title: atypical endìometrial hyperplasia_rep5

source_name: endometrial hyperplasia_atypical

value: endometrial hyperplasia

tag: hyperplasia status

value: atypical

tag: tissue preparation

value: FFPE


title: H3K27ac_left_forebrain_EC_cell_349

status: Public on Jul 15 2019

type: SRA

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

country: China

institute: Peking University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were de-multiplexed to generate single cell profiles by custom scripts. For spliting single cell, we cut the first 21 bp of the read1 and the first 27 bp of the read2.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Cells with less than 3,000 non-duplicated were excluded.
Bed files were generated from bam files using bedtools (v2.25.0) bamToBed.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bed files. Each single cell bed file contain non-duplicated alignments as is in the bam file.

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Following CoBATCH protocol.
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

treatment_protocol: Organs were digested with 0.06 Collagenase II  + 0.08% Trypsin and 0.09% Collagenase II + 0.12% Trypsin  at 37 °C.

tag: strain

tag: tissue

value: left forebrain

tag: cell statement

value: Fixed by formaldehyde

tag: chip antibody


title: H3K27ac_right_forebrain_EC_cell_7

value: right forebrain


title: Vehicle CD44hiCD4+ rep1

city: Rochester

first: B. Paige

last: Lawrence

state: NY

address: 601 Elmwood Ave.

country: USA

institute: University of Rochester

library_source: transcriptomic

data_processing:
Data Formatting - bcltofastq-1.8.4
Data Cleaning - Trimmomatic-0.32, SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10  MINLEN:15
Genome Alignment - STAR-2.4.2a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 - htseq-count-0.6.1 -q -f bam -s no -r pos -i gene_name
Genome_build: GRCm38 + gencode M6
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample

molecule: total RNA

source_name: mediastinal lymph node (MLN)

growth_protocol: not applicable

extract_protocol:
Nine days after infection, lung draining mediastianal lymphnodes (MLNs) were isoalted from influenza A virus infected mice. From MLN cells, CD44hiCD4+ and CD44loCD4+ T cells were purified using flourescent activated cell sorting (FACs). RNA was isolated from purified T cells using the RNeasy Mini kit (Qiagen, Valencia, CA). Total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). RNA (1 ng) was pre-amplified with the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech, Mountain View, CA) following the manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Flourometer (Life Technnologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA).
cDNA (1 ng) was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA). The amplified libraries were hybridized to the Illumina single end flow cell, and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 10 pM per lane. Single end reads of 100nt were generated for each sample using Illumina's HiSeq2500v4.

treatment_protocol: Impregnated and lactating dams were gavaged with vehicle (peanut oil) or 1ug 2,3,7,8-tetrachlorodibenso-p-dioxin (TCDD)/kg body weight on gestational day 0, 7, 14, and post natal day 2. Offspring were aged to maturity (6-10 weeks old), and all mice were infected with 120 HAU Influenza A virus (HKx31).

tag: Sex

value: Female

value: mediastinal lymph node

tag: age

value: 6-10 weeks old

tag: developmental exposure

value: Vehicle (peanut oil)

tag: infection

value: Influenza A virus (120 HAU HKx31)

tag: day post infection


title: Mettl14KO_RNA_seq_1hRecovery-4

city: New York

first: Ryan

middle: J

last: Ries

address: 1300 York Avenue

institute: Weill Cornell Medical College

description:
mES_RNAseq_raw_counts.tab
mES_RiboSeq_WTvMettl14KO_1hRecovery.csv

data_processing:
Fastq files were trimmed based on a phred score cutoff of >30 and reads less than 16 nt were excluded from subsequent analysis of RNA-seq data. Reads less than 17 nt were excluded from subsequent analysis of Ribo-seq data.
The FLEXBAR tool was used to remove adapter sequences.
For Ribo-seq fastq files, reads were demultiplexed based on 5' barcodes for individual replicates using an in-house UNIX shell script.
Ribosomal RNA reads were removed using STAR genome aligner with the mm10 genome used as a reference.
Ribosome protected fragment reads aligning to mRNA sequences were used to construct gene count tables.
For RNA-seq analysis, the R package DESeq2 was used to normalize and process raw sequence data.
For Ribo-seq analysis of translational efficiency, the R package 'xtail' was used. The highest quality ribosome protected fragment replicates were combined during the analysis into two replicates that were matched to the corresponding RNA-seq sample to calculate translational efficiency.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data includes matrix tables with all mRNA-aligned counts from all RNA-seq and Ribo-seq replicates. The processed data used to generate RNA-seq and Ribo-seq comparisons under different stress conditions are included as .csv files and contain the output of the differential expression analysis (RNA-seq) or the translational efficiency analysis (Ribo-seq).

growth_protocol: Mettl14 knockout and wild type mouse ES cells were previously described by Geula et al. and were a generous gift of J. Hanna and S. Geula (Weizmann Institute of Science). mES cells were grown in Knockout DMEM (10829018, Invitrogen) with 15% heat inactivated FBS, 100 U ml−1 penicillin and 100 μg ml−1 of streptomycin, 200 mM L-glutamine, 1% non-essential Amino-Acid (Gibco 11140076), 50 μM β-mercaptoethanol (21985023, Gibco), 1000 U ml-1 mouse LIF (ESG1107, EMD Millipore), 30 μM GSK3 inhibitor CHIR99021 (04-0004-02, Stemgent), 10 μM MEK1 inhibitor PD0325901 (04-0006-02, Stemgent). Media was removed and changed every day. Cells were cultured on 0.1% gelatin-coated (07903, StemCell Technologies Inc.) plates. Cells were passaged every 2-3 days enzymatically using TrypLE Express (Life Technologies) according to the manufacturer’s instructions

extract_protocol:
Cells were rapidly washed twice with ice-cold PBS containing 50 μg/ml of cycloheximide. 5% of the clarified lysate was used for RNA-seq. 30 μg of RNA were used to isolate ribosome-protected fragments following RNase I digestion. After RNase digestion, lysates were loaded on a sucrose gradient and centrifuged at 100,000 rpm to recover ribosome-protected fragments. RNA from the resuspended ribosomal pellet was purified and run on a gel to selectively excise foot-printed RNAs (from 17 nt to 34 nt RNA fragments). To avoid any ribosomal contamination in the library preparation steps, we then performed Ribo-Zero Gold depletion of the foot-printed RNA. The rRNA depleted RNA fragments were dephosphorylated and the linker was added. To specifically deplete unligated linker, yeast 5’-deadenylase and RecJ exonuclease digestion was performed. Subsequent library preparation steps were performed essentially as previously in Linder B., et. al. Nat Methods 12, 767-772 (2015).
To avoid any ribosomal contamination in the library preparation steps, we then performed Ribo-Zero Gold depletion of the foot-printed RNA. The rRNA depleted RNA fragments were dephosphorylated and the linker was added. To specifically deplete unligated linker, yeast 5’-deadenylase and RecJ exonuclease digestion was performed. Subsequent library preparation steps were performed essentially as previously in Linder B., et. al. Nat Methods 12, 767-772 (2015). Library preparation was performed using the NEBNext Ultra Directional RNA Library Prep Kit starting from 1 ug of total input RNA and following the protocol for use with NEBNext rRNA Depletion Kit.

treatment_protocol: mES cells were plated on a 10 cm dish and allowed to reach 70-80% confluence. Heat shock was performed for 30 min in a water bath at 42°C. For the recovery condition, heat shocked cells were placed back at 37°C for 1 h.

tag: cell type

value: mouse embryonic stem cells

tag: passages

tag: origin

value: E6.5 mouse

tag: genotype

value: Mettl14 -/-

tag: stress


title: Mettl14KO_ribo_seq_heatShock-3

data_processing:
Library strategy: Ribo-seq
Fastq files were trimmed based on a phred score cutoff of >30 and reads less than 16 nt were excluded from subsequent analysis of RNA-seq data. Reads less than 17 nt were excluded from subsequent analysis of Ribo-seq data.
The FLEXBAR tool was used to remove adapter sequences.
For Ribo-seq fastq files, reads were demultiplexed based on 5' barcodes for individual replicates using an in-house UNIX shell script.
Ribosomal RNA reads were removed using STAR genome aligner with the mm10 genome used as a reference.
Ribosome protected fragment reads aligning to mRNA sequences were used to construct gene count tables.
For RNA-seq analysis, the R package DESeq2 was used to normalize and process raw sequence data.
For Ribo-seq analysis of translational efficiency, the R package 'xtail' was used. The highest quality ribosome protected fragment replicates were combined during the analysis into two replicates that were matched to the corresponding RNA-seq sample to calculate translational efficiency.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data includes matrix tables with all mRNA-aligned counts from all RNA-seq and Ribo-seq replicates. The processed data used to generate RNA-seq and Ribo-seq comparisons under different stress conditions are included as .csv files and contain the output of the differential expression analysis (RNA-seq) or the translational efficiency analysis (Ribo-seq).

value: heatShock


title: Mettl14KO_RNA_seq_heatShock-4


title: H3K27ac_left_forebrain_EC_cell_345


title: H3K27ac_left_forebrain_EC_cell_346


title: Mettl14KO_RNA_seq_heatShock-3


title: Mettl14KO_ribo_seq_heatShock-4


title: H3K27ac_left_forebrain_EC_cell_344


title: H3K27ac_left_forebrain_EC_cell_347


title: Mettl14KO_RNA_seq_heatShock-2


title: H3K27ac_right_forebrain_EC_cell_15


title: H3K27ac_right_forebrain_EC_cell_1


title: Mettl14KO_ribo_seq_heatShock-1


title: H3K27ac_left_forebrain_EC_cell_343


title: Mettl14KO_RNA_seq_heatShock-1


title: H3K27ac_left_forebrain_EC_cell_341


title: Mettl14KO_ribo_seq_noStress-4

value: noStress


title: Mettl14KO_RNA_seq_noStress-4


title: H3K27ac_left_forebrain_EC_cell_339


title: Mettl14KO_RNA_seq_noStress-3

description:
mES_RNAseq_raw_counts.tab
mES_RiboSeq_WTvMettl14KO_NoStress.csv


title: H3K27ac_left_forebrain_EC_cell_338


title: Mettl14KO_ribo_seq_noStress-3

description:
mES_RiboSeq_raw_counts.tab
mES_RiboSeq_WTvMettl14KO_NoStress.csv


title: Mettl14KO_RNA_seq_noStress-2


title: H3K27ac_left_forebrain_EC_cell_335


title: Mettl14KO_ribo_seq_noStress-2


title: Mettl14KO_ribo_seq_heatShock-2


title: H3K27ac_left_forebrain_EC_cell_334


title: H3K27ac_left_forebrain_EC_cell_336


title: H3K27ac_left_forebrain_EC_cell_337


title: H3K27ac_left_forebrain_EC_cell_333


title: WT_ribo_seq_1hRecovery-4

description:
mES_RiboSeq_raw_counts.tab
mES_RiboSeq_WTvMettl14KO_1hRecovery.csv

value: wild type


title: Mettl14KO_RNA_seq_noStress-1


title: H3K27ac_left_forebrain_EC_cell_331


title: H3K27ac_left_forebrain_EC_cell_332


title: H3K27ac_left_forebrain_EC_cell_342


title: H3K27ac_left_forebrain_EC_cell_329


title: H3K27ac_left_forebrain_EC_cell_330


title: H3K27ac_left_forebrain_EC_cell_340


title: WT_RNA_seq_1hRecovery-4

description:
mES_RNAseq_raw_counts.tab
mES_RiboSeq_WTvMettl14KO_1hRecovery.csv
mES_WT_RNAseq_1hRecoveryvNoStress.csv


