title: Replicate1_2

status: Public on Jul 05 2020

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 1, 10X lane 2

data_processing:
All 10X scRNA-seq data was processed with the default CellRanger v2.1 pipeline (Zheng et al. 2017) for mapping to the mm10 mouse genome assembly. Gene counts were further analysed with scanpy (Wolf et al. 2018). To keep only high-quality cells, we filtered out cells with less than 4,000 UMI counts and/or less than 1,600 detected genes, cells with more than 20000 UMI counts and/or more than 5,000 genes, and cells with more than 5% of UMI reads coming from mitochondrial genes. After this filtering, we kept 109,061 cells from replicate 1, 118,646 cells from replicate 2 and 107,591 cells from replicate 3. Next, we assigned sgRNA expression to every cell using the amplicon sgRNA libraries and we kept only cells assigned to a unique sgRNA: 71,047 cells in replicate 1, 71,188 cells in replicate 2 and 61,729 cells in replicate 3, which summed up 203,964 cells in total across replicates. A gene was considered for downstream analysis if it was detected (UMI count >0) in at least in 10 out of the 203,964 cells that passed filtering. The final dataset after quality control consisted of 20,690 genes. The number of UMIs for every cell was adjusted by library size dividing by the total number of UMIs per cell, log-transformed, and scaled with the factor of 10,000.
Using the amplicon sgRNA libraries, the potential sgRNA sequence (nucleotides 24-43 of the read) was compared to the collection of designed guides. By taking only exact matches to the white list of sgRNAs, the majority of 475 sgRNA sequences were recovered (470-474, variable from one library to another) and 16% of reads on average (15.3%-16.8% for different libraries) were left unassigned to a sgRNA. To correct for sequencing mistakes, we allowed a minimum edit distance (Levenshtein distance – 4 edits) between any two sequences of the designed sgRNAs as well as the CROP-sgRNA-MS2 vector sequence surrounding the potential sgRNA in the read. For the reads left unassigned to a sgRNA at this stage, if there was a sgRNA sequence within Levenshtein distance of 1 or 2 and if the upstream 23 nucleotides and downstream 23 nucleotides matched the CROP-sgRNA-MS2 vector sequence with up to 4 edits each, the respective sgRNA was assigned to the read. After this correction procedure, approximately 2% of reads were left unassigned. Cell barcodes detected in the amplicon libraries were then matched with barcodes detected in the regular 10X scRNA-seq libraries. Out of the 317,847 cells that passed quality control across the three transduction replicates in the regular 10X libraries, 249,767 cell barcodes were captured in the amplicon sgRNA libraries (85,993 in replicate 1, 86,671 in replicate 2 and 77,103 in replicate 3). A sgRNA was assigned to a cell if more than 90% of all the amplicon reads containing the sgRNA had the same cell barcode, with standard error of binomial proportion of less than 10%.
Genome_build: mm10
Supplementary_files_format_and_content: Barcodes detected, genes detected and matrix files are provided for each sample

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem cells (mESCs) were grown under serum/LIF conditions: DMEM (Gibco, 11995-040), 15% fetal bovine serum, 1 U/ml penicillin - 1 mg/ml streptomycin (Gibco, 15140-122), 0.1 mM nonessential amino acids (Gibco, 11140-050), 4 mM GlutaMAX (Gibco, 35050-061), 50 mM β-mercaptoethanol (Gibco, 31350-010), and 103 U/ml LIF (Stem Cell Institute, Cambridge), and cultured at 37 ̊C in 5% CO2 on gelatinized tissue-culture plates. The media was refreshed every day and the cells passaged every other day with Trypsin EDTA (Thermo Fisher Scientific, 25200056).

extract_protocol:
See 10X Genomics V2 Single Cell 3′ Solution kit user guide
For 10X libraries, see 10X Genomics V2 Single Cell 3′ Solution kit user guide. Amplicon sgRNA libraries were performed on full length 10X cDNA samples as previously described (Hill et al. 2018); briefly, 10 ng of full length 10X cDNA were used as starting material and each round of PCR amplification with the primers described in (Hill et al. 2018) was monitored by KAPA SYBR to avoid overcycling.
Each 10X library was sequenced on an Illumina HiSeq4000 lane with 26 cycles for read 1, 98 cycles for read 2 and 8 cycles i7 sample index. The 24 amplicon libraries were multiplexed and sequenced across two lanes of an Illumina Hiseq2500 Rapid Run, with 27 cycles for read 1, 267 cycles for read 2 and 8 cycles for i7 sample index.

treatment_protocol: The lentiviral library of 475 sgRNAs cloned into the CROP-sgRNA-MS2 backbone was transduced in triplicates into SAM mESCs by direct supplementation of the concentrated lentivirus into the medium for 24 hours. The transductions were done at <0.1 multiplicity-of-infection (MOI) into 5 million SAM ESCs, achieving a representation >1000 cells / sgRNA, considering that <10% of the cells were transduced. Two days after transduction, mCherry expression was analysed by flow-cytometry on BD LSR Fortessa and selection with 1 ug/ul puromycin started afterwards. Cells were selected and passaged for 8 days after addition of puromycin before harvesting for 10X single-cell RNA-sequencing library preparation.

tag: strain

value: 129/Ola ES-E14


title: KI-6_S12

status: Public on Jul 09 2020

type: SRA

city: BETHESDA

first: RAJAKUMAR

last: ANBAZHAGAN

state: MD

address: 49 CONVENT DRIVE, NIH

department: NICHD, DDB

country: USA

institute: NICHD, NIH

description: GRTH Knock-In CB-5

library_source: transcriptomic

data_processing:
PartekFlow software was used for read QA/QC report
The sequenced reads were trimmed to remove the adapters
STAR method was used to align the RNA-seq reads with mouse mm10 reference genome
The quantification of transcriptome abundance was performed using Partek E/M algorithm in PartekFlow software.
Differentially expressed genes (DEGs) between WT and KI gentotypes were generated with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files contains results from DESeq2 which includes fold change calculations between KI vs WT along with geneName, total count, p-value, FDR stepup etc.

molecule: total RNA

organism: Mus musculus

source_name: CB in germ cells of GRTH Knock-In

extract_protocol:
Chromatoid bodies isolated from Germ cells of Testis was used to prepare RNA using Phenol:Chloroform:Isoamylalcohol (25:24:1). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Germ cells were fixed in 0.1% Formaldehyde, prior to isolation of chromatoid bodies

tag: strain background

tag: genotype/variation

value: GRTH-KI (R242H)

tag: tissue

value: Testis

tag: cell type

value: Germ Cells

tag: organelle

value: Chromatoid body (CB)


title: KI-4_S10

description: GRTH Knock-In CB-3


title: WT-1_S1

description: Wild Type CB-1

source_name: CB in germ cells of WT

value: WT


title: RNAiPS_1

status: Public on Jun 12 2020

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
Data of RNA-seq (fastq file format) were quality-checked, and low-quality reads (score < 30), adapter sequences, and overrepresented sequences such as poly-A chain were trimmed using the Trim Galore! (ver.0.4.0).
The remaining reads were mapped to the Callithrix jacchus genome (cj3.2.1.86) using the STAR (ver.2.5.3a), and the output file (BAM file format) were summarized using the featureCounts (1.5.2).
Genome_build: cj3.2.1.86
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Callithrix jacchus

source_name: Induced pluripotent stem cells

growth_protocol: See the citation

extract_protocol:
RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: See the citation

value: Induced pluripotent stem cells


title: PC1305 3uM 24h 16hbe

status: Public on May 26 2020

city: GDANSK

first: Rafal

middle: A

last: Bartoszewski

address: Hallera 107

country: Poland

institute: Medical University of Gdansk

description: 3uM C1305 24h hours treated

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
STAR version 2.5.3b was used to align the FASTQ files to the reference genome with parameters --outReadsUnmapped Fastx, --outSAMtype BAM SortedByCoordinate, --outSAMattributes All
For biological replicates, HTSeq-count version 0.9.1 was used to estimate transcript abundances with paramters -r pos, -t exon, -I gene_id, -a 10, -s no, -f bam
For biological replicates, DESeq2 was used to normalize and calculate differentially expressed genes following their default protocol
For samples without biological replicates, Cufflinks version 2.2.1 was used to estimate transcript abundances with parameters --library-type fr-firststrand, -G, -L
For samples without biological replicates, Cuffdiff was used for differential expression using default paramters.
Genome_build: Gencode GRCh38 p7 Release 25
Supplementary_files_format_and_content: tab-delimited Excel file containing raw counts for each gene in each sample

organism: Homo sapiens

source_name: human bronchial epithelial 16HBE14o- cells  (Sigma-Aldrich (Cat. #SCC150)

growth_protocol: 16HBE14o- and cells were cultured in Minimum Essential Modified Eagle's Medium (Invitrogen) with 10% fetal bovine serum (FBS), while HTC 116 cells were cultured in McCoy's 5a Medium (Invitorgen) with 10% FBS and A549 cells were cultured in RPMI 1640 media, supplemented with 10% FBS in a humidified incubator at 37°C in 5% CO2. All experiments were conducted at a final confluence of 70-80%.

extract_protocol: Total RNA containing the small ncRNA fraction was isolated using miRNeasy kit (Qiagen, 217004)

treatment_protocol: Cells were exposed for 24h to C1305 at IC50 concentration, the controls were mantained with DMSO for 8 or 24 hours

value: human bronchial epithelial

tag: cell line

value: HTC 116


title: No40-iNmethod-differentiated-Day20

source_name: ESC-derived neural differentiated cells

value: ESC-derived neural differentiated cells


title: 8h ctrl A549 replicate3

description: DMSO control (8 hours)

source_name: human non-small lung carcinoma A549 cells (ATCC CCL-185)

value: human non-small lung carcinoma


title: C1305 24h htc116 10uM

description: 10uM C1305 24 hours treated

source_name: human colorectal carcinoma HTC 116 (ATCC CCL-247)

value: human colorectal carcinoma


title: 24h ctrl A549 replicate1

description: DMSO control (24 hours)


title: ctrl/htc116 24h

description: DMSO control (24 hours)


title: 24h ctrl A549 replicate2

description: DMSO control (24 hours)


title: 8h ctrl A549 replicate2

description: DMSO control (8 hours)


title: C1305 3uM 24h A549 replicate1

description: 3uM C1305 24h hours treated


title: 24h ctrl A549 replicate3

description: DMSO control (24 hours)


title: Regular

status: Public on Jul 13 2020

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

library_source: genomic

data_processing:
Fastqs were demultiplexed usiing CellRanger-ATAC mkfastq (v1.0.0)
Sequencing reads were aligned to a modified hg19 reference using CellRanger-ATAC count (v1.0.0). Single-cells were called using the default parameters from this step.
Genome_build: hg19
Supplementary_files_format_and_content: Processed fragment files from 10x CellRanger-ATAC count

molecule: genomic DNA

source_name: Cell line mix TF1 and GM11906

growth_protocol: RPMI, 10%FBS, Pen/Strep, 2ng/ml GM-CSF for TF1 cells; RPMI, 15%FBS, Pen/Strep for GM11906 cells

extract_protocol:
Various lysis conditions as indicated above
Custom 10x Genomics scATAC-seq (mtscATAC-seq)

value: Cell line mix TF1 and GM11906

tag: lysis

value: 10x protocol (Omni-ATAC)

tag: decrosslinking

value: regular PCR

tag: fixation

tag: wash

value: Tween wash


title: 8h ctrl A549 replicate1

description: DMSO control (8 hours)


title: C1305 3uM 24h A549 replicate2

description: 3uM C1305 24h hours treated


title: EC-rep1

status: Public on May 18 2020

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

country: China

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BDGP6 genome using STAR v020201 with default parameters
featureCounts v1.6.3 was run for calculating reads counts of genes and relative quantitation of expression. Differential genes expression was analyzed by DESeq2
Genome_build: Ensemble Drosophila melanogaster BDGP6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Drosophila melanogaster

