title: Activated_T_cells_120h_doner_1_2

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
Library strategy: RiboMeth-seq
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 1.12
Mapping to rRNA reference sequence using Bowtie2 v. 2.2.6
Counting read ends and calculating RiboMeth-seq scores using python scripts
Genome_build: Human snRNAs (U1, U2, U4, U5a, and U6)
Supplementary_files_format_and_content: MS Excel files. Contains 5' and 3' read count over the rRNA sequence and the calculated RiboMeth-seq score, read-end count analysis, and statistical analyses

source_name: Whole cell RNA from 1 adult and healthy donor

extract_protocol:
Whole cell total RNA was extracted using Trizol (Thermo Fisher Scientific), according to the manufacturers instructions
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description

tag: tissue

value: CD4+ T cells from blood


title: RIP_Input_1

status: Public on Oct 20 2017

type: SRA

city: Nice

first: Silvia

last: Bottini

address: 299, chemin de la ginestiere

country: France

library_source: transcriptomic

data_processing:
Reads were trimmed with the program cutadapt and reads shorter than 15 nt were discarded
mapping of reads was performed with the webserver "omiRas"
Genome_build: mm10
Supplementary_files_format_and_content: differential smallRNAs were identified with the webtool omiRas and reported in the excel file provided as processed data file.

molecule: total RNA

organism: Mus musculus

source_name: mouse stem cell

extract_protocol:
RNA extraction was performed with miRNeasy columns (Qiagen), according to manufacturer's instructions
small RNA libraries were prepared using the NEBNext® Small RNA Library Prep Set for SOLiD™ kit (New England Biolabs), following the manufacturer’s instructions and performing 11 cycles of PCR

tag: cell type


title: microRNA-seq from neural tube (ENCLB378DWW)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR107JRF/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 12.5 day mouse neural tube
experiment encode accession: ENCSR107JRF
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB378DWW
size range: <30

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (12.5 days)

extract_protocol: not provided

value: neural tube

value: tissue

tag: description

value: Neural tube from 120 embryonic 12.5 day mice

tag: biosample encode accession

tag: age

tag: dev stage

value: embryonic

tag: Sex

value: pooled male and female

tag: health state

value: healthy

tag: lab

value: Len Pennacchio, LBNL

tag: link

value: ENCBS405OOH at ENCODE; https://www.encodeproject.org/ENCBS405OOH/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from MCF-7 (ENCLB844GWF)

description:
https://www.encodeproject.org/experiments/ENCSR042TWZ/
***************
biological replicate number: 2
technical replicate number: 1
description: SNIP1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR042TWZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882IYK
encode release date: 2017-06-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB844GWF
size range: 450-650

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens MCF-7 immortalized cell line

tag: antibody

tag: line

value: immortalized cell line

value: adult

value: female

value: 69 year

value: breast cancer (adenocarcinoma)

value: Michael Snyder, Stanford

value: ENCBS000RXG at ENCODE; https://www.encodeproject.org/ENCBS000RXG/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: microRNA-seq from neural tube (ENCLB941TYL)

description:
https://www.encodeproject.org/experiments/ENCSR107JRF/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 12.5 day mouse neural tube
experiment encode accession: ENCSR107JRF
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB941TYL
size range: <30

value: neural tube

value: Neural tube from 88 embryonic 12.5 day mice

value: ENCBS254TSW at ENCODE; https://www.encodeproject.org/ENCBS254TSW/


title: Activated_T_cells_120h_donor_2_2

value: CD4+ T cells from blood


title: Activated_T_cells_120h_doner_1_3


title: microRNA-seq from embryonic facial prominence (ENCLB941DFN)

description:
https://www.encodeproject.org/experiments/ENCSR005FZJ/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 12.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR005FZJ
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB941DFN
size range: <30

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (12.5 days)

value: embryonic facial prominence

value: tissue

value: Embryonic facial prominence from 120 embryonic 12.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS047UII at ENCODE; https://www.encodeproject.org/ENCBS047UII/


title: RIP_AGO2_3

tag: hits-clip antibody

value: 2D4 clone from Wako Chemicals


title: ChIP-seq from tibial nerve (ENCLB703LVA)

description:
https://www.encodeproject.org/experiments/ENCSR004FGW/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on human tibial nerve
experiment encode accession: ENCSR004FGW
assay title: ChIP-seq
encode release date: 2016-12-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB703LVA
size range: 450-650

source_name: Homo sapiens tibial nerve tissue male adult (37 years)

value: Control

value: tibial nerve

value: male

value: 37 year

value: adult

value: ENCBS168BMV at ENCODE; https://www.encodeproject.org/ENCBS168BMV/

value: derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Activated_T_cells_24h_donor_6_2


title: SC_internal SPEN_HS_43_30'_rec4h

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

data_processing:
Reads were mapped to the mouse genome (mm10) with Bowtie2.
Aligned files were converted to bam and sorted using Samtools.
Peaks detection was carried with case-control strategy (detected peaks are given in bed files)
SPEN target sites were annotated to genomic regions using HOMER software (annotated binding sites are given in text file)
Genome_build: mm10
Supplementary_files_format_and_content: bed - detected peaks, can be open in text editors/Excel; txt - annotated binding sites, can be opened in text editors/Excel.

source_name: spermatocytes

growth_protocol: Testicular cells for ChIP experiments were collected after collagenase type IA digestion of decapsulated testes (1mg/ml in CO2 saturated RPMI medium for 20 min at 32°C in a shaking water bath operated at 120 cycles/min). The dispersed seminiferous tubules were isolated by allowing them to sediment for 2-3 min under 5% CO2 in air and decanting the supernatant. The process was repeated 3 times with 10 ml RPMI to stop the reaction and to ensure removal of the dissociated interstitial cells and blood cells. Cell aggregates were dissociated gently by repeated pipetting for 3-5 min. Cells were suspended in CO2 saturated RPMI medium supplemented with 10% (v/v) fetal bovine serum, 0.004% (v/v) gentamycin (KRKA), and 6mM sodium lactate (Sigma) at 32°C (physiological temperature of testes). Population of cells enriched in spermatocytes (up to 80%) was obtained by unit gravity sedimentation of testicular cells obtained after enzymatic treatment (collagenase type IA, trypsin, and DNase I)  in a Sta-Put chamber (SP-120, ProScience Inc, Ontario, Canada) containing a 1-3% (w/v) linear BSA gradient in PBS. Finally cells were suspended in RPMI medium as the mixture of testicular cells.

extract_protocol:
The ChIP assay was carried out according to the protocol of a ChIP kit from Upstate Biotechnology (Lake Placid, NY) using protein A-sepharose beads (Amersham). Standard crosslinking procedure was used. For each IP reaction 48-50 µg of chromatin sonicated to 100-500 bp fragments and 5 µg of anti-SPEN polyclonal antibodies, or IgG from rabbit serum (Sigma) as a negative control were used. Immunoprecipitated DNA was additionally digested by RNase A (in a final concentration 70 μg/ml, 30 minutes, 37°C) before Proteinase K treatment and organic solvents extraction. Glycogen (70 μg/ml) was added at the precipitation step. DNA was dissolved in H2O. In each experimental point five to six ChIP replicates were collected and combined in one sample before DNA sequencing.
Sequencing libraries were generated using KAPA library preparation kit (for Illumina) KK8201. Template amplification and cluster generation were performed using the TruSeq SBS Kit.

treatment_protocol: For heat shock, equal volumes of CO2 saturated, pre-heated media (to 53°C or 60°C) were added to the cells suspensions, which immediately raised their temperature from 32°C (physiological temperature) to 38°C or 43°C, respectively. Tubes were submerged in a water bath at the appropriate temperature for an additional 15-30 minutes with recovery at 32°C in a cell culture incubator.

tag: strain

value: FVB/N

value: adult (10-16 weeks)

tag: tissue/cells

value: testes/spermatocytes

tag: chip antibody

value: internal SPEN (Abcam, ab72266)

tag: treatment

value: heat shocked at 43°C for 30 min & 4h of recovery


title: microRNA-seq from embryonic facial prominence (ENCLB138SKC)

description:
https://www.encodeproject.org/experiments/ENCSR005FZJ/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 12.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR005FZJ
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB138SKC
size range: <30

value: embryonic facial prominence

value: tissue

value: Embryonic facial prominence from 88 embryonic 12.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS399GYO at ENCODE; https://www.encodeproject.org/ENCBS399GYO/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from MCF-7 (ENCLB091BWC)

description:
https://www.encodeproject.org/experiments/ENCSR042TWZ/
***************
biological replicate number: 1
technical replicate number: 1
description: SNIP1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR042TWZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882IYK
encode release date: 2017-06-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB091BWC
size range: 450-650

value: immortalized cell line

value: female

value: Michael Snyder, Stanford

value: breast cancer (adenocarcinoma)

value: 69 year

value: ENCBS345ZJP at ENCODE; https://www.encodeproject.org/ENCBS345ZJP/

value: derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: Activated_T_cells_24h_donor_6_1

tag: tissue

value: CD4+ T cells from blood


title: Activated_T_cells_120h_donor_2_3


title: HIO_H9B

city: Los Angeles

first: Brendan

middle: H

last: Grubbs

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

description: Processed data file: 25Apr17_TG_Empirical_annotated.txt

data_processing:
Cutadapt 1.13
Trimmomatic 0.35
RNA-star 2.5.2b
Htseq-count 0.6.1p2
EdgeR 3.16.5
Genome_build: GRCh38, gencode v25, Ensembl 87
Supplementary_files_format_and_content: 25Apr17_TG_Empirical_annotated.txt: Tab-delimited text file; Differential expression analysis with edgeR with annotation, counts, and RPKMs.

source_name: Human Intestinal Organoid Tissue-Engineered Small Intestine

growth_protocol: HESC were differentiated into D28-35 HIO as previously published by Spence et al. or separately to unsorted D15 ENCC as previously described by Fattahi et al. ENCC-HIO-TESI was generated by placing 4-6 HIO with 40-60 ENCC onto a PGA/PLLA scaffold and allowing it to grow within the omentum of mice for 3 months. HIO-TESI were generated by placing 4-6 HIO alone onto a PGA/PLLA scaffold and allowing it to grow within the omentum of mice for 3 months.

extract_protocol:
Samples were lysed in RNAlater and processed with Qiagen RNeasy Mini/Midi Prep Kit.
Illumina TruSeq v2

tag: cell type

value: HESC-derived human intestinal organoids


title: HIO_H9E


title: HIO_H9D


title: Activated_T_cells_120h_doner_1_1


title: SC_input DNA mix

value: FVB/N

value: male

value: adult (10-16 weeks)

value: testes/spermatocytes

value: equal mixture of all spermatocyte's inputs


title: Activated_T_cells_24h_donor_6_3


title: ChIP-seq from esophagus squamous epithelium (ENCLB098MSN)

description:
https://www.encodeproject.org/experiments/ENCSR003SZZ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human esophagus squamous epithelium
experiment encode accession: ENCSR003SZZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR710DTC
encode release date: 2016-12-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB098MSN
size range: 450-650

source_name: Homo sapiens esophagus squamous epithelium tissue female adult (51 year)

value: CTCF

value: esophagus squamous epithelium

value: tissue

value: 51 year

value: adult

value: ENCBS969YPI at ENCODE; https://www.encodeproject.org/ENCBS969YPI/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: ENCC_HIO_TESI5

source_name: Enteric Neural Crest Cell and Human Intestinal Organoid Tissue-Engineered Small Intestine

value: HESC-derived enteric neural crest cells and human intestinal organoids


title: SC_internal SPEN_untreated

value: internal SPEN (Abcam, ab72266)

value: untreated control


title: Activated_T_cells_24h_donor_5_1

value: CD4+ T cells from blood


title: ENCC_HIO_TESI2


title: SC_internal SPEN_HS_43_30'_rec2h

value: heat shocked at 43°C for 30 min & 2h of recovery


title: Activated_T_cells_24h_donor_5_3


title: ENCC_HIO_TESI3


title: Man1-GBP Rap1-GFP

city: Bethesda

first: Hani

last: Ebrahimi

address: 7170 Woodmont Ave

department: NCI

institute: NIH

data_processing:
Three bases at the 5’ ends of the reads were trimmed.
The 47 bp post-trimmed reads were aligned to the reference genome using bowtie2, allowing for 50 alignments per repetitive region.
Normalization was performed using a Python script that sequentially executed: 1- Get the number of total aligned reads, reads covering ade6 locus (chr III: 1316291-1318035), and reads covering a euchromatin region adjacent to ade6 locus (chr III: 1304000,1380000); 2- Calculate a normalization scale factor: 10 / (median of reads covering each base within the ade6 locus – median of reads covering each base in the neighboring euchromatic region); 3- Apply the scale factor to the aligned genomic reads (BAM files) using the genomecov function of the BEDTools suit to produce a bedgraph file.
To generate the ribbon-line coverage plots shown in the above figures, an R script was created that imports the bedgraph files and, using a 250 bp sliding window, calculates the median, maximum and minimum of reads from strains with identical genotypes. The scripts used for this study have been deposited at https://www.elucidaid.com/repository/ebrahimih17
We customized the reference genome by replacing the deleted mat region with a contig of the h90 configuration of the mat2P-mat3M region (as described on http://www.pombase.org/status/mating-type-region; accessed July.2017)
Genome_build: ASM294v2
Supplementary_files_format_and_content: bedgraph format with normalized read scores

organism: Schizosaccharomyces pombe

source_name: S. pombe cells

growth_protocol: Cultures were grown overnight in 120 ml YE5S medium to mid-log phase and treated with formaldehyde (1% final conc.) for 10 min at room temperature with occasional swirling.

