title: T24 control_C


title: ACTH Adenomas CU-2015-001

status: Public on Nov 16 2020

type: RNA

city: México City

first: Daniel

last: Marrero-Rodriguez

state: México City

address: Av. Cuauhtémoc 330, Col. Doctores

department: Unidad de Investigacion Medica en Enfermedades Endocrinas

country: Mexico

institute: Instituto Mexicano del Seguro Social

description:
ACTH Adenomas
Adenomas-CU-2015-001
ACTH Adenomas

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Clariom D Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G GeneChip scanner.

data_processing: The data was analyzed with RMA using Partek Genomic Suite default analysis settings .

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Pituitary gland

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip WT Pico Reagent Kit,  Affymetrix).

growth_protocol: Not applicable

extract_protocol: miRNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: With no previous treatment

tag: tissue


title: GH Adenomas AC-2017-006

description:
GH Adenomas
Adenomas-AC-2017-006
GH Adenomas


title: T24 (TRAF4)_D

type: SRA

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

library_source: transcriptomic

data_processing:
FASTQ file sequenced by DNBseq using Phred +33 quality system
Adapter clipping was performed using Cutadapt (v2.8) with default settings.
RNA-Seq reads’ alignment was performed using STAR (v2.7.3a) on GRCh38 reference genome.
The gene read quantification was performed using HTSeq-count (v0.11.2).
The gene annotation used for quantification was Ensembl version 99.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: T24 (TRAF4)

growth_protocol: HT1376 and T24 cell lines were purchased from ATCC. The cells were grown in Dulbecco's modified eagle medium (DMEM) supplemented with 10% feta bovine serum and penicillin/streptomycin. Cells were free of mycoplasma contamination and were genotyped and authenticated. Cells were grown in 5% CO2 atmosphere incubator at 37˚C.

extract_protocol:
Total RNA from cells was isolated using the NucleoSpin RNA II kit (740955, BIOKE) using the manufacturer's instructions. Thereafter, RNA samples were processed for transcriptomic sequencing and analysis.
BGISEQ-500 RNA-Seq Library protocol (SOP-SS-027) was followed. mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. mRNA molecules were fragmented into small pieces using fragmentation reagent after reaction a certain period in proper temperture. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments. PCR process was applied to amplify the cDNA fragments with adapters from previous step. PCR products were purified with Ampure XP Beads (AGENCOURT), and dissolved in EB solution. Library was validated on the Agilent Technologies 2100 bioanalyzer.
DNBSEQ- RNASeq-PolyA – BGI index

treatment_protocol: TRAF4 was knocked down using short-haripin RNAs (shRNAs) in HT1376 using lentiviral transduction. Cells transduced with empty vector (pLKO.1) was used as control. After transduction, cells were grown in puromycin containing media for selection. Four independent experimental replicates were used for each condition. For T24 cell line, stable over-expression of Myc-TRAF4 or empty vector (Myc-tag) cells were generated in a similar manner. Again here, four independent experimental replicates were used.

tag: tag

tag: cell type

value: Bladder cancer cell line

tag: genotype/variation

value: TRAF4 over-expressed


title: Gm4665_1_S1_L001

city: Beijing

first: Zhongyang

last: Chen

address: No.5, Dongdan Santiao, Dongcheng District

country: China

institute: School of Basic Medicine, Peking Union Medical College (PUMC)

data_processing:
the gene cell barcode matrix was filtered based on the number of genes detected per cell (any cells with fewer than 500 or more than 4000 genes per cell were filtered out) and the percentage of mitochondrial UMI counts (any cells with more than 10% of mitochondrial UMI counts were filtered out).
Cell Ranger version 1.3.1 (10×Genomics) were used to process raw sequencing data and Cell Ranger R Kit version 2.0.0 and Seurat suite version 2.0.0 for downstream analysis.
For clustering, principal-component analysis was performed for dimension reduction.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: Testis

extract_protocol:
we employed bilateral testicular microinjection: one testis was injected with AAV9-shCtrl-RFP; the contralateral testis was injected with AAV9-shRNA-RFP. We removed somatic cells and isolated RFP+ germ cells infected with AAV9-RFP from shCtrl or Gm4665-depleted testes by FACS, before performing scRNA-seq.
Single-cell RNA-seq libraries were prepared using Single Cell 3' Library Gel Bead Kit V2 (10x Genomics) following the manufacture’s introduction.

tag: strain background

value: ICR

tag: age

value: post natal day 21 before microinjection

value: RFP+ germ cells


title: Gm4665_2_S1_L001


title: TSH Adenomas TI-2019-001

description:
TSH Adenomas
Adenomas-TI-2019-001
TSH Adenomas


title: CNFPA NF-2018-028

description:
CNFPA
Adenomas-NF-2018-028
CNFPA


title: NC_S1_L001

value: shCtrl


title: ACTH Adenomas CU-2016-003

description:
ACTH Adenomas
Adenomas-CU-2016-003
ACTH Adenomas


title: TSH Adenomas TI-2018-001

description:
TSH Adenomas
Adenomas-TI-2018-001
TSH Adenomas


title: LacZ-3

first: Xu

middle: jia

last: yue

address: NO.3 Dongdan street, Beijing

institute: Peking Union Medical College

library_source: genomic

data_processing:
Library strategy: ChIRP-seq
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,
For each sample, reads from even and odd lanes were aligned separately, and per-base coverage was normalized as if there were 10 M mappable reads. For each base pair of the genome, true coverage of this base in this sample was defined as the minimum coverage of the even lane and odd lane.
Genome-wide signal consists of a combine lane, based on which, a SAM file was generated for peak calling.
Peaks of each sample were called using MACS against its corresponding input with p-value cutoff 1 × 10−5
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include enrichment for each Sample

molecule: genomic DNA

extract_protocol:
Germ cell isolated from the testis of wild-type mouse were cross-linked, lysed and sonicated, and then incubated with probesets of Gm4665.  Following hybridization of biotinylated probesets to Gm4665 transcript, Gm4665-bound chromatin was retrieved. The purified DNA fragments were sequenced using high throughput next generation sequencing (Illumina HiseqXten-PE150)
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

tag: strain

value: Testis

value: post natal day 35


title: LacZ-1


title: TSH Adenomas TI-2018-002

description:
TSH Adenomas
Adenomas-TI-2018-002
TSH Adenomas


title: PRL Adenomas PRL-2018-001

description:
PRL Adenomas
Adenomas-PRL-2018-001
PRL Adenomas


title: TSH Adenomas TI-2017-001

description:
TSH Adenomas
Adenomas-TI-2017-001
TSH Adenomas


title: Non-tumoral gland A18-315

description:
Non-tumoral gland
Control-A18-315
Non-tumoral gland

value: Non-tumoral gland


title: LacZ-2


title: Non-tumoral gland A18-318

description:
Non-tumoral gland
Control-A18-318
Non-tumoral gland


title: Non-tumoral gland Technical replica A18-318T

description:
Non-tumoral gland Technical replica
Control-A18-318T
Non-tumoral gland Technical replica

value: Non-tumoral gland Technical replica


title: Non-tumoral gland A18-310

description:
Non-tumoral gland
Control-A18-310
Non-tumoral gland


title: Input-1


title: LncRNA-20-2


title: LncRNA-20-3


title: LncRNA-20-1


title: Input-2


title: Non-tumoral gland A19-44

description:
Non-tumoral gland
Control-A19-44
Non-tumoral gland


title: Non-tumoral gland A19-33

description:
Non-tumoral gland
Control-A19-33
Non-tumoral gland


title: Non-tumoral gland A19-34

description:
Non-tumoral gland
Control-A19-34
Non-tumoral gland


title: Non-tumoral gland Technical replica A19-33T

description:
Non-tumoral gland Technical replica
Control-A19-33T
Non-tumoral gland Technical replica


title: 24hrs_P4

city: Canberra

first: Regan

last: Ashby

state: ACT

address: University Drive, Bruce

department: Faculty of Science and Technology

country: Australia

institute: University of Canberra

data_processing:
Reads were adaptor stripped using Trimmomatic software (v0.36).
Reads were mapped to the chick genome (GalGal5) using HISAT2 (v2.1).
Counts for ENSEMBL transcripts were obtained using analyzeRNA.pl, script from HOMER package.
Differential gene expression was analysed using EdgeR/limma with sample batch as blocking factor (Bioconductor release 3.6).
Genome_build: GalGal5
Supplementary_files_format_and_content: The CSV file was generated using the data processing steps described above. The table contains raw counts per sample, per condition, per timepoint.