source_name: Wild type_intestinal enteroblast cells

extract_protocol:
Drosophila midgut were removed and digested using Elastase (Sigma, cat. no. E0258). About 10000 green fluorescent protein (GFP) labled cells were sorted using FACSAria II cell sorter (Becton Dickinson) and RNA was harvested using the  Arcturus PicoPure RNA isolation kit (Applied Biosystems). The RNA was then amplified using Arcturus RiboAmp HS PLUS RNA ampliﬁcation kit (Applied Biosystems).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wild type

tag: age

value: adult stage day 3

value: midgut

value: intestinal enterocytes


title: EC-rep2


title: EC-rep3


title: Cochlea_H3K27ac_ChIP-seq

status: Public on Apr 17 2020

first: Eddie

last: Loh

address: 1425 Madison Avenue

department: Department of Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The ChIP-seq data was first checked for quality using the various metrics generated by FastQC (v0.11.2). Raw sequencing reads were then aligned to the mouse mm10 genome using default settings of Bowtie (v2.2.0). Only uniquely-mapped reads were retained and duplicates were removed.
Peak-calling was performed using MACS (v2.1.1) with qvalue (minimum FDR) cutoff of 0.05. Motif enrichment analysis was performed using the Homer package (v4.8.3). The peak annotation and gene ontology analysis was performed using the GREAT program and Panther classification system.
Genome_build: MM10
Supplementary_files_format_and_content: bigwig and bed files

source_name: Mouse cochlea

extract_protocol:
The tissues were fixed with 1%PFA in PBS for 30 min at RT. After washing, the tissues were homogenized to a fine powder using BeadBugTM high-energy benchtop homogenizer in the lysis buffer. Chromatin shearing was performed using the Covaris E220 focused-ultrasonicator system. After preclearing with Protein A beads, the chromatin was immunoprecipitated with antibodies. After IP, the beads were washed in sequential low salt buffer, high salt buffer, LiCl washing buffer and TE buffer.
The libraries were prepared using the ThruPlex DNA-seq Kit (Rubicon Genomics) and according to the manufacturer's instructions.

tag: developmental stage

value: cochlea

tag: antibody

value: H3K27ac (ab4729, Abcam)


title: MED14-IAA7, MED17-IAA7, SUA7-FLAG, DMSO Rep 1

status: Public on Mar 05 2020

city: Bloomington

first: Gabriel

middle: E

last: Zentner

state: IN

address: 915 E 3rd St

department: Biology

institute: Indiana University

data_processing:
alignment with bowtie2, options: `-I 10 -X 700 --no-unal --dovetail --no-discordant --no-mixed’
CPM normalization with deepTools `bamCoverage -b [SAMPLE.BAM]" --normalizeUsing CPM  -bs 1 -p [#PROCS] -e -of bigwig -o [BIGWIG_OUT.bw]'
log2 fold change +IAA / DMSO calculation with deepTools `bamCompare -b1 [IAA.bam] -b2 [DMSO.bam] -e --scaleFactorsMethod SES -bs 1 -p [#PROCS] -of bigwig -o [LOG2_BIGWIG_OUT.bw]’
Genome_build: sacCer3
Supplementary_files_format_and_content: CPM-normalized bigWig files (1 bp resolution)

organism: Saccharomyces cerevisiae

growth_protocol: Yeast were grown at 30C in YPD with shaking at 180 RPM

extract_protocol:
ChIP was performed as described (PMID 19378172) with minor modifications. A 100 mL culture was grown to an OD600 ≥ 0.8 and treated with 500 μM 3-IAA or an equal volume of DMSO for 15 min. After 15 min of 3-IAA or DMSO treatment, the culture was split into two flasks. One culture was treated with 6 μM 1-Napthyl PP1 (NAPP1, Cayman Chemicals) and the other was treated with an equal volume of DMSO for 15 min. Cells were crosslinked using 1% formaldehyde for 30 minutes at 30C and then quenched using Tris pH 8.0 (final concentration of 0.75 M). Crosslinked cells were lysed with bead beating using a Disruptor Genie for 8 cycles of 3 min at 2850 rpm and 1 min on ice. Then, lysate was transferred to a new tube and centrifuged as previously described. Lysate was sonicated using a Bioruptor Pico for 8 cycles of 30 sec on and 30 sec off. Soluble chromatin was immunoprecipitated using 30 μL of serum bovine albumin pre-blocked Sigma FLAG M2 magnetic beads (catalog number M8823) overnight at  4C. Beads were washed as described and and decrosslinked by resuspending the beads in 98 μL of TE/1% SDS and shaking (800 RPM) at 65C for 12 -16 hours. DNA was purified from the supernatant using a Qiagen PCR purification kit per the manufacturer’s protocol. Sequencing libraries were constructed by the Indiana University Center for Genomics and Bioinformatics (CGB) using the NEBNext Ultra II Library Prep Kit for Illumina and sequenced for 80 cycles in paired-end mode on the Illumina NextSeq 500 platform at the CGB.
Libraries were constructed by the Indiana University Center for Genomics and Bioinformatics using the NEB Next Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: 3-IAA in DMSO added to treatment samples at 0.5 mM for 30 m

tag: background strain

tag: treatment

tag: degron

value: MED17-3xV5-IAA7, MED14-3xHA-IAA7

tag: tagged protein

tag: chip antibody

value: Sigma M2 anti-FLAG


title: MED14-IAA7, MED17-IAA7, SUA7-FLAG, +IAA Rep 1


title: MED14-IAA7, TFG2-FLAG, DMSO


title: MED14-IAA7, TFG2-FLAG, +IAA


title: MED17-IAA7, TFG2-FLAG, DMSO


title: MED14-IAA7, TFA2-FLAG, +IAA


title: MED17-IAA7, TFA2-FLAG, +IAA


title: MED17-IAA7, TFA2-FLAG, DMSO


title: 16hbe ctrl 24h

description: DMSO cotrol (24 hours)

value: human bronchial epithelial


title: MED14-IAA7, TFA2-FLAG, DMSO


title: MED17-IAA7, SUA7-FLAG, +IAA Rep 2


title: MED17-IAA7, SUA7-FLAG, DMSO Rep 2


title: MED17-IAA7, SUA7-FLAG, DMSO Rep 1


title: MED17-IAA7, SUA7-FLAG, +IAA Rep 1


title: Day 104 OPC

city: Baltimore

first: Xitiz

last: Chamling

address: 400 N. Broadway

institute: Johns Hopkins University School of Medicine

description: single cell from Dropseq

data_processing:
Fastq files were processed and filtered according to the Dropseq cookbook version 1.0.1
R1 contains cell barcode (bases 1-12) and UMI (13-20). R2 is the biological read.
processed reads were aligned to GRCh38 using the STAR RNA aligner
exons were tagged using the Homo_sapiens.GRCh38.88.gtf annotations file
Genome_build: GRCh38
Supplementary_files_format_and_content: raw UMI count matrices with genes as row names and cells as columns

source_name: stem cell derived PDGFRα+ cells

growth_protocol: hOPCs  differentiation from hES and hIPSCs was initiated using a dual SMAD inhibition and addition of 100 nM all-trans RA. From day 8 to day 12, differentiating cells were maintained in neural induction media supplemented with RA (100nM) and SAG (1 mM). At day 12, adherent cells were lifted and cultured in low-attachment plates to favor sphere aggregation. At day 30, spheres were plated into poly-L-ornithine/laminin-coated dishes in a media supplemented with, B27 (Thermo Fisher, 12587010), N2 supplement (Thermo Fisher, 17502048), PDGF-AA, neurotrophin-3, HGF, and T3.  Once a significant number of tdTomato+ OPCs were visible around day 65-70, a PDGF media without mitogens (PDGF-AA, HGF, NT-3)  was used to drive oligodendrocyte maturation.

extract_protocol:
Differentiating hOPC cultures were were dissociated into single cell suspension by incubating in accutase for ~45 minutes. The single cell suspension was then passed through a ~70 uM cell strainer. To purify PDGFRα expressing cells, the dissociated cells were resuspended in MACS buffer and CD90.2 (THY1.2) or O4  microbeads and incubated at room temperature for 15 minutes for cell binding. Please note that the hES cells used here are knock-in reporter cell lines where the PDGFRα drives the expression of tdTomato and CD90.2, allowing hES-derived OPCs to be purified using CD90.2 microbeads. After incubation with the beads, cells are generally run through the MS column twice without additional supplementation of MicroBeads to increase the purity and achieve ~90% tdTomato+ cells. The purified PDGFRα-tdTomato+ cells are then used to single cell capture by Dropseq.
Illumina nextera XT multiplexed with N70X indices according to the Dropseq protocol

value: hES-derived OPCs

value: Day 104


title: Foreskin fibroblasts, ATAC-seq deep senescence rep2

status: Public on Feb 05 2020

city: Jinan

first: Xianglin

last: Zhang

state: Shandong

address: 247 Beiyuan Street

department: The Second Hospital of Shandong University

institute: Shandong University

data_processing:
ATAC-seq reads were mapped to hg19 genome using bowtie2 (-X2000 --no-mixed --no-discordant).
Duplicate reads were removed by genomic positions.
NFR reads were used to call peaks using MACS2 (--keep-dup all -f BEDPE).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.narrowPeak: Open peaks.

source_name: foreskin fibroblast

growth_protocol: Human diploid BJ fibroblasts purchased from American Type Culture Collection were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and penicillin and streptomycin.

extract_protocol:
~25,000 cells were harvested and then lysed in cold lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.5% Igepal CA-630) for 10 min. Centrifuge at 500× g for 10 min at 4℃. Discard the supernatant and resuspend pellet in a 50 ul transposition mix (TruePrep™ DNA Library Prep Kit V2 for Illumina, TD501). Incubate the transposition system at 37℃ for 1 hour and purify transposed DNA using Zymo DNA Clean & Concentrator™-5 kit. Finally ATAC-seq libraries were PCR amplified for 10 cycles and purified using Zymo DNA Clean & Concentrator™-5 kit.
Illumina HiSeq 2500

