title: i12J-iPSC_RRBS-seq

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

data_processing:
hisat2 -x hg38.idx -U ESO7-CM_rep1.fastq.gz -S ESO7-CM_rep1.sam -p 2
featureCounts -T 2 -t exon -g gene_name -s 1 -a hg38_P2_ERCC.gtf -o MingTao_NT_mRNA.txt 12C-CM_rep1_sorted.bam 12C-CM_rep2_sorted.bam 12C-EC_rep1_sorted.bam
trim_galore --paired ESO7-CM_R1.fq.gz ESO7-CM_R2.fq.gz
bismark bt2_hg38 --bowtie2 -1 ESO7-CM_R1_val_1.fq.gz -2 ESO7-CM_R2_val_2.fq.gz
MethylKit
Genome_build: hg38

source_name: iPSCs

growth_protocol: Pluripotent stem cells (iPSC, nt-ESCs, and IVF-ESCs) were maintained in chemically defined E8 medium on Matrigel-coated plates. PSC-derived cardiomyocytes (PSC-CMs) were cultured in RPMI-1640 medium plus B27 supplement on Matrigel-coated plates. PSC-derived endothelial cells (PSC-ECs) were maintained in EGM2 medium on 0.2% gelatin-coated plates.

extract_protocol:
Total RNAs were extracted by RNeasy Plus Mini kit (Qiagen, cat no. 74134) according to the manufacturer’s protocol. Genomic DNA was isolated using a DNeasy Blood and Tissue kit (Qiagen, cat no. 69506).
For RNA-seq library preparation, mRNAs were isolated from total RNAs using the Dynabeads Oligo (dT)25 in a Dynabeads mRNA DIRECT Micro Kit (Thermo Fisher Scientific, cat no. 61021). ERCC Spike-In Control Mix (Thermo Fisher Scientific, cat no. 4456740) was added to total RNA input before mRNA isolation. RNA-seq libraries were constructed using an Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific, cat no. 4479789). For RRBS-seq library construction, 300 ng of genomic DNA was digested with MspI (NEB, cat no. R0106S) at 37°C for 1 hr. Unmethylated lambda DNA (Promega, cat no. D1521) was spiked in as the quality control for sodium bisulfite conversion. The DNA fragments were then purified and selected using Agencourt AMPure XP beads (Beckman Coulter, cat no. A63880). DNA fragments were repaired to blunt ends by Klenow fragments (NEB, cat no. M0212S). DNA fragments were then ligated to the methylated Illumina adapters (NEB, cat no. E7535L) using a NEBNext Ultra Ligation Module (NEB, cat no. E7445S). The ligation product was purified using Agencourt AMPure XP beads and subsequently subjected to sodium bisulfite conversion using an EZ DNA Methylation-Gold Kit (Zymo Research, cat no. D5005). The purified bisulfite-converted DNA was amplified using the EpiMark Hot Start Taq DNA Polymerase (NEB, cat no. M0490). NEBNext Index Primers were used to barcode different samples during PCR amplification.
RNA-seq and RRBS-seq

treatment_protocol: Different reprogramming mechanisms: iPSCs, somatic cell nuclear transfer, and IVF.

value: Pluripotent stem cells

tag: passage


title: RNA-seq_WT_rep1

status: Public on Dec 06 2017

type: SRA

city: Palo Alto

first: Nian

last: Liu

state: CA

address: 265 Campus Drive, Rm. G3145

department: Chemical and Systems Biology

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
The base calling was done using bcl2fastq v2.17.1.14 (Illumina).
CasTLE analysis for the CRISPR screen was performed as previously described (Morgens et al, 2016)
bigWig files were generated with bedtools genomecov and bedGraphToBigWig
Genome_build: human (hg38)
Supplementary_files_format_and_content: txt files including the name, location and function of identified genes, as well as their effect size and CasTLE scores; wig files for ChIP-Seq and RNA-seq

molecule: total RNA

organism: Homo sapiens

growth_protocol: K562 cells were grown in Roswell Park Memorial Institute (RPMI) 1640 Medium supplemented with 10% Fetal Bovine Serum and 1% penicillin- streptomycin and cultured at 37 ºC with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Total RNA was isolated from K562 cells using the RNAeasy kit (Qiagen # 74104) and treated with RNase-Free DNase Set (Qiagen # 79254) to remove genomic DNA, according to the manufacturer’s instructions.
ChIP DNA, input DNA or cDNA were subject to end repair, A-tailing, adaptor ligation and cleavage with USER enzyme, followed by size selection to 250-500 bp and amplification with NEBNext sequencing primers. Libraries were purified, quantified, multiplexed and sequenced with 1x75bp single-end reads on an Illumina NEXT-seq (Stanford Functional Genomics Facility).
library strategy: CRISPR screen, ChIP-seq and RNA-seq

tag: cell line

tag: cell type

value: Chronic myelogenous leukemia

tag: genotype/variation

value: wild type


title: i12J-EC_RRBS-seq

library_source: genomic

molecule: genomic DNA

source_name: iPSC-ECs

value: Endothelial cells


title: Brain single cell 73

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: processed data column: Brain.EC3_D16

data_processing:
RNA-seq reads were mapped to the mouse reference genome (mm10) using STAR (version STAR_2.4.2a) and the count matrix shows the individual counts aligning to each gene per cell. In order to compare the gene expression counts between different cells, the total gene counts for each cell was normalized to 500,000.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized counts values for each sample

organism: Mus musculus

source_name: Brain

extract_protocol:
We used four different transgenic mouse reporter lines with fluorescent expression in different populations of vascular cells, Cldn5(BAC)eGFP mice that strongly labels brain endothelial cells, mice doubly positive for Pdgfrb(BAC)eGFP and NG2dsRed, in which brain vascular mural cells express both markers whereas each single marker are expressed also in other, non-overlapping cell types, and Pdgfra-H2BGFP that we found labeled a perivascular population of cells distinct from mural cells and astrocytes, in addition to the known labeling of cells of the oligendendrocyte lineage.   We chose to focus our efforts to adult mice 12 to 15 weeks old in order to primarily define fully differentiated and quiescent vascular cells and we chose a methodology based on fluorescence-activated cell sorting (FACS) into 384-well plates
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

tag: strain

tag: tissue

value: brain

tag: age

value: adult mice 12 to 15 weeks old

tag: genotype


title: RNAseq_day12_SSEA1+_cKIT+_rep2

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

description:
polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt
14-13101

data_processing:
CASAVA v1.8.2
For methylC-seq, adapters were trimmed with BBduk with the options mink=3, qtrim=r, trimq=10 minlength=20, before alignment to mm10 with Bowtie and BSseeker2 with the option -n 1. PCR duplicates were removed using Sambamba v.0.5.9 before methylation quantification with BSseeker2. For ATAC-seq, Paired-end ATAC-seq reads were adapter trimmed using the BBduk algorithm, with the option mink=3 and aligned to UCSC mm10 using bowtie227 with the option -X 2000. PCR duplicates were removed using Sambamba v.0.6.3. To call ATAC-seq peaks, we first merged time point replicate BAM files and removed reads aligning to blacklisted genomic regions before calling peaks with MACS2 using the options callpeak --nomodel --keep-dup all --gsize mm. We then created a union peak set by merging all peaks within 100 bp at each time point and removed any peaks with a pileup count in the upper 0.001% quantile being removed as these were typically located in highly repetitive regions. Peak sets from all time points were then merged to generate a consensus union peak set. For ChIP-seq, single-end reads were adapter trimmed using the BBduk algorithm with the options mink=3 qtrim=r minlength=20 and aligned to UCSC mm10 using bowtie2 with the options -m 1 -v 1 -q -S. To call ChIP-seq peaks, reads aligning to blacklisted genomic regions were removed before calling peaks with MACS2 using the options callpeak --call-summits --bdg --gsize mm -q 0.01. For RNA-seq, reads were adapter trimmed using the BBduk algorithm with the options ktrim=r, mink=3, qtrim=rl, minlength=20, forcetrimleft=1. Trimmed reads were aligned to UCSC mm10 reference genome with HISAT2 with the option --rna-strandness FR and with known splice sites from mm10 UCSC gene models. Gene level expression quantification was performed by first counting reads overlapping genes using the summarizeOverlaps function in GenomicRanges with the options mode = "IntersectionNotEmpty", ignore.strand = FALSE, singleEnd=FALSE, fragments=TRUE. Read counts were gene-length normalized by calculating gene level transcripts per million (TPM).
Genome_build: UCSC mm10
Supplementary_files_format_and_content: all_chip_peak_calls.xlsx file contains all ChIP-seq peak calls, with one tab for each time point and antibody. atac_all_peaks_union.bed file contains the union of all ATAC-seq peaks. polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt file contains gene expression data for each sample expressed as TPM. Bigwig files for Bisulfite-Seq data contain CG methylation levels on a 0-1 scale.

growth_protocol: Reprogrammable mouse embryonic fibroblasts (MEF) were extracted from day 13.5 embryos (rtTA3-OKSM-Oct4GFP) and reprogrammed into induced pluripotent stem cells (iPSC). MEF, day3, day6, day9 and day12 reprogramming cultures and iPSC were further processed for analysis.

extract_protocol:
RNA was extracted from approximately 500,000 FACS isolated cells using an RNeasy Micro Kit (Qiagen, Cat. No. 74004) according to the manufacturer’s instructions.
Illumina TruSeq Stranded Total RNA protocol with Ribo-zero.

value: het-het-het

value: day12 MEF reprogramming intermediates


title: ATACseq_day12_SSEA1+_cKIT+_rep1

description:
atac_all_peaks_union.bed
atac_d12_combined_replicates_peaks.xls
RL111

extract_protocol:
DNA was tagnemted with Illumina Tagment DNA Buffer (Cat. No. 15027866) and 2.5 µl of Tagment DNA Enzyme 1 (Cat. No. 15027865).
Transposed DNA libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, Cat. No. A63880).


title: Brain single cell 72

description: processed data column: Brain.EC3_D15


title: 1000nM_JQ1_GM15850_Rep3

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

data_processing:
Base-calling and demultiplexing were performed using Casava (v1.8.2).
Sequences were filtered and trimmed to remove low quality reads, adapters, and other sequencing artifacts.
The remaining reads were aligned to 19084 Refseq genes extracted from the Illumina iGenomes reference, selecting only those with ‘NM_’ annotations. The reference also included 13 mitochondrial mRNAs taken from ENSEMBL build GRCh37.75.
Bowtie (v0.12.9) was used for alignment, allowing two mismatches in a 28 bp seed. Reads with more than 200 alignments were excluded from further analysis.
RSEM (v1.2.3) was used to estimate isoform and relative gene expression levels (expected counts or “EC”).
EBseq was used to determine differential expression.
Genome_build: GRCh37.75
Supplementary_files_format_and_content: ec.tab.txt files containing expected counts for mitochondrial and nuclear protein coding transcripts

source_name: GM15850 LCLs (FRDA)

growth_protocol: RPMI 1640 Medium with 2 mM L-glutamine and 15% FBS

extract_protocol:
After treatment, cells were harvested and total RNA was purified with the RNeasy Mini Kit (Qiagen, Valencia, California), and DNA was removed by on-column DNase I treatment (ZYMO Research) or Ambion TURBO DNA-free Kit, according to manufacturer’s directions.
Final indexed cDNA libraries were pooled with 36 uniquely indexed LM-Seq cDNA libraries per lane and sequenced on an Illumina HiSeq 2500 with a single 64 base pair (bp) read and a 10 bp index read.