extract_protocol:
The frozen pellet was resuspended in 500 µl lysis buffer: 50 mM Hepes pH 7.4, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 1% PMSF and EDTA-free protease inhibitor cocktail (Roch) and lysed using FastPrep (MP Biomedical; setting: 5x 30 Sec cycles at 4.5 m/s). Each lysate was recovered in a 5 ml snap-cap tube by centrifugation at 1500 rpm for 3 min and sonicated using the Covaris E210 instrument. Sonication settings used were: 20%, 8 intensity, 200 cycles per burst for 12 minutes.
Libraries were prepared using DNA SMART ChIP-Seq Kit (Clontech) and Illumina indexed oligomers. Following PCR amplifications (15 cycles), libraries were size selected and purified using Agencourt AMPure XP beads (200-400 bp range). Each library was validated using Quibit 2.0 Fluorometer for concentration, Agilent 2100 Bioanalyzer for fragment size, and NEBNext Library Quant Kit (New England BioLabs) for adaptor presence.
Libraries from 12 samples were pooled in equimolar ratio (10 nM) and submitted for sequencing using Illumina HiSeq2500 Rapid Run mode.

treatment_protocol: 37.5 ml of the spike culture was mixed with 112.5 ml of each sample before treating with formaldehyde. Treated cells were washed with 50 mL refrigerated Milli-Q (Millipore) water. Cells were centrifuged at 2000 rpm for 2 min, resuspended in 1 ml water and centrifuged before adding 1 ml Zirconium beads to the pellet. The pellet and beads mixture was flash frozen in liquid nitrogen and stored at -80 °C in 2 ml screw-cap shatter proof tubes.

tag: genotype

value: h+ Rap1-GFP-kanMX6 man1-GBP-mCherry-hph

value: H3K9-di-methyl (abcam:ab1220)


title: SC_internal SPEN_HS_43_30'

value: FVB/N

value: male

value: adult (10-16 weeks)

value: heat shocked at 43°C for 30 min


title: IgG mix

source_name: testicular cells

value: testes

value: IgG from rabbit serum (Sigma)

value: pooled from all treatments


title: input DNA mix

value: equal mixture of all testicular inputs


title: Skin_3

source_name: Whole cell RNA pooled from 5 adult and healthy donors

value: Skin


title: Man1-GBP Pol Δ-GFP rep3

value: h+ swi7-GFP-kanMX6 man1-GBP-mCherry-hph


title: Skin_1


title: Man1-GBP Pol Δ-GFP rep2


title: Activated_T_cells_24h_donor_5_2


title: Skin_2


title: dcr1Δ

value: h+  dcr1::ura4+


title: Skeletal_muscle_3

value: Skeletal muscle


title: Man1-GBP Pol Δ-GFP rep1


title: internal SPEN_HS_43_30'_rec4h

value: internal SPEN (Abcam, ab72266)

value: heat shocked at 43°C for 30 min & 4h of recovery


title: internal SPEN_HS_43_30'


title: internal SPEN_HS_43_30'_rec2h

value: heat shocked at 43°C for 30 min & 2h of recovery


title: Skeletal_muscle_1


title: bqt4Δ rep3

value: h+ leu1-32 ura4-D18  bqt4::natMX6


title: internal SPEN_HS_43_15'

value: heat shocked at 43°C for 15 min


title: internal SPEN_HS_38_30'_rec4h

value: FVB/N

value: heat shocked at 38°C for 30 min & 4h of recovery


title: bqt4Δ rep2

value: H3K9-di-methyl (abcam:ab1220)


title: Skeletal_muscle_2


title: Pancreas_2

value: Pancreas


title: bqt4Δ rep1


title: WT rep3


title: Pancreas_3


title: internal SPEN_HS_38_30'_rec2h

value: male

value: adult (10-16 weeks)

value: testes

value: heat shocked at 38°C for 30 min & 2h of recovery


title: Pancreas_1


title: internal SPEN_HS_38_30'

value: heat shocked at 38°C for 30 min


title: internal SPEN_HS_38_15'

value: heat shocked at 38°C for 15 min


title: Naive_T_cells_donor_2_3

value: CD4+ T cells from blood


title: WT rep2


title: WT rep1


title: Naive_T_cells_donor_2_2


title: Naive_T_cells_donor_2_1


title: RNAP2_Smarca4_G784E

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

description: anti-RNAP2 ChIP in mES cells expressing G784E Smarca4V5.

data_processing:
Basecalls performed using Illumina CASAVA version 1.8.2.
Reads were aligned to the mm9 genome assembly using bowtie version 2.1.0, requiring mapping qualities > 10. Duplicate reads were discarded.
Peaks were called by comparing ChIP and input samples using MACS 2.1.1 with default settings.
Peaks with less than 30 reads per million were discarded to ensure high-quality peak calls.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigWig files were generated by extending all read fragments to 200 bp, then calculating the basepair coverage for each replicate using Bedtools, normalizing by the total number of reads within called peaks. For samples with multiple replicates, values in the bigWig files represent coverage calculated in this way averaged across both replicates using bwtool.

source_name: Mouse embryonic stem cells, Smarca4_G784E, RNAP2 ChIP

growth_protocol: Cells are grown in DMEM media supplemented with 15% FBS and LIF.

extract_protocol:
Lysates were obtained from sonicated nuclei crosslinked with formaldehyde, and protein-DNA complexes were isolated by immunoprecipitation.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Wild-type and heterozygous Smarca4 mutant cells received no treatment.

tag: strain/background

value: Embryonic stem cells

tag: passage

value: Mouse anti-RNAP2

tag: chip antibody vendor

value: Covance

tag: chip antibody cat. #

tag: chip antibody lot/batch #

value: n/a (monoclonal)


title: Naive_T_cells_donor_1_3


title: Naive_T_cells_donor_1_2


title: input C646 CBP inhibitor rep2

city: Stockholm

first: Mattias

last: Mannervik

address: Arrheniuslaboratories E3

department: Molecular Biosciences, the Wenner-Gren Institute

country: Sweden

institute: Stockholm University

data_processing:
Uniquely mapping reads where mapped to the Drosophila melanogaster genome (release 5, Bowtie2 default parameters)
Log2 ratio between IP and input read density was calculated
Data was median smoothed using 100 bp windows
Smoothed ratio values every 10 bp was extracted
Genome_build: Drosophila melanogaster genome release 5
Supplementary_files_format_and_content: sgr files containing smoothed log2 ratio of IP over input (10 bp resolution)

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: Drosophila S2 cells (catalog #006 from the Drosophila Genomics Resource Center) were grown to a density of 0.2 – 1 x 107 cells/ml and fixed in 1 % formaldehyde for 15 min at ambient temperature. The reaction was quenched by 0.16 M glycine pH 7.0 for 5 min and washed in PBS.

extract_protocol:
After fixation, the cells were washed and sonicated using a Bioruptor (Diagenode) to generate chromatin extract. Chromatin extract was mixed with Drosophila virilis chromatin, cleared by centrifugation and used in ChIP with anti-Drosophila TFIIB antibody, pre-bound to a mix of Protein A and G Dynabeads.
TFIIB bound DNA was purified, and libraries prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina. Illumina sequencing was performed at SciLifeLab, Stockholm, Sweden.

treatment_protocol: Two million S2 cells/ml were centrifuged and dissolved in FCS free media. 30 uM of CBP inhibitor (C646) or control drug (C37) in DMSO was added to the cells for 10 min prior to fixation.


title: TFIIB ChIP-seq C37 control rep2

value: Drosophila TFIIB antibody from Jim Kadonaga (UCSD).


title: input C646 CBP inhibitor rep1


title: input C37 control rep2


title: input C37 control rep1


title: Liver_2

value: Liver


title: Liver_1


title: Liver_3


title: Jurkat_3

source_name: Whole cell RNA from cell culture

value: Jurkat E6-1


title: TFIIB ChIP-seq C37 control rep1


title: Jurkat_2


title: MNase-seq C646 CBP inhibitor rep2

data_processing:
Uniquely mapping reads where mapped to the Drosophila melanogaster genome (release 5, Bowtie2 default parameters)
Only read pairs with insert-size 130-180bp were kept
Read density values every 10 bp was extracted
Genome_build: Drosophila melanogaster genome release 5
Supplementary_files_format_and_content: sgr files containing read density (10 bp resolution)

growth_protocol: Drosophila S2 cells (catalog #006 from the Drosophila Genomics Resource Center) were grown to a density of 0.2 – 1 x 107 cells/ml and fixed in 1 % formaldehyde for 2 min at ambient temperature. The reaction was quenched by 0.16 M glycine pH 7.0 for 5 min and washed in PBS.

extract_protocol:
After fixation, the cells were digested with 150 gel units MNase and mixed with MNase digested Saccharomyces cerevisea chromatin.
Mnase digested DNA was purified, and libraries prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina. Illumina sequencing was performed at SciLifeLab, Stockholm, Sweden.

tag: mnase

value: MNase digestion


title: ATAC_Smarca4_Y860H

description: ATAC-seq in mES cells expressing Y860H Smarca4V5

data_processing:
Basecalls performed using Illumina CASAVA version 1.8.2
Reads were trimmed to remove adapters, then aligned to the mm9 genome assembly using bowtie version 2.1.0, requiring mapping qualities > 10. Duplicate reads were discarded.
Peaks were called by creating pseudofragments of length 200 bp around each ATAC-seq fragment end, then using MACS 2.1.0 with with default settings.
Peaks with less than 10 reads per million were discarded to ensure high-quality peak calls.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated by creating pseudofragments of length 200 bp centered over all ATAC-seq read fragments, then calculating the basepair coverage for each replicate using Bedtools, normalizing by the total number of reads within called peaks. For samples with multiple replicates, values in the bigWig files represent coverage calculated in this way averaged across both replicates using bwtool.

source_name: Mouse embryonic stem cells

extract_protocol:
Isolated nuclei were obtained from lysed cells and transposed with Tn5 transposase. The resulting tagmented fragments were barcoded and sequenced using Illumina sequencing.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

tag: genotype/variation

value: heterozygous Smarca4 mutant


title: ATAC_Smarca4_WT

description: ATAC-seq in mES cells expressing WT Smarca4V5

value: wild type


title: MNase-seq C37 control rep1


title: MNase-seq C646 CBP inhibitor rep1


title: Brain_3

value: Brain


title: internal SPEN_untreated

value: FVB/N

tag: Sex

value: male

tag: age

value: adult (10-16 weeks)

value: internal SPEN (Abcam, ab72266)

value: untreated control


title: ATAC_Smarca4_R885H

description: ATAC-seq in mES cells expressing R885H Smarca4V5


title: TFIIB ChIP-seq C646 CBP inhibitor rep1


title: Brain_2


title: ATAC_Smarca4_G784E

description: ATAC-seq in mES cells expressing G784E Smarca4V5


title: Naive_T_cells_donor_1_1

source_name: Whole cell RNA from 1 adult and healthy donor

value: CD4+ T cells from blood


title: Brain_1


title: ATAC_Smarca4_E882K

description: ATAC-seq in mES cells expressing E882K Smarca4V5


title: siSFPQ_sample3

data_processing:
Reads were trimmed with the program cutadapt and reads shorter than 15 nt were discarded
filtering versus mouse ribosomal RNA with bowtie2
Mapping of reads onto mouse genome mm10 was performed with STAR, than bowtie2
Genome_build: mm10
Supplementary_files_format_and_content: differential spliced events were identified with the software SpliceTrap and reported in the excel file provided as processed data file.

