title: UC_Day28 RNA-seq

city: Hangzhou

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

institute: Westlake University

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Filtering was done by TrimGalore(0.6.4) with default parameters
Reads were aligned to  hg38 ensembl v101 transcriptome using rsem (v1.3.1) and bowtie2 (v2.4.1) (—bowtie2—bowtie2-sensitivity-level very_sensitive— no-bam-output—estimate-rspd).
The gene expression level was calculated by using  RSEM
The gene expression was normalized using EDAseq on a basis of GC-content. RNA-seq data was expressed in units of GC-normalized tag counts.
Genome_build: hg38

source_name: urine cell-induced cardiomyocyte

growth_protocol: Adult human dermal fibroblasts BJ were purchased from ATCC. BJ and hUCs (P0) were plated on culture dishes at a density of 104 cells/cm2 supplemented with 10% FBS of DMEM (Hyclone, high glucose).

extract_protocol: Total RNAs were extracted as described above. The VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (VAHTS, #NR603) was used for RNA library preparation. In brief, 1 μg total RNAs were hybridized with the rRNA probe (H/M/R) and digested by RNase H to remove ribosomal RNAs. After DNase I digestion, the ribosomal-depleted RNAs were fragmented at 94°C for 8min. Then the first-strand and second-strand cDNAs were synthesized successively using the provided reagents. The cDNA was purified by VAHTS DNA Clean Beads (VAHTS, #NR411), followed by end repaired, dA-tailing, adapter ligation, and second strand cDNA digestion. After two-round of purification, the cDNAs was PCR-amplified and purified by VAHTS DNA Clean Beads. High- throughput sequencing was performed using Illumina HiSeq Xten (Illumina) platform with PE150 (pair-end sequencing, 150 bp reads).

treatment_protocol: After 24 hours of replating, Cells were transduced with freshly made viral mixture containing 8 mg/ml polybrene once every 24 hours for two times. 24 hours after the second infection, media was replaced with human induced cardiomyocytes medium [DMEM (Hyclone, high glucose):M199 (GIBCO)(4:1), 10% FBS(GIBCO), 1xNEAA(GIBCO)] containing Vitamin C (50 ųg/ml; Sigma) , SB431542 (2 µM; selleck) and XAV939 (4 µM; selleck) and changed every 3 days. Human maintaining cardiomyocytes medium [RPMI1640(GIBCO), 2%B27(GIBCO), 2%FBS(GIBCO), 0.05%BSA(Sigma), 1xNEAA(GIBCO), 1x GlutaMAX(GIBCO)] containing Vitamin C (50 ųg/ml; Sigma) was used 2 weeks after retroviral infection and changed every 3 days.

value: urine cell-induced cardiomyocyte


title: DS-S3

status: Public on Jun 29 2021

type: SRA

city: Changsha

first: Zekai

last: Cui

state: Hunan

address: 18th floor, the New Century Building, #198, Furong Middle Road

country: China

institute: Aier Eye Institute

description:
DS-S3_S182
processed data file: S_count.txt

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCg6A, hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Human corneal stromal cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: CSCs in the DS model

tag: culture time

value: 7 days


title: H3K9ac WT liver rep 1

city: Baltimore

first: Michael

middle: J.

last: Wolfgang

state: MD

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

country: USA

institute: The Johns Hopkins University School of Medicine

description: WT H3K9ac ChIP in 24hr fasted liver

library_source: genomic

data_processing:
Library construction and base calling were performed according to Active Motif company protocol .
ChIP-seq single-end 75nt sequencing reads were mapped to mm10 genome using the BWA algorthim with “bwaln/samse” default settings.
Uniqely mapped reads were further processed to remove those with mapq score < 25, mitochondria reads, PCR duplicates, and reads with more than 2 mismatches.
To normalize, tag numbers of all samples (within a comparison group) were reduced by random sampling to the number of usable tags present in the smallest sample.
Peaks were identified using the MACS2 (2.1.0) algorithm with default cutoff values. Pooled input samples were used to determine ChIP enrichment over background. ENCODE blacklist regions were removed.
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 peak calling output provided as ENCODE narrowPeak format (BED 6+4)
Supplementary_files_format_and_content: bigWig files were generated using a 32nt bin with a 200bp in silico tag extension
Supplementary_files_format_and_content: Consensus peakset as well as intervals for individual samples are provided in BED format

molecule: genomic DNA

organism: Mus musculus

source_name: Liver

growth_protocol: Mice were housed in a facility with ventilated racks on a 14h light/10h dark cycle with ad libitum access to a standard rodent chow.

extract_protocol:
Genomic DNA was isolated from flash-frozen mouse liver tissue accordng to Active Motif company protocol
Library construction was performed according to Active Motif company protocol.

treatment_protocol: 24 hour fast (3pm-3pm).

tag: strain

tag: antibody

value: H3K9ac Active Motif #39917

tag: tissue

value: Liver

value: 24 hour fast

tag: genotype

value: WT


title: UC_Day21 RNA-seq

tag: cell type


title: A26.13

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

country: United Kingdom

institute: University of Sheffield

data_processing:
Read cleaning and filtering: Raw paired-end ATAC-seq reads were quality controlled using FastQC version 0.11.3. ATAC-seq adapters were removed, uncalled bases (N's) on ends of reads were trimmed using Cutadapt version 1.9.1(Martin, 2011). Only read pairs with both single end fragments remaining were kept. A second quality pass was performed using Sickle version 1.33 (https://github.com/najoshi/sickle), trimming was performed with a sliding window average Phred quality threshold of 30 (without five prime trimming). Only pairs with a minimum of 20 bases in each read were retained.
Mapping: Reads were mapped using Bowtie2 version 2.3.0 in paired-end mode  reporting up to 4 alignments per read, with maximum fragment length 2000bp.
Calling chromatin accessible peaks: Processing was performed using pipeline_atac_consensus_balanced_peaks (https://doi.org/10.15131/shef.data.12280904). Correctly mapped reads were filtered using Samtools version 1.3.1 (samtools view -F 524 -f 2 flags). Read pairs non-overlapping reads in RF orientation were removed with Samtools and Bedtools.  Multimapped reads and duplicates were removed.  Read pairs were converted into two single end tags and Tags. Soft clipped bases re-added and the TN5 added base pairs on the 5' sites of each read were trimmed.   Two consensus peak sets were created: the pan myeloma set and the subgroup set. For the pan myeloma set, the tags in each sample were down-sampled so that each sample had the same number of tags. Samples were then pooled into two categories – MM and NPC.   Broad and narrow peaks were called on each pool using MACS2 version 2.1.1.20160309 (https://github.com/taoliu/MACS)(Zhang, Liu et al. 2008) with the following options for narrow peaks:  -g hs -q 0.01 --nomodel --shift -100 --extsize 200 -B --SPMR --keep-dup all --call-summits  And for broad peaks:  -g hs -q 0.01 --nomodel --shift -100 --extsize 200 --broad --broad-cutoff 0.01 --keep-dup all  Narrow and broad peaks were filtered to remove areas of low mappability and those in ENCODE blacklist reagions,  http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDukeMapabilityRegionsExcludable.bed.gz and  https://www.encodeproject.org/files/ENCFF419RSJ/@@download/ENCFF419RSJ.bed.gz).
MM and PC consensus peak set: for the pan myeloma set, the tags in each sample were down-sampled so that each sample had the same number of tags. Samples were then pooled into two categories – MM and NPC.
MM and PC consensus peak set: for subgroup peak set, samples without a cytogenetic classification were excluded, and the remaining samples downsampled to the new minimum. Tags from samples in the same cytogenetic group (MAF, MMSET, CCND1, HD or ND PC) were pooled and peaks called on each poolSamples were then pooled into two categories – MM and NPC.
Reads in peaks quantification: shifted tags from each sample were transformed to obtain only the initial 1bp reflecting the 5' and filtered to remove tags overlapping with areas of low and high mappability defined previously. The number tags overlapping each peak in the peak set is reported using Bedtools intersect version 2.22.1(Quinlan and Hall, 2010).
Genome_build: hg38 analysis ready
Supplementary_files_format_and_content: Narrowpeak and broadpeak files from each sample. Suppplementary files contain the coordinates for consensus peak sets and the read count in them for each sample.

