicate 2

data_processing:
Reads were aligned using Bowtie
Peaks were called using MACS software with default parameters
Genome_build: Amphioxus Bl71nemr (Genomic sequencing data was submitted to ENA under the master PRJEB13665 accession),
Supplementary_files_format_and_content: Called peaks in BED format

source_name: Whole embryo

growth_protocol: Embryos were cultured at 19°C until 8hpf, 15hpf, 36hpf or 60hpf

extract_protocol:
Batches of embryos from six dishes were transferred into a 2mL tube. After a quick centrifugation at 9000 rpm, the seawater was removed and replaced by 1.5mL of fixation solution (1.85% formaldehyde in MOPS-EGTA buffer: 0.1M MOPS pH 7.5, 2mM MgSO4, 1 mM EGTA, 0.5M NaCl). After 15 minutes at room temperature, 155 µL of Glycine 10% was added and the embryos were allowed to naturally sediment. The solution was then gently removed and the embryos were washed five times at 4°C with cold NaPBS (0.9% NaCl, 20 mM sodium phosphate buffer at pH 7.4). After a quick centrifugation at 13,000 rpm, the liquid was removed and the fixed embryos were frozen in liquid nitrogen and subsequently stocked at -80°C. For the chromatin immunoprecipitation, embryos were homogenized and lysed in order to release the chromatin, which was subsequently sonicated in a Bioruptor (Diagenode). Then the sonicated product was incubated with the specific antibody first, and then with Dynabeads (Thermofisher, cat. 10007D). After washing, pulled down chromatin was eluted from the beads and decrosslinked.
Illumina libraries were prepared following manufacturer's instructions.

tag: antibody


title: liver_MethylC_seq

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
MethylC-seq libraries were sequenced in single-end mode on the Illumina HiSeq 1500 platform. The sequenced reads in FASTQ format were mapped to the in silico bisulfite-converted reference genome Branchiostoma lanceolatum: Bl71nemr) using the Bowtie alignment algorithm with the following parameters: -e 120 -l 20 -n 0 as described before (Bogdanovic et al, Nature Genetics, 2016).
Genome_build: Branchiostoma lanceolatum: Bl71nemr
Supplementary_files_format_and_content: For "*.allC" processed data files (for MethylC-Seq) the column headers are as follows: column 1 - assembly (chromosome).column 2 - position: coordinate for the cytosine position on the chromosome (first base of chromosome = 0).column 3 - strand: + or - strand.column 4 - class: context of the cytosine and the two following bases from the same strand.column 5 - mc: number of reads supporting a methylated cytosine.column 6 - h: total number of reads at that position.

source_name: liver

extract_protocol:
Embryos and adult tissues were homogenized in 3 volumes STOP buffer (15 mM EDTA, 10 mM Tris-HCl pH7.5, 1% SDS, 0.5 mg/mL proteinase K) after which two phenol:chloroform:isoamylalcohol (PCI, 25:24:1) extractions were performed. DNA was then precipitated in 1/5 volume NH4AC 4M and 3 volumes EtOH and dissolved in 100 uL, treated with RNase and purified by a PCI extraction. The precipitation was done with EtOH and the DNA was resuspended in 50 uL H2O.
MethylC-seq library generation was performed as described previously (Ulrich et al, 2015; Nature Protocols). Briefly, the genomic DNA was sonicated to an average size of 200 bp using a Covaris sonicator. Sonicated DNA was then purified and end-repaired followed by the ligation of methylated Illumina TruSeq sequencing adapters. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA), using 6 cycles of amplification.

value: adult


title: 36hpf_MethylC_seq

source_name: whole embryos


title: ATACseq zebra 48 hpf replicate 2

description:
ATAC_seq
ATAC_zebra_48h_idrpeaks.bed


title: ChIPseq amphioxus H3K27ac 8h replicate 1


title: ATACseq amphioxus 60h replicate 1


title: ATACseq amphioxus 36h replicate 1

description:
ATAC_seq
ATAC_amphioxus_36h_idrpeaks.bed


title: 15hpf_MethylC_seq


title: ATACseq amphioxus 15h replicate 2

description:
ATAC_seq
ATAC_amphioxus_15h_idrpeaks.bed


title: ChIPseq amphioxus H3K27ac 15h replicate 2


title: 8hpf_MethylC_seq


title: ATACseq zebra 48 hpf replicate 1

description:
ATAC_seq
ATAC_zebra_48h_idrpeaks.bed


title: ATACseq amphioxus 15h replicate 1


title: acPro (PA002)

city: MADRID

first: PEDRO

middle: JOSÉ

last: ALCOLEA ALCOLEA

address: Ramiro de Maeztu, 9

department: CENTRO DE INVESTIGACIONES BIOLÓGICAS

institute: CONSEJO SUPERIOR DE INVESTIGACIONES CIENTÍFICAS

description: Spliced leader (SL)-based RNA-Seq libraries

library_source: transcriptomic

data_processing:
FastQC for quality check
Bowtie2 for alignment against LinJPCM5 genome sequence version 33 (TriTrypDB)
Samtools to convert SAM into BAM
featureCounts for read counting in CDS
Geneious 10.2.3 to obtain transcript per million (TPM) counts and for normalization and differential gene expression analysis.
Genome_build: LinJPMC5 (TriTrypDB version 33)
Supplementary_files_format_and_content: Tab-delimited files including raw read counts, raw transcript counts, raw transcript per million, normalized TPM, fold changes and p-values (Geneious differential gene expression analysis method)

molecule: total RNA

organism: Leishmania infantum

source_name: Axenic culture

growth_protocol: Cultured promastigotes: RPMI1640 supplemented with heat-inactivated fetal bovine serum, containing penicillin (500IU/mL and streptomycin (500ug/mL); san fly-derived promastigotes were obtained by dissection of the whole midgut after 5 days of feeding with a suspension of late-logarithmic phase promastigotes in rabbit blood over a fresh chicken skin membrane.

extract_protocol:
TRIzol reagent
Multiplexed SL-Seq (Haydock et al., 2015); First strand cDNA synthesis using random primers with adaptor sequence including Illumina sequence. Second strand synthesis using the SL sequence with adaptor including Illumina sequence. PCR primers including adaptor and indexing sequences.

treatment_protocol: Wild type promastigotes in culture vs. sand fly midgut, strain MHOM/MCAN/ES/98/10445

tag: strain

tag: Stage

value: Promastigotes (pool)

tag: origin

value: Culture


title: ChIPseq amphioxus H3K27ac 36h replicate 2


title: sfPro (PA001)

source_name: Whole gut of the sand fly Phlebotomus perniciosus

value: P. perniciosus gut


title: ChIPseq amphioxus H3K27ac 36h replicate 1


title: ChIPseq amphioxus H3K27me3 15h replicate 1


title: ChIPseq amphioxus H3K27ac 15h replicate 1


title: mEB-TE1 RNA-Seq

status: Public on Aug 14 2018

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

description: PolyA RNA amplified by SMARTer kit

data_processing:
Sequences were aligned to the mouse MM9, the cow bosTau and the pig susScr3 reference genome using GSNAP
Only the tags aligning to one position on the genome were considered for further analysis. Further analysis was performed with 36 (single end) or one time 50 bp (paired end) aligned sequence reads.
The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) / BedGraph files for viewing.
Details of the computational analysis performed are described in the Supplementary Information of the accompanying paper
All sequencing analyses were conducted based on the Mus musculus NCBI m37 genome assembly (MM9; assembly July 2007),  the Bos_taurus_UMD_3.1/bosTau6 or the SGSC Sscrofa10.2/susScr3
Genome_build: NCBI37/mm9; Bos_taurus_UMD_3.1/bosTau6; SGSC Sscrofa10.2/susScr3
Supplementary_files_format_and_content: wig file for visualisation in Genome Browsers

molecule: polyA RNA

organism: Mus musculus

source_name: mouse early embryonic material E6.25; Throphoblast

growth_protocol: Mouse ESC and EpiSC culture: 129S2/SvPas and F1 (C57Bl/6xDBA/Ja) mouse ESCs were derived as previously described and cultured using standard protocols (Nagy 2003). Corresponding 129S2/SvPas and F1 mouse EpiSCs were cultured using standard protocols (Brons, Smithers et al. 2007); Embryo sample preparation (embryo collection, dissection): The animal experiments were established in full compliance with European and National laws and regulations. Mouse: 6-12 weeks old C57Bl/6J females and DBA/2J or CBA male mice were used to produce F1 embryos. 6-12 weeks old 129S2 mice were used to produce non-hybrid embryos. All mouse studies complied fully with the UK Animals (Scientific Procedures) Act 1986 as implemented by the University of Cambridge and with the regulation approved by the Regional Animal Health Authorities for BioTalentum Ltd., Hungary (22.1/1970/003/2008). Pre-implantation mouse samples were collected by flushing the embryos out of the uterus. Post-implantation stage mouse epiblasts were dissected as described previously (Nagy 2003) at two time points: at pregastrulation stage (ERSE stage) and at midgastrulation stage (APE stage); Pig: Donor pigs were bred by crossing Danish Landrace females and Yorkshire males after induced oestrus. Farm animals that were too old for further breeding were used. Embryos at E6-E7 (ICM stage); E10-E11 (ERSE stage) and E12-E13 (APE stage) were collected either by gentle flushing of the uterine horns (for stages E6-E7 and E12-E13) or by manually clipping open the uterine horns (E10-E11). For details see Supplemental Information; Bovine: Donor cows were bred by artificial insemination after induced oestrus and super-ovulation. Artificial insemination was performed using the same batch of frozen sperm from a single Holstein bull. Animal care and procedures were completed with the authorization of the French Ministry of Agriculture (B91332). Embryos at E14 (ERSE stage) and at E17 (APE stage) were collected non-surgically by gentle flushing. For details see Supplemental Information.

extract_protocol:
Embryos were depleted of extraembryonic tissues using glass needles, harvested into TriZol and snap frozen. RNA was isolated using TriZol and the PureLink™ RNA Micro Kit (Invitrogen), following the manufacturer’s instructions. Integrity of the RNA samples (Table S1) was confirmed using the Experion Automated Electrophoresis Station (2286; BioRad). Concentration of the RNA samples was determined by a Qubit fluorometer (Invitrogen; Q32857) and the Experion.
In order to generate RNA-Seq expression profiles from the early embryonic stages, the Ovation RNA-Seq kit (Nugen) and the SMARTer Ultra Low RNA kit from Illumina were tested for low quantity RNA-Seq expression profiling on mouse liver RNA. The results were compared to regular RNA-Seq profiling. Regular RNA-Seq profiling was performed on 100 ng of RNA, using the RiboZero kit (EpiBio) to deplete for ribosomal RNA, and hexamers for priming the reverse transcription, followed by regular sample preparation for sequencing. 100 pg of mouse liver total RNA was amplified using the Ovation RNA-Seq kit (7100-08). cDNA was sonicated using the Bioruptor (Diagenode) for 15 min (30 sec on, 30 sec off, high power). Paired-end sequence adaptors were ligated to DNA fragments, followed by size selection (300 bp; E-Gel® Agarose Gel Electrophoresis System of Invitrogen) and 14 cycles of PCR amplification. For the SMARTer Ultra Low RNA kit from Illumina, 100 pg of mouse liver total RNA was amplified as described below. Sequencing was performed as described below. Direct comparisons using RNA-Seq sequencing showed that the SMARTer Ultra Low RNA was clearly superior and this was chosen to be the profiling method of choice. For all samples, 100 pg of RNA was used for cDNA synthesis and amplification using the SMARTer™ Ultra Low RNA Kit for Illumina Sequencing (Clontech; Cat. No. 634935) using 20 PCR cycles. The amplified cDNA was fragmented by sonication (Bioruptor, Diagenode). Paired-end sequence adaptors were ligated to DNA fragments, followed by size selection (300 bp; E-Gel® Agarose Gel Electrophoresis System of Invitrogen) and 14 cycles of PCR amplification.