value: BJ

value: human diploid foreskin fibroblasts

tag: cell state

value: deep senescence


title: Foreskin fibroblasts, ATAC-seq reversal of senescence rep2

value: reversal of senescence


title: Foreskin fibroblasts, ATAC-seq deep senescence rep1


title: Foreskin fibroblasts, ATAC-seq senescence rep2

value: senescence


title: Day 89 OPC

description: single cell from Dropseq

value: Day 89


title: Foreskin fibroblasts, ATAC-seq reversal of senescence rep1


title: Foreskin fibroblasts, ATAC-seq senescence rep1


title: MED17-IAA7, TFG2-FLAG, +IAA


title: Foreskin fibroblasts, ATAC-seq growing rep2

value: growing


title: Foreskin fibroblasts, ATAC-seq growing rep1


title: Foreskin fibroblasts, ATAC-seq quiescence rep2

value: quiescence


title: E14 B6 Library 1

status: Public on Feb 13 2020

city: Utrecht

first: Maya

last: Sen

address: 8 Uppsalalaan

country: Netherlands

institute: Hubrecht Institute

data_processing:
Library strategy: scMspJ1-seq
Fastq files are parsed for library barcodes. Read 1 was mapped to the mm10 or hg19 build using the Bowtie2, filtered for unique mapping full-length reads and demultiplexed. 5mCG positions are obtained from the sequencing data using custom scripts in R and Perl identifying CG dinucleotides in the mm10 or hg19 genome at the expected distance from the mapped read position. Finally, all PCR duplicates are removed. Computer codes will be made available upon request.
Hairpin bisulfite sequencing was performed on bulk mouse embryos samples ( 2-cell to 64 cell stage). The bulk embryos were treated with protease treatment (1 uL of 25 ug/uL Qiagen Protease, 1 uL of 10X NEB Buffer 4, and 8 uL of nuclease free water). Then, 0.5 ng of genomic DNA was digested with 20 mL of MspI master mix (1 uL of MspI R0104L, 2 mL 10X NEB Cutsmart buffer in a total volume of 20 uL) and incubated at 37 C for an hour. After digestion, the digested genomic DNA was ligated with 1 uL of 10 uM phosphorylated hairpin oligo and ligation master mix (1 mL of NEB T4 ligase M0202M, 1 uL of 10X NEB T4 Ligase buffer, 2 uL of 10mM ATP, 5 uL of nuclease free water) and incubated overnight at 16 C. For purification of the ligation mixture, we used Dynabeads? M-280 Streptavidin and followed the recommended protocol with the following exceptions: the bead-ligation mixture was incubated for at least an hour at RT on a rotator and cold 10 mM Tris-HCl wash step was included. Subsequently, we performed BS-seq on the sample using the protocol Clark, et al. 2017. After sequencing the libraries on a Miseq 300x300 or NextSeq 75x75 pair-end kit, we used HBS-tools (Sun, MA et al. 2015) and custom perl scripts were used to analyze the methylated CpG dyads. Hairpin oligo (G/iMe-dC/iMe-dC/G/iMe-dC/iMe-dC/GG/iMe-dC/GG/iMe-dC/AAG/iBiodT/GAAG/iMe-dC/iMe-dC/G/iMe-dC/iMe-dC/GG/iMe-dC/G) was resuspended in 100 uM of Low-TE. The hairpin oligo was phosphorylated (1 uL of 100 uM hairpin oligo, 3 uL of 10X T4 Ligase Buffer, 1 uL T4 PNK and 5 uL of nuclease free water) and incubated at 37 C for an hour. Subsequently the phosphorylated oligo heated at 94 C and placed in ice water to generate the loop.
Published scNMT libraries (GSE109262) analyzed for the bisulfite results were processed as described previously. The first nine bases of the raw reads were trimmed using Trim Galore (v0.5.0) and mapped using Bismark to the mouse genome (mm10) with the 129/CAST background. SNPs specific to 129/CAST mouse genome were prepared using SNPsplit (v0.3.2) and a list of known variant call files from the Mouse Genomes Project (http://www.sanger.ac.uk/resources/mouse/genomes/). After mapping with Bismark, duplicate sequences were removed and CpG methylation calls were extracted with strand-specific information. Further data analysis and visualization of the methylation calls used custom scripts that will be made available upon request.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: mText files with 4 columns: Single Cell ID, chromosome, coordinate, strand, CNNR motif and strain [mouse only])

growth_protocol: Cells were grown on 0.1% gelatin in ES cell culture media; DMEM (1×) high glucose + glutamax (Gibco), supplemented with 10% FCS (Greiner) 100 µM β-mercaptoethanol (Sigma), 100 µM Non-essential amino acids (Gibco), 50 µg/mL Pen/Strep (Gibco) and 1000 U/mL ESGRO mLIF (Millipore).

extract_protocol:
Cells were isolated using hyaluronic acid (Sigma) and trypsin (Life Technologies) and sorted into 384-well plates containing lysis buffer and Vapor-lock.
Single cells were incubated at 50C for 15 hours, 75C for 20 minutes and 80C for 5 minutes. Glucosylation of 5hmC sites followed by dispensing 0.1 L of T4-BGT (NEB), 0.1 L of UDP-Glucose (NEB), 0.05 L of 10X NEB Buffer 4 and 0.25 L of nuclease-free water (final vol 0.5mL). After incubation at 37C for 16 hours, 0.5 L of the following reaction mixture is added: 0.1L of 25g/L Qiagen Protease, 0.05L of 10X NEB Buffer 4 and 0.35 L of nuclease-free water. The plate is then incubated at 50 o C for 5 hours, 75 o C for 20 minutes and 80 o C for 5 minutes. Thereafter, gDNA is digested by the restriction enzyme MspJI by the addition of 0.5 L of the following reaction mixture: 0.02 L of MspJI (NEB), 0.12 L of 30X enzyme activator solution (NEB), 0.05 L of 10X NEB Buffer 4 and 0.31 L of nuclease-free water. The digestion is performed at 37 o C for 5 hours followed by heat inactivation of MspJI at 65 o C for 20 minutes. Next, 0.2 L of cell-specific double-stranded adaptors are added to individual wells and these adapters are ligated to the fragmented gDNA molecules by adding 0.8 L of the following reaction mixture: 0.07 L of T4 DNA ligase (NEB), 0.1 L of T4 DNA ligase buffer (NEB), 0.3 L of 10 mM ATP (NEB) and 0.33 L of nuclease-free water. The ligation is performed at 16 o C for 16 hours. Next, wells containing unique cell-specific adapters are pooled using a multichannel pipette and incubated with 0.8X Agencourt Ampure (Beckman Coulter) beads for 30 minutes, washed twice with 80% ethanol and resuspended in 6.4 L of nuclease-free water. In vitro transcription and Illumina library preparation is performed as described previously in the scAba-seq protocol.

tag: strain


title: Day 77 OPC

description: single cell from Dropseq

tag: cell type

value: Day 77


title: Foreskin fibroblasts, ATAC-seq quiescence rep1


title: Skeletal Muscle 19

status: Public on Jan 31 2020

type: RNA

city: Iowa City

first: Richard

last: Shields

address: 1-252 Medical Education Building

institute: The University of Iowa

description: RMA expression value derived from Partek Genomic Suites

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer and placed onto Affymetrix Human Exon 1.0 ST arrays. Hybridizations were performed by the DNA Core Facility at the University of Iowa.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the GeneChip operating software (GCOS) v1.4.

data_processing: Arrays were normalized using a Robust Multi-array Average (RMA) and transformed into a log2 hybridization signal using Partek Genomic Suites (v6.6 Copyright © 2013 Partek Inc., St. Louis, MO, USA).

label: Biotin

source_name: skeletal muscle, control

label_protocol: 5μg of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

extract_protocol: Following harvest, muscle biopsy samples were immediately placed In RNALater (Ambion) and stored at -80 C until further use. Total RNA was extracted using TRIzol solution (Invitrogen) according to the manufacturer’s instructions. 50 ng of RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN MinElute Reaction Cleanup column (QIAGEN Cat #28204) according to modifications from NuGEN. Four μg of SPIA amplified DNA were used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above.

treatment_protocol: Participants completed a long term unilateral exercise using electrical muscle stimulation before undergoing a bilateral muscle biopsy of the trained versus untrained limb.

tag: tissue

value: muscle

tag: Sex

value: male

tag: intervention

value: CTL

tag: sample type

value: control


title: Skeletal Muscle 29


title: Skeletal Muscle 28


title: Skeletal Muscle 24


title: Skeletal Muscle 11

source_name: skeletal muscle, experiment

value: EXP

value: experiment


title: Skeletal Muscle 18


title: Skeletal Muscle 23


title: Skeletal Muscle 21


title: Skeletal Muscle 16


title: Skeletal Muscle 25


title: Skeletal Muscle 22


title: Skeletal Muscle 15


title: Skeletal Muscle 30


title: Skeletal Muscle 26


title: Skeletal Muscle 27


title: Skeletal Muscle 13


title: Skeletal Muscle 17


title: Skeletal Muscle 20


title: Skeletal Muscle 14


title: Skeletal Muscle 03


title: Skeletal Muscle 04


title: Skeletal Muscle 07


title: Skeletal Muscle 10


title: Skeletal Muscle 08


title: Skeletal Muscle 06


title: Skeletal Muscle 09


title: Skeletal Muscle 12


title: Skeletal Muscle 05


title: Skeletal Muscle 02


title: spr-5; met-2_Rep2 [RNA-seq]

status: Public on Jan 17 2020

city: Atlanta

first: Brandon

middle: S.

last: Carpenter

state: Georgia

address: 615 Michael St., SOM: Cell Biology Dept.

department: Cell Biology

institute: Emory University

description: Replicate 2

data_processing:
Raw RNAseq reads were checked for quality using FastQC (Andrews 2010), filtered using Trimmomatic (Bolger et al. 2014).
Reads were aligned to genome WS220/ce10 using (Kim et al. 2015).
Read count by gene was obtained by FeatureCounts (Yang Liao et al. 2014).
Differentially expressed transcripts were determined using DESEQ2 (v.2.11.40.2) (Love et al 2014)
Genome_build: ce10
Supplementary_files_format_and_content: *.tab: Processed data files from DESEQ2 analysis are in tabular format and contain a list of differentially expressed genes compared to N2.
Supplementary_files_format_and_content: *.rtf: RTF files contain the R-scripts for visualizing the RNAseq data.

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: Animals were cultured with OP50 on 10-cm NGM agar plates at 20C.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) from 200-250 starved L1 larvae born at room temperature (21° C - 22° C) overnight in M9 Buffer.
Libraries were prepared by HAIB-GSL (for HiSeq).

value: whole animal

value: L1 larvae


title: spr-5_Rep2 [RNA-seq]

description: Replicate 2


title: spr-5; met-2_Rep1 [ChIP-seq]

description: Replicate 1

data_processing:
Reads were checked for quality using FastQC (Andrews 2010).
Reads were aligned to genome WS220/ce10 using Bowtie2 (Langmead & Salzberg 2012) using default settings.
bamCoverage in deepTools2 (Ramirez et al. 2016) was used to generate bigwig coverage tracks in 50-bp bins, with blacklisted regions from McMurchy et al. 2017 excluded, using the following parameters: -bs 50, --normalizeUsing RPKM.
MACS2 (Zhang et al. 2008; Feng et al. 2012) default parameters were used to call peaks and create bedgraph files for sequenced and mapped H3K36me3 ChIP samples and Input DNA samples with the following adjustments to account for H3K36me3 broader domains: Broad-cutoff =0.001. Blacklisted regions from McMurchy et al. 2017 were excluded for this analysis. Using published H3K36me3 modMine Chip-chip called broad peaks (modENCODE_3555) from N2 L1 larvae as a guide, we then merged called broad peaks within 1200bp using Bedtools: MergeBED (Quilan and Hall, 2010).
Genome_build: ce10
Supplementary_files_format_and_content: bigWig files, bed files
Supplementary_files_format_and_content: *.rtf: RTF files contain the R-scripts for visualizing the RNAseq data.

extract_protocol:
600 starved L1 larvae born at room temperature (21° C - 22° C) overnight in M9 Buffer were collected, frozen in liquid nitrogen, and stored at -80° C prior to homogenization. Frozen pellets were disrupted by a glass Dounce homogenizer, fixed with formaldehyde (1% final concentration), and quenched with glycine. ChIP samples were processed with a Chromatin Immunoprecipitation Assay Kit (Millipore), according to manufacturer’s instructions. Samples were sonicated using a Diagenode Bioruptor UCD-200 at 4 °C on the “high” setting for a total of 30 min with a cycle of 45 secs on and 15 secs off. A total of 12.5 μL (5 ug) H3K36me3 antibody (cat. 61021; Active motif) was used for immunoprecipitation. The Genomic Services Laboratory (GSL) (HudsonAlpha, Huntsville, Alabama) performed library preparation and sequencing (Illumina HiSeq v4, 50bp single-end reads).
Libraries were prepared by HAIB-GSL (for HiSeq).