source_name: Primary plasma cell multiple myeloma

extract_protocol:
Patient BM aspirates were subjected to red cell lysis. Multiple myeloma plasma cells were purified by two rounds of CD138 immunomagnetic selection (MiltenyiBiotech) following the manufacturer’s instructions. Pre and post selection purity was assessed by FACs analysis (BD LSR-Fortessa) using CD138, CD45, CD19, CD56 and CD38 panel antibodies
ATAC-seq was performed as described(Buenrostro et al., 2013). Briefly, 50,000 purified plasma cells, myeloma plasma cells or cell lines, were washed with cold PBS (Sigma, UK) at 500g at 40C for 5 min. The cells were resuspended in 50 μL of cold Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and washed at 500g at 40C for 10 min. The libraries were sequenced at the Genomics Facility at ICL using the Illumina HiSeq 4000 platform to obtain paired-end 75bp reads.
The nuclei were subjected to transposase reaction for 30 min at 370C; termination of the reaction and DNA purification was performed using a MiniElute Kit (Qiagen) and eluted twice with 10 μL. The purified DNA was amplified as described before with NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs). The PCR amplified product was cleaned twice with (0.9X) AMPure beads (Beckman). The quality of the libraries was assessed with the Bioanalyzer High Sensitivity DNA kit (Agilent). The libraries were quantified using the NEBNext Library Quant Kit for Illumina (New England Biolabs) on a StepOne Plus Real-Time PCR (Applied Biosystems).

value: Bone marrow

tag: condition

value: MM

tag: cytogenetics

value: hyperdiploid

tag: primary subgroup

value: HD

tag: sequencing batch

value: C


title: Liver_NASH_20

type: RNA

city: Barcelona

first: Marta

last: Piqué

state: Barcelona

address: Rosselló, 153

country: Spain

institute: IDIBAPS

hyb_protocol: Total mRNA was prepared for hybridization using the GeneChip 3’ IVT Pico Kit assay (Thermo Fisher) following the manufacturer’s protocols. Samples were hybridized to the Human Genome U219 Array (Affymetrix) also following the manufacturer protocols.

scan_protocol: Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

data_processing: Gene expression profiles that passed the quality control were submitted to the GenePattern ExpressionFileCreator Module20 to generate the final dataset. In this last step, the background was corrected with the Robust Multi-array Average (RMA) algorithm and data were normalized using quantiles.

label: biotin

label_protocol: Double-stranded cDNAs were synthesized from total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA.

extract_protocol: 50ng of total mRNA was isolated from FFPE samples using the miRNeasy FFPE kit (Qiagen). The Qiacube system (Qiagen) was used to automatize the extraction process.  DNA FFPE kits (Qiagen).

value: NASH liver


title: A26.12

value: MAF

tag: selected surface markers


title: A26.10B

value: MMSET


title: UC_Day7 RNA-seq


title: Liver_NASH_18


title: Liver_NASH_21


title: UC_Day14 RNA-seq


title: 4F-MYOCD_Day14 RNA-seq


title: Liver_NASH_19


title: H3K27ac Ppara liver rep 2

description: Ppar⍺ knockout H3K27ac ChIP in 24hr fasted liver

value: H3K27ac Active Motif #39133

value: Ppara -/-


title: H3K27ac DKO liver rep 1

description: Cpt2 liver/Ppar⍺ whole-body double knockout H3K27ac ChIP in 24hr fasted liver

value: Cpt2 L-/- ; Ppara -/-


title: Liver_NASH_22


title: Liver_NASH_17


title: H3K9ac Cpt2 liver rep 2

description: Cpt2 liver knockout H3K9ac ChIP in 24hr fasted liver

value: Cpt2 L-/-


title: 4F-MYOCD_Day10 RNA-seq

value: urine cell-induced cardiomyocyte


title: H3K27ac Ppara liver rep1


title: A27.20

value: TP53 deletion

value: D


title: 4F-MYOCD_Day7 RNA-seq


title: H3K27ac DKO liver rep 2

value: Liver

value: 24 hour fast


title: H3K27ac Cpt2 liver rep2

description: Cpt2 liver knockout H3K27ac ChIP in 24hr fasted liver


title: Liver_NASH_15


title: Liver_NASH_16


title: 4F-MYOCD_Day3 RNA-seq


title: A26.9B

value: Bone marrow

value: hyperdiploid, TP53 del, +1q


title: H3K27ac Cpt2 liver rep1


title: Liver_NASH_14


title: Liver_NASH_12


title: A26.15B

value: MM

value: hyperdiploid (+17, +9, +15)


title: A26.8

value: C


title: 4F-MYOCD_Day0 RNA-seq


title: 4F_Day14 RNA-seq


title: A26.6B

value: hyperdiploid, subclonal +1q (30%)

value: HD


title: H3K27ac WT liver rep2

description: WT H3K27ac ChIP in 24hr fasted liver

value: WT


title: A28.13

value: MMSET

value: singleton


title: 4F_Day10 RNA-seq


title: H3K4me1 DKO liver rep 2

description: Cpt2 liver/Ppar⍺ whole-body double knockout H3K4me1 ChIP in 24hr fasted liver