organism: Gallus gallus

source_name: Retina

extract_protocol:
Total RNA was isolated from the retina using the Trizol/chloroform protocol. RNA quality and quantity was assessed on a 2100 Bioanalyser. All samples had an RNA Integrity Number (RIN) greater than 7.0.
Libraries were prepared using the Ultra Directional RNA Library Kit for Illumina following the manufacturer's instructions. Libraries were validated on a 2100 Bioanalyser. Libraries were normalised to 4 ng/µL in 0.1x TE, pooled and sequenced at the Ramaciotti Centre for Genomics (UNSW, Sydney, Australia) on an Illumina NextSeq 500 platform (paired-end, 75 cycles).

treatment_protocol: Male chicks were raised for 6 days under a 12 hours day/night light cycle. On day 7, chicks were randomly assigned to seven groups (age-matched untreated, FDM, FDM + atropine, FDM + pirenzepine, FDM + ADTN, FDM + TPMPA or recovery from FDM). Following 4 or 24 hours after diffuser attachment and/or intravitreal injection, retinae were collected, total RNA extracted and libraries prepared. For the 24-hour timepoint, a repeat injection was given 4 hours prior to collection. For recovery from FDM, chicks wore translucent diffusers for a period of 3 days to induce myopia before removing the device and collecting the retina 4 or 24 hours later.

value: Retina

tag: breed

value: White Leghorn

tag: Sex

value: Male

tag: treatment

value: FDM + Pirenzepine injection, replicate 4

value: Post-hatch day 8

tag: timepoint

value: 24 hours


title: 24hrs_T4

value: FDM + TPMPA injection, replicate 4


title: 24hrs_AD1

value: FDM + ADTN injection, replicate 1


title: 24hrs_AD4

value: FDM + ADTN injection, replicate 4


title: 24hrs_RF1

value: Recovery from FDM, replicate 1


title: 24hrs_T2

value: FDM + TPMPA injection, replicate 2


title: 24hrs_RF3

value: Recovery from FDM, replicate 3


title: 24hrs_RF4

value: Recovery from FDM, replicate 4


title: 24hrs_AD3

value: FDM + ADTN injection, replicate 3


title: 24hrs_T1

value: FDM + TPMPA injection, replicate 1


title: 24hrs_AD2

value: FDM + ADTN injection, replicate 2


title: 24hrs_T3

value: FDM + TPMPA injection, replicate 3


title: 24hrs_P3

value: Retina

value: FDM + Pirenzepine injection, replicate 3


title: 24hrs_P1

value: White Leghorn

value: Male

value: FDM + Pirenzepine injection, replicate 1


title: 24hrs_A4

value: FDM + Atropine injection, replicate 4

value: Post-hatch day 8

value: 24 hours


title: 24hrs_A3

value: FDM + Atropine injection, replicate 3


title: 24hrs_A2

value: FDM + Atropine injection, replicate 2


title: 24hrs_F4

value: Form-deprivation myopia (FDM), replicate 4


title: 24hrs_F3

value: Form-deprivation myopia (FDM), replicate 3


title: 24hrs_F1

value: Form-deprivation myopia (FDM), replicate 1


title: 24hrs_U2

value: Age-matched untreated, replicate 2


title: 24hrs_U1

value: Age-matched untreated, replicate 1


title: 4hrs_RF2

value: Recovery from FDM, replicate 2

value: Post-hatch day 7

value: 4 hours


title: 4hrs_RF3

value: Retina

value: Recovery from FDM, replicate 3


title: 24hrs_P2

value: White Leghorn

value: Male

value: FDM + Pirenzepine injection, replicate 2


title: 4hrs_T4

value: FDM + TPMPA injection, replicate 4


title: 4hrs_T3

value: FDM + TPMPA injection, replicate 3


title: 24hrs_A1

value: FDM + Atropine injection, replicate 1

value: Post-hatch day 8

value: 24 hours


title: 4hrs_P2


title: 4hrs_P3

value: FDM + Pirenzepine injection, replicate 3


title: 4hrs_P1

value: FDM + Pirenzepine injection, replicate 1


title: 4hrs_AD2

value: FDM + ADTN injection, replicate 2


title: 4hrs_T2

value: FDM + TPMPA injection, replicate 2


title: 4hrs_T1

value: FDM + TPMPA injection, replicate 1


title: 4hrs_AD1

value: FDM + ADTN injection, replicate 1

value: Post-hatch day 7


title: 4hrs_A4

value: Retina

value: FDM + Atropine injection, replicate 4

value: 4 hours


title: 4hrs_P4

value: White Leghorn

value: Male

value: FDM + Pirenzepine injection, replicate 4


title: 4hrs_AD4

value: FDM + ADTN injection, replicate 4


title: 4hrs_A3

value: FDM + Atropine injection, replicate 3


title: 4hrs_A2

value: FDM + Atropine injection, replicate 2


title: 24hrs_F2

value: Form-deprivation myopia (FDM), replicate 2

value: Post-hatch day 8

value: 24 hours


title: 4hrs_A1

value: FDM + Atropine injection, replicate 1


title: 24hrs_U3

value: Age-matched untreated, replicate 3


title: 24hrs_RF2

value: Recovery from FDM, replicate 2


title: 4hrs_RF1

value: Recovery from FDM, replicate 1


title: 4hrs_U4

value: Age-matched untreated, replicate 4

value: Post-hatch day 7


title: 4hrs_AD3

value: Retina

value: FDM + ADTN injection, replicate 3


title: 4hrs_U2

value: White Leghorn

value: Age-matched untreated, replicate 2

value: 4 hours


title: 4hrs_U1

value: Male

value: Age-matched untreated, replicate 1


title: 4hrs_U3


title: IP2

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

description: m6A CLIP rep2

data_processing:
Individual samples were processed using the CLIP Tool Kit (CTK) v1.0.9. (Shah et al. 2017). We largely followed recommended user guide lines specific to CTK iCLIP data analysis as described here (https://zhanglab.c2b2.columbia.edu/index.php/ICLIP_data_analysis_using_CTK).
Briefly, 3’adapter sequences [AGATCGGAAGAGCGGTTCAG] were trimmed using cutadapt v1.8. [--overlap = 5 -m 29].
PCR duplicates were removed using a custom perl script, followed by the extraction of the 9 nucleotide miCLIP barcode and its addition to the read name.
All cDNA libraries were filtered for common Drosophila virus sequences using bowtie v1.1.2 [-p 4 -q (-X 1000) --fr --best].
Next, to avoid sequencing read alignment software biases, we decided to map sequencing reads to the Drosophila melanogaster dm6 genome assembly (ensemble v81)  using novoalign, bwa and STAR v2.4.2a. For STAR alignments, we used a custom python script to transform sam alignment files into the expected format for downstream CITS identification. For STAR alignments, we did not consider spliced reads, soft-clipped reads, mismatches and indels near read start and read end, and reads with more than one indel or mismatch.
Then, unique tags were identified using parseAlignment.pl [-v --map-qual 1 --min-len 18 --indel-to-end 2] to extract unique tags, followed by read collapsing using tag2collapse.pl [-v -big --random-barcode -EM 30 --seq-error-model alignment -weight --weight-in-name --keep-max-score --keep-tag-name].
Crosslinking induced mutation sites (CIMS) indicative for the antibody-m6A interaction were identified running CIMS.pl [-big -n 10], and CIMS with FDR < 0.001 were retained.
Crosslinking induced truncations sites were identified using  CITS.pl [-big -p 0.001 --gap 25]. Sites spanning more than 1 nucleotide were removed.
We further filtered identified CIMS and CITS to be reproducible in at least 2 out of 4 replicate m6A-immunoprecipitation samples and not present in identified CITS from the input control sample for each aligner separately. Moreover, CIMS were filtered to have a minimum of 6 unique tags [k > 5], at least three unique substitutions [m > 2], and be prevalent in less than 20% of the coverage [m/k < 0.2] to avoid calling homozygous and heterozygous single nucleotide variants. CIMS sites were found to be almost exclusive C-to-T conversions (n = 6225, 88% ± 5.8%) independent of the alignment software used (3 aligners n = 2677, 2 n = 2411, 1 n = 1137). For a stringent CITS set, we filtered CITS sites (n = 22917) that mostly truncated at A residues ( n = 11897,  52%), and were followed by C residues (CITS-AC  n = 6799, 57%). Two thousand three hundred and two (37%) of C-to-T CIMS overlapped within a 1nt window to CITS-AC sites, suggesting that in many cases the same nucleotide was identified. Together, we considered a set of 13024 C-to-T conversions CIMS and AC truncation CITS across 2464 genes for our final S2 cell miCLIP data set. CITS site were annotated as described before (Wessels et al. 2019). For representation purposes we simplified the annotation categories. All CITS not annotated to 5’UTR, CDS, 3’UTR or intron were summarized in the category ‘other’. Enrichments were calculated relative to median feature proportions (5'UTR = 0.08 (131nt), CDS = 0.78 (1309.5nt), 3'UTR = 0.14 (234nt)) determined previously for S2 cells (Wessels et al. 2019). Enrichments for sites annotated as intronic or other were set to 1.
Alignment parameters:
Novoalign: [-t 85 -l 20 -s 1 -o Native -r None]
BWA: [-t 4 -n 0.06 -q 20]
STAR: [--alignEndsType EndToEnd --runThreadN 4  --outFilterMultimapNmax 10 --outSAMattributes All --outFilterIntronMotifs RemoveNoncanonical  --outReadsUnmapped Fastx --alignSJoverhangMin 12  --outFilterMatchNmin 15  --outFilterMismatchNmax 1 --outFilterMismatchNoverLmax 0.05 --outFilterMultimapScoreRange 3 --alignIntronMax 20000 --seedMultimapNmax 200000 --seedPerReadNmax 30000 --outSAMtype BAM SortedByCoordinate]
Genome_build: dm6