source_name: mouse stem cell

extract_protocol:
RNA extraction was performed with miRNeasy columns (Qiagen), according to manufacturer's instructions
NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® according to manufacturer's instruction

value: P19 cells

tag: condition

value: SFPQ knockdown


title: siSFPQ_sample2


title: ATAC_Smarca4_K785R

description: ATAC-seq in mES cells expressing K785R Smarca4V5

tag: strain


title: CTRL_sample3

value: control


title: siSFPQ_sample1


title: RNA Smarca4 WT rep 2

description: RNA-seq in mES cells expressing WT Smarca4V5

data_processing:
Basecalls performed using Illumina CASAVA version 1.8.2
Reads were aligned to the mm9 genome assembly using bowtie version 2.1.0, requiring mapping qualities > 10. Duplicate reads were discarded.
Reads within coding regions were counted using htseq, with gene definitions obtained from the refGene table of RefSeq genes in the UCSC Table Browser. The table of all counts was processed using DESeq2, using default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file including total numbers of reads overlapping each gene for each sample

extract_protocol:
RNA was extracted from cells using QIAzol reagent, and mRNA enriched by poly(dT) capture. RNA was converted to DNA, then size-selected for 200-400 bp DNA fragments before PCR amplification.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.


title: RNA Smarca4 WT rep 1


title: RNA Smarca4 G784E rep 2

description: RNA-seq in mES cells expressing G784E Smarca4V5


title: Jurkat_1


title: RNA Smarca4 G784E rep 1


title: Input DNA

city: Miami

first: Matt

middle: C

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

data_processing:
Reads aligned to mm10 with BWA
Peaks called with Macs2
Peaks annotated with Homer
Genome_build: Genome Reference Consortium GRCm38, mm10, Dec 2011
Supplementary_files_format_and_content: Excel file describing the peak data. One line per peak. Describes genomic location, nearest gene, signal in peak, and presence of relevant motifs within each peak.

source_name: whole spinal cord

extract_protocol:
6-week-old male C57BL/6 mice were terminally anesthetized (ketamine/xylazine, 100/15mg, i.p.) and perfused with only cold PBS just prior to removal of the spinal cord  Tissue preparation and ChIP protocol closely adhered to steps outlined in the MAGnify™ Chromatin Immunoprecipitation System manual (Invitrogen, 49-2024) according to manufacturer’s instructions with only a few modifications (see below). Briefly, dissected spinal cords were immediately weighed, cleaned, and minced with a razor blade in ice cold PBS.  Minced tissue was then collectively homogenized by passing repeatedly through 18G and 21G needles before crosslinking chromatin with formaldehyde at a final concentration of 1% at room temperature for 10 minutes.  Glycine was added to a final concentration of 0.125 M to quench formaldehyde crosslinking, and cells were then pelleted and washed with ice-cold PBS.  Cell pellets were resuspended in Lysis Buffer plus Protease Inhibitors at a concentration of 1x10^6 cells / 50 μl.  Nuclear lysates were then sonicated using a Branson® 150 Sonifier (power setting 4, 100% duty cycle for 10 × 30-s on 90-s off intervals), yielding chromatin fragments of 50–300 bp. Dynabeads® Protein A/G (Invitrogen, 10010D) were coupled to either 5 μg of Polyclonal Rabbit anti-Olig2 antibody (Millipore, A9610) or Rabbit IgG (Invitrogen, 100005291) by mixing end-over-end for 4 hours at 4°C prior to introduction to lysates.  Antibody-conjugated beads were then combined with 500 μl of lysate (~1x10^7 cells) plus 500 μl of Dilution Buffer in 1.5 mL LoBind Eppendorf tubes (Sigma-Aldrich, Z666548-250EA) and mixed by end-over-end rotation overnight at 4°C. Approximately 1% of the total sheared chromatin was set aside and served as Input Control.  Beads containing Protein–DNA complexes were subsequently washed with IP Buffer, formaldehyde crosslinking reversed by heat treatment, and the DNA eluted using a 12 Tube Magnetic Separation Rack (NEB, S1509S).  Here, we note that the Magnify™ protocol is designed for use with 0.2 uL tubes, so in all subsequent steps involving end-over-end rotation we instead placed each 1.5 mL LoBind tube on its side and applied gentle agitation using a platform rocker.  This small change to the protocol ensured that the beads remained submerged in solution throughout.  For all steps involving bead collection via magnetic rack, 1.5 mL LoBind tubes were placed in the rack in such a way as to concentrate bead collection toward the bottom of the tube, again to keep them submerged in solution.  Specifically, foam padding was added at the base of the rack to keep the tubes slightly elevated. Input Control samples were processed at the reverse crosslinking step in parallel with the ChIP’d samples. IgG IP’d DNA was analyzed by qPCR but was not included in NGS analysis.
Illumina TruSeq ChIP Library Preparation Kit (Illumina, IP-202-1024) according to manufacturer's instructions. Briefly, DNA libraries were prepared from total sheared chromatin (Input Control Library) and ChIP-enriched fragments (ChIP’d Library) using Illumina TruSeq ChIP Library Preparation Kit (Illumina, IP-202-1024). For this experiment, we used a modified TruSeq® ChIP Sample Preparation Guide protocol (Illumina, PN 15023092 Rev.B; Oct. 2013), omitting only the gel purification step to maximize total yield of adapter-ligated library fragments.  Input Control and ChIP’d libraries were prepared using recommended inputs of 100 pg/μl (50 μl), for a total of 5 ng per library prep.  Libraries were indexed using TruSeq Adapters AR008 (Input Control Library; ACTTGA/A) and AR001 (ChIP’d Library; ATCACG/A).  All QC steps (Input DNA quantification, size distributions, and library traces) were evaluated using a Fragment Analyzer Automated CE system with High Sensitivity NGS Fragment Analysis Kit 1bp-6000bp (Advanced Analytical, DNF-474).  Libraries were sequenced at 2 x 50 bp read lengths using the Illumina MiniSeq Sequencing System and MiniSeq High-Output Reagent Kits (Illumina, FC-420-1001).

tag: developmental stage

value: 6 weeks old


title: CTRL_sample2


title: CTRL_sample1


title: MNase-seq C37 control rep2


title: Olig2_ChIPSeq

tag: chip antibody

value: Olig2 (Millipore #A9610)


title: 10Cu25Ce_b

city: Ann Arbor

first: Wenyu

last: Gu

state: MI

address: 2350 Hayward St, EWRE 283

institute: University of Michigan

data_processing:
The raw reads obtained from the sequencing core were trimmed using Sickle 1.33 with default parameters for single-end reads
The trimmed reads were aligned to the Methylosinus trichosporium OB3b genome (WGS ADVE02) downloaded from Genoscope (https://www.genoscope.cns.fr/agc/microscope/home/index.php) using the  Burrows-Wheeler alignment tool (BWA) backpack 0.7.12 with default parameters.
The quality of sequences was checked at each step by FastQC v0.11.5.
The resulting sequence alignment/map (SAM) files were then sorted using SAMtools-1.3.1
Reads were assigned to features and counted using HTSeq 0.6.1p1 with “intersection-nonempty” and “–a=0” mode
Differential expression was analyzed by DESeq2 v1.12.4
Genome_build: Methylosinus trichosporium OB3b genome (WGS ADVE02) from Genoscope
Supplementary_files_format_and_content: Output file from DESeq2 includes base mean expression level (counts), log2 fold change of expression, uncertainty of estimated fold change (lfcSE, stat), p-values of differential expression tests and BH-adjusted p-values.

organism: Methylosinus trichosporium

source_name: Bacterial cells

growth_protocol: Methylosinus trichosporium OB3b were grown on nitrate mineral salt (NMS) medium (Whittenbury et al., 1970) at 30 °C in 250 ml side-arm Erlenmeyer flasks sealed with rubber stoppers. The flasks are shaken at 200 rpm in dark. CH4 was added at a methane-to-air ratio of 1:2. To investigate the effect of copper and cerium on the transcriptome of M. trichosporium OB3b, this strain was grown under four different conditions using side-arm flasks to noninvasively monitor growth: 0 µM copper + 0 µM cerium, 0 µM copper + 25 µM cerium, 10 µM copper + 0 µM cerium, and 10 µM copper + 25 µM cerium .  All conditions had triplicate biological replicates.  Copper and cerium were added as CuCl2 and CeCl3, respectively.  Growth of these cultures was monitored via OD600 measured using a Genesys 20 Visible spectrophotometer (Spectronic Unicam, Waltham, MA) at 4 h-12 h intervals.

extract_protocol:
RNA was extracted from cultures grown with methane as the sole growth substrate. Cultures were collected in the mid-exponential phase. 20ml from each flask was first mixed with 2.5 ml stop solution [5 % buffer equilibrated phenol (pH 7.3) in ethanol] to stop synthesis of new mRNA and then centrifuged at 4,000 g for 10 minutes at 4 °C 20mL. The cell pellets were then resuspended in 0.75 ml of extraction buffer [100 mM Tris-HCl (pH 8.0), 1.5 M NaCl, 1% (w/v) hexadecyltrimethylammonium bromide (CTAB)] and subjected to lysis by bead beating using 0.5 g 0.1-mm zirconia-silica beads at 4,800 rpm for 1 minute (Biospec Products) in the presence of 35 ml 20% SDS, 35 ml 20% laurylsarcosine, and 750 ml phenol-chloroform-isoamylic alcohol (25:24:1). The samples were then centrifuged at 14,000 rpm for 5 min at 4°C and the upper aqueous phase was transferred to a new tube and mixed with an equal volume of chloroform-isoamylic alcohol (24:1). The mixture was centrifuged again and the upper aqueous phase containing RNA was precipitated in MgCl2, sodium acetate, and isopropanol overnight at -80°C. RNA were recovered the next day by centrifugation at 14,000 rpm for 30 min at 4°C and washed by 75% ethanol. DNA was removed by Qiagen RNase-free DNase through at least two treatments, followed by purification using a Zymo RNA Clean & Concentrator kit (Zymo Research, Irvine, CA) following the manufacturer’s instructions. Removal of all traces of DNA was confirmed by the absence of a 16S rRNA PCR product in reactions using 2 μl of RNA template and 32 PCR cycles. RNA concentrations were estimated by using an ND-1000 spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE). Following the purification of total RNA, ribosomal RNA were removed using the RiboZero kit for Gram-negative bacteria (Illumina, San Diego, CA). The qualities of the samples were checked by Agilent bioanalyzer (Santa Clara, CA).
mRNA-seq libraries were prepared by University of Michigan DNA Sequencing Core (http://seqcore.brcf.med.umich.edu) and sequenced in one lane using Illumina HiSeq4000 SE 50.


title: S11 OX_2

city: Beijing

first: Shanshan

last: Zhao

address: No.5, Yiheyuan Road, Haidian District

country: China

institute: Peking University

data_processing:
The adapter,Ns and low-quality reads were trimmed and filtered by cutadapt.
The clean reads were mapped to rice reference genome by tophat with default parameters in strand-specific mode.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: Text containing  gene id and their expression level (RPKM,Reads Per Kilo Million)in each samples

organism: Oryza sativa Japonica Group

source_name: Oryza sativa, S11 overexpression transgene

growth_protocol: Rcie seedlings were grown in a greenhouse at 28-30℃ with natural light conditions.

extract_protocol:
Total RNA were extracted from 42 days old seedlings using Qiagen RNeasy plant mini kit, one sample pooled from 3 individual palnts.
RNA libraries were prepared for sequencing using standard dUTP strand-specific RNA-seq library  protocols

treatment_protocol: Mock: 14 days old seedlings were inoculated with 3 virus free insect per plant. RDV: 14 days old seedlings were inoculated with 3 viruliferous insect per plant. WT and OsSAMS1 and S11 transgenic rice: grown in a greenhouse at 28-30℃ with natural light conditions without any inoculation.

tag: cultivar

value: Zhonghua 11

value: aboveground part of plant

value: 42 days old seedling

value: S11 overexpression transgene


title: S11 OX_1

tag: tissue


title: S11 OX_3


title: 10Cu0Ce_b


title: 10Cu25Ce_a


title: 10Cu0Ce_a


title: 0Cu25Ce_c


title: Ossams1 KO_2

source_name: Oryza sativa, OsSAMS1 CRISPR/Cas9 transgene

value: OsSAMS1 CRISPR/Cas9 transgene


title: TFIIB ChIP-seq C646 CBP inhibitor rep2

value: Drosophila TFIIB antibody from Jim Kadonaga (UCSD).