value: Throphoblast cells

tag: developmental day


title: mEB-TE2 RNA-Seq

description: PolyA RNA amplified by SMARTer kit


title: m129APE1 RNA-Seq

description: PolyA RNA amplified by SMARTer kit

data_processing:
Sequences were aligned to the mouse MM9, the cow bosTau and the pig susScr3 reference genome using GSNAP
Only the tags aligning to one position on the genome were considered for further analysis. Further analysis was performed with 36 (single end) or one time 50 bp (paired end) aligned sequence reads.
The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) / BedGraph files for viewing.
Details of the computational analysis performed are described in the Supplementary Information of the accompanying paper
All sequencing analyses were conducted based on the Mus musculus NCBI m37 genome assembly (MM9; assembly July 2007),  the Bos_taurus_UMD_3.1/bosTau6 or the SGSC Sscrofa10.2/susScr3
Genome_build: NCBI37/mm9; Bos_taurus_UMD_3.1/bosTau6; SGSC Sscrofa10.2/susScr3
Supplementary_files_format_and_content: BedGraph file for visualisation in Genome Browsers

source_name: mouse early embryonic material; Epiblast elongated along the Anterior-to-Posterior axis (APE) cells


title: mAPE2 RNA-Seq

description: PolyA RNA amplified by SMARTer kit

value: Epiblast elongated along the Anterior-to-Posterior axis (APE) cells


title: mAPE1 RNA-Seq

description: PolyA RNA amplified by SMARTer kit


title: pERSEx RNA-Seq

description: PolyA RNA amplified by SMARTer kit

organism: Sus scrofa

source_name: pig early embryonic material; Epithelial Radially Symmetric Epiblast (ERSE) cells

tag: breed

value: Danish Landrace x Yorkshire males


title: pAPE2x RNA-Seq

description: PolyA RNA amplified by SMARTer kit

source_name: pig early embryonic material; Epiblast elongated along the Anterior-to-Posterior axis (APE) cells


title: pERS5Ex RNA-Seq

description: PolyA RNA amplified by SMARTer kit

value: Epithelial Radially Symmetric Epiblast (ERSE) cells


title: pAPE1x RNA-Seq

description: PolyA RNA amplified by SMARTer kit


title: pEBI6x RNA-Seq

description: PolyA RNA amplified by SMARTer kit

source_name: pig early embryonic material; Inner Cell Mass (ICM) cells

value: Inner Cell Mass (ICM) cells


title: pEBI5x RNA-Seq

description: PolyA RNA amplified by SMARTer kit


title: mERSETroph RNA-Seq

description: PolyA RNA amplified by SMARTer kit

source_name: mouse early embryonic material E3.5; Mural trophectoderm

value: Mural trophectoderm cells


title: mERSEE1 RNA-Seq

description: PolyA RNA amplified by SMARTer kit

source_name: mouse early embryonic material; Epithelial Radially Symmetric Epiblast (ERSE) cells


title: mERSEE2 RNA-Seq

description: PolyA RNA amplified by SMARTer kit


title: pERSEE9x RNA-Seq

description: PolyA RNA amplified by SMARTer kit


title: pAPE3x RNA-Seq

description: PolyA RNA amplified by SMARTer kit


title: mEBI3 RNA-Seq

description: PolyA RNA amplified by SMARTer kit

source_name: mouse early embryonic material; Inner Cell Mass (ICM) cells


title: mEBI2 RNA-Seq

description: PolyA RNA amplified by SMARTer kit


title: pEBI1x RNA-Seq

description: PolyA RNA amplified by SMARTer kit


title: liver_mRNA_bowtie RNA-Seq

description: non-amplified PolyA RNA amplified

source_name: mouse liver

value: Unknown

value: adult mouse liver


title: bERSE7 RNA-Seq

description: PolyA RNA amplified by SMARTer kit

organism: Bos taurus

source_name: bovine early embryonic material; Epithelial Radially Symmetric Epiblast (ERSE) cells

value: Holstein


title: m129ERSEE1 RNA-Seq

description: PolyA RNA amplified by SMARTer kit


title: liver_mRNA_bowtie_SPIA RNA-Seq

description: PolyA RNA amplified by Nugen Ovation SPIA kit


title: mEBI1 RNA-Seq

description: PolyA RNA amplified by SMARTer kit


title: bERSE6 RNA-Seq

description: PolyA RNA amplified by SMARTer kit


title: bEBI7 RNA-Seq

description: PolyA RNA amplified by SMARTer kit

source_name: bovine early embryonic material; Inner Cell Mass (ICM) cells


title: liver_ampl_mRNA_bowtie RNA-Seq

description: PolyA RNA amplified by custom protocol


title: liver_mRNA_SMARTer_bowtie RNA-Seq

description: PolyA RNA amplified by SMARTer kit


title: bEBI8 RNA-Seq

description: PolyA RNA amplified by SMARTer kit


title: NC4

city: Shenzhen

first: Qiangzu

last: Zhang

address: Nan Hai Da Dao Chuang Shi Ji Bin Hai Hua Yuan Building9 9A , Nanshan District, Shenzhen City, Guangdong Province

country: China

institute: Lemondata BioTechnology Limited

data_processing:
Illumina hiseq4000 used for basecalling.
Sequence reads were trimmed for adaptor sequence and 3'-end was trimmed by quality, reads were filtered by quality and mapped to GRCh37 using the HISAT2 software
mapping QC by samtools and picard software
Quantification was done by using Cufflinks to produce gene-level expression values (FPKMs)
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

source_name: breast cancer cell

growth_protocol: cells were cultured in DMEM with 10% FBS.

extract_protocol:
The total RNA was extracted from cells by the qiagen RNA exaction kit
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# 0801-0303).

treatment_protocol: cells were treated with 50nM siSHARPIN or siControl

tag: passages

tag: cell line

tag: transfection

value: scramble siRNA


title: NC1


title: SiZ4

value: siSMURF1 siRNA


title: bAPE20 RNA-Seq

description: PolyA RNA amplified by SMARTer kit

source_name: bovine early embryonic material; Epiblast elongated along the Anterior-to-Posterior axis (APE) cells


title: A704_V5_high_RNASeq

city: New Haven

first: David

middle: Aaron

last: Schoenfeld

state: CT

address: 20 York Street

department: Medical Oncology

country: USA

institute: Yale Cancer Center

data_processing:
FastQC checks were done on the raw data, and the Tuxedo suite of tools was used to align the reads to GRCh37/hg19 and check for differential expression following well established methods.  Briefly, reads were aligned to the hg19 human reference genome using TopHat; the aligned reads were then processed through Cufflinks for assembly and quantification, generating RPKM values. Cuffdiff was used for differential gene expression analysis between samples.
Genome_build: hg19
Supplementary_files_format_and_content: "RNAseq_RPKM_complete_table.txt" is a file that contains a table of RPKM values generated by Cufflinks for transcripts for all 10 samples. "RNASeq_LOWserum_META-analysis.txt" and "RNASeq_HIGHserum_META-analysis.txt" are files that contain tables of the log2-fold-change and associated p-value for each transcript generated by Cuffdiff comparing the PBRM1-decifient condition to the PBRM-containing condition (786-O PBRM1 shRNA #1/control shRNA; 786-O PBRM1 shRNA #2/control shRNA; A-704 EV/V5), and the calculated "meta-p-value" generated by the Fisher's combined probability test.  This method allows one to pool the p-values from independent experiments and perform a meta-analysis, generating a “meta-p-value” for each gene.

growth_protocol: The 786-O and A-704 cell lines were purchased from the ATCC. 786-O were grown in RPMI 1640 medium supplemented with 10% (v/v) fetal bovine serum (FBS). Cells with stable PBRM1 knockdown were produced using  MISSION Lentiviral Transduction Particles  purchased from Sigma-Aldrich (clone IDs: TRCN0000235890 and TRCN0000015994; sh1 and sh2, respectively) and used according to the manufacturer’s instructions. Briefly, 1x10^5 cells were transduced with the viral particles at a MOI = 3, with 12 μg/mL polybrene. Transduced cells were then selected with 3 μg/mL puromycin for 10-14 days. Non-targeting control shRNA (Sigma, SHC016) lentiviruses were produced in HEK-293T cells. A-704 cells were grown in MEM (Cellgro) supplemented with 10% (v/v) FBS. Full-length PBRM1 was cloned into a pBABEpuro vector,  and a C-terminal V5 tag was added to this plasmid using site-directed mutagenesis. Retrovirus was produced by transfection of pBABE constructs into the Phoenix HEK-293 packaging cell line. Transduced A-704 cells were selected in 2 μg/mL puromycin for 10-14 days.

extract_protocol:
Total RNA was collected from healthy cells that were ~70% confluent using the Qiagen RNeasy kit. Poly-A selection of mRNA was then performed.
RNA-seq libraries were made following well-established protocols by the Genomics Core Facility at the Icahn School of Medicine at Mount Sinai. Briefly, 1ug of high quality total RNA was incubated with oligo(dT) magnetic beads (SeraMag or Dynal) in order to enrich for mRNA with poly-A tails. The eluted RNA was incubated at 94°C in Tris buffer with potassium acetate and magnesium acetate. This yielded fractionated RNA in the 200-500 nt range. The RNA was ethanol precipitated with sodium acetate, then resuspended in water. Reverse transcription with random oligonucleotide hexamers (Invitrogen SuperScript III) was performed to generate cDNA. Then, the RNA was degraded by addition of RNAse and DNA polymerase was added to generate a second strand. The DNA was then ready for standard Illumina adaptor ligation for sequencing. 100 bp single-end sequencing was performed on an Illumina HiSeq machine.

treatment_protocol: For reduced serum growth, the cells were washed twice with PBS, and then switched to the appropriate culture media with reduced FBS % (v/v). For low-serum growth, 786-O cells were grown in 1% FBS; A-704 cells were grown in 6% FBS. Before RNA collection, cells were passaged and grown at the specified serum levels for 48 hours.

value: clear cell renal cell carcinoma cell line A-704

tag: shRNA

tag: vector

tag: serum concentration

value: high


title: 786_control_high_RNASeq

value: clear cell renal cell carcinoma cell line 786-O

value: off-target control


title: 786_sh2_high_RNASeq

source_name: clear cell renal cell carcinoma cell line

value: PBRM1 shRNA #2


title: bAPE19 RNA-Seq

description: PolyA RNA amplified by SMARTer kit


title: 786_sh1_low_RNASeq

value: PBRM1 shRNA #1

value: low


title: bAPE17 RNA-Seq

description: PolyA RNA amplified by SMARTer kit

value: Epiblast elongated along the Anterior-to-Posterior axis (APE) cells


title: 786_control_low_RNASeq


title: bEBI5 RNA-Seq

description: PolyA RNA amplified by SMARTer kit


title: A704_EV_high_RNASeq

value: empty-vector


title: SiZ2


title: SiZ3


title: bERSE12 RNA-Seq

description: PolyA RNA amplified by SMARTer kit

value: Epithelial Radially Symmetric Epiblast (ERSE) cells


title: NC2


title: 786_sh2_INPUT_Histone_ChIPSeq

data_processing:
FastQC was run on the ChIP-seq raw data for quality control. Bowtie2 was used to align reads to the genome (GRCh37/hg19). The following settings were used (if not specified, the default settings were applied): a seed length of 75 was used, a maximum of 2 mismatches were allowed, only uniquely aligning reads were used, and the --best option was selected. After aligning, ENCODE-defined blacklisted regions of the genome were removed.
MACS2 was used for peak-calling, with the options --nomodel --extsize 150, --SPMR, and with q-value cutoffs of 0.05. Pileups were generated using MACS2 callpeak.
Galaxy’s deepTools was used to look at the average enrichment profiles at specified regions, for clustering analysis, and to generate heat maps. The genomic location of specific genes was defined according to the human hg19 (GRCh37.p13) gene annotation of Ensembl (gene database version 75), and was provided by the lab of Emily Bernstein.
Genome_build: hg19
Supplementary_files_format_and_content: bigWIg files were generated from MACS2 and represent the pileup signal file of 'fragment pileup per million reads'. narrowPeak files contain significant peaks and were also generated using MACS2, with the following settings:  --nomodel --extsize 150, --SPMR, and q-value cutoffs of 0.05.

