title: primed_primed_Oct4_RNA_2

status: Public on Jul 05 2017

first: Florian

last: Halbritter

institute: St. Anna Children's Cancer Research Institute (CCRI)

description:
other RNA
STARR-RNA-seq for GFP-positve RNA from primed hESCs transfected with a OCT4 ChIP-STARR-seq library generated in primed hESCs

data_processing:
Library strategy: STARR-Seq
Base-calling using default Illumina software by Edinburgh Genomics
Adapter contaminants trimmed using Skewer; 125bp reads were trimmed to 50bp for consistency
Reads aligned to GRCh37/h19 genome using Bowtie2 (default parameters + “--very-sensitive”)
Only properly paired, concordantly aligning and uniquely mapping fragments
Read counts summed up per unique (chromsome,start-read1,end-read2) coordinate
Genome_build: hg19
Supplementary_files_format_and_content: tab-separated text file with read counts per coordinate

source_name: embryonic stem cells

growth_protocol: H9 human embryonic stem cells were cultured on Matrigel coated cell culture plates, using mTesR1 medium (Stem Cell Technology, 05850). Cells were routinely split (ratio 1:3-1:4) using 0.5mM EDTA (Invitrogen, 15575020). For transfection, single cells were obtained by Accutase treatment (Invitrogen, A1110501), in the presence of Rock inhibitor, Y-27632 (10uM, Cambridge bioscience, SM02-10). For conversion to the naive state, cells were split on irradiated MEFs on gelatin coated plates and media was changed to NHSM media, as described by Gafni et al. (Gafni et al., 2013), containing knockout DMEM (Invitrogen ), 20% knockout serum (Invitrogen), human insulin (Sigma, 12.5ug ml-1 final concentration), 20 ng ml-1 recombinant human LIF (Millipore), 8 ng ml-1 recombinant bFGF (Peprotech) and 1 ng ml-1 recombinant TGF-beta1 (Peprotech), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM beta-mercaptoethanol (Invitrogen), penicillin-streptomycin (Invitrogen) and small molecule inhibitors: PD0325901 (1uM, ERK1/2i, Axon Medchem); CHIR99021 (3uM, GSKbetai, Axon Medchem); SP600125 (10uM, JNKi, Abcam ab120065) and SB203580 (10 uM, p38i,Abcam ab120638) Y-27632 (5uM, ROCKi) and protein kinase C inhibitor G06983 (5 uM, PKCi, Abcam, ab144414). Cells were 1:10 passaged using TrypLETM (Invitrogen, 12604021) in the presence of Rock inhibitor and maintained for more than 10 passages in NHSM media prior to analysis. All cells were regularly karyotyped and checked for the presence of mycoplasm.

extract_protocol:
A minimum of 400,000 GFP-positive, sorted cells were used to isolate total RNA using Trizol (Thermo Fisher) according to manufacturer’s instructions.
The mRNA fraction was captured using Oligo (dT)25 beads (61002, Life Technologies) and DNAseI treated (18068-015, Life Technologies), followed by reverse transcription using 2 ul SuperscriptIII (18080-044, Life Technologies) using a GFP-mRNA specific primer (149 STARRseq rep RNA cDNA synth, CAAACTCATCAATGTATCTTATCATG) at 50ᴼC for 90 minutes, in a total reaction volume of 21 ul. To repress residual plasmid DNA contamination, cDNA was PCR amplified using a combination of primers (152 STARR reporter specific primer 2 fw, GGGCCAGCTGTTGGGGTG*T*C*C*A*C and 153 STARR reporter specific primer 2 rv, CTTATCATGTCTGCTCGA*A*G*C, where * represent phosphorothioate bonds) spanning a synthetic intron in the STARR-seq plasmid, as previously described (Arnold et al., 2013). PCR was performed with Phusion polymerase and High-fidelity buffer, in 6 x 50 ul reactions (cycling conditions: 98ᴼC 2 min, (98ᴼC 10 sec, 62ᴼC 30 sec, 72ᴼC 70 sec) x15, 72ᴼC 5 min, 4ᴼC hold). PCR reactions were pooled, purified using AMPureXP beads (1.0x) and eluted in 18 ul 0.1xTE. Absence of significant plasmid contamination in the PCR amplified cDNA was assessed by qPCR using a primer-set amplifying an amplicon from the STARR-seq plasmid backbone (161 STARRseq detect plasmid backbone qPCR fw, CATCATCGGGAATCGTTCTT, and 162 STARRSeq detect plasmid backbone qPCR rv, TGAAGATCAACTGGGTGCAA), relative to a primer-set amplifying GFP (154 STARRseq GFP fw, ACGGCCACAAGTTCTCTGTC, and 155 STARRseq GFP rv, GCAGTTTGCCAGTAGTGCAG). PCR amplified cDNA was then used in a second round of PCR to add Illumina index primers (7335, 7500, NEB) using priming on the adapter sequences added during the plasmid library generation. PCR was performed in 1-4x 50 ul reactions using Phusion polymerase and High-fidelity buffer (NEB)(cycling conditions: 98ᴼC 2 min, (98ᴼC 10 sec, 65ᴼC 30 sec, 72ᴼC 30 sec) x13, 72ᴼC 5 min, 4ᴼC hold), after which PCR reactions were pooled, purified using AMPureXP beads (1.0x) and eluted in 15 ul 0.1xTE. Quantity and quality of generated sequencing libraries was assessed on an Agilent Tapestation.

treatment_protocol: Primed and naive H9 hESCs were transfected using either Nucleofection (Lonza, VPH-5022), or using Lipofectamin3000 according to manufacturer’s instructions. For each transfection, six million cells were used and transfected with 8 ug of plasmid library DNA and 500 ng pmCherry-N1 plasmid (Clonetech) as transfection control. Cells were incubated in 10 cm dishes and 24h post-transfection, single cells were harvested and subjected to FACS. Non-transfected cells were used to set sorting gates, DAPI was used as a marker for dead cells.

tag: cell state source

value: Primed

tag: cell state target

tag: chip target


title: primed_naive_Oct4_RNA_2

type: SRA

city: Vienna

address: Zimmermannplatz 10

country: Austria

description:
other RNA
STARR-RNA-seq for GFP-positve RNA from naive hESCs transfected with a OCT4 ChIP-STARR-seq library generated in primed hESCs

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

value: Naive


title: Yersinia pestis transposon mutant library cultured at 37ºC (replicate 2)

status: Public on Jul 06 2017

city: Exeter

first: ZhengRong

last: Yang

address: Prince of Wales Road

country: United Kingdom

institute: University of Exeter

description: Yersinia pestis mutant library cultured at 37ºC (replicate 2)

library_source: genomic

data_processing:
BWA was used to align the data
RD values - Relative distance to distal ends for each transposon insertion in genes
Supplementary_files_format_and_content: RD
Genome_build: Yersinia pestis CO92 complete genome - AL590842

molecule: genomic DNA

organism: Yersinia pestis

growth_protocol: Grown in blood agar base (BAB) broth

extract_protocol:
genomic DNA extracted using the Gentra Puregene kit (Qiagen)
The gDNA was fragmented to <500 base pairs (bp) using 2 x 15 minute cycles at 4ºC in a BioRuptor sonicator (medium intensity, 30s on/90s off).  A NEBNext DNA library preparation for Illumina kit (NEB) was used according to the manufacturer’s instructions, to end repair, A-tail and ligate adapters to the fragments.  Parallel polymerase chain reaction (PCR) samples were set up with 10 μl JumpStart 10x buffer, 6 μl MgCl2, 2 μl 10mM nucleoside triphosphates (dNTPs), 0.6 μl 100 μM PE_PCR_V3.3 primer, 0.6 μl 100 μM Yp_EzTn_PCR primer, 1 μl JumpStart Taq DNA polymerase and 28.8 μl nuclease-free water per reaction.  Primer sequences are listed in Additional file 2, Table S2.  The reactions were amplified at 94oC for 2 minutes, (94oC for 30 seconds, 60oC for 20 seconds, 72oC for 30 seconds) for 22 cycles, 72oC for 10 minutes, then held at 12oC.  PCR products were pooled and ethanol precipitated before being size selected on a 2% (w/v) agarose tris-borate-EDTA (TBE) gel.  Agarose blocks corresponding to 350-500 bp were excised, and the DNA extracted using a Qiagen MinElute Gel Extraction kit as per the manufacturer’s instructions
The DNA was quantified by qPCR and on an Agilent BioAnalyzer before being submitted for sequencing as 100 bp single end reads on an Illumina HiSeq 2500 standard model.

treatment_protocol: Growth at 28ºC or 37ºC

tag: strain

tag: growth conditions

value: cultured at 37ºC


title: primed_primed_Oct4_RNA_1


title: naive_primed_Oct4_RNA_2

description:
other RNA
STARR-RNA-seq for GFP-positve RNA from primed hESCs transfected with a OCT4 ChIP-STARR-seq library generated in naive hESCs


title: Yersinia pestis transposon mutant library cultured at 28ºC (replicate 1)

description: Yersinia pestis mutant library cultured at 28ºC (replicate 1)

value: cultured at 28ºC


title: primed_naive_Oct4_RNA_1


title: A673/TR/shEF_MRTFB_ChIP_48hdox_rep2

first: Maximilian

last: Kauer

department: Molecular Biology

institute: CCRI, St.Anna Children Cancer Research Institute

description:
ChIP antibody: MKL-2 A302-767A (Bethly laboratories)
MRTFB (MKL-2) ChIP-seq under serum-induced + 1µg/ml dox conditions
MRTFB_SI dox_2

data_processing:
HiSeq Control Software, VN:2.2.58, Basecalling Package, VN:1.18.64.0
reads were aligned to the hs37d5 (ftp://ftp.1000genomes.ebi.ac.uk/) genome assembly using the bwa aligner
ChIP-seq peaks were identified with MACS2
Genome_build: hs37d5 (ftp://ftp.1000genomes.ebi.ac.uk/)
Supplementary_files_format_and_content: output from MACS2 (*peaks.xls)

source_name: Ewing Sarcoma cell line

growth_protocol: The A673/TR/shEF cell line (Carrillo, Garcia-Aragoncillo et al. 2007), stable carrying a sh-EWS-Fli1 construct under a doxycycline-inducible promoter to induce efficient knockdown of the EWS-FLI1 protein was kindly provided by Javier Alonso (Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain) and cultivated in DMEM+Glutamax (Gibco by Life Technologies, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS) (10270) (Gibco by Life Technologies, Carlsbad, CA, USA), 100 U/mL penicillin, and 100 µg/mL streptomycin (Gibco by Life Technologies, Carlsbad, CA, USA) with the addition of blastizidin (2µg/ml) and zeocin (50µg/ml) (InvivoGen, San Diego, CA, USA) at 37°C and 5% CO2.

extract_protocol:
Approximately 10 million cells were harvested and double crosslinked using disuccinimidyl glutarate (DSG) (16434) and formaldehyde (FA) (28906) (Thermo Fisher Scientific, Waltham, MA, USA). ChIP was performed as described previously (Nowak, Tian et al. 2005), with some adaptations. Briefly, cells were harvested and crosslinked with 0.5M DSG for 20 minutes at room temperature. Pellets were washed twice and cells were crosslinked for 5 minutes with 1% FA. Cells were washed and subsequently lysed in the lysis buffers described in the reference above previously to sonication with Covaris ultrasonicator  for 15 minutes. Sheared chromatin was incubated with 5µg of the respective antibody over-night. For immunoprecipitation 50µl/ChIP of the Protein G Dynabeads (10004D) (Thermo Fisher Scientific, Waltham, MA, USA) was used.
Approximately 5ng ChIP-DNA was used for library prep with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina (#E7370S) and the NEBNext® Multiplex Oligos for Illumina®  (Index Primers Set 1) (NEB #E7335) (New England Biolabs, Frankfurt, Germany) were used for adapter labelling in a multiplex sample preparation. The NEBNext Q5 Hot Start HIFI PCR Master mix was used and no size-selection of adapter-ligated DNA was performed. Library preparation was accomplished according to the the manufacturer’s instructions.

treatment_protocol: To efficiently knockdown EWS-FLI1 1µg/ml doxycycline (dox) was added to the medium for 48 h. For serum-induction cells were washed twice with 1Xphosphate-buffered saline (PBS) (14190) (Gibco by Life Technologies, Carlsbad, CA, USA) and starved over-night in medium containing 0.2% FBS. The next day cells were treated for 60 minutes with the respective medium containing 20% FBS.