value: H3K4me1 Active Motif #39297

value: Cpt2 L-/- ; Ppara -/-


title: 4F_Day7 RNA-seq

value: urine cell-induced cardiomyocyte


title: H3K27ac WT liver rep1

description: WT H3K27ac ChIP in 24hr fasted liver

value: H3K27ac Active Motif #39133


title: H3K4me1 DKO liver rep 1


title: A19.6

value: A


title: 4F_Day3 RNA-seq


title: A24.4

value: hyperdiploid, +1q

value: B


title: Liver_NASH_11

value: NASH liver


title: Liver_NASH_10


title: Liver_NASH_13


title: Liver_NASH_9


title: Liver_NASH_8


title: 4F_Day0 RNA-seq


title: H3K4me1 Ppara liver rep 2

description: Ppar⍺ knockout H3K4me1 ChIP in 24hr fasted liver

value: Liver

value: 24 hour fast

value: Ppara -/-


title: A28c.14

source_name: Plasma cell CD19 plus, donor 230218

extract_protocol:
BM-MNCs from BM aspirates were isolated by ficoll (Histopaque, Sigma). The MNCs were pre-cleared of T cells and Monocytes by consecutive immunomagnetic negative selection (CD3 and CD14-EasySep StemCell Technologies) following manufacturer’s instructions. The sample was stained and sorted for positive CD138, CD319, CD27, CD45 and CD38, and negative for CD2, CD3, CD14, CD16, GPA and 7AAD. (FACSAriaII, BD Biosciences) and CD19+or CD19-
ATAC-seq was performed as described(Buenrostro et al., 2013). Briefly, 50,000 purified plasma cells, myeloma plasma cells or cell lines, were washed with cold PBS (Sigma, UK) at 500g at 40C for 5 min. The cells were resuspended in 50 μL of cold Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and washed at 500g at 40C for 10 min. The libraries were sequenced at the Genomics Facility at ICL using the Illumina HiSeq 4000 platform to obtain paired-end 75bp reads.
The nuclei were subjected to transposase reaction for 30 min at 370C; termination of the reaction and DNA purification was performed using a MiniElute Kit (Qiagen) and eluted twice with 10 μL. The purified DNA was amplified as described before with NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs). The PCR amplified product was cleaned twice with (0.9X) AMPure beads (Beckman). The quality of the libraries was assessed with the Bioanalyzer High Sensitivity DNA kit (Agilent). The libraries were quantified using the NEBNext Library Quant Kit for Illumina (New England Biolabs) on a StepOne Plus Real-Time PCR (Applied Biosystems).

value: Bone marrow

value: PC

value: ND

tag: pc cd19 status

value: plus

tag: pc donor id


title: A19.8

value: MM

value: MMSET


title: A24.7

value: hyperdiploid with subclonal gain of 1q

value: HD


title: H3K4me1 Cpt2 liver rep2

description: Cpt2 liver knockout H3K4me1 ChIP in 24hr fasted liver

value: H3K4me1 Active Motif #39297

value: Cpt2 L-/-


title: Liver_NASH_6


title: Liver_NASH_7


title: H3K4me1 Cpt2 liver rep1


title: 5F-MYOCD_Day10 RNA-seq

source_name: fibroblast-induced cardiomyocyte

value: fibroblast-induced cardiomyocyte


title: A19.2

value: A


title: 5F-MYOCD_Day14 RNA-seq


title: A19.5

value: hyperdiploid, +9q subclonal


title: H3K4me1 WT liver rep2

description: WT H3K4me1 ChIP in 24hr fasted liver

value: WT


title: Liver_NASH_4

value: NASH liver


title: A19.1

value: hyperdiploid, +1q


title: 5F-MYOCD_Day7 RNA-seq


title: H3K4me1 Ppara liver rep1

value: Liver

value: 24 hour fast

value: Ppara -/-


title: H3K4me1 WT liver rep1

description: WT H3K4me1 ChIP in 24hr fasted liver


title: Liver_NASH_5


title: 5F-MYOCD_Day3 RNA-seq


title: A17.9

value: Bone marrow

value: hyperdiploid, TP53 deletion, IgH rearranged

value: singleton


title: UC RNA-seq

source_name: urine cell

value: urine cell


title: Liver_NASH_2


title: 5F-MYOCD_Day0 RNA-seq


title: Control_iPSC_EtOH_Bioreplicate_3

city: Bethesda

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

data_processing:
RTA 1.13.48 and CASAVA 1.8.2. software used for basecalling and deplexing.
Raw sequence files generated per library were quality inspected using the FastQC tool (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) then adaptor clipped (TruSeq3-PE-2.fa:2:30:10) and trimmed to remove 5' nucleotide bias (HEADCROP:15) and low quality calls (TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:15) using the Trimmomatic tool (http://www.usadellab.org/cms/?page=trimmomatic). Surviving intact pairs of reads per library were then reference mapped against the current instance of the human genome (GRCh38.82) using the RNA-Seq tool supported in v11 of the CLCbio Genomics Workbench (www.qiagenbioinformatics.com). After, expression per known annotated gene and transcript (Homo_sapiens.GRCh38.82.chr.gtf) were enumerated and exported in Transcripts Per Kilobase Million (TPM) units.
Genome_build: GRCh38.82
Supplementary_files_format_and_content: Two tab-delimited text files per sequenced library are provided; one describing the observed gene expression in Transcript Per Kilobase Million (TPM) units and the other describing the observed transcript expression in Transcript Per Kilobase Million (TPM) units.

source_name: iPSC

extract_protocol:
RNA was extracted from flash-frozen patient samples or cells homogenized in Trizol-Chloroform and purified using the Ambion PureLink RNA Mini kit or Qiagen RNeasy Mini kit.
For library construction, the TruSeq Stranded RiboZero GOLD kit (Illumina) was used in conjunction with 500ng of total RNA per sample with no modification to manufacturer instructions. Per sequencing, the non-iPSC libraries were paired-end sequenced (2x150bp) for a target depth of 40M read pairs each.  For the iPSC libraries, they were paired-end seqeunced (2x75bp) for a target depth of 100M read pairs per each.

treatment_protocol: The non-iPSC samples were provided by the Target ALS Post-Mortem Tissue Core (https://collaborators.nygenome.org/). These samples were acquired through various Institutional Review Board protocols from member sites and transferred to the New York Genomic Consortium in accordance with all applicable foreign, domestic, federal, state, and local laws and regulations for processing, sequencing, and analyses. The iPSCs were generated from patient and control fibroblasts in Dr. Kenneth Fischbeck’s lab at the NIH/NINDS. iPSCs were transfected with the hNIL construct as previously described (Fernandopulle et al., 2018). Briefly, iPSCs were grown to 80% confluency, then digested with accutase solution into single cells. Cells were passaged on matrigel coated plates in E8 Flex media supplemented with 10 μM ROCK inhibitor (Tocris). 3 μg of total DNA (hNIL donor construct and each of the site- specific TALEN or CRISPER/cas9) was added using Lipofectamine Stem (ThermoFisher). 48 hours later, transfected iPSCs were dissociated with accutase and re-plated sparsely onto matrigel coated dishes in E8 flex and 10 μM ROCK inhibitor. Individual clones were manually picked and karyotyped.Differentiation was performed as previously described (Fernandopulle et al., 2018). In brief stably transfected iPSCs with the hNIL cassette were plated at 30,000 cells/cm2 on a Matrigel-coated surface in E8 Flex medium (ThermoFisher) containing 10 μM ROCK inhibitor. 24 hours later, cells were induced with Neural Induction Medium (NIM): DMEM/F12, B27(1x), N2 (1x), NEAA (1x), GlutaMax(1x), compound E (0.2 μg/mL), ROCK inhibitor (10 μM), doxycycline 2 μg/mL, Dihydrotestosterone (DHT) or Ethanol (10 nM). After 48 hours of doxycycline treatment, motor neurons were dissociated with accutase to single cells and re-plated 50,000 cells/cm2 on PDL/Laminin coated surfaces in Neural Differentiation Medium (NDM): DMEM/F12:Brainphys neuronal medium, B27(1x), N2 (1x), NEAA (1x), GlutaMax(1x), compound E (0.2 μg/mL), ROCK inhibitor (10 μM), doxycycline (2 μg/mL), Laminin (1 μg/mL), BDNF (10 ng/mL), GDNF (10 ng/mL), NT3 (10 ng/mL) and DHT or ethanol (10 nM). On day 4 onward, half of cell culture medium was removed and replaced by Neuron medium (NM): Brain phys neuronal medium, B27(1x), N2 (1x), NEAA (1x), GlutaMax(1x), compound E (0.2 μg/mL), ROCK inhibitor (10 μM), doxycycline (2 μg/ml), Laminin (1 μg/ml), BDNF (10 ng/mL), GDNF (10 ng/mL), NT3 (10 ng/mL) and DHT or ethanol (10 nM).