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: S2R+ cells

growth_protocol: S2R+ cells were grown at room temperature in Schneider's medium (Gibco) supplemented with 10% FBS (Sigma) and 1% penicilin-streptomycin (sigma)

extract_protocol:
RNA were harvested using Trizol reagent and mRNA were isolated by two rounds of binding to oligo (dt)25 magnetic beads (NEB). mRNA was fragmented with RNA fragmentation solution (Ambion). Samples IP1, IP2, IP3, IP4 and ctr were immunoprecipitated using anti-m6A antibody. Sample frag-mRNA was purified with RNAClean XP beads (Beckman Coulter).
Library preparation for IP1, IP2, IP3, IP4 and ctr samples was performed as previously described in (Sutandy et al., 2016). Libraries were sequenced on an Illumina NextSeq500. Library preparation for frag_mRNA was performed using the NEBNext Ultra Directional RNA Library Prep Kit.

treatment_protocol: no specific treatment

tag: condition

value: IP

tag: miclip antibody

value: m6A antibody from synaptic systems (lot # 202003/2-82)


title: IP3

description: m6A CLIP rep3


title: 4hrs_F3

value: Form-deprivation myopia (FDM), replicate 3


title: IP4

description: m6A CLIP rep4


title: un-injured (UI), old, replicate 3, 10X chip channel B

city: Berkeley

first: Rebecca

middle: K.

last: Chance

state: CA

department: Molecular and Cell Biology

country: USA

institute: UC Berkeley

description: no lineage trace, propidium iodide sorted cells (alive)

data_processing:
Boying Gong adapted from https://github.com/rkchance/10X-olfactory for 10X v3 chemistry, applied to wholeOE dataset
Genome_build: mm10

source_name: Olfactory Epithelium, YFP+

growth_protocol: olfactory epithelium anatomical dissections were extracted from mice

extract_protocol:
lysates were clarified from alive cells from the sorter
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: in the FACS facility only cells that were alive (PI sorting rule) were taken

tag: mouse strain

value: olfactory epithelium

tag: mouse age

value: 18 months old

tag: animal sex (#)

value: Female (1) / Male (1)


title: un-injured (UI), old, replicate 3, 10X chip channel A


title: un-injured (UI), young, replicate 3, 10X chip channel B

value: 2 months old


title: un-injured (UI), young, replicate 3, 10X chip channel A


title: 4hrs_F4

value: Form-deprivation myopia (FDM), replicate 4


title: un-injured (UI), old, replicate 2, 10X chip channel A


title: un-injured (UI), young, replicate 2, 10X chip channel B


title: 4hrs_F1

value: Form-deprivation myopia (FDM), replicate 1


title: 4hrs_F2

value: Form-deprivation myopia (FDM), replicate 2

value: Post-hatch day 7


title: un-injured (UI), old, replicate 1, 10X chip channel B


title: HA36_TKO_DNMT3A2_R836K_r1

city: Utrecht

first: Tuncay

last: Baubec

address: Padualaan 8

department: Department of Biology

institute: Utrecht University

description: WGBS

data_processing:
Sequencing reads were pre-processed and trimmed using cutadapt v1.16 and sickle v1.33
Trimmed reads were mapped against the mm9 mouse assembly using bwa-meth v0.2.0  running bwa v0.7.12-r1039
Duplicates were removed with Picard MarkDuplicates (picard-tools v1.96, http://broadinstitute.github.io/picard/) with `REMOVE_DUPLICATES=TRUE and REMOVE_SEQUENCING_DUPLICATES=TRUE` flags.
Alignments with MAPQ > 40 were used as input to methylation calling with methyldackel v0.3.0-3-g084d926 (https://github.com/dpryan79/MethylDackel) (using HTSlib v1.2.1) in `cytosine_report` mode for all cytosines in the genome both CpG and CpH contexts (`extract -q 40 --cytosine_report --CHH –CHG`).
Genome_build: mm9
Supplementary_files_format_and_content: Processed tab delimited file contains cytosine report with following information: chromosome, nucleotide position, reported methylated cytosines, reported unmethylated cytosines, sequence context, exact sequence

source_name: Mouse Embryonic Stem Cells

growth_protocol: ES cells were were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol.

extract_protocol:
Genomic DNA extraction, followed by phenol/chloroform extraction and ethanol precipitation. RNaseA treatment was performed for 30 min at 37C
Prior library preparation unmethylated Lambda phage DNA and SssI-methylated T7 DNA were spiked-in to genomic DNA samples to control bisulphite conversion rates. For WGBS, 10ug of DNA was sonicated to ca 500bp using a Bioruptor Pico. DNA was end-repaired and A-tailed using the NEB-Ultra Illumina library preparation kit (E7370). DNA fragments were ligated to methylated adapters (NEB E7535) following the NEB Ultra protocol. After adapter removal using Ampure xp beads (Beckman Coulter), DNA was converted using the Qiagen Epitect bisulphite conversion kit following the FFT sample protocol. After conversion library PCR amplification was performed with 10 cycles following NEB Ultra kit protocol, and cleaned up using Ampure xp beads.

value: embryonic stem cells

tag: genotype


title: HA36_TKO_DNMT3B1_r2

description: WGBS


title: frag_mRNA_input_control

description: fragmented mRNA input control for comparative analysis with IP samples

value: fragmented mRNA input control


title: HA36_TKO_DNMT3A2_R836K_r2

description: WGBS


title: un-injured (UI), old, replicate 1, 10X chip channel A

tag: tissue


title: un-injured (UI), young, replicate 1, 10X chip channel A

value: 2 months


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E5_AD007

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

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.

value: brain

tag: source

value: RSP

tag: target

value: STR

tag: gender

value: male


title: non-crosslinked IP control

description: non-crosslinked control to check for background mRNA binding

value: non-crosslinked IP control

value: m6A antibody from synaptic systems (lot # 202003/2-82)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E1_AD012

value: female


title: IP1

description: m6A CLIP rep1

value: IP


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E1_AD010


title: un-injured (UI), young, replicate 2, 10X chip channel A

value: olfactory epithelium

value: Female (1) / Male (1)


title: Input-3

value: ICR

value: Testis

value: post natal day 35


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E10_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E1_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E11_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E10_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E10_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E10_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D9_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E12_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D7_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D9_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D7_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D9_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D7_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D7_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E4_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D5_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D6_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E11_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_E1_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D6_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D5_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D6_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D11_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D11_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D10_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D5_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D10_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D10_AD012


title: un-injured (UI), young, replicate 1, 10X chip channel B


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D11_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C9_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C7_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C9_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C7_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C7_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C7_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D5_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D10_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C6_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C6_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C6_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C5_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C5_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C5_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_D1_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C5_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C4_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C4_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C4_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C6_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B9_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B9_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B9_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C12_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C10_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C10_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C10_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C12_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C10_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B9_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B7_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C11_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B7_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B6_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B6_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B5_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B6_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B4_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B5_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B5_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B5_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B4_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B7_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B7_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_C12_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B4_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B3_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B4_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B12_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B12_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B12_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B11_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B10_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B10_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B11_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B11_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B10_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B12_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B11_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A9_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_B10_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A9_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A9_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A7_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A7_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A7_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A7_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A6_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A6_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A6_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A5_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A5_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A5_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A5_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A4_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A9_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A4_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A4_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A10_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A11_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A12_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A11_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A11_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A11_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A12_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A6_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A10_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A10_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A10_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H9_AD010

value: AUD


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H9_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H9_AD012


title: un-injured (UI), old, replicate 2, 10X chip channel B

value: 18 months old


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H7_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H7_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H6_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A12_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H7_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H6_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H5_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H6_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H5_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H5_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H7_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H4_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H4_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H3_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H2_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H3_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H3_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H2_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H4_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H2_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P3_180313_P4_A4_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H12_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H2_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H1_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H1_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H1_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H11_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H11_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H11_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H4_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H10_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H10_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G9_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G7_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G9_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G7_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_H12_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G5_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G5_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G6_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G4_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G4_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G3_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G3_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G1_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G1_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G3_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G3_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G1_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G4_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G6_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G1_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G12_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G12_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G11_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G11_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G11_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G10_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G10_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_G10_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F9_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F9_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F9_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F7_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F7_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F7_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F7_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F3_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F3_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F1_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F3_AD007