tag: treatment

value: doxycycline induction:48 h; serum-induction


title: Yersinia pestis transposon mutant library cultured at 37ºC (replicate 3)

description: Yersinia pestis mutant library cultured at 37ºC (replicate 3)


title: primed_primed_Nanog_RNA_2

description:
other RNA
STARR-RNA-seq for GFP-positve RNA from primed hESCs transfected with a NANOG ChIP-STARR-seq library generated in primed hESCs

value: NANOG


title: naive_naive_Oct4_RNA_2

description:
other RNA
STARR-RNA-seq for GFP-positve RNA from naive hESCs transfected with a OCT4 ChIP-STARR-seq library generated in naive hESCs


title: naive_primed_Oct4_RNA_1


title: naive_naive_Oct4_RNA_1


title: primed_primed_Nanog_RNA_1


title: primed_naive_Nanog_RNA_2

description:
other RNA
STARR-RNA-seq for GFP-positve RNA from naive hESCs transfected with a NANOG ChIP-STARR-seq library generated in primed hESCs


title: naive_primed_Nanog_RNA_2

description:
other RNA
STARR-RNA-seq for GFP-positve RNA from primed hESCs transfected with a NANOG ChIP-STARR-seq library generated in naive hESCs


title: naive_primed_Nanog_RNA_1


title: naive_naive_Nanog_RNA_2

description:
other RNA
STARR-RNA-seq for GFP-positve RNA from naive hESCs transfected with a NANOG ChIP-STARR-seq library generated in naive hESCs


title: naive_naive_Nanog_RNA_1


title: primed_primed_Input_RNA_2

description:
other RNA
STARR-RNA-seq for GFP-positve RNA from primed hESCs transfected with a total input STARR-seq library generated in primed hESCs

value: Input


title: primed_naive_Input_RNA_2

description:
other RNA
STARR-RNA-seq for GFP-positve RNA from naive hESCs transfected with a total input STARR-seq library generated in primed hESCs


title: primed_primed_Input_RNA_1


title: primed_primed_H3K4me1_RNA_2

description:
other RNA
STARR-RNA-seq for GFP-positve RNA from primed hESCs transfected with a H3K4me1 ChIP-STARR-seq library generated in primed hESCs


title: primed_naive_Input_RNA_1


title: primed_primed_H3K4me1_RNA_1


title: naive_naive_H3K4me1_RNA_2

description:
other RNA
STARR-RNA-seq for GFP-positve RNA from naive hESCs transfected with a H3K4me1 ChIP-STARR-seq library generated in naive hESCs


title: naive_naive_H3K27ac_RNA_1

description:
other RNA
STARR-RNA-seq for GFP-positve RNA from naive hESCs transfected with a H3K27ac ChIP-STARR-seq library generated in naive hESCs


title: primed_primed_H3K27ac_RNA_2

description:
other RNA
STARR-RNA-seq for GFP-positve RNA from primed hESCs transfected with a H3K27ac ChIP-STARR-seq library generated in primed hESCs


title: naive_naive_H3K4me1_RNA_1


title: naive_naive_H3K27ac_RNA_2


title: primed_Oct4_plasmid_1

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from OCT4 ChIP in primed hESCs

data_processing:
Library strategy: DNA-Seq
Base-calling using default Illumina software by Edinburgh Genomics
Adapter contaminants trimmed using Skewer
Reads aligned to GRCh37/h19 genome using Bowtie2 (default parameters + “--very-sensitive”)
Only properly paired, concordantly aligning and uniquely mapping fragments
Read counts summed up per unique (chromsome,start-read1,end-read2) coordinate
Genome_build: hg19
Supplementary_files_format_and_content: Read counts summed up per unique (chromosome,start-read1,end-read2) coordinate

extract_protocol:
For chromatin immunoprecipitation, 2x10^7 H9 primed or naive hESC were harvested in 9 ml of medium and cross-linked by addition of 270 ul 37% Formaldehyde (Sigma, final concentration of 1%), for 10 min at room temperature under rotation. 1 ml of 1.25 M Glycine was added, cells were incubated on ice for 5 min and 3x washed with ice cold PBS. At this point, cross-linked cell pellets were snap-frozen and stored at -80ᴼC, or immediately processed for sonication. Prior to sonication, cells were resuspended in 1ml TE-I-NP40 (10mM TRIS-HCl pH 8, 1mM EDTA, 0.5% NP40, 1mM PMSF, 1x Protease inhibitor complex (PIC, Complete tablets, 04693116001, Roche)) incubated on ice for 5 min and centrifuged for 5 min at 2500 rpm at 4ᴼC in a refrigerated bench top centrifuge (Eppendorf). Supernatant was removed and nuclei were resuspended in 1 ml ice-cold lysis buffer (50mM TRIS-HCl pH 8, 10mM EDTA, 1% SDS, 1mM PMSF, 1x PIC) and transferred to a 15 ml Falcon tube for sonication, using a Diagenode Bioruptor Next Gen (40 cycles of 30” on, 30” off). After transfer to an Eppendorf tube and centrifugation for 10 min at 13200 rpm at 4ᴼC, chromatin solution was aliquoted and used for immunoprecipitation or snap-frozen and stored at -80ᴼC. A 20 µl sample was taken and served as a total input control. For immunoprecipitation, Protein Dynabeads G (10004D, Life Techology) were washed with PBS and incubated for 6 hours with 5 ug of antibody, at 4ᴼC on a rotating wheel. Antibodies used were: goat-anti-NANOG (AF1997, R&D Systems), rabbit-anti-OCT4 (AB19857, Abcam), rabbit-anti-H3K4me1 (AB8895, Abcam) and rabbit-anti-H3K27ac (AB4729, Abcam); as a control, respective IgG antibodies were used (rabbit-IgG: 10500C, Life Technology, goat-IgG: SC-2028, Santa Cruz Biotechnology). After washing with PBS, antibody-coupled beads were incubated with 200 ul chromatin solution, diluted to a final volume of 2 ml with dilution buffer (167mM NaCl, 16.7mM TRIS-HCl pH 8.1, 1.2mM EDTA, 0.01% SDS, 1.1% Triton-X100, 1mM PMSF, 1x PIC), overnight at 4ᴼC on a rotating wheel. Washing of beads was performed by incubation with ice-cold 1 ml of washing buffer, for 5 min, at 4ᴼC on a rotating wheel, followed by removal of supernatant using a magnetic stand, for each of the following: 2x with wash buffer 1 (10mM TRIS-HCl pH 7.6, 1mM EDTA, 0.1% SDS, 1% Triton-X100, 0.1% NaDeoxychloate), 2x with wash buffer 2 (10mM TRIS-HCl pH 7.6, 1mM EDTA, 0.1% SDS, 1% Triton-X100, 0.1% NaDeoxychloate, 150mM NaCl), 2x with wash buffer 3 (250mM LiCl, 0.5% NP40, 0.1% NaDeoxychloate), 1x with TE 1x with 0.2% TritonX-100 and 1x with TE 1x, after which beads were resuspended in 100ul TE1x. Immunoprecipitated chromatin and total input control were decross-linked, by addition of 3 ul of 10% SDS and 5 ul Proteinase K (20 ug/ul, Roche) and 10 ul RNAse A (50 ug/ul, Roche) to each tube and incubation overnight at 65°C on a shaking thermomixer block, 1400 rpm (Eppendorf). The next day, beads were briefly vortexed and supernatants were transferred to new tubes using the magnetic stand. 100ul of TE1x containing 500mM NaCl was added to the beads and briefly vortexed, after which the supernatant was added to the first fraction of collected supernatant. Following Phenol / chloroform extraction, DNA was precipitated using 1ul glycogen (20mg/ml), 1/10 vol NaOAc (3M) and 100% ice-cold Ethanol, at -20°C for 1 hour, followed by centrifugation at 13200 rpm for 1 hour at 4ᴼC. After a final wash with 70% ethanol, the DNA pellet was dried and resuspended in 50ul H2O. Concentration of ChIP DNA was determined by Qubit measurement following manufacturer’s instructions and sonication was assessed by gel-electrophoresis of total input DNA (target fragment size between 200 and 600 bp).
For ChIP-seq and ChIP-STARR-seq plasmid library generation, 10 ng of ChIP DNA was used as starting material. Using NEB Next ChIP-seq library preparation kit (E6200 or E6240, NEB), DNA was end-repaired, dA-tailed and adapter-ligated according to manufacturer’s instructions. After adapter ligation and purification using AMPure-XP beads (0.8x, Beckman Coulter) and elution into 30ul of 0.1xTE, 25 ul of the reaction product was used for ChIP-seq library preparation, by PCR amplification with Illumina index primers (7335 and 7500, NEB) using the NEB Next Q Hot start high fidelity master mix (M0543S, NEB) according to manufactures instructions (cycle conditions: 98ᴼC 30 sec, (98ᴼC 10 sec, 65ᴼC 75 sec) x15, 65ᴼC 5 min, 4ᴼC hold). After an additional round of AMPureXP bead purification, DNA was eluted in 0.1xTE without further size selection. Quality and quantity of the prepared ChIP-seq libraries was assessed on an Agilent Tapestation.   The remaining 5 ul of purified adapter ligated DNA were used for ChIP-STARR-seq plasmid library generation. Therefore, DNA was diluted to a total volume of 10 ul in 0.1xTE and used as an input in 8 x 50ul PCR reactions using Phusion Polymerase, High-fidelity buffer (M0530L, NEB) and primers 147 STARRseq libr FW (TAGAGCATGCACCGGACACTCTTTCCCTACACGACGCTCTTCCGATCT) and 148 STARRseq libr RV (GGCCGAATTCGTCGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) (Arnold et al., 2013), which prime on the adapter sequences and add a 5’and 3’ 15 nucleotide homology sequence to the reaction products which are used for Gibson assembly. After PCR amplification (cycle conditions: 98ᴼ 2 min, (98ᴼC 10 sec, 62ᴼC 30 sec, 72ᴼC 30 sec) x 15, 72ᴼC 5 min, 4ᴼC hold), PCR reactions were pooled, purified using AMPure XP beads (1.8x), eluted in 30 ul 0.1xTE and used for Gibson assembly. Therefore, 15 ug of the mammalian STARRseq plasmid (a kind gift of A.Stark) (Arnold et al., 2013) were digested with AgeI-HF and SalI-HF (NEB) for 8h at 37ᴼC, column purified (Nucleospin purification columns, 740609250, Machery-Nagel), eluted in 30 ul elution buffer and used as a vector in a Gibson reaction, using 2 ul of digested plasmid, 5 ul purified PCR product, 3 ul H20 and 10 ul of a home-made Gibson reaction (100mM Tris-HCl, 10mM MgCl2, 0.2 mM dNTP (each), 0.5U Phusion DNA polymerase (NEB), 0.16U 5’ T5 exonuclease (Epicentre), 2 Gibson reactions per library. After incubation at 50ᴼC for 1 hour, Gibson reaction were pooled and precipitated by addition of 1 ul Glycogen (20 ug/ul, Roche, 1090139300), 5 ul NaOAc (3M) and 125 ul ice-cold 100% ethanol, incubation at -20ᴼC for 1 hour and centrifugation for 1 hour at 13200 rpm at 4ᴼC, followed by a final wash in 70% ethanol. After air drying, DNA pellet was dissolved in 10 ul water and used for electroporation into electrocompetent MegaX DH10beta E.coli bacteria (Invitrogen), according to manufacturer’s instructions, using a Biorad pulser. A total of 5 electroporations per library were performed with each 2 ul of DNA. After recovery in 1 ml SOCS medium each, bacteria were grown for 1 hour at 37ᴼC in a bacterial shaker in the absence of antibiotics. Then, the remaining 5 ml of bacteria culture were incubated in a total volume of 2 liter of LB-media supplemented with Ampicillin and allowed to grow for 16 hours in a bacterial shaker at 37ᴼC. Plasmid DNA was isolated using a Qiagen Maxiprep kit according to manufacturer’s instructions and eluted in 500 ul 10mM Tris-HCl, pH 7.4. Concentration was determined by Nanodrop measurement. Plasmid DNA was amplified for sequencing by a nested PCR, using primers detecting the STARR-seq plasmid (160 STARR reporter specific primer for plasmid DNA fw, GGGCCAGCTGTTGGGGTG, and 153 STARR reporter specific primer 2 rv, CTTATCATGTCTGCTCGA*A*G*C, where * represent phosphorothioate bonds) and Illumina index primers.

tag: cell state


title: naive_Oct4_plasmid_1

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from OCT4 ChIP in naive hESCs


title: primed_Input_plasmid_1

description:
plasmid DNA
DNA-seq of STARR-seq plasmid library constructed from total input DNA in primed hESCs


title: primed_H3K4me1_plasmid_1

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from H3K4me1 ChIP in primed hESCs


title: primed_naive_Nanog_RNA_1


title: naive_Nanog_plasmid_1

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from NANOG ChIP in naive hESCs


title: primed_Nanog_plasmid_1

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from NANOG ChIP in primed hESCs


title: primed_H3K27ac_plasmid_1

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from H3K27ac ChIP in primed hESCs


title: primed_primed_Oct4_extplasmid_1

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from OCT4 ChIP in primed hESCs after transfection into primed hESCs, replicate 1

data_processing:
Library strategy: DNA-Seq
Base-calling using default Illumina software by Edinburgh Genomics
Adapter contaminants trimmed using Skewer
Reads aligned to GRCh37/h19 genome using Bowtie2 (default parameters + “--very-sensitive”)
Only properly paired, concordantly aligning and uniquely mapping fragments
Read counts summed up per unique (chromsome,start-read1,end-read2) coordinate
Genome_build: hg19
Supplementary_files_format_and_content: tab-separated text file with read counts per coordinate

growth_protocol: H9 human embryonic stem cells were cultured on Matrigel coated cell culture plates, using mTesR1 medium (Stem Cell Technology, 05850). Cells were routinely split (ratio 1:3-1:4) using 0.5mM EDTA (Invitrogen, 15575020). For transfection, single cells were obtained by Accutase treatment (Invitrogen, A1110501), in the presence of Rock inhibitor, Y-27632 (10uM, Cambridge bioscience, SM02-10). All cells were regularly karyotyped and checked for the presence of mycoplasm.

extract_protocol:
24 h post transfection, plasmid was isolated from transfected cells using a Qiagen miniprep isolation kit according to manufacturer’s instructions.
Re-isolated plasmid DNA was amplified in a nested PCR, using primers detecting the STARR-seq plasmid (160 STARR reporter specific primer for plasmid DNA fw, GGGCCAGCTGTTGGGGTG, and 153 STARR reporter specific primer 2 rv, CTTATCATGTCTGCTCGA*A*G*C, where * represent phosphorothioate bonds) and Illumina index primers.  Quantity and quality of generated sequencing libraries was assessed on an Agilent Tapestation.

treatment_protocol: Primed H9 hESCs were transfected using Lipofectamin3000 according to manufacturer’s instructions. For each transfection, six million cells were used and transfected with 8 ug of plasmid library DNA and 500 ng pmCherry-N1 plasmid (Clonetech) as transfection control.