title: H3K27ac_left_forebrain_EC_cell_328


title: WT_RNA_seq_1hRecovery-3


title: WT_ribo_seq_1hRecovery-3


title: H3K27ac_left_forebrain_EC_cell_327


title: Mettl14KO_ribo_seq_noStress-1


title: WT_ribo_seq_1hRecovery-2


title: WT_ribo_seq_1hRecovery-1


title: WT_RNA_seq_1hRecovery-2


title: WT_RNA_seq_1hRecovery-1


title: WT_ribo_seq_heatShock-4


title: H3K27ac_left_forebrain_EC_cell_324


title: WT_RNA_seq_heatShock-4

description:
mES_RNAseq_raw_counts.tab
mES_WT_RNAseq_HeatShockvNoStress.csv


title: H3K27ac_left_forebrain_EC_cell_326


title: H3K27ac_left_forebrain_EC_cell_325


title: H3K27ac_left_forebrain_EC_cell_323


title: H3K27ac_left_forebrain_EC_cell_322


title: WT_RNA_seq_heatShock-3


title: WT_ribo_seq_heatShock-2


title: WT_RNA_seq_heatShock-2


title: H3K27ac_left_forebrain_EC_cell_319


title: WT_RNA_seq_heatShock-1


title: H3K27ac_left_forebrain_EC_cell_320


title: H3K27ac_left_forebrain_EC_cell_318


title: WT_ribo_seq_heatShock-1


title: H3K27ac_left_forebrain_EC_cell_316


title: WT_RNA_seq_noStress-4

description:
mES_RNAseq_raw_counts.tab
mES_RiboSeq_WTvMettl14KO_NoStress.csv
mES_WT_RNAseq_HeatShockvNoStress.csv
mES_WT_RNAseq_1hRecoveryvNoStress.csv


title: H3K27ac_left_forebrain_EC_cell_315


title: WT_ribo_seq_noStress-3


title: H3K27ac_left_forebrain_EC_cell_312


title: H3K27ac_left_forebrain_EC_cell_313


title: H3K27ac_left_forebrain_EC_cell_314


title: WT_RNA_seq_noStress-3


title: WT_ribo_seq_noStress-2


title: H3K27ac_left_forebrain_EC_cell_310


title: H3K27ac_left_forebrain_EC_cell_317


title: WT_RNA_seq_noStress-2


title: WT_ribo_seq_noStress-1


title: WT_RNA_seq_noStress-1


title: WT_ribo_seq_heatShock-3


title: L16_1440_Mouse_18_Adipose

city: Cambridge

first: Sahin

last: Naqvi

state: MA

address: 455 Main St

institute: Whitehead Institute

description:
mouse.salmon.tximport.counts.txt
mouse.salmon.tximport.tpm.txt
mouse.stringtie.gtf
mouse.tx2geneid.txt

data_processing:
Image analysis and base calling was done using the standard Illumina pipeline for HiSeq2500
Libraries from the non-human mammals were mapped to their respective reference genomes using STAR v2.5.0 with the following parameters: --outFilterMultimapNmax 50 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.15
StringTie v1.3.3b with the --rf parameter was run on each resulting .bam file to assemble novel isoforms relative to the reference transcriptome annotation
The sets of novel and existing transcript annotations from each library were then compiled into a single set of annotations for each species using the --merge option in StringTie v1.3.3b
Abundances for these sets of transcripts for each species were then quantified using salmon v0.9.1 with the following parameters/flags: --seqBias, --gcBias, --useVBOpt
The tximport R package (with countsFromAbundance = “lengthScaledTPM”) was used to sum transcript-level counts and transcripts per million (TPM) values from salmon to the gene level for all transcripts with the following class codes: c, j, e, o, =, u
Genome_build: cyno, macFas5; dog, canFam3; mouse, mm10; rat, rn6
Supplementary_files_format_and_content: Transcript annotations for each species are provided as .gtf files. Assignments of transcripts (Ensembl ID for known, Stringtie ID for novel) to genes (Ensembl ID) along with transcript class codes are provided as tab-delimited .txt files. Gene-level TPM and counts are provided as tab-delimited .txt files

molecule: polyA RNA

source_name: Adipose

growth_protocol: standard lab/breeding colony conditions

extract_protocol:
Tissues were isolated from freshly sacrificed animals (< 1 hour from time of death to tissue fixation), washed in cold PBS, and stored in RNALater (Ambion) per the manufacturer’s instructions. Each sample was then homogenized in a bead-mill in Trizol and total RNA was isolated by and treated with DNAse on a Qiagen miRNEasy column
Libraries were prepared using the TruSeq mRNA library kit (Illumina) according to manufacturer’s instructions with the following modifications: After prep, libraries were size-selected using 2% agarose gels on the PippinHT system (Sage Science) with a capture window of 300-600 bases. The size-selected material was then subjected to one additional cycle of PCR with fresh reagents and P5/P7 primers (Illumina) to ensure all library fragments were fully double-stranded. This step significantly reduced the percentage of smaller fragments co-purifying in the final gel size-selection. After PCR, libraries were size-selected a second time on the PippinHT with the same settings

treatment_protocol: RNALater (Ambion)

tag: organism common name

value: Mouse

tag: individual

value: 8 weeks

tag: rna integry number (rin)

tag: library prep batch


title: H3K27ac_left_forebrain_EC_cell_321

tag: strain

tag: tissue


title: H3K27ac_left_forebrain_EC_cell_309

tag: cell statement

tag: chip antibody


title: H3K27ac_left_forebrain_EC_cell_306


title: H3K27ac_left_forebrain_EC_cell_307


title: WT_ribo_seq_noStress-4


title: L16_1413_Mouse_17_Adipose

tag: age


title: H3K27ac_left_forebrain_EC_cell_305


title: L16_1451_Mouse_16_Testis

source_name: Testis


title: L16_1403_Mouse_16_Testis


title: L16_1349_Mouse_16_Testis


title: H3K27ac_left_forebrain_EC_cell_303


title: H3K27ac_left_forebrain_EC_cell_311


title: L16_1301_Mouse_16_Testis


title: L16_1169_Mouse_16_Testis


title: L16_1118_Mouse_16_Testis


title: H3K27ac_left_forebrain_EC_cell_299


title: H3K27ac_left_forebrain_EC_cell_300


title: L16_1263_Mouse_16_Adipose


title: H3K27ac_left_forebrain_EC_cell_298


title: L16_1613_Mouse_16_Testis


title: H3K27ac_left_forebrain_EC_cell_297


title: L16_1400_Mouse_15_Adipose


title: L16_1264_Mouse_14_Adipose


title: H3K27ac_left_forebrain_EC_cell_295


title: H3K27ac_left_forebrain_EC_cell_308


title: H3K27ac_left_forebrain_EC_cell_294


title: L16_1322_Mouse_13_Pituitary

source_name: Pituitary


title: L16_1342_Mouse_13_Thyroid

source_name: Thyroid


title: H3K27ac_left_forebrain_EC_cell_292


title: L16_1500_Mouse_12_Thyroid


title: H3K27ac_left_forebrain_EC_cell_302


title: H3K27ac_left_forebrain_EC_cell_291


title: H3K27ac_left_forebrain_EC_cell_301


title: L16_1535_Mouse_16_Testis


title: L16_1336_Mouse_12_Skin

source_name: Skin


title: H3K27ac_left_forebrain_EC_cell_304


title: H3K27ac_left_forebrain_EC_cell_290


title: L16_1445_Mouse_12_Pituitary


title: L16_1335_Mouse_12_Muscle

source_name: Muscle


title: L16_1414_Mouse_15_Adipose


title: H3K27ac_left_forebrain_EC_cell_288


title: H3K27ac_left_forebrain_EC_cell_287


title: L16_1298_Mouse_12_Lung

source_name: Lung


title: H3K27ac_left_forebrain_EC_cell_286


title: L16_1329_Mouse_12_Liver

source_name: Liver


title: L16_1399_Mouse_12_Colon

source_name: Colon


title: H3K27ac_left_forebrain_EC_cell_283


title: L16_1448_Mouse_12_Brain

source_name: Brain


title: L16_1379_Mouse_12_Heart

source_name: Heart


title: H3K27ac_left_forebrain_EC_cell_285


title: L16_1420_Mouse_11_Thyroid


title: H3K27ac_left_forebrain_EC_cell_296


title: L16_1605_Mouse_12_Adrenal

source_name: Adrenal


title: H3K27ac_left_forebrain_EC_cell_282


title: H3K27ac_left_forebrain_EC_cell_281


title: L16_1357_Mouse_11_Skin


title: H3K27ac_left_forebrain_EC_cell_280


title: H3K27ac_left_forebrain_EC_cell_289


title: L16_1384_Mouse_11_Muscle


title: L16_1382_Mouse_11_Pituitary


title: L16_1259_Mouse_11_Lung


title: H3K27ac_left_forebrain_EC_cell_279


title: H3K27ac_left_forebrain_EC_cell_278


title: H3K27ac_left_forebrain_EC_cell_277


title: H3K27ac_left_forebrain_EC_cell_276


title: L16_1531_Mouse_11_Liver


title: H3K27ac_left_forebrain_EC_cell_275


title: L16_1230_Mouse_11_Heart


title: L16_1396_Mouse_11_Colon


title: H3K27ac_left_forebrain_EC_cell_274


title: H3K27ac_left_forebrain_EC_cell_284


title: L16_1375_Mouse_11_Brain


title: H3K27ac_left_forebrain_EC_cell_273


title: L16_1287_Mouse_11_Adrenal


title: H3K27ac_left_forebrain_EC_cell_272


title: H3K27ac_left_forebrain_EC_cell_271


title: L16_1326_Mouse_10_Thyroid


title: L16_1309_Mouse_10_Skin


title: H3K27ac_left_forebrain_EC_cell_270


title: H3K27ac_left_forebrain_EC_cell_269


title: L16_1442_Mouse_10_Muscle


title: L16_1397_Mouse_10_Lung


title: H3K27ac_left_forebrain_EC_cell_268


title: L16_1269_Mouse_10_Liver


title: H3K27ac_left_forebrain_EC_cell_267


title: L16_1428_Mouse_10_Heart


title: H3K27ac_left_forebrain_EC_cell_265


title: L16_1307_Mouse_10_Brain


title: L16_1331_Mouse_10_Colon


title: L16_1392_Mouse_10_Adrenal


title: L16_1339_Mouse_9_Thyroid


title: L16_1365_Mouse_9_Skin


title: H3K27ac_left_forebrain_EC_cell_263


title: H3K27ac_left_forebrain_EC_cell_262


title: H3K27ac_left_forebrain_EC_cell_260


title: L16_1366_Mouse_9_Muscle


title: H3K27ac_left_forebrain_EC_cell_259


title: L16_1284_Mouse_9_Lung


title: H3K27ac_left_forebrain_EC_cell_258


title: L16_1308_Mouse_9_Liver


title: H3K27ac_left_forebrain_EC_cell_257


title: L16_1600_Mouse_9_Heart


title: H3K27ac_left_forebrain_EC_cell_256


title: H3K27ac_left_forebrain_EC_cell_255


title: L16_1376_Mouse_9_Brain


title: H3K27ac_left_forebrain_EC_cell_254


title: H3K27ac_left_forebrain_EC_cell_266


title: H3K27ac_left_forebrain_EC_cell_253


title: H3K27ac_left_forebrain_EC_cell_264


title: L16_1508_Mouse_8_Skin


title: H3K27ac_left_forebrain_EC_cell_261


title: L16_1441_Mouse_9_Pituitary


title: H3K27ac_left_forebrain_EC_cell_251


title: L16_1430_Mouse_8_Lung


title: L16_1511_Mouse_8_Muscle


title: H3K27ac_left_forebrain_EC_cell_250


title: L16_1272_Mouse_8_Heart


title: H3K27ac_left_forebrain_EC_cell_249


title: H3K27ac_left_forebrain_EC_cell_248


title: L16_1367_Mouse_7_Thyroid


title: L16_1371_Mouse_8_Adrenal


title: H3K27ac_left_forebrain_EC_cell_246


title: L16_1532_Mouse_9_Colon


title: H3K27ac_left_forebrain_EC_cell_245


title: L16_1406_Mouse_7_Skin


title: L16_1374_Mouse_8_Brain


title: L16_1424_Mouse_9_Adrenal


title: H3K27ac_left_forebrain_EC_cell_244


title: L16_1425_Mouse_7_Pituitary


title: H3K27ac_left_forebrain_EC_cell_243


title: L16_1515_Mouse_7_Muscle


title: H3K27ac_left_forebrain_EC_cell_242


title: H3K27ac_left_forebrain_EC_cell_252


title: L16_1265_Mouse_7_Lung


title: H3K27ac_left_forebrain_EC_cell_241


title: H3K27ac_left_forebrain_EC_cell_240


title: L16_1279_Mouse_7_Heart


title: L16_1592_Mouse_7_Liver


title: L16_1419_Mouse_8_Colon


title: H3K27ac_left_forebrain_EC_cell_239


title: L16_1423_Mouse_7_Brain


title: H3K27ac_left_forebrain_EC_cell_238


title: H3K27ac_left_forebrain_EC_cell_237


title: L16_1343_Mouse_7_Adrenal


title: H3K27ac_left_forebrain_EC_cell_247


title: L16_1266_Mouse_7_Colon


title: H3K27ac_left_forebrain_EC_cell_236


title: L16_1595_Mouse_6_Spleen

source_name: Spleen


title: H3K27ac_left_forebrain_EC_cell_235


title: L16_1378_Mouse_5_Spleen


title: L16_1285_Mouse_4_Spleen


title: H3K27ac_left_forebrain_EC_cell_234


title: L16_1268_Mouse_3_Spleen


title: H3K27ac_left_forebrain_EC_cell_233


title: H3K27ac_left_forebrain_EC_cell_232


title: WT3-US_8

city: Charleston

first: Daokum

last: Sun

state: SC

address: 86 Jonathan Lucas St

institute: Medical University of South Carolina

description: raw-counts.xlsx

data_processing:
Illumina HiSeq4000 were used for sequencing
Sequence reads were mapped to mm10 whole genome using STAR v2.5.3 with default parameters
Raw counts were calculated using HTSeq-count v.0.8.0
Genome_build: mm10
Supplementary_files_format_and_content: Excel Worksheet file includes raw counts values for each sample