title: Atf3-cJun_5caC_rep2

type: protein

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

description: Atf3-cJun PBM experiment, 5caC

hyb_protocol: The double-stranded arrays were blocked with 4% milk for 1 hour and washed with 0.1% Tween-20 in 1x PBS.  Freshly synthesized protein (25 µL) was mixed with 125 µL of protein binding reaction mixture consisting of 4% milk in 1x PBS, 50 ng of salmon testes DNA and 0.2 µg/µL bovine serum albumin and added to double-stranded array.  The protein binding reactions were carried out in hydration chamber for 1 hour followed by one wash with 0.5% Tween-20 in 1xPBS.  The protein bound array was incubated with Alexa Fluor 647 conjugated Anti-GST antibody for 1 hour, followed by three washes with 0.05 % Tween-20.  Finally array slides were washed and dried in 1x PBS and scanned using an Agilent Sure Scan II scanner.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 micron resolution. Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 30% PMT (low). The  resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used. Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing:
For all possible 65,536 8-mers, a transformed 8-mer median intensity (Z-score) was calculated from the median signal intensity across array probes containing each 8-mer.  8-mer Z-scores of the modified strand (the reverse complement of the array probe sequence) were used for downstream analyses.
Some of the probes on the array contain multiple 8-mers that are targeted by the proteins which allows for analysis of ~65k 8-mers from ~40K probes.

molecule: protein

source_name: Atf3-cJun, HK design

label_protocol: 180 ng of plasmid containing each binding domain were used to express proteins using PureExpress in-vitro transcription translation kit (NEB) in 25 µL reaction volume as per manufacturer’s instructions.

extract_protocol: The bZIP DNA binding domain (DBD) of of mouse Creb1, Atf2, Zta, and cJun were obtained from Dr. Timothy Hughes, University of Toronto, Canada as chimeric GST constructs.  CREB1, ATF2, and cJun were cloned into the pETGEXCT (C-terminal GST) vector.  Zta was cloned into a modified pDEST15 MAGIC vector (N-terminal GST) (Sharrocks 1994).  The DBD of ATF3 and cFOS were obtained as  constructs cloned into a pT5 expression plasmid  cloned into a modified pDEST15 MAGIC vector.

treatment_protocol: The single-stranded oligonucleotide microarrays were double-stranded by primer extension as described in Badis et al. Science (2009).   Arrays were double-stranded using either cytosine, 5-methylcytosine (5mC, NEB), 5-hydroxymethylcytosine (5hmC, Zymo Research), 5-formylcytosine (5fC, TriLink Biotechnologies),or 5-carboxylcytosine (5caC, TriLink Biotechnologies) . The resulting double-stranded DNA on the array thus contained probes with either cytosine on both strands or modified cytosine (5mC/5hmC/5fC/5caC) on one strand and cytosine on the second strand. This results in a hemi-methylated or hemi-hydroxymethylated state.

tag: dbd

value: bZIP

tag: protein

tag: double-stranding treatment


title: Atf2_5fC_rep1

description: Atf2 PBM experiment, 5fC

source_name: Atf2, HK design


title: cFos-cJun_5caC_rep2

description: cFos-cJun PBM experiment, 5caC

source_name: cFos-cJun, HK design

value: cFos-cJun


title: Atf2_5fC_rep2

description: Atf2 PBM experiment, 5fC


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F1_AD008

tag: strain

tag: age

value: brain


title: Zta_5caC_rep1

description: Zta PBM experiment, 5caC

source_name: Zta, HK design

value: Zta


title: Zta_5caC_rep2

description: Zta PBM experiment, 5caC


title: Atf2_5caC_rep2

description: Atf2 PBM experiment, 5caC


title: Zta_5fC_rep2

description: Zta PBM experiment, 5fC


title: cFos-cJun_5fC_rep1

description: cFos-cJun PBM experiment, 5fC


title: Creb1_5fC_rep2

description: Creb1 PBM experiment, 5fC

source_name: Creb1, HK design


title: Atf3-cJun_5caC_rep1

description: Atf3-cJun PBM experiment, 5caC


title: Atf3-cJun_5fC_rep1

description: Atf3-cJun PBM experiment, 5fC


title: Creb1_5fC_rep1

description: Creb1 PBM experiment, 5fC


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F1_AD007

value: STR


title: Creb1_5caC_rep1

description: Creb1 PBM experiment, 5caC


title: Zta_5fC_rep1

description: Zta PBM experiment, 5fC


title: Atf3-cJun_5fC_rep2

description: Atf3-cJun PBM experiment, 5fC


title: cFos-cJun_5hmC_rep2

description: cFos-cJun PBM experiment, 5hmC


title: Creb1_5hmC_rep2

description: Creb1 PBM experiment, 5mC


title: Creb1_5caC_rep2

description: Creb1 PBM experiment, 5caC


title: cFos-cJun_5caC_rep1

description: cFos-cJun PBM experiment, 5caC


title: Creb1_5hmC_rep1

description: Creb1 PBM experiment, 5mC


title: Atf2_5caC_rep1

description: Atf2 PBM experiment, 5caC


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F10_AD012


title: cFos-cJun_5fC_rep2

description: cFos-cJun PBM experiment, 5fC


title: cFos-cJun_5hmC_rep1

description: cFos-cJun PBM experiment, 5hmC


title: Atf3-cJun_5hmC_rep2

description: Atf3-cJun PBM experiment, 5hmC


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F10_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F10_AD008

value: male


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E9_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_F10_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E9_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E7_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E9_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E7_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E9_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E7_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E6_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E6_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E6_AD008


title: Atf2_5hmC_rep2

description: Atf2 PBM experiment, 5hmC


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E5_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E5_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E6_AD007


title: Atf3-cJun_5mC_rep2

description: Atf3-cJun PBM experiment, 5mC


title: cFos-cJun_5mC_rep1

description: cFos-cJun PBM experiment, 5mC


title: Creb1_5mC_rep2

description: Creb1 PBM experiment, 5mC


title: Atf2_5hmC_rep1

description: Atf2 PBM experiment, 5hmC


title: cFos-cJun_5mC_rep2

description: cFos-cJun PBM experiment, 5mC


title: Atf3-cJun_5hmC_rep1

description: Atf3-cJun PBM experiment, 5hmC


title: Zta_C_rep1

description: Zta PBM experiment, cytosine

value: cytosine


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E1_AD010


title: Creb1_C_rep2

description: Creb1 PBM experiment, cytosine


title: Atf3-cJun_C_rep1

description: Atf3-cJun PBM experiment, cytosine


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E1_AD008


title: Zta_C_rep2

description: Zta PBM experiment, cytosine


title: Trachea_BCR

city: Guangzhou

first: Jin-Xin

last: Bei

state: Guangdong

address: 651 Dongfeng Road East, Yuexiu District, Guanzhou, P.R. China

institute: Sun Yat-sen University Cancer Center

data_processing:
Illumina-implemented software bcl2fastq (version v2.19.0.316) was used for basecalling.
TCR/BCR reads were aligned to human reference VDJ dataset (http://cf.10Xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-2.0.0.tar.gz) using CellRanger (“vdj” option; version 3.1.0; 10x Genomics).
Processed data includes full-length information of TCR and BCR sequences of each cell.

source_name: An adult male donor who died of a traumatic brain injury

extract_protocol:
Viable single cells were prepared from the tissue samples of 15 different organs of a research-consented adult donor.
The concentration of single cell suspension was determined using a Cellometer Auto 2000 instrument (Cellometer) and adjusted to 1,000 cells/μl. Approximately 14,000 cells were loaded into a CHROMIUM instrument (10x Genomics, CA, USA) according to the standard protocol of the Chromium single cell V(D)J kit (v1) in order to capture 5,000 ~ 10,000 cells per channel. In brief, mRNA transcripts from each sample were ligated with barcoded indexes at 5'-end and reverse transcribed into cDNA, using GemCode technology (10x Genomics, USA). cDNA libraries including the enriched fragments spanning the full-length V(D)J segments of T cell receptors (TCR) or B cell receptor (BCR), and 5'-end fragments for gene expression were separately constructed, which were subsequently subjected for high-throughput sequencing.