title: met-2_Rep2 [RNA-seq]

description: Replicate 2


title: N2_Rep2 [ChIP-seq]

description: Replicate 2


title: N2_Rep2_Input [ChIP-seq]

description: Input


title: spr-5; met-2_Rep1 [RNA-seq]

description: Replicate 1


title: Skeletal Muscle 01


title: N2_Rep1 [RNA-seq]

description: Replicate 1


title: spr-5_Rep1 [RNA-seq]

description: Replicate 1


title: spr-5; met-2_Rep2 [ChIP-seq]

description: Replicate 2


title: N2_Rep1 [ChIP-seq]

description: Replicate 1


title: Foreskin fibroblasts, Hi-C reversal of senescence rep2

status: Public on Dec 31 2019

description:
RS_cat_1Mb.iced_contact_map.txt.gz
RS_cat_40kb.iced_contact_map.txt.gz
RS_cat.fithic.txt.gz
genomic_intervals.20kb.bed
genomic_intervals.1Mb.bed
genomic_intervals.40kb.bed
HiC_RS_rep2

data_processing:
Hi-C reads were processed using HiC-Pro 2.7.0, raw and normalized contact maps at various resoultions were obtained both in biological replicates and pooled condtions.
Fit-Hi-C were used to call significant contacts with raw contacts maps of 20kb resolution and biases files from HiC-Pro with noOfPasses of 1 and distUpThres of 2000000.
RNA-seq reads were mapped to hg19 genome assembly with Tophat 2.1.1,and transcript abundance (FPKM) and counts were calculated based on GENCODE annotation using cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: *.raw_contact_map.txt and *.iced_contact_map.txt were the representation of sparse contact matrix, contact scores were stored as 'bin number 1/bin number 2/score'; Bed files showed the corresponding between bin numbers in contact map and genomic regions; *.FPKM.txt and *.Counts.txt showed the transcription abundance of genes and repeated elements in each sample

extract_protocol:
1-2 million of cells were fixed with 1% formaldehyde at room temperature for 10 min. Formaldehyde was quenched with glycine for 10min at room temperature.
cells were lysed and digested with MboI overnight with rotation. MboI was then inactivated at 62℃ for 20 minutes. After filling in with biotin-14-dCTP, the fragments were ligated at room temperature for 5.5 hours with rotation. Then reversal of crosslink and DNA purification was done. The biotin-labeled DNA was sheared to 300-500bp with Covaris M220 and then pulled down with Dynabeads MyOne Streptavidin C1 (Life Technology). Sequencing library preparation was performed on beads, including end-repair, dATP tailing and adaptor-ligation. 9 cycles of PCR amplification were performed with Extaq (Takara). Finally, size selection was done with AMPure XP beads and fragments ranging from 300bp to 500bp were selected.
Truseq

treatment_protocol: BJ fibroblasts stably expressing dcas9/KRAB-rtTA were treated with bleomycin (40 μg/ml; Biorbyt). On the 12th day after treatment, senescent cells were infected with TP53 sgRNA lentivirus and treated with Dox (100ng/ml) to induce dcas9/KRAB expression. Then cells were selected by puromycin (2 μg/ml) for 3 days and cultured for next 12 days

tag: cell line

value: human diploid BJ fibroblasts


title: N2_Rep2 [RNA-seq]

description: Replicate 2


title: met-2_Rep1 [RNA-seq]

description: Replicate 1


title: Foreskin fibroblasts, Hi-C senescence rep2

description:
S_cat_1Mb.iced_contact_map.txt.gz
S_cat_40kb.iced_contact_map.txt.gz
S_cat.fithic.txt.gz
genomic_intervals.20kb.bed
genomic_intervals.1Mb.bed
genomic_intervals.40kb.bed
HiC_S_rep2

treatment_protocol: Cells was induced with bleomycin (40 μg/ml; Biorbyt) for 2 hours and then cultured for 12 days


title: Foreskin fibroblasts, Hi-C deep senescence rep2

description:
DS_cat_1Mb.iced_contact_map.txt.gz
DS_cat_40kb.iced_contact_map.txt.gz
DS_cat.fithic.txt.gz
genomic_intervals.20kb.bed
genomic_intervals.1Mb.bed
genomic_intervals.40kb.bed
HiC_DS_rep2

treatment_protocol: Cells was induced with bleomycin (40 μg/ml; Biorbyt) for 2 hours and then cultured for 28 days


title: Foreskin fibroblasts, Hi-C reversal of senescence rep1

description:
RS_cat_1Mb.iced_contact_map.txt.gz
RS_cat_40kb.iced_contact_map.txt.gz
RS_cat.fithic.txt.gz
genomic_intervals.20kb.bed
genomic_intervals.1Mb.bed
genomic_intervals.40kb.bed
HiC_RS_rep1


title: Foreskin fibroblasts, Hi-C senescence rep1

description:
S_cat_1Mb.iced_contact_map.txt.gz
S_cat_40kb.iced_contact_map.txt.gz
S_cat.fithic.txt.gz
genomic_intervals.20kb.bed
genomic_intervals.1Mb.bed
genomic_intervals.40kb.bed
HiC_S_rep1


title: Foreskin fibroblasts, Hi-C quiescence rep1

description:
Q_cat_1Mb.iced_contact_map.txt.gz
Q_cat_40kb.iced_contact_map.txt.gz
Q_cat.fithic.txt.gz
genomic_intervals.20kb.bed
genomic_intervals.1Mb.bed
genomic_intervals.40kb.bed
HiC_Q_rep1

treatment_protocol: Cells were induced by 0.1% FBS for 4 days


title: Foreskin fibroblasts, RNA-seq reversal of senescence rep1

description:
five_condtions.FPKM.txt.gz
five_conditions.Counts.txt.gz
RNAseq_RS_rep1

molecule: polyA RNA

extract_protocol:
Total RNA was extracted using TRIzol (Life Technologies) and mRNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation kit (New England Biolabs)
Reverse transcription was carried out and cDNA was fragmented, purified, ligated with adapters. PCR was performed using an End Repair/dA-tail ligated DNA template to include unique barcodes to identify each sample.


title: Foreskin fibroblasts, Hi-C growing rep1

description:
G_cat_1Mb.iced_contact_map.txt.gz
G_cat_40kb.iced_contact_map.txt.gz
G_cat.fithic.txt.gz
genomic_intervals.20kb.bed
genomic_intervals.1Mb.bed
genomic_intervals.40kb.bed
HiC_G_rep1


title: Foreskin fibroblasts, Hi-C quiescence rep2

description:
Q_cat_1Mb.iced_contact_map.txt.gz
Q_cat_40kb.iced_contact_map.txt.gz
Q_cat.fithic.txt.gz
genomic_intervals.20kb.bed
genomic_intervals.1Mb.bed
genomic_intervals.40kb.bed
HiC_Q_rep2


title: Foreskin fibroblasts, Hi-C growing rep2

description:
G_cat_1Mb.iced_contact_map.txt.gz
G_cat_40kb.iced_contact_map.txt.gz
G_cat.fithic.txt.gz
genomic_intervals.20kb.bed
genomic_intervals.1Mb.bed
genomic_intervals.40kb.bed
HiC_G_rep2


title: Foreskin fibroblasts, RNA-seq deep senescence rep2

description:
five_condtions.FPKM.txt.gz
five_conditions.Counts.txt.gz
RNAseq_DS_rep2


title: Foreskin fibroblasts, RNA-seq deep senescence rep1

description:
five_condtions.FPKM.txt.gz
five_conditions.Counts.txt.gz
RNAseq_DS_rep1


title: Foreskin fibroblasts, RNA-seq senescence rep2

description:
five_condtions.FPKM.txt.gz
five_conditions.Counts.txt.gz
RNAseq_S_rep2


title: Foreskin fibroblasts, RNA-seq senescence rep1

description:
five_condtions.FPKM.txt.gz
five_conditions.Counts.txt.gz
RNAseq_S_rep1


title: Foreskin fibroblasts, RNA-seq quiescence rep2

description:
five_condtions.FPKM.txt.gz
five_conditions.Counts.txt.gz
RNAseq_Q_rep2


title: Foreskin fibroblasts, RNA-seq growing rep1

description:
five_condtions.FPKM.txt.gz
five_conditions.Counts.txt.gz
RNAseq_G_rep1


title: Foreskin fibroblasts, RNA-seq quiescence rep1

description:
five_condtions.FPKM.txt.gz
five_conditions.Counts.txt.gz
RNAseq_Q_rep1


title: Foreskin fibroblasts, RNA-seq growing rep2

description:
five_condtions.FPKM.txt.gz
five_conditions.Counts.txt.gz
RNAseq_G_rep2


title: Foreskin fibroblasts, Hi-C deep senescence rep1

description:
DS_cat_1Mb.iced_contact_map.txt.gz
DS_cat_40kb.iced_contact_map.txt.gz
DS_cat.fithic.txt.gz
genomic_intervals.20kb.bed
genomic_intervals.1Mb.bed
genomic_intervals.40kb.bed
HiC_DS_rep1


title: L+a-T [Donor135_9]

status: Public on Nov 01 2019

city: Paris

first: Vassili

last: Soumelis

address: 1 avenue Claude Vellefaux

department: U976 - HIPI

country: France

institute: INSERM

description: gene expression data for MoDC stimulated 8 hours with LPS + anti-TNFR blocking antibodies

hyb_protocol: Samples were  amplified and labelled according to the protocol recommended by Affymetrix for hybridization to Human Genome U133 Plus 2.0 arrays.

scan_protocol: Affymetrix GeneTitan device ( combined hybridization oven, fluidics processing, and imaging device )

data_processing: Expression data were normalized with Plier. Transcriptomics analysis was performed in a Matlab environment. For independent filtering, we used the function geneverfilter, which calculates the variance of each probe across the samples and identifies the ones with low variance. Probes with variance less the 40th percentile were filtered out because poorly informative.

label: biotin

source_name: monocyte derived dendritic cells

growth_protocol: Fresh blood samples collected from healthy donors were obtained from Hôpital Crozatier Établissement Français du Sang (EFS), Paris, France, in conformity with Institut Curie ethical guidelines. PBMCs were isolated by centrifugation on a Ficoll gradient (Ficoll-Paque PLUS, GE Healthcare Life Sciences). Monocytes were selected using antibody-coated magnetic beads and magnetic columns according to manufacturer’s instructions (CD14 MicroBeads, Miltenyi Biotec). To generate immature DCs, CD14+ cells were cultured for 5 days with IL-4 (50 ng/mL) and GM-CSF (10 ng/mL) in RPMI 1640 Medium, GlutaMAX (Life Technologies) with 10% FCS.

extract_protocol: Total RNA was extracted using the RNeasy micro kit (Qiagen) in accordance with manufacturer's

treatment_protocol: Monocyte-derived DCs were pre- treated for one hour with mouse IgG1 (20 µg/mL, R&D Systems), mouse anti-IL10R blocking antibody (10 µg/mL, R&D Systems) or mouse anti-TNFα Receptors 1 and 2 (10 µg/mL, R&D Systems) and then cultured with medium or LPS (100 ng/mL, LPS-EB Ultrapure, activates TLR4 only, Invivogen) for additional 4 or 8 hours based on the time point

tag: condition

value: L+a-T

value: blood

tag: time point


title: L+a-10 [Donor135_5]

description: gene expression data for MoDC stimulated 4 hours with LPS + anti-IL10R blocking antibodies

label_protocol: Samples were  amplified and labelled according to the protocol recommended by Affymetrix for hybridization to Human Genome U133 Plus 2.0 arrays.