title: 0Cu25Ce_b


title: ATAC_Smarca4_E861K

description: ATAC-seq in mES cells expressing E861K Smarca4V5

value: heterozygous Smarca4 mutant


title: RDV_3

source_name: Oryza sativa, RDV-infected (inoculated with insect carrying RDV)

value: 42 days old seedling (4 weeks post inoculation)


title: RDV_2

value: RDV-infected (inoculated with insect carrying RDV)


title: 0Cu0Ce_c


title: RDV_1


title: Ossams1 KO_1


title: OsSAMS1 OX_3

source_name: Oryza sativa, OsSAMS1 overexpression transgene

value: OsSAMS1 overexpression transgene


title: Mock_3

source_name: Oryza sativa, wild type (inoculated with virus free insect)


title: 10Cu0Ce_c


title: OsSAMS1 OX_1


title: WT_2

source_name: Oryza sativa, wild type

value: wild type


title: Mock_2

value: wild type (inoculated with virus free insect)


title: 0Cu0Ce_a


title: 0Cu0Ce_b


title: Activated_T_cells_120h_donor_2_1

value: CD4+ T cells from blood


title: Ossams1 KO_3


title: Mock_1


title: 10Cu25Ce_c


title: WT_1


title: FF6mo2

status: Public on Oct 19 2017

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
Reads were mapped to the mm10 murine genome and USCS transcriptome annotation (obtained from Illumina iGenomes) using Tophat 2 and uniquely mapped reads associated with each gene were counted using HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited table of uniquely aligned read counts for each gene in the annotation.

molecule: polyA RNA

source_name: Nf1(flox/flox) mouse

growth_protocol: Optic glioma stem cells (o-GSCs) were isolated from optic glioma mouse models. For NVP-BKM120 treatments, cells were cultured in neural stem cell medium without EGF and bFGF for 1 hour, followed by treatment with DMSO (vehicle) or 0.2 μM NVP-BKM120 for 5 hours at 37°C, and cells harvested for RNA isolation or western blotting.

extract_protocol:
Tissue samples or cell lines were homogenized in Trizol and total RNA was extracted using Trizol and isopropanol precipitation. Poly(A)+ mRNA was then isolated from each total RNA sample using streptavidin-coated superparamagnetic beads (Dynabeads, Life Technologies) coated in biotinylated LNA-oligo(dT) (Exiqon).
Purified poly(A)+ mRNA from each sample was reverse transcribed and Illumina sequencing libraries were enriched usign the SMARTer Stranded RNA-Seq kit (Clontech). The resulting libraries were sequenced on an Illumina HiSeq 2500 or NextSeq 500 with single-end 100-base or 75-base reads, respectively.
template-switching RNA-Seq with random primers

treatment_protocol: 50 mg/kg/day minocycline (Sigma-Aldrich; PBS, vehicle) was delivered by intraperitoneal (i.p.) injection 5 days/week for two weeks. 5 mg/kg/day rapamycin (Selleckchem; 5.2% Tween 80/5.2% polyethylene glycol 400 as vehicle) was administered by i.p. injection 5 days/week for two weeks. 20 mg/kg/day NVP-BKM120 (Selleckchem; N-methyl-2-pyrrolidone/ polyethylene glycol 300 (10/90v/v) as vehicle) was delivered by oral gavage 5 days/week for two weeks [40]. 60 mg/kg/day carboplatin (Sigma-Aldrich; PBS as vehicle) was administered by i.p. injection every other day for 1 week.

value: optic nerve

value: 6 month-old mouse


title: FF6mo3


title: H3K27me3_ChIP_Ezh2cKO_2wk_Cortex_rep2

city: Dallas

first: Hume

last: Stroud

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing:
Reads were mapped to the mm9 genome by allowing up to two mismatches using Bowtie (Langmead et al., 2009). Reads mapping to identical locations were collapsed into one read.
Genome_build: mm9
Supplementary_files_format_and_content: Each line indicates a uniquely mapping read: chromosome, strand (+/-), genomic coordinate
The genomic coordinates represent  the position in leftmost character of the read. These coordinates were taken from the Bowtie output:
http://bowtie-bio.sourceforge.net/manual.shtml

source_name: Cortex

growth_protocol: Brain tissue was taken from wild-type mice or transgenic mice maintained under standard housing conditions.

extract_protocol:
Tissue was crosslinked 1% formaldehyde. The reaction was stopped with 0.125M glycine. After one wash with PBS, samples were lysed twice with L1 buffer (50mM Hepes pH7.5, 140mM NaCl, 1mM EDTA, 1mM EGTA, 0.25% Triton X-100, 0.5% NP40, 10% Glycerol, protease inhibitors). The samples were incubated in L2 buffer (10mM Tris-HCl pH8.0, 200mM NaCl), then lysed in L3 buffer (1M Tris-HCl pH8.0, 5M NaCl, 0.5 M EDTA, 0.5 M EGTA, 10% Na-Deoxycholate, 20% N-lauroylsarcosine), and sonicated with a Bioruptor (Diagenode). Sonicated chromatin was pre-cleared by incubating with Protein A Dynabeads for 2 hours. Pre-cleared chromatin was added to Dynabeads conjugated to specific antibodies and incubating overnight at 4°C, and 1 to 2.5% of chromatin were kept as input material. Antibodies used: DNMT3A (Santa Cruz 20703), H3.1/H3.2 (EMD Millipore ABE154), H3.3 (EMD Millipore 09-838), H2A.Z (EMD Millipore 07-594), H3K4me3 (EMD Millipore 07-473), H3K9me2 (Abcam ab1220), H3K9me3 (Abcam ab8898), H3K27me2 (Cell Signaling 9728), H3K27me3 (EMD Millipore 07-449), H3K36me3 (Abcam ab9050), H3 (Abcam ab1791), MECP2 (Chen et al., 2003), H3K27ac (Abcam ab4729), RNA Pol II (Abcam 817) and RNA Pol II Ser2P (Abcam 5095). Beads were washed twice with Low Salt buffer (0.1% SDS, 1% Triton X-100, 20mM Tris HCl pH8.0, 150mM NaCl, 2mM EDTA), High Salt buffer (0.1% SDS, 1% Triton X-100, 20mM Tris HCl pH8.0, 500mM NaCl, 2mM EDTA) and LiCl buffer (250mM LiCl, 1% NP40, 1mM EDTA, 10mM TrisHCl pH8.0, 1% Sodium Deoxycholate) at 4°C, and washed once with TE buffer at room temperature. Chromatin was eluted off the beads with TE+1%SDS at 65°C, and de-crosslinked by incubating overnight at 65°C. Samples were treated with RNaseA, and then with Proteinase K for 2 hours at 55°C. DNA was extracted by phenol-chloroform extraction and purified with a Minelute PCR cleanup column (Qiagen).
Libraries were constructed by using Ovation Ultralow Library Systems (Nugen) following manufacturer instructions.

value: Nes-cre; Ezh2 fl/fl

tag: background strain

value: Mix

value: 2 week

tag: antibodies

value: Rabbit anti-H3K27me3, EMD Millipore, Cat# 07-449

value: Cortex


title: H3_ChIP_Ezh2cKO_2wk_Cortex_rep2

tag: genotype

value: Rabbit anti-H3, Abcam, Cat# ab1791


title: DNMT3A_ChIP_Ezh2cKO_2wk_Cortex_rep2

value: Rabbit anti-DNMT3A, Santa Cruz, Cat# 20703


title: 0Cu25Ce_a


title: H3_ChIP_Ezh2cKO_2wk_Cortex_rep1


title: DNMT3A_ChIP_Ezh2cKO_2wk_Cortex_rep1


title: H3K27me3_ChIP_Ezh2cKO_2wk_Cortex_rep1


title: OsSAMS1 OX_2

value: Zhonghua 11

value: aboveground part of plant

value: 42 days old seedling


title: H3_ChIP_Ezh2WT_2wk_Cortex_rep2

value: Ezh2 fl/fl


title: H3K27me3_ChIP_Ezh2WT_2wk_Cortex_rep2


title: H3_ChIP_Ezh2WT_2wk_Cortex_rep1


title: Input_Ezh2cKO_2wk_Cortex_rep1


title: MECP2_ChIP_Vip_8wk_Cortex

value: Vip-cre; Sun1

value: 8 week

value: Rabbit anti-MECP2, Chen et al., 2003 (PMID:14593183)


title: Input_Pv_8wk_Cortex

value: Pv-cre; Sun1


title: FF6mo1

value: optic nerve


title: Input_WT_2wk_Visualcortex_Light_rep3

source_name: Visual cortex

value: wild type

tag: treatment

value: Dark reared before eye opening, at P17 exposed to light for 1 hour

value: Visual cortex


title: Input_WT_2wk_Visualcortex_Light_rep1

value: 2 week


title: Input_WT_2wk_Visualcortex_Dark_rep3

value: Dark reared before eye opening until dissection


title: MECP2_ChIP_Pv_8wk_Cortex

value: Cortex


title: DNMT3A_ChIP_WT_2wk_Visualcortex_Light_rep2


title: Input_WT_2wk_Visualcortex_Light_rep2


title: H3K27me3_ChIP_Ezh2WT_2wk_Cortex_rep1

value: Mix

value: Rabbit anti-H3K27me3, EMD Millipore, Cat# 07-449


title: DNMT3A_ChIP_WT_2wk_Visualcortex_Light_rep4

value: Rabbit anti-DNMT3A, Santa Cruz, Cat# 20703


title: Input_WT_2wk_Visualcortex_Dark_rep1


title: DNMT3A_ChIP_Ezh2WT_2wk_Cortex_rep1


title: DNMT3A_ChIP_WT_2wk_Visualcortex_Light_rep3


title: POLII_ChIP_WT_2wk_Cortex_rep2

value: Mouse anti-RNA Pol II, Abcam, Cat# 817


title: DNMT3A_ChIP_Ezh2WT_2wk_Cortex_rep2


title: DNMT3A_ChIP_WT_2wk_Visualcortex_Light_rep1


title: DNMT3A_ChIP_WT_2wk_Visualcortex_Dark_rep3


title: POLII_ChIP_WT_2wk_Cortex_rep1


title: Input_Ezh2WT_2wk_Cortex_rep1


title: Input_WT_2wk_Visualcortex_Light_rep4


title: H3K27me3_ChIP_WT_2wk_Cortex_rep2


title: H3K4me3_ChIP_WT_2wk_Cortex

value: Rabbit anti-H3K4me3, EMD Millipore, Cat# 07-473


title: H3_ChIP_WT_2wk_Cortex_rep2

value: Rabbit anti-H3, Abcam, Cat# ab1791


title: DNMT3A_ChIP_WT_2wk_Visualcortex_Dark_rep2


title: DNMT3A_ChIP_WT_2wk_Visualcortex_Dark_rep1


title: Input_Vip_8wk_Cortex

value: Vip-cre; Sun1


title: POLII_Ser2P_ChIP_WT_2wk_Cortex_rep2

value: Rabbit anti-RNA Pol II Phospho-Ser2, Abcam, Cat# 5095


title: H2AZ_ChIP_WT_2wk_Cortex

value: Rabbit anti-H2A.Z, EMD Millipore, Cat# 07-594


title: POLII_Ser2P_ChIP_WT_2wk_Cortex_rep1


title: H3K36me3_ChIP_WT_2wk_Cortex_rep2

value: Rabbit anti-H3K36me3, Abcam, Cat# ab9050


title: Input_WT_2wk_Visualcortex_Dark_rep2


title: WT rep2 (RNA-Seq)

city: La Jolla

first: Amy

last: Pasquinelli

address: 9500 Gilman Drive

department: Biological Sciences

institute: University of California, San Diego

data_processing:
Read counts were quantified using kallisto.
These were then aligned to C. elegans genome WS247.
Genome_build: WS247
Supplementary_files_format_and_content: Csv; Contains tpm values for each replicate

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: WT Caenorhabditis elegans (N2 Bristol) animals were cultured on OP50 bacteria at 25°C, and collected at the last larval stage (mid-L4 – 29 h time point). Standard worm synchronization methods were used.

extract_protocol:
RNA was extracted with Trizol and DNAse treated.
These samples were prepared for sequencing by rRNA depletion with Ribo-Zero rRNA Removal Mix – Gold (Illumina), and the TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the Low Sample Protocol.

treatment_protocol: No special treatment

value: wildtype N2

value: whole organism


title: H3K27ac_ChIP_WT_2wk_Cortex_rep2

value: wild type

value: Rabbit anti-H3K27ac, Abcam, Cat# ab4729


title: H3_ChIP_Dnmt3acKO_2wk_Cortex

value: Nes-cre; Dnmt3a fl/fl

value: 2 week


title: H3K27ac_ChIP_WT_2wk_Cortex_rep1

value: Cortex


title: WT rep1 (RNA-Seq)


title: Input_Dnmt3aWT_2wk_Cortex

value: Dnmt3a fl/fl


title: H3K36me3_ChIP_WT_2wk_Cortex_rep1


title: FlagPAR

city: Goettingen

first: Markus

middle: T.