title: primed_primed_Oct4_extplasmid_2

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from OCT4 ChIP in primed hESCs after transfection into primed hESCs, replicate 2


title: primed_primed_Nanog_extplasmid_2

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from NANOG ChIP in primed hESCs after transfection into primed hESCs, replicate 2


title: primed_primed_Nanog_extplasmid_1

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from NANOG ChIP in primed hESCs after transfection into primed hESCs, replicate 1


title: primed_primed_Input_extplasmid_2

description:
plasmid DNA
DNA-seq of STARR-seq plasmid library constructed from total input DNA in primed hESCs after transfection into primed hESCs, replicate 2


title: primed_primed_H3K27ac_RNA_1


title: primed_primed_H3K4me1_extplasmid_1

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from H3K4me1 ChIP in primed hESCs after transfection into primed hESCs, replicate 1


title: primed_primed_H3K27ac_extplasmid_2

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from H3K27ac ChIP in primed hESCs after transfection into primed hESCs, replicate 2


title: primed_Oct4_ChIP_1

description: ChIP-seq for OCT4 in primed hESCs

data_processing:
Base-calling using default Illumina software by Edinburgh Genomics
Genome_build: hg19

growth_protocol: H9 human embryonic stem cells were cultured on Matrigel coated cell culture plates, using mTesR1 medium (Stem Cell Technology, 05850). Cells were routinely split (ratio 1:3-1:4) using 0.5mM EDTA (Invitrogen, 15575020). For transfection, single cells were obtained by Accutase treatment (Invitrogen, A1110501), in the presence of Rock inhibitor, Y-27632 (10uM, Cambridge bioscience, SM02-10). For conversion to the naive state, cells were split on irradiated MEFs on gelatin coated plates and media was changed to NHSM media, as described by Gafni et al. (Gafni et al., 2013), containing knockout DMEM (Invitrogen ), 20% knockout serum (Invitrogen), human insulin (Sigma, 12.5ug ml-1 final concentration), 20 ng ml-1 recombinant human LIF (Millipore), 8 ng ml-1 recombinant bFGF (Peprotech) and 1 ng ml-1 recombinant TGF-beta1 (Peprotech), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM beta-mercaptoethanol (Invitrogen), penicillin-streptomycin (Invitrogen) and small molecule inhibitors: PD0325901 (1uM, ERK1/2i, Axon Medchem); CHIR99021 (3uM, GSKbetaetai, Axon Medchem); SP600125 (10uM, JNKi, Abcam ab120065) and SB203580 (10 uM, p38i,Abcam ab120638) Y-27632 (5uM, ROCKi) and protein kinase C inhibitor G06983 (5 uM, PKCi, Abcam, ab144414). Cells were 1:10 passaged using TrypLETM (Invitrogen, 12604021) in the presence of Rock inhibitor and maintained for more than 10 passages in NHSM media prior to analysis. All cells were regularly karyotyped and checked for the presence of mycoplasm.

extract_protocol:
For chromatin immunoprecipitation, 2x10^7 H9 primed or naive hESC were harvested in 9 ml of medium and cross-linked by addition of 270 ul 37% Formaldehyde (Sigma, final concentration of 1%), for 10 min at room temperature under rotation. 1 ml of 1.25 M Glycine was added, cells were incubated on ice for 5 min and 3x washed with ice cold PBS. At this point, cross-linked cell pellets were snap-frozen and stored at -80ᴼC, or immediately processed for sonication. Prior to sonication, cells were resuspended in 1ml TE-I-NP40 (10mM TRIS-HCl pH 8, 1mM EDTA, 0.5% NP40, 1mM PMSF, 1x Protease inhibitor complex (PIC, Complete tablets, 04693116001, Roche)) incubated on ice for 5 min and centrifuged for 5 min at 2500 rpm at 4ᴼC in a refrigerated bench top centrifuge (Eppendorf). Supernatant was removed and nuclei were resuspended in 1 ml ice-cold lysis buffer (50mM TRIS-HCl pH 8, 10mM EDTA, 1% SDS, 1mM PMSF, 1x PIC) and transferred to a 15 ml Falcon tube for sonication, using a Diagenode Bioruptor Next Gen (40 cycles of 30” on, 30” off). After transfer to an Eppendorf tube and centrifugation for 10 min at 13200 rpm at 4ᴼC, chromatin solution was aliquoted and used for immunoprecipitation or snap-frozen and stored at -80ᴼC. A 20 µl sample was taken and served as a total input control. For immunoprecipitation, Protein Dynabeads G (10004D, Life Techology) were washed with PBS and incubated for 6 hours with 5 ug of antibody, at 4ᴼC on a rotating wheel. Antibodies used were: goat-anti-NANOG (AF1997, R&D Systems), rabbit-anti-OCT4 (AB19857, Abcam), rabbit-anti-H3K4me1 (AB8895, Abcam) and rabbit-anti-H3K27ac (AB4729, Abcam); as a control, respective IgG antibodies were used (rabbit-IgG: 10500C, Life Technology, goat-IgG: SC-2028, Santa Cruz Biotechnology). After washing with PBS, antibody-coupled beads were incubated with 200 ul chromatin solution, diluted to a final volume of 2 ml with dilution buffer (167mM NaCl, 16.7mM TRIS-HCl pH 8.1, 1.2mM EDTA, 0.01% SDS, 1.1% Triton-X100, 1mM PMSF, 1x PIC), overnight at 4ᴼC on a rotating wheel. Washing of beads was performed by incubation with ice-cold 1 ml of washing buffer, for 5 min, at 4ᴼC on a rotating wheel, followed by removal of supernatant using a magnetic stand, for each of the following: 2x with wash buffer 1 (10mM TRIS-HCl pH 7.6, 1mM EDTA, 0.1% SDS, 1% Triton-X100, 0.1% NaDeoxychloate), 2x with wash buffer 2 (10mM TRIS-HCl pH 7.6, 1mM EDTA, 0.1% SDS, 1% Triton-X100, 0.1% NaDeoxychloate, 150mM NaCl), 2x with wash buffer 3 (250mM LiCl, 0.5% NP40, 0.1% NaDeoxychloate), 1x with TE 1x with 0.2% TritonX-100 and 1x with TE 1x, after which beads were resuspended in 100ul TE1x. Immunoprecipitated chromatin and total input control were decross-linked, by addition of 3 ul of 10% SDS and 5 ul Proteinase K (20 ug/ul, Roche) and 10 ul RNAse A (50 ug/ul, Roche) to each tube and incubation overnight at 65°C on a shaking thermomixer block, 1400 rpm (Eppendorf). The next day, beads were briefly vortexed and supernatants were transferred to new tubes using the magnetic stand. 100ul of TE1x containing 500mM NaCl was added to the beads and briefly vortexed, after which the supernatant was added to the first fraction of collected supernatant. Following Phenol / chloroform extraction, DNA was precipitated using 1ul glycogen (20mg/ml), 1/10 vol NaOAc (3M) and 100% ice-cold Ethanol, at -20°C for 1 hour, followed by centrifugation at 13200 rpm for 1 hour at 4ᴼC. After a final wash with 70% ethanol, the DNA pellet was dried and resuspended in 50ul H2O. Concentration of ChIP DNA was determined by Qubit measurement following manufacturer’s instructions and sonication was assessed by gel-electrophoresis of total input DNA (target fragment size between 200 and 600 bp).
For ChIP-seq library generation, 10 ng of ChIP DNA was used as starting material. Using NEB Next ChIP-seq library preparation kit (E6200 or E6240, NEB), DNA was end-repaired, dA-tailed and adapter-ligated according to manufacturer’s instructions. After adapter ligation and purification using AMPure-XP beads (0.8x, Beckman Coulter) and elution into 30ul of 0.1xTE, 25 ul of the reaction product was used for ChIP-seq library preparation, by PCR amplification with Illumina index primers (7335 and 7500, NEB) using the NEB Next Q Hot start high fidelity master mix (M0543S, NEB) according to manufactures instructions (cycle conditions: 98ᴼC 30 sec, (98ᴼC 10 sec, 65ᴼC 75 sec) x15, 65ᴼC 5 min, 4ᴼC hold). After an additional round of AMPureXP bead purification, DNA was eluted in 0.1xTE without further size selection. Quality and quantity of the prepared ChIP-seq libraries was assessed on an Agilent Tapestation.


title: primed_primed_H3K27ac_extplasmid_1

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from H3K27ac ChIP in primed hESCs after transfection into primed hESCs, replicate 1


title: primed_Nanog_ChIP_1

description: ChIP-seq for NANOG in primed hESCs


title: naive_Oct4_ChIP_1

description: ChIP-seq for OCT4 in naive hESCs


title: naive_Nanog_ChIP_1

description: ChIP-seq for NANOG in naive hESCs


title: primed_Input_ChIP_1

description: ChIP-seq total input control in primed hESCs


title: naive_Input_ChIP_1

description: ChIP-seq total input control in naive hESCs


title: primed_H3K4me1_ChIP_1

description: ChIP-seq for H3K4me1 in primed hESCs


title: naive_H3K4me1_ChIP_1

description: ChIP-seq for H3K4me1 in naive hESCs


title: primed_H3K27ac_ChIP_1

description: ChIP-seq for H3K27ac in primed hESCs


title: naive_H3K4me1_plasmid_1

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from H3K4me1 ChIP in naive hESCs


title: naive_H3K27ac_ChIP_1

description: ChIP-seq for H3K27ac in naive hESCs


title: naive_H3K27ac_plasmid_1

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from H3K27ac ChIP in naive hESCs


title: Doc1_IgG

city: Rotterdam

first: C. Peter

last: Verrijzer

address: Dr Molewaterplein 50

department: Department of Biochemistry

country: Netherlands

institute: Erasmus MC

data_processing:
Reads were trimmed prior to alignment with Trimmomatic (v0.33) to remove Illumina adapters.
The trimmed ChIP-Seq reads were aligned to the human genome (hg19) using bwa mem (v0.7.12-r1039).
Sambamba (v0.5.9) was used to sort and generate BAM index files and retrieve post-alignment statistics.
Non-uniquely mapped reads were removed using samtools (v1.2) (bitwise flag 3844) prior to downstream peak analysis.
Narrow peak calling was performed by MACS2 (v2.1.1.20160309) with a q-value cutoff of 0.01 using respective mock controls (LacZ_IgG/DOC1_IgG) per sample to reduce background noise and artifacts.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *narrowPeak files were generated by running MACS2 (v2.1.1.20160309) with a q-value cutoff of 0.01 using respective mock controls (LacZ_IgG/DOC1_IgG) per sample to reduce background noise and artifacts. These files contain the MACS2-called ChIP-Seq peaks.

source_name: Squamous cell carcinoma cell line SCC9, +DOC1, IgG ChIP

growth_protocol: Squamous cell carcinoma cell line SCC9 was cultured at 37 degrees Celsius in Dulbecco’s modified Eagle’s medium (DMEM/F12). Media was supplemented with 10% fetal calf serum (FCS), 1% penicillin/streptomycin and 400 ng/ml hydrocortisone.

extract_protocol:
Elution buffer (1% SDS, 100 mM NaHCO3) followed by PCR purification kit/columns.
Samples were prepared for ChIP sequencing according to the NEXTflex ChIP-Seq kit (Bioo Scientific). Briefly, 10 ng of chromatin was end repaired and enriched for the 300-400 bp fraction using Ampure XP beads (Agencourt). The repaired DNA library was 3’ end adenylated and barcoded Illumina adaptors were ligated followed by bead purification. The adaptor modified library was enriched by PCR for 18 cycles. The ChIP libraries were sequenced according to the Illumina TruSeq Rapid v2 protocol on the HiSeq2500 for a single read 50bp in length and a 7bp index read.

treatment_protocol: Cells were fixed with 1% formaldehyde for 10-15 minutes at RT, crosslinking was stopped by the addition of glycine (0.125 M) for 5-10 minutes. After washes with ice-cold PBS, cells were collected by scraping and pelleted in ice-cold PBS. Cells were lysed in ChIP buffer (50 mM Tris-HCl, pH 8.1, 1% SDS, 10 mM EDTA, and protease inhibitors PMSF, aprotinin, leupeptin, pepstatin).

tag: cell type

value: Squamous cell carcinoma cell line

tag: doc1 status

tag: chip antibody

value: anti-IgG


title: primed_primed_Input_extplasmid_1

description:
plasmid DNA
DNA-seq of STARR-seq plasmid library constructed from total input DNA in primed hESCs after transfection into primed hESCs, replicate 1


title: lacZ-CHD4_ChIP-1

source_name: Squamous cell carcinoma cell line SCC9, -DOC1, CHD4 ChIP


title: DOC1-CHD4_ChIP-2

source_name: Squamous cell carcinoma cell line SCC9, +DOC1, CHD4 ChIP


title: DOC1-CHD4_ChIP-3


title: LacZ_IgG

source_name: Squamous cell carcinoma cell line SCC9, -DOC1, IgG ChIP


title: lacZ-CHD4_ChIP-3


title: DOC1-CHD4_ChIP-1


title: hu_lean NK IL6Ra- replicate 4

city: Köln (Cologne)

first: Sebastian

last: Theurich

address: Gleueler Str. 50

country: Germany

institute: Max-Planck-Institute for Metabolism Research and University Hospital of Cologne

description:
FPKM_RUN1861.xlsx
hNKctrl23-

data_processing:
Illumina Casava software used for basecalling
RNAseq reads were aligned homo_sapiens and mus_musculus
Fragments Per Kilobase of exon per Million mapped fragments (FPKM) were calculated using a Cufflinks
Genome_build: human genome build 38.p10 and mm10
Supplementary_files_format_and_content: excel files
Single cell Data
Read 2 of each read pair was first 3' trimmed for adapters, base quality and poly-A tails using cutadapt 1.9.1 (http://dx.doi.org/10.14806/ej.17.1.200). Remaining sequences were mapped to the mouse genome GRCm38 (primary assembly) using STAR-2.5.2b (https://www.ncbi.nlm.nih.gov/pubmed/23104886). Gene models were used according to gencode version M9 (https://www.ncbi.nlm.nih.gov/pubmed/26187010). Gene summarization was done using featureCounts 1.5.0-p1 (https://www.ncbi.nlm.nih.gov/pubmed/24227677) collapsing exons to genes and excluding pseudogenes and transcripts with a biotype related to "decay". Multimapping reads were discarded.
Cell and gene demultiplexing was done using the cell-barcode and the unique molecular identifier (UMI) present in the first 12nt of Read 1 of the read pair. Libraries L1/L3/L5/L7 use cell barcodes 1-96 and libraries L2/L4/L6/L9 use cell barcodes 97-192. Only exact matches were counted.
Data analysis was performed using RaceID2 and StemID algorithm (Grün et al., 2016). Downsampling to 800 transcripts was used for data normalization. K-medoids clustering was performed using log-pearson  correlation as a distance metric. The minimum suitable cluster number (=3) characterizing the dataset was determined by computing Jaccard’s similarity for each cluster by bootstrapping for k-medoids clustering with different cluster numbers. The minimum number yielding a Jaccard’s similarity >0.6 for all clusters was selected. The t-distributed stochastic neighbor embedding (t-SNE) algorithm was used for dimensional reduction and cell cluster visualization (Maaten and Hinton, 2008). RaceID2 was executed with the probability threshold value for outlier identification set to <10 -3. The StemID algorithm was used to infer a dedifferentiation trajectory. A p-value threshold of 0.05 was chosen to assign significance to the links.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-separated text file with transcript counts per gene (corrected for UMI saturation effects according to Grün, Kester and van Oudenaarden (2014) ), text file with cell barcodes

source_name: Sorted NK cells from PBMC

growth_protocol: Diet induced obesity model: Mice were set on ad libitum high-fat-diet (HFD) or normal control diet (CD).