title: L+a-T [Donor135_4]

description: gene expression data for MoDC stimulated 4 hours with LPS + anti-TNFR blocking antibodies


title: L+a-10 [Donor135_10]

description: gene expression data for MoDC stimulated 8 hours with LPS + anti-IL10R blocking antibodies


title: L+IgG [Donor134_8]

description: gene expression data for MoDC stimulated 8 hours with LPS + isotype ctrl

value: L+IgG


title: M+IgG [Donor135_7]

description: gene expression data for MoDC after 8 hours in medium + isotype ctrl

value: M+IgG


title: L+IgG [Donor135_8]


title: L+a-T [Donor134_9]


title: L+a-both [Donor134_6]

description: gene expression data for MoDC stimulated 4 hours with LPS + anti-IL10R and anti-TNFR blocking antibodies

value: L+a-both


title: M+IgG [Donor135_2]

description: gene expression data for MoDC after 4 hours in medium + isotype ctrl


title: L+a-both [Donor135_6]


title: L+a-both [Donor127_11]

description: gene expression data for MoDC stimulated 8 hours with LPS + anti-IL10R and anti-TNFR blocking antibodies


title: M+IgG [Donor134_7]


title: L+a-10 [Donor134_10]


title: L+a-both [Donor134_11]


title: L+a-T [Donor134_4]


title: L+a-10 [Donor134_5]


title: L+IgG [Donor134_3]

description: gene expression data for MoDC stimulated 4 hours with LPS + isotype ctrl


title: L+a-both [Donor135_11]


title: time0 [Donor134_1]

description: gene expression data for MoDC after differentiation and before stimulation


title: L+IgG [Donor135_3]


title: L+a-10 [Donor127_10]


title: time0 [Donor135_1]


title: L+IgG [Donor127_8]


title: L+a-10 [Donor127_5]


title: M+IgG [Donor127_7]

description: gene expression data for MoDC after 8 hours in medium with isotype ctrl


title: M+IgG [Donor134_2]


title: L+a-both [Donor127_6]


title: L+a-T [Donor127_9]


title: Foreskin fibroblasts, RNA-seq reversal of senescence rep2

description:
five_condtions.FPKM.txt.gz
five_conditions.Counts.txt.gz
RNAseq_RS_rep2

value: reversal of senescence


title: M+IgG [Donor127_2]


title: L+IgG [Donor127_3]


title: L+a-both [Donor125_11]


title: L+IgG [Donor122_8]


title: time0 [Donor127_1]


title: L+a-T [Donor125_9]


title: time0 [Donor125_1]


title: L+a-T [Donor122_9]


title: L+a-10 [Donor125_5]


title: L+a-10 [Donor122_10]


title: M+IgG [Donor125_2]


title: M+IgG [Donor122_7]


title: M+IgG [Donor125_7]


title: L+IgG [Donor125_3]


title: L+a-both [Donor125_6]


title: L+a-10 [Donor122_5]


title: L+a-both [Donor122_6]


title: L+IgG [Donor122_3]


title: L+a-T [Donor125_4]


title: L+a-T [Donor122_4]


title: L+a-both [Donor122_11]


title: L+IgG [Donor121_8]


title: time0 [Donor122_1]


title: L+a-T [Donor121_9]


title: L+a-10 [Donor125_10]


title: M+IgG [Donor122_2]


title: L+a-both [Donor121_11]


title: M+IgG [Donor121_7]


title: LPS+anti-TNFRs+anti-IL-10R(L+a-both) [Donor121_6]


title: LPS+anti-IL-10R(L+a-10) [Donor121_5]


title: LPS+anti-TNFRs(L+a-T) [Donor121_4]

value: LPS+anti-TNFRs(L+a-T)


title: RNAseq_Parental_2

status: Public on Aug 30 2019

city: Santiago de Compostela

first: Carmen

last: Rivas

address: Avda Barcelona

department: CIMUS

country: Spain

institute: Universidad de Santiago de Compostela

data_processing:
Raw ChIP sequencing reads were aligned using BWA version 0.7.17 with default parameters. After alignment, we sorted the bam files using samtools, then igvtools was used to generate wig files (igvtools count -w 25 -e 200). Finally, bigWig files were obtained using wigToBigWig.
Raw RNA sequencing reads were aligned using STAR version 2.5.3a with default parameters. The bigWig files were generated similarly as ChIP-seq.
Raw reads from whole-genome bisulfite sequencing were aligned using BWA (version 0.6.1). Low-quality sequence at the 3′ ends were trimmed. After alignment, we filtered duplicated or poorly mapping reads (>2% mismatches or aberrant insert size). Samtools (version 0.1.18) in mpileup mode was applied to call CpG methylation. We used igvtools to generate the tdf files.
Genome_build: hg19, mm10 and dm6 for human, mouse and drosophila data, respectively
Supplementary_files_format_and_content: bigWig, tdf

source_name: C3H10T1/2 cells

growth_protocol: C3H10T1/2 cells were cultured in Dulbecco's modified Eagles' medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, Sigma).

extract_protocol:
RNA was purified from C3H10T1/2 cells using Qiagen RNAeasy kit
Ribo Zero rRNA removal Kit (H/M/R)

value: C3H embryo-derived mesenchymal progenitor cells

tag: genotype

value: wild-type


title: RNAseq_Parental_3


title: RNAseq_Parental_1


title: Hmgcs2-KO rep2

status: Public on Jul 19 2019

first: Chia-Wei

last: Cheng

state: MA

address: 500 Main St

institute: Koch Institute at MIT

data_processing:
Alignment to the mm10 mouse genome and unique molecular identifier (UMI) collapsing was performing using the Cellranger toolkit (version 1.3.1, 10X Genomics). For each cell, we quantified the number of genes for which at least one UMI was mapped, and then excluded all cells with fewer than 1,000 detected genes.
Supplementary_files_format_and_content: counts for ensembl genes

source_name: Intestinal crypt cells

extract_protocol: As previously reported and briefly summarized here, small intestines were removed, washed with cold PBS, opened longitudinally and then incubated on ice with PBS−/− EDTA (10 mM) for 30-45 min. Tissues were then moved to PBS. Crypts were then mechanically separated from the connective tis-sue by shaking, and then filtered through a 70-μm mesh into a 50-ml conical tube to remove villus material and tissue fragments. Crypts were removed from this step and dissociated into single cells and sorted by flowcytometry.

value: small intestine

tag: age

value: adult


title: WT rep2

value: wild type


title: Hmgcs2-KO rep1


title: L+a-10 [Donor121_10]


title: Medium+IgG(M+IgG) [Donor121_2]

value: Medium+IgG(M+IgG)


title: LPS+IgG(L+IgG) [Donor121_3]

value: LPS+IgG(L+IgG)


title: time0 [Donor121_1]


title: WT rep1


title: 10-39 Control neuron

status: Public on Apr 17 2019

city: South San Francisco

first: Brad

last: Friedman

state: CA

address: 1 DNA Way

institute: Genentech, Inc.

data_processing: Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from sorted cells

extract_protocol: Frozen tissue was dissociated on ice as described in manuscript and ethanol-fixed single-positive cells were sorted for each of four cell type markers, Astrocyte (Gfap+), Endothelial (Cd31+), Myeloid (CD11b+) and Neuron (NeuN+). RNA was extracted and amplified using Nugen Ovation V2. Libraries were then sequenced and analyzed as described in manuscript.

value: Male

value: neuron

tag: diagnosis

value: Control

tag: apoe

tag: pmi

value: I


title: 10-39 Control endothelial

value: endothelial


title: 10-26 Control astrocyte

value: Female

value: astrocyte

value: III


title: 05-10 Control myeloid

value: myeloid

value: II


title: 05-10 Control neuron


title: 10-39 Control astrocyte


title: 10-39 Control myeloid


title: 10-26 Control neuron


title: 05-10 Control astrocyte


title: 07-04 Control astrocyte


title: 05-10 Control endothelial


title: 07-04 Control neuron


title: 10-26 Control endothelial


title: 09-20 Control neuron


title: GMPSiglecF-5

status: Public on Nov 29 2018

city: Parkville

first: Carolyn

last: de Graaf

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

description:
CAGRF11700.1635
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

data_processing:
Sequence reads were aligned using the Subread aligned.
Genewise counts were obtained using FeatureCounts.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Haemopedia-Mouse-RNASeq_raw.txt is the raw counts as given by featureCounts.
Supplementary_files_format_and_content: Haemopedia-Mouse-RNASeq_tpm.txt gives genewise TPM.

source_name: SiglecF Positive Granulocyte Macrophage Progenitor

growth_protocol:
All cells were purified from mice between 7 and 12 weeks of age.
Bone marrow was harvested from femurs and tibias, flushed with a needle and processed to a single cell suspension. Red cell removal buffer was applied

extract_protocol:
RNA was isolated from two biological replicates (RNeasy plus micro kit, Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type short

value: GMPSiglecF

tag: strain/background

tag: antibodies

value: PI:- CD4:- CD8:- CD19:- B220:- Ter119:- Ly6C:+/- SiglecF:+ Ly6G:- SSC-A:v.lo FSC-A:In

value: Bone Marrow

tag: lineage

value: Restricted Potential Progenitor


title: 10-26 Control myeloid

tag: cell type


title: 07-04 Control endothelial


title: EoSSCLo-5

description:
CAGRF11700.1634
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Eosinophil Low Side Scatter

value: Eosinophil Low Side Scatter

value: EoSSCLo

tag: tissue

value: Eosinophil Lineage


title: SAMPLE 10: genomic DNA from SCC_1

status: Public on Oct 26 2019

type: genomic

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

description: SqCC IPF10

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: lung squamous cell carcinoma with idiopathic pulmonary fibrosis

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cell lines or clinical samples using QIAquick DNA mini kit according to standard instructions

tag: gender

value: Male

value: clinical sample

tag: disease state

value: lung cancer

value: squamous cell carcinoma


title: SAMPLE 11: genomic DNA from SCC_39

description: SqCC nonIPF1

source_name: lung squamous cell carcinoma without idiopathic pulmonary fibrosis

tag: sample type


title: SAMPLE 8: genomic DNA from SCC_8

description: SqCC IPF8


title: SAMPLE 1: genomic DNA from SCC_13

description: SqCC IPF1


title: SAMPLE 20: genomic DNA from SCC_33

description: SqCC nonIPF10


title: SAMPLE 16: genomic DNA from SCC_35

description: SqCC nonIPF6


title: SAMPLE 15: genomic DNA from SCC_31

description: SqCC nonIPF5


title: MacCult-3

description:
CAGRF11700.1610
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Mac1+ F4/80+ cultured macrophage

growth_protocol:
All cells were purified from mice between 7 and 12 weeks of age.
Fetal livers were harvested at embryonic day 10.5 and processed to a single cell suspension

value: Mac1+ F4/80+ cultured macrophage

value: MacCult

value: Embryonic day 10.5 Fetal liver

value: Macrophage Lineage

value: Day5 Cultured M-CSF Fetal liver


title: GMPSiglecF-4

description:
CAGRF11700.1631
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: SiglecF Positive Granulocyte Macrophage Progenitor


title: EoSSCHi-6

description:
CAGRF11700.1632
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Eosinophil High Side Scatter

value: Eosinophil High Side Scatter

value: EoSSCHi


title: SAMPLE 9: genomic DNA from SCC_2

description: SqCC IPF9


title: SAMPLE 2: genomic DNA from SCC_11

description: SqCC IPF2


title: SAMPLE 5: genomic DNA from SCC_3

description: SqCC IPF5


title: SAMPLE 4: genomic DNA from SCC_12

description: SqCC IPF4


title: EoCult-2

description:
CAGRF11700.1597
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Cultured Eosinophils

value: Cultured Eosinophils

value: EoCult

value: Cultured Fetal liver


title: SAMPLE 13: genomic DNA from SCC_21

description: SqCC nonIPF3


title: SAMPLE 7: genomic DNA from SCC_5

description: SqCC IPF7


title: EoSSCHi-5

description:
CAGRF11700.1576
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Bone Marrow


title: EoSSCHi-4

description:
CAGRF11700.1571
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Eosinophil Lineage


title: SAMPLE 18: genomic DNA from SCC_37

description: SqCC nonIPF8

value: Male


title: MacCult-2

description:
CAGRF11700.1600
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: EoSSCLo-4