value: iPSC

tag: culture condition

value: EtOH

tag: biological replicate

tag: sample group

value: Control

tag: donor

tag: age

tag: gender

value: Male

tag: race

value: Asian

tag: author sample id

tag: author reference id


title: 5F_Day14 RNA-seq

tag: cell type

value: fibroblast-induced cardiomyocyte


title: Control_iPSC_DHT_Bioreplicate_3

tag: tissue

value: DHT


title: DKO liver rep 2

description: Cpt2 liver/Ppar⍺ whole-body double knockout ATAC-seq in 24hr fasted liver

data_processing:
Library construction and base calling were performed according to Active Motif company protocol .
ATAC-seq paired-end 42nt sequencing reads were mapped to mm10 genome using the BWA algorthim with default settings. Only reads mapping as matched pairs were used in the analysis.
Mapped reads were further processed to remove those with mapq score < 25, mitochondria reads, PCR duplicates, and reads with more than 2 mismatches.
Samples were normalized to the same number of unique alignments by downsampling to 38.3 million.
Peaks were identified using the MACS2 (2.1.0) algorithm at a cutoff of p-value 1e-7, without control file, and with the – nomodel option. Paired reads were treated as a independent events. ENCODE blacklist regions were removed.
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 peak calling output provided as ENCODE narrowPeak format (BED 6+4)
Supplementary_files_format_and_content: bigWig files were generated using a 32nt bin with a 200bp in silico tag extension
Supplementary_files_format_and_content: Consensus peakset as well as intervals for individual samples are provided in BED format

extract_protocol:
Genomic DNA was isolated from flash-frozen mouse liver tissue accordng to Active Motif company protocol.
Library construction was performed according to Active Motif company protocol.

tag: strain

tag: treatment

tag: genotype

value: Cpt2 L-/- ; Ppara -/-


title: Ppara liver rep 2

description: Ppar⍺ knockout ATAC-seq in 24hr fasted liver


title: Control_iPSC_EtOH_Bioreplicate_2


title: 5F_Day10 RNA-seq


title: Ppara liver rep1


title: Control_iPSC_DHT_Bioreplicate_2


title: Liver_Cirrhotic_7

value: Cirrhotic liver


title: 5F_Day7 RNA-seq


title: Liver_Cirrhotic_8


title: Cpt2 liver rep2

description: Cpt2 liver knockout ATAC-seq in 24hr fasted liver

value: Cpt2 L-/-


title: Cpt2 liver rep1

value: Liver


title: Liver_NASH_1

value: NASH liver


title: Liver_Cirrhotic_6


title: Liver_NASH_3


title: DKO liver rep 1

value: 24 hour fast


title: 5F_Day3 RNA-seq


title: BJ RNA-seq

source_name: fibroblast

value: fibroblast


title: Liver_Cirrhotic_4


title: Liver_Cirrhotic_3


title: WT liver rep2

description: WT ATAC-seq in 24hr fasted liver

value: WT


title: 5F_Day0 RNA-seq


title: Liver_Cirrhotic_5


title: Liver_Cirrhotic_2


title: Control_iPSC_DHT_Bioreplicate_1

value: Caucasian


title: WT liver rep1

description: WT ATAC-seq in 24hr fasted liver


title: 4F-MYOCD_D14 ATAC-seq

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the genome(hg38) with bowtie2
The idea of analyzing ATAC-seq data was follow from previous published paper (Li et al., 2017). The data was mapped to hg38 using bowtie2 (Langmead and Salzberg et al, 2012) with options "-p 10 --very-sensitive --end-to-end --no-unal --phred33 --no-mixed -X2000". Low quality reads were filtered by samtools (Li, H. et al. , 2009) with parameter (view -q 35). Unique reads mapping to a single genomic location and strand were remained.  Mitochondrial sequences were removed using "grep –v 'chrM'". BigWig files were generated by BamCoverage from deeptools (Ramírez et al., 2014) with parameters "-bs 20 --smoothLength 60 -p=4 --normalize RPKM -e 300 –ignoreDuplicates".
Genome_build: hg38

extract_protocol: Fifty thousand cells were collected and centrifuged. The cells were lysed to collect the nuclei, which were broken down with transposase. Fragmented product was purified by VAHTS DNA Clean Beads. After purification, the DNAs was PCR-amplified and purified by VAHTS DNA Clean Beads. High- throughput sequencing was performed using Illumina HiSeq Xten (Illumina) platform with PE150 (pair-end sequencing, 150 bp reads).

value: urine cell-induced cardiomyocyte


title: Liver_Cirrhotic_1


title: SBMA_iPSC_EtOH_Bioreplicate_2

value: iPSC

value: SBMA


title: SBMA_iPSC_DHT_Bioreplicate_3


title: 4F-MYOCD_D10 ATAC-seq


title: SBMA_iPSC_DHT_Bioreplicate_2


title: SBMA_iPSC_EtOH_Bioreplicate_1

value: EtOH


title: 4F-MYOCD_D7 ATAC-seq


title: 4F-MYOCD_D3 ATAC-seq


title: 4F-MYOCD_D0 ATAC-seq


title: Liver_Healthy_6

value: Healthy liver


title: Liver_Healthy_3


title: Liver_Healthy_5


title: SBMA_iPSC_DHT_Bioreplicate_1

value: Male


title: NonNeurological_Control_Medial_Motor_Cortex_Bioreplicate_2

value: Female

value: Hispanic or Latino


title: Pneumosphere day10 rep2

city: Melbourne

first: Casey

last: Ah-Cann

state: Victoria

address: 1G Royal Parade, Parkville

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description:
gene_counts.txt
S10

data_processing:
Rsubread package (version 1.22.2) was used for read mapping and summarisation.
Sequenced reads were mapped using the align function with default parameters.
Gene-level summarisation was carried out using the featureCounts and in-built mm10 annotation to get gene counts.
Genome_build: mm10
Supplementary_files_format_and_content: Text file containing Entrez gene identifiers and gene counts.

molecule: polyA RNA

source_name: Pneumosphere

growth_protocol: Lungs were dissected from E11.5 embryos and dissociated in 0.05% Trypsin-EDTA (Gibco). Cells were filtered and resuspended at 200,000 cells/ml/well and plated in pneumosphere media (PSM: DMEM-Ham’s F-12 + Glutamax (Gibco), 2% B27 supplement (Life Technologies), 1 x ITS (Gibco), 20 ng/ml bFGF (Becton-Dickinson), Heparin (Sigma), 10 ng/ml EGF (Becton-Dickinson)) for 1hr in a 6-well regular tissue culture plate. Supernatant was harvested and cells were then resuspended at 50,000 cells/ml/well in PSM in a 24-well ultra-low attachment plate (Corning) in 10% CO2, 5% O2 at 37 C. Cells were split at day 3 and day 7 and replated at 50,000 cells/ml/well.