source_name: Embryo

extract_protocol:
Embros were minced and flow-sorted. Total RNA was purified using the Norgen Bioteck Total RNA Purification Plus Micro Kit (Norgen; 48500). 200 ng of rRNA-depleted RNA was used for the construction of the library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB/NJ

value: Embryo day 11.5

value: Embryo

tag: cell phases

value: US:unsorted cells


title: WT3-US_7

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_230

value: left forebrain

value: Fixed by formaldehyde


title: H3K27ac_left_forebrain_EC_cell_231


title: L16_1393_Mouse_1_Spleen


title: H3K27ac_left_forebrain_EC_cell_229


title: H3K27ac_left_forebrain_EC_cell_228


title: L16_1411_Mouse_2_Spleen


title: WT3-US_6

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_227


title: H3K27ac_left_forebrain_EC_cell_224


title: H3K27ac_left_forebrain_EC_cell_226


title: YVG00044

city: Madrid

first: Kevin

last: Troulé

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: SPANISH NATIONAL CANCER CENTER

data_processing:
RNA-seq processing:
RNA-seq data was analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Reads are quality-checked with FastQC, and aligned to the mouse genome (GRCh38/mm10) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 20 multihits
Genome_build: GRCh38/mm10
Supplementary_files_format_and_content: FPKM values calculated with Cufflinks

source_name: B220+ sorted cells from VavPBcl2/RagC S74C/+ lymphoma

extract_protocol: Samples of 500ng of total RNA (but 100ng for YRT-236, and 200-300ng for YRT-224, -230 and -235)  were used as provided by the user. Average sample RNA Integrity Number was 8.5 (range 7.9-10) when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760) [this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced]. Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: GC B cells were induced with SRBC. GC B cells were sorted using CD19+/CD95+/CD38- gating strategy, B220+ were sorted using B220 magnetic beads from Miltenyi

tag: genotype/variation

value: B220+ sorted cells from lymphoma


title: H3K27ac_left_forebrain_EC_cell_223


title: YVG00090

source_name: B220+ sorted cells from VavPBcl2/RagC +/+ lymphoma

value: VavPBcl2/RagC +/+


title: YVG00039


title: WT3-US_4

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_225


title: WT3-US_3

description: raw-counts.xlsx


title: YVG00030


title: H3K27ac_left_forebrain_EC_cell_221


title: H3K27ac_left_forebrain_EC_cell_222


title: H3K27ac_left_forebrain_EC_cell_220


title: H3K27ac_left_forebrain_EC_cell_219


title: YVG00019


title: WT3-US_2

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_218


title: H3K27ac_left_forebrain_EC_cell_217


title: H3K27ac_left_forebrain_EC_cell_216


title: WT3-P5_8

description: raw-counts.xlsx

value: DR:G1 phase cells


title: WT3-P5_7

description: raw-counts.xlsx


title: YRT236

source_name: GCB cells from RagC +/+ mice

value: RagC +/+

value: Germinal Center B cells


title: YRT234

source_name: GCB cells from RagC T89N/+ mice

value: RagC T89N/+


title: H3K27ac_left_forebrain_EC_cell_212


title: WT3-US_5

description: raw-counts.xlsx


title: YRT235


title: WT3-P5_5

description: raw-counts.xlsx


title: WT3-P5_6

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_213


title: H3K27ac_left_forebrain_EC_cell_215


title: H3K27ac_left_forebrain_EC_cell_211


title: YRT231


title: H3K27ac_left_forebrain_EC_cell_209


title: H3K27ac_left_forebrain_EC_cell_210


title: H3K27ac_left_forebrain_EC_cell_207


title: H3K27ac_left_forebrain_EC_cell_205


title: H3K27ac_left_forebrain_EC_cell_208


title: H3K27ac_left_forebrain_EC_cell_206


title: YRT230


title: H3K27ac_left_forebrain_EC_cell_204


title: H3K27ac_left_forebrain_EC_cell_214


title: L16_1338_Mouse_13_Pituitary


title: YRT229


title: H3K27ac_left_forebrain_EC_cell_293


title: WT3-US_1

description: raw-counts.xlsx


title: WT3-P5_1

description: raw-counts.xlsx


title: WT3-P5_2

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_201


title: H3K27ac_left_forebrain_EC_cell_203


title: H3K27ac_left_forebrain_EC_cell_202


title: H3K27ac_left_forebrain_EC_cell_200


title: YRT223


title: YRT224


title: XBH20036


title: WT3-P5_4

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_199


title: H3K27ac_left_forebrain_EC_cell_195


title: H3K27ac_left_forebrain_EC_cell_198


title: WT3-P4_5

description: raw-counts.xlsx

value: YE:G1-S phase cells


title: XBH17907


title: H3K27ac_left_forebrain_EC_cell_197


title: XBH17903


title: WT3-P4_7

description: raw-counts.xlsx


title: WT3-P5_3

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_196


title: WT3-P4_6

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_193


title: H3K27ac_left_forebrain_EC_cell_191


title: WT3-P4_4

description: raw-counts.xlsx


title: XBH17125


title: H3K27ac_left_forebrain_EC_cell_192


title: WT3-P4_3

description: raw-counts.xlsx


title: XBH17126


title: YRS94

description: 47456_GTGGCC_CACJGANXX_6_20161213B_20161213

extract_protocol: Total RNA samples were used as provided by the user. Average sample RNA Integrity Number was 9.75 (range 9.0 - 10) when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was extracted from 1µg of total RNA, randomly fragmented and converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: GC B cells were induced with SRBC. GC B cells were sorted using CD19+/CD95+/CD38- gating strategy.

value: Germinal Center (GC) B cells


title: YRS93

description: 47455_GTGAAA_CACJGANXX_6_20161213B_20161213

source_name: GCB cells from RagC S74C/+ mice

value: RagC S74C/+


title: H3K27ac_left_forebrain_EC_cell_187


title: H3K27ac_left_forebrain_EC_cell_190


title: H3K27ac_left_forebrain_EC_cell_189


title: WT3-P4_2

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_186


title: WT3-P4_8

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_194


title: XBH17189


title: WT3-P4_1

description: raw-counts.xlsx


title: YRS89

description: 47454_GTCCGC_CACJGANXX_6_20161213B_20161213


title: WT3-P3_8

description: raw-counts.xlsx

value: GR:S-G2-M phase cell


title: H3K27ac_left_forebrain_EC_cell_184


title: H3K27ac_left_forebrain_EC_cell_185


title: YRS88

description: 47453_ATTCCT_CACJGANXX_6_20161213B_20161213


title: H3K27ac_left_forebrain_EC_cell_183


title: H3K27ac_left_forebrain_EC_cell_182


title: H3K27ac_left_forebrain_EC_cell_178


title: H3K27ac_left_forebrain_EC_cell_181


title: WT3-P3_5

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_179


title: WT3-P3_6

description: raw-counts.xlsx


title: WT3-P3_7

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_188


title: YRS82

description: 47450_AGTTCC_CACJGANXX_6_20161213B_20161213


title: H3K27ac_left_forebrain_EC_cell_180


title: H3K27ac_left_forebrain_EC_cell_176


title: H3K27ac_left_forebrain_EC_cell_177


title: YRS81

description: 47449_AGTCAA_CACJGANXX_6_20161213B_20161213


title: YRS83

description: 47451_ATGTCA_CACJGANXX_6_20161213B_20161213


title: WT3-P3_4

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_175


title: H3K27ac_left_forebrain_EC_cell_174


title: WT3-P3_2

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_173


title: TS cells treated with ethanol (control) replicate 3

city: Otsu

first: Eiichi

last: Okamura

state: Shiga

address: Seta, Tsukinowa-cho

department: Research Center for Animal Life Science

country: Japan

institute: Shiga University of Medical Science

data_processing:
FASTQ sequences were aligned to the mm9 genome using STAR v2.3.1z12 with default parameters
Gene expression was quantified using HTSeq v0.6.1, using genic GTF from mm9 refGene
Genome_build: mm9
Supplementary_files_format_and_content: Individual count tables generated as output from HTSeq

source_name: TS cells treated with ethanol (control)

growth_protocol: TS cells were maintained in RPMI1640 (Sigma) supplemented with 20% FBS (Life Technologies), 1mM sodium pyruvate (Life Technologies), 50U/ml penicillin, 50μg/ml streptomycin, 100mM 2-mercaptoethanol (Sigma), 2mM Glutamax (Life Technologies), 25ng/ml FGF4 (R & D Systems), and 1μg/ml heparin (Sigma), with 70% of the media preconditioned by mitotically inactivated E12.5 embryonic fibroblasts (70CM + F4H medium)

extract_protocol:
Total RNA was extracted from TS cells treated with DES or vehicle (ethanol) for 2 days using TRIzol reagent with PureLink RNA Micro Kit
Single-end 100bp RNA-sequencing libraries were prepared using TruSeq Stranded Sample Prep Kit with human/mouse/rat Ribo Zero Gold

treatment_protocol: 1.6 x 10^5 TS cells were grown in 6-well plates for 2 days in 70CM + F4H medium in the presence of DES (20 μM) or the vehicle (ethanol)

tag: cell line

value: Trophoblast stem cells (TSCs)

tag: treatment

value: ethanol (vehicle control)


title: WT3-P3_3

description: raw-counts.xlsx

value: FVB/NJ

value: Embryo day 11.5


title: H3K27ac_left_forebrain_EC_cell_170


title: H3K27ac_left_forebrain_EC_cell_171


title: H3K27ac_left_forebrain_EC_cell_172


title: TS cells treated with ethanol (control) replicate 2

tag: cell type


title: WT3-P3_1

description: raw-counts.xlsx

value: Embryo


title: TS cells treated with ethanol (control) replicate 1


title: YRS87

description: 47452_CCGTCC_CACJGANXX_6_20161213B_20161213


title: H3K27ac_left_forebrain_EC_cell_169

value: left forebrain


title: H3K27ac_left_forebrain_EC_cell_167

value: Fixed by formaldehyde


title: TS cells treated with DES replicate 3

source_name: TS cells treated with DES

value: 20 μM diethylstilbestrol (DES, Esrrb inhibitor)


title: H3K27ac_left_forebrain_EC_cell_166


title: WT3-P1_8

description: raw-counts.xlsx

value: BR:G0 phase cells


title: TS cells treated with DES replicate 2


title: WT3-P1_6

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_164


title: WT3-P1_7

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_165


title: WT3-P1_5

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_162


title: H3K27ac_left_forebrain_EC_cell_168


title: H3K27ac_left_forebrain_EC_cell_163


title: TS cells treated with DES replicate 1


title: WT3-P1_4

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_160


title: H3K27ac_left_forebrain_EC_cell_159


title: WT3-P1_3

description: raw-counts.xlsx


title: WT3-P1_2

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_158


title: H3K27ac_left_forebrain_EC_cell_155


title: H3K27ac_left_forebrain_EC_cell_156


title: WT3-P1_1

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_161


title: H3K27ac_left_forebrain_EC_cell_154


title: H3K27ac_left_forebrain_EC_cell_153


title: H3K27ac_left_forebrain_EC_cell_149


title: H3K27ac_left_forebrain_EC_cell_152


title: WT2-US_7

description: raw-counts.xlsx

value: Embryo day 10.5

value: US:unsorted cells


title: H3K27ac_left_forebrain_EC_cell_151


title: H3K27ac_left_forebrain_EC_cell_150


title: H3K27ac_left_forebrain_EC_cell_147


title: H3K27ac_left_forebrain_EC_cell_146


title: NP day8_3

type: RNA

city: Kyoto

first: Akira

last: Hirasawa

state: Kyoto

address: 46-29 Yoshida Shimoadachi-cho, Sakyo-ku

department: Genomic Drug Discovery Science

institute: Kyoto University Graduate School of Pharmaceutical Sciences

description: NP day8

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

scan_protocol: The probe arrays were scanned with the GeneChip(R) Scanner.