description:
CAGRF11700.1633
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Eosinophil Low Side Scatter

value: EoSSCLo


title: SAMPLE 6: genomic DNA from SCC_9

description: SqCC IPF6

value: clinical sample

value: lung cancer

value: squamous cell carcinoma


title: SAMPLE 19: genomic DNA from SCC_29

description: SqCC nonIPF9


title: EoSSCHi-3

description:
CAGRF11700.1568
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: SAMPLE 14: genomic DNA from SCC_38

description: SqCC nonIPF4


title: SAMPLE 12: genomic DNA from SCC_41

description: SqCC nonIPF2


title: GMPSiglecF-3

description:
CAGRF11700.1570
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: GMPSiglecF

value: Restricted Potential Progenitor


title: SAMPLE 3: genomic DNA from SCC_15

description: SqCC IPF3


title: EoSSCLo-1

description:
CAGRF11700.1557
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: GMPSiglecF-1

description:
CAGRF11700.1555
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: EoSSCHi-1

description:
CAGRF11700.1556
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: GMPSiglecF-2

description:
CAGRF11700.1559
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: EoSSCHi-2

description:
CAGRF11700.1560
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: cDC2-1

description:
CAGRF11700.1545
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Conventional DC type 2

growth_protocol:
All cells were purified from mice between 7 and 12 weeks of age.
After harvesting spleens they were processed to single cell suspension and put through a sieve. Red Cell removal buffer was applied before staining with antibodies and sorting on fluorescence cytometer

value: Conventional DC type 2

value: CD11c:+ 120G8:- Sirp alpha:+ CD8alpha:- F4/80:- or Lo

value: Spleen

value: Dendritic Cell Lineage


title: pDC-2

description:
CAGRF11700.1544
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Plasmacytoid DC

value: Plasmacytoid DC

value: pDC


title: MegCD8T-1

description:
CAGRF11700.1541
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: CD8+ Memory T

growth_protocol:
All cells were purified from mice between 7 and 12 weeks of age.
After harvesting spleens and lymph nodes they were processed to single cell suspension and put through a sieve. Red Cell removal buffer was applied before staining with antibodies and sorting on fluorescence cytometer

value: CD8+ Memory T

value: Spleen and Lymph nodes

value: T Cell Lineage


title: pDC-1

description:
CAGRF11700.1543
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: MemCD4T-2

description:
CAGRF11700.1540
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: CD4 Memory T

value: CD4 Memory T


title: RegT-2

description:
CAGRF11700.1539
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Regulatory T

value: Regulatory T

value: RegT

value: CD4:+ CD25:Hi


title: EoSSCLo-2

description:
CAGRF11700.1558
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Eosinophil Low Side Scatter

value: EoSSCLo

value: Bone Marrow

value: Eosinophil Lineage


title: NeutPB-4

description:
CAGRF11700.1536
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Neutrophil Peripheral Blood

growth_protocol:
All cells were purified from mice between 7 and 12 weeks of age.
Peripheral blood was obtained by retro-orbital bleed

value: Neutrophil Peripheral Blood

value: NeutPB

value: Peripheral Blood

value: Neutrophil Lineage


title: NveCd8T-2

description:
CAGRF11700.1533
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: CD8+ Naive T

value: CD8+ Naive T


title: SAMPLE 17: genomic DNA from SCC_27

description: SqCC nonIPF7

value: Male

value: clinical sample

value: lung cancer

value: squamous cell carcinoma


title: NveCd8T-1

description:
CAGRF11700.1532
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Spleen and Lymph nodes

value: T Cell Lineage


title: MemCD8T-1

description:
CAGRF11700.1530
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: CD8+ Memory T


title: NK-1

description:
CAGRF11700.1523
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Mature NK

value: Mature NK

value: NK

value: Spleen

value: NK Cell Lineage


title: NeutPB-3

description:
CAGRF11700.1535
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: NveCD4T-1

description:
CAGRF11700.1519
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: CD4 Naive T

value: CD4 Naive T


title: RegT-1

description:
CAGRF11700.1522
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Regulatory T

value: RegT

value: CD4:+ CD25:Hi


title: NK-2

description:
CAGRF11700.1524
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: cDC2-2

description:
CAGRF11700.1546
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Conventional DC type 2

value: CD11c:+ 120G8:- Sirp alpha:+ CD8alpha:- F4/80:- or Lo

value: Dendritic Cell Lineage


title: EffCD4T-2

description:
CAGRF11700.1518
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: CD4 Effector T

value: CD4 Effector T


title: BasoBM-2

description:
CAGRF11700.1503
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Basophil

growth_protocol:
All cells were purified from mice between 7 and 12 weeks of age.
Bone marrow was harvested from femurs and tibias by crushing, processed to a single cell suspension and filtered through a sieve. Red cell removal buffer was applied

value: Basophil

value: BasoBM

value: Bone Marrow (Crush)

value: Basophil Lineage


title: BasoBM-1

description:
CAGRF11700.1502
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: EryBlPB-3

description:
CAGRF9188.1472
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Polychromatic erythroblasts (some Basophillic erythroblasts)

value: EryBlPB

value: Bone Marrow

value: Erythrocyte Lineage


title: MemCD4T-1

description:
CAGRF11700.1516
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: CD4 Memory T

value: Spleen and Lymph nodes

value: T Cell Lineage


title: MacCult-1

description:
CAGRF11700.1599
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Mac1+ F4/80+ cultured macrophage

value: MacCult

value: Embryonic day 10.5 Fetal liver

value: Macrophage Lineage

value: Day5 Cultured M-CSF Fetal liver


title: NveCD4T-2

description:
CAGRF11700.1520
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: CD4 Naive T


title: EryBlPO-3

description:
CAGRF9188.1471
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Polychromatic erythroblasts (some Orthochromatic erythroblasts)

value: EryBlPO


title: EryBlPO-2

description:
CAGRF9188.1462
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Polychromatic erythroblasts (some Orthochromatic erythroblasts)


title: BasoSpl-1

description:
CAGRF9188.1460
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Basophil

value: BasoSpl

value: Spleen


title: Retic-3

description:
CAGRF9188.1446
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Reticulocytes

value: Reticulocytes

value: Retic


title: Retic-2

description:
CAGRF9188.1445
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Bone Marrow

value: Erythrocyte Lineage


title: CLP-2

description:
CAGRF9188.1437
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Common Lymphoid Progenitor

value: Common Lymphoid Progenitor

value: CLP

value: Lin:- cKit:Lo Sca1:Lo CD127rec:Lo CD135(Flt3):+

value: Restricted Potential Progenitor


title: NeutPB-2

description:
CAGRF9188.1438
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Neutrophil Peripheral Blood

value: NeutPB

value: IL-5:Hi Ly6G:Hi Siglec-F:lo Ly6C:+ B220:- CD4:- CD8:- CD19:- Ter119:-

value: Peripheral Blood

value: Neutrophil Lineage


title: Retic-1

description:
CAGRF9188.1428
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: Eo-2

description:
CAGRF9188.1422
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Eosinophils

value: Eosinophils

value: Eo

value: Eosinophil Lineage


title: NeutPB-1

description:
CAGRF9188.1420
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: IL-5:Hi Ly6G:Hi Siglec-F:lo Ly6C:+


title: EryBlPB-2

description:
CAGRF9188.1410
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Polychromatic erythroblasts (some Basophillic erythroblasts)

value: EryBlPB

value: Lin:- CD44:+ Ter119:+ FSC:Hi


title: EffCD4T-1

description:
CAGRF11700.1517
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: CD4 Effector T

value: Spleen and Lymph nodes

value: T Cell Lineage


title: EryBlPB-1

description:
CAGRF9188.1409_1465
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Bone Marrow

value: Erythrocyte Lineage


title: STHSC-2

description:
CAGRF9188.1400
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Short Term HSC

value: Short Term HSC

value: STHSC

value: Multi Potential Progenitor


title: STHSC-1

description:
CAGRF9188.1399
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: MPP-2

description:
CAGRF9188.1396
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Multi Potential Progenitor

value: MPP


title: MPP-1

description:
CAGRF9188.1395
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: InfMono-2

description:
CAGRF9188.1392
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Inflammatory Monocyte

value: Inflammatory Monocyte

value: InfMono

value: IgG:Lo Ly6C:Hi CD115:+ Ly6G:- CD11c:- CD62L:+

value: Macrophage Lineage


title: InfMono-1

description:
CAGRF9188.1390
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: 07-04 Control myeloid

source_name: RNA from sorted cells

tag: Sex

value: Male

value: myeloid

value: Control

value: III


title: CMP-2

description:
CAGRF9188.1373
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Common Myeloid Progenitor

value: Common Myeloid Progenitor

value: CMP

value: Restricted Potential Progenitor


title: MonoBM-2

description:
CAGRF9188.1334
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Total Monocyte

value: Total Monocyte

value: MonoBM

value: Bone Marrow


title: MEP-1

description:
CAGRF9188.1369
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Megakaryocyte Erythrocyte Progenitor

value: Megakaryocyte Erythrocyte Progenitor

value: MEP


title: MonoBM-1

description:
CAGRF9188.1333
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: BCell-1

description:
CAGRF9188.1278
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Total B Cells

growth_protocol:
All cells were purified from mice between 7 and 12 weeks of age.
Peritoneal cavity was flushed with PBS to harvest the cells, before staining with antibodies and sorting on fluorescence cytometer

value: Total B Cells

value: BCell

value: Peritoneal Cavity Lavage

value: B Cell Lineage


title: BCell-2

description:
CAGRF9188.1283
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: Mast-2

description:
CAGRF9188.1246_1248_1289
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Mast Cell

value: Mast Cell

value: Mast

value: Mast Cell Lineage


title: Eo-3

description:
CAGRF9188.1423
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Eosinophils

value: Eo

value: Eosinophil Lineage


title: CLP-1

description:
CAGRF9188.1073_1074_1406_1407
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Common Lymphoid Progenitor

value: CLP

value: Lin:- cKit:Lo Sca1:Lo CD127rec:Lo CD135(Flt3):+


title: Mast-1

description:
CAGRF7126.1413
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: MonoPB-1

description:
CAGRF7126.1414
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Total Monocyte

value: MonoPB

value: Peripheral Blood

value: Macrophage Lineage


title: GMP-2

description:
CAGRF7126.1379
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Granulocyte Macrophage Progenitor

value: Granulocyte Macrophage Progenitor

value: GMP

value: Bone Marrow

value: Restricted Potential Progenitor


title: EryBlPO-1

description:
CAGRF9188.1408_1463
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Polychromatic erythroblasts (some Orthochromatic erythroblasts)

value: EryBlPO

value: Erythrocyte Lineage


title: GMP-1

description:
CAGRF7126.1377
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: EoP-2

description:
CAGRF7126.1376
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Eosinophil Progenitor

value: Eosinophil Progenitor

value: EoP


title: BasoCult-2

description:
CAGRF7126.1332
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Basophil

value: Basophil

value: BasoCult

value: Basophil Lineage

value: day 10 BM culture with SCF + IL-3


title: EoP-1

description:
CAGRF7126.1375
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Eosinophil Lineage


title: LSK-2

description:
CAGRF7126.1294
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: LSK MultiPotential Progenitor

value: LSK MultiPotential Progenitor

value: LSK

value: Lin-, c.Kit+ Sca-1+

value: Multi Potential Progenitor


title: Mac-2

description:
CAGRF7126.1286
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Macrophage

value: Macrophage

value: Mac

value: Peritoneal Cavity Lavage

value: Macrophage Lineage


title: CD4T-2

description:
CAGRF7126.1274
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Total CD4+ T

value: Total CD4+ T

value: Spleen and Lymph nodes

value: T Cell Lineage


title: CD4T-1

description:
CAGRF7126.1273
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: MEP-2