extract_protocol:
RNA from pneumospheres and sorted E11.5 cells was extracted using RNeasy Minikit (Qiagen).
Libraries were prepared using the Illumina TruSeq RNA kit from 1 µg total RNA

value: Embryonic lung


title: 4F_D14 ATAC-seq


title: primary fibroblasts, 36906-C

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

description: Sample 9

data_processing:
Indexed sequences were checked by FastQC | version: 0.11.5
Trimed adapter by TrimGalore-0.4.5
Reads were mapped to the Pman2.1 reference genome using STAR | version 2.7.2b with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes Peromyscus_maniculatus_bairdii.HU_Pman_2.1.98.gtf were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -T 10
Genome_build: Pman_2.1.dna.toplevel
Supplementary_files_format_and_content: tab-delimited text file includes gene counts for each sample

organism: Peromyscus maniculatus

source_name: Fibroblasts

growth_protocol: Deer mice, P. maniculatus were obtained from the Peromyscus Genetic Stock Center (PGSC), University of South Carolina (USC), Columbia, SC (RRID:SCR_002769). P. maniculatus bairdii (BW Stock), was closed colony bred in captivity since 1948 and descended from 40 ancestors wild-caught near Ann Arbor, Michigan.

extract_protocol:
Total RNA was extracted from primary fibroblasts using the RNeasy Mini Kit (Qiagen).
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit(NEB#E7490/NEB#E7760)

treatment_protocol: Ear tissue was collected from 3-week old males of P. maniculatus, digested with colleganase and cultured with complete RPMI medium to get fibroblasts.

tag: stock

value: BW

tag: age of animal at termination

value: 3 weeks

value: Fibroblasts


title: primary fibroblasts, 36907-C

description: Sample 10


title: Pneumosphere day10 rep3

description:
gene_counts.txt
S14


title: 4F_D10 ATAC-seq


title: Liver_Healthy_2


title: NonNeurological_Control_Medial_Motor_Cortex_Bioreplicate_1

value: Not known Â


title: NonNeurological_Control_Lumbar_Spinal_Cord_Bioreplicate_2


title: Pneumosphere day10 rep1

description:
gene_counts.txt
S7


title: primary fibroblasts, 36905-C

description: Sample 8


title: Pneumosphere day7 rep3

description:
gene_counts.txt
S13


title: 4F_D3 ATAC-seq


title: primary fibroblasts, 36798-C

description: Sample 7


title: Liver_Healthy_1


title: NonNeurological_Control_Lumbar_Spinal_Cord_Bioreplicate_1


title: primary fibroblasts, 36797-C

description: Sample 6


title: Liver_Healthy_4


title: Pneumosphere day7 rep2

description:
gene_counts.txt
S9


title: NonNeurological_Control_Lateral_Motor_Cortex_Bioreplicate_1


title: UC ATAC-seq

value: urine cell


title: Pneumosphere day7 rep1

description:
gene_counts.txt
S6


title: primary fibroblasts, 36789-C

description: Sample 5


title: Control_iPSC_EtOH_Bioreplicate_1

value: Control


title: 5F-MYOCD_D14 ATAC-seq

value: fibroblast-induced cardiomyocyte


title: Neurological_Control_Medial_Motor_Cortex_Bioreplicate_2

value: Caucasian


title: 4F_D7 ATAC-seq

value: urine cell-induced cardiomyocyte


title: primary fibroblasts, 36772-C

description: Sample 3


title: NonNeurological_Control_Lateral_Motor_Cortex_Bioreplicate_2


title: 5F-MYOCD_D10 ATAC-seq


title: Neurological_Control_Lumbar_Spinal_Cord_Bioreplicate_1


title: primary fibroblasts, 36764-C

description: Sample 2


title: primary fibroblasts, 36787-C

description: Sample 4


title: Pneumosphere day3 rep2

description:
gene_counts.txt
S8


title: Pneumosphere day3 rep1

description:
gene_counts.txt
S5


title: Pneumosphere day3 rep3

description:
gene_counts.txt
S12


title: 5F-MYOCD_D3 ATAC-seq


title: 5F-MYOCD_D7 ATAC-seq


title: 4F_D0 ATAC-seq


title: Neurological_Control_Lateral_Motor_Cortex_Bioreplicate_2


title: 5F-MYOCD_D0 ATAC-seq


title: RAW 264.7 4-OHT replicate C

city: Montreal

first: Gerardo

last: Ferbeyre

address: 2900 Edouard Montpetit Boulevard

department: Department of Biochemistry and Molecular Medicine

country: Canada

institute: Université de Montréal

data_processing:
Illumina Real Time Analysis 2.4.11 Software was used for basecalling.
Demultiplexing was performed with Illumina bcl2fastq 2.20 Software allowing 1 mismatch per 6 bp index.
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference mouse genome version GRCm38 (or mm10, gene annotation from Gencode version M13, based on Ensembl 88) using STAR version 2.5.1b.
Gene expressions were obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain gene and transcript level expression, either in TPM or FPKM values, for these stranded RNA libraries.
DESeq2 version 1.18.1 was then used to normalize gene readcounts.
Genome_build: GRCm38 (or mm10, gene annotation from Gencode version M13, based on Ensembl 88)
Supplementary_files_format_and_content: excel file
Supplementary_files_format_and_content: baseMean : average normalized gene expression counts across all samples
Supplementary_files_format_and_content: Log2FoldChange : normalized fold change which has been adjusted to penalize variations in low expression genes
Supplementary_files_format_and_content: lfcMLE: unshrunken maximum likelihood estimate of the Log2FoldChange values
Supplementary_files_format_and_content: lfcSE : standard error of the log2FoldChange estimate
Supplementary_files_format_and_content: stat : Wald statistic
Supplementary_files_format_and_content: pvalue: Wald test p-value
Supplementary_files_format_and_content: padj: Benjamini-Hochberg adjusted p-value
Supplementary_files_format_and_content: Condition Mean (Log2) : normalized read counts (log2) means and standard deviation per group
Supplementary_files_format_and_content: Log2FoldChange (unshrunken) : unshrunken log2FoldChange values
Supplementary_files_format_and_content: EnsembleID: Ensembl gene identifier
Supplementary_files_format_and_content: Gene name: common feature name
Supplementary_files_format_and_content: Category : type of feature (if available)
Supplementary_files_format_and_content: Sample: normalized read counts per sample (DESeq2 analysis)

growth_protocol: RAW 264.7 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin G/streptomycin sulphate. Cells were put in DMEM supplemented with 1% penicillin G/streptomycin sulphate without serum 24 hours prior to RNA extraction.

extract_protocol:
RNA was harvested using Trizol reagent. RNA phase separation was obtained by choloroform extraction. RNA from the aqueous phase was precipitated with isopropanol and purified using RNeasy Mini kit (Qiagen #74106) according to manufacturer’s instructions.
1000 ng of total RNA was used for library preparation. Quality of total RNA was assessed with the BioAnalyzer Nano (Agilent) and all samples had a RIN above 9.5. Library preparation was done with the KAPA mRNAseq Hyperprep kit (KAPA, Cat no. KK8581). Ligation was made with 64 nM final concentration of Illumina index and 9 PCR cycles was required to amplify cDNA libraries. Libraries were quantified by QuBit and BioAnalyzer DNA1000. All libraries were diluted to 10 nM and normalized by qPCR using the KAPA library quantification kit (KAPA; Cat no. KK4973). Libraries were pooled to equimolar concentration. Sequencing was performed with the Illumina Nextseq500 using the Nextseq High Output Kit (86 cycles) using 2.2 pM of the pooled library. Around 20 M single-end PF reads was generated per sample. Library preparation and sequencing was made at the Institute for Research in Immunology and Cancer’s Genomics Platform (IRIC).

