title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G12_ad006

value: PTLp


title: 20FS146A_P1

status: Public on Dec 01 2020

type: SRA

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

country: Canada

institute: McGill University

library_source: genomic

data_processing:
Trimming of adapter and poor quality reads with trim_galore_v0.3.3
Align to genome and get methylation calls with bsmap-2.74
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing information for each sample: chrBase, chr, base, strand, coverage, FreqC (methylation), FreqT

molecule: genomic DNA

organism: Mus musculus

source_name: Placenta

extract_protocol:
Frozen tissue samples were homogenized using mortar and pestle and DNA was isolated from ~10mg of samples using the DNeasy Blood and Tissue kit (Qiagen)
Reduced representation bisulfite sequencing (RRBS) libraries were prepared according to previously published protocols using gel-free technique (Boyle, P. Genome Biol., 2012).  Briefly, ~500ng of  DNA was digested with MspI restriction enzyme, followed by size selection, gap filling and 3'-A-tailing.  Ligation of NEBNext methylated adaptors was performed, followed by bisulfite conversion and index PCR amplification.

treatment_protocol: F1 females were exposed to folic acid control (FCD; 2mg/kg), folic acid deficient (7FD; 0.3mg/kg), 10-fold folic acid supplement (10FS; 20mg/kg) or a 20-fold folic acid supplement (20FS; 40mg/kg) diets throughout their gestation, lactation and until weaning, at which point they were weated onto FCD. At 8-10 weeks of age, F1 females mated and throughout mating and gestation, the F1 females were fed the FCD (2mg/kg).  Embryonic tissues from E18.5 embryos were collected (a total of 43 placental samples and 24 cortex samples), flash frozen and kept at -80oC until use for DNA methylation analyses (i.e. RRBS)

tag: strain

value: BALB/c

tag: gender

value: female

tag: tissue

value: Placenta

tag: treatment


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G12_ad004

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: age

value: brain

tag: source

tag: target

value: VISp


title: Empty Vector Sub-Confluent Rep 3 (rnaseq_3T3)

city: Iowa City

first: Michael

middle: S

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were demultiplexed and converted from the native Illumina BCL format to fastq format using an in-house python wrapper to Illumina’s ‘bcl2fastq’ conversion utility.
FASTQ data were processed with ‘bcbio’, a best-practices pipeline available at the open-source ‘bcbio-nextgen’ project
Reads from the NIH 3T3 line was aligned against the ensembl reference ‘mm10'
Transcript-level abundances were converted to gene-level counts using the ‘tximport’ package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample ...

molecule: polyA RNA

source_name: NIH 3T3 murine fibroblast cells ATCC

growth_protocol: NIH3T3 cells were stably transduced and grown to confluence 48 hrs before collection (except CAMTA1 collected at sub-confluence)

extract_protocol:
Total RNA was isolated using the PureLink™ RNA mini kit (Invitrogen-ThermoFisher Scientific).  On-column DNase (Invitrogen) treatment was performed according to manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: NIH 3T3 murine fibroblast cells


title: E50_R_MeRIP-ip_1

city: shenzhen

first: Xin

middle: xin

last: Zhang

state: china/guangdong

address: No.7 pengfei road Dapend

department: agricultural genomics institute at shenzhen

country: China

institute: chinese academy of agricultural science

description: m6A immunoprecipitate rRNA_depleted RNA

data_processing:
Trimmomatic was used for trimming adapters and filtering on length and quality of the raw sequencing reads with default settings
Clean reads were mapped to respective reference genome using hisat2 with default settings.
reference genome:Sscrofa11.1 (GCA_000003025.6)

molecule: total RNA

organism: Sus scrofa

source_name: longissimus dorsi

extract_protocol:
Total RNA (PK15 and skeletal muscle) was purified using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions.
To degrade any possible DNA contamination, the total RNA samples were dissolved in diethylpyrocarbonate (DEPC)-treated water and treated with DNaseI. Paired-end sequencing libraries with insert size of 300 bp were conducted on the HiSeq 2,500 platform following the Illumina’s protocols.
MeRIP-seq/R-MeRIP-seq

value: skeletal muscle

tag: developmental stage

value: 50 days post coitus

tag: m6a antibody

value: Synaptic systems, 202003


title: Empty Vector Sub-Confluent Rep 2 (rnaseq_3T3)


title: 20FS121B_P1


title: Empyt Vector Sub Confluent Rep 1 (rnaseq_3T3)


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G12_ad002

value: male


title: E50_R_MeRIP-in_1

description:
rRNA_depleted RNA
E50-1-n.TPM


title: Empty Vector Rep 3 (rnaseq_3T3)


title: E40_R_MeRIP-ip_3

description: m6A immunoprecipitate rRNA_depleted RNA

value: 40 days post coitus


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G11_ad012

value: RSP


title: 20FS120A_P1


title: 20FS111E_P5


title: E40_R_MeRIP-in_3

description:
rRNA_depleted RNA
E40-3-n.TPM


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G11_ad010


title: Empty Vector Rep 1 (rnaseq_3T3)


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G11_ad008


title: Empty Vector Rep 2 (rnaseq_3T3)


title: 20FS104B_P2


title: CAMTA1 Rep 3 (rnaseq_3T3)


title: E40_R_MeRIP-ip_2

description: m6A immunoprecipitate rRNA_depleted RNA


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G11_ad007


title: 20FS105A_P4


title: E40_R_MeRIP-ip_1

description: m6A immunoprecipitate rRNA_depleted RNA


title: 10FS146C_P1


title: E40_R_MeRIP-in_2

description:
rRNA_depleted RNA
E40-2-n.TPM


title: E40_R_MeRIP-in_1

description:
rRNA_depleted RNA
E40-1-n.TPM


title: 10FS148C_P4


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G11_ad004


title: FAK-WT–expressing SCC cells, replicate 3

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh, The Institute of Genetics and Cancer

data_processing:
Transcript level abundance analysis was performed by kallisto (v0.43.1, default parameters) on the mouse transcriptome database generated using kallisto index (default parameters), ftp://ftp.ensembl.org/pub/release-90/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz
Transcript level abundance were summarised to gene level (EnsDb.Mmusculus.v79) and imported into differential expression analysis R package DESeq2 for analysis using the R package tximport.
Genome_build: mm10
Supplementary_files_format_and_content: abundances.tsv is a plaintext file of the transcript-level abundance estimates generated by kallisto. The combined_gene_level_counts.txt file is a gene-level count summarised text file.

source_name: Squamous cell carcinoma (SCC)

growth_protocol: Mouse SCC cells were grown at 37°C, 5% (v/v) CO2, in Glasgow minimum essential medium (MEM) (Sigma-Aldrich) supplemented with 10% (v/v) foetal bovine serum, 1× MEM nonessential amino acids (both Life Technologies), 2 mM L-glutamine, 1 mM sodium pyruvate and 1× MEM vitamins (all Sigma-Aldrich) (complete medium) and maintained as previously described (Serrels et al. 2012, Serrels et al. 2015).

extract_protocol:
RNA was extracted from SCC FAK-WT and FAK–/– cells using an RNeasy kit (Qiagen) following the manufacturer’s instructions, using 350 μl buffer RLT with 0.1% (v/v) β-mercaptoethanol for the initial step of the protocol. To verify sample quality, RNA samples were assessed using the Bioanalyzer RNA 6000 pico assay (Agilent) run on a 2100 Bioanalyzer instrument (Agilent). All samples had an RNA integrity number (RIN) of at least 9.6 (RIN ≥ 8 considered a suitable quality for sequencing).
Samples were prepared using the TruSeq RNA Library Prep Kit v2 (low-sample protocol) (Illumina), validated using the High Sensitivity DNA assay (Agilent) run on a 2100 Bioanalyzer instrument and paired-end sequenced using a HiSeq 4000 platform (Illumina) at BGI.

treatment_protocol: The mouse SCC FAK cellular model and the FAK-NLS mutant were generated as previously described (Serrels et al. 2012, Serrels et al. 2015). SCC ILK-KO cells were generated by CRISPR/Cas9 technology using the Multiplex CRISPR/Cas9 Assembly System (Addgene) according to manufacturer’s instructions.

value: Wildtype


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G11_ad001


title: E33_R_MeRIP-ip_3

description: m6A immunoprecipitate rRNA_depleted RNA

value: 33 days post coitus


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G11_ad002


title: FAK-WT–expressing SCC cells, replicate 2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G10_ad012


title: E33_R_MeRIP-in_3

description:
rRNA_depleted RNA
E33-3-n.TPM


title: 10FS143BC_P1


title: 10FS127C_P5


title: 10FS128F_P2


title: FAK-WT–expressing SCC cells, replicate 1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G10_ad010


title: E33_R_MeRIP-ip_2

description: m6A immunoprecipitate rRNA_depleted RNA


title: CAMTA1 Rep 2 (rnaseq_3T3)


title: CAMTA1 Rep 1 (rnaseq_3T3)


title: FAK-deficient (FAK−/−) SCC cells, replicate 3


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G10_ad007


title: 10FS119B_P3


title: 7FD125E_P4


title: E33_R_MeRIP-ip_1

description: m6A immunoprecipitate rRNA_depleted RNA


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G10_ad006


title: FAK-deficient (FAK−/−) SCC cells, replicate 1


title: FAK-kinase dead–expressing SCC cells, replicate 3

value: Kinase-dead


title: E33_R_MeRIP-in_1

description:
rRNA_depleted RNA
E33-1-n.TPM


title: FAK-deficient (FAK−/−) SCC cells, replicate 2


title: 7FD115A_P5


title: 7FD114B_P5


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G10_ad002


title: PK15_R_MeRIP_ip_2

description: m6A immunoprecipitate rRNA_depleted RNA

source_name: kidney

value: kidney cell (PK15)

value: adult


title: 7FD112C_P5

value: BALB/c


title: FAK-kinase dead–expressing SCC cells, replicate 2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G10_ad001

value: PTLp


title: PK15_R_MeRIP_in_2

description: rRNA_depleted RNA


title: FAK-kinase dead–expressing SCC cells, replicate 1


title: 7FD108A_P3

value: female

value: Placenta


title: 7FD106AC_P3


title: PK15_R_MeRIP_ip_1

description: m6A immunoprecipitate rRNA_depleted RNA


title: LL-PM2.5_RNASeq_2

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to mouse genome release mm10 using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: TSV text file containing FPKM for all samples and genes

extract_protocol:
Liver were removed, snap frozen on liquid Nitrogen and stored at -80, and RNA was harvested using RNeasy Micro Kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Wild type