description:
CAGRF9188.1370
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Megakaryocyte Erythrocyte Progenitor

value: MEP

value: Bone Marrow

value: Restricted Potential Progenitor


title: CMP-1

description:
CAGRF9188.1371
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Common Myeloid Progenitor

value: CMP


title: CD8T-2

description:
CAGRF7126.1269
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Total CD8+ T

value: Total CD8+ T


title: NeutBM-2

description:
CAGRF7126.1250
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Neutrophil Bone Marrow

value: Neutrophil Bone Marrow

value: NeutBM

value: IL-5:hi, Ly6G:hi, Siglec-F-

value: Neutrophil Lineage


title: CD8T-1

description:
CAGRF7126.1267
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: NeutBM-1

description:
CAGRF7126.1249
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: PreCFUE-2

description:
CAGRF7126.1229
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Pre CFU-E

value: Pre CFU-E

value: PreCFUE

value: Lin- cKit+ Sca1- CD150- FcgRII/III (CD16/32)- Endoglinhi

value: Bone Marrow (Crush)

value: Erythrocyte Lineage


title: Eo-1

description:
CAGRF7126.1260
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Eosinophil

value: Eosinophil

value: Eo

value: IL-5:lo, Ly6G:-, Siglec-F+

value: Eosinophil Lineage


title: LSK-1

description:
CAGRF7126.1232
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: LSK MultiPotential Progenitor

value: LSK

value: Lin- cKit+ Sca1-

value: Multi Potential Progenitor


title: CFUE-2

description:
CAGRF7126.1223
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: CFU-E

value: CFU-E

value: CFUE


title: CFUE-1

description:
CAGRF7126.1222
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: MonoPB-2

description:
CAGRF7126.1415
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Total Monocyte

value: MonoPB

value: Peripheral Blood

value: Macrophage Lineage


title: BasoCult-1

description:
CAGRF7126.1213
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Basophil

value: BasoCult

value: Gr-1:- c.Kit:- CD49b:+ FcepsilonR1:+

value: Bone Marrow

value: Basophil Lineage

value: day 10 BM culture with SCF + IL-3


title: PreCFUE-1

description:
CAGRF7126.1217
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Pre CFU-E

value: PreCFUE

value: Bone Marrow (Crush)

value: Erythrocyte Lineage


title: MegSCF-2

description:
CAGRF7658.1385
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: MegSCF

value: Lin:- cKit:+ Sca1:- CD150:+

value: Megakaryocyte Lineage

value: day 3 BM culture with SCF


title: MegTPO-2

description:
CAGRF7658.1339
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: MegTPO

value: day 3 BM culture with TPO


title: MegSCF-1

description:
CAGRF7658.1384
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt


title: Mac-1

description:
CAGRF7126.1282
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Macrophage

value: Mac

value: Peritoneal Cavity Lavage

value: Macrophage Lineage


title: L1

status: Public on Jan 22 2017

city: Montpellier

first: Hervé

last: Seitz

address: 141 rue de la Cardonille

department: IGH (UMR 9002)

institute: CNRS

description:
Sample obtained from L1 starving larvae
L1_ctrl

hyb_protocol: Performed according to NimbleGen protocols

data_processing:
Array data was normalized using the Lowess method, then background-subtracted (defining background as the measured values in the L1_ctrl negative control, and subtracting only when both values are positive), then smoothed over a 5-probe sliding window (attributing the median value across all 5 probes to the middle probe)
The supplemental .txt files contains log-ratios (i.e.: log2(Cy5/Cy3) ) after normalization, background subtraction and smoothing (along with other data described in the readme.txt).

source_name: Negative control (L1 larvae)

growth_protocol: Synchronious culture in bioreactor

extract_protocol: Embryo and L1 pellets were thawed at 56°C for 2 min and lysed in lysis buffer (0.1M Tris-HCl pH 8.5, 0.1M NaCl, 30 mM EDTA, 0.5% SDS) at 56°C for 3 hr. Samples were digested with 200 μg/ml proteinase K at 37°C for 2 hr. After phenol/chloroform extraction and precipitation with 0.2 M NaCl and 2.5 vol of 100% ethanol, DNA was transferred into a new tube and washed with 5 ml of 70% ethanol at room temperature (RT) for 5 min and dried at 37°C. DNA was resuspended in 2 ml TEN20 (10 mM Tris-HCl pH 7.9, 2 mM EDTA, 20 mM NaCl, 0.1% SDS, 1000 U RNasin) at 65°C, boiled for 10-15 min and chilled on ice. For the RNase A negative control, two rounds of RNase A treatment (200 μg/ml) were performed before boiling. NS purification was carried out following the protocol described before (Cayrou, C.,et al. Methods 2012( except for two main modifications. The size of the selected fractions ranged from 300 bp to 2 kb, and three rounds of lambda exonuclease digestion were performed to decrease the signal from background DNA and to ensure the specific purification of replication origins. Purified NS samples and negative controls were amplified using the WGAII Kit (Sigma-Aldrich), omitting the first step of fragmentation. Amplification products were purified using Qiagen PCR purification columns.

tag: strain

tag: developmental stage/tissue

value: L1 larvae

source_name: L1 (hybridization control)


title: Mixed-embryos_1

description:
Sample obtained from embryos in all embryonic stages
Mixa

scan_protocol: Performed according to NimbleGen protocols

source_name: Mixed stage embryos

value: Mixed stage embryos


title: Mixed-embryos_3

description:
Sample obtained from embryos in all embryonic stages
Mixc

label_protocol: Performed according to NimbleGen protocols


title: ESC_PE_mRNA-Seq

status: Public on Jan 19 2017

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

department: Biological Chemistry

institute: UCLA

data_processing:
Basecalls performed using CASAVA version 1.4
Reads from RNA-seq experiments were mapped to the mouse genome (mm9) using TopHat software and only those reads that aligned with no more than two sequence mismatches were retained. RPKM values of mm9 RefSeq genes were calculated as described
HTSeq  was used to determine gene counts from replicate experiments, and DESeq2 for differential analysis
Genome_build: mm9
Supplementary_files_format_and_content: RPKM values are provided as part of table2

source_name: ESC

growth_protocol: All cell types (MEFs, 48h-OSKM inducing MEFs, pre-iPSCs, ESCs) were grown in standart mouse ESC media containing KO DMEM, 15% FBS, leukemia inhibiotry factor (Lig), b-mercaptoethanol, penicillin/streptomycin, L-glutamine and non-essential amino acids. Additionally, pre-iPSCs and ESCs were grown on irradiated feeders, but feeder-depleted and grown on gelatin overnight for genomics experiments. For the 48h reprogramming time-point, tetO-OSKM MEFs were cultures in ESC media containing 2ug/mL doxycycline for 48h to induce the expression of OSKM.

extract_protocol:
oligodt-selected mRNA
RNA was treated on column with 0.5 kunitz units of DNAse prior to elution according to manufacturers instructions. RNA from MEF cultures induced for 48h to express OSKM/Esrrb, OSKM/Fra1, OSKM/cJun or a single reprogramming factor (tetO-Oct4, tetO-Sox2, or tetO–Klf4, tetO–Myc) was also isolated. Messenger RNA was captured using oligodT Dynabeads (Life Technologies). Strand-specific RNA-seq libraries were constructed using a TruSeq Stranded mRNA library Prep Kit, following the manufacturers instructions (RS-122-2101). Stranded mRNA Library

value: ESC


title: Pre-Gastrula-embryos_1

description:
Sample obtained from embryos containing form 2 to 28 cells
2.40a

source_name: 2-28 cell embryos

treatment_protocol: Performed according to NimbleGen protocols

value: 2-28 cell embryos


title: Mixed-embryos_2

description:
Sample obtained from embryos in all embryonic stages
Mixb


title: RNase A

description:
Sample obtained from embryos in all embryonic stages and treated with RNAse A previous to NS purification
Rnase_ctrl

source_name: Negative control (Rnase A-treated)

value: Negative control


title: preiPSC1_PE_mRNA-Seq

source_name: pre-iPSC line 1(12.1)

value: pre-iPSC


title: Pre-gastrula-embryos_3

description:
Sample obtained from embryos containing form 2 to 28 cells
2.40c


title: 48h_OSKMcJun_mRNA-Seq

source_name: MEFs expressing OSKM and Flag-cJun for 48h

value: MEF


title: Pre-Gastrula-embryos_2

description:
Sample obtained from embryos containing form 2 to 28 cells
2.40b


title: 48h_OSKMEsrrb_repA_mRNA-Seq

source_name: MEFs expressing OSKM and Esrrb for 48h


title: 48h_OSKMEsrrb_repC_mRNA-Seq


title: MEF_PE_mRNA-Seq

source_name: mouse embryonic fibroblasts with incorporated but not expressing tetO-OSKM cassette


title: 48h_OSKMEsrrb_repB_mRNA-Seq


title: 48h_OSKM_PE_mRNA-Seq

source_name: MEFs expressing OSKM for 48h


title: MegTPO-1

description:
CAGRF7658.1338
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

value: Bone Marrow


title: 48h_OSKMFra1_mRNA-Seq

source_name: MEFs expressing OSKM and Flag-Fra1 for 48h


title: MEF_Klf4pMX_mRNA-Seq

source_name: MEFs expressing Klf4 from pMX vector for 48 h


title: MEF_Sox2tetO_mRNA-Seq

source_name: MEFs expressing Sox2 from inducible system for 48h


title: ESC_mRNA-Seq


title: preiPSC2_repA_mRNA-Seq

source_name: pre-iPSC line 2(1A2)


title: MEF_Oct4tetO_mRNA-Seq

source_name: MEFs expressing Oct4 from inducible system for 48h


title: preiPSC2_repB_mRNA-Seq


title: preiPSC1_mRNA-Seq


title: 48h_OSKM_repC_mRNA-Seq


title: EoSSCLo-3

description:
CAGRF11700.1567
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Eosinophil Low Side Scatter

value: Eosinophil Low Side Scatter

value: EoSSCLo

value: Eosinophil Lineage


title: 48h_OSKM_repB_mRNA-Seq


title: MEF_repC_mRNA-Seq


title: 48h_OSKM_repA_mRNA-Seq


title: adult wild type Muller glia (adult MG)_normalized

status: Public on Oct 31 2017

first: Stefanie

middle: G

last: Wohl

state: NY

address: 33w 42nd Street

department: Biological and Vision Sciences

institute: SUNY Optometry

description: pooled from 40 adult retinas

hyb_protocol: The miRtagged mature miRNA was then hybridized to a probe pair (reporter probe and capture probe) in the standard nCounter gene expression array workflow.

scan_protocol: 200 ng of total RNA per sample (33 ng/μl, n = 13 mice, pooled sample) was submitted for NanoString analysis, performed at the Fred Hutchinson Cancer Center in Seattle, WA, USA.

data_processing: Values from adult Dicer-CKO and wild type MG were normalized against 4 housekeeping genes (β -actin, GAPDH, Rpl19, and B2m), 8 negative controls, and 6 positive controls that were run simultaneously with the samples.

source_name: mouse retina_wildtype

label_protocol: NanoString nCounter® was used for miRNA expression analysis. DNA sequences called miRtags were ligated to the mature miRNAs through complementary oligonucleotides with sequence-specific binding (bridges). All excess tags and ridges were removed, resulting in sequence-specific tagging of mature miRNAs.

extract_protocol: The sorts of 26 retinas were pooled for the RNA-purification. RNA was extracted and purified with a miRNeasy Micro Kit in accordance with manufacturer’s instructions (Qiagen). For miRNA RT-qPCR, DNA stem-loop RT primers were used to produce cDNA for specific miRNAs.

treatment_protocol: Tamoxifen for cre activation: Tamoxifen (Sigma) was administered intraperitoneally at 75 mg/kg in corn oil at P11-14.