treatment_protocol: GM15850 cells were treated with the indicated molecules for 24 h

value: GM15850 LCLs (FRDA)

tag: treatment

tag: treatment time


title: ChIP:Input(H3K9me2or3)_Cell:MPP8-KO_rep2

value: MPP8 KO


title: RNAseq_day9_SSEA1+_cKIT+_rep2

description:
polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt
14-13100

value: day9 MEF reprogramming intermediates


title: i12J-CM_RRBS-seq

source_name: iPSC-CMs

value: Cadiomyocytes

value: Day 30


title: ChIP:Input(H3K9me2or3)_Cell:MPP8-KO_rep1


title: Brain single cell 71

description: processed data column: Brain.EC3_D14


title: i12C-iPSC_RRBS-seq


title: Brain single cell 70

description: processed data column: Brain.EC3_D13


title: RNAseq_day3_SSEA1+_rep2

description:
polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt
14-13098

value: day3 MEF reprogramming intermediates


title: ChIP:Input(H3K9me2or3)_Cell:WT_rep1


title: Brain single cell 69

description: processed data column: Brain.EC3_D12


title: i12C-EC_RRBS-seq


title: ChIP:Input(H3K9me2or3)_Cell:WT_rep2


title: RNAseq_MEF_rep2

description:
polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt
14-13097

value: MEF


title: i12C-CM_RRBS-seq


title: ChIP:H3K9me3_Cell:MPP8-KO_rep2

tag: chip antibody

value: H3K9me3 (ab8898, Abcam)


title: RNA-seq_WT_rep2


title: Brain single cell 68

description: processed data column: Brain.EC3_D11


title: NT2-NT_RRBS-seq

source_name: nt-ESCs


title: NT2-EC_RRBS-seq

source_name: nt-ESC-ECs


title: ChIP:H3K9me3_Cell:MPP8-KO_rep1


title: Brain single cell 66

description: processed data column: Brain.EC3_C9


title: RNAseq_Oct4_IPSC_GFP+_rep1

description:
polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt
14‐13096

value: MEF derived induced pluripotent stem cells


title: NT2-CM_RRBS-seq

source_name: nt-ESC-CMs


title: ChIP:H3K9me3_Cell:WT_rep4


title: ChIP:H3K9me3_Cell:WT_rep3

value: H3K9me2 (ab1220, Abcam)


title: Brain single cell 67

description: processed data column: Brain.EC3_D10


title: RNAseq_day9_SSEA1+_cKIT+_rep1

description:
polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt
14-13093


title: Brain single cell 65

description: processed data column: Brain.EC3_C8


title: RNAseq_day6_SSEA1+_rep2

description:
polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt
14‐13099

value: day6 MEF reprogramming intermediates


title: Brain single cell 64

description: processed data column: Brain.EC3_C7


title: RNAseq_day6_SSEA1+_rep1

description:
polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt
14‐13092


title: NT1-EC_RRBS-seq


title: ChIP:H3K9me2_Cell:MPP8-KO_rep2

value: Chronic myelogenous leukemia


title: NT1-CM_RRBS-seq


title: RNAseq_day3_SSEA1+_rep1

description:
polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt
14-13091


title: NT1-NT_RRBS-seq

value: Pluripotent stem cells


title: Brain single cell 63

description: processed data column: Brain.EC3_C6

value: brain


title: ChIP:H3K9me2_Cell:WT_rep2


title: ChIP:H3K9me2_Cell:MPP8-KO_rep1


title: ESO8-ESC_RRBS-seq

source_name: IVF-ESCs


title: RNAseq_MEF_rep1

description:
polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt
14-13090


title: ChIP:H3K9me2_Cell:WT_rep1


title: ChIPseq_Sox2_IPSC_GFP+_rep2

description:
all_chip_peak_calls.xlsx
RL265

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared using the ThruPLEX DNA-seq 12S kit (Rubicon Genomics, R400429). After PCR amplification, libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, Cat. No. A63880).

value: Abcam Cat#ab59776


title: RNAseq_day12_SSEA1+_cKIT+_rep1

description:
polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt
14‐13094

value: het-het-het


title: Brain single cell 61

description: processed data column: Brain.EC3_C4

value: adult mice 12 to 15 weeks old


title: ChIPseq_Sox2_day12_SSEA1+_cKit+_rep2

description:
all_chip_peak_calls.xlsx
RL264

value: day12 MEF reprogramming intermediates


title: ChIP:Input(H3K9me3)_Cell:TASOR-KO_rep2


title: ESO8-EC_RRBS-seq

source_name: IVF-ESC-ECs

value: Endothelial cells


title: ESO8-CM_RRBS-seq

source_name: IVF-ESC-CMs


title: Brain single cell 60

description: processed data column: Brain.EC3_C3


title: ChIPseq_Sox2_day9_SSEA1+_cKit+_rep2

description:
all_chip_peak_calls.xlsx
RL263

value: day9 MEF reprogramming intermediates


title: ChIP:Input(H3K9me3)_Cell:TASOR-KO_rep1


title: ESO7-ESC_RRBS-seq


title: ChIPseq_Sox2_day6_SSEA1+_rep2

description:
all_chip_peak_calls.xlsx
RL262


title: ChIPseq_Sox2_day6_Thy1+_rep2

description:
all_chip_peak_calls.xlsx
RL261

value: day6 cells refractory to MEF reprogramming


title: ChIP:Input(H3K9me3)_Cell:MORC2-KO_rep2


title: Brain single cell 58

description: processed data column: Brain.EC3_C23


title: ESO7-EC_RRBS-seq


title: Brain single cell 62

description: processed data column: Brain.EC3_C5


title: ChIP:Input(H3K9me3)_Cell:MORC2-KO_rep1


title: ChIPseq_Sox2_day3_SSEA1+_rep2

description:
all_chip_peak_calls.xlsx
RL260


title: Brain single cell 57

description: processed data column: Brain.EC3_C22


title: ESO7-CM_RRBS-seq

value: Cadiomyocytes

value: Day 30


title: Brain single cell 56

description: processed data column: Brain.EC3_C21


title: ChIP:Input(H3K9me3)_Cell:WT_rep1


title: ChIPseq_Sox2_day3_Thy1+_rep2

description:
all_chip_peak_calls.xlsx
RL259

value: day3 cells refractory to MEF reprogramming


title: ChIP:Input(H3K9me3)_Cell:WT_rep2


title: Brain single cell 55

description: processed data column: Brain.EC3_C20


title: ChIPseq_Sox2_MEF_rep2

description:
all_chip_peak_calls.xlsx
RL258

value: day3 MEF reprogramming intermediates


title: ChIP:H3K9me3_Cell:TASOR-KO_rep2

value: H3K9me3 (ab8898, Abcam)


title: Brain single cell 54

description: processed data column: Brain.EC3_C19


title: Brain single cell 59

description: processed data column: Brain.EC3_C2


title: ChIPseq_Oct4_IPSC_GFP+_rep2

description:
all_chip_peak_calls.xlsx
RL257

value: MEF derived induced pluripotent stem cells

value: Santa Cruz Biotechnology Cat#sc-9081, Santa Cruz Biotechnology Cat#sc-8628, Abcam Cat#ab19857


title: Diabetic_EP300_siRNA_R3

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

institute: Baker Heart and Diabetes Institute

data_processing:
Fastq files were aligned to the hg19 human genome (ensembl GRCh37 release 75) using STAR
The tool featureCounts was used to generate a matrix of read counts per gene
edgeR software was then used to determine differential gene expression
Genome_build: hg19
Supplementary_files_format_and_content: Matrix (text file) of raw reads for each gene (ensembl GRCh37 release 75) for all samples

source_name: Diabetic endothelial cells_EP300_siRNA

growth_protocol: Human aortic endothelial cells (HAEC) from diabetic (CC-2919) and non-diabetic (CC-2535) individuals were maintained in endothelial cell basal growth media-2 (EBM-2, Lonza) with additional EBM-2 growth factors and supplements and with 10% heat-inactivated fetal bovine serum (Gibco). HAECs used in this study were between 5-9 passages.

extract_protocol:
Total RNA was extracted in TRIzol (Invitrogen) and purified using the Direct-zolTM RNA MiniPrep kit (cat. no: R2052, Zymo Research) according to the manufacturers instructions. RNA was quantified on the MultiNA bioanalyzer (Shimadzu).
NEBNext® Poly(A) mRNA Magnetic Isolation Module was used to enrich mRNA from 1 μg of total RNA. The NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® was used to generate barcodes. Libraries were quantified on the MultiNA bioanalyzer (Shimadzu) and pooled to equimolar ratios for sequencing. Cluster generation was performed at a concentration of 12 pM (TruSeq SR Cluster Kit v4-cBot-HS) and the flow cell was run on Illumina HiSeq2500 generating 50 nt reads.

treatment_protocol: Cells were stimulated with DMSO, SAHA (2 μM) or C646 (10 μM) for 12 hours. EP300 knock-down was generated using ON-TARGETplus Human EP300 (2033) siRNA – SMARTpool (L-003486-00-0005, Dharmacon). Cells were cultured in Opti-MEM® (Life Technologies) media with Lipofectamine® RNAiMAX Reagent (13778-075, Life Technologies) with either non-target (ON-TARGETplus Non-targeting Pool, D-001810-10-05, Dharmacon) or 25 nM EP300 siRNA for four hours. Media was replaced with EBM-2 and RNA was harvested after 48 hours.

value: Human aortic endothelial cell

tag: disease state

value: diabetic

tag: passages


title: Diabetic_EP300_siRNA_R1


title: Diabetic_NT_siRNA_R3

source_name: Diabetic endothelial cells_NT_siRNA


title: Brain single cell 53

description: processed data column: Brain.EC3_C18

value: brain


title: Diabetic_EP300_siRNA_R2


title: ChIPseq_Oct4_day12_SSEA1+_cKit+_rep2

description:
all_chip_peak_calls.xlsx
RL256


title: ChIP:H3K9me3_Cell:MORC2-KO_rep2

value: Chronic myelogenous leukemia

value: MORC2 KO


title: ChIP:H3K9me3_Cell:TASOR-KO_rep1


title: Brain single cell 52

description: processed data column: Brain.EC3_C17

value: adult mice 12 to 15 weeks old


title: ChIP:H3K9me3_Cell:MORC2-KO_rep1


title: ChIPseq_Oct4_day9_SSEA1+_cKit+_rep2

description:
all_chip_peak_calls.xlsx
RL255

value: het-het-het


title: ChIPseq_Oct4_day6_SSEA1+_rep2

description:
all_chip_peak_calls.xlsx
RL254

value: day6 MEF reprogramming intermediates


title: ChIP:H3K9me3_Cell:WT_rep2

value: wild type


title: Diabetic_NT_siRNA_R1


title: Diabetic_C646_R3

source_name: Diabetic endothelial cells_C646


title: ChIPseq_Oct4_day6_Thy1+_rep2

description:
all_chip_peak_calls.xlsx
RL253

value: day6 cells refractory to MEF reprogramming


title: Diabetic_C646_R2


title: Brain single cell 49

description: processed data column: Brain.EC3_C13


title: Brain single cell 48

description: processed data column: Brain.EC3_C12


title: Diabetic_C646_R1


title: ChIPseq_Oct4_day3_Thy1+_rep2

description:
all_chip_peak_calls.xlsx
RL251


title: ChIP:Input(MORC2, MPP8, TASOR)_Cell:TASOR-KO_rep1

value: TASOR KO


title: ChIPseq_Oct4_day3_SSEA1+_rep2

description:
all_chip_peak_calls.xlsx
RL252


title: ChIPseq_Oct4_MEF_rep2

description:
all_chip_peak_calls.xlsx
RL250


title: Brain single cell 46

description: processed data column: Brain.EC3_C10


title: ChIP:Input(MORC2, MPP8, TASOR)_Cell:MPP8-KO_rep2

value: MPP8 KO


title: Brain single cell 51

description: processed data column: Brain.EC3_C16


title: Brain single cell 47

description: processed data column: Brain.EC3_C11


title: Diabetic_SAHA_R2

source_name: Diabetic endothelial cells_SAHA


title: ChIPseq_Input__IPSC_GFP+_rep2

description:
all_chip_peak_calls.xlsx
RL249

value: day12 MEF reprogramming intermediates

value: Input


title: Brain single cell 45

description: processed data column: Brain.EC3_B9


title: ChIPseq_Input_day12_SSEA1+_cKit+_rep2

description:
all_chip_peak_calls.xlsx
RL248


title: Diabetic_SAHA_R3


title: Brain single cell 50

description: processed data column: Brain.EC3_C14


title: ChIP:Input(MORC2, MPP8, TASOR)_Cell:MORC2-KO_rep2


title: Diabetic_SAHA_R1


title: Brain single cell 44

description: processed data column: Brain.EC3_B8


title: ChIP:Input(MORC2, MPP8, TASOR)_Cell:MORC2-KO_rep1


title: ChIPseq_Input_day9_SSEA1+_cKit+_rep2

description:
all_chip_peak_calls.xlsx
RL247

value: day9 MEF reprogramming intermediates


title: ChIP:H3K9me3_Cell:WT_rep1

value: H3K9me3 (ab8898, Abcam)