extract_protocol:
NK cell subpopulations from murine organs and blood or human blood were purified from single cell suspensions using FACSAria-III or FACSAria-Fusion cell sorters (BD Bioscience) after immunostainings as described above. In mice, NK cells were sorted from obese versus lean animals identified as single, viable CD45+ CD3- NK1.1+ CD11b+ mature NK cells. Final sorting gates of human NK cells identified IL6Ra+ versus IL6Ra- CD3- CD56+ single cells. Purified cells were directly sorted into RNA-protect cell reagent (Qiagen, Germany).   Stabilized, purified NK cell populations were pelleted by centrifugation and total RNA was extracted using the Arcturus RNA picopure Kit (KIT0204, ThermoFisher Scientific) following the manufacturer´s instructions. RNA integrity was assessed with the Agilent 2100 Bioanalyzer.
For organs and bulk sorted NK cells: RNA libraries were prepared from a minimum of 100ng total RNA using the TruSeq® RNA sample preparation Kit v2 (Illumina). Complementary DNA (cDNA) was transcribed from poly-A selected RNA, which served for library generation. Libraries were sequenced in replicates for 30 million reads on an Illumina HiSeq 2000 sequencer with a paired-end (101x7x101 cycles) protocol.
Single cells were sorted in 384-well plates containing 240nL of primer mix and 1.2uL of PCR encapsulation barrier, Vapor-Lock (Qiagen GmbH, Germany). Single cell RNA sequencing was performed using CEL-Seq2 method (Hashimshony et al., 2016) with several modifications.  Importantly, a fivefold volume reduction was achieved using a nanoliter-scale pipetting robot, Mosquito HTS (TTP Labtech).  Sorted plates were centrifuged at 2200g for 10min at 4°C, snap-froze in liquid nitrogen and stored at -80°C until processed. 160nL of reverse transcription reaction mix and 2.2μl of second strand reaction mix was used to convert RNA into cDNA. cDNA from 96-cells was pooled together before clean up and in vitro transcription, generating 4 libraries from one 384-well plate. 0.8μl of AMPure/RNAClean XP beads (Beckman Coulter GmbH, Germany) per 1μl of sample were used during all the purification steps including library cleanup. 8 libraries (768 single cells) were sequenced in a single lane (pair-end multiplexing run, Read 1 30bp Read 2 120bp read length) of Illumina NextSeq 500 sequencing system generating 200 million sequence fragments.

treatment_protocol: Organs and / or cells were harvested and isolated after completion of the diet periods of time indicated in the manuscript.

tag: il6ra expression

value: negative

tag: organ

value: PBMC

tag: bmi

value: lean


title: hu_lean NK IL6Ra- replicate 3

description:
FPKM_RUN1861.xlsx
hNKctrl21-


title: hu_lean NK IL6Ra+ replicate 4

description:
FPKM_RUN1861.xlsx
hNKctrl23+

value: positive


title: hu_lean NK IL6Ra+ replicate 3

description:
FPKM_RUN1861.xlsx
hNKctrl21+


title: mu_CD_IL6Raflox_Liver replicate 3

description:
FPKM_RUN1666.xlsx
IL6Ra_flox_Liv_CD_3

data_processing:
Illumina Casava software used for basecalling
RNAseq reads were aligned homo_sapiens and mus_musculus
Fragments Per Kilobase of exon per Million mapped fragments (FPKM) were calculated using a Cufflinks
Genome_build: human genome build 38.p10 and mm10
Supplementary_files_format_and_content: excel files
Single cell Data
Read 2 of each read pair was first 3' trimmed for adapters, base quality and poly-A tails using cutadapt 1.9.1 (http://dx.doi.org/10.14806/ej.17.1.200). Remaining sequences were mapped to the mouse genome GRCm38 (primary assembly) using STAR-2.5.2b (https://www.ncbi.nlm.nih.gov/pubmed/23104886). Gene models were used according to gencode version M9 (https://www.ncbi.nlm.nih.gov/pubmed/26187010). Gene summarization was done using featureCounts 1.5.0-p1 (https://www.ncbi.nlm.nih.gov/pubmed/24227677) collapsing exons to genes and excluding pseudogenes and transcripts with a biotype related to "decay". Multimapping reads were discarded.
Cell and gene demultiplexing was done using the cell-barcode and the unique molecular identifier (UMI) present in the first 12nt of Read 1 of the read pair. Libraries L1/L3/L5/L7 use cell barcodes 1-96 and libraries L2/L4/L6/L9 use cell barcodes 97-192. Only exact matches were counted.
Data analysis was performed using RaceID2 and StemID algorithm (Grün et al., 2016). Downsampling to 800 transcripts was used for data normalization. K-medoids clustering was performed using log-pearson  correlation as a distance metric. The minimum suitable cluster number (=3) characterizing the dataset was determined by computing Jaccard’s similarity for each cluster by bootstrapping for k-medoids clustering with different cluster numbers. The minimum number yielding a Jaccard’s similarity >0.6 for all clusters was selected. The t-distributed stochastic neighbor embedding (t-SNE) algorithm was used for dimensional reduction and cell cluster visualization (Maaten and Hinton, 2008). RaceID2 was executed with the probability threshold value for outlier identification set to <10 -3. The StemID algorithm was used to infer a dedifferentiation trajectory. A p-value threshold of 0.05 was chosen to assign significance to the links.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text file with transcript counts per gene (corrected for UMI saturation effects according to Grün, Kester and van Oudenaarden (2014) ), text file with cell barcodes

organism: Mus musculus

source_name: Liver

tag: diet

value: CD

value: Liver

tag: il6ra deletion in nk cells (del or flox)

value: flox


title: mu_CD_IL6Raflox_Liver replicate 2

description:
FPKM_RUN1666.xlsx
IL6Ra_flox_Liv_CD_1


title: hu_lean NK IL6Ra- replicate 2

description:
FPKM_RUN1861.xlsx
hNKctrl8-


title: primed_primed_H3K4me1_extplasmid_2

description:
plasmid DNA
DNA-seq of ChIP-STARR-seq plasmid library constructed from H3K4me1 ChIP in primed hESCs after transfection into primed hESCs, replicate 2


title: hu_lean NK IL6Ra+ replicate 2

description:
FPKM_RUN1861.xlsx
hNKctrl8+


title: mu_CD_IL6Raflox_Liver replicate 1

description:
FPKM_RUN1666.xlsx
IL6Ra_flox_Liv_CD_2


title: mu_CD_IL6RaNKdel_Liver replicate 3

description:
FPKM_RUN1666.xlsx
IL6Ra_delNK_Liv_CD_3

value: del


title: mu_CD_IL6RaNKdel_Liver replicate 2

description:
FPKM_RUN1666.xlsx
IL6Ra_delNK_Liv_CD_2


title: mu_HFD_IL6Raflox_PGAT replicate 3

description:
FPKM_RUN1666.xlsx
IL6Ra_flox_VAT_HFD_3

source_name: PGAT

value: HFD

value: PGAT


title: mu_HFD_IL6Raflox_PGAT replicate 2

description:
FPKM_RUN1666.xlsx
IL6Ra_flox_VAT_HFD_2


title: mu_CD_IL6RaNKdel_Liver replicate 1

description:
FPKM_RUN1666.xlsx
IL6Ra_delNK_Liv_CD_1


title: hu_lean NK IL6Ra- replicate 1

description:
FPKM_RUN1861.xlsx
hNKctrl1-


title: mu_HFD_IL6Raflox_PGAT replicate 1

description:
FPKM_RUN1666.xlsx
IL6Ra_flox_VAT_HFD_1


title: mu_HFD_IL6RaNKdel_PGAT replicate 3

description:
FPKM_RUN1666.xlsx
IL6Ra_delNK_VAT_HFD_3


title: mu_HFD_IL6RaNKdel_PGAT replicate 2

description:
FPKM_RUN1666.xlsx
IL6Ra_delNK_VAT_HFD_2


title: hu_lean NK IL6Ra+ replicate 1

description:
FPKM_RUN1861.xlsx
hNKctrl1+


title: lacZ-CHD4_ChIP-2


title: mu_HFD_IL6RaNKdel_PGAT replicate 1

description:
FPKM_RUN1666.xlsx
IL6Ra_delNK_VAT_HFD_1


title: mu_CD_IL6Raflox_PGAT replicate 2

description:
FPKM_RUN1666.xlsx
IL6Ra_flox_VAT_CD_2


title: mu_CD_IL6Raflox_PGAT replicate 3

description:
FPKM_RUN1666.xlsx
IL6Ra_flox_VAT_CD_3


title: hu_obese NK IL6Ra- replicate 2

description:
FPKM_RUN1861.xlsx
hNKob8-

value: obese


title: mu_CD_IL6RaNKdel_PGAT replicate 2

description:
FPKM_RUN1666.xlsx
IL6Ra_delNK_VAT_CD_2


title: mu_CD_IL6Raflox_PGAT replicate 1

description:
FPKM_RUN1666.xlsx
IL6Ra_flox_VAT_CD_1


title: hu_obese NK IL6Ra+ replicate 2

description:
FPKM_RUN1861.xlsx
hNKob8+


title: mu_CD_IL6RaNKdel_PGAT replicate 3

description:
FPKM_RUN1666.xlsx
IL6Ra_delNK_VAT_CD_3


title: hu_obese NK IL6Ra- replicate 3

description:
FPKM_RUN1861.xlsx
hNKob7-


title: mu_HFD_IL6Raflox_Liver replicate 3

description:
FPKM_RUN1666.xlsx
IL6Ra_flox_Liv_HFD_3


title: mu_CD_IL6RaNKdel_PGAT replicate 1

description:
FPKM_RUN1666.xlsx
IL6Ra_delNK_VAT_CD_1


title: mu_HFD_IL6Raflox_Liver replicate 2

description:
FPKM_RUN1666.xlsx
IL6Ra_flox_Liv_HFD_2


title: hu_obese NK IL6Ra- replicate 1

description:
FPKM_RUN1861.xlsx
hNKob2-


title: mu_HFD_IL6Raflox_Liver replicate 1

description:
FPKM_RUN1666.xlsx
IL6Ra_flox_Liv_HFD_1


title: mu_HFD_IL6RaNKdel_Liver replicate 3

description:
FPKM_RUN1666.xlsx
IL6Ra_delNK_Liv_HFD_3


title: hu_obese NK IL6Ra+ replicate 1

description:
FPKM_RUN1861.xlsx
hNKob2+


title: mu_single NK cells PGAT HFD_CD_IL6Ra Library 8

description:
all_cells_mouse_mm10.txt
L8_P2_96cells

molecule: polyA RNA

source_name: Flow sorted NK cells isolated from PGAT

tag: library no.

tag: plate no.