value: retina

tag: genotype

tag: condition

value: FACS-sorted

value: adult


title: EoCult-1

description:
CAGRF11700.1596
processed data file: Haemopedia-Mouse-RNASeq_raw.txt
processed data file: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Cultured Eosinophils

value: Cultured Eosinophils

value: EoCult

value: Embryonic day 10.5 Fetal liver

value: Cultured Fetal liver


title: adult Muller glia Dicer-CKO_normalized

description: pooled from 26 adult retinas

source_name: mouse retina_dicer

tag: age


title: MEF_repB_mRNA-Seq


title: 48h_Oct4_OSKMEsrrbChIP-Seq

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie aligner only those reads that aligned to a unique position with no more than two sequence mismatches were retained for further analysis
Histone mark signal was converted into wig files at 25 bp resolution
Histone marks were binarised using a p-value cut-off of 1e-4 and chromatin states were derived using chromHMM v1.1.0
TF peaks were called using MACS2 with the following setting:q-val <0.005 and Enrichment Fold (>=4).
Genome_build: mm9
Supplementary_files_format_and_content: peaks calls are provided as part of  Peak_calls_table

growth_protocol: All cell types (MEFs, 48h-OSKM inducing MEFs, pre-iPSCs, ESCs) were grown in standard mouse ESC media containing KO DMEM, 15% FBS, leukemia inhibiotry factor (Lig), b-mercaptoethanol, penicillin/streptomycin, L-glutamine and non-essential amino acids. Additionally, pre-iPSCs and ESCs were grown on irradiated feeders, but feeder-depleted and grown on gelatin overnight for genomics experiments. For the 48h reprogramming time-point, tetO-OSKM MEFs were cultures in ESC media containing 2ug/mL doxycycline for 48h to induce the expression of OSKM.

extract_protocol:
Histone Modifications were assesed by means of Native ChIP. 50 x 106 Nuclei were isolated from non-crosslinked cells (MEFs, 48hOSKM, pre-i#1 and ESC) by incubation in 2 mL of a hypotonic solution (0.3M sucrose, 60mM KCl, 15mM NaCl, 5mM MgCl2, 15mM Tris-HCl pH 7.5, 0.5mM DTT, 0.1% NP40, and protease inhibitor cocktail) followed by subsequent centrifugation through a sucrose cushion (1.2M sucrose, 60mM KCL, 15mM NaCl, 5mM MgCl2, 0.1mM EGTA, 15 mM Tris-HCl pH 7.5, 0.5mM DTT, and protease inhibitor cocktail). Nuclei were then re-suspended in MNAse-digestion buffer (0.32M sucrose, 50mM Tris-HCl pH 7.5, 4mM MgCl2, 1mM CaCl2, and protease inhibitor cocktail) and digested with 3 units of MNase (Roche 10107921001) for 10 minutes at 37oC. The first soluble fraction (S1) was recovered by centrifugation for 10 min at 10,000 rpm. The nuclei pellet was then dialyzed overnight in 1l of dialysis buffer (1mM Tris-HCl pH7.5, 0.2mM EDTA, protease inhibitors) to more completely release the chromatin fraction (S2) from nuclei. 10 ug of soluble chromatin (S1 and S2) was then incubated with 5 ug of antibodies targeting histone modifications-conjugated to magnetic beads (Active Motif; 53014) under constant stirring at 4oC for 16 hrs. The antibodies used were anti-H3K9ac (Abcam; ab4441), anti-H3K4me3 (Abcam; ab8580), anti-H3K4me2 (Abcam ab7766), anti-H3K4me1 (Abcam; ab8895), anti-H3K27me3 (Active Motif; 39155), antiH3K27ac (Abcam; ab4729), and anti-H3K36me3 (Abcam; ab9050). Beads were washed twice with wash buffer A (50mM Tris-HCl pH 7.5, 10mM EDTA, 75mM NaCl), wash buffer B (50mM Tris-HCl pH 7.5, 10mM EDTA, 125mM NaCl), and wash buffer C (50mM Tris-HCl pH 7.5, 10mM EDTA, 175 mM NaCl). DNA was extracted using phenol:chloroform:iso-amylacohol and used for downstream library construction. DNA from fractions S1 and S2 was also isolated directly using phenol:chloroform:iso-amylacohol extraction and used as an whole genome input control (native Input). All protocols for Illumina/Solexa sequencing library preparation, sequencing, and quality control were performed as recommended by Illumina, with the minor modification of limiting the PCR amplification step to 10 cycles. All constructed libraries were sequenced using single-end 50 bp sequencing reactions.
Transcription factor occupancy data generated in this study were acquired using ChIP after crosslinking cells. X-ChIP was also employed for mapping H3K79me2 (Active Motif, 39143), H3K9me3 (abcam, ab8898 or Millipore, 05-1242), H3 (abcam, ab1791) and H3.3 (Abnova, H00003021-M01). Briefly, cells were grown to a final concentration of 5x107 cells for each ChIP-seq experiment. To stabilize HATs/HDACs (p300, Hdac1) and Brg1 on chromatin, cells were treated with 2 mM disuccinimidyl glutarate (DSG) for 10 minutes prior to formaldehyde crosslinking. For all other antibodies used, cells were chemically cross-linked at room temperature by the addition of formaldehyde to 1% final concentration for 10 minutes and quenched with 0.125 M final concentration glycine. Cross-linked cells were re-suspended in sonication buffer (50mM Hepes-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% TritonX-100, 0.1% Na-deoxycholate, 0.1% SDS) and sonicated using a Diagenode Bioruptor for three 10-minute rounds using pulsing settings (30 sec ON; 1 min OFF). 10 ug of sonicated chromatin was then incubated overnight at 4oC with 5 ug of antibodies-conjugated to magnetic beads. The antibodies used were: anti-Esrrb (RnD; H6705), anti-Klf4 (RnD; AF3158), anti-cMyc (RnD; AF3696), anti-Nanog (cosmobio REC-RCAB001P), anti-Oct4 (RnD; AF1759), anti-Sox2 (RnD AF2018), anti-p300 (SantaCruz;sc-585), anti-Runx1 (Novus Biologicals NBP1-61277), anti-Fra1 (SantaCruz;sc-183X), anti-Cebpa (SantaCruz; sc-61X), anti-Cebpb (SantaCruz;sc-150X), anti-Hdac1(abcam; ab7028) and anti-Brg1(abcam; ab110641). Following the IP the beads were washed twice with RIPA buffer (50mM Tris-HCl pH8, 150 mM NaCl, 2mM EDTA, 1% NP-40, 0.1% Na-deocycholate, 0.1% SDS), low salt buffer (20mM Tris pH 8.1, 150mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), high salt buffer (20mM Tris pH 8.1, 500mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), LiCl buffer (10mM Tris pH 8.1, 250mM LiCl, 1mM EDTA, 1% Na-deoxycholate, 1% NP-40), and 1xTE. Finally, DNA was extracted by reverse crosslinking at 60oC overnight with proteinase K (20ug/ul) and 1% SDS followed by phenol:chloroform:iso-amylacohol purification. Libraries were constructed as indicated above and sequenced using single-end 50 bp sequencing reactions
Libraries were prepared according to Illumina's instructions accompanying the TruSeq library preparation kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: MEF_repA_mRNA-Seq


title: 48h_Klf4_OSKMEsrrbChIP-Seq


title: preiPSC#1_Cebpb_ChIP-Seq


title: MEF_Cebpb_ChIP-Seq

source_name: mouse embryonic fibroblasts


title: ESC_Nanog_ChIP-seq

source_name: ESC


title: ESC_Esrrb_ChIP-seq


title: 48h_FlagFra1_OSKMFra1ChIP-Seq


title: 48h_Oct4_OSKMFra1ChIP-Seq


title: 48h_Cebpa_ChIP-Seq


title: 48h_Fra1_ChIP-Seq


title: 48h_Runx1_ChIP-Seq


title: MEF_Cebpa_ChIP-Seq


title: MEF_Runx1_ChIP-Seq


title: MEF_Fra1_ChIP-Seq


title: 48h_Brg1_ChIP-Seq


title: ESC_Brg1_ChIP-Seq


title: MEF_Brg1_ChIP-Seq


title: preiPSC#1_Brg1_ChIP-Seq


title: 48h_H3K27ac_OSKMEsrrbChIP-Seq


title: 48h_Klf4_OSKMFra1ChIP-Seq


title: 48h_Esrrb_OSKMEsrrbChIP-Seq


title: ESC_Hdac1_ChIP-Seq


title: 48h_Cebpb_ChIP-Seq


title: preiPSC#1_Hdac1_ChIP-Seq


title: ESC_p300_ChIP-Seq


title: MEF_Hdac1_ChIP-Seq


title: 48h_Klf4_OSKpMX_ChIP-seq

source_name: MEFs expressing Oct4,Sox2,Klf4 from pMX vector for 48h


title: 48h_p300_ChIP-Seq


title: MEF_p300_ChIP-Seq


title: preiPSC#1_p300_ChIP-Seq

source_name: pre-iPSC line 1(12.1)


title: 48h_endoKlf4_OSpMX_ChIP-seq

source_name: MEFs expressing Oct4,Sox2 from pMX vector for 48h


title: 48h_Sox2_OSpMX_ChIP-seq


title: 48h_Sox2_OSKpMX_ChIP-seq


title: 48h_Klf4_SKpMX_ChIP-seq

source_name: MEFs expressing Sox2,Klf4 from pMX vector for 48h


title: 48h_Sox2_SKpMX_ChIP-seq


title: 48h_Oct4_OSpMX_ChIP-seq


title: 48h_Klf4_OKpMX_ChIP-seq

source_name: MEFs expressing Oct4,Klf4 from pMX vector for 48h


title: 48h_Sox2_SpMX_ChIP-seq

source_name: MEFs expressing Sox2 from pMX vector for 48h


title: 48h_Hdac1_ChIP-Seq

source_name: MEFs expressing OSKM for 48h


title: 48h_Oct4_OpMX_ChIP-seq

source_name: MEFs expressing Oct4 from pMX vector for 48h


title: 48h_endoK_OtetO_ChIP-seq

source_name: MEFs expressing Oct4 from inducible system for 48


title: 48h_H3K27ac_OtetO_ChIP-seq


title: 48h_Oct4_OKpMX_ChIP-seq


title: 48h_Sox2_StetO_ChIP-seq

source_name: MEFs expressing Sox2 from inducible system for 48h


title: 48h_endoK_StetO_ChIP-seq


title: 48h_Oct4_OtetO_ChIP-seq

source_name: MEFs expressing Oct4 from inducible system for 48h


title: 48h_Klf4_KtetO_ChIP-seq

source_name: MEFs expressing Klf4 from inducible system for 48h


title: ESC_cMyc_ChIP_seq


title: pre-iPSC#2_Klf4_ChIP_seq

source_name: pre-iPSC line 2(1A2)


title: pre-iPSC#2_cMyc_ChIP_seq


title: ESC_Klf4_ChIP_seq


title: ESC_Sox2_ChIP_seq


title: ESC_Oct4_ChIP_seq


title: 48h_Klf4_KpMX_ChIP-seq

source_name: MEFs expressing Klf4 from pMX vector for 48h


title: pre-iPSC#2_Sox2_ChIP_seq


title: pre-iPSC#1_cMyc_ChIP_seq


title: 48h_Oct4_OSKpMX_ChIP-seq


title: pre-iPSC#1_Oct4_ChIP_seq


title: pre-iPSC#1_Klf4_ChIP_seq


title: pre-iPSC#1_Sox2_ChIP_seq


title: 48h_cMyc_OSKM_ChIP_seq


title: pre-iPSC#2_Oct4_ChIP_seq


title: 48h_Klf4_OSKM_ChIP_seq


title: 48h_Oct4_OSKM_ChIP_seq