title: Diabetic_DMSO_R3

source_name: Diabetic endothelial cells_DMSO


title: Diabetic_DMSO_R2


title: ChIP:Input(MORC2, MPP8, TASOR)_Cell:TASOR-KO_rep2


title: ChIPseq_Input_day6_SSEA1+_rep2

description:
all_chip_peak_calls.xlsx
RL246


title: Brain single cell 42

description: processed data column: Brain.EC3_B6


title: ChIP:Input(MORC2, MPP8, TASOR)_Cell:WT_rep2

source_name: ChIP:Input(MORC2, MPP8, TASOR)_Cell:WT


title: ChIP:Input(MORC2, MPP8, TASOR)_Cell:WT_rep1


title: ChIPseq_Input_day6_Thy1+_rep2

description:
all_chip_peak_calls.xlsx
RL245


title: Brain single cell 41

description: processed data column: Brain.EC3_B4


title: Diabetic_DMSO_R1


title: ChIP:TASOR_Cell:TASOR-KO_rep2

value: TASOR (HPA006735, Atlas Antibodies)


title: Healthy_EP300_siRNA_R3

source_name: Healthy endothelial cells_EP300_siRNA

value: Human aortic endothelial cell

value: healthy


title: Healthy_EP300_siRNA_R2


title: ChIPseq_Input_day3_Thy1+_rep2

description:
all_chip_peak_calls.xlsx
RL243

value: day3 cells refractory to MEF reprogramming


title: ChIP:TASOR_Cell:TASOR-KO_rep1

value: Chronic myelogenous leukemia


title: Brain single cell 39

description: processed data column: Brain.EC3_B2

value: brain


title: Brain single cell 40

description: processed data column: Brain.EC3_B3

value: adult mice 12 to 15 weeks old


title: ChIPseq_Input_day3_SSEA1+_rep2

description:
all_chip_peak_calls.xlsx
RL244

value: het-het-het

value: day3 MEF reprogramming intermediates


title: ChIPseq_Input_MEF_rep2

description:
all_chip_peak_calls.xlsx
RL242


title: Brain single cell 43

description: processed data column: Brain.EC3_B7


title: Brain single cell 38

description: processed data column: Brain.EC3_B24


title: ChIP:TASOR_Cell:MPP8-KO_rep2


title: ChIP:TASOR_Cell:MPP8-KO_rep1


title: Healthy_NT_siRNA_R3

source_name: Healthy endothelial cells_NT_siRNA


title: Healthy_EP300_siRNA_R1


title: ChIPseq_Sox2_day6_Thy1+_rep1

description:
all_chip_peak_calls.xlsx
RL182

value: Abcam Cat#ab59776


title: Brain single cell 37

description: processed data column: Brain.EC3_B23

source_name: Brain


title: ChIP:TASOR_Cell:MORC2-KO_rep2

value: MORC2 KO


title: Brain single cell 36

description: processed data column: Brain.EC3_B22


title: ChIPseq_Input_day6_Thy1+_rep1

description:
all_chip_peak_calls.xlsx
RL180

value: day6 cells refractory to MEF reprogramming


title: ChIP:TASOR_Cell:MORC2-KO_rep1


title: Healthy_NT_siRNA_R1


title: ChIPseq_Oct4_day6_Thy1+_rep1

description:
all_chip_peak_calls.xlsx
RL181

value: Santa Cruz Biotechnology Cat#sc-9081, Santa Cruz Biotechnology Cat#sc-8628, Abcam Cat#ab19857


title: Brain single cell 35

description: processed data column: Brain.EC3_B21


title: Brain single cell 34

description: processed data column: Brain.EC3_B20


title: Healthy_C646_R3

source_name: Healthy endothelial cells_C646


title: ChIPseq_Oct4_day3_Thy1+_rep1

description:
all_chip_peak_calls.xlsx
RL178


title: ChIPseq_Sox2_day3_Thy1+_rep1

description:
all_chip_peak_calls.xlsx
RL179


title: Healthy_C646_R2


title: ChIP:TASOR_Cell:WT_rep1

value: wild type


title: Healthy_C646_R1


title: ChIPseq_Sox2_IPSC_GFP+_rep1

description:
all_chip_peak_calls.xlsx
RL150

value: MEF derived induced pluripotent stem cells


title: ChIPseq_Sox2_day12_SSEA1+_cKIT+_rep1

description:
all_chip_peak_calls.xlsx
RL149

value: day12 MEF reprogramming intermediates


title: Brain single cell 33

description: processed data column: Brain.EC3_B1


title: ChIP:MPP8_Cell:TASOR-KO_rep2

value: TASOR KO

value: MPP8 (16796-1-AP, Protein Technologies Inc)


title: Healthy_NT_siRNA_R2

value: Human aortic endothelial cell


title: Healthy_SAHA_R3

source_name: Healthy endothelial cells_SAHA

value: healthy


title: Healthy_SAHA_R2


title: MethylCseq_MEF

extract_protocol:
DNA methylation analysis was performed using approximately 1 x 10^6 FACS isolated cells. Genomic DNA was isolated with the Qiagen Blood and Tissue Kit according to manufacturer's instructions. 0.5% (w/w) of unmethylated lambda phage DNA (Promega) was added to the sample genomic DNA for the purpose of an unmethylated control to measure the bisulfite non-conversion frequency in each sample.
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, and subjected to 4 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).

value: MEF


title: ChIP:MPP8_Cell:TASOR-KO_rep1

value: Chronic myelogenous leukemia


title: Brain single cell 31

description: processed data column: Brain.EC3_B18

value: brain


title: ChIP:MPP8_Cell:MPP8-KO_rep2

value: MPP8 KO


title: Brain single cell 30

description: processed data column: Brain.EC3_B17

value: adult mice 12 to 15 weeks old


title: ChIP:MPP8_Cell:MPP8-KO_rep1


title: Brain single cell 29

description: processed data column: Brain.EC3_B16


title: Healthy_SAHA_R1


title: ChIP:TASOR_Cell:WT_rep2

value: TASOR (HPA006735, Atlas Antibodies)


title: Healthy_DMSO_R3

source_name: Healthy endothelial cells_DMSO


title: ChIPseq_Sox2_day6_SSEA1+_rep1

description:
all_chip_peak_calls.xlsx
RL147

value: het-het-het

value: day6 MEF reprogramming intermediates

value: Abcam Cat#ab59776


title: Brain single cell 32

description: processed data column: Brain.EC3_B19


title: Healthy_DMSO_R2


title: ChIPseq_Input_day3_Thy1+_rep1

description:
all_chip_peak_calls.xlsx
RL177

value: day3 cells refractory to MEF reprogramming

value: Input


title: Brain single cell 28

description: processed data column: Brain.EC3_B15


title: ChIP:MPP8_Cell:MORC2-KO_rep1

value: MORC2 KO


title: Brain single cell 27

description: processed data column: Brain.EC3_B14


title: ChIP:Input(MORC2, MPP8, TASOR)_Cell:MPP8-KO_rep1


title: ChIPseq_Sox2_MEF_rep1

description:
all_chip_peak_calls.xlsx
RL145


title: ChIP:MPP8_Cell:WT_rep2

value: wild type


title: Brain single cell 26

description: processed data column: Brain.EC3_B13


title: ChIP:MPP8_Cell:WT_rep1


title: Healthy_DMSO_R1


title: Prep1down cells 1 day rep2

city: Milan

first: Marco

middle: J.

last: Morelli

address: via Adamello 16

department: Center for Genomic Science of IIT@SEMM

country: Italy

institute: Istituto Italiano di Tecnologia

data_processing:
Artifacts eliminated with FASTX-Toolkit v.0.0.13.2
Reads were aligned to the mm9 reference using  Tophat v2.0.9
GenomicFeatures, GenomicRanges and GenomicAligments R libraries were used to count the number of reads with respect to the annotation reference (UCSC, genome='mm9', tablename='refGene’).
Differentially expressed genes between different conditions were retrieved using DESEQ R library
Genome_build: mm9
Supplementary_files_format_and_content: read count table

organism: Mus

source_name: Prep1down cells 1 day

growth_protocol: 3T3-L1 control and Prep1 down-regulated cells were grown in a complete DMEM medium using BCS serum. The cells were splitted every 2 days

extract_protocol:
Total RNA was extracted usinf trizol and then purified using RNAesy kit
RNA libraries were prepared for sequencing using standard Ion-Torrent protocols

treatment_protocol: For adipogenic differentiation of 3T3-L1 cells, two days after confluence the medium was changed to differentiation medium I containing 1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxanthine, and 1 μg/ml insulinin DMEM containing 10% of FBS. Two days after the induction of differentiation the medium was changed do differentiation medium II containing only 1 μg/ml insulin in the presence of 10% of FBS. After 4 days of differentiation the medium was changed to differentiation medium III containing only 10% of FBS.

value: mouse preadipocyte cells

tag: processed data column


title: Brain single cell 25

description: processed data column: Brain.EC3_B12


title: ChIPseq_Sox2_day9_SSEA1+_cKIT+_rep1

description:
all_chip_peak_calls.xlsx
RL148

value: day9 MEF reprogramming intermediates


title: ChIPseq_Oct4_day12_SSEA1+_cKIT+_rep1

description:
all_chip_peak_calls.xlsx
RL143

value: day12 MEF reprogramming intermediates

value: Santa Cruz Biotechnology Cat#sc-9081, Santa Cruz Biotechnology Cat#sc-8628, Abcam Cat#ab19857


title: Prep1down cells 1 day rep1


title: Brain single cell 24

description: processed data column: Brain.EC3_B11


title: ChIPseq_Oct4_day9_SSEA1+_cKIT+_rep1

description:
all_chip_peak_calls.xlsx
RL142


title: Control cells 1 day rep2

source_name: Control cells 1 day


title: ChIP:MPP8_Cell:MORC2-KO_rep2

value: MPP8 (16796-1-AP, Protein Technologies Inc)


title: ChIPseq_Sox2_day3_SSEA1+_rep1

description:
all_chip_peak_calls.xlsx
RL146

value: day3 MEF reprogramming intermediates


title: Control cells 1 day rep1


title: Prep1down cells -2 day rep2

source_name: Prep1down cells -2 day


title: Brain single cell 22

description: processed data column: Brain.EC3_A9

value: brain


title: ChIPseq_Oct4_day3_SSEA1+_rep1

description:
all_chip_peak_calls.xlsx
RL140


title: ChIPseq_Oct4_day6_SSEA1+_rep1

description:
all_chip_peak_calls.xlsx
RL141


title: ChIP:MORC2_Cell:TASOR-KO_rep1

value: Chronic myelogenous leukemia

value: TASOR KO

value: MORC2 (A300-149A, Bethyl Laboratories)


title: ChIP:MORC2_Cell:MPP8-KO_rep2

value: MPP8 KO


title: Prep1down cells -2 day rep1


title: ChIPseq_Oct4_IPSC_GFP+_rep1

description:
all_chip_peak_calls.xlsx
RL144

value: het-het-het

value: MEF derived induced pluripotent stem cells


title: Diabetic_NT_siRNA_R2

value: Human aortic endothelial cell

value: diabetic


title: Brain single cell 20

description: processed data column: Brain.EC3_A7

value: adult mice 12 to 15 weeks old


title: ChIP:MORC2_Cell:MORC2-KO_rep1

value: MORC2 KO


title: ChIPseq_Input_IPSC_GFP1+_rep1

description:
all_chip_peak_calls.xlsx
RL138

value: Input


title: Control cells -2 days rep2

source_name: Control cells -2 days

value: mouse preadipocyte cells


title: ChIP:MORC2_Cell:MPP8-KO_rep1


title: Brain single cell 21

description: processed data column: Brain.EC3_A8


title: ChIPseq_Input_day12_SSEA1+_cKIT+_rep1

description:
all_chip_peak_calls.xlsx
RL137

value: day12 MEF reprogramming intermediates


title: Control cells -2 days rep1


title: Brain single cell 19

description: processed data column: Brain.EC3_A6


title: ChIP:MORC2_Cell:WT_rep2

value: wild type


title: ChIP:MORC2_Cell:TASOR-KO_rep2


title: ChIP:MORC2_Cell:MORC2-KO_rep2


title: ChIPseq_Oct4_MEF_rep1

description:
all_chip_peak_calls.xlsx
RL139

value: MEF

value: Santa Cruz Biotechnology Cat#sc-9081, Santa Cruz Biotechnology Cat#sc-8628, Abcam Cat#ab19857