growth_protocol: The 786-O cell line was purchased from the ATCC. Cells were grown in RPMI 1640 medium supplemented with 10% (v/v) fetal bovine serum. Cells with stable PBRM1 knockdown were produced using  MISSION Lentiviral Transduction Particles  purchased from Sigma-Aldrich (clone IDs: TRCN0000235890 and TRCN0000015994; sh1 and sh2, respectively) and used according to the manufacturer’s instructions. Briefly, 1x10^5 cells were transduced with the viral particles at a MOI = 3, with 12 μg/mL polybrene. Transduced cells were then selected with 3 μg/mL puromycin for 10-14 days. Non-targeting control shRNA (Sigma, SHC016) lentiviruses were produced in HEK-293T cells.

extract_protocol:
Briefly, 20-50x10^6 cells were swelled and lysed using 0.1% IGEPAL, nuclei were collected by centrifugation through a sucrose gradient, and micrococcal nuclease digestion was optimized for each cell collection to primarily generate mononucleosomes, without overdigesting. For the ChIP step, 3 μg of each histone mark antibody was used, and 50 μg of chromatin was used for methyl marks, and 100 μg was used for acetyl marks.
ChIP-seq libraries were made following well-established protocols. Briefly, 2-10 ng of DNA was end-repaired, an A-overhang was added, Illumina Truseq adapters were ligated, DNA was run on an agarose gel and size-selected using the Qiagen Gel Extraction Kit from between 300-400 bp to exclude polynucleosomes, which produced amplified libraries with sharp peaks of ~280 bp, as seen on the Bioanalyzer.  Finally, libraries were PCR amplified for 10-14 cycles using KAPA Biosystems HiFi PCR Master Mix. Where not indicated, all library preparation steps involved New England Biolabs enzymes. 75 bp single-end sequencing was performed on an Illumina NextSeq 500 machine.

tag: chip antibody


title: A704_V5_low_RNASeq


title: 786_control_INPUT_Histone_ChIPSeq


title: A704_EV_low_RNASeq


title: 786_sh1_high_RNASeq


title: 786_sh2_H3K4me1_ChIPSeq

value: Abcam H3K4me1 rabbit polyclonal ab (ab8895) - 3 ug (lot# GR141677-4)


title: 786_control_H3K27ac_ChIPSeq

value: Millipore H3K27ac rabbit polyclonal ab (07-360) - 3 ug (lot# 1959680)


title: 786_sh1_H3K4me1_ChIPSeq


title: 786_sh2_low_RNASeq


title: 786_sh2_H3K4me3_ChIPSeq

value: Abcam H3K4me3 rabbit polyclonal ab (ab8580) - 3 ug (lot# GR190202-1)


title: 786_control_H3K4me3_ChIPSeq


title: 786_sh1_INPUT_ARID2_ChIPSeq

data_processing:
FastQC was run on the ChIP-seq raw data for quality control. Bowtie2 was used to align reads to the genome (GRCh37/hg19). The following settings were used (if not specified, the default settings were applied): a seed length of 75 was used, a maximum of 2 mismatches were allowed, only uniquely aligning reads were used, and the --best option was selected. After aligning, ENCODE-defined blacklisted regions of the genome were removed. MACS2 was used to generate pileups.
SICER-df was used for ARID2 peak-calling with the following options: genome build – hg19; effective genome size – 0.793; redundancy threshold – 2; window size – 200; fragment size – 400; gap size – 600; and an FDR threshold of less than 0.05 for peak identification. Input DNA was used as the control sample for each cell line. ARID2 enrichment levels were also generated using SICER, comparing the ARID2 signal to the input DNA.
HOMER’s annotatePeaks was used for genomic annotation.
Galaxy’s deepTools was used to look at the average enrichment profiles at specified regions, for clustering analysis, and to generate heat maps. The genomic location of specific genes was defined according to the human hg19 (GRCh37.p13) gene annotation of Ensembl (gene database version 75), and was provided by the lab of Emily Bernstein.
Genome_build: hg19
Supplementary_files_format_and_content: bigWIg files were generated from MACS2 and represent the pileup signal file of 'fragment pileup per million reads'. Wig peak files were generated using SICER-df with the above settings and show peaks with an FDR threshold of less than 0.05.

extract_protocol:
Briefly, 15x10^6 786-O cells were cross-linked with 1% formaldehyde (Pierce, #28908) for 5 min at 4⁰C with gentle rocking. The fixed cells were sonicated using the TruChIP Chromatin Shearing Reagant Kit (Covaris, # PN 520154) following the manufacturer’s instructions. The IP step was carried out for 4 hr at 4⁰C with 5 μg of ARID2 (E-3) antibody (Santa Cruz), followed by a 2 hr incubation with Magna ChIP Protein A+G Magnetic Beads (Millipore, #16-663). After washing and chromatin elution, DNA was extracted via phenol/chloroform followed by DNA purification using Qiagen MiniElute PCR purification tubes. The amount and size of the precipitated DNA was evaluated using the Bioanalyzer. To generate enough DNA to make ChIP-seq libraries for sequencing, the entire process was repeated on a different batch of cells for each cell line. The precipitated DNA was then pooled for each cell line.
ChIP-seq libraries were made following well-established protocols. Briefly, 2-10 ng of DNA was end-repaired, an A-overhang was added, Illumina Truseq adapters were ligated, DNA was run on an agarose gel and size-selected at 350-500 bp using the Qiagen Gel Extraction Kit, and finally libraries were PCR amplified for 10-14 cycles using KAPA Biosystems HiFi PCR Master Mix. Where not indicated, all library preparation steps involved New England Biolabs enzymes. The quality and concentration of the prepared libraries were assessed on the Bioanalyzer - the libraries produced U-shaped DNA profiles, with an average peak around 400bp. 75 bp single-end sequencing was performed on an Illumina NextSeq 500 machine.


title: 786_sh1_INPUT_Histone_ChIPSeq


title: 786_control_INPUT_ARID2_ChIPSeq


title: 786_sh2_H3K9ac_ChIPSeq

value: Abcam H3K9ac rabbit polyclonal ab (ab10812) - 3 ug (lot# GR194223-1)


title: 786_sh2_ARID2_ChIPSeq

value: Santa Cruz ARID2 (E-3) sc-1666117 mouse monoclonal ab - 5 ug (lot# G2712)


title: 786_sh1_H3K9ac_ChIPSeq


title: 786_sh2_H3K27ac_ChIPSeq


title: 786_control_ARID2_ChIPSeq


title: 786_control_H3K9ac_ChIPSeq


title: 786_sh2_ATACSeq

data_processing:
Reads were trimmed for Illumina adapter sequences using in-house scripts and aligned to the GRCh37/hg19 using Bowtie2 (version 2.1.0) with parameters –S –X 2000. Reads that align to mtDNA, with quality value Q<30, as well as duplicated reads, were discarded using in-house scripts and Samtools. Coverage tracks were generated using deepTools bamCoverage with parameters –normalizeUsingRPKM –binsize 10.
Genome_build: hg19
Supplementary_files_format_and_content: bigWIg coverage tracks were generated using deepTools bamCoverage with parameters –normalizeUsingRPKM –binsize 10. The bed files represent significant peaks.

extract_protocol:
150,000 cells were harvested, tagmented with 5 μL Nextera Tn5 Transposes from Nextera kit (Illumina) for 30 min, amplified up to 13 cycles and purified.
Purified libraries were size selected on 2% agarose gel (150-700bp). Libraries were sequenced on Illumina Hi-Seq2500 (40 bp paired-end).


title: trachea_GFP

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: Tas2r143-reporter mice

data_processing:
Basecalls with RTA v2 (Illumina)
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Mapping: alignment versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1"
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers.
Genome_build: mm10
Supplementary_files_format_and_content: library size normalized counts per sample

source_name: EGFP-positive cells stomach

extract_protocol:
Same number of EGFP- and Tomato-positive cells were isolated by FACS from tracheas and stomachs of three tamoxifen-treated Tas2r143-reporter mice. RNA was isolated using the RNeasy Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA was verified with a BioAnalyzer 2100 (Agilent) or LabChip Gx Touch 24 (Perkin Elmer). RNA amount was adjusted on number of isolated cells by FACS and approx. 250ng of total RNA was used as input for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Clontech) for cDNA pre-amplification.
Clontech SMART-Seq® v4 Ultra® Low Input RNA Kit; Briefly, RNA amount was adjusted on number of isolated cells by FACS and approx. 250pg of total RNA was used as input for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Clontech) for cDNA pre-amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine (Covaris). Final Library Preparation was performed by Low Input Library Prep Kit v2 (Takara Clontech).

treatment_protocol: Tas2r143-reporter mice were treated with tamoxife for 5 days to induce the activiation of cre recombinase and were analyzed 5 days after the last injection .

tag: tissue

value: Stomach

tag: genotype


title: 786_sh1_H3K27ac_ChIPSeq


title: stomach_GFP

description: Tas2r143-reporter mice

source_name: EGFP-positive cells trachea

value: Trachea


title: SC_control [GE18S12]

status: Public on Aug 13 2018

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

data_processing:
The reads data were processed using BaseSpace software (Illumina)
Reads were aligned to R. norvegicus genome (version Rn5) using STAR aligner with default settings.
Statistical data processing and differential transcript expression was determined using the Cufflinks package (http://cufflinks.cbcb.umd.edu/).
Biological pathway analysis and comparison were performed using Ingenuity Pathway Analysis (Qiagen).
Genome_build: Rn5

organism: Rattus norvegicus

growth_protocol: Primary Schwann cells were isolated from sciatic nerves of postnatal (day 1-3) Sprague-Dawley rats. Cells were purified from fibroblasts using 10 M cytosine arabinoside (AraC), an anti-fibronectin Thy1.1 antibody, and the rabbit complement. Schwann cell purity was confirmed by S100B staining. Schwann cells (purity >99%) were plated in a 75 cm2 flask coated with 50 µg/ml poly-D-lysine (EMD Millipore) in DMEM containing 1 g/L glucose, 10% FBS, 100 μg/ml primocin (Invivogen), 21 μg/ml bovine pituitary extract and 4 μM Forskolin (EMD Millipore). Cells (90-100% confluent) were used in our experiments at passages 3-10. Cultures were routinely maintained at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from Schwann cells using TRI reagent (Zymo Research) and purified using Direct-zol microRNA system (Zymo Research). The RNA purity was estimated by measuring the OD260/280 ratio using a ND-1000 spectrophotometer (Thermo Scientific). RNA integrity was determined using 2100 Bioanalyser (Agilent Technologies).
Poly(A) RNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Ribosomal RNA was depleted using NEBNext rRNA Depletion reagents (New England Biolabs). A NEBNext Ultra Directional II RNA Library Preparation Kit for Illumina (New England Biolabs) was used to obtain barcoded cDNA libraries from total RNA. Barcoded libraries were pooled and the High Output v2 kit (IlluminaO) was employed to prepare the sequencing libraries. Libraries were sequenced on a NextSeq 500 DNA sequencer (Illumina).