tag: exposure

value: Light/Light cycle, PM2.5

value: Liver


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F9_ad010

value: brain

value: VISp


title: E33_R_MeRIP-in_2

description:
rRNA_depleted RNA
E33-2-n.TPM

value: skeletal muscle


title: PK15_R_MeRIP_in_1

description: rRNA_depleted RNA


title: LL-PM2.5_RNASeq_1


title: FCD133G_P1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G10_ad004


title: PK15_MeRIP_ip_2

description: m6A immunoprecipitate polyA RNA

value: Synaptic systems, 202003


title: FCD127A_P4


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F9_ad007

value: RSP

value: male


title: PK15_MeRIP_in_2

description: polyA RNA


title: LL-FA_RNASeq_1

source_name: LL-FA

value: Light/Light cycle, Filtered air


title: LL-FA_RNASeq_2


title: FCD122E_P3


title: FCD123A_P1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F9_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F9_ad001


title: PK15_MeRIP_in_1

description: polyA RNA


title: FCD103F_P1


title: PK15_MeRIP_ip_1

description: m6A immunoprecipitate polyA RNA


title: LD-PM2.5_RNASeq_2

value: Light/Dark cycle, PM2.5


title: LD-PM2.5_RNASeq_1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F9_ad012


title: Day 13 post 1x0Gy - 4

city: Melbourne

last: Sia

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina bcl2fastq v2.20.0.422 software used for base calling
Sequenced reads were trimmed using CutAdapt v1.5 software for random primer (12 bases) and poly-A, per Lexogen Quantseq data analysis guidelines
Reads aligned using HISAT2 v2.0.4, gene abundance calculated using HTSEQ v0.9.1 with transcript annotation Ensembl GRCm38 v73
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing gene count (from HTSEQ software) for each sample

source_name: Tumor

extract_protocol:
For extraction of RNA, QIAzol-treated samples were thawed gently on ice and processed using the Direct-zol™ RNA MicroPrep kit (Zymo Research) as per manufacturer’s instructions.  Prior to sequencing, the quality of extracted RNA was assessed using the Aligent 2100 Bioanalyzer (Aligent Technologies). Only samples with an RNA integrity number (RIN) of greater than 8.5 were processed for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were anaesthetized with a ketamine/xylazine mix (ketamine 100 mg/kg [Baxter Pharmaceuticals] + xylazine 20 mg/kg [Troy Laboratories] in 200 mL PBS, injected intraperitoneally). Mice were positioned on a specially designed Perspex plate and covered by a 3 mm thick lead shield containing 0.8 cm2 square holes in designated areas to allow localized radiation to be administered to the site of tumor growth, while minimising delivery of radiation to the rest of the animal. Irradiation was delivered using a 6 MeV electron beam at a dose rate of 20 Gy / minute using a megavoltage linear accelerator (Varian Medical Systems). Each fraction of radiation was delivered at 24 hour intervals. Control mice were anaesthetized but not exposed to radiation.

tag: cell type

value: CD45.2+ immune cells

value: Day 13 post 1x0Gy


title: LD-FA_RNASeq_2

source_name: LD-FA

value: Light/Dark cycle, Filtered air


title: Day 13 post 1x0Gy - 3


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F8_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F8_ad008


title: 20FS146A_C1

source_name: Cortex

value: BALB/c

value: Cortex


title: LD-FA_RNASeq_1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F9_ad008

value: female


title: Day 13 post 1x0Gy - 2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F8_ad007


title: 20FS121B_C1


title: mouse5_retina_IOP-GCV

first: Michal

last: Krawczyk

address: 9500 Gilman Dr

department: Ophthalmology

institute: UCSD

data_processing:
Read mapping was done using Tophat2/Bowtie2 using default parameters
Transcript abundances (FPKM) were calculated using cuffdiff from cufflinks package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited output file from cufflinks containing FPKM values for all transcripts

source_name: retina

growth_protocol: Mice were housed in 20 ºC environment with standard (12 h light/dark) cycling, food and water available ad libitum.

extract_protocol:
Retinas were dissected and directly collected in Trizol Reagent for RNA isolation.
Illumina TruSeq stranded mRNA Library Prep Kit  (Cat 20020597) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol:
Animals were anesthetized with an intraperitoneal injection of ketamine/xylazine cocktail, (100 mg/kg and 10 mg/kg, respectively), their eyes anesthetized with one drop of proparacaine (0.5 %, Bausch-Lomb) and dilated with one drop  f tropicamide (1 %, Alcon Laboratories).
Unilateral elevation of IOP was achieved by infusing Balanced Salt Solution (Alcon Laboratories) into the anterior chamber of the eye through using an intravenous (IV) infusion set
The level of IOP increase was determined by the height of the saline bottles on the IV infusion set
Stable elevated IOP of 85-90mm Hg was maintained for 60 minutes, and controlled by IOP measurements using a veterinary rebound tonometer (Tonovet).
Animals recovered on a Deltaphase isothermal pad (Braintree Scientific) until awake
The contralateral eye without IOP elevation served as a healthy non-IOP control (CTRL)
The experimental group of animals was treated by intraperitoneal (IP) administration of GCV (Sigma, 25mg/kg once a day)
Control group of mice was sham-treated with PBS

value: 12-16 weeks

tag: condition

value: IOP

value: GCV

value: retina


title: Day 13 post 1x0Gy - 1


title: 20FS120A_C1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F8_ad006

value: brain

value: PTLp

value: VISp


title: mouse2_retina_IOP-GCV


title: 20FS111E_C5


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F8_ad004


title: mouse1_retina_IOP-GCV


title: 20FS105A_C4


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F8_ad002


title: FCD101F_P5

value: Placenta


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F8_ad001

value: male


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F7_ad008

value: RSP


title: Day 13 post 1x20Gy - 5

value: Day 13 post 1x20Gy


title: Day 13 post 1x20Gy - 6

value: CD45.2+ immune cells


title: 10FS148C_C4


title: mouse2_retina_ctrl-GCV

value: ctrl


title: 10FS146C_C1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F7_ad006


title: mouse1_retina_ctrl-GCV


title: Day 13 post 1x20Gy - 3


title: Day 13 post 1x20Gy - 7


title: mouse5_retina_ctrl-GCV


title: 10FS128F_C2


title: mouse6_retina_IOP

value: control


title: Day 13 post 1x20Gy - 2


title: Day 13 post 1x20Gy - 1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F7_ad004


title: 10FS119B_C3

value: BALB/c


title: mouse4_retina_IOP


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F6_ad012


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F7_ad001


title: mouse3_retina_IOP


title: 7FD115A_C5

value: Cortex


title: Day 5 post 1x0Gy - 4

value: Day 5 post 1x0Gy


title: mouse6_retina_ctrl

value: 12-16 weeks


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F6_ad008

value: female


title: 10FS127C_C5


title: 7FD114B_C5


title: Day 5 post 1x0Gy - 3


title: Day 13 post 1x20Gy - 4


title: mouse4_retina_ctrl


title: 7FD112C_C5


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F5_ad012


title: 7FD108A_C3


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F6_ad007


title: Day 5 post 1x0Gy - 1


title: Day 5 post 1x20Gy - 6

value: Day 5 post 1x20Gy


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F5_ad010


title: Wildtype_scRNA_hindlimb_2

city: New Haven

first: James

middle: P.

last: Noonan

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University

data_processing:
For ChIP-seq: Humanized and chimpanzee ortholog reference genomes were edited to replace the mouse ortholog of HACNS1 with the human or chimpanzee sequence, respectively, using using bowtie2-build in Bowtie 2 (v2.2.8). ChIP-seq raw reads were aligned to the mm9, mm9 with chimpanzee ortholog, or humanized HACNS1 mm9 reference genome using Bowtie (v2.2.8) with --sensitive and --no-unal settings. All peaks were called with HOMER (v4.9.1) with --histone (IP vs input fold change=4, p=0.0001, peak size=500, minDist=1000). Bigwig files were generated with the HOMER v4.9.1 command makeUCSCfile. For scRNA-seq: Count matrices were produced from fastqs using the Cell Ranger v3.0.2 package from 10X Genomics (cellranger count --transcriptome=refdata-cellranger-mm10-3.0.0).
Genome_build: For ChIP-seq: mm9; For scRNA-seq: mm10
Supplementary_files_format_and_content: bigWig (.bw) files contain ChIP-seq signal data; text (.txt) files contain peak coordinates for ChIP-seq experiments; HDF5 (.h5) files contain count matrices for scRNA-seq experiments.

source_name: E11.5 hindlimb bud

extract_protocol:
Tissue was collected in 1x Calcium–magnesium-free phosphate buffered saline with 0.1% glucose. Cells were dissociated using Gibco TrypLE Express (Thermo Fisher Scientific # 2605010). Cells were filtered through a 40 μM strainer and harvested by centrifugation at 4°C. Cells were washed and resuspended in 1x Calcium–magnesium-free phosphate buffered saline with 0.04% BSA (Sigma-Aldrich #SRE0036).
Libraries were prepared using Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X Genomics PN-1000075) and sequenced (2×75 bp) on an Illumina HiSeq 4000.

value: hindlimb bud

value: wild type


title: Wildtype_scRNA_hindlimb_1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F5_ad008

value: brain


title: Day 5 post 1x20Gy - 5


title: FCD_122_C3


title: ChimpanzeeOrtholog_scRNA_hindlimb_1

value: chimpanzee ortholog+/+


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F5_ad007

value: VISp


title: Day 5 post 1x20Gy - 4


title: Humanized_scRNA_hindlimb_2


title: Day 5 post 1x20Gy - 3


title: FCD133G_C1


title: FCD127A_C4


title: Humanized_scRNA_hindlimb_1


title: Day 5 post 1x0Gy - 2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F4_ad012


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F4_ad010

value: male


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F5_ad004

value: PTLp


title: FCD123A_C4


title: Day 5 post 1x20Gy - 2


title: Day 5 post 1x20Gy - 1


title: mouse3_retina_ctrl

value: retina


title: FCD103F_C1


title: Chimpanzee_ChIP_arch_H3K4me2_chimpOrtholog_rep2

source_name: E11.5 pharyngeal arch

extract_protocol:
Crosslinked E11.5 limb bud or pharyngeal arch tissue was used for nuclei isolation, sonication, and chromatin extraction. Chromatin immunopecipitation was performed with H3K27ac (Active Motif #39133) or H3K4me2 (Active Motif #39913) antibody-coated magnetic beads (Protein G Dynabeads, Invitrogen).
Libraries were prepared and sequenced (2×100 bp) using standard Illumina protocols on an Illumina HiSeq 4000.