title: Brain single cell 18

description: processed data column: Brain.EC3_A4

value: brain


title: Prep1down cells 4hours input

description:
processed data file:
Prep1down_4h.narrowPeaks

data_processing:
Artifacts were eliminated with FASTX-Toolkit v.0.0.13.2
Reads were aligned to the mm9 genome using Bowtie v.0.12.8
Duplicate reads were removed using Samtool rmdup v 0.1.18
Mapped reads were down-sampled 8mln using Samtools  v 1.3.1
Enriched domains were identified using MACS version 2.0.10.20131028 with default parameters and p-value threshold (10e-5)
Genome_build: mm9
Supplementary_files_format_and_content: bed files

source_name: Prep1down cells 4hours

extract_protocol:
Cells were lysed and nuclei sonicated. The chromatin-Cebpß complexes were obtained using Cebpß Ab.
Libraries were prepared according to Ion_torrent's instructions


title: ChIP:MORC2_Cell:WT_rep1

value: Chronic myelogenous leukemia


title: Brain single cell 17

description: processed data column: Brain.EC3_A3


title: Control cells 4hours input

description:
processed data file:
Control_4h.narrowPeak

source_name: Control cells 4hours


title: ChIPseq_Input_day6_SSEA1+_rep1

description:
all_chip_peak_calls.xlsx
RL135

value: day6 MEF reprogramming intermediates


title: Batch-screen_G418_rep2

description:
processed data file:
Batch_screen_result


title: Brain single cell 23

description: processed data column: Brain.EC3_B10


title: Brain single cell 16

description: processed data column: Brain.EC3_A2


title: Prep1down cells -2days input

description:
processed data file:
Prep1down_-2d.narrowPeaks

source_name: Prep1down cells -2days


title: ChIPseq_Input_day3_SSEA1+_rep1

description:
all_chip_peak_calls.xlsx
RL134

value: day3 MEF reprogramming intermediates


title: Batch-screen_G418_rep1


title: Brain single cell 15

description: processed data column: Brain.EC3_A24


title: Control cells -2days input

description:
processed data file:
Control_-2d.narrowPeak

source_name: Control cells -2days


title: ChIPseq_Input_MEF_rep1

description:
all_chip_peak_calls.xlsx
RL133


title: Batch-screen_untreated_rep2


title: Brain single cell 14

description: processed data column: Brain.EC3_A23


title: Y41F-2

city: Singapore

first: Ee Sin

last: Chen

address: 8 Medical Drive, MD7 level 5

department: Biochemistry

country: Singapore

institute: National University of Singapore

data_processing:
Illumina GA Pipeline v1.5 used for base calling
Sequenced reads were filtered to remove reads with adaptors, reads with more than 10% unknown bases, low quality reads
Clean reads were mapped to genome reference using BWA (Li H and Durbin R, 2009) and to gene reference using Bowtie (Langmead B et al., 2009)
Gene expression level are quantified by a software package RSEM (RNASeq by Expectation Maximization). FRKM method is used in calculating expression level.
Genome_build: ASM294v2.25
Supplementary_files_format_and_content: xls files contains: gene ID number; transcript list of gene; length of gene; support reads number to this gene after model regulation; FPKM value of this gene

organism: Schizosaccharomyces pombe

source_name: Log phase cell culture

growth_protocol: Cells were grown in YEA media at 30°C to log phase.

extract_protocol:
Cell pellets harvested from mid-log phase cultures were homogenised using glass beads (0.5 mm; BioSpec, Bartlesville, OK) and Fastprep homogenizer (MP Biomedicals, Switzerland). RNA samples were extracted using TRIzol (Thermo Scientific, Waltham, MA) and purified by phenol:chloroform:isoamyl alcohol (25:24:1) (PCI) (Nacalai Tesque, Kyoto, Japan) extraction thrice. Total RNA (50 μg) was treated with DNase I (Thermo Scientific) in the manufacturer-supplied buffer following the manufacturer’s protocol.
RNA-seq and primary data analyses were supplied by BGI (Shenzhen, China) using an Illumina HiSeqTM 2000 platform (Illumina, San Diego, CA).


title: Batch-screen_untreated_rep1


title: Brain single cell 13

description: processed data column: Brain.EC3_A22


title: Prep1down cells 4hours ChIP

value: Cebpß Santa-Cruz C19 (sc-150)


title: Genome-wide-screen_G418_rep2

description:
processed data file:
Genome_wide_screen_result


title: Y41F-1


title: Control cells 4hours ChIP


title: ChIPseq_Input_day9_SSEA1+_cKIT+_rep1

description:
all_chip_peak_calls.xlsx
RL136

value: het-het-het

value: day9 MEF reprogramming intermediates


title: Prep1down cells -2days ChIP


title: Genome-wide-screen_G418_rep1


title: Brain single cell 11

description: processed data column: Brain.EC3_A20


title: Control cells -2days ChIP


title: Brain single cell 12

description: processed data column: Brain.EC3_A21


title: WT-1


title: Genome-wide-screen_untreated_rep2


title: Genome-wide-screen_untreated_rep1


title: Brain single cell 9

description: processed data column: Brain.EC3_A19


title: f30_Adult_SPF_F_rep3

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

institute: Singapore Immunology Network

data_processing:
Alignment of reads using to the mouse genome version mm10 with Bowtie v1.1.1
Duplicate reads were flagged with Picard v1.134
Peak calling using MACS2 v2.1.0.20140616 using default parameters
Consensus peak regions across all 30 samples were generated with the ‘reduce’ function of the Bioconductor GenomicRanges v1.28.4 package and read counting per sample was performed using the ‘summarizeOverlaps’ function of the Bioconductor GenomicAlignments v1.12.2 package
Blacklisted genomic regions for mm10 defined by ENCODE as well as regions that were inconsistently present across samples of the same analysis group were excluded from the analysis.
Regions were annotated using the HOMER v4.9.1 command annotatePeaks.pl
Genome_build: mm10
Supplementary_files_format_and_content: Count table of all unified peak counts before cpm filtering

source_name: FACS-purified microglia from brains of GF and SPF adults (P60)

extract_protocol:
Sorted cells were resuspended in Lysis buffer (10mM Tris-HCl pH 7.4, 10mM MgCl2, 0.1% IGEPAL CA-630) and underwent Transposase reaction with Tn5
For library amplification, two sequential 9-cycle PCR were performed in order to enrich small tagmented DNA fragments. 2μl of indexing primers included in the Nextera Index kit and KAPA HiFi  HotStart ready mix were used, then after the first PCR, the libraries were selected for small fragments (less than 600 bp) using SPRI cleanup. A second PCR was performed with the same conditions in order to obtain the final library. DNA concentration was  measured with a Qubit fluorometer (Life Technologies) and library sizes were determined using TapeStation (Agilent Technologies). Libraries where sequenced on a NextSeq for an average of 10 million unique reads per sample.

tag: developmental stage

value: Adult

tag: Sex

value: Female

tag: conditions

value: SPF

value: whole brain


title: Brain single cell 10

description: processed data column: Brain.EC3_A1

value: adult mice 12 to 15 weeks old


title: RD peel at 30 DAFB

city: Changsha

first: Lu

last: Xiaopeng

address: 1 Nongda Rad.

country: China

institute: Hunan Agricultural University

data_processing:
Data were filtered using SOAPnuke
Mapping were using Bowtie / BWA
Gene/Transcript expression were using RSEM
Differrentially expressed gene screening were using Possion Distribution method
Genome_build: http://citrus.hzau.edu.cn/orange/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Citrus unshiu

source_name: citrus fruit peel

growth_protocol: regular growth and managment in the orchard

extract_protocol:
Total RNA was isolated using TRIzol reagent according to the manufacturer’s instructions, and the mRNA was enriched using magnetic oligo (dT) beads and used for RNA-Sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: roughing disorder was induced by defruiting with normal growth as a control

tag: development stage

value: 30 days after full bloom

value: fruit peel


title: f29_Adult_SPF_F_rep2


title: Brain single cell 7

description: processed data column: Brain.EC3_A17


title: RD peel at 80 DAFB

value: 80 days after full bloom


title: RD peel at 170 DAFB

value: 170 days after full bloom


title: f28_Adult_SPF_F_rep1


title: f27_Adult_SPF_M_rep3

value: Male


title: Brain single cell 5

description: processed data column: Brain.EC3_A14

value: brain


title: Brain single cell 6

description: processed data column: Brain.EC3_A15


title: WT-2


title: CK peel at 30 DAFB


title: Brain single cell 4

description: processed data column: Brain.EC3_A13


title: f25_Adult_SPF_M_rep1


title: lasR rhlR stat-phase replicate 3

city: Seattle

first: Kyle

middle: Lowe

last: Asfahl

state: Washington

address: 1705 NE Pacific St

department: Microbiology

institute: University of Washington

data_processing:
Illumina bcl2fastq2 Conversion Software v2.18 for fastq file generation
BWA-MEM alignment
tRNA/rRNA filtering using bowtie
Duplicate filtering using samtools
Count matrix generation using idxstats
Genome_build: PAO1_107 (NC_002516.2)
Supplementary_files_format_and_content: Raw count data with genes as rows and samples as columns

organism: Pseudomonas aeruginosa

source_name: Bacterial cells

growth_protocol: All cells were grown in 4 ml M9-casamino acids in a 18 mm diameter standard glass testtube incubated at 37C with 250 rpm shaking from a starting OD600 of 0.01.

extract_protocol:
mRNA was preserved immediately upon cell harvest using Qiagen RNAprotect. Cells were lysed using sonication and mRNA was extracted using Qiagen RNEasy miniprep columns, followed by DNAse I treatment and cleanup using another round of RNEasy-based purification. rRNA was removed using Illumina RiboZero protocol.
100bp PE Illumina TruSeq using Wafergen Apollo protocol
Sequencing performed on Illumina HiSeq 3000, 30 samples in 1 lane

value: PAO lasR rhlR

tag: growth phase

value: early stationary phase

tag: media

value: M9-casamino acids


title: lasR rhlR stat-phase replicate 2


title: Brain single cell 2

description: processed data column: Brain.EC3_A11


title: f24_Adult_GF_F_rep3

value: GF


title: Brain single cell 3

description: processed data column: Brain.EC3_A12


title: f23_Adult_GF_F_rep2


title: Brain single cell 1

description: processed data column: Brain.EC3_A10


title: f22_Adult_GF_F_rep1


title: f21_Adult_GF_M_rep3


title: qteE qslA stat-phase replicate 1

value: PAO qteE qslA


title: CK peel at 170 DAFB


title: Brain single cell 8

description: processed data column: Brain.EC3_A18


title: qslA stat-phase replicate 3

value: PAO qslA


title: f19_Adult_GF_M_rep1

value: Adult


title: f18_E18.5_SPF_F_rep3

source_name: FACS-purified microglia from brains of embryos of GF and SPF dams (E18.5)

value: Female


title: qslA stat-phase replicate 1


title: f17_E18.5_SPF_F_rep2

value: SPF


title: qteE stat-phase replicate 3

value: PAO qteE


title: qteE stat-phase replicate 2


title: f16_E18.5_SPF_F_rep1

value: whole brain


title: qteE qslA stat-phase replicate 3


title: lasR rhlR stat-phase replicate 1


title: NAA RNA-seq repeat3

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

data_processing:
The paired-end reads were aligned to the moso bamboo genome using tophat-2.0.11 with anchor length more than 8nt for spliced alignments (Kim et al. 2013).
Genome_build: P.heterocycla-v1.0; http://202.127.18.221/bamboo/down.php
Supplementary_files_format_and_content: bigwig files were generated using wig2bw program

organism: Phyllostachys edulis

source_name: One-month-old seedlings_NAA treated

growth_protocol: For materials used for RNA-Seq analysis, seeds were sterilized with chlorine gas for 3-5 hours, and then were put on MS agar for germination and growth vertically over a 1-month period.

extract_protocol:
Total RNA from bamboo root was extracted using the RNeasy Mini Kit (QIAGEN, China) according to the manufacturer’s instructions.
In total, there were 6 strand-specific RNA-Seq libraries that were sequenced in this study using dUTP method (Parkhomchuk et al. 2009).

treatment_protocol: One-month-old seedlings were sprayed with 5μM NAA for 4 hours with 1-hour interval, and the root part were dissected for RNA extraction.