value: Trachea

value: 31 years


title: Stomach_BCR

value: Stomach


title: Creb1_5mC_rep1

description: Creb1 PBM experiment, 5mC


title: cFos-cJun_C_rep2

description: cFos-cJun PBM experiment, cytosine


title: Atf2_5mC_rep1

description: Atf2 PBM experiment, 5mC


title: Atf2_5mC_rep2

description: Atf2 PBM experiment, 5mC


title: cFos-cJun_C_rep1

description: cFos-cJun PBM experiment, cytosine


title: Creb1_C_rep1

description: Creb1 PBM experiment, cytosine


title: Atf2_C_rep2

description: Atf2 PBM experiment, cytosine


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E2_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E4_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E1_AD007


title: Spleen_BCR

value: Spleen


title: Small.intestine_BCR

value: Small intestine


title: Atf3-cJun_C_rep2

description: Atf3-cJun PBM experiment, cytosine


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E11_AD010

value: female


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E11_AD012


title: Rectum_BCR

value: Rectum


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E11_AD008


title: Marrow_BCR

value: Marrow


title: Skin_BCR

value: Skin


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E11_AD007

value: AUD


title: Lymph.node_BCR

value: Lymph node


title: Atf2_C_rep1

description: Atf2 PBM experiment, cytosine

value: bZIP


title: Atf3-cJun_5mC_rep1

description: Atf3-cJun PBM experiment, 5mC


title: Heart_BCR

value: Heart


title: Liver_BCR

value: Liver


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E10_AD012

value: brain

value: STR


title: Esophagus_BCR

value: Esophagus

value: male


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D9_AD012


title: Blood_BCR

value: Blood

value: 31 years


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D7_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D9_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D9_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D9_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D7_AD010


title: Stomach_TCR

value: Stomach


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D7_AD007


title: Muscle_BCR

value: Muscle


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_E10_AD010

value: female


title: Spleen_TCR

value: Spleen


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D6_AD012


title: Small.intestine_TCR

value: Small intestine


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D6_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D5_AD010


title: Rectum_TCR

value: Rectum


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D5_AD012

value: AUD


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D5_AD008


title: Common.bile.duct_BCR

value: Common bile duct


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D4_AD007


title: Lymph.node_TCR

value: Lymph node


title: Muscle_TCR


title: Bladder_BCR

value: Bladder


title: Trachea_TCR

value: Trachea


title: Liver_TCR

value: Liver


title: Marrow_TCR

value: Marrow


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D2_AD010

value: brain

value: STR


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D3_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D7_AD008

value: male


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D1_AD010


title: Heart_TCR

value: Heart

value: 31 years


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D1_AD008


title: Esophagus_TCR

value: Esophagus


title: Common.bile.duct_TCR


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D6_AD010

value: female


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D10_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D10_AD010


title: Skin_TCR

value: Skin


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_D10_AD007


title: Bladder_TCR


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C9_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C9_AD008


title: angveg12

city: Cambridge

first: Michael

last: Nagle

state: MA

address: 1 Portland Street

department: Internal Medicine Research Unit

institute: Pfizer

data_processing:
Reads were assessed for quality and aligned to the GRCm38 mus musculus genome using STAR (v.2.5.3a) with these options selected: --alignSJDBoverhangMin 1 --outFilterMismatchNoverLmax 0.05 --outFilterScoreMinOverLread 0.90 --outFilterMatchNminOverLread 0.90 --alignIntronMax 1000000. Quantmode TranscriptomeSam was also selected to allow for input to Salmon for read counts
Aligned reads were quantified using Salmon (v.0.12.0) in alignment-based mode with gcBias option selected and mapped to the Ensembl 95 mus musculus gene annotation.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file containing gene summarized TPM values, with samples across columns and genes, given by ensembl identifiers, by row

extract_protocol:
Cardiomyocytes, lymphatic endothelial cells and blood endothelial cells were isolated from mouse heart and lymphatic endothelial cells were isolated from mouse diaphragm using an optimized protocol with FACS
Total RNA was converted into cDNA using the Smart-Seq ultra low input RNA kit and cDNA was converted into libraries using Nextera DNA XT Library Prep Kit

treatment_protocol: Angiotensin II infusion was used to induce chronic cardiac dysfunction and VEGFCc156s, a lymphangiogenic therapy, was infused concomintantly with angiotensin II as a treatment for some of the animals.

value: heart

tag: cell type

value: cardiomyocytes

tag: treatment

value: angiotensin II and VEGFCc156s

tag: age (months)

tag: animal id

tag: sequencing batch


title: angveg9

value: lymphatic endothelial cells


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C9_AD007

value: AUD


title: angveg10

value: blood endothelial cells


title: angveg11

value: diaphragm


title: angveg8


title: angveg7


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C7_AD010


title: angveg5


title: angveg4


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C7_AD007


title: angveg6


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C6_AD012


title: Blood_TCR

value: Blood


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C6_AD008


title: angveg3


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C6_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C6_AD007


title: angii20

value: angiotensin II


title: angveg1


title: angveg2


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C5_AD012

value: brain


title: angii19


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C5_AD010

value: STR


title: angii18


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C5_AD008

value: male


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C7_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C9_AD010


title: angii17


title: angii16


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C4_AD012


title: angii15


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C4_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C4_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C12_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C7_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C12_AD008


title: angii12


title: angii13


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C12_AD007


title: angii11


title: angii10


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C11_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C11_AD008


title: angii8


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C11_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C10_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C11_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C10_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C10_AD008


title: angii7


title: angii5


title: angii4


title: angii6


title: angii14


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_C10_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B9_AD010


title: angii2


title: angii1


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B9_AD012


title: angii3


title: ctrl16

value: Control


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B9_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B7_AD012


title: angii9


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B7_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B7_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B7_AD010


title: ctrl14


title: ctrl15


title: ctrl12


title: ctrl11


title: ctrl13


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B6_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B6_AD012


title: ctrl8


title: ctrl6


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B6_AD008


title: ctrl7


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B5_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B5_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B9_AD008


title: ctrl5


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B5_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B4_AD012


title: ctrl4


title: ctrl2


title: ctrl3


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B4_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B4_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B12_AD012


title: WT_aorta_2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: repeat 2 -Total RNA was prepared using isolated mouse aortic SMC of wild-type (WT) amice  after 18 days tamoxifen injection

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC. Reaper version 15-065 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides.
Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.5.2b with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.14.1. Only genes with a minimum fold change of +- 1.5 (log2 +-0.59), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
The Ensemble annotation was enriched with UniProt data (release 24.03.2017) based on Ensembl gene identifiers.
Genome_build: mm10
Supplementary_files_format_and_content: library-size normalized counts

source_name: primary mouse aortic SMC of wild-type (WT) amice  after 18 days tamoxifen injection

extract_protocol:
Total RNA was isolated using the RNeasy lipid tissue Mini Kit (Qiagen, Valencia, CA, USA), and DNA was removed using the QIAGEN RNase-Free DNaseSet following the manufacturer’s instructions.
200ng of total RNA was used as starting material for ribosomal depletion with RiboGone-Mammalian (Clontech) followed by library preparation using SMARTer Stranded Total RNA Sample Prep Kit (Clontech).

value: aortic smooth muscle cells

value: WT


title: KO_aorta_1

description: repeat 1 -Total RNA was prepared using isolated mouse aortic SMC of  Sm-Yap/Taz-KO mice (KO) after 18 days tamoxifen injection

source_name: primary mouse aortic SMC of  Sm-Yap/Taz-KO mice (KO) after 18 days tamoxifen injection

value: Yap/Taz-KO


title: WT_aorta_1

description: repeat 1 -Total RNA was prepared using isolated mouse aortic SMC of wild-type (WT) amice  after 18 days tamoxifen injection


title: ctrl10


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B12_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B12_AD007


title: KO_aorta_2

description: repeat 2 -Total RNA was prepared using isolated mouse aortic SMC of Sm-Yap/Taz-KO mice (KO) after 18 days tamoxifen injection


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B12_AD010

value: female


title: ctrl9

value: heart


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B5_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B11_AD012


title: sgKDM5A_REP2

city: Boston

first: Matthew

last: Oser

address: 450 Brookline Avenue, Mayer 457

institute: Dana-Farber Cancer Institute

data_processing:
Basecalls
For RNA-Seq: gene counts were done using STAR (v2.5.1b) {Dobin A., etal (2013), Bioinformatics 29: 15.} and normalized gene counts (RPKM) were calculated using Cufflinks (v2.2.1) {Trapnell C., etal (2010), Nat. Biotech. 28: 511.}. Analysis was performed using the VIPER snakemake pipeline {Cornwell M., etal (2018), BMC Bioinformatics 19: 135.}
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-Seq, cufflinks file shows normalized RPKM values.