data_processing: The data were analyzed with R software. The MAS 5.0 normalization were performed using the justMAS function in the simpleaffy package from Bioconductor.

label: biotin

source_name: NP day8

label_protocol: The labeled cDNA were then hybridized on Affimetrix gene chip and stained.

growth_protocol: ES cells were cultured on MMC treated mouse embryonic fibroblast and differentiated by embryo body formation

extract_protocol: cDNA labeling was performed according to the manufacturer’s instructions.

treatment_protocol: Total RNA was extracted byspin column method and transcribed to cDNA.

tag: agent

value: NP

value: Differentiated ES cells D3


title: BPA day8_3

description: BPA day8

source_name: BPA day8

value: BPA


title: NP day8_1

description: NP day8


title: WT2-US_5

description: raw-counts.xlsx


title: WT2-US_6

description: raw-counts.xlsx


title: BPA day8_2

description: BPA day8


title: H3K27ac_left_forebrain_EC_cell_157


title: NP day8_2

description: NP day8


title: H3K27ac_left_forebrain_EC_cell_145


title: H3K27ac_left_forebrain_EC_cell_144


title: H3K27ac_left_forebrain_EC_cell_143


title: WT2-US_4

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_148


title: WT2-US_3

description: raw-counts.xlsx


title: WT2-US_8

description: raw-counts.xlsx


title: BPA day8_1

description: BPA day8


title: H3K27ac_left_forebrain_EC_cell_141


title: H3K27ac_left_forebrain_EC_cell_139


title: H3K27ac_left_forebrain_EC_cell_140


title: H3K27ac_left_forebrain_EC_cell_138


title: WT2-US_2

description: raw-counts.xlsx


title: WT2-US_1

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_134


title: H3K27ac_left_forebrain_EC_cell_136


title: H3K27ac_left_forebrain_EC_cell_135


title: H3K27ac_left_forebrain_EC_cell_137


title: WT2-P5_8

description: raw-counts.xlsx

value: DR:G1 phase cells


title: WT2-P5_7

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_133


title: control day8_1

description: control day8

source_name: control day8


title: control day0_3

description: control day0

source_name: control day0

value: ES cells D3


title: control day8_3

description: control day8


title: control day0_1

description: control day0


title: ROBO-Crainbow 8

city: Durham

first: Joshua

middle: C

last: Snyder

state: North Carolina

address: 203 Research Dr

department: Surgery

institute: Duke University

description:
2 Cartridges used for isolation (up to 2400 cells isolated) per genotype.
mRNA isolation
processed data file: ROBO_Cell_Matrix.tsv

data_processing:
BaseSpace Sequence Hub was used to build cell matrix files using the SureCell RNA Single-Cell App. 1,348 WT and 1,249 ROBO cells passed QC, aligned to Mus musculus UCSC mm10).
Genome_build: Mus musculus UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: *_Cell_Matrix.tsv: Cell matrix file (gene symbol, UMI counts, cell ID).

source_name: Crypt isolates

growth_protocol: Harvested from mice (Postnatal age day 16).

extract_protocol:
Intestinal crypts were isolated by mechanical disruption and EDTA treatment. Single cell suspensions were made with a 1 hr 0.25% trypsin incubation + 1mg/ml Collagenase/Dispase, DNaseI, and Q-VD-OPH. For more information, please see the reference publication. 2 Cartridges were used per genotype for a theoretical isolation of 2400 cells per genotype.
Following manufacturer's protocol: SureCell WTA 3' Library Prep Kit.
68bp:Read1 and 75bp:Read2, paired-end reads. Sequenced on Illumina NextSeq 500 (hi-output mode).

treatment_protocol: Untreated

tag: strain/background

value: Outbred mice

value: ROBO-Crainbow

value: Postnatal day 16

value: Intestinal crypt cells

tag: cell isolation

value: Biorad-ddSEQ

tag: library construction

value: SureCell WTA 3' Library Prep Kit


title: control day0_2

description: control day0


title: H3K27ac_left_forebrain_EC_cell_142

value: left forebrain


title: ROBO-Crainbow 7


title: ROBO-Crainbow 6


title: control day8_2

description: control day8


title: H3K27ac_left_forebrain_EC_cell_132

value: Fixed by formaldehyde


title: WT2-P5_6

description: raw-counts.xlsx

value: FVB/NJ

value: Embryo


title: ROBO-Crainbow 5


title: H3K27ac_left_forebrain_EC_cell_130


title: WT2-P5_5

description: raw-counts.xlsx

value: Embryo day 10.5


title: WT2-P5_4

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_131


title: ROBO-Crainbow 4


title: H3K27ac_left_forebrain_EC_cell_129


title: H3K27ac_left_forebrain_EC_cell_128


title: H3K27ac_left_forebrain_EC_cell_127


title: WT2-P5_3

description: raw-counts.xlsx


title: ROBO-Crainbow 3


title: WT2-P5_2

description: raw-counts.xlsx


title: ROBO-Crainbow 2


title: H3K27ac_left_forebrain_EC_cell_124


title: H3K27ac_left_forebrain_EC_cell_123


title: H3K27ac_left_forebrain_EC_cell_122


title: WT2-P5_1

description: raw-counts.xlsx


title: ROBO-Crainbow 1


title: H3K27ac_left_forebrain_EC_cell_121


title: Wild-type (WT) 8

description:
2 Cartridges used for isolation (up to 2400 cells isolated) per genotype.
mRNA isolation
processed data file: WT_Cell_Matrix.tsv

value: Wild-type


title: H3K27ac_left_forebrain_EC_cell_120


title: WT2-P4_8

description: raw-counts.xlsx

value: YE:G1-S phase cells


title: Wild-type (WT) 7


title: WT2-P4_7

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_118


title: H3K27ac_left_forebrain_EC_cell_119


title: WT2-P4_5

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_117


title: H3K27ac_left_forebrain_EC_cell_113


title: H3K27ac_left_forebrain_EC_cell_115


title: H3K27ac_left_forebrain_EC_cell_116


title: WT2-P4_6

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_114


title: H3K27ac_left_forebrain_EC_cell_125


title: H3K27ac_left_forebrain_EC_cell_126


title: H3K27ac_left_forebrain_EC_cell_112


title: WT2-P4_4

description: raw-counts.xlsx


title: Wild-type (WT) 4


title: Wild-type (WT) 6


title: Wild-type (WT) 3


title: H3K27ac_left_forebrain_EC_cell_111


title: WT2-P4_3

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_109


title: H3K27ac_left_forebrain_EC_cell_107


title: Wild-type (WT) 1


title: WT2-P4_2

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_108


title: Wild-type (WT) 2


title: H3K27ac_left_forebrain_EC_cell_106


title: WT2-P3_8

description: raw-counts.xlsx

value: GR:S-G2-M phase cell


title: H3K27ac_left_forebrain_EC_cell_105


title: WT2-P4_1

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_102


title: 65_MII_KO

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Raw reads were trimmed for adapters with cutadapt (1.12) using the Trim Galore! (0.4.4) wrapper (default settings) and subsequently mapped to the complete rRNA sequence with Bowtie2 (2.2.9).
Reads that did not map to rRNA were then mapped with STAR (2.5.3a) to the full reference genome.
Gene counts were generated using STAR --quant_mode.
Genome_build: hg19 (ipNF05.5 cells)
Genome_build: GRCm38/mm10 (spermatogonia and oocytes)
Supplementary_files_format_and_content: gene counts

source_name: oocytes

extract_protocol:
RNA Picopure Extraction Kite KIT0204, Life Tech
SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing, Ref-634888

value: MII oocytes

tag: genotype

value: CXORF67 KO/KO


title: H3K27ac_left_forebrain_EC_cell_104


title: Wild-type (WT) 5


title: H3K27ac_left_forebrain_EC_cell_100


title: H3K27ac_left_forebrain_EC_cell_101


title: WT2-P3_7

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_103


title: WT2-P3_6

description: raw-counts.xlsx


title: WT2-P3_5

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_98


title: H3K27ac_left_forebrain_EC_cell_110


title: 63_MII_KO


title: 61_MII_KO


title: H3K27ac_left_forebrain_EC_cell_99


title: H3K27ac_left_forebrain_EC_cell_97


title: 62_MII_KO


title: H3K27ac_left_forebrain_EC_cell_95


title: 60_MII_KO


title: H3K27ac_left_forebrain_EC_cell_94


title: 64_MII_KO


title: H3K27ac_left_forebrain_EC_cell_93


title: WT2-P3_3

description: raw-counts.xlsx


title: WT2-P3_2

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_92


title: 58_MII_KO


title: 57_MII_KO


title: H3K27ac_left_forebrain_EC_cell_90


title: 56_MII_KO


title: WT2-P1_8

description: raw-counts.xlsx

value: BR:G0 phase cells


title: H3K27ac_left_forebrain_EC_cell_87


title: H3K27ac_left_forebrain_EC_cell_88


title: H3K27ac_left_forebrain_EC_cell_86


title: H3K27ac_left_forebrain_EC_cell_89


title: WT2-P1_7

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_96


title: WT2-P3_1

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_84


title: 55_MII_WT

value: CXORF67 KO/WT


title: WT2-P3_4

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_85


title: WT2-P1_6

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_83


title: H3K27ac_left_forebrain_EC_cell_82


title: H3K27ac_left_forebrain_EC_cell_91


title: WT2-P1_5

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_81


title: H3K27ac_left_forebrain_EC_cell_80


title: WT2-P1_4

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_79


title: 59_MII_KO


title: 51_MII_WT


title: WT2-P1_3

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_77


title: 50_MII_WT


title: WT2-P1_2

description: raw-counts.xlsx


title: 54_MII_WT


title: H3K27ac_left_forebrain_EC_cell_75


title: H3K27ac_left_forebrain_EC_cell_76


title: 49_MII_WT


title: 48_MII_WT


title: WT1-US_6

description: raw-counts.xlsx

value: US:unsorted cells


title: H3K27ac_left_forebrain_EC_cell_74


title: H3K27ac_left_forebrain_EC_cell_72


title: WT2-P1_1

description: raw-counts.xlsx


title: WT1-US_5

description: raw-counts.xlsx


title: 47_MII_WT


title: 52_MII_WT


title: H3K27ac_left_forebrain_EC_cell_71


title: H3K27ac_left_forebrain_EC_cell_70


title: 46_MII_WT


title: H3K27ac_left_forebrain_EC_cell_69


title: H3K27ac_left_forebrain_EC_cell_78


title: H3K27ac_left_forebrain_EC_cell_66


title: WT1-US_3

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_67


title: WT1-US_4

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_68


title: H3K27ac_left_forebrain_EC_cell_65


title: H3K27ac_left_forebrain_EC_cell_64


title: P30_3_S10

city: Copenhagen

first: Svetlana

last: Ulyanchenko

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research and Innovation Centre

data_processing:
Data basecalled in BaseSpace
Sequenced reads were trimmed with Trimmomatic (v0.32) with paramaters: HEADCROP:3 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
Trimmed reads were mapped to the canonical chromosomes in the mm10 genome assembly using STAR allignment tool (v2.5.1a) with parameters: --outFilterMatchNmin 16 --outFilterMismatchNmax 5 --outFilterMismatchNoverLmax 0.1 --sjdbOverhang 69 --twopassMode Basic
Aligned reads were assigned genes using featureCounts (v1.5.1) with parameters: –primary -s 2 -J
RefSeq gene annotation (downloaded from UCSC 2018/08/05) was used both in alignment and count assignment steps
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text of with three columns containing: Gene symbol, RefSeq ID and raw counts.