value: One-month-old seedlings

tag: treated with

value: 5μM NAA for 4 hrs with 1-hr interval


title: Mock RNA-seq repeat1

source_name: One-month-old seedlings_mock treated

value: mock control


title: NAA RNA-seq repeat1


title: NAA RNA-seq repeat2


title: Mock RNA-seq repeat3


title: Mock RNA-seq repeat2


title: qteE stat-phase replicate 1

tag: strain


title: f15_E18.5_SPF_M_rep3

tag: tissue


title: qteE qslA stat-phase replicate 2


title: f14_E18.5_SPF_M_rep2


title: wild-type stat-phase replicate 1

value: PAO1 wild-type


title: IC.C

city: Jouy-en-Josas

first: Tatiana

last: Rochat

address: Domaine de Vilvert

country: France

institute: INRA

description: replicate C

data_processing:
Trimming of adapter sequences with cutadapt-1.9.1.
PRINSEQ (Schmieder and Edwards 2011) for read quality with filtering (-min_len 20 -min_qual_mean 20 -min_qual_score 10) and trimming (trim_qual_right 10) options.
Mapping performed on Refseq NC_015844.1 by Bowtie2 software with the --very-sensitive option (Langmead and Salzberg 2012).
The number of reads mapping to each predicted CDS was calculated by HTSeq-count (Anders, Pyl et al. 2015) with the -m union option.
Differential expression analysis (normalisation and statistical tests) was performed using the SARTools with DESeq2 software (Varet, Brillet-Gueguen et al. 2016) and a bonferroni p-value adjustment was used to correct for multiple testing. Genes with an adjusted p-value < 0.05 were considered as differentially expressed.
Genome_build: NC_015844.1
Supplementary_files_format_and_content: Full results of DEseq2 analysis for all annotated CDS (expression values before and after normalization, statistical analysis results). Column legends : Id=Accession number retrieved from MicroScope platform ; start=Coordinates according to NC_015844.1 genome sequence ; end=Coordinates according to NC_015844.1 genome sequence ; strand=(+) for positive, (-) for negative strand ; gene=Gene name, if available, according to the MicroScope platform ; product=Description of gene product according to the MicroScope platform ; eC_number=eC_number, if available, according to the MicroScope platform ; KCvsGal log2FoldChange=Log2-fold change of Z. galactanivorans grown on KC relative to D-gal as unique carbon source. Boldface type indicates significant changes (FWER 5%) and if red-colored a log2-change of at least 3.32 (= 10-fold change in linear scale). Padj=Bonferroni adjusted p-values ; ICvsGal log2FoldChange=Log2-fold change of Z. galactanivorans grown on IC relative to D-gal as unique carbon source. Boldface type indicates significant changes (FWER 5%) and if red-colored a log2-change of at least 3.32 (= 10-fold change in linear scale). Padj=Bonferroni adjusted p-values ; ADGvsGal log2FoldChange=Log2-fold change of Z. galactanivorans grown on D-AnG relative to D-gal as unique carbon source. Boldface type indicates significant changes (FWER 5%) and if red-colored a log2-change of at least 3.32 (= 10-fold change in linear scale), padj=Bonferroni adjusted p-values ; Gal=Means of normalized counts for 'D-gal' biological condition ; ADG=Means of normalized counts for 'D-AnG' biological condition ; IC=Means of normalized counts for 'IC' biological condition ; KC=Means of normalized counts for 'KC' biological condition ; Function=Functional categories, if available, according to the MicroScope platform ; condition.replicat=Raw counts for 'condition.replicat' sample ('condition' and 'replicat' take the possible values 'D-gal', 'KC', 'IC' or 'D-AnG' and 'A', 'B' or 'C', resp.) ; norm.condition.replicat=Rounded normalized counts for 'condition.replicat' sample ; baseMean=Base mean over all samples ; FoldChange=Fold change of expression, calculated as 2log2(FC) ; log2FoldChange=Log2(FC) as estimated by the GLM model. It reflects the differential expression between Test ('KC', 'IC' or 'D-AnG') and Ref ('D-gal') and can be interpreted as log2(Test/Ref). If this value is around 0 : the feature expression is similar in both conditions; positive: the feature is up-regulated; negative: the feature is down-regulated ; pvalue=Raw p-value from the statistical test ; dispGeneEst=dispersion parameter estimated from feature counts ; dispFit=dispersion parameter estimated from the model ; dispMAP=dispersion parameter estimated from the Maximum A Posteriori model ; dispersion=final dispersion parameter used to perform the test ; betaConv=convergence of the coefficients of the model (TRUE or FALSE) ; maxCooks=maximum Cook's distance of the feature.

organism: Zobellia galactanivorans

source_name: Bacteria

growth_protocol: Cells were cultivated in synthetic Marine Mineral Medium supplemented with different carbon sources: D-galactose (Sigma-Aldrich #G0750), iota-carrageenan (Danisco, 2544-88-20), kappa-carrageenan (Coffoni x6913) or D-AnG (Dextra Laboratories #G0002) used at 0.4 g/L.

extract_protocol:
Cells pellets were resuspended into Lysis buffer (4 M guanidine thiocyanate, 25 mM sodium acetate pH 5.2, 5 g/L N-laurylsarcosinate), mixed to hot acid phenol and incubated during 5 min at 65°C for efficient cell lysis. Total RNAs were recovered, after at least four times of acid phenol:chloroform:IAA (25:24:1, [pH 4.5]) extractions and once with chloroform, by ethanol precipitation. Total RNA extracts were treated using DNase I (Qiagen) to remove residual genomic DNA. mRNA enrichment was performed using the Illumina Ribo-Zero rRNA Removal Kit (Bacteria).
Strand-specific RNA-seq libraries were generated with the ScriptSeq V2 RNA-Seq Library Preparation Kit (Illumina), according to the manufacturer's instructions. The sequencing was performed with a NextSeq 500 platform using a single-end 75 bases run.

treatment_protocol: When cell density reached an OD600 of 0.7, bacteria were harvested by centrifugation for 3 min at 4 °C after addition of ½ volume of frozen killing buffer (20 mM Tris/HCl pH 7.5, 5 mM MgCl2, 20 mM NaN3) to the culture sample. Cell pellets were frozen in liquid nitrogen and stored at -80 °C until RNA extraction.

value: DsijT

tag: c-source

value: Iota-carrageenan


title: f11_E18.5_GF_F_rep2


title: f20_Adult_GF_M_rep2

value: Male


title: D-AnG.C

description: replicate C


title: qslA stat-phase replicate 2

value: early stationary phase


title: KC.C

description: replicate C

value: Kappa-carrageenan


title: f10_E18.5_GF_F_rep1

value: GF


title: D-gal.C

description: reference condition, replicate C

value: Galactose


title: lasR rhlR log-phase replicate 2

value: PAO lasR rhlR

value: logarithmic phase

value: M9-casamino acids


title: IC.B

description: replicate B


title: f13_E18.5_SPF_M_rep1

value: SPF


title: wild-type stat-phase replicate 2


title: f08_E18.5_GF_F_rep2

value: Female


title: KC.B

description: replicate B


title: f09_E18.5_GF_M_rep3

value: whole brain


title: D-AnG.B

description: replicate B


title: lasR rhlR log-phase replicate 3


title: qteE qslA log-phase replicate 3

value: PAO qteE qslA


title: qteE qslA log-phase replicate 2


title: D-gal.B

description: reference condition, replicate B


title: f06_E14.5_SPF_UD_rep3

source_name: FACS-purified microglia from brains of embryos of GF and SPF dams (E14.5)

value: not determined


title: f26_Adult_SPF_M_rep2

value: Adult


title: wild-type stat-phase replicate 3

value: PAO1 wild-type


title: lasR rhlR log-phase replicate 1


title: f12_E18.5_GF_M_rep3


title: f07_E18.5_GF_M_rep1


title: D-AnG.A

description: replicate A

value: DsijT


title: CK peel at 80 DAFB

value: 80 days after full bloom

value: fruit peel


title: qteE qslA log-phase replicate 1


title: IC.A

description: replicate A

value: Iota-carrageenan


title: f05_E14.5_SPF_UD_rep2


title: qslA log-phase replicate 3

value: PAO qslA


title: f04_E14.5_SPF_UD_rep1


title: qslA log-phase replicate 1


title: D-gal.A

description: reference condition, replicate A


title: qslA log-phase replicate 2


title: KC.A

description: replicate A

value: Kappa-carrageenan


title: f02_E14.5_GF_UD_rep2

value: GF


title: qteE log-phase replicate 3

value: PAO qteE


title: YED3

city: Barcelona

first: Dietmar

last: Fernandez Orth

state: Barcelona

address: C/Doctor Aiguader 88 Primera Planta, 08003, Isglobal CREAL

country: Spain

institute: IsGlobal

data_processing:
Fastq files were quality checked with FASTQC
Reads were mapped onto the reference genome using EDGEpro with default parameters
Resulting count datasets were exported to the DESeq2 for normalization, and pair-wise differential expression was carried out for each gene
Genome_build: SL1344 NC_016810.1
Supplementary_files_format_and_content: tab-delimited text file includes read counts for each Sample.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: bacterial strain

extract_protocol:
RNA of the strains studied was obtained from exponential cultures using the Maxwell® 16 Research Instrument (Promega) and the Maxwell® 16 LEV simplyRNA Blood Kit according to the manufacturer’s recommendations. Then, ribosomal RNA was depleted with the Ribo-Zero TM Magnetic Kit for Gram-negative bacteria (Epicentre).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: mutant for the gene yedF


title: f01_E14.5_GF_UD_rep1


title: qteE log-phase replicate 2

value: logarithmic phase

value: M9-casamino acids


title: YED2


title: Potato_D114-T01_good

city: Fuzhou

first: Haifeng

last: Wang

state: Fujian

address: Shangxia dian

data_processing:
For BS-seq, reads were aligned to potato reference genome (Stuberosum_448_V4.03) by using Bsmap 2.9. Only unique mapping reads were used to estimate methylation ratio. Methylation ratios were calculated as the number of Cs divided by Cs plus Ts (#C/(#C+#T)).
For mRNA-seq, total reads were aligned to the potato reference genome (Stuberosum_448_v4.03) by using Tophat 2.1.0 using default paramters, then quantified by using CufflinksV2.2.1. Expression values were expressed in FPKM.
Supplementary_files_format_and_content: For mRNA-seq, the format is "tracking id, FPKM" of merged three replicates. For Bsseq, the format is cytosine location and corresponding methylation levels as data process step.

organism: Solanum tuberosum

source_name: tuber

extract_protocol:
Total RNA was extracted from tuber tissue of potato following the cetyltrimethylammonium bromide (CTAB) protocol (Doyl and Doyl 1990). Genomic DNA was removed by TURBO DNA-free™ Kit (Ambion) and RNA quality and quantity was assessed, respectively, by Agilent 2100 BioAnalyzer (Agilent Technologies Inc. Santa Clara, CA) and NanoDrop2000c (Thermo Scientific). One microgram of total RNA per sample was utilized for library preparation using the Illumina TruSeq sample preparation kit (v2) with polyA mRNA selection as per manufacturer’s instructions (Illumina, San Diego, CA). three libraries were pooled and sequenced using an Illumina HiSeq2500 with paired end reads of 150 bp at Biomarker technologies company.
BS-seq libraries were prepared using the TruSeq DNA LT kit (Illumina), except that EZ DNA Methylation-Lightning Kit (Qiagen) was used for bisulfite conversion of the DNA. BS-Seq libraries were sequenced on a HiSeq 2500 system (Illumina) to obtain paired-end 150bp reads per manufacture instructions.