value: pharyngeal arch

tag: chip antibody

value: H3K4me2 (Active Motif, #39913)


title: FCD101F_C5


title: Day 5 post 3x0Gy - 4

value: CD45.2+ immune cells

value: Day 5 post 3x0Gy


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F4_ad007

value: RSP


title: 7FD106AC_C3

value: BALB/c

value: Cortex


title: Day 5 post 3x0Gy - 3


title: Chimpanzee_ChIP_arch_H3K4me2_chimpOrtholog_rep1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F4_ad006

value: female


title: Chimpanzee_ChIP_arch_H3K4me2_wildtype_rep2


title: Chimpanzee_ChIP_arch_H3K4me2_wildtype_rep1


title: Day 5 post 3x0Gy - 2


title: Chimpanzee_ChIP_limb_H3K4me2_wildtype_rep2

source_name: E11.5 limb bud

value: limb bud


title: Sample 22 Smart-Seq_wildtype

city: Beijing

first: Xu

middle: jia

last: yue

address: NO.3 Dongdan street, Beijing

institute: Peking Union Medical College

description:
single cell
Switching mechanism at 5’ end of the RNA transcript
T1preHSC_RPKM.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome
Gene expression levels were expected of fragments per kilobase of transcript sequence per millions base pairs mapped (FPKM) using Cufflinks v2.1.0
genome build: mm10
supplementary file format and content: tab-delimited text files include RPKM values for  lncRNA genes in each sample

source_name: T1 pre-HSC

growth_protocol: Wildtype and mutant T1 pre-HSCs were sorted from the E11 embryonic AGM region. Adult  HSCs were sorted from the bone marrow of C57 mice.

extract_protocol: Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette; 0.05 μl of 1:200,000 dilution of External RNA Controls. Consortium (ERCC) RNA spike-in Mix1 (Ambion) was added to lysis buffer per reaction.

treatment_protocol: FACS-enriched cells were kept on ice until lysed and reverse transcribed.

value: T1 pre-HSC

value: mH19 flDMR/+

value: E11 embryo


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F4_ad004

value: brain


title: Day 5 post 3x0Gy - 1


title: Sample 21 Smart-Seq_wildtype


title: E14_Setdb1_SC

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
fastq files were mapped using STAR aligner. Maximum of 3 mismatches were allowed and reads mapping to more than 500 loci were filtered out. The options –alignIntronMax and –alignEndsType were set to 1 and EndToEnd respectively.
Tag directories were created using makeTagDirectory of HOMER with the option -keepOne.
Peaks were called with findPeaks of HOMER with the -style set to factor.
Bedgraphs were generated using makeUCSCfile of HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text files containing the bound sites for each library and bedgraphs indicating the enrichment of the libraries over the genome.

source_name: E14 mESCs

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured using mouse ES medium prepared in DMEM high glucose (Hyclone) supplemented with 15 percent ES cell FBS (Gibco), 2mM L-glutamine (Gibco), 1X Pen-Strep (Gibco), 100 µM MEM non-essential amino acids (Gibco), 100 micromolar 2-mercaptoethanol (Gibco), and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore). The mouse ES line was cultured on plates pre-coated with 0.1 percent gelatine (porcine).

extract_protocol:
Cells were trypsinized, harvested and the cell number was estimated. Cross-linking was performed using 1 percent formaldehyde for 10 min at room temperature followed by quenching with 0.125 M Glycine. Cross-linked pellets were washed twice with ice-cold 1X PBS (with 0.1 percent Triton X-100) and then subjected to lysis with a lysis buffer (10 mM Tris-Cl (pH 8), 100 mM NaCl, 10 mM EDTA, 0.25 percent Triton X-100 and protease inhibitor cocktail (Roche)). Pellets were resuspended after centrifugation, in 1 percent SDS lysis buffer (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 percent SDS, 2 mM EDTA, 1 percent Triton X-100, 0.1 percent NaDOC and protease inhibitor cocktail). For every 10 million cells, 14 cycles of sonication were carried out using the Bioruptor (Diagenode) with 30 sec pulses and 60 sec halts in each cycle. Pre-clearing of the chromatin was carried out with 100 uL of Protein G Dynabeads (Life Technologies) for 2 hours at 4 degree Celsius. Simultaneously, 100 uL of Protein G Dynabeads were also bound to 5 microgram (per 10 million cells) of the antibodies (Setdb1 – home-made Ab; Setdb1 - Santa Cruz #sc-66884; Smc1a - Bethyl #A300-055A; Flag - Sigma-Aldrich #F1804; Pan Methyl Lysine - Biorbyt #orb100017). After separation of a small amount as input - the remaining pre-cleared chromatin was used to bind to the antibody-bound beads at 4 degree Celsius, overnight. Elution involved three washes with 0.1 percent SDS lysis buffer, one with 0.1 percent SDS lysis buffer/0.35 M NaCl, one with 10 mM Tris-Cl (pH 8), 1 mM EDTA, 0.5 percent NP40, 0.25 LiCl, 0.5 percent NaDOC, and one with TE buffer (pH 8.0). The immunoprecipitated chromatin was eluted out from the beads by heating the beads resuspended in 50 mM Tris-HCl (pH 7.5), 10 mM EDTA, 1 percent SDS, for 1 hour at 68 degree Celsius while shaking at 1400 rpm. Cross-links were reversed by incubating the eluted samples and inputs at 42 degree Celsius for 2 hours and 67 degree Celsius for 6 hours in the presence of Pronase (Sigma) and TE buffer, after which the DNA was purified using the QIAGEN PCR Purification kit (for inputs) and the QIAGEN MinELute PCR Purification kit (for samples).
Following qPCR validation of the samples, libraries were prepared by using Illumina reagents with TruSeq adapters and the TruSeq ChIP Library Preparation kit, as per the manufacturer’s instructions. The quality and concentration of each sample was assessed by using Agilent High Sensitivity chips on the Agilent 2100 Bioanalyzer.

treatment_protocol: E14 cells were harvested using trypsinization and were counted and further processed for the wild-type ChIP-Seq libraries. For the tagged Flag-Setdb1 cell line (C1), the cells were trypsinized, harvested, counted and then processed for ChIP-Seq. For treated ChIP-Seq samples, cultured E14 cells were harvested and re-seeded at 300,000 cells per well of the plates. These cells were cultured at 37 degree Celsius for 20-24 hours and the cells were replenished with fresh medium at least 2 hours prior to transfection. The cells were then transfected with 3 microgram of the plasmid constructs (shControl, shSetdb1) using 4.5 microliters of Lipofectamine 2000 (Thermofisher), as per the manufacturer’s protocol. Puromycin (1 microgram/millliter) containing mESC medium was added to the cells 24 hours after transfection to select for the transfected plasmids. This process of selection was repeated once more 48 hours after transfection. The cells were finally harvested 72 hours after transfection and then processed for ChIP-Seq.

value: E14 embryonic stem cells (ESCs)

value: Wild-type

value: Setdb1 (Santa Cruz #sc-66884)


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F4_ad008

value: VISp


title: Day 5 post 3x4Gy - 4

value: Day 5 post 3x4Gy


title: Chimpanzee_ChIP_limb_H3K4me2_chimpOrtholog_rep1

value: chimpanzee ortholog+/+

value: H3K4me2 (Active Motif, #39913)


title: Chimpanzee_ChIP_limb_H3K4me2_wildtype_rep1

value: wild type


title: Sample 19 Smart-Seq_wildtype


title: Sample 20 Smart-Seq_wildtype


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F3_ad012

value: RSP


title: Sample 18 Smart-Seq_wildtype


title: Day 5 post 3x4Gy - 5

value: CD45.2+ immune cells


title: Chimpanzee_ChIP_arch_input_chimpOrtholog_rep2

value: pharyngeal arch

value: none (input control)


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F3_ad006

value: PTLp

value: female


title: Chimpanzee_ChIP_arch_input_wildtype_rep2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F3_ad007

value: male


title: Day 5 post 3x4Gy - 3


title: C1_FLAG

value: Flag-Setdb1 cell line (C1) derived from E14

value: FLAG (Sigma-Aldrich #F1804)


title: Day 5 post 3x4Gy - 2


title: Sample 17 Smart-Seq_wildtype

value: T1 pre-HSC

value: mH19 flDMR/+

value: E11 embryo


title: Chimpanzee_ChIP_limb_H3K4me2_chimpOrtholog_rep2

value: limb bud


title: Chimpanzee_ChIP_arch_input_chimpOrtholog_rep1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F3_ad004

value: brain

value: VISp


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F4_ad001


title: Day 5 post 3x4Gy - 6

value: Day 5 post 3x4Gy


title: Day 5 post 3x4Gy - 1


title: Sample 16 Smart-Seq_wildtype


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F3_ad008


title: Chimpanzee_ChIP_arch_input_wildtype_rep1

value: wild type


title: Sample 15 Smart-Seq_wildtype


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F3_ad001


title: Chimpanzee_ChIP_limb_input_chimpOrtholog_rep2

value: chimpanzee ortholog+/+


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F2_ad012

value: RSP


title: Myc/Akt1 driven liver tumors 2

city: Tübingen

first: Omelyan

last: Trompak

state: BW

address: Otfried-Müller-Straße 14

department: Internal Medicine VIII

country: Germany

institute: University Hospital of Tübingen

data_processing:
Basecalling was assessed using ngs-bits to identify and trimm sequencing cycles with low average quality, adaptor contamination, or repetitive sequences from PCR amplification
Reads were aligned using STAR v2.6.1c (Dobin et al.,2013) to the grcm38
Normalized read counts for all genes were obtained using Subread (v1.6.3) and edgeR (v3.22.5)
Genome_build: grcm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver tumors

growth_protocol: To generate murine liver tumors, we co-delivered transposable elements encoding for Myc and NrasG12V or Akt1 via hydrodynamic injection into the hepatocytes of C57BL/6 wildtype mice.

extract_protocol:
RNA was isolated from tumor samples via TRIZOL (Invitrogen) and the RNeasy Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina TruSeq stranded protocol. mRNA fraction was enriched using polyA capture from 100ng of total RNA using the  TruSeq stranded protocol (Illumina). The libraries were denaturated according to the manufacturer’s instructions and sequenced as single-end using the 75 cycle chemistry on an Illumina NextSeq500 (Illumina).