source_name: sebaceous gland basal cells laser dissection

growth_protocol: Samples isolated from fresh frozen tissue

extract_protocol:
laser capture microdissection
smarter stranded total RNAseq kit v2 -pico input

tag: sample type

value: sebaceous gland basal cells isolated at P30 HF are in anagen

tag: material

value: total RNA

tag: transgenic


title: P30_2_S5

tag: strain


title: H3K27ac_left_forebrain_EC_cell_63

tag: tissue

tag: cell statement


title: WT1-US_2

description: raw-counts.xlsx

tag: age


title: H3K27ac_left_forebrain_EC_cell_62

tag: chip antibody


title: H3K27ac_left_forebrain_EC_cell_73


title: H3K27ac_left_forebrain_EC_cell_60


title: WT1-P5_6

description: raw-counts.xlsx

tag: cell phases

value: DR:G1 phase cells


title: WT1-US_1

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_61


title: WT1-P5_5

description: raw-counts.xlsx


title: P10_3_S9

value: sebaceous gland basal cells isolated at P10


title: P30_1_S4


title: H3K27ac_left_forebrain_EC_cell_59

value: left forebrain


title: H3K27ac_left_forebrain_EC_cell_58

value: Fixed by formaldehyde


title: P10_2_S3


title: H3K27ac_left_forebrain_EC_cell_57


title: H3K27ac_left_forebrain_EC_cell_56


title: WT1-P5_4

description: raw-counts.xlsx

value: FVB/NJ


title: P10_1_S2


title: P4_4_S13

value: sebaceous gland basal cells isolated at P4


title: WT1-P5_3

description: raw-counts.xlsx

value: Embryo day 10.5

value: Embryo


title: H3K27ac_left_forebrain_EC_cell_54


title: P4_3_S12


title: H3K27ac_left_forebrain_EC_cell_52


title: WT1-P5_2

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_55


title: H3K27ac_left_forebrain_EC_cell_50


title: WT1-P5_1

description: raw-counts.xlsx


title: WT1-P4_6

description: raw-counts.xlsx

value: YE:G1-S phase cells


title: H3K27ac_left_forebrain_EC_cell_48


title: H3K27ac_left_forebrain_EC_cell_51


title: WT1-P4_5

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_46


title: H3K27ac_left_forebrain_EC_cell_44


title: P8_7Sham_rep1_input

first: Zhaoning

last: Wang

state: New York

address: 701 West 168th Street Hammer 14 - 1410

department: Genetics and Development

institute: Columbia University

data_processing:
Quality control of RNA-Seq data was performed using FastQC Tool (Version 0.11.4).
ChIP-seq raw reads were aligned to mouse (mm10) genome assembly using Bowtie2 (Version 2.3.4) with default parameters.
For H3K27ac samples, duplicated reads were removed from further analysis. MACS2 (Version 2.1.1) was first applied to each sample to perform peaking calling using the “-nomodel” parameter and was next applied to merged pseudo samples of the biological duplicates14. Only the peaks that are present in both replicates as well as the merged pseudo sample, defined by at least 50% overlapping of the peak coordinates, were kept as real peaks for further analyses.
To compare ChIP-seq signal intensities between MI and sham samples, diffbind (Version 1.16.3) was applied to calculate the normalized ChIP-seq enrichment score with summits=250. Cutoff values of absolute fold change greater than 2.0 and false discovery rate less than 0.05 were used for differential peak analysis between sample groups.
The normalized peak scores calculated using the TMM function in edgeR were plotted in the heatmaps to show peak intensity across timepoints.
For H3K27me3 samples, duplicates and X-chromosome mapped reads were removed. MACS2 was applied to each biological sample using “--broad-cutoff 0.01 –nomodel” parameter.
Diffbind was applied to calculate the differentially bound peak with summits=500. Fold change value of two and FDR less than 0.05 were used as cutoffs.
Genome_build: mm10

source_name: Mouse ventricle approximate to below left anterior descending artery ligation plane in age-matched MI samples

extract_protocol:
Each heart was dissected in ice-cold PBS and a transverse cut on ligation plane was made, separating it into above ligation plane (ALP) part and below ligation plane (BLP) part. BLP parts were flash-frozen with liquid nitrogen and stored in -80°C for RNA-Seq. The collected tissue samples were ground to powder in liquid nitrogen, and crosslinked with 2% formaldehyde in PBS for 30 min and quenched with 0.125M glycine for 10 min at room temperature. Crosslinked samples were then washed with cold PBS and further homogenized with a Dounce tissue grinder. Samples were collected by a brief spin, and treated with 10 mM Tris-HCl (pH 8.0), 10mM NaCl and 0.2% NP-40 for 30 min to collect nuclei. After nuclear extraction, chromatin was sheared on a Bioruptor Pico (Diagenode) for 20 cycles (30 sec on/ 30 sec off for each cycle) at 4°C in sonication buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.25% sarkosyl, 1 mM DTT, 1x cOmplete Protease Inhibitor Cocktail (Roche), and 1 mM PMSF, pH 8.0). After sonication, 1% of the sonicated chromatin from each sample was taken out as “input” samples. The remaining sonicated chromatin was evenly split for H3K27ac or H3K27me3 ChIP. Sonication buffer was added to make the final volume to 1 mL. NaCl was then added to a final concentration of 300 mM for each sample. 1 µg H3K27ac antibody (Diagenode, C15410196) or H3K27me3 (Diagenode, C15410195) was added to each sample and incubated at 4°C overnight with gentle rotation. The next day, 30 µL of pre-washed Dynabeads Protein G (Invitrogen, 10004D) was added to each sample for a two-hour incubation. After that, the beads were washed twice with 1 mL RIPA 0 buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, pH 8.0), twice with 1 mL RIPA 0.3 buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, 300 mM NaCl, pH 8.0), twice with 1 mL LiCl wash buffer (250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.0), and finally twice with 1 mL TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0). For each ChIP sample or input sample, 100 uL of SDS elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0) was added and incubation was done at 65°C overnight on a ThermoMixer (Eppendorf) at 1000 rpm. The next day, supernatant was collected and further treated with 0.5 µg RNaseA (Sigma, 11119915001) for 30 min at 37°C, followed by 20 µg Proteinase K (NEB, P8107S) treatment at 37°C for 2h. DNA was recovered using MinElute PCR Purification Kit (QIAGEN, 28004) according to manufacturer’s protocol.
ChIP-Seq libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) according to manufacturer’s protocol.

tag: surgery performed at developmental age

value: Postnatal day 8

tag: sample collected at post-surgical day

value: day 7

tag: surgery type

value: Sham

tag: antibody

value: input


title: H3K27ac_left_forebrain_EC_cell_47


title: WT1-P4_4

description: raw-counts.xlsx


title: P8_7Sham_rep2_H3K27me3


title: H3K27ac_left_forebrain_EC_cell_42


title: WT1-P4_3

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_43


title: P8_7Sham_rep1_H3K27me3


title: P8_7Sham_rep2_input


title: H3K27ac_left_forebrain_EC_cell_53


title: P8_7Sham_rep2_H3K27ac


title: WT1-P4_2

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_40


title: P4_2_S8


title: H3K27ac_left_forebrain_EC_cell_39


title: P8_7Sham_rep1_H3K27ac


title: H3K27ac_left_forebrain_EC_cell_49


title: H3K27ac_left_forebrain_EC_cell_38


title: H3K27ac_left_forebrain_EC_cell_36


title: WT1-P4_1

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_45


title: H3K27ac_left_forebrain_EC_cell_37


title: WT1-P3_6

description: raw-counts.xlsx

value: GR:S-G2-M phase cell


title: H3K27ac_left_forebrain_EC_cell_35


title: WT1-P3_5

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_33


title: H3K27ac_left_forebrain_EC_cell_41


title: H3K27ac_left_forebrain_EC_cell_34


title: WT1-P3_4

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_30


title: H3K27ac_left_forebrain_EC_cell_32


title: P8_7MI_rep2_input

source_name: Mouse ventricle below left anterior descending artery ligation plane

value: MI


title: H3K27ac_left_forebrain_EC_cell_28


title: P8_7MI_rep2_H3K27ac


title: P8_7MI_rep2_H3K27me3


title: P8_7MI_rep1_input


title: H3K27ac_left_forebrain_EC_cell_29


title: P8_7MI_rep1_H3K27me3


title: WT1-P3_2

description: raw-counts.xlsx

source_name: Embryo


title: H3K27ac_left_forebrain_EC_cell_26


title: WT1-P3_1

description: raw-counts.xlsx


title: P8_7MI_rep1_H3K27ac


title: P8_3Sham_rep2_input

value: day 3


title: WT1-P1_6

description: raw-counts.xlsx

value: BR:G0 phase cells


title: WT1-P1_5

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_24


title: H3K27ac_left_forebrain_EC_cell_25


title: H3K27ac_left_forebrain_EC_cell_31


title: P8_3Sham_rep2_H3K27me3


title: P8_3Sham_rep1_input


title: WT1-P3_3

description: raw-counts.xlsx


title: WT1-P1_4

description: raw-counts.xlsx


title: P8_3Sham_rep1_H3K27me3


title: H3K27ac_left_forebrain_EC_cell_22


title: WT1-P1_3

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_27


title: WT1-P1_2

description: raw-counts.xlsx


title: EB-dHey RNAi 2

city: Seattle

first: Hector

last: Rincon-Arano

state: Washington

address: 1100 Fairview Ave N

department: Basic Science Division

institute: Fred Hutchinson Cancer Research Center

description: This sample is of  purifed dHey-depleted Ebs  (dHey-Gal4>UAS-dHey RNAi) derived from  drosophila melanogaster female guts. It is the second of three biological replicates.

hyb_protocol: Hybridiztion was performed using a Nimblegen hybridization system on a Drosophila melanogaster gene expression 4x72K Array (A4509001-00-01) according to Nimblegene expression array protocol.

scan_protocol: arrays were scanned on a Genepix 4000B Microarray scanner (Molecular Devices) and Data was extracted using Nimblegen V2.4 software.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version ? (Roche NimbleGen, Inc.).

organism: Drosophila melanogaster

source_name: drosophila melanogater dHey depleted enteroblast cells

label_protocol: Samples were labled using Nimblegene One-Color DNA labeling Kit using standard Nimblegene  protocol.

growth_protocol: Flies were cultured at 18°C prior to eclosion and 0-2 days post-eclosion

extract_protocol: Guts were dissociated and  RNA extracted either from whole guts or  from isolated EBs using  a RNAeasy extraction Kit (Qiagene), followed by cDNA synthesis (Invitrogene), cRNA amplification (Epicenter biotechnologies),and Double stranded cDNA synthesis.

treatment_protocol: 2-4 days adult femlaes flies were transferred to 29°C for 2 days prior to RNA extraction.