value: seed tubers

tag: cultivar

value: pacific


title: qteE log-phase replicate 1


title: Potato_D114-T02_good


title: Potato_D114-T03_good


title: SL3

value: wild type


title: wild-type log-phase replicate 3


title: Potato_D113-J03_good


title: ChIP:Input_Cell_mESC:WT_rep2

data_processing:
The base calling was done using bcl2fastq v2.17.1.14 (Illumina).
CasTLE analysis for the CRISPR screen was performed as previously described (Morgens et al, 2016)
Genome_build: human (hg38)
Supplementary_files_format_and_content: txt files including the name, location and function of identified genes, as well as their effect size and CasTLE scores

growth_protocol: K562 cells (ATCC) were grown in Roswell Park Memorial Institute (RPMI) 1640 Medium (11875093, Life Technologies) supplemented with 10% Fetal Bovine Serum (Fisher, Cat# SH30910), 2 mM L-glutamine (Fisher, Cat# SH3003401) and 1% penicillin-streptomycin (Fisher, Cat#SV30010), and cultured at 37 C with 5% CO2. HeLa cells (ATCC) were grown in Dulbecco’s Modified Eagle’s Medium (Life Technologies, Cat# 11995073) supplemented with 10% FBS (Fisher, Cat# SH30910), 2 mM L-glutamine (Fisher, Cat# SH3003401), and 1% penicillin-streptomycin (Fisher, Cat# SV30010), and cultured at 37 C with 5% CO2. Human ES cells (H9 line) were expanded in feeder-free, serum-free medium mTeSR-1 from StemCell technologies. Cells were passaged 1:6 every 5–6 days by incubation with accutase (Invitrogen) and the resulting small cell clusters (50–200 cells) were subsequently re-plated on tissue culture dishes coated overnight with growth-factor-reduced matrigel (BD Biosciences). Cell cultures were routinely tested and found negative for mycoplasma infection (MycoAlert, Lonza).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Total RNA was isolated from K562 cells using the RNAeasy kit (Qiagen # 74104) and treated with RNase-Free DNase Set (Qiagen # 79254) to remove genomic DNA, according to the manufacturer’s instructions.
ChIP DNA, input DNA or cDNA were subject to end repair, A-tailing, adaptor ligation and cleavage with USER enzyme, followed by size selection to 250-500 bp and amplification with NEBNext sequencing primers. Libraries were purified, quantified, multiplexed and sequenced with 1x75bp single-end reads on an Illumina NEXT-seq (Stanford Functional Genomics Facility).

tag: cell line

value: mESC

tag: cell type

value: Mouse embryonic stem cell lines

tag: genotype/variation


title: ChIP:Input_Cell_mESC:WT_rep1


title: wild-type log-phase replicate 2

value: PAO1 wild-type


title: Potato_D113-J02_good


title: SL1


title: wild-type log-phase replicate 1


title: ChIP:MPP8_Cell_mESC:WT_rep1

tag: chip antibody

value: MPP8 (16796-1-AP, Protein Technologies Inc)


title: SL2


title: Potato_D113-J01_good


title: f03_E14.5_GF_UD_rep3

value: not determined

value: whole brain


title: C380_CMP_high

status: Public on Dec 05 2017

city: manchester

first: Muhammmad

middle: Zaki

last: Fadlullah Wilmot

address: Wilmslow Road

country: United Kingdom

institute: Cancer Research UK Manchester Institute

data_processing:
Basecall files generated from NextSeq sequencing run were converted to FASTQ format with Illumina bcl2fast converter (v2.17.1.14). Each lane-wise fastq files of the same sample was merged into one fastq file.  Read trimming was performed with trimmomatic (v0.36) with the following settings “CROP:75 HEADCROP:5 SLIDINGWINDOW:20:20 MINLEN:36”. Mouse reference genome GRCm38 (Ensembl release 87) and ERCC reference sequence (downloaded from Thremo Fisher) was combined and used as the reference genome for alignment.  Alignment was performed by STAR (version 2.4.2a) to the reference genome (GRCm38 + ERCC). The expression levels of 49,585 features annotated in the GENCODE mouse genome (GRCm38, version M12 [Ensembl 87]) and 92 ERCC features were determined using the htseq program (version 0.6.1p1).  The following parameters was specified for the htseq quantification `--format=bam --stranded=no --type=exon --idattr=gene_id`.
Genome_build: GRCm38
Supplementary_files_format_and_content: abundance measurements in count table; Ensembl gene annotation; cell annotation

extract_protocol:
E14.5 Runx1 P1-GFP::P2-hCD4/+ fetal livers (from two litters) were isolated, pooled and manually disaggregated in DMEM supplemented with 10% Fetal Bovine Serum. They were then stained with fluorescently conjugated antibodies in preparation for FACS sorting.  Single P2-hCD4-/+ MEPs and CMPs were sorted into 384-well plates containing lysis buffer and snap frozen.
cDNA was prepared using a Mantis platform (Formulatrix) and quantified with quantIT picogreen reagent (Thermo Fisher). Dual indexed sequencing libraries were prepared from 0.1ng cDNA using an Echo525 automation system (Labcyte) in miniaturized reaction volumes.  The library pool was quantified by qPCR using a Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems).

tag: strain background

value: C57BL/6 crossed with ICR

value: Runx1 P2-GFP::P2-hCD4/+

value: Fetal Liver

value: 14.5 days post fertilization

value: E14.5 Fetal Liver Hematopoietic Progenitor Cell

tag: cell subtype

value: Common Myeloid Progenitors (CMPs)

tag: sorted single cell


title: C381_CMP_high

tag: developmental stage


title: C382_CMP_high


title: C378_CMP_high


title: C376_CMP_high


title: C379_CMP_high


title: C377_CMP_high


title: C375_CMP_high


title: C374_CMP_high


title: YED1

value: mutant for the gene yedF


title: ChIP:MPP8_Cell_mESC:WT_rep2


title: C371_CMP_high


title: C373_CMP_high


title: C369_CMP_high


title: C368_CMP_high


title: C367_CMP_high


title: C366_CMP_high


title: C370_CMP_high


title: C372_CMP_high


title: C363_CMP_high


title: C364_CMP_high


title: C365_CMP_high


title: C361_CMP_high


title: C359_CMP_high


title: C358_CMP_high


title: C360_CMP_high


title: C357_CMP_high


title: C356_CMP_high


title: C353_CMP_high


title: C355_CMP_high


title: C352_CMP_high


title: C350_CMP_high


title: C351_CMP_high


title: C345_CMP_high


title: C349_CMP_high


title: C344_CMP_high


title: C343_CMP_high


title: C348_CMP_high


title: C362_CMP_high


title: C339_CMP_low


title: C341_CMP_high


title: C338_CMP_low


title: C342_CMP_high


title: C346_CMP_high


title: C332_CMP_low


title: C336_CMP_low


title: C335_CMP_low


title: C337_CMP_low


title: C340_CMP_high


title: C334_CMP_low


title: C333_CMP_low


title: C330_CMP_low


title: C328_CMP_low


title: C329_CMP_low


title: C331_CMP_low


title: C354_CMP_high


title: C326_CMP_low


title: C347_CMP_high


title: C325_CMP_low


title: C324_CMP_low


title: C327_CMP_low


title: C323_CMP_low


title: C320_CMP_low


title: C321_CMP_low


title: C322_CMP_low


title: C319_CMP_low


title: C317_CMP_low


title: C316_CMP_low


title: C315_CMP_low


title: C313_CMP_low

value: Megakaryocyte Erythroid Progenitors (MEPs)


title: C314_CMP_low


title: C309_MEP_pos


title: C308_MEP_pos


title: C310_MEP_pos


title: C312_MEP_pos


title: C311_MEP_pos


title: C304_MEP_pos


title: C306_MEP_pos


title: C307_MEP_pos


title: C305_MEP_pos


title: C302_MEP_pos


title: C301_MEP_pos


title: C303_MEP_pos


title: C318_CMP_low


title: C296_MEP_pos


title: C300_MEP_pos


title: C298_MEP_pos


title: C294_MEP_pos


title: C299_MEP_pos


title: C295_MEP_pos


title: C297_MEP_pos


title: C293_MEP_pos


title: C290_MEP_pos


title: C292_MEP_pos


title: C291_MEP_pos


title: C287_MEP_pos


title: C288_MEP_pos


title: C289_MEP_pos


title: C285_MEP_pos


title: C284_MEP_pos


title: C282_MEP_pos


title: C283_MEP_pos


title: C280_MEP_pos


title: C281_MEP_pos


title: C279_MEP_pos


title: C278_MEP_pos


title: C276_MEP_pos


title: C274_MEP_pos


title: C277_MEP_pos


title: C275_MEP_pos


title: C273_MEP_pos


title: C270_MEP_pos


title: C269_MEP_pos


title: C272_MEP_pos


title: C266_MEP_pos


title: C265_MEP_pos


title: C271_MEP_pos


title: C286_MEP_pos


title: C261_MEP_neg


title: C259_MEP_neg


title: C263_MEP_neg


title: C262_MEP_neg


title: C260_MEP_neg


title: C258_MEP_neg


title: C255_MEP_neg


title: C256_MEP_neg


title: C257_MEP_neg


title: C253_MEP_neg


title: C251_MEP_neg


title: C247_MEP_neg


title: C252_MEP_neg


title: C245_MEP_neg


title: C249_MEP_neg


title: C268_MEP_pos


title: C264_MEP_neg


title: C267_MEP_pos


title: C238_MEP_neg


title: C243_MEP_neg


title: C244_MEP_neg


title: C239_MEP_neg


title: C241_MEP_neg


title: C242_MEP_neg


title: C236_MEP_neg


title: C237_MEP_neg


title: C234_MEP_neg


title: C233_MEP_neg


title: C235_MEP_neg


title: C232_MEP_neg


title: C231_MEP_neg


title: C250_MEP_neg


title: C248_MEP_neg


title: C246_MEP_neg


title: C229_MEP_neg


title: C228_MEP_neg


title: C254_MEP_neg


title: C227_MEP_neg


title: C225_MEP_neg


title: C224_MEP_neg


title: C221_MEP_neg


title: C220_MEP_neg


title: C223_MEP_neg


title: C222_MEP_neg


title: C240_MEP_neg


title: C219_MEP_neg


title: C218_MEP_neg


title: C230_MEP_neg


title: C215_MEP_neg


title: C214_MEP_neg


title: C209_MEP_neg


title: C216_MEP_neg


title: C212_MEP_neg


title: C208_MEP_neg


title: C217_MEP_neg


title: STEM-seq E7.5PS rep3

city: Beijing

first: Wei

last: Xie

address: Zhongguancun north street

institute: Tsinghua University

description: Processed data file: stage.mCG.gz in STEM-seq-methylC_mCG.tar.

data_processing:
Base calls were performed using CASAVA version 1.8. Early embryo STEM-seq reads were aligned to the mm9 genome using BSseeker2.0.8. Replicates of same stage were pooled together and methylation values in wiggle files were computed for each single base. ES cell STEM-seq and MethylC-seq reads were aligned to the mm9 genome using BSseeker2.0.8. Replicates of same stage were pooled together and methylation values in wiggle files were computed by the number of reads falling into 1,000bp bin in the genome.
 Genome_build: mm9.
Supplementary_files_format_and_content: The bedgraph files counted the number of reads falling on each base or 1,000bp bin in the genome.

source_name: postimplantation embryo

extract_protocol: Embryos were washed with PBS and incubated in lysis buffer. STEM-seq libraries were constructed following the protocol described in this study (Zhang et al., Nature Genetics, 2017).

treatment_protocol: C57BL/6N female mice were induced for superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin and 5 IU of human chorionic gonadotrophin (44-48 hours apart) and mated to DBA/2N males.

value: C57BL/6N x DBA/2N

value: Primitive streak


title: ATAC-seq distal femur E15.5

city: Cambridge

first: Terence

middle: D

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard Univserity

description: The original SRA runs were withdrawn on Jan 12 2018 and replaced with current runs.