treatment_protocol: Cells were grown to 80-90% confluency before transfection. Cells (1X106) were transfected using the recombinant DNA (1 µg) and Lipofectamin 3000. Cells were analyzed after 48 h post-transfection. Positive cells were enriched by passaging in the medium containing 10 µg/ml blasticidin S (Invivogen). Cells were stimulated by MBP peptides at the concentration of 10 uM added to the culture medium. Cells were collected after 24h in culture.

value: Sprague-Dawley

tag: cell type

value: primary Schwann cells (SC)

tag: treatment


title: SC_SCR [GE18S10]


title: 786_sh1_ATACSeq

value: clear cell renal cell carcinoma cell line 786-O


title: SC_84-105WT [GE18S07]


title: 786_control_H3K4me1_ChIPSeq

value: off-target control


title: 786_sh1_ARID2_ChIPSeq


title: 786_control_ATACSeq


title: MB7F1

city: Norfolk

first: Elena

last: Galkina

state: VA

address: 700 West Olney Road

department: Microbiology and Molecular Cell Biology

institute: Eastern Virginia Medical School

description: Single CD4+CD73+PD1+CD25+CCR5+ T cell library. The file name contains the C1 IFC Chip number, well position, and illumina Nextera indexing primer sequences

data_processing:
Illumina indexing primer sequences located in the file names were trimmed using the Fastx toolkit clipper function (Hannon lab). Trimmed Fastq files were then aligned to the mouse genome (UCSC mm10) using the Illumina Basespace Tophat 2 application (v1.0.0) with the default parameters to generate FPKM values. The FPKM values were exported and aggregated into a tab-delimited text file and analyzed for differential gene expression using R (v3.0.3, R. Foundation for Statistical Computing) and the SINGuLAR R library (v3.5.2, Fluidigm). Single T cell libraries that had under 100,000 reads were excluded from the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Butcher.All single T cell FPKM data.txt: The aligned and aggregated FPKM values for all of the single T cell libraries.  Butcher.Single T cell library groups: The Th1, Treg, and Th1/Treg groups analyzed

source_name: Splenic CD4+ T cells

extract_protocol:
40 week old Apoe-/- spleens (4-5 spleens/C1 IFC preparation, six independent IFC preparations) were collected, and CD4+ T cells were isolated by negative selection (Stem cell Technologies, Murine CD4+ EasySep kits). After extracellular staining with antibodies, CD4+CD73+PD1+CD25+CCR5+ T cells were isolated by cell sorting, as this population contains a mixture of Th1, Treg, and Th1/Treg cells. Isolated CD4+CD73+PD1+CD25+CCR5+ T cells were loaded onto 5-10um Fluidigm C1 IFCs in C1 suspension reagent to capture single cells, following the manufacturer's protocol. cDNA was prepared and amplified using the SMARTer Ultra Low RNA Kit and Advantage 2 PCR kits (Clontech), following the Fluidigm C1 Auto-prep mRNA seq: RT & Amp script (1772x/1773x) and C1 protocol. The single T cell cDNA yeilds were determined using the Quant-iT PicoGreen dsDNA assay (Life Technologies). 0.1-0.3 ng of cDNA was used to prepare the Nexterra cDNA libraries for illumina sequencing.
Nextera XT cDNA libraries were tagmented and indexed using the Nextera XT  DNA Sample Preparation kit, Nextera XT indexing primers (Illumina), and AMPure XP beads (Agencourt), following the Fluidigm C1 protocol and the manufacturer's instructions. 48 indexed libraries were pooled/lane and sequenced with an Illumina HiSeq 2000 (50bp, single ended reads, six lanes total). Base calling and demultiplexing was conducted using CASAVA to generate Fastq files. The Illumina indexing primer sequences are included in the Fastq file name.

value: Splenic CD4+CD73+PD1+CD25+CCR5+ T cell

value: Apoe-/-

tag: source

value: Spleen


title: MB7E11

tag: strain


title: MB7F2


title: 786_sh1_H3K4me3_ChIPSeq

value: PBRM1 shRNA #1


title: Med17AA_Veh_lab_RNA

city: Geneva

first: Maria

middle: Jessica

last: Bruzzone

address: 30, quai Ernest-Ansermet

department: Molecular Biology Department

country: Switzerland

institute: Univeristy of Geneva

data_processing:
ForRNA-Seq raw reads were aligned to the sacCer3 and 972-h pombe genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
For RNA-Seq, data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For RNA-Seq, reads that mapped to both sacCer3 and 972-h genomes were discarded.
For RNA-Seq, reads were extended by 50 bp
For RNA-Seq, reads mapped uniquely to the sacCer3 genome were first normalized to total number of mapped reads in sacCer3 and then to total number of uniquely mapped reads in 972-h pombe in the same sample as described in (Hu et al. 2015)
Genome_build: sacCer3, 972-h pombe
Supplementary_files_format_and_content: wig files were obtained using HTSStation (http://htsstation.epfl.ch)

organism: Saccharomyces cerevisiae

source_name: whole organism

growth_protocol: cells were grown at 30 degrees in YPAD to mid-log phase before treatment

extract_protocol:
Before extraction, previously 4-tU labeled S.pombe cells were mixed to S.cerevisiae cells to a ratio of 1:6. RNA was extracted with the standard hot phenol method and treated with DNAse I for 15' at room temperature. 4-tU labeled RNA was purified as described in (Baptista, T. 2017; PMID: 28918903)
TruSeq stranded mRNA kit (Illumina)

treatment_protocol: 4-tU labeling was performed as described in (Baptista, T. 2017; PMID: 28918903). After 54 minutes of rapamycin or vehicle treatement 4-tU was added to the cells. Cells were then harvested after 6 minutes of 4-tU labeling.

value: W303 mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 MED17-FRB::HIS3

value: no rapamycin, 6 minutes 4-tU labeling


title: MB5H2


title: MB5G10


title: MB5G12


title: MB5H1


title: 786_sh2_INPUT_ARID2_ChIPSeq

value: PBRM1 shRNA #2


title: trachea_TOM

description: Tas2r143-reporter mice

source_name: Tomato-positive cells stomach


title: stomach_TOM

description: Tas2r143-reporter mice

source_name: Tomato-positive cells trachea


title: MB5G9


title: MB5G6


title: SC_MBP84-104-mCherry [GE18S11]

value: expression of MBP84-104-mCherry


title: SC_mimTT [GE18S09]


title: MB5F12


title: MB5F7


title: MB7E9


title: MB7E7


title: SC_84-105WT [GE18S08]


title: MB7F4


title: MB5G11


title: MB5H5


title: MB5H3


title: MB5G2


title: MB5H9


title: MB5F8


title: MB5F10


title: MB5F2


title: MB5E4


title: MB5F3


title: MB5E10


title: MB5E1


title: MB5F6


title: MB5D10


title: MB5G5


title: MB5E7


title: MB5E2


title: MB5E8


title: MB5D9


title: MB5E3


title: MB5F5


title: MB5D6


title: MB5D8


title: MB5F9


title: MB5D5


title: MB5D12


title: MB5C12


title: MB7F5


title: MB5E5


title: MB5D7


title: MB5D3


title: MB5C10


title: MB5D1


title: MB5C9


title: MB5C8


title: MB5B6


title: MB5B7


title: MB5B3


title: MB5C6


title: MB5C2


title: MB5B2


title: MB5A12


title: MB5B1


title: MB5A8


title: MB5A3


title: MB5A2


title: MB4H8


title: MB4H7


title: MB5D4


title: MB5A1


title: MB4H5


title: MB4H3


title: MB4H4


title: MB4H1


title: MB4G2


title: MB4G9


title: MB4F9


title: MB5B10


title: MB5B11


title: MB4G3


title: MB4F8


title: MB4F2


title: MB4F6


title: MB4F10


title: MB4F1


title: MB7F6


title: MB7G1


title: MB2H10


title: MB7G4


title: MB7G5


title: MB7G3


title: MB2G12


title: MB2G11


title: MB2G7


title: MB2G10


title: MB2G9


title: MB2G8


title: MB2G6


title: MB2G5


title: MB2G4


title: MB2G2


title: MB2F12


title: MB2F11


title: MB2F10


title: MB2F8


title: MB2F7


title: MB2F6


title: MB7G6


title: MB7E12


title: MB2H3


title: MB2F3


title: MB2H1


title: MB2F5


title: MB2F2


title: MB2E8


title: MB2E12


title: MB2E9


title: MB2E6


title: MB2E7


title: MB2E2


title: MB2E4


title: MB2E3


title: MB2E5


title: MB2D7


title: MB2D11


title: MB2D6


title: MB2D5


title: MB2D2


title: MB2D3


title: MB2D1


title: MB2C9


title: MB2E11


title: MB2C8


title: MB2C7


title: MB2C6


title: MB2C2


title: MB2C3


title: MB2B12


title: MB2C5


title: MB2E10


title: MB2C1


title: MB2B7


title: MB2B8


title: MB2B4


title: MB2B6


title: MB2D8


title: MB2B11


title: MB2A12


title: MB2A11


title: MB2D4


title: MB2A9


title: MB2A8


title: MB2A7


title: MB2A6


title: MB2A1


title: MB1H10


title: MB1H6


title: MB1H11


title: MB2A3


title: MB1H9


title: MB1G12


title: MB1F11


title: MB1G3


title: MB1F1


title: MB1F4


title: MB1E12


title: MB1G8


title: MB1D11


title: MB2B3


title: MB2B2


title: MB2B1


title: MB1D10


title: MB2A10


title: MB1C9


title: MB1A11


title: MB1B9


title: MB7E5


title: MB7E6


title: MB1A12


title: MB1B1


title: MB7E2


title: MB7D8


title: MB7D10


title: MB1D7


title: MB7E1


title: MB7D1


title: MB1C3


title: MB7D4


title: MB7D3


title: MB7D12


title: MB2A2


title: MB7C12


title: MB7C10


title: MB7C11


title: MB7C9


title: MB7C6


title: MB7C5


title: MB7C7


title: MB7C4


title: MB7E4


title: MB7C3


title: MB7C2


title: MB7D7


title: MB7B10


title: MB7B7


title: MB7B12


title: MB7C1


title: MB7D6


title: MB7B4


title: MB7B6


title: MB7B1


title: MB7A12


title: MB7B2


title: MB7B3


title: Control rep3

city: Debrecen

first: Lilla

last: Ozgyin

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

description: Sample 3

data_processing:
Base calling and quality scoring are performed by RTA v2, demultiplexing was performed using CASAVA 1.4.
We used TopHat version 2.0.7 for read alignment with the option --max-multihits 1.
We used Cufflinks for calculating FPKM values using UCSC GRCh37/hg19 annotation track.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files for each sample containing gene IDs, genomic location and FPKM values.

source_name: B-lymphoblastoid cell line

growth_protocol: GM12873 cells were grown in RPMI-1640 medium supplemented with 15% FBS, 1v/v% Penicillin-Streptomycin and 2mM L-glutamine until sub-confluency (up to 0.8*10-5 cells/ml) before experiments.

extract_protocol:
Control cells were resuspended in 1 ml trizol after PBS washing, vortexed for 5 min at room temperature and stored at -20°C until RNA isolation. Lyophilized cells after two weeks of room temperature storage were directly resuspended in 1 ml trizol, vortexed for 5 min at room temperature and stored at -20°C until RNA isolation. Phase separation was performed by adding 1:5 volume of chloroform, vortexing for 5 min and subjecting to high-speed centrifugation at 4°C. RNA was precipitated from the aqueous phase using 1:1 volume of isopropanol at room temperature for 10 min. Pellets were washed twice with chilled 75% ethanol, vacuum-dried and redissolved in nulcease-free water at 65°C for 10 min.
Sequencing libraries were prepared following Illumina’s TruSeq RNA Sample Preparation v2 Guide with poly(A) selection from 1 μg total RNA. Indexed libraries were pooled and sequenced on the NextSeq 500 platform (75 bp, single-end).