treatment_protocol: RAW 264.7 cells were retrovirally infected with a ∆Raf-1:ER construction. Cells successfully transfected were selected with hygromycin B treatment (70 µg/mL) for 7 days

tag: cell line

value: macrophage

tag: treatment protocol

value: 100 nM 4-hydroxytamoxifen (4-OHT) treatment


title: D-D3

description:
D-D3_S173
processed data file: DRG_count.txt

organism: Gallus gallus

source_name: Chicken embryo DRG

value: DRG in the D model

tag: culture time

value: 7 days


title: SBMA_Medial_Motor_Cortex_Bioreplicate_1

tag: culture condition

tag: biological replicate

tag: sample group

value: SBMA

value: Male


title: primary fibroblasts, 36746-C

description: Sample 1


title: D-D2

description:
D-D2_S172
processed data file: DRG_count.txt


title: 5F_D14 ATAC-seq


title: SBMA_Lumbar_Spinal_Cord_Bioreplicate_1

tag: donor

tag: age

tag: gender


title: 5F_D10 ATAC-seq


title: RAW 264.7 Vehicle replicate C

value: Vehicle (Ethanol) treatment


title: Neurological_Control_Medial_Motor_Cortex_Bioreplicate_1

tag: race

tag: author sample id

tag: author reference id


title: SBMA_Lateral_Motor_Cortex_Bioreplicate_1

tag: tissue


title: DS-D3

description:
DS-D3_S179
processed data file: DRG_count.txt

tag: treatment

value: DRG in the DS model


title: RAW 264.7 Vehicle replicate B

tag: cell type


title: RAW 264.7 Vehicle replicate A


title: DS-D2

description:
DS-D2_S178
processed data file: DRG_count.txt


title: XP12RO-siTENT4A_8

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

description:
DEoutput_XP_A.xlsx
XP_A_siPOLS_8

data_processing:
Reads were trimmed using cutadapt
After trimming, the reads were mapped to the human genome (GRCh38) using STAR  v2.4.2a (using options alignEndsType EndToEnd and outFilterMismatchNoverLmax set to 0.04)
Counting proceeded over genes annotated in Ensembl release 88, using htseq-count (version 0.6.1p1, with the stranded option set to reverse)
Normalization and differential expression was performed using DESeq2 (Version 1.10.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed files include DESeq2 normalized counts as well as adjusted p-values and log 2 ratios.

source_name: Skin

growth_protocol: U2OS epithelial cells were cultured in DMEM (Gibco)  supplemented with  2 mM L-Alanyl-L-Glutamine, 100 units/ml of penicillin, 100 µg/ml of streptomycin, 1 mM sodium pyruvate (Biological Industries), and 10% fetal bovine serum (HyClone). XP12RO  human fibroblasts cells were cultured in MEM Eagle (Biological Industries) supplemented with  2 mM L-Alanyl-L-Glutamine, 100 units/ml of penicillin, 100 µg/ml of streptomycin (Biological Industries) and 15% fetal bovine serum (HyClone). The cells were incubated at 37°C in a humidified incubator with 5% atmosphere, and periodically examined for Mycoplasma contaminations by EZ-PCR test kit (Biological Industries).

extract_protocol:
Total RNA was isolated using RNeasy plus mini kit (Qiagen) according to the manufacturer’s instructions. The quality of all RNA samples was examined by using the Agilent 2200 TapeStation system. The efficiencies of knocked down the TENT4A expression were assessed by qPCR.
Total RNA was processed using the Illumina TruSeq Strand Specific total RNA with RiboZero Gold protocol (Illumina). Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing. Single-end 61-bp reads were sequenced on Illumina HiSeq 2500 instrument.

treatment_protocol: Lentiviral pLKO.1-puro empty vector control plasmid and human TENT4A shRNA pLKO.1-puro plasmid (clone TRCN0000053036, target sequence CCAACAATCAGACCAGGTTTA) were obtained from Sigma (Mission shRNA library). Lentiviruses were produced in 293FT cells, by co-transfecting pLKO-derived plasmids and the second-generation packaging plasmids using JetPrime (Polyplus). Lentiviral particles were harvested 48 h post-transfection. The resulting lentiviral particles were used to infect the U2OS cells in the presence of 8 mg/ml polybrene (Sigma). 48 h post-infection, infected cells were treated 2 µg/ml of puromycin (Invivogen) for the selection of stably-transduced clones. The stably-transduced clone of U2OS and XP12RO cells were transfected with 25 nM of siGENOME Non-Targeting Control siRNA #5 (D-001210-05, Dharmacon) and SMARTpool siGENOME TENT4A siRNA (M-009807-01, Dharmacon) using Lipofectamine RNAiMAX (Invitrogen) as recommended transfection protocols by the manufacturer. After 48 h post-transfection, total RNA was extracted and expression profiles were analyzed.

value: Xeroderma pigmentosum, complementation group A, SV-40 transformed fibroblast

tag: RNAi

value: siGENOME SMART pool TENT4A siRNA


title: XP12RO-siTENT4A_7

description:
DEoutput_XP_A.xlsx
XP_A_siPOLS_7


title: Neurological_Control_Lateral_Motor_Cortex_Bioreplicate_1

source_name: characteristics: tissue+D43:D71


title: XP12RO-siTENT4A_5

description:
DEoutput_XP_A.xlsx
XP_A_siPOLS_5


title: 5F_D3 ATAC-seq


title: DS-D1

description:
DS-D1_S177
processed data file: DRG_count.txt


title: BJ ATAC-seq

value: fibroblast


title: JK12

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

country: Japan

institute: National cancer center research institute

description: COPD.rds

data_processing:
Raw sequencing data were processed with the CellRanger pipeline (version 3.0.2, 10X Genomics) and mapped to the human genome (GRCh38) to generate matrices of gene counts by cell barcodes.
Genome_build: GRCh38
Supplementary_files_format_and_content: COPD.rds

source_name: Human lung from Never smokers

extract_protocol:
Single cells were isolated from patient-derived lungs using Lung Dissociation Kit protocol (Miltenyi Biotec, 130-095-927).  Single cells  were processed using the Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 and Chromium Next GEM Chip G Single Cell Kit according to the manufacturer’s instructions in the Chromium Next GEM Single Cell 3′ Reagents Kits V3.1 User Guide(10X Genomics). Briefly, 6,000 cells were loaded into each chip channel and partitioned into Gel Beads-in-emulsion (GEMs) on the Chromium Controller, followed by cell lysis and barcoded RNA reverse transcription.
Library preparation was performed after breaking of single-cell emulsions, and included cDNA amplification, fragmentation, hearing and 5′ adaptor and sample index attachment. Sequencing was performed on a HiSeq X (Illumina, Inc., San Diego, CA)

value: lung

tag: disease

value: Never smokers


title: M21-AP2A

city: Iowa City

first: Jeffrey

last: White

state: Iowa

address: 285 Newton Road 5269 CBRB

institute: University of Iowa

data_processing:
Raw sequences generated from Illumina/Solexa sequencer were aligned using NCBI Build 36.1 (UCSC hg18) of the human genome. Only sequences that mapped uniquely to the genome with zero or one mismatch were used for further analysis. When multiple sequences mapped to the same genomic position, a maximum of two reads mapping to the same position were used. The sequenced reads represent only the ends of each immunoprecipitated fragments instead of the precise protein-DNA binding sites. To illustrate the entire DNA fragment, the 3’ end of each read was extended 250 bp. The reference genome was partitioned into 25 bp bins and the total reads (including partial reads) in each bin were summed and used to generate the visualization file in wiggle (WIG) format.
Genome_build: hg18 (NCBI36)
Supplementary_files_format_and_content: bedGraph files

source_name: Human Melanoma

extract_protocol: ChIP using TFAP2A monoclonal antibody.