data_processing:
alignment to mm10:Bowtie2 version 2.2.8 default parameters for mm10 alignment
filter for duplicates:MACS2 version 2.1.1 macs2 filterdup -i file -g mm --keep-dup 1 -o outfile
peak calling:MACS2 version 2.1.1 macs2 callpeak -B -t rep1file -n name --nomodel --shift -100 --extsize 200
peak filtering
IDR https://sites.google.com/site/anshulkundaje/projects/idr
batch-consistency-script.R rep1file rep2file -1 outdir 0 F p.value
MACS2 .narrowPeak output was cut using the number of peaks below the IDR threshold, sorting by MACS2 reported p-value
Genome_build: mm10
Supplementary_files_format_and_content: ProximalFemur_IDR0.05_peaks.txt
Supplementary_files_format_and_content: bed format; contains the coordinates of the peaks called and filtered as described for the proximal femur ATAC-seq experiment
Supplementary_files_format_and_content: DistalFemur_IDR0.05_peaks.txt
Supplementary_files_format_and_content: bed format; contains the coordinates of the peaks called and filtered as described for the distal femur ATAC-seq experiment

source_name: Distal femoral growth plates E15.5

growth_protocol: in vivo collected E15.5 growth plate chondrocytes

extract_protocol:
The samples were collected in microcentrifuge tubes containing 200ul 5% FBS/DMEM. To generate a single cell chondrocyte suspension, each pooled sample was then subjected to 1% Collagenase II (VWR 80056-222) digestion for 2hrs at 37C rocking, mixing every 30 minutes. After placing on ice, samples were filtered using a micro-centrifuge filter set-up by gently mashing the residual tissues through the filter followed by rinsing with 5% FBS/DMEM. Samples were then spun down at 500g at 4C for 5 min. We next performed cell counting methods using trypan blue and a hemacytometer and performed subsequent ATAC-seq steps on those samples that had cell death rates well below 25%. On average we acquired 500,000-1,000,000 living cells per harvest. Next, cells were resuspended in concentrations of 50,000 cells in 1x PBS.  Cell samples then subjected to the ATAC-seq protocol as described in Buenrostro et al., 2015, modifying the protocol by using 2 ul of transposase per reaction. The transposase reaction product was then purified using the Omega MicroElute DNA Clean Up Kit following manufacturers protocols, eluted in 10 ul of warmed ddH20, and stored at -20C.
Samples were subjected to PCR amplification and barcoding following Buenrostro et al., 2015. 10 ul of transposed DNA was then placed in a reaction containing NEBNext High-Fidelity PCR Master Mix, ddH20, and primers. After amplification, samples were transferred to micro-centrifuge tubes and subjected to the OMEGA Bead Purification Protocol following manufacturers protocol. The samples were eluted in 30 ul of TE, run on a nanodrop, diluted to 5 ng/ul and run on a bioanalyzer. Prior to sequencing sample concentrations were determined using the KAPA Library Quantification Complete Kit (KK4824). Samples were then sent out to the Harvard University Bauer Core Facility for sequencing on one lane of the Illumina NextSeq 500

treatment_protocol: All experiments were performed following protocols approved by the Harvard University IACUC committee. Timed matings were established between FVB mice, and pregnant females were euthanized at E15.5 in order to acquire embryonic long bone growth plates. Embryos were dissected in PBS1X on ice under a dissection scope and the proximal and distal growth zones of the right and left femur were stripped clear of soft tissues. Each proximal or distal cartilaginous end was then micro-dissected from the bony diaphysis and separately pooled from a single litter, consisting on average of 8 animals. Two biological replicates were collected in line with previous ATAC-seq studies.

value: chondrocytes

value: FVBNJ

tag: reagent

value: tn5 transposase


title: C211_MEP_neg


title: ATAC-seq proximal femur E15.5

source_name: Proximal femoral growth plates E15.5


title: C210_MEP_neg


title: STEM-seq E7.5Mes rep3

value: Mesoderm


title: C226_MEP_neg


title: STEM-seq mES 500cells rep1 R1 cell line

description: STEM-seq-methylC processed data file: STEM-seq_mESC_mCG.tar.gz.

source_name: Embryonic stem cell

growth_protocol: mESCs were cultured routinely in LIF and serum medium.

value: Embryonic stem cell


title: C213_MEP_neg


title: STEM-seq mES 500cells rep2 R1 cell line


title: STEM-seq IVC+2d rep1

description: STEM-seq-methylC processed data file: GSE76505_STEM-seq_IVC_mCG.tar.

source_name: Embryo_in vitro culture

treatment_protocol: C57BL/6N female mice were induced for superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin and 5 IU of human chorionic gonadotrophin (44-48 hours apart) and mated to DBA/2N males. Embryos were flushed out from uterus at E4.5 and cultured 1, 2 or 4 days in CMRL 1066 supplemented with 1mM glutamine, 1mM sodium pyruvate and 20% fetal bovine serum.

value: C57BL/6N x DBA

value: Epiblast


title: STEM-seq IVC+2d rep2


title: STEM-seq E6.5Epi_tetDKO_rep1

description: STEM-seq-methylC processed data file: GSE76505_E6.5Epi_tetDKO_merge_mCG.txt

source_name: Embryo_Tet1/2 double knockout

treatment_protocol: Tet1+/- mice (B6;129S4-Tet1tm1.1Jae/J) and Tet2-/- mice (B6;129S-Tet2tm1.1Iaai/J ) were purchased from The Jackson Laboratory. After mating Tet1+/-/Tet2-/- heterozygotes, E6.5 epiblast from embryonic regions was collected from Tet1/2 DKO embryos as described above. Extraembryonic regions were used for genotyping.

value: Tet1/2 double knockout


title: STEM-seq E6.5Epi_tetDKO_rep3

description: STEM-seq-methylC processed data file: GSE76505_E6.5Epi_tetDKO_merge_mCG.txt.

source_name: embryo_Tet1/2 double knockout


title: STEM-seq E6.5Epi_tetDKO_rep2


title: STEM-seq IVC+1d rep1


title: SAM rep2

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

data_processing:
After removing bacodes, adapters and low-quality reads, clean reads of size 18-28 nt were mapped to the Arabidopsis genome (TAIR10 version) with Bowtie (Langmead et al., Genome Biology, 2009, 10, R25) allowing no mismatches. sRNA abundance was calculated as reads per million (RPM).
Genome_build: TAIR10
Supplementary_files_format_and_content: Genome-matched unique reads

organism: Arabidopsis thaliana

source_name: Seven-days-old seedlings

growth_protocol: Plants were grown in a standard chamber under long-day conditions (16 h of light/8 h of darkness, 22°C).

extract_protocol:
Total RNA were extracted by Trizol reagent (Invitrogen) followed by PEG precipitation to enrich low molecular-weight sRNAs. The resulting sRNAs were resolved on a 17% denaturing PAGE gel, and visualized by SYBR-Gold (Invitrogen) staining. Gel slices within the range of 18-28nt were excised, and the RNAs were eluted and purified for small RNA library contruction.
Small RNA libraries were constructed as previously described (Mi et al., Cell, 2008, 133, 116-175).

value: Wild type

tag: ecotype

value: Columbia

tag: age

value: Seven-days-old


title: Root rep2


title: Bent torpedo embryo rep2

source_name: Seven-weeks-old seedlings

value: Seven-weeks-old


title: Flower carpel 13 rep2

source_name: Five-weeks-old seedlings

value: Five-weeks-old


title: Flower_stage_13 rep2


title: Seedling rep2


title: Green leaf embryo rep2


title: Flower stage 9 rep2


title: Seed rep2

source_name: 24 hours on moist paper

value: 24 hours on moist paper


title: Flower petal 12 rep2


title: STEM-seq E4.0ICM rep3

source_name: Periimplantation embryo

value: inner cell mass


title: Stem first node rep2

source_name: Four-weeks-old seedlings

value: Four-weeks-old


title: Flower stamen 12 rep2


title: Flower stage 10_11 rep2


title: Flower carpel 12 rep2


title: Inflorescence rep2


title: Cotyledon rep2


title: Flower stage 12 rep2


title: Flower sepal 12 rep2


title: Cauline leaf rep2


title: Adult leaf 2 rep2


title: Hypocotyl rep2


title: Adult leaf 1 rep2


title: Juvenile leaf rep2


title: Silique 5d rep2

source_name: Six-weeks-old seedlings

value: Six-weeks-old


title: Silique 7d rep2


title: Silique 2d rep2


title: PIR-_KO_3

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dymanics Research

country: Japan

institute: RIKEN

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
"_A" and " _B" files are merged
Reads were aligned to the mm10 genome assebly using TopHat2
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each was counted, which provides the number of molecules detected for each gene
The copy number of RNA moelcules per cell for each gene is calculated based on spike-in RNA detection efficiency
Genome_build: mm10
Supplementary_files_format_and_content: The calculated copy number of RNA moelcules per cell for each gene is listed.  P-value is obtained using DESeq2.

source_name: E14.5 liver cell

extract_protocol:
RNAs from cell lysate obtained by heat elevation is directly used for the next RT reaction
Libraries were prepared by using molecular barcoding technique. First, for normalization, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains 100 cells. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

treatment_protocol: PIR+ or PIR- cells were isolated from fetal liver cells using FACS cell sorter

tag: markers

value: PIR- KO


title: 5'OH_ev_20m

city: Boston

first: Peter

last: Culviner

address: 677 Huntington Ave

department: IID

institute: Harvard School of Public Health

data_processing:
Library strategy: 5'OH-seq
Single-end reads were mapped using bowtie2 default settings.
A single count was added at the 5' end of all reads.
Samples were sequencing depth normalized using by calculating reads per million mapped.
A 5'-OH ratio was determined by log transforming the + MazF to empty vector ratio.
Genome_build: NCBI reference sequence: NC_000913.2
Supplementary_files_format_and_content: 5OH_counts_and_ratio.csv.gz contains single-nucleotide mapping of read 5' ends after reads per million correction for both empty vector and MazF as well as the log2 5'OH ratio (+ mazF / empty vector) calculated at each position

organism: Escherichia coli

source_name: Bacterial liquid culture

growth_protocol: Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2.

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo).
See publication for complete protocol. Briefly, 5’-P terminated RNA was degraded with terminator exonuclease (Epicentre) and then 5’-OH terminated RNA was phosphorylated with optikinase (USB). An RNA linker containing an amplification region was then ligated onto phosphorylated RNA. Reverse transcription was conducted with a primer with a randomized region as well as an amplification region. Finally, libraries were amplified and sequenced.

tag: strain

tag: plasmid

tag: time induction

value: 20 minutes


title: PIR+_KO_3

source_name: E12.5 liver cell

value: PIR+ KO


title: PIR-_KO_2


title: PIR+_KO_2


title: PIR-_KO_1


title: 5'OH_mazF_20m


title: swine milk_3

city: Hohhot

first: Zhihong

last: Liu

address: 306 Zhao Wu Da

institute: inner Mongolia agricultural university

description: Samples were placed in a refrigerator at -80C

data_processing:
the raw reads were subjected to the Illumina pipeline  lter (Solexa 0.3), and thenthe dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) toremove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
unique sequences with length in 18~26 nucleotide were mapped to speci c species precursors in miRBase20.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3.and 5. ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mappingto speci c species mature miRNAs in hairpin arms were identi ed as known miRNAs.
The unique sequences mappingto the other arm of known speci c species precursor hairpin opposite to the annotated mature miRNA-containing armwere considered to be novel 5p- or 3pderived miRNA candidates.
The remaining sequences were mapped to otherselected species precursors (with the exclusion of speci c species) in miRBase 20.0 by BLAST search, and the mappedpre-miRNAs were further BLASTed against the speci c species genomes to determine their genomic locations.
Theabove two we de ned as known miRNAs. The unmapped sequences were BLASTed against the speci c genomes,and the hairpin RNA structures containing sequences were predicated from the ank 80 nt sequences using RNAfoldsoftware (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi)
Genome_build: 84
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Sus scrofa

source_name: swine

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer.s procedure. Thetotal RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA,USA) with RIN number >7.0. Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA). And then we performed the single-endsequencing (36 bp) on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China) following the vendor.s recommended  protocol.

tag: breed

value: rongchang pig

tag: tissue

value: milk


title: PIR+_KO_1


title: PIR-_wt_1

value: PIR- wt


title: PIR+_wt_2

value: PIR+ wt


title: PIR-_wt_2


title: PIR+_wt_3


title: swine milk_2


title: PIR-_wt_3


title: PIR+_wt_1


title: swine milk_1


title: Silique 3d rep2

tag: genotype


title: MB_05_EN_rep3

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

institute: Karolinska institute

data_processing:
Illumina Casava1.7 software used for basecalling.
The clean reads (quality checked by FastQC) were aligned to the reference genome twice. At first, clean reads were mapped to B73 reference using Tophat aligner(with 4 mismatch) and the unmapped reads were remapped to SNPs-substituted reference (B73 reference substituted to MO17 reference by replacing SNPs between B73 and MO17) using the Tophat aligner (with 2 mismatches). Reads with no more than five best mapped positions were retained for further analysis. After combining above mapping results, read counts of annotated genes (filtered gene set version 5b.60) were summarized by HTSeq-count. Gene expression [Reads per kilobase of transcript per million fragments mapped] (FPKM) was estimated by Cufflinks (V2.2.1) software.
Genome_build: REL5b.60
Supplementary_files_format_and_content: Tab-delimited text file include Reads and FPKM values for 48 Samples .