title: mu_HFD_IL6RaNKdel_Liver replicate 2

description:
FPKM_RUN1666.xlsx
IL6Ra_delNK_Liv_HFD_2


title: mu_HFD_IL6RaNKdel_Liver replicate 1

description:
FPKM_RUN1666.xlsx
IL6Ra_delNK_Liv_HFD_1


title: mu_HFD_PGAT_NK_IL6Ra+ replicate 3

description:
FPKM_RUN1675.xlsx
B5HVAThi

source_name: Sorted NK cells from PGAT

tag: il6ra expression in nk cells


title: mu_single NK cells PGAT HFD_CD_IL6Ra Library 7

description:
all_cells_mouse_mm10.txt
L7_P2_96cells


title: mu_single NK cells PGAT HFD_CD_IL6Ra Library 6

description:
all_cells_mouse_mm10.txt
L6_P2_96cells


title: mu_CD_PGAT_NK_IL6Ra- replicate 3

description:
FPKM_RUN1675.xlsx
B3CVATmat


title: mu_CD_PGAT_NK_IL6Ra- replicate 2

description:
FPKM_RUN1675.xlsx
B2CVATmat


title: mu_CD_Blood_NK_IL6Ra- replicate 2

description:
FPKM_RUN1675.xlsx
B2CpBmat

source_name: Sorted NK cells from blood

value: Blood


title: mu_HFD_PGAT_NK_IL6Ra+ replicate 2

description:
FPKM_RUN1675.xlsx
B4HVAThi


title: mu_single NK cells PGAT HFD_CD_IL6Ra Library 5

description:
all_cells_mouse_mm10.txt
L5_P2_96cells


title: mu_CD_Blood_NK_IL6Ra- replicate 1

description:
FPKM_RUN1675.xlsx
B1CpBmat


title: mu_CD_PGAT_NK_IL6Ra- replicate 1

description:
FPKM_RUN1675.xlsx
B1CVATmat


title: hu_obese NK IL6Ra+ replicate 3

description:
FPKM_RUN1861.xlsx
hNKob14+


title: mu_HFD_PGAT_NK_IL6Ra+ replicate 1

description:
FPKM_RUN1675.xlsx
B3HVAThi


title: mu_HFD_PGAT_NK_IL6Ra- replicate 2

description:
FPKM_RUN1675.xlsx
B2HVATmat


title: mu_single NK cells PGAT HFD_CD_IL6Ra Library 4

description:
all_cells_mouse_mm10.txt
L4_P1_96cells


title: mu_single NK cells PGAT HFD_CD_IL6Ra Library 2

description:
all_cells_mouse_mm10.txt
L2_P1_96cells


title: mu_single NK cells PGAT HFD_CD_IL6Ra Library 3

description:
all_cells_mouse_mm10.txt
L3_P1_96cells


title: mu_HFD_Blood_NK_IL6Ra+ replicate 3

description:
FPKM_RUN1675.xlsx
B3HpBhi


title: mu_HFD_PGAT_NK_IL6Ra- replicate 1

description:
FPKM_RUN1675.xlsx
B1HVATmat


title: mu_HFD_PGAT_NK_IL6Ra- replicate 3

description:
FPKM_RUN1675.xlsx
B3HVATmat


title: mu_single NK cells PGAT HFD_CD_IL6Ra Library 1

description:
all_cells_mouse_mm10.txt
L1_P1_96cells


title: mu_HFD_Blood_NK_IL6Ra- replicate 3

description:
FPKM_RUN1675.xlsx
B3HpBmat


title: mu_HFD_Blood_NK_IL6Ra- replicate 1

description:
FPKM_RUN1675.xlsx
B1HpBmat


title: mu_HFD_Blood_NK_IL6Ra+ replicate 2

description:
FPKM_RUN1675.xlsx
B2HpBhi


title: tw18 /tw18

city: Berlin

first: Jinhua

last: Liu

address: Ihnestra§e 73

institute: Max Planck Institute for Molecular Genetics

description: embryos obtained from matings of tw18/+ mice

data_processing:
Reads were mapped to the mm10 genome (containing chromosomes 1-19, X, Y and M) with TopHat2 (version 2..0.8b) using bowtie (version 1.0.0) and providing refSeq annotations in gtf format (UCSC) and the options  -g1 --library-type fr-firststrand.
For calculation of FPKM’s, we used Cuffdiff, part of Cufflinks (version 2.2.1) with the options -u --no-effective-length-correction -b.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-seperated file containing gene symbols and the corresponding FPKM values.

source_name: tw18 homozygote epiblast

extract_protocol:
RNA was extracted embryo epiblasts using the RNeasy Micro Kit (Qiagen).
Total RNA-Seq were generated using the TotalScript RNA-Seq-Seq Kit (Epicentre) with random hexamers according to manufacturer’s instructions with slight modifications. Briefly, all reagents during the cDNA synthesis steps were scaled down in order to achieve a total volume of 39µl, allowing all of the material to be used in the subsequent tagmentation procedure. To further improve strand-specificity of the libraries, Actinomycin D was added to the first strand cDNA synthesis reaction at 5ng/µl final concentration and the libraries were finally amplified using 14 PCR cycles. Quantification was performed using the Qubit high sensitivity DNA assay (Invitrogen) and the libraries were verified using the DNA HS Bioanalyzer chips (Agilent).

tag: developmental stage

tag: genotype

tag: tissue

value: epiblast


title: S._tsukubaensis_32_h_R2_TEX_pos

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
FastQ quality trimming using FastX (version 0.0.13)  and a cut-off value of 20
Adaptor trimming using cutadapt version 1.10
Fastq to fasta conversion using FastX  FastX (version 0.0.13)
PolyA removal and size filtering by READemption 0.4.3
Read alignment using READemption 0.4.3 and segemehl 0.2.0
Coverage calculation using READemption 0.4.3
Genome_build: AJSZ00000000.1
Supplementary_files_format_and_content: wiggle

organism: Streptomyces tsukubensis NRRL18488

source_name: gram positive bacteria

growth_protocol: Precultures of S. tsukubaensis NRRL18488 were grown from spore stocks in TSB medium for 2 days at 28°C at 200 rpm. Microtiter plates were prepared with 3 mL of MGm 2.5  medium per well, inoculated with 75 μL preculture and cultures were grown at 28°C at 300 rpm. Mycelia for RNA extraction and sequencing were harvested after 16 and 32 h of growth.

extract_protocol:
For stabilization of the RNA the culture was mixed with twice the amount of RNA protect, incubated for 5 min at RT and centrifuged. The resulting pellet was stored until RNA extraction at -80°C. After cell lysis RNA was extracted using the hot phenol method.
The RNA samples were poly(A)-tailed using poly(A) polymerase. Then, the 5'PPP structures were removed using RNA 5' Polyphosphatase (5'PP, Epicentre). Afterwards, an RNA adapter was ligated to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified to about 10-20 ng/µl using a high fidelity DNA polymerase. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and were analyzed by capillary electrophoresis.

treatment_protocol: Sample were collected after 16 or 32 h

value: Terminator Exonuclease treated

tag: strain


title: S._tsukubaensis_16_h_3_TEX_pos

tag: treatment


title: tw18/+

source_name: tw18 heterozygote epiblast


title: S._tsukubaensis_32_h_R1_TEX_neg


title: mu_HFD_Blood_NK_IL6Ra+ replicate 1

description:
FPKM_RUN1675.xlsx
B1HpBhi


title: S._tsukubaensis_16_h_5_TEX_pos


title: S._tsukubaensis_16_h_5_TEX_neg


title: B.Fem.Sp#1

status: Public on Jul 04 2017

city: Boston

first: Liang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

country: USA

institute: Harvard Medical School

description:
Female, CD19+Igm+TCRb-CD4-
B.Fem.Sp.bw

data_processing:
Trimming for adapter sequences and low quality reads (original script and sickle1.2)
Mapping of reads to the mouse reference genome (mm10) with bowtie aligner version 2.2.4
Filtering out non-uniquely mapped reads by samtools view -q 30 (samtools 0.1.19)
Removing chrM mapped reads (0.1~20%, median=4.1%) and duplicated reads (7~69%, median=22%) by Picard Tools (picard-1.138) to prepare bam files for each sample
Removing mapped fragments which are spanning more than 120bp to improve resolutions and decrease technical sample-to-sample deviations in pile-up tarces
Merging replicates for a population and computing piling-up traces with macs2 (2.1.1)
Normalization of pile-up traces by quantile normalization taking every 25bp bin to make bigwig files for each population
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Spleen

extract_protocol:
Immunocytes were isolated to high purity by flow cytometry according to ImmGen SOP using the antibodies and gates manifested in ImmGen website (www.immgen.org). After the 2nd rounds of sorting, 10,000 cells (except very rare cell populations including LTHSC.34-.BM, LTHSC.34+.BM and STHSC.150-.BM which were sorted 677, 2483 and 3660 cells respectively) were collected in 100uL of BAMBANKER (serum-free cell freezing medium, No.302-14681, Wako, Osaka, Japan) pre-chilled on ice. Tubes were kept on ice at most 30min until frozen in a cell freezing container with isopropyl alcohol (-1°C/min rate, 4C to -80C) and stored at -80C until preparing ATAC-seq libraries.
Frozen cells were thawed, washed with 1mL of PBS containing protease inhibitors (cOmplete EDTA-free protease inhibitor cocktail, Roche Diagnostics, Basel, Switzerland) and cell pellets were resuspended in 10uL of Tn5transposase mixture: 1xTagment DNA Buffer, 0.5uL Tagment DNA Enzyme (Nextera DNA Library Preparation Kit, illumine, CA, USA) and 0.2mg/ml digitonin (#G9441, Promega, WI, USA) on ice. Then, the cells were incubated at 37C for 30min with agitation followed by DNA isolation using MinElute Reaction Cleanup Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction. To construct libraries, the 1st round of PCR was performed in 50uL using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, MA, USA) with a set of primers (0.5uM each) and following thermal cycles: 5min at 72°C, 30 sec at 98°C, followed by 7 cycles [98°C for 10 sec, 63°C for 30 sec and 72°C for 60 sec] and a final extension at 72°C for 5mn. The PCR products were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter, CA, USA) (0.65x and 1.8x volume to remove long and short fragments respectively) and eluted in 18uL of EB (Qiagen). For avoiding an over amplification which can produce more GC bias, 2uL of the eluted DNA were subjected to qPCR (StepOnePlus Real-Time PCR System, Life Technologies, CA, USA) in 20uL employing SYBR GreenI (final 0.6x SYBR GreenI, Life Technologies) and the same set of primers (1.25uM each) as in the 1st round of PCR. After running qPCR (30sec at 98°C, followed by 30 cycles [98°C for 10 sec, 63°C for 30 sec and 72°C for 60 sec]), amplification curves were examined and the optimal number of PCR cycles were estimated as the cycles where amplifications reach 1/4 of maximum. 12.5uL of the eluted DNA were subjected to the 2nd round of PCR in 50uL with NEBNext High-fidelity 2x PCR master mix, a set of primers (1.25uM each) and following thermal cycles: 30 sec hot-start at 98°C, followed by 7~13 cycles [98°C for 10 sec, 63°C for 30 sec and 72°C for 60 sec] and a final extension at 72°C for 5mn. The libraries were purified by Agencourt AMPure XP beads (x1.8 vol.), quantified by qPCR employing Power SYBR Green PCR Master mix (ThermoFisher scientific, MA, USA) and a common set of primers (P5_FW and P7_RV, 0.2uM each) and pooled, which were sequenced for paired-end (38+37bp) on an Illumina Next-seq 500 instrument in a high-output mode.

value: B Cell


title: S._tsukubaensis_16_h_3_TEX_neg


title: B.PC.Sp#2

description:
Blimp1hi CD138hi MHCIIlo TCRb- NK1.1- CD11b-
B.PC.Sp.bw


title: S._tsukubaensis_32_h_R2_TEX_neg


title: Treg.4.25hi.Sp#1

description:
CD4+CD8-TCRbhiCD62LhiCD44loCD25hiDump-
Treg.4.25hi.Sp.bw

value: CD4 Treg Cell


title: T.8.Nve.Sp#2

description:
CD4-CD8+TCRbhiCD62LhiCD44loDump-
T.8.Nve.Sp.bw

value: CD8 Naive T Cell


title: B.PB.Sp#2

description:
Blimp1lo CD138hi MHCIIhi TCRb- NK1.1- CD11b-
B.PB.Sp.bw


title: Treg.4.25hi.Sp#2


title: mu_HFD_Blood_NK_IL6Ra- replicate 2

description:
FPKM_RUN1675.xlsx
B2HpBmat

value: negative


title: FRC.CD140a+.Madcam-.CD35-.SLN#2

description:
CD45-Epcam-Ter119-LiveDead-CalceinViolet+PDPN+CD31-CD35-Madcam-CD140a+
FRC.CD140a+.Madcam-.CD35-.SLN.bw

source_name: Skin draining lymph node

value: Stromal Cell


title: GN.Thio.PC#3

description:
ip 1ml of 3% thioglycate 18hrs before sac, CD11b+ Ly6G+
GN.Thio.PC.bw

source_name: Peritoneal cavity

value: Neutrophil


title: BEC.SLN#2

description:
CD45-Epcam-Ter119-LiveDead-CalceinViolet+PDPN-CD31+
BEC.SLN.bw


title: GN.Thio.PC#2


title: T.DP.Th#2

description:
SSCsmallCD4+CD8+TCRbloCD69-Dump-
T.DP.Th.bw

source_name: Thymus

value: DP Thymocytes


title: DC.8+.Sp#2

description:
CD45+ MHCII+ CD11c+ CD8+ CD4-
DC.8+.Sp.bw

value: Dendritic Cell


title: T.DP.Th#1


title: B.Fem.Sp#2

description:
Female, CD19+Igm+TCRb-CD4-
B.Fem.Sp.bw


title: preT.DN3.Th#2

description:
Lin-(CD4,CD8,CD11b,CD11c-,CD19,TCRb,TCRgd,NK1.1,Gr1,Ter119)CD44-CD25hi
preT.DN3.Th.bw