value: Liver tumors


title: Sample 14 Smart-Seq_wildtype


title: Myc/Akt1 driven liver tumors 3


title: Sample 13 Smart-Seq_wildtype


title: Chimpanzee_ChIP_limb_input_wildtype_rep2

value: none (input control)


title: Myc/NrasG12V driven liver tumors 3


title: Chimpanzee_ChIP_limb_input_wildtype_rep1


title: Sample 12 Smart-Seq_H19 DMR KO

value: mH19 delta_DMR/+


title: Myc/Akt1 driven liver tumors 1


title: Myc/NrasG12V driven liver tumors 2


title: Chimpanzee_ChIP_arch_H3K27ac_chimpOrtholog_rep2

value: pharyngeal arch

value: H3K27ac (Active Motif, #39133)


title: Myc/NrasG12V driven liver tumors 1


title: Sample 11 Smart-Seq_H19 DMR KO


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F2_ad007

value: male


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F2_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F2_ad004

value: PTLp

value: female


title: Chimpanzee_ChIP_arch_H3K27ac_wildtype_rep2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F2_ad002


title: Perturb-seq18

city: Cambridge

first: Joshua

last: Levin

state: MA

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description:
Perturb-seq sample
Same underlying biological sample as for Dialout18

data_processing:
10X fastqs were run through CellRanger (v2.1.0) count using the standard mm10 reference
Count matrices were extracted.
Perturb-seq count matrices were combined, and cells with <500 gene were removed, as was sample 17.
Perturb-seq cells were clustered with Seurat (v 2.2), and cell types identified
The same pipeline was run with the single perturbation samples
For samples with multiple dialout fastqs, the fastqs were combined if they had the same tag (TAG or GCA)
Dialout reads were run through our dialout pipeline (https://github.com/klarman-cell-observatory/ivPerturbSeq) using the cell barcodes produced by CellRanger to extract a perturbation by cell count matrix. For samples with both tags, the one with more assigned cells was used.
For downstream analysis, cells were assigned to a pertubation if they had UMI supporting that perturbation and the number of UMI supporting it were >1.3 times the next highest.
Perturbation labels were uploaded to the Seurat object
Uploaded fastq are from the dialout library, uploaded bam files are from the single cell expression data.
Genome_build: mm10
Supplementary_files_format_and_content: csv matrix containing perturbation barcode by cell barcode UMI counts from dialout
Supplementary_files_format_and_content: h5 containing raw count data from CellRanger

source_name: Whole Cortex

extract_protocol:
Each single-cell library was made by combining the BFP+ cells from 1-3 litters (4-20 animals) of P7 animals harvested on the same day. The FACS-purified cells were sorted into cold Hibernate A/B27 medium and subjected to single-cell RNA sequencing library preparation.
Single-cell RNA sequencing libraries were created using the Chromium Single Cell 3' Solution v2 kit (10x Genomics) following the manufacturer’s protocol.
We used the Chromium Single Cell 3' Solution v2 kit (10x Genomics) to construct all the libraries, which are experimental replicates for the pooled Perturb-Seq.

treatment_protocol: In utero lentiviral injection into the lateral ventricles was performed at E12.5 in Cas9 transgenic mice (4-6 month old, Jax #026179).

tag: targeted genes

value: All 35 genes

tag: data type

value: 10X v2 single cell


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F2_ad001

source_name: C57BL/6J P56 Mouse Brain

tag: strain


title: Sample 10 Smart-_H19 DMR KO

value: T1 pre-HSC

value: E11 embryo


title: Sample 8 Smart-Seq_H19 DMR KO


title: Chimpanzee_ChIP_limb_input_chimpOrtholog_rep1

value: limb bud


title: Chimpanzee_ChIP_arch_H3K27ac_chimpOrtholog_rep1


title: Chimpanzee_ChIP_arch_H3K27ac_wildtype_rep1


title: Perturb-seq16

description:
Perturb-seq sample
Same underlying biological sample as for Dialout16


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F1_ad010

value: brain

value: VISp

tag: gender


title: Perturb-seq15

description:
Perturb-seq sample
Same underlying biological sample as for Dialout15


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F1_ad012

tag: tissue


title: Sample 7 Smart-Seq_H19 DMR KO


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F2_ad006


title: Chimpanzee_ChIP_limb_H3K27ac_chimpOrtholog_rep2

value: chimpanzee ortholog+/+


title: Chimpanzee_ChIP_limb_H3K27ac_wildtype_rep2

value: wild type


title: Perturb-seq14

description:
Perturb-seq sample
Same underlying biological sample as for Dialout14


title: Sample 5 Smart-Seq_H19 DMR KO


title: Sample 6 Smart-Seq_H19 DMR KO


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F1_ad008

value: RSP


title: Chimpanzee_ChIP_limb_H3K27ac_chimpOrtholog_rep1


title: Sample 9 Smart-Seq_H19 DMR KO


title: Perturb-seq13

description:
Perturb-seq sample
Same underlying biological sample as for Dialout13


title: Sample 4 Smart-Seq_H19 DMR KO


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F1_ad007


title: Chimpanzee_ChIP_limb_H3K27ac_wildtype_rep1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F1_ad006


title: Perturb-seq17

description:
Perturb-seq sample
Same underlying biological sample as for Dialout17


title: HACNS1_ChIP_arch_H3K4me2_humanized_rep2

value: H3K4me2 (Active Motif, #39913)


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F1_ad004


title: Perturb-seq11

description:
Perturb-seq sample
Same underlying biological sample as for Dialout11


title: Perturb-seq10

description:
Perturb-seq sample
Same underlying biological sample as for Dialout10


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F1_ad002


title: HACNS1_ChIP_arch_H3K4me2_wildtype_rep2


title: HACNS1_ChIP_arch_H3K4me2_humanized_rep1


title: Sample 1 Smart-Seq_H19 DMR KO

extract_protocol:
Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette; 0.05 μl of 1:200,000 dilution of External RNA Controls. Consortium (ERCC) RNA spike-in Mix1 (Ambion) was added to lysis buffer per reaction.
The cDNA libraries from single cells were generated as described previously. "Tang, F. et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nature  Methods 6, 377–382 (2009)."

value: mH19 delta_DMR/+


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F1_ad001


title: Perturb-seq9

description:
Perturb-seq sample
Same underlying biological sample as for Dialout9


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F12_ad012


title: Sample 4 DNA methylation Seq (WGBS)_wildtype

description:
pool of 200 cells
DNA methylation

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome by Bismark
genome build: mm10
supplementary file format and content: wig files to satistics the coverage for each sample

extract_protocol:
FACS-enriched cells  were  rinsed in PBS-BSA and centrifuged, then cells were  transferred into cell lysis buffer.
Genomic DNA with 0.5% unmethylated lambda DNA (Fermentas) spike-in was first sonicated into 200–300-bp fragments using Covaris S2 system. After being concentrated, the shearedDNAwas end-repaired, dA-tailed and ligated with pre-methylated TruSeqDNAadapters (illumina). Bisulphite conversionwas  conductedwithMethylCode Bisulphite Kit (Invitrogen), after bisulphite conversion, the converted templates were PCR amplified and quantified using Qubit  ds DNA high sensitivity dye (Invitrogen), and standard-curve-based qPCR assay (Agilent). The final quality-insured libraries were sequenced onHiSeq2000 sequencer.

value: mH19 flDMR/+


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F12_ad010


title: Sample 5 DNA methylation Seq (WGBS)_wildtype

description:
pool of 200 cells
DNA methylation


title: Perturb-seq7

description:
Perturb-seq sample
Same underlying biological sample as for Dialout7


title: HACNS1_ChIP_limb_H3K4me2_wildtype_rep2


title: HACNS1_ChIP_arch_H3K4me2_wildtype_rep1

value: pharyngeal arch


title: Sample 3 DNA methylation Seq (WGBS)_wildtype

description:
pool of 200 cells
DNA methylation


title: Perturb-seq8

description:
Perturb-seq sample
Same underlying biological sample as for Dialout8


title: Perturb-seq6

description:
Perturb-seq sample
Same underlying biological sample as for Dialout6

value: GFP, Dyrk1a, Mll1


title: Sample 3 Smart-Seq_H19 DMR KO


title: Sample 2 DNA methylation Seq (WGBS)_H19 DMR KO

description:
pool of 200 cells
DNA methylation


title: Perturb-seq12

description:
Perturb-seq sample
Same underlying biological sample as for Dialout12


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F12_ad008


title: Sample 1 DNA methylation Seq (WGBS)_H19 DMR KO

description:
pool of 200 cells
DNA methylation


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F12_ad007

value: male


title: Sample 2 Smart-Seq_H19 DMR KO


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F12_ad006

value: PTLp

value: female


title: HACNS1_ChIP_limb_H3K4me2_wildtype_rep1


title: Perturb-seq4

description:
Perturb-seq sample
Same underlying biological sample as for Dialout4

value: All 35 genes

value: 10X v2 single cell


title: HACNS1_ChIP_arch_input_humanized_rep2

value: none (input control)