last: Bohnsack

address: Humboldtallee 23

department: Institute for Molecular Biology

country: Germany

institute: Goettingen University

description: FlagPARsnRNAs.txt

data_processing:
Sequencing reads for each experimental sample were demultiplexed using their 5' barcode sequences and barcodes were then clipped
Reads of identical sequence that contained identical 5-nucleotide random barcodes (NNNNNAGC) were collapsed
Reads were trimmed and quality controlled using flexbar and aligned to the human genome (Ensembl GRCh 37.75) by Bowtie2 (version 2.2.4)
The data from the two sequecing runs of METTL16UV (METTL16UV-1 and METTL16UV-2) and the two sequecing runs of METTL16PAR (METTL16PAR-1 and METTL16PAR-2) the were combined for the generation of the METTL16 mRNA, lncRNA and ncRNA lists.
Genome_build: GRCh 37.p13
processed data files format and content: The "FlagUVoverview" file indicates the relative proportion of reads mapping to different classes of RNAs in the Flag control sample crosslinked by UV (254nm)
processed data files format and content: The "METTL16UVoverview" file indicates the relative proportion of reads mapping to different classes of RNAs in the METTL16 sample crosslinked by UV (254nm)
processed data files format and content: The "FlagUVsnRNA" file shows the distribution of reads between snRNAs in the Flag control sample crosslinked by UV (254nm)
processed data files format and content: The "METTL16UVsnRNA" file shows the distribution of reads between snRNAs in the METTL16 sample crosslinked by UV (254nm)
processed data files format and content: The "FlagPARsnRNA" file shows the distribution of reads between snRNAs in the Flag control sample crosslinked after 4-thiouridine incorporation at 365nm
processed data files format and content: The "METTL16PARsnRNA" file shows the distribution of reads between snRNAs in the METTL16 sample crosslinked after 4-thiouridine incorporation at 365nm

source_name: HEK293 cell culture

growth_protocol: Flp-In T-Rex HEK293 cells expressing His-FLAG-tagged METTL16 or the His-FLAG tag only were grown at 37°C in 5% CO2 in high glucose DMEM supplemented with 10% foetal bovine serum, 2 mM L-glutamine.

extract_protocol:
Crosslinked RNA-protein complexes were purified under denaturing conditions and RNAs associated with His-FLAG-tagged proteins were trimmed (Bohnsack et al., 2012).
3' and 5' adapters were ligated and a cDNA library was prepared by reverse transcription and amplified by PCR (Bohnsack et al., 2012).

treatment_protocol: Expression of tagged proteins was induced by addition of tetracycline for 24 h before crosslinking/harvesting. Cells were crosslinked as previously described (Memet et al., 2017).

tag: expressing

value: His-Prc-FLAG

tag: cell line


title: H3K27me3_ChIP_WT_2wk_Cortex_rep1

value: Rabbit anti-H3K27me3, EMD Millipore, Cat# 07-449


title: DNMT3A_ChIP_Dnmt3aWT_2wk_Cortex

value: Rabbit anti-DNMT3A, Santa Cruz, Cat# 20703


title: H3K9me2_ChIP_WT_2wk_Cortex

value: Mouse anti-H3K9me2, Abcam, Cat# ab1220


title: H3_ChIP_WT_2wk_Cortex_rep1

value: Rabbit anti-H3, Abcam, Cat# ab1791


title: FlagUV

description:
FlagUVoverview.txt
FlagUVsnRNAs.txt


title: H3K9me3_ChIP_WT_2wk_Cortex

value: Rabbit anti- H3K9me3, Abcam, Cat# ab8898


title: METTL16PAR-2

description:
METTL16PAR-1 and METTL16PAR-2 represent two sequencing runs of the same library
METTL16mRNAs.txt
METTL16lncRNAs.txt
METTL16ncRNAs.txt


title: Input_Dnmt3acKO_2wk_Hippocampus

source_name: Hippocampus

value: Hippocampus


title: METTL16PAR-1

description:
METTL16PAR-1 and METTL16PAR-2 represent two sequencing runs of the same library
METTL16PARsnRNAs.txt
METTL16mRNAs.txt
METTL16lncRNAs.txt
METTL16ncRNAs.txt


title: H3_ChIP_Dnmt3aWT_2wk_Cortex


title: DNMT3A_ChIP_Dnmt3aWT_2wk_Hippocampus


title: Input_Dnmt3aWT_2wk_Hippocampus


title: METTL16UV-2

description:
METTL16UV1 and METTL16UV2 represent two sequencing runs of the same library
METTL16mRNAs.txt
METTL16lncRNAs.txt
METTL16ncRNAs.txt


title: DNMT3A_ChIP_WT_8wk_Cortex_rep1

value: 8 week


title: WT rep3 (RNA-Seq)


title: Input_WT_2wk_Cortex_rep1


title: METTL16UV-1

description:
METTL16UV1 and METTL16UV2 represent two sequencing runs of the same library
METTL16UVoverview.txt
METTL16UVsnRNAs.txt
METTL16mRNAs.txt
METTL16lncRNAs.txt
METTL16ncRNAs.txt


title: H3K27me2_ChIP_WT_2wk_Cortex

value: Rabbit anti-H3K27me2, Cell Signaling, Cat# 9728


title: Input_WT_2wk_Cortex_rep2


title: Cortex_OX_12wk

data_processing:
Reads were mapped to the mm9 genome using Bsmap (Xi et al., 2009). Duplicate reads were removed and only uniquely mapping reads were kept.
Genome_build: mm9 genome + lambda genome (NC_001416.1)
Supplementary_files_format_and_content: Each line indicates a cytosine in the genome with the following information listed for each column: Chromosome, nucleotide position, sequence context of cytosine (CG or CA), number of non-converted base-calls at this position (#C), total number of reads for the base at this position (# of C and T base-calls).

growth_protocol: Brain tissue was taken from wild-type mice maintained under standard housing conditions.

extract_protocol:
Genomic DNA was isolated from each brain region at the indicated ages.
WGBS libraries were constructed by using a similar method as previously described (Mo et al., 2015) except that NEXTflex methylated adapters (Bioo Scientific) were used.
Briefly, DNA was sonicated to 200 bp using a Covaris S2. Bisulfite treatment was performed using EZ DNA Methylation-Gold kit (Zymo). Unmethylated lambda DNA (0.1-0.5%; Promega D1521) was spiked in to assess conversion rates.

value: 12 week

value: Oxidized treatment using Truemethyl-seq kit (Cambridge Epigenetix) following manufacturer instructions


title: Cortex_BS_12wk


title: DNMT3A_ChIP_WT_2wk_Cortex_rep1

value: wild type


title: DNMT3A_ChIP_Dnmt3acKO_2wk_Hippocampus


title: Sample_86-5_il6-tnfa

city: Frederick

first: Dennis

last: Klinman

state: Maryland

address: 1050 Boyles St

department: Cancer and Inflammation Program

institute: National Institutes of Health

data_processing:
Basecall by Illumina RTA 1.18.66.3
demultiplex by Illumina Bcl2fastq 2.17
data was aligned to hg19 using CLC genomics workbench v 10
RNA seq analysis and differential expression for RNA-seq preformed by CLC genomics workbench
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with RPKM for each Sample

source_name: FACS sorted MDSC cells

extract_protocol:
cells from stimulated mMDSC were stored in RNA protect (Qiagen, Frederick, MD).  Total RNA was isolated using the RNeasy micro kit (Qiagen) and RNA quality was assessed using an Agilent 2200 TapeStation
Clonetech SMART er Ultra Low Input RNA Kit
Illumina TruSeq V4.0

tag: treatment group

tag: donor number


title: WT_Hippocampus_BS_8wk_Control_rep3

value: Control


title: WT_Hippocampus_BS_8wk_Control_rep2


title: Sample_79-6_r848


title: Sample_85-6_r848


title: Input_WT_8wk_Cortex


title: DNMT3A_ChIP_Dnmt3acKO_2wk_Cortex

value: Nes-cre; Dnmt3a fl/fl


title: WT_Hippocampus_BS_8wk_Control_rep1


title: Sample_82-6_r848


title: Sample_81-6_r848


title: WT_Hippocampus_BS_8wk_DailyKA_rep2

value: Injection of kainic acid (Sigma Aldrich K0250) daily from postnatal day10  (P10) to P20


title: Sample_84-5_il6-tnf


title: Sample_85-5_il6-tnf


title: WT_Hippocampus_BS_8wk_Control_rep4


title: WT_Hippocampus_BS_8wk_DailyKA_rep1


title: Sample_84-1_untreated

value: untreated


title: Ezh2cKO_Cortex_BS_2wk

value: Nes-cre; Ezh2 fl/fl

value: Cortex

value: 2 week


title: Sample_86-1_untreated


title: Sample_79-1_untreated


title: WT_Hippocampus_BS_8wk_DailyKA_rep3


title: Sample_82-1_untreated


title: Sample_76-5_il6-tnfa


title: Ezh2WT_Cortex_BS_2wk

value: Ezh2 fl/fl


title: Sample_76-1_untreated


title: RNAseq_WT_P20_Hippocampus_DailyKA_rep2

description: total RNA

data_processing:
Reads were mapped to annotated genes and the genome using Tophat2 (Kim et al., 2013) and quantified with HTseq (Anders et al., 2015). Gene expression levels were quantified by calculating reads per kilobase of transcript per million mapped reads (RPKM). For the nuclear RNA dataset, duplicated reads were collapsed into one read.
Genome_build: mm9
Supplementary_files_format_and_content: Column 1: Ensembl gene identifier; Column 2: Gene expression (RPKM)

extract_protocol:
Total RNA was isolated from each brain region, and nuclear RNA was isolated from neuronal subtypes at the indicated ages using TRIzol (Invitrogen) and purified with an RNeasy kit (with on-column DNase treatment) (Qiagen) following manufacturer instructions
Libraries were generated with either the Tru-Seq Strand Specific RNA-Sequencing kit (Illumina) or NEBNext Ultra Directional RNA Library Prep Kits (NEB) following manufacturer instructions

tag: background

value: 3 week

value: Kainic acid injection daily from postnatal day 10 to 20


title: RNAseq_WT_2wk_Visualcortex_Light_rep3

description: total RNA

value: Dark reared before eye opening, at P17 exposed to light for 1 hour


title: RNAseq_Dnmt3aWT_2wk_Hippocampus

description: total RNA

value: Dnmt3a fl/fl


title: RNAseq_Dnmt3aWT_2wk_Cortex

description: total RNA


title: RNAseq_WT_P20_Hippocampus_Control_rep1

description: total RNA


title: RNAseq_WT_2wk_Visualcortex_Light_rep1

description: total RNA


title: RNAseq_WT_2wk_Visualcortex_Dark_rep1

description: total RNA

value: Dark reared before eye opening until dissection


title: RNAseq_WT_2wk_Visualcortex_Dark_rep2

description: total RNA


title: RNAseq_Dnmt3acKO_2wk_Hippocampus

description: total RNA


title: RNAseq_WT_2wk_Visualcortex_Light_rep4

description: total RNA


title: RNAseq_WT_P20_Hippocampus_DailyKA_rep1

description: total RNA


title: RNAseq_WT_P20_Hippocampus_Control_rep2

description: total RNA


title: RNAseq_WT_2wk_Visualcortex_Light_rep2

description: total RNA


title: RNAseq_Ezh2cKO_2wk_Cortex_B_rep1

description: total RNA

value: Mix


title: RNAseq_Ezh2cKO_2wk_Cortex_A_rep2

description: total RNA


title: RNAseq_Dnmt3acKO_2wk_Cortex

description: total RNA


title: RNAseq_Ezh2cKO_2wk_Cortex_A_rep1

description: total RNA


title: RNAseq_Ezh2WT_2wk_Cortex_B_rep1

description: total RNA


title: RNAseq_Ezh2WT_2wk_Cortex_A_rep1

description: total RNA


title: RNAseq_Vip_3wk_rep2

description: nuclear RNA

value: Vip-cre; Sun1


title: RNAseq_Vip_8wk_rep2

description: nuclear RNA

value: 8 week


title: RNAseq_Vip_3wk_rep1

description: nuclear RNA


title: RNAseq_Vip_1wk

description: nuclear RNA

value: 1 week


title: RNAseq_Pv_8wk_rep1

description: nuclear RNA

value: Pv-cre; Sun1


title: RNAseq_Pv_8wk_rep2

description: nuclear RNA


title: RNAseq_InputforVip_3wk

description: nuclear RNA


title: RNAseq_Pv_1wk_rep2

description: nuclear RNA


title: MNase_WT_2wk_Cortex

data_processing:
Reads were mapped to the mm9 genome by allowing up to two mismatches using Bowtie (Langmead et al., 2009). For the analysis reads were normalized to the total number of uniquely mapping reads.
Genome_build: mm9
Supplementary_files_format_and_content: Each line indicates a uniquely mapping read: chromosome, strand (+/-), genomic coordinate

extract_protocol:
Tissue were homogenized in L1 buffer (50mM Hepes pH7.5, 140mM NaCl, 1mM EDTA, 1mM EGTA, 0.25% Triton X-100, 0.5% NP40, 10% Glycerol, protease inhibitors) and spun down. Pellets were resuspended in L2 buffer (10mM Tris-HCl pH8.0, 200mM NaCl) and rotated at room temperature for 10 min. Tubes were spun down and the pellet was resuspended in 100 µl MNase digestion buffer (20mM Tris-Cl, pH 7.5, 10mM NaCl, 2.5mM CaCl2, 0.01 mM PMSF, 1x Roche protease inhibitors) and incubated with 40µg of RNase A (Qiagen), and incubated at room temperature for 10 min. Treated samples with 1 µl MNase (NEB) for 4min at 37C. The reaction was stopped with addition of 2 µl 0.5M EDTA. Triton X-100 was added to a final concentration of 1%, and samples were rotated at 4°C for 30 min. DNA was subsequently purified using Qiagen PCR purification kit.
Libraries were constructed by using Ovation Ultralow Library Systems (Nugen) following manufacturer instructions.