treatment_protocol: Three million cells were washed in PBS and either resuspended in trizol or lyophilized in 0.5 ml 0.1 M trehalose (in PBS).

value: B-lymphocyte

value: non-lyophilized (control)

tag: sample pairing

value: paired to sample 6


title: Lyo rep3

description: Sample 6

value: Lyophilized

value: paired to sample 3


title: Lyo rep2

description: Sample 5

value: paired to sample 2


title: Lyo rep1

description: Sample 4

value: paired to sample 1


title: MB7A10


title: MB7C8


title: MB7A9


title: MB7A8


title: Control rep2

description: Sample 2

value: paired to sample 5


title: MB7A11


title: MB7A7


title: MB7B11


title: Control rep1

description: Sample 1

value: paired to sample 4


title: MB7A5

value: Splenic CD4+CD73+PD1+CD25+CCR5+ T cell


title: CTSK-cre positive cells - plate48

city: New York

first: Matthew

last: Greenblatt

state: NY

address: 1161 York Ave APT 1a

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICAL COLLEGE

data_processing:
Illumina CASAVA was used for basecalling.
Read 1 is composed of the barcode + UMI sequences while read 2 is the sequence of sample.
The data were processed using the NYGC re-tooled pipeline based on Drop-seq Core tools (McCarroll lab) which provides basic QC and expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: txt file recording the UMI counts for each gene in each cell

source_name: CTSK-cre positive cells sample 2

extract_protocol:
Skeletal tissue from postnatal day 6, mice was subjected to both mechanical and enzymatic digestion. Single cells were obtained, stained for Flow cytometry antibodies and FACS was conducted to sort CTSK-mGFP positive single cells.
cDNA synthesis was performed in individual wells using a template-switching mechanism followed by PCR amplification. All barcoded amplified cDNA was then pooled and run on a pico-green assay and Fragment Analyzer to evaluate sample concentration and quality, respectively. Libraries were generated from 300 pg of pooled cDNA using the Nextera XT library preparation kit (Illumina). The library was then sequenced with custom sequencing primers across two lanes of a 25bp x 75bp rapid run (HiSeq 2500 instrument).

value: Mouse femur

value: Mesenchymal cells

tag: age

value: Day 6

value: CTSK-cre+ mTMG


title: CTSK-cre positive cells - plate47

source_name: CTSK-cre positive cells sample 1


title: MB6H10

value: Apoe-/-

value: Spleen


title: dKOsham3

city: Rochester

first: Eric

last: Small

address: 601 Elmwood Avenue, Box CVRI

institute: University of Rochester

description:
Strain from: PMID 11440973, PMID 16847332, PMID 20534669
Processed data file: raw_counts.txt.gz

data_processing:
DEMULTIPLEXING - bcltofastq-2.19.0
CLEANING - Trimmomatic-0.36 "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15"
MAPPING - STAR_2.5.2b "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - subread-1.5.0p3, featurecounts, "-s 2 -t exon -g gene_name"
Genome_build: GRCm38.p5 + Gencode-M12 Annotation
Supplementary_files_format_and_content: raw_counts.txt: Tab-delimited text file includes raw expression counts.

source_name: MRTF dKO cardiomyocytes, sham surgery

growth_protocol: Single cells were isolated from mouse hearts by langendorff perfusion and cardiomyocytes were separated from non-myocytes by gravity sedimentation for 10min at 37∘C. Cardiomyocytes were then revived in a calcium ramping protocol, pelleted, and then immediately isolated in Trizol reagent.

extract_protocol:
RNA was isolated using Trizol reagent (Ambion) and treated with TURBO DNase I (Ambion) per manufacturer's instructions.
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next-generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified using Ampure beads and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA). Single end reads of 100nt were generated for each sample using Illumina’s HiSeq2500v4.

treatment_protocol: Eight-week-old male mice received three daily injections of tamoxifen at 30ug/g, were maintained for two weeks and then administered trans-aortic or sham surgery at 10 weeks of age. Hearts were isolated 7 days post-surgery (at 11 weeks of age).

tag: genotype/variation

tag: Sex

value: male

value: 11 weeks at isolation

value: cardiomyocytes

value: sham surgery


title: dKOTAC3

source_name: MRTF dKO cardiomyocytes, TAC surgery

value: trans-aortic constriction (TAC) surgery


title: dKOTAC2


title: MB7B5


title: dKOsham2


title: MB7A6


title: MB6H9


title: MB6H6


title: controlTAC2

description:
Strain from: PMID 11440973
Processed data file: raw_counts.txt.gz

source_name: Control cardiomyocytes, TAC surgery

value: alphaMHC-MerCreMre/+


title: dKOTAC1


title: controlTAC3


title: MB6H8


title: controlTAC1


title: dKOsham1


title: controlsham3

source_name: Control cardiomyocytes, sham surgery


title: MB6H3


title: controlsham2


title: MB6H1


title: MB6G9


title: controlsham1


title: MB6G7


title: MB6G10


title: MB6G3


title: MB6G4


title: MB6G6


title: MB6G2


title: MB6F2


title: MB6E10


title: MB6F4


title: MB6G1


title: MB6F12


title: MB6E9


title: MB6E11


title: MB6F7


title: MB6G8


title: MB6E8


title: MB6E2


title: MB6E7


title: MB6E1


title: MB6E5


title: MB6D12


title: MB6D11


title: MSC_4

data_processing:
Illumina bcl2fastq2 v2.17 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the UCSC mm10 mouse reference genome using tophat v2.0.11.
Raw reads counts were extracted using htseq-count v0.6.1.
Differential expression analysis was performed by using DESeq2 package v1.6.3.
Genome_build: mm10
Supplementary_files_format_and_content: excel file including gene name, Ensembl gene id, normalized read counts for each gene in each sample

source_name: CTSK-mGFP negative mesenchymal stem cells (MSC)

extract_protocol:
Skeletal tissue from postnatal day 6, mice was subjected to both mechanical and enzymatic digestion. Single cells were obtained, stained for Flow cytometry antibodies and FACS was conducted to sort the desired cell types. RNA samples were prepared using the RNeasy Plus Micro kit Cat no 74034.
cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation kit and sequenced on HiSeq4000 sequencer.

value: Endosteal mesenchymal stem cells


title: MSC_3


title: MSC_1


title: MB6D4


title: MB6D6


title: MB6D8


title: PP2_4

source_name: Progenitor population type 2

value: Periosteal progenitor cells


title: MB6D3


title: MB6D2


title: MB6D1


title: PP1_4

source_name: Progenitot population type 1


title: PP2_1


title: MB6C7


title: MB6E3


title: MB6C10


title: MB6C11


title: PP2_3


title: PP1_2


title: PP1_1


title: PSC_4

source_name: Persiosteal stem cells (PSC)

value: Periosteal stem cells


title: PP1_3


title: MB6C5


title: MB6C1


title: MB6D7


title: PSC_3


title: MB6C2


title: MB6B11


title: MSC_2


title: MB6B9


title: PSC_1


title: MB6B5


title: SCL KO Bio Rep 2

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

institute: Monash University

data_processing:
STAR (v2.5.2b) Alignment
featureCounts in Subread v1.5.2
DE analysis by LIMMA/VOOM
Genome_build: GRCm38 Ensembl
Supplementary_files_format_and_content: txt

source_name: Pooled e9.5 embryos

growth_protocol: Not applicable

extract_protocol:
Trizol and RNAeasy Mini according to manufacturer's instructions
TruSeq Stranded mRNA Library preparation

treatment_protocol: Not applicable

value: SCL KO

value: embryo


title: MB6B1

value: Splenic CD4+CD73+PD1+CD25+CCR5+ T cell


title: PP2_2

value: Mouse femur


title: SCL KO Bio Rep 1


title: LYL1 KO Bio Rep 2

value: LYL1 KO


title: MB6A9


title: MB6A11


title: LYL1 SCL DKO Bio Rep 2

value: LYL1 SCL DKO


title: Wildtype Bio Rep 3

value: WT


title: LYL1 SCL DKO Bio Rep 1


title: MB6A3

value: Apoe-/-

value: Spleen


title: MB6B2


title: LYL1 KO Bio Rep 1


title: MB6A1


title: PSC_2

value: Day 6

value: CTSK-cre+ mTMG


title: Wildtype Bio Rep 2


title: SCL KO Bio Rep 3


title: Wildtype Bio Rep 1


title: LYL1 KO Bio Rep 3


title: MB6F9


title: hs_rna_b_control_C3

status: Public on Aug 11 2018

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: processed data: human_gene_counts.txt (RNA-seq counts table)

data_processing:
Raw reads were aligned to the reference genome using STAR v2.4.2a.
Counts per gene were generated using featureCounts v1.5.0.
genome build: hg19
processed data files format and content: Read counts per gene: tab-delimited text table

source_name: Human B cells - control

extract_protocol: RNA was isolated from flow sorted B cell populations with the Qiagen RNeasy kit (Qiagen). Concentration and purity was analyzed on a Nanodrop 1000 Spectrophotometer. mRNA was isolated by oligo-dT beads and library was prepared using standard Illumina library protocol (Kit: RS-122-2101 TruSeq® Stranded mRNA LT-SetA). Libraries were sequenced on the Illumina Hiseq2500.

value: B cells


title: hs_rna_b_CVID4

source_name: Human B cells - common variable immune deficiency


title: hs_rna_b_CVID3


title: hs_rna_b_control-C5

source_name: Human B cells – control


title: hs_rna_b_CVID1


title: hs_rna_b_PM

description:
mother of patients 1 and 2.
processed data: human_gene_counts.txt (RNA-seq counts table)

source_name: Human B cells – patient's mother (control)


title: hs_rna_b_brwd1mut-P2

description:
patient 2. Brother of patient 1.
processed data: human_gene_counts.txt (RNA-seq counts table)

source_name: Human B cells – Brwd1 mutation


title: hs_rna_b_control_C4


title: hs_rna_b_control-C2


title: hs_rna_b_brwd1mut-P1

description:
patient 1. Brother of patient 2.
processed data: human_gene_counts.txt (RNA-seq counts table)


title: hs_rna_b_control-C1


title: LYL1 SCL DKO Bio Rep 3


title: hs_atac_b_CVID4

description:
processed data: ChIP and ATAC peak calls (*bed)
processed data: ATAC-seq open chromatin enrichment (*open.bw)
processed data: ATAC-seq read start position enrichment (*starts.bw)