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F12_ad004


title: Sample 25 poly A enriched RNA-Seq

description:
single cell
poly-A (riched) RNA
adult_HSC_expression_matrix.txt.gz

source_name: Bone marrow cells

value: HSC

value: wildtype

value: adult


title: Perturb-seq3

description:
Perturb-seq sample
Same underlying biological sample as for Dialout3


title: HACNS1_ChIP_arch_input_wildtype_rep2


title: HACNS1_ChIP_limb_H3K4me2_humanized_rep2

value: limb bud


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F12_ad002

value: brain

value: VISp


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F11_ad012

value: RSP


title: HACNS1_ChIP_arch_input_humanized_rep1


title: Perturb-seq1

description:
Perturb-seq sample
Same underlying biological sample as for Dialout1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F11_ad010


title: Sample 23 poly A enriched RNA-Seq


title: HACNS1_ChIP_arch_input_wildtype_rep1

value: wild type


title: Perturb-seq2

description:
Perturb-seq sample
Same underlying biological sample as for Dialout2


title: Perturb-seq5

description:
Perturb-seq sample
Same underlying biological sample as for Dialout5


title: HACNS1_ChIP_limb_input_humanized_rep2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F11_ad008


title: Singleton1

description: Single perturbation

value: GFP


title: HACNS1_ChIP_limb_H3K4me2_humanized_rep1

value: H3K4me2 (Active Motif, #39913)


title: Sample 22 poly A enriched RNA-Seq


title: Sample 21 poly A enriched RNA-Seq


title: HACNS1_ChIP_limb_input_wildtype_rep2


title: Dialout18

description:
Dialout for sample 18
Same underlying biological sample as for Perturb-seq18

molecule: other

value: Dialout for perturbation barcode


title: Sample 26 poly A enriched RNA-Seq


title: HACNS1_ChIP_limb_input_humanized_rep1


title: Sample 20 poly A enriched RNA-Seq


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F11_ad007

value: male


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F11_ad006

value: PTLp


title: Dialout17

description:
Dialout for sample 17
Same underlying biological sample as for Perturb-seq17


title: Sample 19 poly A enriched RNA-Seq


title: Sample 24 poly A enriched RNA-Seq


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F11_ad004

value: female


title: HACNS1_ChIP_limb_input_wildtype_rep1


title: Dialout16

description:
Dialout for sample 16
Same underlying biological sample as for Perturb-seq16

value: All 35 genes


title: Singleton2

description: Single perturbation

value: 10X v2 single cell


title: Sample 18 poly A enriched RNA-Seq


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F11_ad002


title: HACNS1_ChIP_arch_H3K27ac_humanized_rep2

value: pharyngeal arch

value: H3K27ac (Active Motif, #39133)


title: Dialout15

description:
Dialout for sample 15
Same underlying biological sample as for Perturb-seq15


title: Sample 17 poly A enriched RNA-Seq

value: HSC

value: wildtype


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F11_ad001


title: HACNS1_ChIP_arch_H3K27ac_wildtype_rep2


title: Dialout14

description:
Dialout for sample 14
Same underlying biological sample as for Perturb-seq14


title: Sample 16 poly A enriched RNA-Seq

value: adult


title: Sample 15 poly A enriched RNA-Seq


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F10_ad012

value: brain


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F10_ad010

value: VISp


title: HACNS1_ChIP_arch_H3K27ac_wildtype_rep1


title: N6 DMBA HFD Liver RNA

city: GARY

first: Dipika

last: Gupta

state: IN

address: 3400 BROADWAY

institute: INDIANA UNIV SCHOOL MEDICINE-NORTHWEST

data_processing:
Reads were adapter trimmed and quality filtered using Trimmomatic ver. 0.33 (http://www.usadellab.org/cms/?page=trimmomatic), with the cutoff threshold for average base quality score set at 20 over a window of 3 bases.
Reads shorter than 20 bases post-trimming were excluded.
Cleaned reads were mapped to mouse reference genome GRCm38 (gencode M16), using TopHat2 ver. 2.1.1 (https://doi.org/10.1186/gb-2013-14-4-r36).
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Differential expression with statistical analysis was calculated using the software DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: countstable.txt

source_name: Liver RNA

extract_protocol:
RNA was isolated from the liver using TRIZOL and purified on RNeasy spin columns. The purity was checked with Agilent Tapestation.
Libraries were prepared according to Illumina's TruSeq Stranded mRNA library preparation kit protocol.
The cleaned adapter ligated libraries were pooled and loaded on the NextSeq 500 with a 75 cycle sequencing module to generate paired-end reads (43bp+43bp+6bp).

treatment_protocol: Mice were treated with the carcinogen DMBA and maintained on high fat diet for 30 weeks.

value: BALB/c

value: 30 weeks

tag: organ

value: Liver

tag: treatment

value: DMBA and high fat diet

tag: disease state

value: cancer


title: N7 DMBA HFD Liver RNA

tag: age


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F10_ad008

tag: source

value: RSP

tag: target


title: HACNS1_ChIP_limb_H3K27ac_humanized_rep2

tag: developmental stage

value: limb bud


title: Sample 14 poly A enriched RNA-Seq

tag: genotype


title: Sample 13 poly A enriched RNA-Seq


title: HACNS1_ChIP_arch_H3K27ac_humanized_rep1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F10_ad007

value: male


title: N4 DMBA HFD Liver RNA


title: HACNS1_ChIP_limb_H3K27ac_wildtype_rep2

value: wild type


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F10_ad006

value: PTLp

value: female


title: HACNS1_ChIP_limb_H3K27ac_humanized_rep1

value: H3K27ac (Active Motif, #39133)


title: HACNS1_ChIP_limb_H3K27ac_wildtype_rep1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F10_ad004


title: Sample 10 poly A enriched RNA-Seq

value: HSC


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F10_ad002


title: lib4_LEC

city: Heidelberg

first: Nicolas

last: Gengenbacher

address: Im Neuenheimer Feld 280

department: Vascular Oncology and Metastasis

institute: German Cancer Research Center

data_processing:
Sequencing strategy: 26+74 bp Paired-End
RTA 2.7.7
The sequenced reads were aligned to the mouse reference genome mm10 using Cell Ranger (v 2.1.1).
Low-quality cells containing less than 200 detected genes or more than 10% of transcripts from mitochondrial genes were filtered out.
Genome_build: mm10
Supplementary_files_format_and_content: BEC_LEC.Gene-Cell.UMI.Matrix.csv includes UMI raw count matrix per cell as calculated by Cell Ranger.

source_name: MT-ret melanoma

growth_protocol: MT-ret tumor fragments were implanted on the ventral flank of 10 C57BL/6N mice.

extract_protocol:
10000 Blood (BEC) and 10000 lymphatic (LEC) endothelial cells were isolated by FACS, and directly processed for single-cell library generation with 10x Genomics reagents.
Libraries were prepared using the Chromium Single Cell 3′ Reagent Kits (v2) (10x Genomics) according to the manufacturer’s protocol.

value: MT-ret tumor tissue

value: endothelial cells

tag: ec type

value: lymphatic


title: N1 DMBA HFD Liver RNA


title: N2 DMBA HFD Liver RNA


title: lib3_LEC

tag: cell type


title: W6 DMBA HFD Liver RNA

value: WT


title: Sample 9 poly A enriched RNA-Seq

value: wildtype

value: adult


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_F10_ad001

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

value: brain

value: VISp


title: Sample 8 poly A enriched RNA-Seq


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E9_ad010


title: Sample 7 poly A enriched RNA-Seq


title: lib2_LEC


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E9_ad008


title: W5 DMBA HFD Liver RNA

value: BALB/c

value: 30 weeks

value: Liver

value: DMBA and high fat diet

value: cancer


title: lib1_LEC


title: Sample 6 poly A enriched RNA-Seq


title: W4 DMBA HFD Liver RNA


title: N3 DMBA HFD Liver RNA


title: lib4_BEC

value: blood vascular


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E9_ad007

value: RSP

value: male


title: Sample 5 poly A enriched RNA-Seq

value: HSC


title: W3 DMBA HFD Liver RNA


title: lib3_BEC

value: MT-ret tumor tissue


title: Sample 11 poly A enriched RNA-Seq


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E9_ad006

value: PTLp

value: female


title: W2 DMBA HFD Liver RNA

value: WT


title: Sample 4 poly A enriched RNA-Seq

value: wildtype


title: lib2_BEC

value: endothelial cells


title: W1 DMBA HFD Liver RNA


title: lib1_BEC


title: treatment05

data_processing:
Sequencing strategy: 50bp Single-Read
RTA 2.7.7
The sequenced reads were aligned to the mouse reference genome mm10 using STAR aligner. Featurecounts was used to perform gene specific read counting. A custom script was used to calculate FPKM and TPM expression values.
DEseq2 was used to test for differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Bulk_LEC_TUMOR_Count.FPKM.TPM_FC.csv includes gene counts, FPKM and TPM values for each sample

extract_protocol:
MT-ret tumor LEC were isolated by FACS, and RNA was extracted using the Arcturus PicoPure RNA Isolation Kit (Life Technologies).
Libraries were prepared with 0.5 ng of total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (SMARTer) and the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (NEBNext)

treatment_protocol: Mice were i.p. injected with anti-Ang2 or IgG and sacrificed after 12h.

value: LEC


title: Liver_Adult

city: Houston

first: Manuel

middle: Eliezer

last: Cantu Gutierrez

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Data was mapped to the Mus musculus reference genome (mm9 and mm10) using Bowtie2 v2.4
Mitochondiral and undetermined reads were filtered using samtools v1.10
Data was sorted using samtools v1.10 (samtools sort {} -o {}.sorted.bam')
Duplicate reads were filtered using Picard Tools ($PICARD MarkDuplicat\es I={} ASSUME_SORTED=true METRICS_FILE={}.markdup.metrics VALIDATION_STRINGENC\ Y=LENIENT OUTPUT={}.md.bam')
MACS2 v2.1.2 was used to call peaks (macs2 callpeak -t {} -g mm --nomodel --shift -100 --extsize 200 -B --broad -n {}-nm-broad -q 0.05 --outdir {}-nm.broad.peaks 2> {}-nm.broad.stder')
bigwig files for visualization were created using bedgraphtobigwig
Genome_build: M. musculus, UCSC mm9 and M. musculus, UCSC mm10
Supplementary_files_format_and_content: bigwig files for visualization in genome browser

source_name: Mouse liver

extract_protocol:
Briefly, fresh tissue was harvested on ice and immediately dissected and minced into small 1mm by 1mm portions with curved scissors prior to dounce homogenization. Nuclei were isolated via density gradient centrifugation with optiprep density gradient medium (Sigma, D1556). Nuclei were collected from the 30-40% interface. Approximately 50,000 nuclei from murine tissues were used as input for ATAC-seq.
ATAC-Seq libraries for murine cells were generated as previously described (Buenrostro et al. 2013). Paired-end 2x75 bp sequencing was performed on an Illumina Nextseq 500 instrument.