value: Enteroblasts depleted for dHey


title: H3K27ac_left_forebrain_EC_cell_21


title: P8_3Sham_rep1_H3K27ac


title: WT1-P1_1

description: raw-counts.xlsx


title: 8-US_2

description: raw-counts.xlsx

value: Embryo day 13.5

value: US:unsorted cells


title: P8_3MI_rep2_input


title: H3K27ac_left_forebrain_EC_cell_20

value: left forebrain

value: Fixed by formaldehyde


title: H3K27ac_left_forebrain_EC_cell_19


title: P8_3Sham_rep2_H3K27ac


title: 8-US_1

description: raw-counts.xlsx

value: FVB/NJ


title: P8_3MI_rep1_input


title: H3K27ac_left_forebrain_EC_cell_18


title: P8_3MI_rep2_H3K27me3


title: H3K27ac_left_forebrain_EC_cell_17


title: H3K27ac_left_forebrain_EC_cell_23


title: EB-GFP 2

description: This sample is of control  (dHey-Gal4>UAS-GFP) purifed Ebs derived from  drosophila melanogaster female guts. It is the second of three biological replicates.

source_name: drosophila melanogater enteroblast cells control

value: Enteroblasts cells control


title: EB-GFP 1

description: This sample is of control  (dHey-Gal4>UAS-GFP) purifed Ebs derived from  drosophila melanogaster female guts. It is the first of three biological replicates.


title: EC-dHey RNAi 2

description: This sample is of drosophila melanogaster female gut where dHey was depleted in ECs (Myo-Gal4> dHey RNAi) . It is the second of three biological replicates.

source_name: drosophila melanogater dHey depleted in EC

value: dHey RNAi gut


title: EB-dHey RNAi 1

description: This sample is of  purifed dHey-depleted Ebs  (dHey-Gal4>UAS-dHey RNAi) derived from  drosophila melanogaster female guts. It is the first of three biological replicates.


title: EB-GFP 3

description: This sample is of control  (dHey-Gal4>UAS-GFP) purifed Ebs derived from  drosophila melanogaster female guts. It is the third of three biological replicates.


title: 8-P5_DR_2

description: raw-counts.xlsx

value: Embryo

value: DR:G1 phase cells


title: EC-dHey RNAi 3

description: This sample is of drosophila melanogaster female gut where dHey was depleted in ECs (Myo-Gal4> dHey RNAi) . It is the third of three biological replicates.


title: EB-dHey RNAi 3

description: This sample is of  purifed dHey-depleted Ebs  (dHey-Gal4>UAS-dHey RNAi) derived from  drosophila melanogaster female guts. It is the third of three biological replicates.


title: P8_3MI_rep1_H3K27me3

value: Postnatal day 8


title: 8-P5_DR_1

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_16


title: 8-P4_YE_2

description: raw-counts.xlsx

value: YE:G1-S phase cells


title: EC-GFP 3

description: This sample is of  control  (Myo-GAL4> UAS-GFP)  drosophila melanogaster female gut. It is the third of three wild-type biological replicates.

source_name: drosophila melanogater control

value: controlgut


title: H3K27ac_left_forebrain_EC_cell_15


title: TSC Input control

data_processing:
FASTQ sequences were aligned to the mm9 genome using Bowtie2 v.2.2.3
Peak-calling was performed on the ChIP-Seq library using MACS v.2.2.1, using the following parameters (-g mm -q 0.01)
Genome_build: mm9
Supplementary_files_format_and_content: NarrowPeak (BED) file generated by MACS peakcalling

extract_protocol:
The lysate is incubated with 15ug anti-Esrrb antibody, ), washed, and the bound chromatin eluted. The eluate was reverse-crosslinked, and treated with proteinase K
The ChIP-enriched and corresponding input genomic DNA libraries were prepared using the Illumina Genomic Sample Preparation Kit (Illumina) according to the manufacturer’s instruction

treatment_protocol: trophoblast stem cells were fixed with formaldehyde, lysed and then sonicated with a Misonix Sonicator 3000.

tag: cell line

tag: cell type

value: Trophoblast stem cells (TSCs)


title: EC-GFP 2

description: This sample is of  control  (Myo-GAL4> UAS-GFP) drosophila melanogaster female gut. It is the second of three wild-type biological replicates.

value: control gut


title: TSC Esrrb ChIP

value: anti-Esrrb antibody (Perseus Proteomics)


title: 8-P3_GR_2

description: raw-counts.xlsx

value: GR:S-G2-M phase cell


title: H3K27ac_left_forebrain_EC_cell_13


title: H3K27ac_left_forebrain_EC_cell_14


title: EC-GFP 1

description: This sample is of control  (Myo-GAL4> UAS-GFP) drosophila melanogaster female gut. It is the first of three wild-type biological replicates.


title: P8_1.5Sham_rep2_input

value: day 1.5

value: Sham

value: input


title: P8_1.5Sham_rep1_input


title: P8_3MI_rep1_H3K27ac

value: day 3

value: MI


title: 8-P3_GR_1

description: raw-counts.xlsx

value: FVB/NJ

value: Embryo day 13.5


title: H3K27ac_left_forebrain_EC_cell_12

value: left forebrain

value: Fixed by formaldehyde


title: EC-dHey RNAi 1

description: This sample is of drosophila melanogaster female gut where dHey was depleted in ECs (Myo-Gal4> dHey RNAi) . It is the first of three biological replicates.

value: dHey RNAi gut


title: P8_1.5Sham_rep2_H3K27me3

value: Postnatal day 8


title: 8-P1_BR_2

description: raw-counts.xlsx

value: Embryo

value: BR:G0 phase cells


title: P8_3MI_rep2_H3K27ac


title: P8_1.5Sham_rep1_H3K27me3


title: T6g2-27

city: Heidelberg

first: Haikun

last: Liu

address: INF 581

country: Germany

institute: DKFZ

data_processing:
Raw reads from Gpd1 sgRNA-knockout RNA-seq experiments were aligned to mm10 (ensemble version 86) by  STAR (2.4.1d) with default parameters.
The aligned reads were quantified by the featureCounts in Rsubread package.
We used DESeq2 to identify the differentially expressed genes between control and sgRNA1 knock out samples with the option “cooksCutoff = FALSE”.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated count data

growth_protocol: For the GPD1 KO with CRISPR /Cas9 the vector lentiCRISPv2 was used following the protocol published by the Zhang lab on the GeCKO (genome-scale CRISPR knock-out)40. We used the CRISPR Design tool provided in GeCKO, which is based on the specificity analysis performed in Hsu et al., Nature Biotechnology, 2013. Five gRNAS were used to transfect mouse BTSCs with lipofectamine LTX&PLUS reagent (Invitrogen) according to the manufacturer’s protocol. After two days puromycin was added to the media for one week to select transfected cells. These cells were seeded as 1000/10 cm coated dish to grow colonies deriving from one single cell. Once the colonies were visible they were gently picked with a pipette tip and resuspended in a coated 24 well plate to expand. Western blots were performed to confirm the GPD1 KO in the expanded colonies.

extract_protocol:
For RNA isolation from cultured NSCs, BTSCs and cells were harvested in TRI Reagent (Sigma) following the protocol.
After chloroform phase separation the transparent upper phase was added to an equal volume of 70 % ethanol and transferred to an RNeasy Mini spin column (Qiagen). The RNA was purified according to the protocol and send for library preparation and Illumina HiSeq sequencing to our in house facility.

treatment_protocol: From the colonies of interest DNA was purified and sequenced to prove the GPD1 KO. All five gRNAs could knock-out GPD1. We chose the two gRNAs closest to the start ATG of the GPD1 gene and used the colonies established with them. gRNA1: AAAGTCTGCATTGTCGGCTC, gRNA2: TGCATTGCTACCCACGATCT.

value: brain

value: brain tumor stem cells Gpd1 knock-out by Crispr-cas9


title: T6g1-8


title: H3K27ac_left_forebrain_EC_cell_11


title: H3K27ac_left_forebrain_EC_cell_9


title: 5_US_2

description: raw-counts.xlsx

value: US:unsorted cells


title: T6g2-10


title: T6g1-18


title: 8-P1_BR_1

description: raw-counts.xlsx


title: P8_1.5Sham_rep1_H3K27ac


title: P8_1.5Sham_rep2_H3K27ac


title: H3K27ac_left_forebrain_EC_cell_10


title: 5_US_1

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_8


title: T6g2-9


title: P8_1.5MI_rep2_input


title: H3K27ac_left_forebrain_EC_cell_6


title: T6g1_10


title: T6_2

value: brain tumor stem cells


title: P8_1.5MI_rep2_H3K27me3

value: day 1.5


title: 5_P5_DR_1

description: raw-counts.xlsx

value: DR:G1 phase cells


title: 5_P4_YE_2

description: raw-counts.xlsx

value: YE:G1-S phase cells


title: H3K27ac_left_forebrain_EC_cell_5


title: 5_P5_DR_2

description: raw-counts.xlsx


title: H3K27ac_left_forebrain_EC_cell_4


title: P8_1.5MI_rep1_H3K27me3


title: T6_1


title: P8_1.5MI_rep2_H3K27ac


title: 5_P3_GR_2

description: raw-counts.xlsx

value: GR:S-G2-M phase cell


title: BTSC Tum6

data_processing:
Sequences were aligned analysis with TopHat v1.4.0 using the reference genome mm10.
To analyse the differentially expressed genes between we used Cuffdiff v2.2.1 with classic fpkm as library normalization method and a FDR of 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated results

value: brain tumor stem cell


title: P8_1.5MI_rep1_H3K27ac

value: MI


title: 5_P3_GR_1

description: raw-counts.xlsx

value: FVB/NJ

value: Embryo day 13.5


title: H3K27ac_left_forebrain_EC_cell_2

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were de-multiplexed to generate single cell profiles by custom scripts. For spliting single cell, we cut the first 21 bp of the read1 and the first 27 bp of the read2.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Cells with less than 3,000 non-duplicated were excluded.
Bed files were generated from bam files using bedtools (v2.25.0) bamToBed.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bed files. Each single cell bed file contain non-duplicated alignments as is in the bam file.

value: left forebrain

value: Fixed by formaldehyde


title: P8_1.5MI_rep1_input

value: Postnatal day 8

value: input


title: H3K27ac_left_forebrain_EC_cell_7


title: T6_3


title: H3K27ac_left_forebrain_EC_cell_1


title: 5_P1_BR_2

description: raw-counts.xlsx

value: Embryo

value: BR:G0 phase cells


title: H3K27ac_left_forebrain_EC_cell_3


title: NSC2

value: brain

value: neural stem cells


title: P1_7Sham_rep2_input

value: Postnatal day 1

value: day 7

value: Sham


title: NSC1


title: 5_P1_BR_1

description: raw-counts.xlsx


title: P1_7Sham_rep1_input


title: Embryo p53Mut (ChIP-seq)

city: Dallas

first: John

middle: M

last: Abrams

state: TX

address: 6000 Harry Hines Blvd., NL7.110L

department: Cell Biology

institute: UT Southwestern Medical Center

description:
ChIP_Embryo_WT_FoldChangeOverp53mut.bw
ChIPmacs2CalledPeaks_Embyo.narrowPeak

data_processing:
Cutadapt to remove adapters
Prinseq to remove low quality reads/bases
Alignment using bowtie2
Picard marked PCR duplicates
SAMtools to remove PCR duplicates and low quality alignments.  Peaks were called with MACS2.
Genome_build: dm6
Supplementary_files_format_and_content: MACS2 called peak output files, bw files.

source_name: 4.5-5.5 hour embryos

growth_protocol: Flies grown in standard media at room temperature for 1-2 weeks with genotypes age matched. Embryos were collected on standard grapejuice agar plates and aged to 4.5-5.5 hours and dechorionated. Adult heads were harvested from age matched adults. collected using a series of sieves.

extract_protocol:
Tissue was fixed in 1% formaldehyde for 10 minutes at room temperature, cells were lysed, and chromatin fragmented in a Bioruptor to an average lengthy of approximately 200-300 base pairs. ChIPs were performed with the sc-25767 p53 d200 antibody (2ug/ChIP), precipitated with Protein A/G beads, eluted in 1% SDS and reverse crosslinked at 65C overnight.  DNA was purified by standard phenol:choloroform extraction followed by isopropanol precipitation.
Libraries were prepared from purified DNA with an illumina compatible protocol.

treatment_protocol: Flash freeze and sieve sorting to extract fly heads. Embryos were dechorionated with 50% bleach.