data_processing:
Raw reads were aligned to the reference genome using BWA MEM v0.7.5a. Apparent PCR duplicates were removed using Picard MarkDuplicates v1.107.
Read alignments were first adjusted to account for TAC transposon binding: +4bp for + strand alignments, -5bp for - strand alignments. The open chromatin enrichment track was generated by first creating a bedGraph from the raw reads using bedtools genomcov v2.18.2, then coverted to bigWig using UCSC tool bedGraphToBigWig; tracks were normalized by the sum of alignment lengths over 1 billion. The start position track was generated by taking just the first base of the alignment for + strand alignments or the last base of the alignment for - strand alignments, then creating bedGraph and bigWig tracks as for the open chromatin; tracks were normalized to the alignment count over 1 million. Open chromatin peaks were called using Macs2 (v2.1.0) with --nomodel set and no background provided; peaks with a score >5 were retained.
Properly paired read pairs were first put into nucleosome-free or nucleosome-containing bins, based on their fragment size. Fragments <=100bp were considered nucleosome free (background) and converted to a single read covering the length of the fragment. Fragments 180-247bp were considered single-nucleosome-containing and converted to a single read the length of the fragment; similarly, fragments 315-473bp or 558-615bp were considered two- or three-nucleosome containing, and split into 2 or 3 reads covering half or 1/3 of the total fragment length. Single-, two-, and three- nucleosome reads were combined into the nucleosome signal read set. Nucleosome positioning analysis was run using danpos v2.2.2 with command dpos and parameters -m 1 -a 10 -jd 20 --clonalcut 0, and contrasting nucleosome signal to nucleosome background for each sample. Wig tracks from danpos were re-normalized to counts per billion bases using the sum of alignment lengths over 1 billion from the original BAM file, and converted to bigWig using UCSC tool wigToBigWig.
genome build: hg19
processed data files format and content: ChIP and ATAC peak calls: Peak calls from Macs2 (bed format).
ATAC-seq open chromatin enrichment, normalized to counts per billion bases (bigWig format)
ATAC-seq read start position enrichment: Track of read start positions for ATAC-seq (used for motif footprinting), normalized to counts per million reads (bigWig format)

extract_protocol: To prepare Nuclei, respective flow sorted mouse or EBV transformed human peripheral B cells (1x105) cultured in RPMI media (with L- glutamine, 10% FBS, 1mM Sodium pyruvate, 10mM HEPES, 100units/ml penicillin, 100µg/ml Streptomycin) were centrifuged at 500g for 5 min, which was followed by a wash with ice-cold PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min at 40C and supernatant removed. The nuclei pellet was resuspended in the transposase reaction mix (25 μL 2X Tagment buffer, 2.5 μL Tagment DNA enzyme (Illumina, FC-121-1030) and 22.5 μL nuclease-free water). The transposition reaction was carried out at 37 °C for 30 min. Directly following transposition the sample was purified using a Qiagen MinElute kit. Following purification, we amplified library fragments using Nextera PCR Primers (Illumina Nextera Index kit) and NEBnext PCR master mix (New England lab, 0541) for a total of 10-12 cycles. The libraries were then purified using a Qiagen PCR cleanup kit.   The amplified, adapter ligated libraries were size selected using Life Technologies' E-Gel® SizeSelect™ gel system in the 150-650bp range. The size-selected libraries were quantified using the Agilent Bioanalyzer and via q-PCR in triplicate using the KAPA Library Quantification Kit on the Life Technologies Step One System. Libraries were sequenced on the Illumina Hiseq2500 system to generate 75-100M, 50bp paired end reads.


title: hs_atac_b_control-C5


title: hs_atac_b_CVID3


title: hs_atac_b_CVID1


title: hs_atac_b_CVID2


title: hs_atac_b_brwd1mut-P1

description:
patient 1. Brother of patient 2.
processed data: ChIP and ATAC peak calls (*bed)
processed data: ATAC-seq open chromatin enrichment (*open.bw)
processed data: ATAC-seq read start position enrichment (*starts.bw)


title: hs_atac_b_control-C2


title: hs_atac_b_control_C3


title: hs_atac_b_control-C1


title: Control23

city: London

first: Sarah

last: Marzi

address: DeCrespigny Park

department: Institute of Psychiatry, Psychology and Neuroscience

country: United Kingdom

institute: King's College London

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version with the following configurations: Aligned files were output to SAM format and alignment was calculated across 64 cores.
For samples profiled across more than one lane, aligned reads across lanes were merged. Data were filtered using the following specifications: Any reads of sequencing quality score q < 30 were filtered out. Non-aligned and non-uniquely aligned reads were filtered out. PCR duplicates were removed.
All samples were merged into one large BAM file, on which peaks were called using MACS2 with the following configurations: Sequencing length 50, keep duplicates = all (because of prior removal of duplicates), genoome = hs, output format = BED.
Peaks were filtered using the following specifications: Peaks mapping to unmapped contigs or mitochondrial DNA were filtered out
Read counts per peak and sample were generated: The peak locations were converted to gff format and read counts per peak were generated for each sample using HTSeq.
Genome_build: hg19
Supplementary_files_format_and_content: The bed file H3K27ac_EntorhinalCortex.bed contains the location of all 182065 peaks called on the merged set of all samples and was generated using MACS2
Supplementary_files_format_and_content: Text files xxx.txt were generated using HTSeq. For each sample these show the number of reads mapping to each peak listed in H3K27ac_EntorhinalCortex.bed. Statistical analyses of differential acetylation were performed on these read counts using EdgeR.

source_name: Entorhinal cortex

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the MicroPlex Library Preparation kit v2 (Diagenode, Cat #C05010013) according to the manufacturer’s protocol.  Libraries were sequenced on the on an Illumina HiSeq-2500 using single-end sequencing and a read length of 50bp.

tag: disease status

value: C

tag: age at death

value: M

tag: neuronal proportion estimate

value: H3K27ac (Diagenode, catalog #C15410196, lot# A1723-0041D)


title: Control22

value: F


title: hs_atac_b_brwd1mut-P2

description:
patient 2. Brother of patient 1.
processed data: ChIP and ATAC peak calls (*bed)
processed data: ATAC-seq open chromatin enrichment (*open.bw)
processed data: ATAC-seq read start position enrichment (*starts.bw)


title: hs_atac_b_PM

description:
mother of patients 1 and 2.
processed data: ChIP and ATAC peak calls (*bed)
processed data: ATAC-seq open chromatin enrichment (*open.bw)
processed data: ATAC-seq read start position enrichment (*starts.bw)


title: Control19


title: Control20


title: hs_atac_b_control_C4


title: Control18


title: Control17


title: Control9


title: Control10


title: Control14


title: Control13


title: Control12


title: Control11


title: Control15


title: hs_rna_b_CVID2


title: Control21


title: Control6


title: Control5


title: Control7


title: Control2


title: Control4


title: Control3


title: AD23

value: AD


title: AD24


title: Control1


title: AD20


title: AD21


title: Control16


title: Control8


title: AD17


title: AD18


title: mm_rna_prob.1

description: processed data: mouse_gene_counts.txt (RNA-seq counts table)

data_processing:
Raw reads were aligned to the reference genome using STAR v2.4.2a.
Counts per gene were generated using featureCounts v1.5.0.
genome build: mm9
processed data files format and content: Read counts per gene: tab-delimited text table

source_name: Pro-B

value: Pro-B


title: AD15


title: AD16


title: mm_rna_spreb_brwd1ko.2

source_name: small Pre-B - BRWD1-Mut

value: small Pre-B


title: AD13


title: AD14


title: AD12


title: mm_rna_spreb_brwd1ko.1


title: mm_rna_spreb.2

source_name: small Pre-B


title: AD11


title: mm_rna_spreb.1


title: AD19


title: mm_chip_spreb_irf4_lowdna.2

description:
processed data: ChIP and ATAC peak calls (*bed)
processed data: ChIP enrichment tracks (*pileup.bw)

data_processing:
Raw reads were aligned to the reference genome using BWA MEM v0.7.5a. Apparent PCR duplicates were removed using Picard MarkDuplicates v1.107.
Peaks were called against specified inputs using Macs2 (v2.1.0); normalized bedgraph tracks were generated using the --SPMR flag, and converted to bigWig using UCSC tool bedGraphToBigWig. Peaks with a score >5 were retained.
genome build: mm9
processed data files format and content: ChIP and ATAC peak calls: Peak calls from Macs2 (bed format).
ChIP enrichment tracks: ChIP-seq enrichment tracks from Macs2, normalized to counts per million reads (bigWig format)

source_name: SpreB – low DNA

extract_protocol: Chromatin from flow sorted small pre-B cells (20×10^6 or 2×10^6 for lowdna samples) was used for each ChIP experiment with anti-IRF4 (M-17, Santa Cruz Biotechnogy, sc-6059X, lot#J2015) antibody. DNA libraries were prepared from the sheared chromatin (200–600 bp). Libraries were sequenced on the Illumina Hiseq2500.

tag: input used for chip-seq peak calling


title: AD8


title: AD10


title: AD9


title: mm_rna_prob.2


title: mm_chip_spreb_irf4_lowdna.1


title: mm_chip_spreb_irf4.1

source_name: SpreB


title: AD7


title: AD5


title: mm_chip_spreb_irf4_brwd1ko-lowdna.1

source_name: Spre-B Brwd1 KO – low DNA


title: AD4


title: AD3


title: mm_chip_spreb_irf4_brwd1ko-lowdna.2


title: AD6


title: mm_input_spreb.2

description: processed data: none (input)


title: mm_chip_spreb_irf4_brwd1ko.1

source_name: Spre-B Brwd1 KO


title: AD2


title: mm_input_spreb_tag.1

description: processed data: none (input)

source_name: SpreB – input tagmentation


title: mm_atac_immatureb.1

description:
processed data: ChIP and ATAC peak calls (*bed)
processed data: ATAC-seq open chromatin enrichment (*open.bw)
processed data: ATAC-seq read start position enrichment (*starts.bw)
processed data: ATAC-seq nucleosome signal enrichment (*nucl.signal.bw)
processed data: ATAC-seq nucleosome background enrichment (*nucl.bkgrnd.bw)
processed data: ATAC-seq nucleosome differential enrichment (*nucl.diff.bw)

data_processing:
Raw reads were aligned to the reference genome using BWA MEM v0.7.5a. Apparent PCR duplicates were removed using Picard MarkDuplicates v1.107.
Read alignments were first adjusted to account for TAC transposon binding: +4bp for + strand alignments, -5bp for - strand alignments. The open chromatin enrichment track was generated by first creating a bedGraph from the raw reads using bedtools genomcov v2.18.2, then coverted to bigWig using UCSC tool bedGraphToBigWig; tracks were normalized by the sum of alignment lengths over 1 billion. The start position track was generated by taking just the first base of the alignment for + strand alignments or the last base of the alignment for - strand alignments, then creating bedGraph and bigWig tracks as for the open chromatin; tracks were normalized to the alignment count over 1 million. Open chromatin peaks were called using Macs2 (v2.1.0) with --nomodel set and no background provided; peaks with a score >5 were retained.
Properly paired read pairs were first put into nucleosome-free or nucleosome-containing bins, based on their fragment size. Fragments <=100bp were considered nucleosome free (background) and converted to a single read covering the length of the fragment. Fragments 180-247bp were considered single-nucleosome-containing and converted to a single read the length of the fragment; similarly, fragments 315-473bp or 558-615bp were considered two- or three-nucleosome containing, and split into 2 or 3 reads covering half or 1/3 of the total fragment length. Single-, two-, and three- nucleosome reads were combined into the nucleosome signal read set. Nucleosome positioning analysis was run using danpos v2.2.2 with command dpos and parameters -m 1 -a 10 -jd 20 --clonalcut 0, and contrasting nucleosome signal to nucleosome background for each sample. Wig tracks from danpos were re-normalized to counts per billion bases using the sum of alignment lengths over 1 billion from the original BAM file, and converted to bigWig using UCSC tool wigToBigWig.
genome build: mm9
processed data files format and content: ChIP and ATAC peak calls: Peak calls from Macs2 (bed format).
ATAC-seq open chromatin enrichment, normalized to counts per billion bases (bigWig format)
ATAC-seq read start position enrichment: Track of read start positions for ATAC-seq (used for motif footprinting), normalized to counts per million reads (bigWig format)
ATAC-seq nucleosome signal enrichment: Track of nucleosome signal read pairs (inferred presences of nucleosomes), normalized to counts per billion bases (bigWig format)
ATAC-seq nucleosome background enrichment: Track of nucleosome background read pairs (inferred absence of nucleosomes), normalized to counts per billion bases (bigWig format)
ATAC-seq nucleosome differential enrichment: Track of nucleosome signal minus background, normalized to counts per billion bases (bigWig format)

source_name: ImmatureB

value: ImmatureB


title: AD1


title: mm_atac_spreb_brwd1ko.2


title: mm_atac_spreb.2


title: mm_atac_spreb_brwd1ko.1


title: ACC_ATRA_1

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description:
rRNA depleted RNA
JMG_8_ACCx9_2-16
Barcode: ACTTGA