value: 2 month old

value: liver


title: Sample 2 poly A enriched RNA-Seq

value: adult


title: Sample 1 poly A enriched RNA-Seq


title: treatment04


title: Brain_Adult

source_name: Mouse brain

value: brain


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E9_ad002

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

value: VISp


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E9_ad001


title: Brain_P6


title: treatment03


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E8_ad012


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E8_ad010


title: treatment02


title: Brain_E12


title: N5 DMBA HFD Liver RNA

value: BALB/c

value: 30 weeks

value: Liver

value: DMBA and high fat diet

value: cancer


title: treatment01

value: MT-ret tumor tissue


title: sample_08

city: Boston

first: Beth

last: Stevens

state: Massachusetts

address: 3 Blackfan Circle, 12220 Center for Life Sciences

institute: Boston Children's Hospital

data_processing:
Bcl2fastq & Demultiplex by sample: 'mkfastq' Cell Ranger 2.2.0
Alignment/Counts: 'count' Cell Ranger 2.2.0
Aggregate: 'Aggr' Cell Ranger 2.2.0 (normalize = none)
Analysis: Seurat
i7 (Sample Index: 8bp)
Read 1: 26 bp (Barcode:16 bp UMI: 10 bp)
Read 2: 98 bp (Transcript)
Genome_build: 10X Default 2.2.0 (GRCm38 (mm10); Annotation: Filtered Ensembl v84)
Supplementary_files_format_and_content: 10X Cell Ranger Count Output (.tsv & .mtx)

source_name: brain

extract_protocol: 10X Genomics 3' Version 2 Single Cell Kit

tag: digestion type

value: Cold Dounce

tag: Sex

value: Male

value: PBS (tail vein; 24hrs prior to sac)

tag: brain region

value: Cortex & Hippocampus


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E8_ad007

value: RSP

value: male


title: sample_06


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E9_ad004

value: PTLp

value: female


title: Sample 3 poly A enriched RNA-Seq

value: HSC

value: wildtype

value: adult


title: control05

value: LEC

value: IgG


title: control04


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E7_ad012

value: brain

value: VISp


title: control02


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E7_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E8_ad008


title: control03


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E7_ad006


title: sample_02


title: control01


title: Dounce_IN_sample_06

data_processing:
Bcl2fastq & Demultiplex by sample: 'mkfastq' Cell Ranger 3.0.0
Alignment/Counts: 'count' Cell Ranger 3.0.0
Aggregate: 'Aggr' Cell Ranger 3.0.0 (normalize = none)
Analysis: Seurat
Genome_build: 10X Default 3.0 (GRCm38 (mm10); Annotation: Filtered Ensembl v93)
Supplementary_files_format_and_content: 10X Cell Ranger Count Output (.tsv & .mtx)

tag: inhibitors

value: Yes

tag: batch

value: Batch 2

value: M

value: Whole Brain


title: Miltenyi_NO_sample_06

value: Enzymatic

value: No

tag: strain


title: Miltenyi_IN_sample_03


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E7_ad004

tag: tissue

tag: gender


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E8_ad006


title: Dounce_NO_sample_03

value: Cold Dounce


title: Bmal1Mut_ZT22_71814

city: Philadelphia

first: Shirley

state: Pennsylvania

address: 3400 Civic Center Blvd, Bldg 421, Rm 10-162

institute: University of Pennsylvania

data_processing:
Raw RNA-Seq reads were aligned to the reference genome using STAR v2.5.3a with the following command line options: --outSAMtype BAM Unsorted; --outSAMunmapped Within KeepPairs; --outFilterMismatchNmax 33; --seedSearchStartLmax 33; --alignSJoverhangMin 8. Additionally, STAR was provided with the gene models (Ensembl v91) in GTF format during alignments and the “—outSAMattrRGline” was used to add a unique read group to each of the resulting BAM files. Note that the three pairs of FASTQ files per library (two for each sequencing lane) were aligned separately.
Following alignment, the three BAM files for each library were combined using the SAMtools v1.3.1 merge command with the “-n” argument, which maintains the BAM files in “unsorted” order (i.e. sorted by read ID).
The Pipeline Of RNA-seq Transformations (PORT) v0.8.5-beta (https://github.com/itmat/Normalization) was used to perform gene-level normalization and quantification of the merged, aligned data.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt files contain PORT-normalized and quantified read counts for each gene in each sample

source_name: Blood brain barrier endothelial cells

growth_protocol: Animals were fed ad libitum and entrained to 12h:12h light:dark cycles and given at least 1 day per hour of phase shift prior to experiments.

extract_protocol:
RNA was extracted from sorted cells using RNeasy Plus Micro Kit (Qiagen) following the manufacturer’s protocol.
RNA quality was assessed using 2100 Bioanalyzer Instrument (Agilent). RNA integrity numbers (RIN) of 6-8 were used to construct libraries. Strand-specific libraries were constructed using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech). Each library was prepared using a unique adapter barcode index to allow for multiplexing. All libraries were pooled together and sequenced across three lanes of an Illumina HiSeq 4000 Sequencer.

treatment_protocol: Brains were harvested from mice at time points around the circadian day (ZT2, 6, 10, 14, 18, 22). Brains were finely minced in RPMI media containing 10% CCS, incubated at 37°C with 2 mg/ml collagenase IV (Gibco) and 200 μg/mL DNase I (Roche) for 30 mins with shaking at 250 rpm, pipetting up and down once during incubation. Brain homogenate was demyelinated using myelin removal beads II (Miltenyi Biotec) as instructed by the manufacturer’s protocol. Cell suspensions were then filtered using a 100um cell strainer. Endothelial cells were then labeled with fluorescence-conjugated anti-CD31 antibody and sorted using either a BD FACSAria or BD FACSMelody (BD Biosciences). Between 10000 and 20000 cells were sorted from a single mouse.

value: Bmal1fl/fl; Tie2cre

tag: timepoint

tag: replicate

tag: library barcode

value: AGCGATAG-ATAGAGGC


title: DN18

type: RNA

city: San Francisco

first: Swastika

last: Sur

address: 513 Parnassus Ave

department: Surgery

institute: UCSF

hyb_protocol: We followed Agilent’s hybridization protocol. Equal amounts of the exposed and negative control sample (825 ng) were competitively hybridized onto Agilent Whole 4×44K Human oligonucleotide arrays in a hybridization oven at 65°C for 17 hours. Slides were washed according to the manufacturer’s instructions with washing buffers and finally dipped in Stabilization and Drying Solution (Agilent Technologies, Palo Alto, CA) to protect them from environmental ozone.

scan_protocol: We followed Agilent’s scan protocol. The arrays were scanned on an Agilent scanner (G2565BA, Agilent Technologies, Palo Alto, CA), and further processed using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software was used for background subtraction GeneSpring was used for normalization

organism: Homo sapiens

source_name: blood

label_protocol: Cy5-CTP (exposed samples) and Cy3-CTP (negative control samples) were fluorescently labeled during the step of cDNA was transcribed into complimentary RNA (cRNA). We used Agilent LIRAK PLUS, two color Low Input RNA Linear Amplification Kit method according manufacturer’s instructions

extract_protocol: The blood was drawn in the presence of sodium heparin. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA).

value: peripheral blood

tag: diagnosis

value: ESRD

source_name: human reference total RNA pool

value: 10 human cell lines


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E7_ad001

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

tag: age

tag: source

value: PTLp

tag: target

value: male


title: sample_03

value: Male

tag: treatment

value: PBS (tail vein; 24hrs prior to sac)

value: Cortex & Hippocampus


title: Miltenyi_IN_sample_02

value: Yes


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E6_ad012

value: brain

value: RSP

value: VISp

value: female


title: DN14


title: DN15


title: Bmal1Mut_ZT18_71801

tag: genotype

value: TAATGCGC-TATAGCCT


title: DN17


title: DNG5-5

value: diabetic nephropathy


title: DN13


title: DN8


title: Dounce_IN_sample_05

tag: digestion type

value: Cold Dounce

value: Batch 2

value: M

value: Whole Brain


title: Bmal1Mut_ZT18_71800

value: Bmal1fl/fl; Tie2cre

value: CTGAAGCT-TATAGCCT


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E6_ad010

value: male


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E6_ad008


title: Bmal1Mut_ZT14_71351

value: TCCGCGAA-ATAGAGGC


title: Bmal1Mut_ZT22_71813

value: TCTCGCGC-ATAGAGGC


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E6_ad007


title: DNG5-4

value: peripheral blood

value: 10 human cell lines


title: DN2

value: ESRD


title: DNG5-3


title: DNG5-1


title: Bmal1Mut_ZT14_71350

value: CGGCTATG-ATAGAGGC


title: Miltenyi_NO_sample_05

value: Enzymatic

value: No

value: Batch 1

tag: Sex


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E6_ad001

value: brain

value: PTLp

value: VISp


title: Dounce_NO_sample_02

value: Cold Dounce

value: M

tag: brain region


title: DNG5-2

value: diabetic nephropathy


title: Miltenyi_IN_sample_01

tag: inhibitors

value: Yes

value: Whole Brain


title: Dounce_IN_sample_04

tag: batch


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E5_ad012

tag: strain

value: RSP

value: female


title: Bmal1Mut_ZT06_71799

value: Bmal1fl/fl; Tie2cre

value: GAATTCGT-TATAGCCT


title: Miltenyi_NO_sample_04


title: Dounce_NO_sample_01


title: DNG4-13

tag: tissue

value: peripheral blood

value: 10 human cell lines


title: Bmal1Mut_ZT06_71798

value: ATTCAGAA-TATAGCCT


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E5_ad010

tag: gender

value: male


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E5_ad008


title: All_INHIB_sample_02

data_processing:
Bcl2fastq & Demultiplex by sample: 'mkfastq' Cell Ranger 3.0.0
Alignment/Counts: 'count' Cell Ranger 3.0.0
Aggregate: 'Aggr' Cell Ranger 3.0.0 (normalize = none)
Analysis: Seurat
Genome_build: 10X Default 3.0 (GRCm38 (mm10); Annotation: Filtered Ensembl v93)

value: Enzymatic

value: Batch 1


title: DNG4-26


title: All_INHIB_sample_01


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E3_ad012

value: brain


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E5_ad001

value: PTLp

value: VISp


title: Bmal1Mut_ZT02_71810

tag: timepoint

value: GAATTCGT-ATAGAGGC


title: Bmal1Mut_ZT10_71812

tag: replicate

value: TAATGCGC-ATAGAGGC


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E5_ad007


title: Control_ZT22_71808

tag: library barcode

value: GAGATTCC-ATAGAGGC


title: DNG4-16

tag: diagnosis

value: diabetic nephropathy


title: All_NO_sample_02

value: No

value: M

value: Whole Brain

tag: age


title: Bmal1Mut_ZT10_71811

value: Bmal1fl/fl; Tie2cre

value: CTGAAGCT-ATAGAGGC


title: DNG4-10

value: peripheral blood

value: 10 human cell lines


title: DNG4-4


title: Bmal1Mut_ZT02_71809

value: ATTCAGAA-ATAGAGGC


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E3_ad010

tag: source

value: RSP

value: male


title: All_NO_sample_01

value: Enzymatic

value: Batch 1


title: Control_ZT22_71807

value: CGCTCATT-ATAGAGGC


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E3_ad008

value: brain

tag: target

value: VISp

value: female


title: DNG3-7

value: diabetic nephropathy


title: DNG4-1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E3_ad007


title: Control_ZT18_71797

value: GAGATTCC-TATAGCCT


title: Sample 12 poly A enriched RNA-Seq

tag: cell type

value: HSC

value: wildtype

tag: developmental stage

value: adult


title: Control_ZT18_71796

tag: genotype

value: CGCTCATT-TATAGCCT


title: Colonic Epithelial Cells, Ccna2-KO rep3

city: Marseille

first: Quentin

last: Da Costa

address: 232 boulevard de Sainte Marguerite

country: France

institute: Institut Paoli-Calmettes

data_processing:
The quantification of the gene transcripts was performed using the Kallisto program, which is based on pseudo-alignment principle, with default settings.
GRCm38 Refseq was used to annotate the transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: A tab-delimited text file include raw transcript counts for each Sample.