value: wild type


title: RNAseq_Pv_3wk

description: nuclear RNA


title: RNAseq_Pv_1wk_rep1

description: nuclear RNA


title: Vip_BS_8wk_rep1

data_processing:
Reads were mapped to the mm9 genome using Bsmap (Xi et al., 2009). Duplicate reads were removed and only uniquely mapping reads were kept.
Genome_build: mm9
Supplementary_files_format_and_content: Each line indicates a cytosine in the genome with the following information listed for each column: Chromosome, nucleotide position, sequence context of cytosine (CG or CA), number of non-converted base-calls at this position (#C), total number of reads for the base at this position (# of C and T base-calls).


title: RNAseq_InputforPv_3wk

description: nuclear RNA


title: Vip_BS_3wk_rep1


title: RNAseq_WT_2wk_Hippocampus_Control

description: polyA RNA

value: PBS injection


title: Vip_BS_3wk_rep2


title: Pv_BS_8wk_rep1


title: Pv_BS_1wk_rep1


title: Vip_BS_8wk_rep2


title: 6_LXRalpha_H3K27ac_(ANTAGONIST)

city: Madrid

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

country: Spain

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

data_processing:
Basecalls performed using Casava version 1.8.4
For ChIP-Seq, reads were aligned to the mm10 genome using default parameter for bowtie2 (v2.2.9).
Aligned read files were analyzed with HOMER software (v4.9) to find peaks, perform sequence motif finding and other analyses in the study.
Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped.
annotation was performed with HOMER software v4.9 annotatePeaks.pl using default parameters
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

source_name: mouse macrophage

growth_protocol: Immortalized bone marrow derived macrophages (iBMDM) from LXRαβ-/- mice have previously been described (Ito et al. Elife. 2015 Jul 14;4:e08009. doi: 10.7554/eLife.08009). LXR-null iBMDM were reconstituted with N-terminus 3xFLAG-tagged LXRα or LXRβ using a pBabe-puro retroviral expression system as described (Chen M et al. FEBS Lett. 2006;580(20):4835-41). Different clones of LXRα and LXRβ reconstituted lines were isolated by selection with 2-10 ug/ml Puromycin (not shown). A control LXRαβ-/- iBMDM line was also prepared by transduction with an empty pBabe-puro vector.  Macrophages were regularly cultured in complete DMEM media with 10%FBS without any macrophage growth factor. To analyze LXR-dependent responses, cells were cultured in DMEM supplemented with 1% FFA-free BSA (SIGMA# A8806), 50nM of Zaragozic acid (Squalene Synthase inhibitor; SIGMA# Z2626), and 1 uM of either GW3965 LXR agonist or GW2033 LXR antagonist (both kindly provided by Glaxo SmithKline) for 24 h.

extract_protocol:
Lysates were clarified from sonicated nuclei and LXR-DNA or H3K27ac-DNA complexes were isolated with indicated antibodies.
Libraries were prepared using the NEBNext Ultra DNA Library Prep kit for Illumina (Ref.:#7370) following the manufacture instructions. 12 cycles of PCR were done for the final library amplification for all samples.

tag: cell type

value: bone marrow-derived immortalized macrophage

value: GW2033 Antagonist 1 uM 24 hours

value: anti-H3K27ac (Abcam #ab4729)


title: Vip_BS_1wk

tag: age


title: Pv_BS_8wk_rep2


title: 8_LXRbeta_H3K27ac_(ANTAGONIST)


title: 7_LXRbeta_H3K27ac_(AGONIST)

value: GW3965 1uM agonist 24 hours


title: Dnmt3aWT_Cortex_BS_10wk_rep1

value: Dnmt3a flx/flx

value: 10 week


title: RNAseq_Vip_8wk_rep1

description: nuclear RNA


title: Dnmt3acKO_Cortex_BS_10wk_rep1

value: Dnmt3a flx/flx Tg(Nes-cre)1Kln/J


title: Pv_BS_1wk_rep2


title: Hippocampus_BS_8wk


title: 4_LXRbeta_(FLAG)

value: anti-FLAG M2 (SIGMA #F3165)


title: Dnmt3acKO_Cortex_BS_10wk_rep2


title: 5_LXRalpha_H3K27ac_(AGONIST)


title: 1_input_control


title: Pv_BS_3wk

value: 3 week


title: Hippocampus_BS_2wk

value: 2 week


title: Dnmt3aWT_Cortex_BS_10wk_rep2


title: Cortex_BS_8wk


title: Hippocampus_BS_1wk


title: 3_LXRalpha_(FLAG)


title: 2_LXR-DKO_neg_control


title: RNAseq_WT_2wk_Hippocampus_KA

description: polyA RNA

value: Kanic acid injection


title: H3.1_ChIP_WT_2wk_Cortex

value: Rabbit anti-H3.1/H3.2, EMD Millipore, Cat# ABE154

value: Cortex


title: Cortex_BS_2wk


title: Cortex_BS_1wk

value: 1 week


title: H3.3_ChIP_WT_2wk_Cortex

value: Rabbit anti-H3.3, EMD Millipore, Cat# 09-838


title: Input_WT_2wk_Hippocampus_KA

value: wild type

value: Hippocampus


title: WT rep2 (mTAIL-seq)

description: mTAIL-seq Rep2

data_processing:
Base calling, trimming of adapter sequences, removal of duplicated reads and determination of poly(A) tail sizes were performed by tailseeker2.
Reads were analyzed by mapping to the WS247 assembly of the C. elegans genome using RNA-STAR.
Poly(A) lengths were then assigned to individual coding genes by intersecting the mapped sequences with WormBase.org WS247 gene annotations using BEDTools.
Genome_build: WS247
Supplementary_files_format_and_content: Csv; contains the number of hits per gene, and the mean, median, standard deviation, and range of poly(A) tail lengths for RNAs that had more than 10 reads, as well as each individual poly(A) tail length that was read for each gene.

extract_protocol:
RNA was extracted with Trizol and DNAse treated.
A splint oligo was used to favor poly(A)+ RNAs being ligated to a 3′ adapter. After partially digesting the RNA from the ligation reaction with RNAse T1, RNAs were pulled down using Streptavidin beads, then 5' phosphorylated by PNK reaction. RNA was eluted and size selected for 250-1000 nt fragments. This was done by gel extraction and purification from a 6% Urea-PAGE gel. Libraries were normalized, pooled and then sequenced in the Illumina MiSeq platform (51 x 251 bp paired end run) with PhiX control library and the spike-in controls mixture. The quantified fluorescent signals were saved and processed by tailseeker2.

value: wildtype N2

value: whole organism


title: Input_WT_2wk_Hippocampus

value: PBS injection


title: WT rep1 (mTAIL-seq)

description: mTAIL-seq Rep1


title: DNMT3A_ChIP_WT_2wk_Hippocampus_KA_rep1

value: Rabbit anti-DNMT3A, Santa Cruz, Cat# 20703


title: As 1.0 mM 1

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

data_processing:
Sequencing tags were mapped to SmaI sites in the Danio rerio genome (danRer7) and signatures corresponding to methylated (starting with CCGGG) and unmethylated (starting with GGG) CpG were enumerated for each SmaI/XmaI site.
At each SmaI/XmaI site, let sm be the number of tags corresponding to methylated CpG (i.e., tags starting with CCGGG) and u be the number of tags corresponding to unmethylated CpG (i.e., tags starting with GGG), the methylation value was calculated as 100%*(c*sm/(c*sm+u)), where c is the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: danRer7
Supplementary_files_format_and_content: tab delimited text file with numbers of reads and percent methylation at individual CCCGGG sites

organism: Danio rerio

source_name: embryo 72 hours post fertilization

growth_protocol: Danio rerio adults were commercially obtained wild-type import (Ruinemans Aquarium BV, Montfoort, the Netherlands) and maintained and bred for more than 8 years/generations in our lab. Adult zebrafish were kept as groups of 20-30 in 7.5L tanks in a ZebTec system with automatically controlled water parameters at 26.5 ± 1°C with a day-night cycle of 14-10h. Small spawning groups of 2m/2f, which had been separated 3 days before, were composed on the day before spawning, which was triggered by morning light on the next day. Eggs were collected within the next 2 hours and assessed for quality. Spawns with >10% coagulations or deformities, i.e. damaged membranes or embryo asymmetries, were discarded.

extract_protocol:
DNA was extracted from the exposed pools of embryos using the Gentra Puregene Tissue kit (Qiagen, Hilden, Germany).
Genomic DNA (2.5 micrograms) was spiked with 8 methylation standards with defined methylation levels of ranging from 0 to 100%. Spiked DNA was digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. SmaI cuts only unmethylated sites leaving blunt ends. The enzyme is completely blocked by CpG methylation. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. XmaI can cut both unmethylated and CpG methylated sites (CCmeCGGG) leaving 5’CCGG overhangs. The unmethylated sites thus have the GGG signature whereas the methylated sites have the CCGGG signature at the 5’ ends of the restriction fragments. Digested DNA was supplemented with dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Restriction fragments with methylation-specific signatures were ligated to NEBNext Illumina adapters and amplified using NEBNext® Multiplex Oligos for Illumina®, KAPA HiFi HotStart ReadyMix PCR Kit and 12 PCR cycles.

treatment_protocol: Arsenic was presented to the zebrafish embryos in the form of sodium arsenite (NaAsO2; CAS 7784-46-5; Sigma-Aldrich, St. Louis, MO, USA), further referred to as arsenite. A stock solution of arsenite was prepared in and further diluted with OECD medium (294.0 mg/L CaCl2∙2H2O, 123.3 mg/L MgSO4∙7H2O, 64.7 mg/L NaHCO3, 5.7 mg/L KCl; (OECD, 2002)). The concentrations of arsenite were in the range of 0, 0.1 and 1 mM. The collected fertilized eggs were rinsed with OECD medium, distributed among the test concentrations, and embryos of matched developmental stage were then distributed over triplicate experimental units which were 20 embryos in 2 mL per embryo per well in a 24-wells plate for the range finding experiment or pools of embryos (n=20) in petri dish at 2 mL per embryo, and further kept in an incubator at 26.5 ± 1 °C with a day-night cycle of 14-10 h. The embryos were scored for morphological development and teratogenicity using a standardized scoring system (Hermsen et al., 2011), which considers 9 develomental parameters, such as development of the eyes, pectoral fins, head, and pigmentation, with a maximum score of 15 points at 72 hours post fertilization (hpf).

value: sodium arsenite 1 mM for 72 hours


title: caNIK HSPC rep2

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

data_processing:
The sequencing quality of RNA-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA-Seq libraries were mapped to mouse genome using Tophat (v2.1.0, Trapnell et al., Bioinformatics). UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Mapped reads were then processed by featureCounts (v1.5.0) to estimate expression levels of all genes  Deseq2 (v1.10.1) was used to identify differentially expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: Raw unnormalized counts.