source_name: GLC16 small cell lung cancer cells engineered to express Cas9

growth_protocol:
GLC16 cells engineered to express Cas9 (plentiCAS9-P2A-Blast) were counted and plated at 2 X 10^6 cells/mL in 1 mL lentivirus with 8 ug/mL polybrene and centrifuged at 434 x g for 2 hours at 30 C.
Day 4 after infection, cells were selected with 1 ug/mL of puromycin. Media was subsequently changed every 3 days. On day 11 after infection, cells were plated at 200,000 cell/mL in 8 mLs on a petri dish and harvested for RNA on day 14 after infection.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen #74106) per the manufacturer's instructions
Libraries were constructed as per the manufacturers instructions. For RNASeq: 500 ng RNA was used with the Illumina stranded total RNASeq protocol; whereas, for ChIP-Seq the Illumina Nextera protocol was used.

tag: cell line

value: small cell lung cancer

tag: genotype/variation

value: Infected with lentivirus plentiguide puro containing an sgRNA targeting KDM5A


title: sgControl_REP1

value: Infected with lentivirus plentiguide puro containing non-targeting sgRNA (sgControl C0111)


title: sgKDM5A_REP1


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B11_AD010

value: AUD


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B11_AD008


title: sgControl_REP2


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B10_AD012


title: Glucose-free media IP Rep2

first: Amy

middle: Si-Ying

last: Lee

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

data_processing:
Reads were quality filtered and adapter trimmed using Cutadapt.
Trimmed reads were mapped to the human genome (GRCh38) using HiSat2.
Mapping was converted to indexed bam files using SAMtools.
In R Studio, mapped reads were summarized to gene-level counts using SummarizeOverlaps from GenomicAlignments
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx, RPKM

source_name: HEK293T cells expressing eIF3d-TEV

growth_protocol: HEK293T cells expressing eIF3d-TEV were grown in complete media (DMEM+10%FBS) or glucose-free media (glucose-free DMEM + 10% dialyzed FBS)

extract_protocol:
cDNA libraries were constructed from polyA-containing RNA using standard RNA-Seq library protocol
Subunit-Seq

value: expressing eIF3d-TEV

tag: growth

value: glucose-free media

tag: antibody

value: anti-HA


title: Glucose-free media IP Rep1


title: ctrl1

tag: tissue

value: lymphatic endothelial cells


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B10_AD008

value: brain

tag: source

tag: target


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B10_AD010

value: STR

tag: gender


title: Glucose-free media Input Rep2

value: input


title: Complete media IP Rep2

value: complete media


title: Glucose-free media Input Rep1


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B10_AD007

value: male


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A9_AD012


title: Complete media IP Rep1


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A9_AD010


title: Complete media Input Rep1


title: Complete media Input Rep2


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A7_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A7_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A7_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_B11_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A7_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A6_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A6_AD010


title: HH779 AR

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

country: Italy

institute: Università degli Studi di Udine

data_processing:
Basecalls performed using the ShortRead R/Biocoductor package
Quality, adapters and contamination filtering were performed using the ERNE-FILTER and the Cutadapt command-line tools
The STAR aligner was used to align reads to the NCBI GRCh38 human genome reference assembly
Transcript assembly and the number of reads per gene were determined using Stringtie (RNA-seq)
Differentially expressed genes were identified using the DESeq2 R/Bioconductor package. Extended gene annotations (including HGNC gene symbol, description and transcript type) were obtained using the biomaRt R/Bioconductor package
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample (RNA-seq)

source_name: Explanted failing heart

growth_protocol: Isolation and cell growth as in: Cesselli, D.; D'Aurizio, F.; Marcon, P.; Bergamin, N.; Beltrami, C.A.; Beltrami, A.P. Cardiac stem cell senescence. Methods in molecular biology 2013, 976, 81-97, doi:10.1007/978-1-62703-317-6_7.

extract_protocol:
RNA was extracted with RNeasy (Qiagen), according to manufacturer’s instructions
RNA libraries were prepared for single-end sequencing following the TruSeq Stranded mRNA kit Illumina protocol, loading 100 ng RNA per sample

treatment_protocol: None performed

value: Atrial heart tissue

tag: tissue type

value: End stage ischemic heart disease

value: Pericytes


title: HH801 AR


title: HH815 AR


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A6_AD008


title: HH734 AR


title: HH789 AR


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A6_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A5_AD012

value: female


title: GR50 AD

source_name: Donated heart

value: Healthy tissue


title: GR128 AD


title: GR96 AD


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A5_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A5_AD010


title: GR146 AD


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A9_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A5_AD007


title: Adult_DP_ELW33

city: Taichung

first: Yung-Chih

last: Lai

address: 7F., No. 6, Xueshi Road, North District

department: Integrative Stem Cell Center

country: Taiwan

institute: China Medical University Hospital

data_processing:
Low quality of sequencing bases were trimmed based on the Phred+33 quality score (> 20) from both of the 5'- and 3'-ends of reads. After trimming, reads are discarded, if they are shorter than 50bp, or have one or more ambiguous base.
RefGene annotation were downloaded from the UCSC Genome Browser on 2016.2.6.
The alignment, quantification, normalization, and differential expression analysis were performed by STAR 2.4.1d, htseq-count 0.6.0, TMM, and edgeR 3.10.5, respectively.
Genes with count-per-million (CPM) values above 1 in at least two samples were retained, and genes with no or low expression levels were discarded.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: The tab-delimited text files: (1) 8 files with count values of 26669 genes for each sample produced by htseq-count (2) 1 file with count-per-million (CPM) values of 16623 genes produced by edgeR

source_name: scalp hair follicles

extract_protocol:
total RNA with primers allows for preferential priming of non-rRNA sequences with reduced number of reads from rRNA
NuGEN Ovation RNA-Seq System V2
NuGEN Ovation Ultralow Library Systems V2 kit

value: Adult

value: Dermal papilla (DP)

tag: sample label


title: Adult_DP_ELW30


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A4_AD010

tag: strain

value: AUD


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A4_AD012

tag: age


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A3_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A4_AD008


title: Fetus_IFD_ELW28

value: Fetus

value: Interfollicular dermis (IFD)


title: Fetus_DSC_ELW27

value: Dermal sheath cup (DSC)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A3_AD010


title: Fetus_DSC_ELW25


title: Fetus_DP_ELW24


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A3_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A1_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A12_AD008


title: BT12 cells, mithramycin 18h_MMAC, RNA-seq

city: Philadelphia

first: Patrick

last: Grohar

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Libraries were sequenced using 1x75 bp sequencing on the Illumina NextSeq 500 platform at the Van Andel Research Institute.  Data were demultplexed using bcl2fastq v2.20.0.
Supplementary_files_format_and_content: Text file containing filtered gene transcripts per million matrix (TPM) from all samples.

source_name: Atypical Teratoid/Rhabdoid Tumor

growth_protocol: BT12 cells were grown in RPMI-1640 medium (Invitrogen) supplemented with 10% fetal bovine serum (Gemini Bio-Products), 2 mM L-glutamine (Invitrogen), 100 U/mL penicillin and 100 μg/mL streptomycin (Invitrogen). Cell lines were maintained at less than 80% confluency at 37°C and 5% CO2 and confirmed to be mycoplasma negative every 6-months.

extract_protocol:
RNA was extracted with the RNeasy kit (Qiagen).
Sequencing libraries were prepared using the Kapa Biosystems stranded mRNA-Seq kit for the Illumina platform.

treatment_protocol: BT12 cells were treated with 100nM mithramycin for 8-hours or 18-hours continous treatment then collected.

value: Mithramycin

tag: timepoint

tag: replicate


title: Fetus_DP_ELW26


title: HH797 AR

tag: cell type


title: BT12 cells, mithramycin 18h_MMAA, RNA-seq

tag: treatment


title: BT12 cells, mithramycin 18h_MMAB, RNA-seq


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A12_AD007

value: brain


title: BT12 cells, mithramycin 8h_MMAC, RNA-seq


title: BT12 cells, mithramycin 8h_MMAB, RNA-seq


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A11_AD008

value: STR


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A11_AD007


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A11_AD010


title: BT12 cells, SolvC, RNA-seq

description: SolvC

value: Solvent


title: BT12 cells, mithramycin 8h_MMAA, RNA-seq


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A10_AD012


title: BT12 cells, SolvB, RNA-seq

description: SolvB


title: BT12 cells, SolvA, RNA-seq

description: SolvA


title: Fetus_IFD_ELW29


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A10_AD010


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A11_AD012


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A10_AD008


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A10_AD007


title: BT12 cells, mithramycin 18h_C, ATAC-seq

data_processing:
Libraries were sequenced using 2x75 bp sequencing on the Illumina NextSeq 500 platform at the Van Andel Research Institute.  Data were demultplexed using bcl2fastq v2.20.0.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files for raw and lambda corrected (lambda_corrected) peaks from all samples.

extract_protocol:
ATAC-seq samples were extracted as described in Corces et al., Nature Methods, 2017.
ATAC-seq libraries were prepared as described in Buenrostro et al., Corces et al., Nature Methods, 2017 with the addition of lambda phage and phiX spike-ins.