tag: cell line

value: Melanoma cell line

tag: chip antibody

value: TFAP2A monoclonal antibody


title: JK11

description: COPD.rds


title: RAW 264.7 4-OHT replicate B

tag: treatment protocol


title: 5F_D0 ATAC-seq

value: fibroblast-induced cardiomyocyte


title: CLL BMMC RNA

city: Pleasanton

first: Joseph

middle: G

last: Arthur

state: CA

address: 6230 Stoneridge Mall Road

institute: 10x Genomics

data_processing:
Raw base calls from the NovaSeq 6000 sequencer were converted from BCL to FASTQ and demultiplexed using an in-house pipeline.
ATAC FASTQs were processed using the `cellranger-atac count` pipeline (pre-release 1.0 version) with the option `--force-cells 4200`. Reads were aligned to the hg19 genome reference. A single set of peaks was called based on genome coverage across all barcodes. ATAC fragment ends (cut sites) were counted within each peak and for each barcode to produce the unfiltered peak-barcode matrix. Barcodes were ranked according to the number of high-quality fragments lying within peaks, and the top 4200 barcodes were selected as cell-associated (4200 determined manually based on knowledge of input material and data inspection). This filtered set of barcodes was used to construct the filtered peak-barcode matrix. A full description of the cellranger-atac pipeline can be found at https://support.10xgenomics.com/single-cell-atac/software/pipelines/1.0/algorithms/overview
RNA FASTQs were processed using the `cellranger count` pipeline (pre-release 3.0 version) with default parameters. Reads were aligned to the GRCh38 genome reference and alignments assigned to genes based on the Ensembl 93 transcriptome annotation. Alignments for each barcode were deduplicated using the UMI sequences, then counted to form the unfiltered feature-barcode matrix. Cell-associated barcodes were called using high UMI counts as the primary signal, followed by a second pass to detect barcodes with gene expression significantly different than a putative background distribution. This filtered set of barcodes was used to construct the filtered peak-barcode matrix. A full description of the cellranger pipeline can be found at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/3.0/algorithms/overview
Genome_build: Single Cell ATAC: hg19  Single Cell RNA: GRCh38 genome reference and Ensembl 93 transcriptome reference (Cell Ranger GRCh38 3.0.0)
Supplementary_files_format_and_content: RNA feature-barcode matrices contain UMI counts in a sparse matrix format (Matrix Market exchange format) with .mtx file extensions. The .mtx files contain three lines of metadata followed by the list of matrix entries. The third line of metadata contains three entries: the total number of genes (matrix rows), the total number of barcodes (matrix columns), and the total number of non-zero entries in the matrix. From line 4 onwards, the three data columns contain the gene index, the barcode index, and the UMI count for that gene-barcode combination. All indices start from 1, and only the matrix entries that are larger than 0 are included. The raw feature-barcode matrices contain data for all valid barcodes in the experiment, and the filtered feature-barcode matrices contain data only from barcodes determined to be cells. The list of these barcode sequences can be found in the raw and filtered barcodes.tsv files, respectively. Raw and filtered matrices from both datasets contain the same genes, listed in the features.tsv files.
Supplementary_files_format_and_content: ATAC peak-barcode matrices counts of transposase cut sites in a sparse matrix format (Matrix Market exchange format) with .mtx file extensions. The .mtx files contain three lines of metadata followed by the list of matrix entries. The third line of metadata contains three entries: the total number of peaks (matrix rows), the total number of barcodes (matrix columns), and the total number of non-zero entries in the matrix. From line 4 onwards, the three data columns contain the peak index, the barcode index, and the count of fragment ends (cut sites) within the given peak region and for the given barcode . All indices start from 1, and only the matrix entries that are larger than 0 are included. The raw peak-barcode matrices contain data for all valid barcodes in the experiment, and the filtered peak-barcode matrices contain data only from barcodes determined to be cells. The list of these barcode sequences can be found in the raw and filtered barcodes.tsv files, respectively. Raw and filtered matrices for each experiment use both contain all peaks detected in that experiment; these are listed in standard BED format in the peaks.bed files.

source_name: Bone Marrow Mononuclear Cells

extract_protocol:
Single Cell ATAC: Cryopreserved bone marrow mononuclear cells (BMMCs) from a healthy donor and a patient with chronic lymphocytic leukemia (CLL) were obtained from AllCells. Cells were isolated and lysed following the Nuclei Isolation for Single Cell ATAC Sequencing Demonstrated Protocol (10x Genomics: CG000169) following guidance for primary cells.
Single Cell RNA: Cryopreserved bone marrow mononuclear cells (BMMCs) from a healthy donor and a patient with chronic lymphocytic leukemia (CLL) were obtained from AllCells. Cells were isolated following the Sample Preparation Demonstrated Protocol: Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing (10x Genomics: CG00039).
Single Cell ATAC: Libraries for 10x Genomics Single Cell ATAC-seq were generated following the Chromium Single Cell ATAC Reagent Kits User Guide (10x Genomics: CG000168). Briefly, nuclei were tagmented in bulk. Single nuclei were encapsulated in GEMs containing a gel bead with a unique cell barcode, and genomic material was amplified in a linear amplification reaction. GEMs were broken, and genomic material was amplified via PCR appending a sample index and Illumina sequencing handles (P5/P7). Libraries were sequenced on the Illumina NovaSeq 6000 System according to the manufacturer’s protocols.
Single Cell RNA: Libraries for Single Cell Gene Expression were generated following the Single Cell 3’ Reagent Kits v2 User Guide (10x Genomics: CG00052). Briefly, cells were encapsulated in GEMs containing a gel bead with a unique cell barcode, and mRNA was reverse transcribed. GEMs were broken, and cDNA was amplified and fragmented. Ends were blunted, A-tailed, and adapter oligos were ligated. Samples were amplified via PCR appending a sample index and Illumina sequencing handles (P5/P7). Libraries were sequenced on the Illumina NovaSeq 6000 System according to the manufacturer’s protocols.