value: Double Negative Thymocytes


title: MF.ICAM+480hi.PC#3

description:
CD115+CD11b+F4/80+CD102+MHCIIloCD226-
MF.ICAM+480hi.PC.bw

value: Macrophage


title: MF.ICAM+480hi.PC#4


title: Mo.6C-II-.Bl#3

description:
B220-CD3-Ly6G-CD45+CD115+CD11b+Ly6C-
Mo.6C-II-.Bl.bw

source_name: Blood

value: Monocyte


title: Mo.6C+II-.Bl#3

description:
B220-CD3-Ly6G-CD45+CD115+CD11b+Ly6C+
Mo.6C+II-.Bl.bw


title: LTHSC.34-.BM#1

description:
Lin-Sca1+ckit+CD135-CD150+CD48-CD34-
LTHSC.34-.BM.bw

source_name: Bone marrow

value: Stem Cell


title: LTHSC.34+.BM#1

description:
Lin-Sca1+ckit+CD135-CD150+CD48-CD34+
LTHSC.34+.BM.bw


title: MF.microglia.CNS#2

description:
CD19-CD3-Ly6G-CD45loCD11b+ CD64+ F4/80loCD206-
MF.microglia.CNS.bw

source_name: brain

value: Microglia


title: STHSC.150-.BM#1

description:
Lin-Sca1+ckit+CD135-CD150-CD48-
STHSC.150-.BM.bw


title: Tgd.Sp#2

description:
TCRd+CD3+CD4-CD8-
Tgd.Sp.bw

value: gdT Cell


title: DC.pDC.Sp#2

description:
CD45lo CD11b+
DC.pDC.Sp.bw


title: WT

description: embryos obtained from matings of tw18/+ mice

source_name: wild type epiblast

value: wildtype


title: MF.Fem.PC#2

description:
Female, F4/80+ICAM2+CD5-CD19-CD43-
MF.Fem.PC.bw


title: proB.CLP.BM#1

description:
CD93+CD117+IL7Ra+CD45R-
proB.CLP.BM.bw


title: T.4.Nve.Fem.Sp#2

description:
Female, CD4+CD8-TCRbhiCD62LhiCD44loCD25-Dump-
T.4.Nve.Fem.Sp.bw

value: CD4 Naive T Cell


title: MF.Fem.PC#1


title: T.4.Nve.Fem.Sp#1


title: MF.PC#1

description:
F4/80+ICAM2+CD5-CD19-CD43-
MF.PC.bw


title: MPP4.135+.BM#1

description:
Lin-Sca1+ckit+CD135+
MMP4.135+.BM.bw


title: MF.PC#2

description:
F4/80+ICAM2+CD5-CD19-CD43-
MF.PC.bw


title: DC.103+11b+.SI#2

description:
CD45+ MHCII+ CD11c+/loCD64-CD103+CD11b-
DC.103+11b+.SI.bw

source_name: Small intestine


title: MPP3.48+.BM#1

description:
Lin-Sca1+ckit+CD135-CD150-CD48+
MMP3.48+.BM.bw


title: DC.103+11b+.SI#1

description:
CD45+ MHCII+ CD11c+/loCD64+CD103-CD11b+
DC.103+11b+.SI.bw


title: DC.103+11b-.SI#1

description:
CD45+ MHCII+ CD11c+/loCD64-CD103+CD11b-
DC.103+11b-.SI.bw


title: DC.103+11b-.SI#2

description:
CD45+ MHCII+ CD11c+/loCD64-CD103+CD11b+
DC.103+11b-.SI.bw


title: MF.LP.SI#1

description:
CD45+ MHCII+ CD11c+/loCD64-CD103+CD11b+
MF.SI.LP.bw

source_name: Small intestine lamina propria


title: MF.LP.SI#2

description:
CD45+ MHCII+ CD11c+/loCD64+CD103-CD11b+
MF.SI.LP.bw


title: MF.pIC.Alv.Lu#2

description:
50ug pIC intratracheal, CD45+ SiglecF+ CD11c+
MF.pIC.Alv.Lu.bw

source_name: Lung


title: MF.pIC.Alv.Lu#1


title: MF.Alv.Lu#2

description:
CD45+ SiglecF+ CD11c+
MF.Alv.Lu.bw


title: B1b.PC#2

description:
CD19+CD45R+IgM++CD93-CD23-CD43+CD5-
B1b.PC.bw


title: MF.Alv.Lu#1

description:
CD45+ SiglecF+ CD11c+
MF.Alv.Lu.bw


title: B.T3.Sp#2

description:
CD19+CD45R+IgM+CD93+CD23+
B.T3.Sp.bw


title: B.MZ.Sp#2

description:
CD19+CD45R+IgM++CD93-CD23-CD21/35++
B.MZ.Sp.bw


title: B.T2.Sp#2

description:
CD19+CD45R+IgM++CD93+CD23+
B.T2.Sp.bw


title: B.Fo.Sp#2

description:
CD19+CD45R+IgM+CD93-CD23+CD43-CD5-
B.Fo.Sp.bw


title: IAP.SLN#1

description:
CD45-Epcam-Ter119-LiveDead-CalceinViolet+PDPN-CD31-
IAP.SLN.bw


title: BEC.SLN#1

description:
CD45-Epcam-Ter119-LiveDead-CalceinViolet+PDPN-CD31+
BEC.SLN.bw


title: B.T1.Sp#2

description:
CD19+CD45R+IgM++CD93+CD23-
B.T1.Sp.bw


title: S._tsukubaensis_32_h_R1_TEX_pos

value: Terminator Exonuclease treated


title: LEC.SLN#1

description:
CD45-Epcam-Ter119-LiveDead-CalceinViolet+PDPN+CD31-
LEC.SLN.bw


title: LEC.SLN#2


title: FRC.CD140a+.Madcam-.CD35-.SLN#1

description:
CD45-Epcam-Ter119-LiveDead-CalceinViolet+PDPN+CD31-CD35-Madcam-CD140a+
FRC.CD140a+.Madcam-.CD35-.SLN.bw


title: MF.microglia.CNS#1

description:
CD19-CD3-Ly6G-CD45loCD11b+ CD64+ F4/80loCD206-
MF.microglia.CNS.bw


title: DC.4+.Sp#2

description:
CD45+ MHCII+ CD11c+ CD8- CD4+
DC.4+.Sp.bw


title: DC.pDC.Sp#1

description:
CD45lo CD11b+
DC.pDC.Sp.bw


title: DC.8+.Sp#1

description:
CD45+ MHCII+ CD11c+ CD8+ CD4-
DC.8+.Sp.bw


title: MF.RP.Sp#2

description:
CD19-Ly6G-CD115- CD45+CD11bloF4/80+MerTK+CD64+
MF.RP.Sp.bw


title: MF.RP.Sp#1


title: MF.ICAM+480hi.PC#2

description:
CD115+CD11b+F4/80+CD102+MHCIIloCD226-
MF.ICAM+480hi.PC.bw


title: MF.ICAM+480hi.PC#1


title: MF.226+II+480lo.PC#2

description:
CD115+CD11b+F4/80loCD102loMHCII+CD226+
MF.226+II+480lo.PC.bw


title: Mo.6C+II-.Bl#1

description:
B220-CD3-Ly6G-CD45+CD115+CD11b+Ly6C+
Mo.6C+II-.Bl.bw


title: Mo.6C+II-.Bl#2


title: Mo.6C-II-.Bl#2

description:
B220-CD3-Ly6G-CD45+CD115+CD11b+Ly6C-
Mo.6C-II-.Bl.bw


title: Mo.6C-II-.Bl#1


title: ILC3.NKp46+.SI#2

description:
CD3-CD19-Tcrb-CD5-Thy1+KLRG1-CCR6-NKp46+
ILC3.NKp46+.SI.bw

value: Innate Lymphocytes


title: MF.226+II+480lo.PC#1


title: ILC3.NKp46+.SI#1


title: ILC3.NKp46-CCR6-.SI#2

description:
CD3-CD19-Tcrb-CD5-KLRG1-Thy1+CCR6–NKp46-
ILC3.NKp46-CCR6-.SI.bw


title: ILC3.CCR6+.SI#2

description:
CD3-CD19-Tcrb-CD5-Thy1+KLRG1-CCR6+NKp46-
ILC3.CCR6+.SI.bw


title: ILC3.CCR6+.SI#1


title: ILC2.SI#2

description:
CD3-CD19-Tcrb-CD5- CD127+ KLRG1+ ST2+ Sca1+
ILC2.SI.bw


title: IAP.SLN#2


title: ILC3.NKp46-CCR6-.SI#1


title: NKT.Sp.LPS.3d#2

description:
3d post-LPS 165ug i.v. , [CD19-Gr1-Ter119-CD8-] TCRbMedCD1dTetramer(alphaGalCer)+
NKT.Sp.LPS.3d.bw

value: NKT Cell


title: ILC2.SI#1


title: NKT.Sp.LPS.3d#1


title: DC.4+.Sp#1


title: NKT.Sp.LPS.3hr#1

description:
3h post-LPS 165ug i.v. , [CD19-Gr1-Ter119-CD8-] TCRbMedCD1dTetramer(alphaGalCer)+
NKT.Sp.LPS.3hr.bw


title: NKT.Sp.LPS.3hr#2


title: NKT.Sp#2

description:
[CD19-Gr1-Ter119-CD8-] TCRbMedCD1dTetramer(alphaGalCer)+
NKT.Sp.bw


title: NKT.Sp.LPS.18hr#1

description:
18h post-LPS 165ug i.v. , [CD19-Gr1-Ter119-CD8-] TCRbMedCD1dTetramer(alphaGalCer)+
NKT.Sp.LPS.18hr.bw


title: B.Sp#2

description:
CD19+ IgM+ TCRb-
B.Sp.bw

value: B Cell


title: NKT.Sp.LPS.18hr#2


title: NKT.Sp#1


title: B.Fo.Sp#3

description:
B220+ CD19+ IgM+ CD23+ CD5- CD43- CD93-
B.Fo.Sp.bw


title: B.PC.BM#1

description:
Blimp1hi CD138hi TCRb- NK1.1- CD11b-
B.PC.BM.bw


title: B.PC.Sp#1

description:
Blimp1hi CD138hi MHCIIlo TCRb- NK1.1- CD11b-
B.PC.Sp.bw


title: B.Sp#1

description:
CD19+ IgM+ TCRb-
B.Sp.bw


title: B.mem.Sp#1

description:
NP-KLH/alum D14, B220+ TCRb- CD138- Gr1- IgD-IgM- Fas- CD38+ IgG+
B.mem.Sp.bw


title: B.mem.Sp#2


title: B1b.PC#1

description:
CD19+CD45R+IgM++CD93-CD23-CD43+CD5-
B1b.PC.bw


title: B.GC.CB.Sp#1

description:
NP-KLH/alum D14, B220+ TCRb- CD138- Gr1- Fas+ CD38- CXCR4hi CD84lo
B.GC.CB.Sp.bw


title: B.T3.Sp#1

description:
CD19+CD45R+IgM+CD93+CD23+
B.T3.Sp.bw


title: B.GC.CB.Sp#2


title: B.FrE.BM#2

description:
CD93+IgM+CD19+CD43-HSA+
B.FrE.BM.bw


title: B.T1.Sp#1

description:
CD19+CD45R+IgM++CD93+CD23-
B.T1.Sp.bw


title: B.MZ.Sp#1

description:
CD19+CD45R+IgM++CD93-CD23-CD21/35++
B.MZ.Sp.bw


title: B.FrE.BM#1

description:
CD93+IgM+CD19+CD43-HSA+
B.FrE.BM.bw


title: B.Fo.Sp#1

description:
CD19+CD45R+IgM+CD93-CD23+CD43-CD5-
B.Fo.Sp.bw


title: preB.FrD.BM#2

description:
CD93+IgM-CD19+CD43-HSA+
preB.FrD.BM.bw


title: proB.FrBC.BM#2

description:
CD93+IgM-CD19+CD43+HSA+
proB.FrBC.BM.bw


title: B.GC.CC.Sp#1

description:
NP-KLH/alum D14, B220+ TCRb- CD138- Gr1- Fas+ CD38- CXCR4lo CD84hi
B.GC.CC.Sp.bw


title: proB.FrA.BM#2

description:
CD93+CD117+IL7Ra+CD45R+
proB.FrA.BM.bw


title: T8.IEL.LCMV.d7.SI#1

description:
LCMV infection day7, CD8+CD45.1+CD4-MHCII-B220-Gr1-
T8.IEL.LCMV.d7.Gut.bw

source_name: Small Intestine

value: CD8 T Cell


title: B.PC.BM#2


title: T8.IEL.LCMV.d7.SI#2


title: B.PB.Sp#1

description:
Blimp1lo CD138hi MHCIIhi TCRb- NK1.1- CD11b-
B.PB.Sp.bw


title: Tgd.Sp#1

description:
TCRd+CD3+CD4-CD8-
Tgd.Sp.bw


title: T8.Tem.LCMV.d180.Sp#2

description:
LCMV infection day180, CD8+CD44+CD62L-CD45.1+CD4-MHCII-B220-Gr1-Ter119-
T8.Tem.LCMV.d180.Sp.bw


title: T8.Tcm.LCMV.d180.Sp#1

description:
LCMV infection day180, CD8+CD44+CD62L+CD45.1+CD4-MHCII-B220-Gr1-Ter119-
T8.Tcm.LCMV.d180.Sp.bw


title: T8.Tem.LCMV.d180.Sp#1


title: B.GC.CC.Sp#2


title: B.T2.Sp#1

description:
CD19+CD45R+IgM++CD93+CD23+
B.T2.Sp.bw


title: T8.Tcm.LCMV.d180.Sp#2


title: T8.TE.LCMV.d7.Sp#2

description:
LCMV infection day7, CD8+KLRG1+CD127-CD45.1+CD4-MHCII-B220-Gr1-Ter119-
T8.TE.LCMV.d7.Sp.bw


title: T8.MP.LCMV.d7.Sp#1

description:
LCMV infection day7, CD8+KLRG1-CD127+CD45.1+CD4-MHCII-B220-Gr1-Ter119-
T8.MP.LCMV.d7.Sp.bw


title: T8.TN.P14.Sp#2

description:
CD8+CD44-CD4-MHCII-B220-Gr1-Ter119-
T8.TN.P14.Sp.bw


title: T8.TE.LCMV.d7.Sp#1


title: preB.FrD.BM#1

description:
CD93+IgM-CD19+CD43-HSA+
preB.FrD.BM.bw


title: Tgd.g2+d1.LN#2

description:
TCRvg2+TCRd+CD24-CD27+CD4-CD8-
Tgd.g2+d1.LN.bw

source_name: Lymph nodes


title: Tgd.g1.1+d1.LN#1

description:
TCRvg1.1+TCRd+CD24-CD27+CD4-CD8-
Tgd.g1.1+d1.LN.bw


title: Tgd.g2+d17.LN#1

description:
TCRvg2+TCRd+CD24-CD27-CD4-CD8-
Tgd.g2+d17.LN.bw


title: Tgd.g1.1+d1.24a+.Th#2

description:
TCRvg1.1+TCRd+CD24hiScart2-CD4-CD8-
Tgd.g1.1+d1.24a+.Th.bw


title: Tgd.g2+d1.LN#1


title: proB.FrA.BM#1

description:
CD93+CD117+IL7Ra+CD45R+
proB.FrA.BM.bw


title: Tgd.g1.1+d1.24a+.Th#1


title: proB.FrBC.BM#1

description:
CD93+IgM-CD19+CD43+HSA+
proB.FrBC.BM.bw


title: Tgd.g2+d1.24a+.Th#1

description:
TCRvg2+TCRd+CD24hiScart2-CD4-CD8-
Tgd.g2+d1.24a+.Th.bw


title: NK.27+11b-.BM#2

description:
PI- CD3-PECy7- CD19-PECy7- NK1.1-PCPCy5.5+ CD127-BV421- CD51-BV421- CD49a-BV421- DX5-FITC+ CD27-APC+ CD11b-PE-
NK.27+11b-.BM.bw