source_name: Colonic Epithelial Cells, Ccna2-KO

extract_protocol:
Colons were removed from mice and flushed with cold PBS. Colons were treated with 10 ml of CEC buffer to release CECs. RNA was extracted using the Roche High Pure RNA isolation kit (Roche Molecular Systems, Inc.) according to the manufacturer protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colon

value: Colonic Epithelial Cells

value: 4 weeks


title: DNG3-5

value: peripheral blood

value: 10 human cell lines


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E3_ad006

value: PTLp


title: Control_ZT14_71806

last: Zhang

value: TCCGGAGA-ATAGAGGC


title: Colonic Epithelial Cells, WT rep4

source_name: Colonic Epithelial Cells, WT

value: wild type


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E3_ad004

value: brain


title: Colonic Epithelial Cells, Ccna2-KO rep2


title: DNG2-30


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E3_ad002

value: VISp

value: male


title: Colonic Epithelial Cells, WT rep3


title: Control_ZT10_71804

value: AGCGATAG-TATAGCCT


title: Colonic Epithelial Cells, Ccna2-KO rep1


title: Control_ZT14_71805

value: ATTACTCG-ATAGAGGC


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E2_ad012

value: RSP

value: female


title: Colonic Epithelial Cells, Ccna2-KO rep4


title: DNG4-6

value: diabetic nephropathy


title: Colonic Epithelial Cells, WT rep2


title: Control_ZT06_71795

value: TCCGGAGA-TATAGCCT


title: Colonic Epithelial Cells, WT rep1

value: Colon


title: Control_ZT06_71794

value: ATTACTCG-TATAGCCT


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E2_ad008


title: Control_ZT02_71802

value: TCCGCGAA-TATAGCCT


title: Control_ZT02_71349

value: CGGCTATG-TATAGCCT


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E2_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E2_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E2_ad010


title: shControl_Setdb1_In

tag: cell line

value: E14 embryonic stem cells (ESCs)

tag: treatment

value: shControl

tag: chip antibody


title: DNG2-27

value: peripheral blood

value: 10 human cell lines


title: DNG2-20


title: DNG2-26


title: Control_ZT10_71803

value: TCTCGCGC-TATAGCCT


title: BAT3-a452

city: Leiden

first: Roel

last: Bijkerk

address: Albinusdreef 2

department: Nephrology

country: Netherlands

institute: LUMC

data_processing:
The reads were mapped to the reference sequences using a short-read aligner based on the Burrows-Wheeler Transform.
The default mismatch rate of 2% (2 mismatches in a read of 100 bases) was used. Based on the mapped locations in the alignment file, the frequency of reads mapping to a transcript was determined.
Read counts served as input for downstream RNA-seq differential expression analysis.RPKM/FPKM (reads/fragments per kilobase of exon per million reads mapped) values were calculated.
The read counts were loaded into the DESeq package v 1.10.1, a statistical package within the R platform v2.15.3.
Genome_build: Mus musculus reference version GRCm38.p4 was used for alignment of samples
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each group including  differential expression compared to scramblemir control group

source_name: brown adipose tissue

extract_protocol:
adipose tissues were removed, snap frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
The NEB Next Ultra Directional RNA Library Prep Kit for Illumina was used to process samples according to the manufacturer’s protocol. Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed for ligation of with the sequencing adapters and PCR amplification of the resulting product.

treatment_protocol: mice received two subcutaneous injections of 25 mg/kg locked nucleic acid (LNA) modified antisense miR-224 (antimiR-224), miR-452 (antimiR-452) or scrambled miR sequence (scramblemiR

value: brown adipose tissue

value: mir-452 inhibitor


title: BAT1-a452


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E2_ad002

value: brain

value: PTLp

value: VISp

value: male


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E2_ad004

value: female


title: BAT4-a452


title: BAT2-a452


title: shControl_Setdb1

value: Setdb1 (home-made)


title: DNG2-21

value: diabetic nephropathy


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E2_ad001


title: BAT4-a224

value: miR-224 inhibitor


title: DNG1-8

value: healthy control


title: DNG2-8


title: shSetdb1_SMC1a_In


title: DNG2-23


title: DNG2-2


title: BAT3-a224


title: DNG1-6


title: DNG1-9


title: DNG1-5


title: shSetdb1_SMC1a

value: SMC1a (Bethyl #A300-055A)


title: BAT2-a224


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E1_ad010

value: RSP


title: DNG2-24


title: DNG1-4


title: BAT4-scr

description: BAT224_res.all.tab and BAT452_res.all.tab

value: control


title: BAT1-a224


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E1_ad008


title: E14_PML

value: E14 embryonic stem cells (ESCs)

value: Wild-type

value: PML (Biorbyt #orb100017)


title: shControl_SMC1a_In

value: shControl


title: shControl_SMC1a


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E1_ad007


title: E14_Setdb1


title: DNG1-2

value: peripheral blood

value: 10 human cell lines


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E1_ad006

value: brain

value: PTLp


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E1_ad012

value: VISp


title: BAT2-scr

value: brown adipose tissue


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E1_ad004

value: female


title: BAT1-scr


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E1_ad002

value: male


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E1_ad001


title: shSetdb1 E14 RNA-Seq 2

data_processing:
fastq files were mapped using STAR aligner. Maximum of 3 mismatches were allowed. Reads mapping to more than one locus were filtered out.
Cuffdiff was used to normalize the libraries and calculate differential gene expression.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited txt file containing the FPKM values of every gene in each condition.

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured using mouse ES medium prepared in DMEM high glucose (Hyclone) supplemented with 15 percent ES cell FBS (Gibco), 2mM L-glutamine (Gibco), 1X Pen-Strep (Gibco), 100 micromolar MEM non-essential amino acids (Gibco), 100 micromolar 2-mercaptoethanol (Gibco), and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore). The mouse ES line was cultured on plates pre-coated with 0.1 percent gelatine (porcine).

extract_protocol:
Total RNA was extracted for each of the transfected cells using Trizol reagent (Ambion). DNA contamination for the samples was minimized by using the QIAGEN RNeasy Kit. The RNA sample quality control was performed by qPCR for constitutive genes (Actin, Gapdh) as well as by determination of knock-down efficiency.
TruSeq Stranded mRNA Library Prep Kit (RS-122-2101, Illumina) was used and the libraries were prepared as per the recommended kit protocol.

treatment_protocol: E14 cells were harvested using trypsinization and were re-seeded into 6-well plates which were pre-coated with gelatine. The seeding density was 300,000 cells per well of the plates. These cells were cultured at 37 degree Celsius for 20-24 hours and the cells were replenished with fresh medium at least 2 hours prior to transfection. The cells were then transfected with 3 microgram of the plasmid constructs (shControl, shSetdb1, shSmc1a) using 4.5 microliters of Lipofectamine 2000 (Thermofisher), as per the manufacturer’s protocol. Puromycin (1 microgram/millliter) containing mESC medium was added to the cells 24 hours after transfection to select for the transfected plasmids. This process of selection was repeated once more 48 hours after transfection. The cells were finally harvested 72 hours after transfection.


title: shSetdb1 E14 RNA-Seq 1


title: BAT3-scr


title: shSmc1a E14 RNA-Seq 2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E12_ad010


title: WAT2-a452

source_name: white adipose tissue

value: white adipose tissue

value: mir-452 inhibitor


title: WAT4-a452


title: shControl E14 RNA-Seq 2

source_name: E14 mESCs


title: WAT3-a452


title: DNG1-1

value: healthy control


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E12_ad008

value: RSP


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E12_ad007


title: DNG1-3


title: shSmc1a E14 RNA-Seq 1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E12_ad006


title: N7


title: WAT3-a224

value: miR-224 inhibitor


title: cc2∆:cc1_msc1∆_CENP-ACnp1

city: Edinburgh

first: Alastair

middle: Robert

last: Kerr

state: Midlothian

address: 2.21 Michael Swann Building, Kings Buildings, Mayfield Road

department: Wellcome Centre for Cell Biology

institute: University of Edinburgh

data_processing:
BWA (Li, 2010 #9905;Li, 2009 #9908) or BOWTIE2 (Langmead, 2012 #9901) was used to map ChIP-seq reads onto the S. pombe genome assembly EF2 (ASM294v2) or modified genome assembly generated based on ASM294v2, where centromere 2 was replaced with sequence from centromere 1 to mimic (cc2∆::cc1) and to include pHCC2 plasmid sequence.
Indexed, sorted bam files were created for each dataset using SAMtools (Li, 2009 #9907).
The program bamCoverage from the deepTools suite version 2.5.3 (Ramirez, 2016 #9919) or BEDtools (Quinlan, 2014 #9916;Quinlan, 2010 #9917) was used to create bigwig files from the mapped bam files and scaled using reads per kilobase of transcript per million mapped reads [RPKM]
SeqPlots (Stempor, 2016 #9923) was used to plot the occupancy over transcription start sites [TSS] as annotated in PomBase.
Genome_build: S. pombe EF2 genome assembly; ASM294v2
Genome_build: S. pombe +pHCC2 genome (see pombe.ASM294v2.20.cc2_D.gtf.gz, pombe_cc2D_pHcc2.bed.gz, pombe_cc2_D_pHetcc2.ann.gz, pombe_cc2_D_pHetcc2.fa.gz)
Supplementary_files_format_and_content: bigWig

organism: Schizosaccharomyces pombe

growth_protocol: S.pombe strains were grown in YES media. ~150x107 cells were harvested from o/n cultures and processed for ChIP