title: BT12 cells, mithramycin 18h_A, ATAC-seq


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P1_180313_P2_A12_AD010


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H9_AD012

value: AI


title: BT12 cells, mithramycin 18h_B, ATAC-seq


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H9_AD010


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H9_AD008

value: male


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H9_AD007


title: BT12 cells, mithramycin 8h_C, ATAC-seq


title: BT12 cells, mithramycin 8h_B, ATAC-seq


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H9_AD006

value: ACA


title: BT12 cells, Solv_C, ATAC-seq


title: BT12 cells, Solv_B, ATAC-seq


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H9_AD002


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H9_AD004


title: BT12 cells, Solv_A, ATAC-seq


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H8_AD012


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H8_AD010


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H8_AD006


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H8_AD004


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H8_AD002


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H6_AD012


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H8_AD001


title: BT12 cells, mithramycin 8h_A, ATAC-seq


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H6_AD008


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H6_AD007


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H6_AD006


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H6_AD010


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H6_AD004


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H9_AD001


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H6_AD002


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H6_AD001


title: STAT6-KO _ bone marrow -derived CD11b+ cells _MI 2 weeks

city: Shanghai

first: Xiangdong

last: Yang

state: China

address: 180 Fenglin Road, Xuhui District, Shanghai

institute: Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University

description:
Gene expression in bone marrow-derived CD11b+ cells of STAT6-KO mice after MI for 2 weeks
DM23

hyb_protocol: Microarray hybridization and scanning were performed with the Agilent Scanner G2505C. Pooled samples from each mixture were hybridized to three arrays.

data_processing: Raw CEL files were subject to an established battery of quality tests using the Bio-conductor package. Arrays were normalized using GCRMA algo-rithm.

source_name: STAT6-KO, bone marrow -derived CD11b+ cells, MI 2 weeks

label_protocol: cRNA synthesis and labeling were performed according to the protocol of Agilent's Amp Labeling protocol (version 5.7) by KangChen Bio-tech.

extract_protocol: RNA was prepared using the TRIzol reagent (Invitrogen, MA, USA) following the manufacturer's recommendations. RNA concentration and integrity were measured using standard pro-tocols.

treatment_protocol: The model of acute myocardial infarction. After the mice were sacrificed, CD11b+ cells were isolated from the spleen or bone marrow from mice, and the number of cells per tube was more than 5 x 106. CD11b+ cells of each sample were isolated from the spleen or bone marrow of 5 mice.

tag: genotype

value: bone marrow

tag: group

value: MI + 2 weeks


title: STAT6-KO _ bone marrow -derived CD11b+ cells _MI 1 week

description:
Gene expression in bone marrow-derived CD11b+ cells of STAT6-KO mice after MI for 1 week
DM22

scan_protocol: Microarray hybridization and scanning were performed with the Agilent Scanner G2505C. Pooled samples from each mixture were hybridized to three arrays.

source_name: STAT6-KO, bone marrow -derived CD11b+ cells, MI 1 week

value: MI + 1 week


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H5_AD008

source_name: C57BL/6J P56 Mouse Brain


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H5_AD006

value: female


title: HDC-KO _ bone marrow -derived CD11b+ cells _MI 1 week

description:
Gene expression in bone marrow-derived CD11b+ cells of HDC-KO mice after MI for 1 week
DM18

source_name: HDC-KO, bone marrow -derived CD11b+ cells, MI 1 week

value: HDC-KO


title: HDC-KO _ bone marrow -derived CD11b+ cells _MI 2 weeks

description:
Gene expression in bone marrow-derived CD11b+ cells of HDC-KO mice after MI for 2 weeks
DM19

source_name: HDC-KO, bone marrow -derived CD11b+ cells, MI 2 weeks


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H5_AD004


title: STAT6-KO _ bone marrow -derived CD11b+ cells _MI 4 weeks

description:
Gene expression in bone marrow-derived CD11b+ cells of STAT6-KO mice after MI for 4 weeks
DM24

source_name: STAT6-KO, bone marrow -derived CD11b+ cells, MI 4 weeks

value: MI + 4 weeks


title: HDC-KO_ bone marrow-derived CD11b+ cells _control

description:
Gene expression in bone marrow-derived CD11b+ cells of HDC-KO control mice
DM17

source_name: HDC-KO, bone marrow -derived CD11b+ cells, control

value: control


title: STAT6-KO_ bone marrow-derived CD11b+ cells _control

description:
Gene expression in bone marrow-derived CD11b+ cells of STAT6-KO control mice
DM21

source_name: STAT6-KO, bone marrow -derived CD11b+ cells, control


title: HDC-KO _ bone marrow -derived CD11b+ cells _MI 4 weeks

description:
Gene expression in bone marrow-derived CD11b+ cells of HDC-KO mice after MI for 4 weeks
DM20

source_name: HDC-KO, bone marrow -derived CD11b+ cells, MI 4 weeks


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H5_AD002


title: WT_ bone marrow -derived CD11b+ cells _MI 4 weeks

description:
Gene expression in bone marrow-derived CD11b+ cells of WT mice after MI for 4 weeks
DM16

source_name: WT, bone marrow -derived CD11b+ cells, MI 4 weeks

value: WT


title: WT_ bone marrow -derived CD11b+ cells _MI 2 weeks

description:
Gene expression in bone marrow-derived CD11b+ cells of WT mice after MI for 2 weeks
DM15

source_name: WT, bone marrow -derived CD11b+ cells, MI 2 weeks


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H5_AD001


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H2_AD010


title: STAT6-KO _ spleen-derived CD11b+ cells _MI 4 weeks

description:
Gene expression in spleen-derived CD11b+ cells of STAT6-KO mice after MI for 4 weeks
DS12

source_name: STAT6-KO, spleen-derived CD11b+ cells, MI 4 weeks

value: spleen


title: WT_ bone marrow-derived CD11b+ cells _control

description:
Gene expression in bone marrow-derived CD11b+ cells of WT control mice
DM13

source_name: WT, bone marrow -derived CD11b+ cells, control


title: WT_ bone marrow -derived CD11b+ cells _MI 1 week

description:
Gene expression in bone marrow-derived CD11b+ cells of WT mice after MI for 1 week
DM14

source_name: WT, bone marrow -derived CD11b+ cells, MI 1 week


title: STAT6-KO _ spleen-derived CD11b+ cells _MI 1 week

description:
Gene expression in spleen-derived CD11b+ cells of STAT6-KO mice after MI for 1 week
DS10

source_name: STAT6-KO, spleen-derived CD11b+ cells, MI 1 week


title: STAT6-KO_ spleen-derived CD11b+ cells_ control

description:
Gene expression in spleen-derived CD11b+ cells of STAT6-KO control mice
DS9

source_name: STAT6-KO, spleen-derived CD11b+ cells, control


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H2_AD006


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H2_AD001


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H2_AD002


title: M1_cp531_1

first: liu

last: xincheng

address: zhongshan Road 74 Street

institute: sysu

data_processing:
We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC:RNA concentration, RIN value,28S/18S and the fragment length distribution.
We use internal software SOAPnuke to filter reads
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.
We mapped clean reads to reference using Bowtie2 and then calculate gene expression  level with RSEM
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: The cells were cultured according to the guideline of ATCC

extract_protocol:
Total RNA was isolated from cultured cell lines. Beads containing oligo (dT) were used to isolate poly(A) mRNA from total RNA. Purified mRNA was then fragmented in fragmentation buffer. Using these short fragments as templates, random hexamer-primers ere used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I. Short double-stranded cDNA fragments were purified with a QIAquick PCR extraction kit (vendor) and eluted with EB buffer for end repair and the addition of an ‘A’ base. Next, the short fragments were ligated to Illumina sequencing adaptors. DNA fragments of a selected size were gel-purified and amplified by PCR. The amplified library was sequenced using Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT 116 tumor cells were treated with control, M1 (MOI=1 pfu/cell), Lonidamine (50 μM) or M1 (MOI=1 pfu/cell) plus Lonidamine (50 μM) for 24 hours. Total RNA was extracted from 1×106 cells with TRIzol Reagent (Thermo Fisher Scientific) and was sent for RNA sequencing

tag: cell line

value: HCT 116


title: M1_cp531_2


title: Myeloid cells sorted from juxta tumoral tissue

city: San Francisco

first: Bushra

last: Samad

address: 505 Parnassus Ave

institute: USCF Immunoprofiler

description: Droplet based Single cell RNAseq (10x genomics. 3 prime v2)

data_processing:
Alignement in human genome
Cell ranger processing
Geneation of Seurat object using Seurat V3
Genome_build: GRCh38
Supplementary_files_format_and_content: genes count and barcodes list
Supplementary_files_format_and_content: Matrix of genes and barcodes