value: NK Cell


title: Tgd.g2+d17.24a+.Th#1

description:
TCRvg2+TCRd+CD24hiScart2+CD4-CD8-
Tgd.g2+d17.24a+.Th.bw


title: T8.MP.LCMV.d7.Sp#2


title: NK.27+11b+.BM#2

description:
PI- CD3-PECy7- CD19-PECy7- NK1.1-PCPCy5.5+ CD127-BV421- CD51-BV421- CD49a-BV421- DX5-FITC+ CD27-APC+ CD11b-PE+
NK.27+11b+.BM.bw


title: Tgd.g2+d1.24a+.Th#2


title: T8.TN.P14.Sp#1


title: Tgd.g1.1+d1.LN#2


title: NK.27+11b-.Sp#1

description:
PI- CD3-PECy7- CD19-PECy7- NK1.1-PCPCy5.5+ CD127-BV421- CD51-BV421- CD49a-BV421- DX5-FITC+ CD27-APC+ CD11b-PE-
NK.27+11b-.Sp.bw


title: NK.27+11b-.Sp#2


title: NK.27+11b+.BM#1


title: NK.27+11b+.Sp#2

description:
PI- CD3-PECy7- CD19-PECy7- NK1.1-PCPCy5.5+ CD127-BV421- CD51-BV421- CD49a-BV421- DX5-FITC+ CD27-APC+ CD11b-PE+
NK.27+11b+.Sp.bw


title: NK.27-11b+.BM#1

description:
PI- CD3-PECy7- CD19-PECy7- NK1.1-PCPCy5.5+ CD127-BV421- CD51-BV421- CD49a-BV421- DX5-FITC+ CD27-APC- CD11b-PE+
NK.27-11b+.BM.bw


title: proB.CLP.BM#2

description:
CD93+CD117+IL7Ra+CD45R-
proB.CLP.BM.bw


title: Tgd.g2+d17.24a+.Th#2


title: NK.27+11b+.Sp#1


title: GN.Sp#2

description:
CD11b+ Ly6G+
GN.Sp.bw

value: Neutrophil


title: NK.27+11b-.BM#1


title: GN.Sp#1

description:
CD11b+ Ly6G+
GN.Sp.bw


title: GN.BM#1

description:
CD11b+ Ly6G+
GN.BM.bw


title: GN.BM#2

description:
CD11b+ Ly6G+
GN.BM.bw


title: Treg.4.FP3+.Nrplo.Co#2

description:
Foxp3+CD4+TCRb+NrploDump-
Treg.4.FP3+.Nrplo.Co.bw

source_name: Colon

value: CD4 Treg Cell


title: Treg.4.FP3+.Nrplo.Co#1


title: T.4.Sp.aCD3+CD40.18hr#1

description:
ip 60ug CD3(KT3) and 100ug CD40(FGK4.5) 18hrs before sac. , CD4+CD8-TCRb-Dump-
T.4.Sp.aCD3+CD40.18hr.bw

value: Activated T Cell


title: T.4.Sp.aCD3+CD40.18hr#2


title: Tgd.g2+d17.LN#2


title: NK.27-11b+.Sp#2

description:
PI- CD3-PECy7- CD19-PECy7- NK1.1-PCPCy5.5+ CD127-BV421- CD51-BV421- CD49a-BV421- DX5-FITC+ CD27-APC- CD11b-PE+
NK.27-11b+.Sp.bw


title: NK.27-11b+.BM#2


title: T.8.Th#2

description:
CD4-CD8+TCRbhiCD24int-Dump-
T.8.Th.bw

value: CD8 SP Thymocytes


title: T.8.Th#1

description:
CD4-CD8+TCRbhiCD24int-Dump-
T.8.Th.bw


title: NK.27-11b+.Sp#1


title: T.4.Th#2

description:
CD4+CD8-TCRbhiCD24int-Dump-
T.4.Th.bw

value: CD4 SP Thymocytes


title: T.4.Th#1

description:
CD4+CD8-TCRbhiCD24int-Dump-
T.4.Th.bw


title: T.DN4.Th#2

description:
Lin-(CD4,CD8,CD11b,CD11c-,CD19,TCRb,TCRgd,NK1.1,Gr1,Ter119)CD44-CD25-CD28+
T.DN4.Th.bw

value: Double Negative Thymocytes


title: T.ISP.Th#1

description:
CD4-CD8+TCR-/loCD24hiDump-
T.ISP.Th.bw

value: Immature Single Positive Thymocytes


title: T.DN4.Th#1


title: preT.DN2a.Th#2

description:
Lin-(CD4,CD8,CD11b,CD11c-,CD19,TCRb,TCRgd,NK1.1,Gr1,Ter119)CD44hiCD117hiCD25hi
preT.DN2a.Th.bw


title: preT.DN2a.Th#1


title: Ep.MEChi.Th#2

description:
CD45-Ly51loMHC-IIhiEPCAMhi
Ep.MEChi.Th.bw

value: Thymic epithelial Cell


title: preT.DN3.Th#1

description:
Lin-(CD4,CD8,CD11b,CD11c-,CD19,TCRb,TCRgd,NK1.1,Gr1,Ter119)CD44-CD25hi
preT.DN3.Th.bw


title: preT.DN1.Th#2

description:
Lin-(CD4,CD8,CD11b,CD11c-,CD19,TCRb,TCRgd,NK1.1,Gr1,Ter119)CD44hiCD117hiCD25-/lo
preT.DN1.Th.bw


title: preT.DN2b.Th#2

description:
Lin-(CD4,CD8,CD11b,CD11c-,CD19,TCRb,TCRgd,NK1.1,Gr1,Ter119)CD44hiCD117intCD25hi
preT.DN2b.Th.bw


title: T.ISP.Th#2

description:
CD4-CD8+TCR-/loCD24hiDump-
T.ISP.Th.bw


title: Ep.MEChi.Th#1


title: preT.DN1.Th#1


title: preT.DN2b.Th#1


title: T.8.Nve.Sp#1

description:
CD4-CD8+TCRbhiCD62LhiCD44loDump-
T.8.Nve.Sp.bw

value: CD8 Naive T Cell


title: 4C_WT_IhhTSS_rep2

first: Darío

middle: G

last: Lupiáñez

address: Ihnestrasse 73

description:
Processed data file: 4C_Ratio_Dup-int_vs_WT.bedgraph
Processed data file: 4C_Ratio_Dup-syn_vs_WT.bedgraph

data_processing:
Library strategy: 4C-seq
4C-seq reads were cleaned of the primer sequence and mapped to a corresponding reference (NCBI37/mm9) using BWA-MEM (v0.7.12-r1044) with default settings.
4C-seq contacts were analyzed in the murine region chr1:74500000-75500000.
To calculate read count profiles, the viewpoint and adjacent fragments 1.5 kb up- and downstream were removed. A sliding window of 2 fragments was chosen to smooth the data and data was normalized to reads per million mapped reads (RPM).
To compare interaction profiles of different samples, we obtained the log2 fold change for each window of normalized reads.
To obtain ratios, duplicated regions were excluded for calculation of the scaling parameter used in RPM normalization.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bedGraph files of the coverage and the calculated ratios.

source_name: E14.5 digit forelimb, WT

extract_protocol:
4C-seq libraries were generated from microdissected E14.5 mouse forelimb tissues (digit 2-5) as described previously (van de Werken et al., 2012). The starting material for all 4C-seq libraries was 5000000-10000000 cells. All 4C-seq experiments were carried out in heterozygous animals and were compared to wildtype. 4-bp cutters were used as primary (Csp6I) and secondary (BfaI) restriction enzymes. A total of 1 to 1.6 µg DNA was amplified by PCR (Primer sequence: Ihh_promoter_1:ACAGCTGGGGACCCTATAC; Ihh_promoter_2:CCCGTCAGGAGGACAATC). 4C-seq experiments were carried out in two biological replicates in wildtype, Dupint/+ and Dupsyn/+ mutants.
All samples were sequenced with Illumina Hi-Seq technology according to standard protocols.

tag: strain/background

tag: genotype/variation

value: Wild type

tag: age

value: forelimb (digit 2-5)

tag: viewpoint

value: Ihh TSS


title: Nef-sp -/-;rep2

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description:
SS2
Processed data file: Nef_table.txt

data_processing:
Reads were sorted into individual libraries based on the barcodes, the 3′ adapter sequences were removed and mapped to the mouse genome (mm9). The software used for processing the data (genomic coordinates, etc.) from the raw data files are in-house tools developed by the Sachidanandam lab (Olson et al., 2008). Only reads perfectly matching the genome were kept for further analysis.
Only the reads having at least 5 counts, when summed from all the libraries, were kept for the analysis. The reads were divided into groups based on their annotation (repeat_sense, repeat_antisense, gene_exon_sense, gene_exon_antisense, gene_intron_sense, gene_intron_antisense, ncRNA_sense, ncRNA_antisense, miRNA_sense, miRNA_antisense, none) and their counts were compared between Nef-sp -/- and Nef-sp +/-. DESeq2 Bioconductor package was used to search for differentially expressed transcripts.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Nef_table.txt: The processed data file contains the read counts produced from individual transcripts together with the statistics calculated by DESeq2.

source_name: testis, Nef-sp -/-

extract_protocol:
Total testicular RNA was isolated by TRI-reagent (Life Tech, AM9738).
Strand-specific RNA-seq libraries were prepared using TruSeq Stranded Total RNA Sample Preparation Kit (Illumina) after removal of abundant ribosomal RNAs with Ribo-Zero (mouse). Libraries were sequenced with the Illumina HiSeq 2000 platform (EMBL Heidelberg Gene core facility) for 50 cycles.

treatment_protocol: Nef-sp null allele was created using the RNA-guided Cas9 endonuclease [Cas9 nickase (Cas9n)] and a pair of guide RNAs (gRNAs). The Cas9n mRNA and the in vitro transcribed gRNAs were used for injection into C57Bl/6J host embryos for mouse generation using one-cell stage injection. The founder females carrying a 23 bp out-of-frame deletion were crossed with wildtype C57Bl/6J Rj males (Janvier labs, France) to establish the mutant line.

value: Nef-sp -/-

value: testis

value: adult (P60)


title: Nef-sp +/-;rep1

description:
SS3
Processed data file: Nef_table.txt

source_name: testis, Nef-sp +/-

value: Nef-sp +/-


title: Nef-sp +/-;rep2

description:
SS4
Processed data file: Nef_table.txt


title: 4C_WT_IhhTSS_rep1


title: Nef-sp -/-;rep1

description:
SS1
Processed data file: Nef_table.txt


title: T.4.Nve.Sp#2

description:
CD4+CD8-TCRbhiCD62LhiCD44loCD25-Dump-
T.4.Nve.Sp.bw

source_name: Spleen

tag: cell type

value: CD4 Naive T Cell


title: mESC [86_plus_2]

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Genome reconstruction: The VCF file (mgp.v3.snps.rsIDdbSNPv137.vcf) reporting all SNP sites from 36 mouse strains based on mm10 was downloaded from the Sanger database and used to reconstruct the Cast and 129S1 genomes from mm10 genome assembly.
Mapping: Single-end reads were then aligned to the mouse 129S1 and Cast/EiJ genomes using the TopHat2 software (v2.0.6). Only random best alignments with less than 2 mismatches were reported for downstream analyses. The resulting mapping files for both parental genomes were then merged for each sample.
Allelic Ratio: The SAMtools mpileup utility  was then used to extract base-pair information at each genomic position from the merged alignment file. At each SNP position, the number of paternal and maternal allele was counted. The allele-specific origin of the transcripts (or allelic ratio) has been measured by the total number of reads mapped on the paternal genome divided by the total number of reads for each gene: allelic ratio = paternal reads / (paternal+maternal) reads.
Estimation of gene expression levels: To estimate the transcript abundance, count tables of gene expression were generated using HTSeq v0.6.1 software.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files (tab-delimited format) contain the allelic ratio and raw counts expression of each gene

source_name: mESC

growth_protocol: mESC were grown in 2i+LIF conditions containing DMEM, 100 U/ml penicillin/streptomy¬cin, 20% KnockOut Serum Replacement (Gibco), 0.1 mM NEAA, 0.1 mM 2-mer¬captoethanol, 5000 U/ml LIF, 1μM MEK inhibitor PD0325901 (Stemgent) and 3 μM GSK3 inhibitor CH99021 (Stemgent).

extract_protocol:
total RNA was extracted according to the manufacturer’s instructions (Invitrogen),1 μg of RNA was reverse transcribed by Superscript II reverse transcriptase with random hexamers (Invitrogen).
RNA samples were prepared with the Truseq RNA kit, sequenced according to the Illumina TruSeq v3 protocol on the HiSeq2000

treatment_protocol: Cells were lysed by direct addiction of 500 μg of TRIZOL and stored at -80°C

tag: Sex

value: Female

value: mESC

value: Inducible Xist transgene

tag: transgene location

value: Xist Tg on chromosome X

tag: ectopic transgene expression

value: plus


title: mESC [87_minus_2]

value: minus


title: mESC [87_plus_1]


title: mESC [87_minus_1]


title: mESC [87_plus_2]


title: mESC [86_minus_1]


title: mESC [85_plus_1]


title: SDE_2

city: Beijing

first: Kehkooi

last: Kee

state: Beijing

address: Room D110, Medical Science Building, School of Medicine, Tsinghua University

department: Basic Medical Sciences

country: China

institute: Tsinghua University

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were firstly trimmed to remove low qulifty bases and the adapter sequences.
Secondly, the cleaned reads were aligned to the human hg19 reference by using  Tophat (v.2.0.12) according to Trapnell et al., 2009.
Thirdly, the transcripts were assembled by using Cufflinks (v2.2.1) with default parameters.
Forthly, the ranscription levels (FPKM, fragments per kilobase of transcript per million mapped reads) of annotated genes were quantified by using Cufflinks (v2.2.1) according to Trapnell et al., 2010.
Genome_build: hg19
Supplementary_files_format_and_content: processed data files are txt files. FPKM values of RefSeq genes are included

source_name: human embryonic stem cells, spontaneous differentiation

extract_protocol:
Each sample was picked out from the plate and lysed in 1ml TRIzol reagent (Invitrogen, 15596026).  A total amount of 125ng RNA of each sample was used for RNA-seq according to Guo, F. et al. NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, E7370) was used for the construction of sequencing library.
Sequencing library was prepared according to the protocol of NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, E7370).