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to hg19 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: hg19
Supplementary_files_format_and_content: excel file includes FPKM values for each Sample

growth_protocol: ACCx9 tumor fragments from host animals were implanted subcutaneously into the flank of nude mice (CRL: ATH/NU). Mice were randomized to receive vehicle or ATRA diluted in 10:90 DMSO:10%hydroxypropyl-beta-cyclodextrin orally.

extract_protocol:
Frozen primagrafts were mechanically dissociated, and total RNA was extracted with the RNeasy mini plus kit from Qiagen.
Total RNA was depleted of ribosomal RNA with the RiboZero gold kit (Epicentre). Enriched mRNA was then applied to library preparation according to manufacturer’s protocol (NEBNext Ultra). After repeated quality control for average DNA input size of 300 bp, the samples were sequenced on a Hi-Seq2500 Illumina sequencer with 2x100bp paired-end reads.

treatment_protocol: Mice were randomized and treated with vehicle or ATRA (3 mg/mL, 0.2 mL flat dose) for 3 days. Tumors were collected and flash frozen.

tag: xenograft

tag: agent

value: ATRA


title: mm_atac_spreb.1


title: ACC_vehicle_3

description:
rRNA depleted RNA
JMG_6_ACCx9_1-8
Barcode: GCCAAT

value: vehicle


title: mm_atac_lpreb.2

source_name: Large Pre-B

value: Large Pre-B


title: ACC_vehicle_1

description:
rRNA depleted RNA
JMG_3_ACCx9_1-1
Barcode: TTAGGC


title: 1673_SHR

city: Muenster

last: Barysenka

address: Domagkstrasse 3

department: Genetic Epidemiology

institute: Institute of Human Genetics, University of Muenster

description: SHR Rep3

data_processing:
Basecalls performed using NextSeq 500 RTA software, v. 2.4.6
FASTQ files were generated using bcl2fastq, v.2.16
Raw reads were quality trimmed using Cutadapt v. 1.9 program with the following configurations: minimal base quality: 25, minimal read length after trimming: 70 nt
RNA-seq reads were aligned to the rn6 genome assembly using TopHat2 (v. 2.1.0) and Bowtie2 (v. 2.2.3)
Cufflinks version 2.2.1 program together with Ensembl (release 81) gene annotation were used to assemble transcripts and estimate their abundances
Differential expression analysis was performed using Cuffdiff version 2.2.1 software package and DESeq2 R package version 1.12.4
Genome_build: rn6
Supplementary_files_format_and_content: cuffdiff.gene_exp.diff: gene differential expression produced by Cuffdiff
Supplementary_files_format_and_content: deseq2.results.csv: gene differential expression produced by DeSeq2

source_name: spontaneously hypertensive rats

extract_protocol:
Total RNA of glomeruli preparations was isolated and DNase-treated by RNeasy Purification Kits (Qiagen)
The NEBNext Poly(A) mRNA magnetic isolation module followed by library preparation using NEBNext Ultra RNA Library Prep Kit for Illumina (New England BioLabs) was applied on 1 µg total RNA to generate a cDNA library

value: glomerular cells


title: 2139_MWF

description: MWF Rep1

source_name: Munich Wistar Frömter


title: RAR ChIP on ATRA-treated ACC

description:
ACC9_2_18_RAR
Barcode: TTAGGC

data_processing:
ChIP-Seq aligned to hg19 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph pileup from MACS 2.0 output

source_name: RAR ChIP on ATRA-treated ACC

extract_protocol:
Frozen primagrafts were mechanically dissociated, formaldehyde cross-linked, and collected. ChIP was performed with 10 antibodies against c-myb (Bethyl, A304-136A), RAR (Santa Cruz, sc-773X), and H3K27ac (Abcam, ab4729). DNA was then de-cross-linked from pulled down proteins and purified by phenol:chloroform:isoamyl alcohol extraction.
The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified for 150 and 350 bp.  The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2500. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script.

tag: chip antibody

value: RAR (Santa Cruz, catalog# sc-773X, lot# B1715)


title: mm_atac_lpreb.1


title: ACC_vehicle_2

description:
rRNA depleted RNA
JMG_5_ACCx9_1-3
Barcode: ACAGTG


title: mm_atac_prob.1


title: 1671_SHR

description: SHR Rep1

tag: tissue


title: Input RAR ChIP on ATRA-treated ACC

description:
ACC9_2_18_input
Barcode: TAGCTT

source_name: Input RAR ChIP on ATRA-treated ACC


title: ACC_ATRA_2

description:
rRNA depleted RNA
JMG_11_ACCx9_2-22
Barcode: GGCTAC


title: ACC_ATRA_3

description:
rRNA depleted RNA
JMG_12_ACCx9_2-30
Barcode: CTTGTA


title: mm_atac_prob.2


title: 2142_MWF

description: MWF Rep3


title: Input H3K27ac ChIP on ATRA-treated ACC

description:
ACC9_2_16_input
Barcode: AGTCAA

source_name: Input H3K27ac ChIP on ATRA-treated ACC


title: H3K27ac ChIP on ATRA-treated ACC

description:
ACC9_2_16_H3K27ac
Barcode: TGACCA

source_name: H3K27ac ChIP on ATRA-treated ACC

value: H3K27ac (Abcam, catalog# ab4729, lot# GR261979-1)


title: 2141_MWF

description: MWF Rep2


title: mm_atac_pre-prob.2

source_name: Pre-Pro-B

value: Pre-Pro-B


title: Myb ChIP on ATRA-treated ACC

description:
ACC9_2_30_MYB
Barcode: CGATGT

source_name: Myb ChIP on ATRA-treated ACC

value: c-myb (Bethyl, catalog# A304-136A, lot# A304-136A-1)


title: Input RAR ChIP on vehicle-treated ACC

description:
ACC9_1_8_input
Barcode: GATCAG

source_name: Input RAR ChIP on vehicle-treated ACC


title: 1672_SHR

description: SHR Rep2


title: H3K27ac ChIP on vehicle-treated ACC

description:
ACC9_1_3_H3K27ac
Barcode: TTAGGC

source_name: H3K27ac ChIP on vehicle-treated ACC


title: RAR ChIP on vehicle-treated ACC

description:
ACC9_1_8_RAR
Barcode: ATCACG

source_name: RAR ChIP on vehicle-treated ACC


title: Myb ChIP on vehicle-treated ACC

description:
ACC9_1_1_MYB
Barcode: ATCACG

source_name: Myb ChIP on vehicle-treated ACC


title: mm_atac_pre-prob.1


title: Input myb ChIP on vehicle-treated ACC

description:
ACC9_1_1_input
Barcode: CAGATC

source_name: Input myb ChIP on vehicle-treated ACC


title: pMrpJ-His replicate 2

status: Public on Aug 10 2018

city: Ann Arbor

first: Melanie

middle: M

last: Pearson

state: MI

address: 1150 W Medical Center Dr

department: Microbiology and Immunology

institute: University of Michigan Medical School

data_processing:
Sequence reads were aligned to the HI4320 genome and normalized sequence read density across the genome was determined using Rockhopper (version 2.02; default parameters)
Each anti-His ChIP-seq dataset was arbitrarily paired with a control dataset and the sequence read coverage from the control dataset was subtracted from that for the paired anti-His dataset. These background-subtracted data were then used to call peaks. Peaks within 100 bp of each other were considered to be representative of single binding events.
The peak corresponding to the MrpJ gene was manually removed because sequence read coverage in this genomic region is due predominantly to mrpJ present on the multi-copy plasmid.
101 bp sequences centered on each peak were extracted for motif analysis. Overlapping sequences were merged. This yielded 79 sequences that were analyzed for enriched sequence motifs using MEME-ChIP (version 4.10.2; default parameters except that the HI4320 genome sequence was used as a background model)
Genome_build: Proteus mirabilis HI4320 accession numbers NC_010554 (chromosome) and NC_010555 (plasmid)
Supplementary_files_format_and_content: As in Singh et al, 2014 Genes & Development doi: 10.1101/gad.234336.113

organism: Proteus mirabilis

source_name: Bacterial culture

growth_protocol: 300 ml of LB supplemented with ampicillin was inoculated with a 1:100 dilution of an overnight culture and was grown at 37°C with 225 rpm agitation. Cultures were harvested when OD600 reached ~ 2.

extract_protocol:
Formaldehyde-crosslinked frozen pellets were thawed on ice followed by cell lysis in 8 ml of ChIP lysis buffer (1% Triton X-100, 1mM EDTA, 15mM Tris-Cl pH 7.5, 150mM NaCl) that was fortified with protease inhibitor cocktail (Thermo Fisher). Cells were broken by French press (3 passes) followed by centrifugation of 800 ul lysate aliquots at 17115 x g for 10 minutes to get rid of cellular debris. Each 800ul clean lysate corresponds to 10 ml of cell pellet.
As in Singh et al, 2014 Genes & Development doi: 10.1101/gad.234336.113

treatment_protocol: Cells were collected by centrifugation of 50 ml aliquots at 1500 x g for 15 min. Pellets were washed twice in 5 ml sterile 1X PBS (pH 7.4) prior to resuspension in 10 ml final volume. 37% formaldehyde solution (Fisher Scientific) was added as an in vivo cross-linker to reach a final concentration of 1% and the tubes were gently rocked for 10 min at room temperature followed by the addition of glycine (final concentration of 0.75M) to cease cross linking (5 min rocking at room temperature). Cells were spun down followed by the washing of pellets in 5 ml sterile 1X PBS as described above. These treated pellets were snap frozen in dry-ice/ethanol and stored in -80 C.

tag: plasmid

value: pNB010 (pMrpJ)

value: penta-His (Qiagen #34660)


title: empty vector-His replicate 1

value: pLX3607 (empty vector)


title: pMrpJ-no Ab replicate 1


title: pMrpJ-His replicate 1


title: empty vector-no Ab replicate 1


title: empty vector-no Ab replicate 2


title: pMrpJ-no Ab replicate 2


title: mm_atac_immatureb.2

tag: cell type


title: young_rep2_Ribo-seq

city: Houston

first: Bo

last: Xia

state: TX

address: 6670 Bertner Ave, R10-414D

institute: Houston Methodist

description:
ribosome-protected mRNA
all_sample_normalized.xls

data_processing:
Library strategy: Ribo-seq
Reads were quality trimmed and filtered using fastqx to remove reads containing low-quality bases.
Genome Index were built with bowtie-build
Reads were mapped with tophat2 and calculated for each gene using HtSeq v0.6.1
RNA abundance analysis, Translation efficiency, Ribosome binding analysis were performed with meV, David, R packages & scripts
Wig file are generated from bam by bedtools2 and kent package from ucsc, and normalized by danpos
Genome_build: sacCer3

source_name: yeast

growth_protocol: Cells were grown under standard conditions, unless otherwise noted. Yeast strains, plasmids, and oligonucleotides are listed in Table S2. Epitope-tagged sORFs were generated using homologous recombination (Longtine et al., 1998) or standard molecular cloning strategies. For isolating old cells, we used the MEP (Lindstrom and Gottschling, 2009) with the previously described slight modifications (Hu et al., 2014). Middle-aged cells were isolated after 15hr in estradiol while old cells were isolated after 30 hours in estradiol. Yeast were grown in YEP + 2% glucose or 0.5% galactose.