source_name: Kidney biopsy

value: Juxta tumoral tumor tissue


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H1_AD010

value: brain


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H1_AD007

value: STR


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H1_AD008


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H1_AD004


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H1_AD006


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H2_AD004


title: M1_cp531_3


title: M1_1


title: M1_2


title: STAT6-KO _ spleen-derived CD11b+ cells _MI 2 weeks

description:
Gene expression in spleen-derived CD11b+ cells of STAT6-KO mice after MI for 2 weeks
DS11

source_name: STAT6-KO, spleen-derived CD11b+ cells, MI 2 weeks


title: M1_3


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H1_AD001


title: cp531_3


title: cp531_2


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H12_AD012


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H12_AD010


title: HDC-KO _ spleen-derived CD11b+ cells _MI 2 weeks

description:
Gene expression in spleen-derived CD11b+ cells of HDC-KO mice after MI for 2 weeks
DS7

source_name: HDC-KO, spleen-derived CD11b+ cells, MI 2 weeks


title: HDC-KO _ spleen-derived CD11b+ cells _MI 4 weeks

description:
Gene expression in spleen-derived CD11b+ cells of HDC-KO mice after MI for 4 weeks
DS8

source_name: HDC-KO, spleen-derived CD11b+ cells, MI 4 weeks


title: HDC-KO _ spleen-derived CD11b+ cells _MI 1 week

description:
Gene expression in spleen-derived CD11b+ cells of HDC-KO mice after MI for 1 week
DS6

source_name: HDC-KO, spleen-derived CD11b+ cells, MI 1 week


title: HDC-KO_ spleen-derived CD11b+ cells_ control

description:
Gene expression in spleen-derived CD11b+ cells of HDC-KO control mice
DS5

source_name: HDC-KO, spleen-derived CD11b+ cells, control


title: WT_ spleen-derived CD11b+ cells _MI 4 weeks

description:
Gene expression in spleen-derived CD11b+ cells of WT mice after MI for 4 weeks
DS4

source_name: WT, spleen-derived CD11b+ cells, MI 4 weeks


title: cp531_1


title: WT_ spleen-derived CD11b+ cells _control

description:
Gene expression in spleen-derived CD11b+ cells of WT control mice
DS1

source_name: WT, spleen-derived CD11b+ cells, control


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H12_AD008

source_name: C57BL/6J P56 Mouse Brain


title: WT_ spleen-derived CD11b+ cells _MI 2 weeks

description:
Gene expression in spleen-derived CD11b+ cells of WT mice after MI for 2 weeks
DS3

source_name: WT, spleen-derived CD11b+ cells, MI 2 weeks


title: WT_ spleen-derived CD11b+ cells _MI

description:
Gene expression in spleen-derived CD11b+ cells of WT mice after MI for 1 week
DS2

source_name: WT, spleen-derived CD11b+ cells, MI 1week


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H1_AD002


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H12_AD007


title: control_2


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H12_AD006


title: control_3


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H12_AD004


title: control_1


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H11_AD010


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H10_AD008


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H11_AD002


title: TB_validation_8

city: Reno

first: Musheng

last: Li

address: North Virginia Street

institute: University of Nevada, Reno

data_processing:
Our newly developed pipeline, SPORTS1.0 (https://github.com/junchaoshi/sports1.0), was used to parse the raw sequencing data.
Genome_build: hg19

source_name: PBMC

extract_protocol:
We extracted total RNA from PBMCs using TRIzol reagent (Invitrogen) and purified it with a mirVana miRNA Isolation Kit (Ambion, Thermo Fisher Scientific) according to the manufacturer’s protocol.
The sequencing libraries were constructed using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina.

tag: type

value: TB


title: TB_validation_6


title: TB_validation_7


title: HFW3_Δcnb1

city: Taipei

first: YI-HSUAN

last: HOU

address: Roosevelt Rd

institute: National Taiwan University

data_processing:
RNA-seq reads were processed using "Trinity v2.3.2".
Read quality was evaluated using "MultiQC v1.2".
The alignment and the alignment QC report was evaluated using "Qualimap v2"
The gene expression level is calculated by using FPKM method.
Genome_build: Fusarium oxysporum f. sp. lycopersici 4287
Supplementary_files_format_and_content: A tab-delimited text file includes FPKM. BLASTP, BLASTX, and annotation

source_name: F. oxysporum f. sp. lycopersici 4287 CNB1 single deletion mutant strain cells

growth_protocol: The F. oxysporum f. sp. lycopersici WT and calcineurin mutants spores were cultured in PDB at 25°C for 14 h with shaking at 200 rpm.

extract_protocol:
For total RNA extraction, mycelia were collected and frozen in liquid nitrogen, then grownd into powder. Transfer the powder to 1.5 mL centrifuge tube followed by adding an equal volume of TRIzol reagent (Invitrogen) and 100 μL chloroform, mixed well and centrifuged at 14,000 rpm for 5 min at 4℃. The upper phase was collected and precipitated with isopropanol by centrifuged at 14,000 rpm for 10 min at 4℃. The supernatants were discarded, and the nucleic acid pellets were serial washed by 70% and 100% ethanol. The RNA was then re-suspended with DEPC water.
The mRNA was enriched with oligo(dT) magnetic beads and shortened into approximately 200-base fragments in fragmentation buffer. The first strand of cDNA as synthesized by the use of a random hexamer, buffer, dNTPs, and RNase H, and the second by the use of DNA polymerase I. The double strand cDNAs were purified with magnetic beads. After end preparation and 3' end single nucleotide adenine addition were performed, sequencing adaptors were ligated to the fragments, and amplified by PCR. An Aglient 2100 bioanalyzer and ABI StepOnePlus real-time PCR system were used to qualify and quantify the sample library, and the library products were sequenced via an illumina HuSeq 2000 instrument.

value: CNB1 single deletion mutant


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H10_AD007

value: AI

value: male


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H10_AD006

value: ACA


title: TB_validation_5


title: TB_validation_4


title: TB_validation_3


title: WT_4287

organism: Fusarium oxysporum f. sp. lycopersici 4287

source_name: F. oxysporum f. sp. lycopersici 4287 cells

value: wild type


title: CD8_033G

city: Hannover

first: Christian

last: Schultze-Florey

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

data_processing:
MIXCR (v2.1.11): alignment based on the IMGT database (22.05.2018) followed by assembling of clonotypes to correct PCR-errors.
random normalization to 20000 reads to avoid bias due to diverging sequencing depths
decompression, conversion into the FASTQ-file format, subsequent formatting
TCR repertoire analysis was based on usage of VDJtools, tcR-package
All bash and R scripts used are available at: https://github.com/MHHIMMUNOLOGY/MHHTCR_ANALYSIS
Supplementary_files_format_and_content: CDR3 sequences

source_name: CD8 from PBMC_donor

extract_protocol:
sorted CD8+ - RNA extr - RACE - CDR3 amplification - MiSeq TRB sequencing
libraries were prepared for sequencing using standard Illumina protocols

tag: patient id

tag: sample tp, refer to stable 1 and 2 for further details

value: donor

tag: dli sample

value: yes

value: CD8 from PBMC

tag: molecule subtype

value: cDNA:CDR3 amplicon


title: MO24_sgKdm5a RPP_Tumor8

data_processing:
Basecalls
For RNA-Seq: gene counts were done using STAR (v2.5.1b) {Dobin A., etal (2013), Bioinformatics 29: 15.} and normalized gene counts (RPKM) were calculated using Cufflinks (v2.2.1) {Trapnell C., etal (2010), Nat. Biotech. 28: 511.}. Analysis was performed using the VIPER snakemake pipeline {Cornwell M., etal (2018), BMC Bioinformatics 19: 135.}
Genome_build: mm9
Supplementary_files_format_and_content: For RNA-Seq, cufflinks file shows normalized RPKM values.

source_name: Lung Tumor 236 sgKdm5a RPP

growth_protocol:
sgControl RPP or sgKdm5a RPP adenovirus that were titered diluted in PBS were intratracheally injected in H11 LSL-Cas9 mice (2-4 months of age) at 4 X 10^8 VP/mouse.
At the study endpoint, mice were euthanized and lung tumors harvested

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen #74106) per the manufacturer's instructions
Libraries were constructed as per the manufacturers instructions. For RNASeq: 500 ng RNA was used with the Illumina stranded total RNASeq protocol.

value: B6;129-Igs2tm1(CAG-cas9*)Mmw/J. Also known as H11-LSL-Cas9. Jackson Labs catalog number 026816

tag: tissue

value: Small cell lung cancer lung tumor from mouse infected with sgKdm5a RPP adenovirus


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_G8_AD012

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

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.

tag: source

tag: target

tag: gender

value: female


title: TB_validation_2


title: MO23_sgKdm5a RPP_Tumor7

source_name: Lung Tumor 190 sgKdm5a RPP

tag: strain


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_H10_AD012

tag: age