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma) for 15 min at room temperature and lysed using a bead beater (Biospec Products). Cell lysates were sonicated in a Bioruptor (Diagenode) (30/40 min, 30 s On and 30 s Off at ‘High’ (200W) position). For CENP-ACnp1 ChIPs, anti-CENP-ACnp1 serum was used with Protein G sephrose beads (Roche). For all other ChIPs, Protein G Dynabeads (Life Technologies) were used along with anti-Myc 9B11 (Cell Signaling) or anti-Flag M2 antibody (Sigma), as appropriate. Immunoprecipitated DNA was recovered using Qiagen Min-Elute PCR purification kit.
ChIP-seq libraries were generated using an Illumina-based protocol with custom reagents using NEXTFlex-96 DNA Barcodes (Bioo Scientific). Briefly, immunoprecipitated DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina adapters, which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA fragments were size-selected using AmpureXP beads to remove excess adapters and adapter-modified DNA fragments were enriched by PCR amplification with Illumina primers for 12 cycles. The purified ChIP-seq libraries thus generated were validated and subsequently captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500/ HiSeq4000 system following the manufacturer's protocols.

tag: antibody

value: anti-Cnp1 (sheep)


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E12_ad004

tag: strain


title: WAT2-a224

tag: tissue


title: cc2∆:cc1_swr1∆_CENP-ACnp1


title: WAT1-a224


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E12_ad002

tag: gender


title: AGR-2

city: West Lafayette

first: Michael

last: Wendt

address: 201 S. University St.

department: MCMP

institute: Purdue University

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

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

label: biotin

source_name: cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical manual, 2001, Affymetrix)

growth_protocol: DMEM containing 10% FBS and 10mg/ml Insulin

extract_protocol: Quaigen RNAeasy

treatment_protocol: AGR cells were isolated from 3D culture in which NME cells were grown in 5% cultrex on top of a layer of solidified 100% cultrex. These cells were treated with AG1478 (1 micromolar) untill a distintinct, large colony was identified and physically isolated. These cells were expanded using tradidtional 2D culture and demonstrated to be AG4178 resistant before RNA was extracted.

tag: group

value: AG1478 resistant


title: AGR-3


title: cc2∆:cc1_wt_CENP-ACnp1

value: wt


title: WAT1-a452


title: shControl E14 RNA-Seq 1

value: E14 embryonic stem cells (ESCs)

value: shControl


title: cc2∆:cc1_pht1∆_CENP-ACnp1


title: WAT4-a224


title: N5

value: peripheral blood

value: 10 human cell lines


title: NME-2

value: overexpression of EGFR


title: AGR-1


title: NME-1


title: WAT4-scr

description: WAT224_res.all.tab and WAT452_res.all.tab

value: control


title: WAT3-scr


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E12_ad012

value: brain

value: VISp


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E12_ad001

value: PTLp

value: male


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E11_ad010


title: WAT2-scr

value: white adipose tissue


title: WAT1-scr


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E11_ad007


title: NME-3


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E11_ad004

value: female


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E11_ad006


title: Homo_input

first: Catherine

last: Wu

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description:
ChIP DNA
Homo_input.bigwig

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to the mouse reference genome using STAR (v2.4.0.1). ChIP-seq reads were aligned to the mouse reference genome using using Bowtie2 (v2.3.4.1).
TPM (Transcripts Per Kilobase Million) value was used to measure gene expression. Peak detection was performed with MACS2 (v2.2.0).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for all samples
Supplementary_files_format_and_content: bigwig

source_name: B cell

growth_protocol: Chromatin immunoprecipitation (ChIP) was performed on splenic B cells (80x106) from 2-3 months old Ikzf3 wild-type and homozygous mutant mice.

extract_protocol:
Cells were washed in cold PBS, fixed in 1% formaldehyde at room temperature for 10 min and the fixation reaction was quenched with 0.125M glycine for 5 min at room temperature. The nuclei were resuspended and lysed in 500µl of shearing buffer containing 0.5% SDS, 10mM EDTA pH8, 50mM Tris-HCl pH8, 5mM sodium butyrate and protease inhibitor. The chromatin was sheared on the Covaris E220 sonifiyer, according to the following program: PIP70, 5% duty factor, 200 cycles per burst, 25min. The sheared chromatin was diluted in 1% Triton, 2Mm EDTA, 150 Mm NaCL, 20Mm Tris-HCl pH8 plus protease inhibitor. A small portion of the shearded chromatin was set aside as total input, reverse crosslinked with 1 µl of 10mg/ml RNAase for 30 min at 37°C and 5µl of 20mg/ml Proteinase K at 65°C overnight, purified using the Qiagen PCR purification Kit and DNA is quantify on Qubit 3.0 fluorimeter.
The immunoprecipitated chromatin was cleaned up using the Qiagen PCR purification Kit. Input and ChIP Libraries were prepared with the Rubicon ThruPLEX FD kit (ref. R400429, Takara Bio USA) and sequenced on Illumina NextSeq instrument to generate 75bp single-end sequencing reads.

value: Splenic B cell

value: Ikzf3 fl/fl

value: 3 months


title: Homo_H3K4me2_ChIPSeq

description:
ChIP DNA
Homo_H3K4me2_ChIPSeq.bigwig


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E11_ad002

source_name: C57BL/6J P56 Mouse Brain


title: ST at timepoint t2, biological repC

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

institute: Quantitative Biology Center (QBiC)

description: Gene expression data from HEK293 cells treated with mock control for 120min

hyb_protocol: The samples were hybridized to the Affymetrix GeneTitan:HumanGene 2.1 ST Array Plate for 16 h at 48 ºC.

scan_protocol: HT Array Plates were scanned using the HT Scanner (Affymetrix GeneChip®HT)

data_processing: The data was analyzed using robust multi-array average (RMA) analysis using the rma() function from the R package oligo (version 1.30.0) with default setting (target=core).

source_name: TLR5 overexpressing human embryonic kidney cells (HEK293) treated with flagellin of Salmonella Typhimurium SL1344 (FliCS.T., acronym=ST) for 120min (t2)

label_protocol: 100 ng of quality controlled (using Bioanalyzer) total RNA were used for processing of the biotinylated cRNA.

growth_protocol: Murine TLR5 overexpressing HEK cells were cultured in custom- made SILAC-DMEM media (SILAC heavy label (Lys8Arg10), SILAC medium label (Lys4Arg6) and SILAC light label (Lys0Arg0) at 37°C and 5% CO2. At a passage number of seven the cells were highly incorporated and used for stimulation.

extract_protocol: 60 minutes or 120 minutes stimulated murine TLR5 overexpressing HEK cells were resuspended in RLT buffer containing 1% ß-mercaptoethanol for total RNA isolation with Qiagen RNeasy kit following the manufacturer’s instructions (Qiagen).

treatment_protocol: 6.6 x106 murine TLR5 overexpressing HEK cells per flask were stimulated with isolated flagellin of E. coli Nissle (EcN) or isolated flagellin of Salmonella Typhimurium SL1344 (ST) with a concentration according to MOI 10 for 60 minutes (t1) or 120 minutes (t2).

value: TLR5 overexpressing HEK293

value: ST

tag: time

value: 120 minutes


title: ST at timepoint t2, biological repB


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E10_ad012

value: RSP


title: ST at timepoint t2, biological repA


title: ST at timepoint t1, biological repB

description: Gene expression data from HEK293 cells treated with mock control for 60min

source_name: TLR5 overexpressing human embryonic kidney cells (HEK293) treated with flagellin of Salmonella Typhimurium SL1344 (FliCS.T., acronym=ST) for 60min (t1)

value: 60 minutes


title: Homo_IKZF3_ChIPSeq

description:
ChIP DNA
Homo_IKZF3_ChIPSeq.bigwig


title: WT H3K4me2_ChIPSeq

description:
ChIP DNA
WT H3K4me2_ChIPSeq.bigwig

value: wild type


title: ST at timepoint t1, biological repC


title: WT_input

description:
ChIP DNA
WT_input.bigwig


title: EcN at timepoint t2, biological repC

description: Gene expression data from HEK293 cells treated with flagellin of E. coli Nissle for 120min

source_name: TLR5 overexpressing human embryonic kidney cells (HEK293) treated with flagellin of E. coli Nissle (FliCEcN, acronym=EcN) for 120min (t2)

value: EcN


title: ALLSIL_PHF6_siRNA2_repl3

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

description: Gene expression 72h post-electroporation of ALLSIL T-ALL cells with PHF6 siRNA2, replicate 3

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to the array for 17 hours at 65°C in a rotating  hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner with SureScan High-Resolution Technology using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed using the VSN-package (Bioconductor) and background correction was performed during the normalization process, selecting those probes detecting at least a two-fold higher expression than the negative control probes of the array design in at least 60% of either treatment groups.

source_name: ALLSIL, PHF6 siRNA2, 96h, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labling kit (Agilent) according to the manufacturer's instructions, followed by miRNeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown in RPMI supplemented with 20% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin

extract_protocol: Total RNA was harvested with the miRNeasy micro kit (Qiagen) with Dnase treatment on-column.

treatment_protocol: ALLSIL cells were electroporated with  control or PHF6 targeting siRNA and cells were harvested 96h post-electroporation

value: ALLSIL

value: PHF6 siRNA2

value: 96h post-electroporation


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E10_ad010

value: brain

value: VISp


title: ALLSIL_control_siRNA_repl3

description: Gene expression 72h post-electroporation of ALLSIL T-ALL cells with control siRNA, replicate 3

source_name: ALLSIL, control siRNA, 96h, replicate 3

value: control siRNA


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_E10_ad008

value: female


title: EcN at timepoint t2, biological repB


title: EcN at timepoint t1, biological repC

description: Gene expression data from HEK293 cells treated with flagellin of E. coli Nissle for 60min

source_name: TLR5 overexpressing human embryonic kidney cells (HEK293) treated with flagellin of E. coli Nissle (FliCEcN, acronym=EcN) for 60min (t1)


title: ST at timepoint t1, biological repA


title: WT IKZF3_ChIPSeq

description:
ChIP DNA
WT_IKZF3_ChIPSeq.bigwig

value: Splenic B cell


title: ALLSIL_PHF6_siRNA2_repl2

description: Gene expression 72h post-electroporation of ALLSIL T-ALL cells with PHF6 siRNA2, replicate 2

source_name: ALLSIL, PHF6 siRNA2, 96h, replicate 2


title: ALLSIL_PHF6_siRNA1_repl2

description: Gene expression 72h post-electroporation of ALLSIL T-ALL cells with PHF6 siRNA1, replicate 2

source_name: ALLSIL, PHF6 siRNA1, 96h, replicate 2

value: PHF6 siRNA1