source_name: Hematopoietic stem/progenitor cells

extract_protocol:
Hematopoietic stem/progenitor cells were sort-purified and total RNA was extracted using standard Qiagen RNease columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

value: Hematopoietic stem/progenitor cells

tag: genotype/variation

value: cross of Rosa-loxp-STOP-loxp-NIK mice with Vav-iCre mice (caNIK mice)


title: caNIK HSPC rep1


title: Control HSPC rep2

value: control


title: As 1.0 mM 3


title: Control HSPC rep1


title: DNMT3A_ChIP_WT_2wk_Hippocampus_rep1


title: As 0.1 mM 4

value: sodium arsenite 0.1 mM for 72 hours


title: DNMT3A_ChIP_WT_2wk_Hippocampus_KA_rep2

value: 2 week


title: Control_Lambda_BS

data_processing:
Reads were mapped to the phage lambda genome using Bsmap (Xi et al., 2009). Duplicate reads were removed and only uniquely mapping reads were kept.
Genome_build: lambda genome (NC_001416.1)
Supplementary_files_format_and_content: Each line indicates a cytosine in the genome with the following information listed for each column: Chromosome, nucleotide position, sequence context of cytosine (CG or CA), number of non-converted base-calls at this position (#C), total number of reads for the base at this position (# of C and T base-calls).

organism: Lambdavirus lambda

source_name: Unmethylated cl857 Sam7 Lambda DNA

value: Incubated with SAM, histone H3


title: As 1.0 mM 2


title: As 0.1 mM 3


title: DNMT3A_ChIP_WT_2wk_Hippocampus_rep2


title: DNMT3A_Lambda_BS_rep2

value: Incubated with human DNMT3A, SAM, histone H3


title: As 0.1 mM 2


title: DNMT3A_ChIP_WT_8wk_Cortex_rep2

value: 8 week

value: Cortex


title: DNMT3A_ChIP_WT_2wk_Cortex_rep3


title: TNFalpha_treated

city: Neuherberg

first: Dietrich

last: Trümbach

address: Ingolstädter Landstraße 1

department: Institute for Developmental Genetics

institute: Helmholtz Zentrum München German Research Center for Environmental Health

description: treated with TNFalpha

data_processing:
The Fastq Filter Module (FFM) of the custom Java program ENCoRE was applied to identify all single reads in the FASTQ file containing reads with the sequence motif ‘gaaacaccg’.
Sequencing reads were trimmed directly after the search sequence ‘gaaacaccg’ at 3’ ends consisting of 19 bp in the FFM module.
The filtered 19 bp sequence directly corresponds to the CRISPR guide RNA sequence.
The dataset was then compressed and repetitive guides were counted and integrated into unique guide sequences.
Next, the CRISPR Report Module (CRM) of the ENCoRE program was used to compare the counts of individual guides from selected libraries with the unselected library and the total starting library.
Genome_build: mm10
Supplementary_files_format_and_content: A CSV file containig the gene symbol, log2(fold change), p-value as well as log2(p-value) was generated by the ENCoRE program including the following steps: Each guide was annotated to its corresponding gene by using the reference file (containing guide cross-references) from Koike-Yusa et al., 2014 Nat Biotechnol 32(3): 267-273; After counting sgRNA sequences of the TNFalpha treated and the untreated (total) library a normal z-score was computed for each gene (i.e. all guides per gene). A median imputation strategy was defined before calculation of the z-test. This means that missing or zero counts were replaced by the median of the counts with missing or zero counts set to 1.

source_name: Fibroblast cells

growth_protocol: 10% FCS/DMEM +pen/strep

extract_protocol:
After TNFa treatment was applied, mutant cell pools were harvested and genomic DNA was extracted. Genomic DNA isolated from unselected cells served as a control population as well as from pure plasmid preparation of the sgRNA library. Ion Torrent sample preparation (see Supplementary Table Primer Sequences) and sequencing was carried out on a Ion Torrent P1 chip (PrimBio Research Institute, Exton, PA), producing separate .fastq files from individual barcodes.
Individual gene knockouts in mouse fibroblasts were performed using guide sequences cloned into the BbsI-digested pKLV-U6gRNA(BbsI)-PGKpuro2aBFP vector and infected as above. Infected BFP positive colonies were then screened for mutations using PCR primers were designed outside the guide sequence. PCR products were cloned using the Zero Blunt TOPO PCR Cloning Kit (ThermoFisher) and Sanger sequenced.

treatment_protocol: Immortalized mouse fibroblasts were infected with ecotropic lentivirus particles containing the Cas9-Blasticidin construct. Cells were treated with 10 µg/ml blasticidin for five days and resistant cells were used for a second infection with ecotropic lentivirus particles containing sgRNA expressing library (pKLV-U6gRNA-PGKpuro2ABFP). Following infection, cells were sorted using Blue Fluorescent Protein (BFP) as a marker. The BFP-positive cell population was seeded onto a 15 cm dish at low density (100-500 cells per 15 cm plate) and cells were treated with TNFa or control for 11 days.

tag: strain

value: TNFalpha

tag: period

value: 11 days


title: Control_unselected

description: infected, no selection

value: unselected


title: As 0.1 mM 1


title: Control 3

value: no exposure


title: Synthesized DNAs with index A

city: Suita

first: TAISAKU

last: OGAWA

state: Osaka

address: 6-2-3 Furuedai

country: Japan

institute: RIKEN

data_processing:
Library strategy: Amplicon Seq
Basecalls performed by Illumina MiSeq
Sequenced reads were sorted by indexes in Illumina MiSeq
indexA and  indexB files are merged
Reads were aligned to template sequences using Bowtie2
Mapped reads seperated by templates, and the reads mapped for each tempalte were clusterd by molecular barcode
Sample contamination and misidentification were removed
The number of cluteres for each was counted, which provides the number of molecules detected for each template

organism: synthetic construct

source_name: Index A

extract_protocol: Libraries were prepared by PCR amplification

tag: source

value: synthetic DNA


title: Control_Library

description: all guides before virus production (total starting library)

value: untreated


title: Control 4


title: As 1.0 mM 4


title: Synthesized DNAs with index B

source_name: Index B


title: Control 2


title: DNMT3A_ChIP_WT_2wk_Cortex_rep2

value: wild type

value: Rabbit anti-DNMT3A, Santa Cruz, Cat# 20703


title: DNMT3A_Lambda_BS_rep1


title: w1118_WB_f_r4

status: Public on Oct 18 2017

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description: mixed-species [D. melanogaster (w1118), D. pseudoobscura, and D. virilis] RNA preparation

data_processing:
De-multiplexed reads (Chastity > 0.6) were generated by Illumina CASAVA (v.1.8.2) as fastq files.  For the single-species samples (i.e., D. melanogaster genitalia samples), we provided the raw de-multiplexed fastq files without processing.  For the multi-species samples, we first made merged genome and annotation of appropriate Drosophila species plus corrected ERCC standards (Lee et al., Journal of Genomics, 2016, PMID 27512518).  Additionally, we added a four-letter prefix for each chromosome or scaffold in the merged genome or annotation (e.g., 2L => dmel_2L).  ERCC names were unchanged due to their specific prefix.  The de-multiplexed reads from the multi-species samples were then mapped to the appropriate merged genome and annotation using STAR (v2.4.2a) (Doblin et al., Bioinformatics, 2012, PMID 23104886) with default parameters.  We used an in-house python script to fetch the prefix of read names in the bam alignments, and obtained all uniquely-mapped and multi-hit (2-10 hits) reads (in bam format) that were mapped exclusively to a single species or exclusively to ERCC.  We converted the bam reads to fastq reads by BEDTools (2.25.0; bamtofastq) (Quinlan and Hall, 2010, Bioinformatics, PMID 20110278).  After this step, reads of each multi-species sample were split into five categories – species 1, species 2, species 3, ERCC, and leftover, which includes unmapped reads and reads mapped to multiple species (or multiple species plus ERCC).  For multi-species samples, the original fastq file can be restored by merging the reads of appropriate three species as well as the ERCC and leftover reads.
We provide both STAR (SRR5639* and SRR6181*) and HiSAT2 (SRR724*) fastq and associated matrices of raw gene-level read counts in this GEO entry. For STAR read count files, we used the FlyBase (FB) annotations (version 2017_03). For HiSAT2 read count files, we used both FB and updated (YO) annotations (data in Supplementary Files of this GEO). For the latter one, we also provide two extra columns in the expression matrix, showing the maximum exon-level Jaccard index overlap between our YO annotation gene IDs and FlyBase ones. In addition, we provided bigWig tracks for all samples (replicated merged), YO annotation files (in both gtf and gff3 format), ortholog look up table (among YO gene ID, FlyBase gene ID, and dmel gene), gene-level normalized read counts based on either YO or FlyBase annotation, and transcript-level transcripts per million (TPM) based on YO or FlyBase annotation.
Supplementary_files_format_and_content: counts

source_name: whole body

growth_protocol: D. melanogaster stocks were obtained from the Drosophila Stock Center (Bloomington IN, NIH P40OD018537, http://fly.bio.indiana.edu), and were reared at the NIH (Bethesda MD).  Fly food for D. melanogaster was a medium of water (8.5 L), agar (79 g), torumel yeast (275 g), cornmeal (520 g), granulated sugar (1,100 g), p-hydroxy-benzoic acid methyl ester (23.8 g), and 95% ethanol (91.8 mL) (LabExpress, Ann Arbor MI). All non-melanogaster flies were reared and dissected at the Drosophila Species Stock Center (San Diego CA, NSF CSBR 1351502, https://stockcenter.ucsd.edu).  D. yakuba, D. ananassae, D. pseudoobscura, D. willistoni, and D. virilis were grown on a medium of de-ionized water (28 L), agar (300 g), soy flour (700 g), cornmeal (2,940 g), molasses (2,230 g), yeast (860 g), propionate (135 g), and nipogen (200 g) (https://stockcenter.ucsd.edu/info/food_cornmeal.php). D. persimilis and D. mojavensis were grown on a medium of agar (85 g), yeast (165 g), methylparaben (13.4 g), blended bananas (825 g), syrup (570 g), liquid malt extract (180 g), and 100% ethanol (134 mL) (https://stockcenter.ucsd.edu/info/food_banana_Opuntia.php).  All flies were reared at 23-25 oC.

extract_protocol:
Flies were anesthetized using CO2, and all samples were dissected in phosphate buffered saline solution (PH 7.4, Life Technologies, Carlsbad CA) and transferred to 56 or 112 μL of RNAlater (Life Technologies, Carlsbad CA) in 96-well 1.5 mL plates at room temperature after being macerated with forceps. Plates were stored at -80 oC at the NIH after dissection (melanogaster samples) or after dissection and shipping (non-melanogaster samples).  For RNA extraction, we added 20-30 1.0 mm glass beads (BioSpec Products, Bartlesville OK) to each sample and added RLT buffer from the RNeasy 96 kit (Qiagen, Valencia CA) to 712 μL (final volume).  We homogenized the samples three times for 60 seconds each with a mini-beadbeater (Biospec Products, Bartlesville OK). Extraction of total RNA was performed using the RNeasy 96 kit (spin version), except that we used 712 μL of 70% ethanol due to the increased volumes of RNAlater/RLT mixture.  RNA was quantified using Quant-iT RiboGreen (Life Technologies, Carlsbad CA).  We spot checked RNA integrity by capillary electrophoresis on a TapeStation 2200 (Agilent Technologies, Santa Clara CA) and found that the rRNA bands were distinct. We used 33 ng aliquots of RNA of three genetically distant species for each library, except for thorax, where we used 17 ng due to lower yield. The mixing of RNA was performed using a pipetting robot (Andrew Alliance, Vernier CH). RNA from D. melanogaster genitalia was not mixed with tissues of the other species.
We used 100 ng of total RNA as input (except thorax samples: 50 ng), and followed the TruSeq PolyA+ stranded mRNA kit protocol with half volume reactions (Illumina, San Diego CA).  For each sample, we also added 10 pg Standard Reference Material 2374 beta (Pool 78A or 78B) ERCC spike-ins (Lee et al., Journal of Genomics, 2016, PMID 27512518) to the Fragment-Prime-Finish Mix during the mRNA fragmentation step.  We used 96-plex molecular barcoding (Kozarewa and Turner, Methods in Molecular Biology, 2011, PMID 21431778) from the Illumina TruSeq kit for all samples. Libraries were quantified with Quant-iT PicoGreen (Life Technologies, Carlsbad CA). For each sample, we conducted RNA-seq for the three libraries with the highest DNA concentration out of four libraries. The quality (i.e., no overt primer dimers or low complexity) of all selected libraries were confirmed by capillary electrophoresis on a TapeStation 2200 (Agilent Technologies, Santa Clara CA). We performed single-end 76 bp PolyA+ sequencing on the HiSeq2000 Sequencing System (Illumina, San Diego CA).