extract_protocol:
For ribosome footprinting, the clarified lysate from the same number of young and old cells were digested with RNase I and separated through a 10.5-ml 10%–50% sucrose gradient. 80S monosome fractions were collected and the RNA was extracted following the same procedure as for global footprints.
The TruSeq Ribo Profile kit RPYSC12116 (formerly ARTseq) was used to sequence ribosome-protected mRNA fragments. The Ambion ERCC RNA spike-in control (#4456740, Life Technology) was sonicated to reach an average size of 28nt and included in the library construction.


title: Input myb ChIP on ATRA-treated ACC

description:
ACC9_2_30_input
Barcode: ACTTGA

source_name: Input myb ChIP on ATRA-treated ACC


title: young_rep3_Ribo-seq


title: old30h_rep2_Ribo-seq


title: old30h_rep1_Ribo-seq


title: H30

city: Pacific Grove

first: Luke

last: Gardner

state: California

address: 120 Ocean View Blvd, Hopkins Marine Station

institute: Stanford University

data_processing:
Illumina Casava 1.7 software was used for basecalling.
Trimmomatic software was used to trim any remaining sequencing adapter and filter low quality reads
Bowtie 2 software was used align filtered reads to the Oncorhynchus gorbuscha cardiac transcriptome
Read count values were genereated from aligment files by using Samtools software
Unnormalized read counts were used with Deseq2 software to perform statistical analysis
Genome_build: GFUW00000000

organism: Oncorhynchus gorbuscha

source_name: Pink salmon cardiac ventricle

growth_protocol: After intail oil exposure animals were reared in clean water raceway systems until approximately 8-10 months of age.

extract_protocol:
Trizol total RNA protocol
TruSeq RNA library prep kit v2 protocol

treatment_protocol: Pink salmon embryos were exposed from fertilization through late organogenesis to a graded series of environmentally relevant doses of Alaskan crude oil, yielding total PAH concentrations in water ranging from 10 to 45 µg/L.

tag: developmental stage

value: juvenile

value: cardiac ventricle

tag: cude oil exposure treatment

value: High


title: old15h_rep3_Ribo-seq

tag: strain


title: young_rep1_Ribo-seq


title: old15h_rep2_Ribo-seq


title: M32

value: Medium


title: old30h_rep3_Ribo-seq


title: L10

value: Low


title: C8

value: Control


title: M28


title: old15h_rep1_Ribo-seq


title: young_rep3_RNA-seq

description:
total RNA
all_sample_normalized.xls

data_processing:
Reads were quality trimmed and filtered using fastqx to remove reads containing low-quality bases.
Genome Index were built with bowtie-build
Reads were mapped with tophat2 and calculated for each gene using HtSeq v0.6.1
RNA abundance analysis, Translation efficiency, Ribosome binding analysis were performed with meV, David, R packages & scripts
Wig file are generated from bam by bedtools2 and kent package from ucsc, and normalized by danpos
Genome_build: sacCer3

extract_protocol:
Total RNA isolation was performed using the MasterPure Yeast RNA Isolation Kit from Epicentre Biotechnologies (# MPY03100) following the manufacturer’s instructions.
All RNA fragments were converted into deep-sequencing libraries using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (#RSS-122-2301, Illumina). The Ambion ERCC RNA spike-in control (#4456740, Life Technology) was included in the library construction.


title: empty vector-His replicate 2


title: L17


title: young_rep2_RNA-seq

description:
total RNA
all_sample_normalized.xls


title: old30h_rep3_RNA-seq

description:
total RNA
all_sample_normalized.xls


title: young_rep1_RNA-seq

description:
total RNA
all_sample_normalized.xls


title: H27


title: M24


title: L9


title: old30h_rep1_RNA-seq

description:
total RNA
all_sample_normalized.xls


title: C6


title: Input H3K27ac ChIP on vehicle-treated ACC

description:
ACC9_1_3_input
Barcode: GATCAG


title: old15h_rep3_RNA-seq

description:
total RNA
all_sample_normalized.xls


title: old15h_rep2_RNA-seq

description:
total RNA
all_sample_normalized.xls


title: H18


title: H36


title: L13


title: C3


title: HEK293T AlkB treated, Queuosine Supplemented

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description:
HEK293T - 100% Queuosine, DM
tRNA

data_processing:
Raw reads were processed using Trimmomatic v 0.32n and custom Python scripts to fully remove traces of adapter.
Processed reads were aligned in Bowtie 1.0 according to the parameters of -t -v 3 -m 10 --best --strata -p 12
Fragments shorter than 18 base pairs during alignment were removed during subsequent analysis.
Further processing using custom C and Python scripts were used to map reads onto tRNA isodecoders/rRNAs for visualization and modification index analysis.
Lastly, charging ratios were determined using strict read criteria to determine whether an aligned read was both A or C ending as well as aligned to the 3' end 20 nucleotides.
Genome_build: hg19

growth_protocol: Human HEK293T cell line was cultured in DMEM (Thermo) media supplemented with 10% FBS and 1% 100 × Pen Strep (Gibco)

extract_protocol:
Total RNA was isolated by using mirVana miRNA Isolation Kit (Life Technologies).
5' and 3' tRNA fragments at 20-60 nt were gel-size selected and RNAs were eluted with crush and soak buffer at 4°C overnight. The eluted RNA was recovered by ethanol precipitation and dissolved in water. 1 μg of purified tRNA (~40 pmole) were treated with 2× molar ratio of wild-type AlkB enzyme (80 pmole) and 4× molar ratio of D135S mutant (160 pmole). Purified total RNA was deacylated by incubating in 0.1 M tris-HCl, pH 9 at 37°C for 45 min, followed by T4 kinase (NEB) treatment to remove 3' and 2',3' cyclic phosphates at the 3'-end of tRNA fragments. RNAs were extracted using acid Phenol/CHCl3 (pH 4.0??) with 0.3 M NaOAc/HOAc, pH 4.8, followed by ethanol precipitation.
Directional ligation of adapters, cDNA generation, and PCR amplification were performed using the TruSeq Small RNA Sample Prep kit (Illumina) according to the manufacturer’s protocol. The PCR products were sequenced on Illumina HiSeq 1000 system.

treatment_protocol: Cells were supplemented with queuine at 1 µM for 24 h

tag: treatment

value: AlkB-derived enzyme mixture

value: queuosine


title: M41


title: old15h_rep1_RNA-seq

description:
total RNA
all_sample_normalized.xls

tag: age


title: HEK293T AlkB treated, Queuosine Unsupplemented

description:
HEK293T - 0% Queuosine, DM
tRNA

value: no queuosine


title: HEK293T AlkB untreated, Queuosine Supplemented

description:
HEK293T - 100% Queuosine
tRNA

value: no AlkB-derived enzyme mixture


title: M36


title: T9

value: Trace


title: L8


title: HEK293T AlkB untreated, Queuosine Unsupplemented

description:
HEK293T - 0% Queuosine
tRNA


title: C7


title: old30h_rep2_RNA-seq

description:
total RNA
all_sample_normalized.xls


title: C21


title: H26


title: L12


title: siCon-1

first: Suowen

last: Xu

address: 603 Elmwood Avenue

department: Medicine

data_processing:
Sequenced reads were cleaned using Trimmomatic-0.32 before mapping some of to the human reference genome (GRCh38.p2) with STAR-2.4.2a. Raw read counts were obtained using HTSeq and gencode 23 human gene annotations. DESeq2-1.10.1 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05. Then, Cufflinks-2.0.2 Software was used with the gencode 23 human gene annotations to perform differential expression analysis with an FDR cutoff of 0.05.
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - htseq-count v0.6.1 "-q -f bam -s no -r pos -i gene_name"
Genome_build: GRCh38.p2 (hg38) + Gencode-23 Annotation

source_name: Human coronary artery endothelial cells

growth_protocol: Human Coronary Artery Endothelial Cells (HCAECs, Cell Application Inc.) were cultured in M200 media supplemented with 5% FBS and 1X ECGS ( Cell Application Inc.).

extract_protocol:
Total RNA was harvested using RNAeasy Mini Kit from Qiagen. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: 80% confluent HCAECs were transfected with 100 nM non-targetting control siRNA (siCon)  or JCAD siRNA  (siJCAD) using Lipofectamine 2000 for 48 hours, n=2-3. Note: siCon biological replicate#3 alignes poorly to human reference genome for unknown reasons, was thus not included for analysis .

value: Human coronary artery endothelial cells

value: non-targetting siRNA


title: T7


title: siJCAD-2

value: JCAD siRNA


title: siCon-2


title: siJCAD-3


title: T6


title: H23


title: M29


title: WT_ST3_rep2

city: Shanghai

first: Yu

address: 320 Yueyang Road

institute: Shanghai Institue of Biochemistry and Cell Biology

data_processing:
After quality filteration and removing the sequencing adapters with Trimmomatic (version 0.36), the RNA-seq reads were aligned to mouse genome (mm10) using HISAT2, and only reads hitting no more than 2 genomic loci were used to quantify gene expressions with StringTie.
The gtf file of mouse genes was downloaded from GENCODE (vM12).
The gene expressions were normalized as FPKM.
The fold change and p-value of all the detected genes were estimated by Ballgown.

source_name: thymus, iNKT cells at stage3

extract_protocol:
All the RNA was extracted using Trizol reagent, purified and checked for integrity using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Libraries were generated for sequencing using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Illumina).
RNA libraries were prepared for sequencing using standard illumina protocols

value: iNKT cells at stage3

value: thymus


title: H24


title: L16


title: C24


title: WT_ST2_rep3

source_name: thymus, iNKT cells at stage2

value: iNKT cells at stage2


title: WT_ST2_rep2


title: WT_ST2_rep1


title: M39

value: juvenile


title: H22

value: cardiac ventricle


title: T3


title: L6


title: mIMCD3 WT clone#3

city: Minneapolis

first: Siu Chiu

last: Chan

state: MN

address: MCB-5148 420 Washington Ave SE

institute: University of Minnesota

description: Sample name: WT-3_S15

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence quality was accessed via FastQC, and none of the preprocessing (trimming, filtering or masking) is necessary.
Raw paired-reads were mapped to mouse genome (GRCm8) using HiSAT2 with Ensembl (GRCm38.83) reference and following parameters: --dta-cufflinks --threads 8
Various Picard tools (CleanSam, Sort, CollectInsertSizeMetrics) have been used to clean the resulted sam files.
Read counts per gene were calculated using featureCounts (Liao Y. et al, Bioinformatics 2013) and following parameters: -p 8
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts of reads mapped per gene for each Sample.

source_name: mIMCD3 cells

growth_protocol: mIMCD3 WT and HNF-1β deficient cells were maintained in DMEM with 10% FBS until 80-90% confluent and changed to fresh medium for 24hrs, cells were fully confluent for total RNA harvesting.

extract_protocol:
Total RNA was isolated using a Qiagen RNA Easy kit.
RNA samples passed the quality control (RIN>8) were used to create a polyA barcoded RNAseq libraries using standard Illumina TruSeq protocols.

tag: genotype

value: WT

tag: cell line


title: mIMCD3 WT clone#2

description: Sample name: WT-2_S14


title: siJCAD-1


title: M26

value: Medium


title: mIMCD3 WT clone#1

description: Sample name: WT-1_S13


title: AD22

source_name: Entorhinal cortex

tag: disease status

value: AD

tag: Sex

value: M

value: H3K27ac (Diagenode, catalog #C15410196, lot# A1723-0041D)


title: C19

value: Control


title: WT_ST3_rep3


title: C29


title: WT_ST3_rep1


title: T10


title: HNF-1β KO clone#3

description: Sample name: HNF1bKO-3_S18

value: HNF-1beta -/-


title: HNF-1β KO clone#2

description: Sample name: HNF1bKO-2_S17