tag: stress treatment

value: p53 d200 antibody (Santa Cruz Biotechnology, sc-25767)

value: embryos


title: PR5 BTSC

description: ribosome protected mRNA

data_processing:
Bowtie2 was used to align the reads against mouse rRNA sequences.
Only the non-aligned reads were used for further analysis with TopHat v1.4.0 using the reference genome mm10.
To analyse the differentially expressed genes between we used Cuffdiff v2.2.1 with classic fpkm as library normalization method and a FDR of 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: deferentially expressed genes between BTSCs and NSCs under the cut-off of FDR < 0.1

extract_protocol:
The cells of a 15 cm culture plate were lysed with lysis buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, 200 mM KCl, 1 % Triton, 2 mM DTT, 100 µg/ml Cyclohexamide, 25 U/ml DNase and EDTA-free protease inhibitors, Roche). The mRNA not protected by ribosomes was digested with RNAseI and the ribosome footprints were collected by centrifugation with a continuous sucrose gradient (10-50 %) with DTT, cyclohexamideand 20 U/ml SUPERaseIN. The fraction with the ribosome footprint RNA was used for acid phenol extraction.
Precipitated RNA was resuspended in 10 mM Tris pH7, mixed with 2x sample buffer (TBE-urea, NOVEX, Invitrogen) and loaded on a 15 % TBE-urea gel. The region between 26-34 nt was excised and used for library generation exactly as described previously (Ingolia et al, Nat Protoc 2012). The library was sequenced on the Illumina HiSeq system according to the manufacturer’s protocol.

value: mouse brain tumor stem cells


title: 5_P4_YE_1

description: raw-counts.xlsx

value: YE:G1-S phase cells


title: Embryo WT (ChIP-seq)

value: yw


title: P1_7Sham_rep2_H3K27me3


title: P1_7Sham_rep1_H3K27me3


title: PR4 BTSC

description: ribosome protected mRNA


title: UAS-Dm0 3

city: Haifa

first: Amir

last: Orian

address: Efron 1

country: Israel

institute: technion

data_processing:
50 bp single-end reads were aligned to Drosophila reference genome and annotation file (Drosophila_melanogaster.BDGP6 downloaded from ENSEMBL) using TopHat (v2.0.13) allowing 2 mismatches per read with options -very-sensitive and –GTF.
The number of reads per gene was counted using Htseq (0.6.0).
The number of reads per sample and the number of aligned reads suggest that reads' quality and number are good and that data analysis using all 12 samples can proceed.
Samples' clustering and differential expressed genes (DEGs) were calculated using Deseq2 package (version 1.10.1).
Genome_build: Drosophila_melanogaster.BDGP6
Supplementary_files_format_and_content: counts

source_name: Gut

extract_protocol:
Guts were dissociated and RNA was extracted with Rneasy Mini Kit (Qiagene)
Twelve  RNAseq libraries were produced using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, cat no. E7420) according to manufacture protocol and starting with 100 ng of total RNA. mRNA pull-up was performed using the Magnetic Isolation Module (NEB, cat no. E7490). libraries were mixed into a single tube at an equal molar concentration. The RNAseq data was generated on two lanes of HiSeq2500, 50SR.

tag: genotype

value: Dmo overexpression in EC


title: BTSC Tum1

value: brain tumor stem cell


title: UAS-Dm0 4


title: Head p53Mut (ChIP-seq)

description:
ChIP_Head_WT_FoldChangeOverp53mut.bw
ChIPmacs2CalledPeaks_Head.narrowPeak

source_name: Mixed adult heads

value: head


title: PR3 BTSC

description: ribosome protected mRNA


title: P1_7Sham_rep2_H3K27ac


title: UAS-Dm0 2


title: P1_7Sham_rep1_H3K27ac


title: PR2 NSC

description: ribosome protected mRNA

value: mouse brain neural stem cells


title: Head WT (ChIP-seq)


title: UAS-Dm0 1


title: Embryo p53Mut IR (RNA-Seq)

data_processing:
Cutadapt to remove adapters
Prinseq to remove low quality reads/bases
Alignment using Tophat2 (-p 10 --mate-inner-dist=200 --mate-std-dev=40 --library-type fr-firststrand --no-coverage-search )
Picard marked PCR duplicates
SAMtools to remove PCR duplicates and low quality alignments
Genome_build: dm6
Supplementary_files_format_and_content: Txt file includes a table with FPKM values generated by CuffDiff and pseudocount1 log2 fold change between groups of interest.

growth_protocol: Flies grown in standard media at room temperature for 1-2 weeks, after IR treatment flies were allowed recovery for 3 hours before RNA extraction, genotypes age matched. Embryos were collected on standard grapejuice agar plates and aged to 3-4 hours when either IR/mock treatment was performed, embryos were allowed recovery for 1.5 hour when total RNA was extracted.

extract_protocol:
Trizol total RNA extraction followed by DNase treatment
Poly(A) enrichment followed by illumina standard library prep for paired-end stranded RNA-seq

value: 40gy Ionizing Radiation


title: Control 4

value: wt


title: P1_7MI_rep1_input

value: MI

value: input


title: P1_7MI_rep2_input


title: Embryo p53Mut Ctr (RNA-Seq)

value: mock


title: PR1 NSC

description: ribosome protected mRNA

value: brain


title: P1_7MI_rep2_H3K27me3

value: Postnatal day 1

value: day 7


title: Embryo WT IR (RNA-Seq)


title: Control 2


title: Embryo WT Ctr (RNA-Seq)


title: Control 1


title: P1_7MI_rep1_H3K27me3


title: p53Mut IR (RNA-Seq)

growth_protocol: Flies grown in standard media at room temperature for 1-2 weeks, genotypes age matched.

treatment_protocol: Flash freeze and sieve sorting to extract fly heads


title: p53Mut Ctr (RNA-Seq)


title: P1_3Sham_rep2_input

value: day 3

value: Sham


title: P1_7MI_rep2_H3K27ac


title: WT IR (RNA-Seq)


title: P1_3Sham_rep1_input


title: Control 3


title: L16_1614_Rat_14_Testis

description:
rat.salmon.tximport.counts.txt
rat.salmon.tximport.tpm.txt
rat.stringtie.gtf
rat.tx2geneid.txt

data_processing:
Image analysis and base calling was done using the standard Illumina pipeline for HiSeq2500
Libraries from the non-human mammals were mapped to their respective reference genomes using STAR v2.5.0 with the following parameters: --outFilterMultimapNmax 50 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.15
StringTie v1.3.3b with the --rf parameter was run on each resulting .bam file to assemble novel isoforms relative to the reference transcriptome annotation
The sets of novel and existing transcript annotations from each library were then compiled into a single set of annotations for each species using the --merge option in StringTie v1.3.3b
Abundances for these sets of transcripts for each species were then quantified using salmon v0.9.1 with the following parameters/flags: --seqBias, --gcBias, --useVBOpt
The tximport R package (with countsFromAbundance = “lengthScaledTPM”) was used to sum transcript-level counts and transcripts per million (TPM) values from salmon to the gene level for all transcripts with the following class codes: c, j, e, o, =, u
Genome_build: cyno, macFas5; dog, canFam3; mouse, mm10; rat, rn6
Supplementary_files_format_and_content: Transcript annotations for each species are provided as .gtf files. Assignments of transcripts (Ensembl ID for known, Stringtie ID for novel) to genes (Ensembl ID) along with transcript class codes are provided as tab-delimited .txt files. Gene-level TPM and counts are provided as tab-delimited .txt files

organism: Rattus norvegicus

source_name: Testis

extract_protocol:
Tissues were isolated from freshly sacrificed animals (< 1 hour from time of death to tissue fixation), washed in cold PBS, and stored in RNALater (Ambion) per the manufacturer’s instructions. Each sample was then homogenized in a bead-mill in Trizol and total RNA was isolated by and treated with DNAse on a Qiagen miRNEasy column
Libraries were prepared using the TruSeq mRNA library kit (Illumina) according to manufacturer’s instructions with the following modifications: After prep, libraries were size-selected using 2% agarose gels on the PippinHT system (Sage Science) with a capture window of 300-600 bases. The size-selected material was then subjected to one additional cycle of PCR with fresh reagents and P5/P7 primers (Illumina) to ensure all library fragments were fully double-stranded. This step significantly reduced the percentage of smaller fragments co-purifying in the final gel size-selection. After PCR, libraries were size-selected a second time on the PippinHT with the same settings

tag: organism common name

value: Rat

value: Brown Norway

tag: individual

value: 9 weeks

tag: rna integry number (rin)

tag: library prep batch


title: WT Ctr (RNA-Seq)

tag: strain

value: yw

tag: tissue


title: P1_3Sham_rep2_H3K27me3


title: L16_1536_Rat_14_Testis

tag: age


title: U2OS_dCXORF67_2

description: Cell Signaling Technology (9733)

data_processing:
Reads were mapped to the concatenated human reference genome (GRCh37/hg19) and Drosophila melanogaster (dm6) with Bowtie2 (2.2.9) using the following parameters: --very-sensitive --end-to-end --reorder.
PCR duplicates were removed with Picard Tools MarkDuplicates (1.97)
BAM files were filtered exclude artifact regions. The merged consensus blacklist was obtained from the Kundaje lab at Stanford University (Stanford, CA, USA).
Reads were extended to 200bp and RPKM normalized counting only reads in bins of length 50 and converted to bigWig format using DeepTools (2.4.1).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigWig

organism: Homo sapiens

source_name: osteosarcoma-derived cell line

growth_protocol: ipNF05.5 cells were cultured in DMEM media supplemented with 10% FBS and 1% L-Glutamine and 1% non essential amino acids.

extract_protocol:
Libraries were prepared according to Illumina's DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
ChIP-Seq/CUT&RUN

value: CXORF67 KO

tag: chip antibody


title: WT  replicate 2

hyb_protocol: cDNA was then hybridized to Mouse 1.0 ST gene array v1 according to the manufacturer’s protocol

scan_protocol: Chip was scanned with an Affymetrix GeneChip Scanner 7G

data_processing: The raw data was imported and normalized using the affy R package v.1.44.0

label: Biotin

source_name: WT_extraembryonic ectoderm

label_protocol: 100 ng of RNA from each pooled sample was used to generate cDNA, which was then fragmented and labeled using the Ambion WT Expression Kit according to the manufacturer's protocol

extract_protocol: Total RNA was extracted using Trizol, and the quality of the RNA was assessed using a BioAnalyzer

treatment_protocol: Post-implantation embryos were dissected from the uteri of pregnant females at E6.5. Extraembryonic ectoderm was separated and pooled (~20-25 per replicate)

tag: strain background

tag: developmental stage

value: E6.5 embryo

tag: genotype/variation

value: wild type

value: Extraembryonic ectoderm


title: L16_1452_Rat_14_Testis


title: U2OS_dCXORF67_1

description: Cell Signaling Technology (9733)


title: WT  replicate 3


title: WT  replicate 1


title: P1_3Sham_rep1_H3K27me3

tag: surgery performed at developmental age

tag: sample collected at post-surgical day

tag: surgery type


title: P1_7MI_rep1_H3K27ac

tag: antibody


title: P1_3Sham_rep2_H3K27ac


title: L16_1404_Rat_14_Testis


title: U2OS_dEED_2

description: Cell Signaling Technology (9733)

tag: cell type

value: EED KO


title: ExE mutant replicate 3

source_name: mutant_extraembryonic ectoderm

value: Esrrb mutant


title: ExE mutant replicate 1


title: 8-P4_YE_1

description: raw-counts.xlsx

data_processing:
Illumina HiSeq4000 were used for sequencing
Sequence reads were mapped to mm10 whole genome using STAR v2.5.3 with default parameters
Raw counts were calculated using HTSeq-count v.0.8.0
Genome_build: mm10
Supplementary_files_format_and_content: Excel Worksheet file includes raw counts values for each sample

extract_protocol:
Embros were minced and flow-sorted. Total RNA was purified using the Norgen Bioteck Total RNA Purification Plus Micro Kit (Norgen; 48500). 200 ng of rRNA-depleted RNA was used for the construction of the library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB/NJ

value: Embryo day 13.5

value: Embryo

tag: cell phases

value: YE:G1-S phase cells


title: HIV_specific_CD4_ T cells_EC15

city: Montreal

first: Daniel

middle: Elias

last: Kaufmann

state: Quebec

address: 900 Rue St. Denis

country: Canada

institute: CRCHUM

hyb_protocol: 5 µg DNA target was hybridized on GeneChip® Clariom™ D, human (ThermoFisher Scientific) and incubated at 450C in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (Affymetrix) using Applied Biosystems™ Hybridization Wash and Stain kit according to the manufacturer’s instructions (Applied Biosystems™)

scan_protocol: The microarrays were finally scanned on a GeneChip® scanner 3000 (Affymetrix).