tag: cell line

value: ES-derived spontaneous differentiation

tag: gender

value: female

tag: days

value: after differentiation, day 11


title: FLC_2 (H9)

description: polyA RNA

source_name: human embryonic stem cells, induction

value: ES-derived human follicle-like cells


title: mESC [85_plus_2]


title: FLC_1 (HSF6)

description: polyA RNA


title: mESC [38_plus_2]

value: Xist Tg on chromosome 12


title: mESC [86_minus_2]


title: mESC [68_plus_1]


title: SDE_1

description: polyA RNA


title: mESC [86_plus_1]


title: mESC [85_minus_2]


title: ES_2

description: polyA RNA

source_name: human embryonic stem cells， untreated

value: human embryonic stem cells

value: before differentiation,  day 0


title: mESC differentiated into neurons [38_plus_N]

source_name: mESC differentiated into neurons

value: mESC differentiated into neurons


title: mESC [38_plus_1]


title: mESC differentiated into neurons [38_minus_N]


title: mESC [38_minus_1]


title: mESC [38_minus_2]


title: mESC [339_plus_1]

value: Xist Tg on chromosome X:8


title: mESC [339_plus_2]


title: T.4.Nve.Sp#1


title: mESC [339_minus_1]


title: mESC [85_minus_1]


title: mESC differentiated into neurons [292_plus_1N]


title: mESC differentiated into neurons [292_plus_2]


title: mESC differentiated into neurons [292_plus_2N]


title: mESC differentiated into neurons [292_minus_2]


title: mESC differentiated into neurons [292_minus_2N]


title: ES_1

description: polyA RNA


title: mESC [292_minus_1]


title: mESC differentiated into neurons [292_plus_1]


title: mESC [267_plus_2]


title: mESC [273_plus_1]


title: Hiseq_Newman_SprC_rep3

city: RENNES

first: Yoann

last: AUGAGNEUR

address: 2 Avenue du Pr Leon Bernard

department: Pharmaceutical Biochemistry

institute: University Rennes 1

data_processing:
Sequenced reads were verified by a fastqc report
reads were mapped using the BWA aligner
Reads were filtered for reads properly paired and sorted by pairs
Read pairs were counted using HTSeq count
Genome_build: Staphylococcus aureus subps, aureus Newman
Supplementary_files_format_and_content: Excel file include raw counting

organism: Staphylococcus aureus

source_name: ribosomal-depleted RNA

growth_protocol: exponential phase of growth

extract_protocol:
Cells were lyzed with glass beads in a Fast Prep instrument and RNAs extract with Phenol/Chloroform. Ribosomal RNAs were depleted using the Ribo-zero rRNA remmoval kit (bacteria).
NEBNext ultra directional RNA library prep kit (E7420)

tag: strain/genotype


title: mESC [267_minus_1]


title: mESC [267_plus_1]


title: mESC [273_minus_3]


title: mESC [267_minus_2]


title: mESC [228_plus_1]


title: mESC [228_plus_2]


title: Hiseq_Newman_SprC_rep1


title: input_H3K9me2_set-25_eemb_20°C_rep2

city: Mainz

first: Jan

last: Padeken

address: Ackermannweg 4

institute: Institute of Molecular Biology

description: chromatin

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the ce6 (WS190) genome assembly using the qAlign function from the QuasR R package (v. 3.2).
The qCount function in the QuasR package was used to count reads overlapping the ce6 genome assembly split into fragments of 500bp.
Genome_build: ce6 (WS190)
Supplementary_files_format_and_content: Tab-delimited file. First column contains seqnames, followed by start and end position and columns contain raw counts of reads overlapping each fragment for each sample of replica 1 as shown in the linked manuscript.

organism: Caenorhabditis elegans

source_name: early embryo

growth_protocol: Chromatin was isolated from early embryos (before bean stage) grown after L1 synchronization (60–65 h depending on each strain) in two independent biological replicates.

extract_protocol:
Embryos were fixed with 2% Formalin for 30min at room temperature. Fixed chromatin was extracted using the FastPrep-24™ (MPI) homogenizer and sonicated using the Bioruptor (Diagenode)
Libraries were prepared from chromatin IP and input samples using the NEBNext ultra DNA library prep kit for Illumina (NEB # 7370) and the NEBNext Multiplex Oligos for Illumina (NEB # E7335)

value: early embryo


title: mESC [228_minus_2]


title: mESC [228_minus_1]


title: Hiseq_Newman_SprC_rep2


title: input_H3K9me2_set-25_eemb_20°C_rep1

description: chromatin


title: mESC differentiated into neurons [20_plus_N]


title: mESC differentiated into neurons [20_minus_N]


title: mESC [292_minus_1N]


title: mESC [273_minus_1]


title: input_H3K9me3_set-25_eemb_20°C_rep1

description: chromatin


title: mESC [273_plus_3]


title: input_H3K9me2_met-2_eemb_20°C_rep2

description: chromatin


title: Newman_SprC_rep3


title: input_H3K9me2_met-2_eemb_20°C_rep1

description: chromatin


title: Newman_SprC_rep2


title: input_H3K9me3_met-2_eemb_20°C_rep2

description: chromatin


title: mESC [190_plus_2]


title: mESC [203b_minus_1]


title: mESC [190_minus_1]


title: mESC [203b_minus_2]


title: mESC [190_minus_2]


title: ChIP_H3K9me2_set-25_eemb_20°C_rep2

description: chromatin


title: Newman_rep3

value: Newman


title: mESC [160_plus_1]

value: Female


title: mESC [190_plus_1]

value: mESC


title: Newman_rep2


title: mESC [160_plus_2]

value: Inducible Xist transgene


title: ChIP_H3K9me2_set-25_eemb_20°C_rep1

description: chromatin


title: mESC [339_minus_2]


title: input_H3K9me3_set-25_eemb_20°C_rep2

description: chromatin


title: mESC [203b_plus_2]


title: ChIP_H3K9me3_set-25_eemb_20°C_rep2

description: chromatin


title: Newman_rep1


title: input_H3K9me3_met-2_eemb_20°C_rep1

description: chromatin


title: Newman_MiSeq


title: ChIP_H3K9me3_set-25_eemb_20°C_rep1

description: chromatin


title: mESC [109_plus_2]

value: Xist Tg on chromosome X


title: mESC [160_minus_1]


title: Newman_SprC_rep1


title: 4C_Dup-syn_IhhTSS_rep_2

description: Processed data file: 4C_Ratio_Dup-syn_vs_WT.bedgraph

source_name: E14.5 digit forelimb, Dup-syn

value: Dupsyn/+

value: forelimb (digit 2-5)

value: Ihh TSS


title: mESC [109_plus_1]

value: plus


title: ChIP_H3K9me2_met-2_eemb_20°C_rep1

description: chromatin


title: 4C_Dup-syn_IhhTSS_rep_1


title: ChIP_H3K9me2_met-2_eemb_20°C_rep2

description: chromatin


title: mESC [109_minus_2]

value: minus


title: ChIP_H3K9me3_met-2_eemb_20°C_rep1

description: chromatin


title: mESC [109_minus_1]


title: RNA_met-2_set-25_eemb_20°C_rep2

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the ce6 (WS190) genome assembly using the qAlign function from the QuasR R package (v. 3.2) with the parameter "splicedAlignment = TRUE", which calls the SpliceMap aligner with default parameters.
Gene expression was quantified using WS190 annotations downloaded from UCSC. The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Genome_build: ce6 (WS190)
Supplementary_files_format_and_content: Tab-delimited file. First column contains gene names (Sanger identifiers) and width of genes, following columns contain raw counts of reads overlapping each gene for each sample.

growth_protocol: RNA was isolated from early embryos (before bean stage) grown after L1 synchronization (60–65 h depending on each strain) in two independent biological replicates.

extract_protocol:
Extraction of RNA was performed according to the WormBook protocol (Stiernagle, 2006). Total RNA was purified using RNeasy kit (QIAGEN 74104) including DNase treatment. Depletion of ribosomal RNA was done for 5 ľg of total RNA with Ribo-Zero Margnetic Gold Kit (Epicentre MRGZG12324) and further concentrated with RNA Clean & Concentrator kit (Zymo Research R1015) according to corresponding manufacturers instructions.
Libraries were prepared using the TruSeq Standard mRNA Library Prep Kit (Illumina, San Diego, CA, USA).


title: RNA_set-25_eemb_20°C_rep3


title: 4C_Dup-int_IhhTSS_rep1

description: Processed data file: 4C_Ratio_Dup-int_vs_WT.bedgraph

source_name: E14.5 digit forelimb, Dup-int

value: Dupint/+


title: RNA_set-25_eemb_20°C_rep2


title: RNA_met-2_set-25_eemb_20°C_rep3


title: 4C_Dup-int_IhhTSS_rep2


title: RNA_set-25_eemb_20°C_rep1


title: mESC [160_minus_2]


title: RNA_met-2_eemb_20°C_rep3


title: RNA_met-2_eemb_20°C_rep2


title: RNA_met-2_eemb_20°C_rep1


title: RNA_N2_eemb_20°C_rep1

value: N2 (Bristol)


title: RNA_N2_eemb_20°C_rep3


title: RNA_N2_eemb_20°C_rep2


title: VPA P21 male litter 8

status: Public on Jul 03 2017

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Sample reads were demultiplexed and processed in the Illumina BaseSpace Environment
Reads were mapped to the mm10 mouse genomic reference with ethe STAR aligner
Abundance estimate of raw read counts per transcript was done with the htseq-count algorithm
Library size normalization to produced normalized expression (normalized read counts) was performed with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Rattus norvegicus

source_name: basolateral amygdala

extract_protocol:
Subjects were deeply anaesthetized with isofluorane, decapitated, and brains were frozen on dry ice and stored at -80˚C. On a microtome, punches (~1uM3) were be collected of the BLA, as well as the prefrontal cortex, nucleus accumbens, bed nucleus of the stria terminalis, and the hippocampus. Transcriptomics was assessed in male amygdala micropunches from P10 (n = 4 saline, 4 vpa) and P21 (n = 7 saline, 6 vpa). RNA sequencing libraries were prepared by the Yerkes Nonhuman Primate Genomics Core (NHPGC). Total RNA was prepared using the QIAGEN RNEasy Micro Kit. Libraries were generated from 5 ng of Total RNA using the CLONTECH SMARTer HV kit, and barcoding and sequencing primers were added using NexteraXT DNA kit. Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell. The clustered flowcell was sequenced on an Illumina HiSeq 1000 in 100-base single-read reactions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Pregnant females were orally gavaged with either 500 mg/kg of VPA (Sigma-Aldrich, St. Louis, Missouri) diluted in 0.9% saline or saline alone once daily on embryonic days 11-13.

value: basolateral amygdala

value: Sprague-Dawley

tag: develpmental stage

value: male


title: VPA P21 male litter 5


title: VPA P10 male litter 6

source_name: amygdala

value: amygdala


title: Saline P21 male litter 4


title: ChIP_H3K9me3_met-2_eemb_20°C_rep2

description: chromatin

value: early embryo


title: Saline P21 male litter 1


title: Saline P21 male litter 3


title: VPA P10 male litter 8


title: Saline P21 male litter 2


title: VPA P10 male litter 7


title: VPA P10 male litter 5


title: Saline P10 male litter 4


title: Saline P10 male litter 2


title: Saline P10 male litter 3


title: VPA P21 male litter 7


title: ACT88F-Foxo RNAi Carcass Fat Body

city: College Station

first: Jason

last: Karpac

state: Texas

address: Reynolds Medical Building

department: Molecular and Cellular Medicine

institute: Texas A&M University Health Sciences Center

data_processing:
Sample libraries were sequenced using the Illumina HiSeq 2500.
Sequence cluster identification, quality pre-filtering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.58 and RTA 1.18.64 software with default parameter settings.
Between 7 and 12 million (1X50) base pair reads were generated per library and mapped to the Drosophila genome (Release 6).
Expression was recorded as RPKM: reads per kbp per million reads.
Gene Ontology clustering analysis was performed using FlyMine
Genome_build: Drosophila genome (Release 6)
Supplementary_files_format_and_content: Expression was recorded as RPKM: reads per kbp per million reads.

organism: Drosophila melanogaster

source_name: Carcass Fat Body

growth_protocol: All flies were reared on standard yeast and cornmeal based food at 25°C and 65% humidity on a 12 hr light/dark cycle, The standard yeast and cornmeal based food was made with the following protocol: 14g Agar/165.4g Malt Extract/ 41.4g Dry yeast/ 78.2g Cornmeal/ 4.7ml propionic acid/ 3g Methyl 4-Hydroxybenzoate/ 1.5L water.

extract_protocol:
Intact fly thorax, carcass (with all of the eggs and intact intestines removed) and intestines were dissected in PBS. Total RNA was extracted using Trizol reagent and used as template to generate sample libraries for RNA sequencing
sample libraries for RNA sequencing were generated using the TruSeq Stranded Total RNA Library Prep Kit.

treatment_protocol: In order to standardize metabolic results, 2-3 days after eclosion, adult flies were placed on a simple sugar-yeast (SY) diet for 10 days. The standard SY diet was made with the following protocol (as previously described in (Skorupa et al., 2008)); 1.0g agar/10g sucrose/ 10g yeast/ 0.3 ml propionic acid/100 ml water. Ingredients were combined, heated to at least 102°C, and cooled before pouring.

value: ACT88F>Foxo RNAi

tag: ages

value: 10 days

value: Carcass Fat Body


title: ACT88F-W1118 Carcass Fat Body

tag: tissue


title: GN.Thio.PC#1

description:
ip 1ml of 3% thioglycate 18hrs before sac, CD11b+ Ly6G+
GN.Thio.PC.bw

source_name: Peritoneal cavity

tag: strain

value: Neutrophil


title: ACT88F-W1118 Gut

source_name: Gut

value: Gut


title: ACT88F-Foxo RNAi Thorax Skeletal muscle

source_name: Thorax Skeletal muscle

value: Thorax Skeletal muscle