organism: Zea mays

source_name: 05DAP Endosperm

growth_protocol: The two inbred lines B73 and Mo17 were grown in the China Agriculture university experiment station of Beijing, and they were used as two parental lines for reciprocal crosses. Before pollination, the ear and the tassel of B73 and Mo17 were bagged with kraft paper on the day before pollination. The next day, each paper bag was patted to collect the pollens from one parental, which were used to pollinate the ear of the other parental.

extract_protocol:
As described above, 15 kinds of embryo samples and one endosperm sample were collected for RNA-seq analysis. For each sample, hundreds(9DAP,11DAP,13DAP) or thousands(5DAP,7DAP) individual embryos were put into one tube containing RNA storing liquid buffer (Hueyueyang, China) (three replicates). The embryo and endosperm were collected from at least three ears in each replicate. RNA samples were isolated by Quick RNA isolation Kit (Huayueyang, China) and were checked on 1% agarose gels to avoid possible degradation and contamination. Then examined by a Nano Photometer spectrophotometer (IMPLEN, CA, USA) for RNA purity and sent to the Novogene for mRNA library construction and high-throughput sequencing using the Illumina HiSeq2500 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: This was followed by two kinds of treatments during the pollination:(1) the B73 inbred lines as the female treatment, before pollination, the ear of B73 and the tassel of Mo17 were bagged with kraft paper on the day before pollination. The next day, each paper bag of Mo17 was patted to collect the pollens to pollinate the ear of B73. (2) the Mo17 inbred lines as the female treatment, before pollination, the ear of Mo17 and the tassel of B73 were bagged with kraft paper on the day before pollination. The next day, each paper bag of B73 was patted to collect the pollens to pollinate the ear of Mo17.


title: MB_05_EN_rep2


title: MB_05_EN_rep1


title: WB_Liver_90d_miRNA-seq

city: Wuhan

first: Yuhua

last: Fu

state: Hubei

address: No.1, Shizishan Street, 430070, Wuhan, China

department: College of Animal Science and Technology

institute: Huazhong Agricultural University

data_processing:
All reads were counted and the identical reads were combined into a single kind. The raw reads were subjected to a series of additional strict filters (such as the digital filters of base-call quality, reads length, and sequence comparison) with acceptance criteria derived from the statistics of mammalian miRNAs in miRBase 21.0. The reads originated from porcine known classes of RNAs (i.e., mRNA; rRNA, tRNA, snRNA, and snoRNA; and repetitive sequence elements) were also filtered.In addition, to ensure higher reliability of the reported results, only the reads that were observed more than 10 times for each library were used in subsequent analyses.
To conduct differential analysis, miRNA read in each library was normalized to obtain the expression of transcripts per million (RPM).
Genome_build: Genome database:Sus scrofa (Sscrofa10.2); miRbase version: V21.0
Supplementary_files_format_and_content: Identified miRNAs in each library with reads and normalized data

source_name: Liver

growth_protocol: The liver tissues were obtained from three male pigs at Postnatal day 90.

extract_protocol:
Total RNA was extracted from the three liver samples using TRIzol (Invitrogen). RNase-free DNase I (TaKaRa) was used to remove genomic DNA from the RNA samples. The integrity of total RNA was determined by the Agilent Technologies of Bioanalyzer 2100 and RNA 6000 Nano Labchip Kit (Agilent, CA, USA) with RIN number >6.0.
According to the Illumina EAS Small RNA Sample Prep Protocol. In general, approximately 15 ug of small RNA-enriched total RNA was prepared for High-throughput sequencing. In brief, High-throughput sequencing was performed as following successive step: For each library, the small RNA ranged from 14 to 40 nt were purified by polyacrylamide gel electrophoresis (PAGE) and ligated with proprietary adaptors (Illumina). Then the modified small RNA was reverse transcribed and amplified by RT-PCR. Finally, the enriched cDNA were sequenced on the Illumina Hiseq 2500/2000 platform and 50 bp single-end reads were generated.

tag: breeds

value: Chinese wild boar

value: Postnatal 90 day

tag: Sex

value: male

value: liver


title: ES_Liver_90d_miRNA-seq

value: Enshi black pig


title: swine milk exosome_2

value: milk exosome


title: swine milk exosome_3


title: swine milk exosome_1


title: BM_05_EN_rep1


title: MB_13_EM_rep3

source_name: 13DAP Embryo


title: BM_05_EN_rep2


title: BM_05_EN_rep3


title: MB_13_EM_rep2


title: BM_13_EM_rep3


title: BM_13_EM_rep2


title: LW_Liver_90d_miRNA-seq

value: Large White pig


title: AbaSeq_rep21

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Library strategy: Aba-seq
FASTQ reads were filtered based on a quality score greater than 30 and were then aligned to the human reference genome (UCSC Hg19) using Bowtie 2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml), with the preset parameters of very-sensitive (−D 20 -R 3 -N 0 -L 20 -i S,1,0.50).
Duplicates were removed using Picard (http://broadinstitute.github.io/picard/) and realignment was performed using the GATK alignment procedures from the Broad Institute (https://www.broadinstitute.org/gatk/).
Subsequent filtering of aligned reads was based on a quality score of greater or equal to 10.
5hmC sites were identified using a custom PERL script [19] that detected potential 5hmC sites based on their expected distance from the AbaSI enzymatic cleavage site.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include read count values for each sample.

source_name: Prefrontal cortex

growth_protocol: Post-mortem human brain tissue from the prefrontal cortex was obtained from the Douglas – Bell Canada Brain Bank. The prefrontal cortex was chosen given its diverse functions relative to human cognition and of importance to neuropsychiatric phenotypes. Additionally, the prefrontal cortex has been widely implicated in a variety of mental illnesses through dysregulation of epigenetic mechanisms [50, 51, 52, 53, 54, 55, 56]. Brain tissue used in this study was dissected at 4 °C, snap-frozen in liquid nitrogen, and stored at −80 °C following standard procedures. The Quebec Coroner’s office assessed the cause of death for each subject, and subsequently, we obtained information on the subjects’ mental health using psychological autopsies using the Structured Clinical Interviews for DSM-IV Axis 1 [57]. In addition, brain tissue samples from all subjects were assessed for absence of pathological processes by a neuropathologist. Subjects died from either natural (n = 11) or accidental (n = 13) causes, and all were psychiatrically and neurologically healthy. All subjects were French-Canadian. Mean age was 43.33 ± 4.46 years. Written informed consent was obtained from next-of-kin for all subjects, and the Douglas Institute Research Ethics Board approved this study.

extract_protocol:
Genomic DNA was extracted from the prefrontal cortex using QIAGEN’s QIAamp DNA Mini Kit (QIAGEN, cat. # 51304).
DNA was glucosylated by using UDP-glucose and T4-β-glucosyltransferase (New England Biolabs, cat. #M0357L). The DNA was then digested using AbaSI (New England Biolabs, cat. #R0665S) and custom biotinylated adaptors were ligated to DNA ends. The DNA was then sheared using the Covaris S220 Focused-Ultrasonicator (peak incident power = 140; duty % = 10; cycles per burst = 200; time = 120 s). Sheared DNA was captured using Dynabeads® MyOne™ Streptavidin C1 beads (Life Technologies, cat. # 65001). NEBNext™ End Repair Module (New England Biolabs, cat. #E6050L) and NEBNext™ dA-Tailing Module (New England Biolabs, cat. #E6053L) were used to generate blunt ended fragments and create an adenosine tail, respectively. A second set of custom adaptors were ligated to the DNA, followed by PCR amplification using NEBNext™ High-Fidelity 2x PCR Master Mix (New England Biolabs, cat. #E6013AA). Illumina TruSeq indices 1 through 12 were used to barcode samples. 50 cycle, single-read sequencing was performed on Illumina’s HiSeq 2000. A minimum of 60,000,000 sequencing reads was obtained per subject.

value: Prefrontal cortex

tag: gender

value: Female

tag: refrig delay

tag: ph


title: AbaSeq_rep20

value: Male


title: AbaSeq_rep19


title: AbaSeq_rep23


title: AbaSeq_rep18


title: BM_13_EM_rep1


title: AbaSeq_rep15


title: AbaSeq_rep14


title: MB_11_EM_rep3

source_name: 11DAP Embryo


title: MB_11_EM_rep2


title: AbaSeq_rep13

tag: brain id


title: MB_11_EM_rep1


title: AbaSeq_rep11


title: AbaSeq_rep10


title: BM_11_EM_rep3


title: AbaSeq_rep24


title: AbaSeq_rep9


title: AbaSeq_rep16


title: MB_13_EM_rep1


title: AbaSeq_rep17


title: BM_11_EM_rep2


title: AbaSeq_rep4


title: AbaSeq_rep6


title: AbaSeq_rep8


title: AbaSeq_rep2


title: AbaSeq_rep22


title: AbaSeq_rep7


title: MB_09_EM_rep3

source_name: 09DAP Embryo


title: BM_11_EM_rep1


title: AbaSeq_rep1


title: AbaSeq_rep5


title: MB_09_EM_rep2


title: BM_09_EM_rep2


title: BM_09_EM_rep3


title: AbaSeq_rep12


title: MB_07_EM_rep3

source_name: 07DAP Embryo


title: MB_07_EM_rep1


title: MB_07_EM_rep2


title: MB_05_EM_rep3

source_name: 05DAP Embryo


title: BM_07_EM_rep1


title: BM_07_EM_rep3


title: BM_07_EM_rep2


title: MB_05_EM_rep2


title: MB_05_EM_rep1


title: BM_05_EM_rep3


title: MB_LCM_05_EM_rep1

source_name: LCM 05DAP Embryo


title: MB_LCM_05_EM_rep2


title: BM_LCM_05_EM_rep3


title: BM_05_EM_rep1


title: MB_LCM_05_EM_rep3


title: MB_09_EM_rep1


title: BM_LCM_05_EM_rep2


title: MB_LCM_03_EM_rep3

source_name: LCM 03DAP Embryo


title: MB_LCM_03_EM_rep2


title: BM_LCM_05_EM_rep1


title: BM_09_EM_rep1


title: ribo_footprints_mazF_25m

description:
Ribosome protected mRNA
ribosome_footprint_ends.csv.gz

data_processing:
Library strategy: Ribo-Seq
Single-end reads were mapped using bowtie2 default settings after trimming off adapter sequences.
A single count was added at the 5' end or 3' end of reads.
Samples were sequencing depth normalized using by calculating reads per million mapped.
Genome_build: NCBI reference sequence: NC_000913.2
Supplementary_files_format_and_content: ribosome_footprint_ends.csv.gz uniquely mapping 5' and 3' end footprints are recorded for each sample at all positions in the genome. Counts are sequencing-depth normalized using reads per million mapped.

growth_protocol: Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%.

extract_protocol:
Cells were harvested by filtration and were scraped into liquid nitrogen. Lysis was conducted on a mixer mill (Qiagen) and lysate was treated with MNase and separated on a sucrose gradient to yield ribosome protected mRNA fragments. RNA was harvested by phenol chloroform extraction.
See publication for details. RNA fragments were size-selected, dephosphorylated, and ligated to a linker RNA. RNA was then reverse transcribed using an oligo recognizing the ligated linker. cDNA was circularized and cDNA arising from rRNA was subtracted using custom oligos. Finally, libraries were PCR amplified and sequenced.

value: MG1655 delta_mazF

value: 25 minutes


title: BM_LCM_03_EM_rep2


title: MB_LCM_03_EM_rep1


title: AbaSeq_rep3


title: BM_LCM_03_EM_rep3


title: ribo_footprints_mazF_5m

value: 5 minutes


title: MazF_totalRNA_60m_rep2

description:
[processed data file: ]
total_RNA_rpm.csv.gz

data_processing:
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping.
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added.
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples).
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts.
Genome_build: NCBI reference sequence: NC_000913.2
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples.

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo).
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols.

tag: ribozero

value: No

tag: ercc spike-in

value: Prior to extraction

value: 60 minutes


title: BM_05_EM_rep2


title: ribo_footprints_empty_vector_15m

value: 15 minutes


title: MazF_totalRNA_5m_rep2


title: MazF_totalRNA_30m_rep1

value: 30 minutes


title: MazF_totalRNA_5m_rep1


title: MazF_totalRNA_60m_rep1


title: emptyvec_totalRNA_30m_rep1


title: emptyvec_totalRNA_5m_rep2