data_processing: The preprocessing of the microarray data was done in R v3.3.3 using the oligo package47 v1.38.0 using rma function.

source_name: CD154+ CD69+ HIV-specific CD4 T cells from PBMCs

label_protocol: Sense-strand cDNA was synthesized from total RNA using a fixed volume of 3µL. Fragmentation and labeling were performed to produce ss-DNA with the Applied Biosystems™ GeneChip® WT Pico Terminal Labeling Kit according to manufacturer’s instructions (Applied Biosystems™).

growth_protocol: Cryopreserved PBMCs were thawed and rested at 37°C for 3 hours.

extract_protocol: Total RNA was purified using the RNeasy Plus Micro Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: A CD40 blocking antibody (Miltenyi Biotec, clone HB14) was added 15 minutes prior to stimulation with a gag peptide pool.  Following a 9 hr incubation, HIV-specific CD4 T cells were identified based on the co-upregulation of CD40L and CD69 and were live-sorted directly in RLT lysis buffer (Qiagen).

tag: disease status

value: Elite Controller

value: PBMCs


title: U2OS_dEED_1

description: Cell Signaling Technology (9733)

tag: genotype


title: L16_1302_Rat_14_Testis

tag: organism common name

tag: individual

tag: rna integry number (rin)


title: ExE mutant replicate 2

tag: tissue


title: L16_1131_Rat_14_Testis

tag: strain

tag: age

tag: library prep batch


title: P1_3Sham_rep1_H3K27ac

value: Postnatal day 1

value: day 3

value: Sham


title: U2OS_WT_2

description: Cell Signaling Technology (9733)

value: WT

tag: chip antibody


title: L16_1085_Rat_14_Testis

value: Rat

value: Brown Norway

value: 9 weeks


title: P1_3MI_rep1_input

value: MI

value: input


title: U2OS_WT_1

description: Cell Signaling Technology (9733)


title: HIV_specific_CD4_ T cells_EC13


title: HIV_specific_CD4_ T cells_EC12


title: P1_3MI_rep2_input


title: P1_3MI_rep2_H3K27me3


title: HIV_specific_CD4_ T cells_EC11


title: HIV_specific_CD4_ T cells_EC10


title: WT2

data_processing:
Raw reads were trimmed for adapters with cutadapt (1.12) using the Trim Galore! (0.4.4) wrapper (default settings) and subsequently mapped to the complete rRNA sequence with Bowtie2 (2.2.9).
Reads that did not map to rRNA were then mapped with STAR (2.5.3a) to the full reference genome.
Gene counts were generated using STAR --quant_mode.
Genome_build: hg19 (ipNF05.5 cells)
Genome_build: GRCm38/mm10 (spermatogonia and oocytes)
Supplementary_files_format_and_content: gene counts


title: L16_1389_Rat_12_Adipose

source_name: Adipose


title: P1_3MI_rep1_H3K27me3


title: L16_1054_Rat_11_Adipose


title: HIV_specific_CD4_ T cells_EC8


title: dEEDcl72

value: EED KO


title: P1_3MI_rep2_H3K27ac


title: dEEDcl71


title: L16_1434_Rat_10_Adipose


title: dHey chromatin profiling 2

type: genomic

description: DamID-based dHey chromatin profiling

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: For DamID chromatin profiling, raw signals of corresponding experimental replicates were loess normalized and averaged. Signal were mapped and lifted to DM3 genome build and repeated or umapable probes were removed. dHey enrichment statistics were cumputed using a two state HMM according to  Filion et al Cell 2010. Probes were considered to be bound significantly if the posterior probability of the HMM was greater than 0.9 and the enriched region was larger than 3Kb. Meta-analysis were performed as described (Henikoff, S., et al., 2009 Genome research, 19(3), 460–469.) (Deal, R. B., et al., Science (New York, NY), 328(5982), 1161–1164) or using cistrome (Liu T et al. 2011. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biology 12: R83).

source_name: Dam_dHey expressed in Kc cells

label_protocol: 1 µg DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers ( DNA isolated from DamdHey transfected cells) or with Cy3 nonamers (DNA isolated from Dam transfected cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Dam_dHey transfected cells cell were incubated for 72h at 25C

extract_protocol: For DamID experiments, genomic DNA samples from Dam-dHey or Dam- control transfected cells were recovered, DpnI digested and fractionated according to Orian A. Methods in molecular biology (2009), 567, 155–169.

treatment_protocol: 16 ug of DamdHey plasmid was electroporated in Kc cells

tag: cell line

value: Kc cell

source_name: Dam expression in Kc cells

growth_protocol: Dam transfected cells cells were incubated for 72h at 25C

treatment_protocol: 16 ug of Dam plasmid was electroporated in Kc cells


title: WT1


title: HIV_specific_CD4_ T cells_EC9


title: L16_1427_Rat_9_Adipose


title: HIV_specific_CD4_ T cells_EC7


title: P1_1.5Sham_rep2_input

data_processing:
Quality control of RNA-Seq data was performed using FastQC Tool (Version 0.11.4).
ChIP-seq raw reads were aligned to mouse (mm10) genome assembly using Bowtie2 (Version 2.3.4) with default parameters.
For H3K27ac samples, duplicated reads were removed from further analysis. MACS2 (Version 2.1.1) was first applied to each sample to perform peaking calling using the “-nomodel” parameter and was next applied to merged pseudo samples of the biological duplicates14. Only the peaks that are present in both replicates as well as the merged pseudo sample, defined by at least 50% overlapping of the peak coordinates, were kept as real peaks for further analyses.
To compare ChIP-seq signal intensities between MI and sham samples, diffbind (Version 1.16.3) was applied to calculate the normalized ChIP-seq enrichment score with summits=250. Cutoff values of absolute fold change greater than 2.0 and false discovery rate less than 0.05 were used for differential peak analysis between sample groups.
The normalized peak scores calculated using the TMM function in edgeR were plotted in the heatmaps to show peak intensity across timepoints.
For H3K27me3 samples, duplicates and X-chromosome mapped reads were removed. MACS2 was applied to each biological sample using “--broad-cutoff 0.01 –nomodel” parameter.
Diffbind was applied to calculate the differentially bound peak with summits=500. Fold change value of two and FDR less than 0.05 were used as cutoffs.
Genome_build: mm10

source_name: Mouse ventricle approximate to below left anterior descending artery ligation plane in age-matched MI samples

tag: surgery performed at developmental age

value: day 1.5


title: L16_1412_Rat_13_Adipose


title: L16_1063_Rat_8_Adipose


title: P1_1.5Sham_rep1_input

tag: sample collected at post-surgical day


title: dCXorf67cl29_2

value: CXORF67 KO


title: dHey chromatin profiling 3

description: DamID-based dHey chromatin profiling (dye swap)

source_name: Dam_expressed in Kc cells

growth_protocol: Dam transfected cells cell were incubated for 72h at 25C

treatment_protocol: 16 ug of Damd plasmid was electroporated in Kc cells

source_name: Dam_dHey expression in Kc cells

growth_protocol: Dam_dHey transfected cells cells were incubated for 72h at 25C

treatment_protocol: 16 ug of Dam_dHey plasmid was electroporated in Kc cells


title: P1_3MI_rep1_H3K27ac

source_name: Mouse ventricle below left anterior descending artery ligation plane

tag: surgery type


title: L16_1134_Rat_7_Thyroid

source_name: Thyroid

treatment_protocol: RNALater (Ambion)


title: miCLIP_ZCCHC4_KO_2

first: Samie

last: Jaffrey

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

description: miCLIP

data_processing:
For miCLIP,  adapters and low-quality based were trimmed using flexbar v2.5: flexbar -n 20 -as AGATCGGAAGAGCGGTTCAG -f i1.8 --pre-trim-phred 30 -t output -r Read1.fastq -p Read2.fastq
Reads were then demultiplexed using pyBarcodeFilter.py and de-deduplicted using pyFastqDuplicateRemover.py from the pyCRAC software suite, and processed for the CTK iCLIP/miCLIP protocol. Second mate reads were reverse complimented and concatenated a with the first read file and aligned to GRCh38 using bwa v0.7.17: bwa aln -t 4 -n 0.06 -q 20 GRCh38.fasta ConcatendatedReads.fasta > AlignedReads.sai
Aligned reads were then processed as in miCLIP using C to T transitions to identify m6A sites.
To determine significantly different coverage across transcripts in the knockout cells, aligned reads were converted to transcript (exonic) (Ensembl GRCh38.93 annotation) coordinates for the long isoform of each gene, using the GenomicFeatures library in R. Coverage within 80 nt sliding windows (step size of 40 nt) was then calculated for each replicate. These were normalized to the median window coverage per gene. To remove variabilty due to low coverage, the bottom 2% of covered transcripts were removed. Differential enrichment between each bin was then calculated between the wild-type and each knockout using the EdgeR package (exactTest()).
Genome_build: hg38
Supplementary_files_format_and_content: bed files: called m6A sites; tsv files: output of EdgeR exactTest() function with BH p-value corrections for multiple comparions (FDR)

growth_protocol: Cells were cultured in McCoy’s 5A Medium (Lonza™ BE12-168F) in a New Brunswick Galaxy 170R incubator at 37°C and under 5% CO2.

extract_protocol:
Total RNA from wild-type, mettl5-knockout, and zcchc4-knockout HCT116 cells was extracted in Tri Reagent (AM9738, Thermo-Fisher Scientific). Any contaminating genomic DNA was degraded with DNase I, and Poly(A) RNA was purified with an mRNA isolation kit (NEB #S1550) according to the manufacturer’s recommendations.
Five micrograms of poly(A)-selected RNA was then used as input for single-nucleotide resolution m6A mapping according to the miCLIP protocol.

value: ZCCHC4 knockout

tag: antibody


title: dCXorf67cl29_1

extract_protocol:
RNA Picopure Extraction Kite KIT0204, Life Tech
SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing, Ref-634888

tag: cell type


title: P1_1.5Sham_rep2_H3K27me3


title: HIV_specific_CD4_ T cells_EC4


title: P1_1.5Sham_rep1_H3K27me3


title: HIV_specific_CD4_ T cells_EC1


title: dHey chromatin profiling 1

description: DamID-based dHey chromatin profiling


title: HIV_specific_CD4_ T cells_EC2


title: HIV_specific_CD4_ T cells_EC5


title: miCLIP_ZCCHC4_KO_1

description: miCLIP


title: HIV_specific_CD4_ T cells_VC12

value: Viremic Controller


title: miCLIP_METTL5_KO_2

description: miCLIP

value: METTL5 knockout


title: HIV_specific_CD4_ T cells_VC11

value: PBMCs


title: L16_1179_Rat_7_Skin

source_name: Skin

growth_protocol: standard lab/breeding colony conditions


title: P1_1.5Sham_rep2_H3K27ac

value: Postnatal day 1


title: P1_1.5Sham_rep1_H3K27ac


title: miCLIP_METTL5_KO_1

description: miCLIP


title: miCLIP_WT_2

description: miCLIP

value: Wild type


title: P1_1.5MI_rep2_input


title: L16_1319_Rat_7_Pituitary

source_name: Pituitary


title: L16_1369_Rat_7_Muscle

source_name: Muscle


title: L16_1363_Rat_7_Spleen

source_name: Spleen


title: L16_1416_Rat_7_Lung

source_name: Lung


title: HIV_specific_CD4_ T cells_VC9


title: L16_1180_Rat_7_Heart

source_name: Heart


title: miCLIP_WT_1

description: miCLIP


title: P1_1.5MI_rep2_H3K27ac


title: P1_1.5MI_rep1_H3K27me3


title: L16_1291_Rat_7_Colon

source_name: Colon