tag: flybase species id

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: developmental stage

value: adult

value: whole body

tag: Sex

value: Female

tag: age post eclosion (days)

tag: fly culture temperature (oc)

tag: replicate

tag: illumina barcode

value: CTGAAGCT-TATAGCCT

tag: plate and well id

tag: ercc infomation

value: without ERCC


title: Control 1

tag: treatment


title: w1118_TX_f_r4

source_name: thorax without digestive system

tag: tissue

value: thorax without digestive system

value: ATTCAGAA-CCTATCCT


title: w1118_HD_f_r4

source_name: head

value: head

value: GAATTCGT-ATAGAGGC


title: w1118_RE_m_r4

source_name: reproductive system without gonad and genitalia

value: Male

value: GAGATTCC-TAATCTTA


title: w1118_WB_m_r4

value: GAGATTCC-TATAGCCT


title: Input_WT_2wk_Cortex_rep3

source_name: Cortex

tag: genotype

tag: background strain

tag: age

value: 2 week

value: Cortex


title: w1118_GE_f_r4

description: single-species [D. melanogaster (w1118)] RNA preparation

source_name: genitalia

value: genitalia

value: CTGAAGCT-CAGGACGT

value: ERCC SetB


title: w1118_RE_f_r4

value: adult

value: reproductive system without gonad and genitalia

value: GAATTCGT-TAATCTTA


title: w1118_GE_m_r4

value: GAGATTCC-CAGGACGT


title: w1118_AC_m_r4

source_name: abdomen without digestive or reproductive system

value: TCCGGAGA-GGCTCTGA

value: without ERCC


title: w1118_GO_m_r4

source_name: gonad

value: gonad

value: ATTACTCG-AGGCGAAG


title: w1118_DG_f_r4

source_name: digestive plus excretory system

value: digestive plus excretory system

value: Female

value: ATTCAGAA-GTACTGAC


title: w1118_GO_f_r4

value: GAATTCGT-AGGCGAAG


title: w1118_DG_m_r4

value: Male

value: GAGATTCC-GTACTGAC


title: w1118_HD_m_r4

value: head

value: ATTACTCG-ATAGAGGC


title: w1118_TX_m_r4

value: thorax without digestive system

value: TCCGGAGA-CCTATCCT


title: orgR_RE_f_r4

description: mixed-species [D. melanogaster (Oregon-R), D. mojavensis, and D. persimilis] RNA preparation

value: Oregon-R  (FBst0005905)

value: adult

value: reproductive system without gonad and genitalia

value: CTGAAGCT-TAATCTTA


title: orgR_WB_m_r4

value: whole body

value: CGCTCATT-TATAGCCT

value: without ERCC


title: w1118_AC_f_r4

value: abdomen without digestive or reproductive system

value: TAATGCGC-GGCTCTGA


title: orgR_GO_f_r4

value: gonad

value: Female

value: CTGAAGCT-AGGCGAAG


title: orgR_GE_m_r4

description: single-species [D. melanogaster (Oregon-R)] RNA preparation

value: genitalia

value: Male

value: ATTACTCG-CAGGACGT

value: ERCC SetA


title: orgR_HD_f_r4

value: head

value: TAATGCGC-ATAGAGGC


title: orgR_RE_m_r4

value: Oregon-R  (FBst0005905)

value: adult

value: TCCGGAGA-TAATCTTA


title: orgR_TX_f_r4

value: thorax without digestive system

value: GAATTCGT-CCTATCCT


title: orgR_DG_m_r4

value: digestive plus excretory system

value: ATTACTCG-GTACTGAC

value: without ERCC


title: orgR_TX_m_r4

value: ATTACTCG-CCTATCCT


title: orgR_DG_f_r4

value: Female

value: CTGAAGCT-GTACTGAC


title: orgR_HD_m_r4

value: TCCGGAGA-ATAGAGGC


title: orgR_GO_m_r4

value: gonad

value: Male

value: ATTACTCG-AGGCGAAG


title: orgR_GE_f_r4

value: genitalia

value: ATTCAGAA-CAGGACGT

value: ERCC SetA


title: orgR_AC_f_r4

value: Oregon-R  (FBst0005905)

value: adult

value: abdomen without digestive or reproductive system

value: GAATTCGT-GGCTCTGA


title: orgR_AC_m_r4

value: TCCGGAGA-GGCTCTGA


title: RS_KO_rep1

city: Cincinnati

first: So

last: Maezawa

address: 3333 Burnet Ave.

department: Reproductive Sciences

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Data analysis was performed using the BioWardrobe (PMID: 26248465 )
Fastq files from Illumina pipeline were aligned by bowtie (version 1.1.1 PMID: 19261174) with maximum one allowed error in a sequence and no more than one number of hits was allowed. MACS2 (version 2.1.0.20140616 PMID: 18798982) were used to estimate fragment size and to find islands of enrichment. MACS2 were used with q-value threshold less than 0.2.
Genome_build: mm10

source_name: Round spermatides

extract_protocol: The ATAC-seq libraries were prepared as previously described (Buenrostro et al. 2013). Around 500,000 of Thy1+ or c-Kit+ spermatogonia, 250,000 of pachytene spermatocytes, and 1,000,000 of round spermatids were used. Briefly, samples were lysed in 50 μl of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40). Immediately after lysis, nuclei were spun at 500g for 5 min to remove the supernatant. Nuclei were then incubated with the Tn5 transposes and tagmentation buffer at 37 °C for 30 min (Illumina). After the tagmentation, the transposed DNA was purified by MinElute kit (Qiagen). PCR was performed to amplify the library using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min; following by 72 °C 5 min. qPCR was used to estimate of the number of additional cycles needed to generate products at 25% saturation. Typically, two to five additional PCR cycles were added to the initial set of five cycles. The library was purified by AMPure XP beads (Beckman). Size selection of library pools were achieved by running on agrose gel electrophoresis and excising gel slices in the 250- to 500-bp size range. The pool purified from the gel slices was analyzed on an Agilent Bioanalyzer, and 75-bp single-read sequencing was performed using an Illumina HiSeq 2500 platform according to standard oper¬ating procedures.

tag: strain

value: testis

tag: biowardrobe ides


title: RS_KO_rep2


title: dvir_RE_f_r4

city: Bethesda

organism: Drosophila virilis

source_name: reproductive system without gonad

tag: flybase species id

value: reproductive system without gonad

value: GAATTCGT-TAATCTTA

value: without ERCC


title: RS_WT_rep2

value: wild type


title: RS_WT_rep1


title: dvir_RE_m_r4

tag: strain (strain name or flybase id or drosophila species stock center id)

value: GAGATTCC-TAATCTTA


title: orgR_WB_f_r4

tag: developmental stage

value: whole body

value: Female

value: GAATTCGT-TATAGCCT


title: dvir_TX_f_r4

value: thorax without digestive system

tag: Sex

value: ATTCAGAA-CCTATCCT


title: dvir_TX_m_r4

value: Male

tag: age post eclosion (days)

value: TCCGGAGA-CCTATCCT


title: dvir_WB_f_r4

value: adult

tag: fly culture temperature (oc)

value: CTGAAGCT-TATAGCCT


title: dvir_WB_m_r4

tag: replicate

value: GAGATTCC-TATAGCCT


title: PS_WT_rep2

source_name: Pachyten spermatocytes


title: dvir_HD_m_r4

value: head

tag: illumina barcode

value: ATTACTCG-ATAGAGGC


title: PS_WT_rep1

value: testis


title: cKit_KO_rep1

source_name: c-Kit+ spermatogonia


title: dvir_GO_f_r4

value: gonad

value: GAATTCGT-AGGCGAAG

tag: plate and well id


title: cKit_WT_rep2

value: wild type


title: dvir_AC_f_r4

value: abdomen without digestive or reproductive system

value: TAATGCGC-GGCTCTGA

tag: ercc infomation

value: without ERCC


title: dvir_DG_f_r4

value: digestive plus excretory system

value: Female

value: ATTCAGAA-GTACTGAC


title: PS_KO_rep2


title: cKit_KO_rep2


title: PS_KO_rep1


title: w1118_dpse_dvir_TX_f_r4.ERCC

description: ERCC SetA

source_name: ERCC that merged to the multi-species sample (Drosophila melanogaster; Drosophila pseudoobscura; Drosophila virilis)

value: not applicable

value: ATTCAGAA-CCTATCCT

value: ERCC SetA


title: Vγ2+ G rep1

city: Copenhagen

first: Terkild

middle: Brink

last: Buus

address: Blegdamsvej 3

department: ISIM

institute: University of Copenhagen

description:
V2G_1
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: ACAGTG

data_processing:
Standard Illumina Casava software used for basecalling.
Sequenced reads were pseudoaligned to the mouse transcriptome (ENSEMBL, GRCm38 release 79) using the Kallisto pipeline
Kallisto abundance matrices imported to R with tximport
Normalized Expression values were calculated by DEseq2 taking transcript lengths into account
Genome_build: GRCm38 release 79 (ENSEMBL)
Supplementary_files_format_and_content: Expression_Matrix.csv (semicolon separated)

source_name: Thymus, γδT, TCRVγ2+CD73+CD117-CD24-

extract_protocol:
TRI Reagent (ThermoFisher) and 1-Bromo-3-chloropropane (BCP). Extracted upper phase and precipitated with 99.9% ethanol.
SMARTer Ultra Low Input RNA v4 (cDNA synthesis and amplification) and SMARTer Low Input Library Prep Kit V2 (library prep from cDNA) using vendor provided protocols.

tag: gender

value: female

value: 8 weeks

value: Thymus

tag: cell type

value: TCRdelta+ thymocytes

tag: cell population


title: dvir_DG_m_r4

value: adult

tag: tissue

value: Male

value: GAGATTCC-GTACTGAC


title: dvir_HD_f_r4

value: head

value: GAATTCGT-ATAGAGGC


title: Vγ2+ E rep1

description:
V2E_1
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: TTAGGC

source_name: Thymus, γδT, TCRVγ2+CD73+CD200+CD117+

tag: age


title: dvir_AC_m_r4

value: abdomen without digestive or reproductive system

value: TCCGGAGA-GGCTCTGA


title: Thy1_KO_rep1

source_name: Thy1+ spermatogonia

tag: strain

value: testis

tag: genotype


title: w1118_dpse_dvir_DG_m_r4.ERCC

description: ERCC SetB

tag: flybase species id

value: ERCC SetB


title: cKit_WT_rep1

value: wild type

tag: biowardrobe ides


title: dvir_GO_m_r4

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: developmental stage

value: gonad

value: ATTACTCG-AGGCGAAG

value: without ERCC


title: w1118_dpse_dvir_WB_m_r4.ERCC

description: ERCC SetB

value: not applicable

tag: Sex

tag: age post eclosion (days)

value: GAGATTCC-TATAGCCT


title: w1118_dpse_dvir_HD_f_r4.ERCC

description: ERCC SetA

tag: fly culture temperature (oc)

tag: replicate

value: ERCC SetA


title: w1118_dpse_dvir_DG_f_r4.ERCC

description: ERCC SetA

tag: illumina barcode

value: ATTCAGAA-GTACTGAC

tag: plate and well id


title: Vγ2+ D rep2

description:
V2D_2
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: GGCTAC

tag: gender

value: female

value: 8 weeks

value: Thymus

value: TCRdelta+ thymocytes


title: Vγ2+ D rep1

description:
V2D_1
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: CGATGT

tag: cell type


title: Vγ2+ C rep2

description:
V2C_2
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: TAGCTT

tag: cell population


title: w1118_dpse_dvir_WB_f_r4.ERCC

description: ERCC SetB

tag: tissue

value: CTGAAGCT-TATAGCCT

tag: ercc infomation


title: Vγ2+ F rep1

description:
V2F_1
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: TGACCA

source_name: Thymus, γδT, TCRVγ2+CD73+CD117-CD24+

tag: age

tag: strain


title: w1118_dpse_dvir_TX_m_r4.ERCC

description: ERCC SetA

tag: flybase species id

value: TCCGGAGA-CCTATCCT


title: Thy1_WT_rep1

tag: genotype

tag: biowardrobe ides


title: Thy1_WT_rep2


title: Vγ2+ G rep2

description:
V2G_2
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: CGATGT


title: w1118_dpse_dvir_RE_m_r4.ERCC

description: ERCC SetB

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: developmental stage

value: GAGATTCC-TAATCTTA