tag: subject id

value: Donor 2

tag: subject status

value: chronic lymphocytic leukemia

value: bone marrow mononuclear cells


title: XP12RO-siControl_3

description:
DEoutput_XP_A.xlsx
XP_A_Control_3

value: Non-Targeting Control siRNA


title: JK06

description: COPD.rds


title: RAW 264.7 4-OHT replicate A

value: macrophage

value: 100 nM 4-hydroxytamoxifen (4-OHT) treatment


title: XP12RO-siControl_2

description:
DEoutput_XP_A.xlsx
XP_A_Control_2


title: D-D1

description:
D-D1_S171
processed data file: DRG_count.txt

value: DRG in the D model

tag: culture time

value: 7 days


title: 5F_D7 ATAC-seq


title: XP12RO-siControl_1

description:
DEoutput_XP_A.xlsx
XP_A_Control_1


title: KO2-AP2A

value: CRISPR Knockout of TFAP2A


title: CLL BMMC ATAC


title: Healthy BMMC RNA

value: Donor 1

value: healthy


title: JK03

description: COPD.rds

source_name: Human lung from Non-COPD smokers

value: Non-COPD smokers


title: ChIP WT LL37

city: Boston

last: Wessels

state: MA

address: 330 Longwood Ave

department: Medicine

institute: Boston Children's Hospital

data_processing:
Paired ChIP-Seq reads corresponding to fragment sizes of  200 bp were aligned  to the S. pyogenes MGAS5005 genome (NCBI RefSeq NC_007297) using bowtie2 version 2.3.1 allowing up to one mismatch per seed
The program samtools (version 1.3.1) was used to extract read 1 from each mapped read pair.
Biological replicates of mock IP data (WT samples for each condition) were merged and used as background for each biological replicate of CsrR-FLAG samples grown in the same media condition
Regions of enrichment were called using QuEST, version 2.42
Regions in each biological replicate were considered peaks if they were 2-fold enriched for reads over background, had a positive peak shift and strand correlation, and had a q-value of less than 0.01.
Custom scripts were used to combine peaks identified in each biological replicate of sample 1, keeping the maximual region identified in at least two biological replicates (final enriched regions).
Genome_build: NC_007297
Supplementary_files_format_and_content: wig files were generated using QuEST; Scores represent normalized smoothed read density
Supplementary_files_format_and_content: bed intervals reflect regions with signicant (as defined above in data processing steps) enrichment of reads in the experimental condition in comparision to the mock control condition.

organism: Streptococcus pyogenes

source_name: Bacterial cells grown to OD ∼0.4

growth_protocol: Cultures were grown to mid-log-phase (OD600 of ~0.4)

extract_protocol:
Samples were crosslinked with 1% formaldehyde for 30 min and reactions were quenched with 250 mM glycine for 15 min
Cells were lysed and DNA sheared using a Bioruptor water bath sonicator. Lysates were incubated with anti-FLAG magnetic beads (Sigma). The co-purifying nucleic acid were purified after crosslink reversal at 65°C overnight.
Libraries were prepared from 25 ng DNA using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB). Adapters were diluted 10-fold before ligation and samples underwent 5 rounds of amplification without size selection.

treatment_protocol: See media conditions, above

tag: genotype

value: 854 wild-type

tag: media

value: THY broth with 300 nM LL-37

value: anti-FLAG magnetic beads (Sigma)


title: JK10

description: COPD.rds

source_name: Human lung from COPD patients

value: lung

value: COPD patients


title: U2OS-sh/siTENT4A-5

description:
DEoutput_U2OS.xlsx
U2OS_siPOLS_5

source_name: Bone

value: bone osteosarcoma epithelial

value: pLKO.1-empty vector +siGENOME SMART pool TENT4A siRNA


title: A549 dnCRTC, biological rep2 [W16_A549_dnC_B]

city: Gainesville

first: Lizi

last: Wu

state: FL

address: 2033 Mowry Road

institute: University of Florida

data_processing:
Illumina’s bcl2fastq was used to convert bcl files to FASTQ files and de-multiplex the samples.
Sequenced reads were mapped to hg38 using HISAT2 with default parameters. Only alignment with the minimum mapping quality greater than 10 were used for downstream analysis.  Quantification was performed using Partek Genomics Suite, and the raw read counts and normalized read count (RPKM) were obtained.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw read count and RPKM values for each Sample

source_name: A549 dnCRTC

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% inactivated fetal bovine serum and penicillin/streptomycin (100U/ml) at 37°C under 5% CO2.

extract_protocol:
RNA was isolated with the Trizol Reagent (Invitrogen) and purified by the Qiagen Column with in column DNase digestion.
RNA-seq libraries (non-strand-specific, paired end) were prepared with the NEBNext® Ultra™ RNA Library Prep Kit (Illumina, San Diego, CA) and were sequenced according to the paired-end 150bp protocol using NovaSeq 6000.

treatment_protocol: GFP control and dnCRTC

value: human lung carcinoma epithelial cells, dnCRTC

value: dnCRTC


title: ChIP CsrR-FLAG LL37

source_name: Bacterial cells grown to OD ∼0.8

value: 854 CsrR-FLAG


title: JK04

description: COPD.rds


title: U2OS-sh/siTENT4A-6

description:
DEoutput_U2OS.xlsx
U2OS_siPOLS_6


title: Healthy BMMC ATAC

value: bone marrow mononuclear cells


title: JK08

description: COPD.rds


title: A375-AP2A

value: Melanoma cell line

value: TFAP2A monoclonal antibody


title: A549 GFP, biological rep2 [W14_A549_GFP_B]

source_name: A549 GFP

value: human lung carcinoma epithelial cells, GFP control

value: GFP Control


title: U2OS-sh/siTENT4A-1

description:
DEoutput_U2OS.xlsx
U2OS_siPOLS_1


title: ChIP WT Mg2+

source_name: Bacterial cells grown to OD ∼0.7

value: THY broth with 15 mM MgCl2


title: ChIP CsrR-FLAG Mg2+

source_name: Bacterial cells grown to OD ∼0.6


title: A549 dnCRTC, biological rep1 [W15_A549_dnC_A]


title: U2OS-sh/siControl-6

description:
DEoutput_U2OS.xlsx
U2OS_Control_6

value: pLKO.1-empty vector +Non-Targeting Control siRNA


title: U2OS-sh/siControl-5

description:
DEoutput_U2OS.xlsx
U2OS_Control_5


title: JK05

description: COPD.rds


title: A549 GFP, biological rep1 [W13_A549_GFP_A]


title: JK07

description: COPD.rds


title: ChIP CsrR-FLAG

value: THY broth


title: U2OS-sh/siControl-1

description:
DEoutput_U2OS.xlsx
U2OS_Control_1


title: LTi cells, Gata3-KO_rep2

status: Public on Jun 28 2021

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Reads were aligned to mouse genome (mm10) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Genome_build: mm10
Supplementary_files_format_and_content: GATA3.rpkm.count.gs.txt  (First column: entrez ID; second column: gene symbol; columns thereafter: RPKMs for each sample in log2 scale)

source_name: Gata3fl/fl-VavCre #2

extract_protocol:
Total RNA was extracted with miRNeasy Micro kit (50) (1071023; Qiagen)
RNA-Seq libraries were prepared through the Smart-seq2 method (PMID: 24385147) as previously described (PMID: 29466755).

value: small intestine lamina propria

tag: strain


title: JK09

description: COPD.rds


title: IFIH1KO_P3_9

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

country: Germany

institute: University Medical Center Freiburg

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: library of 96 IFIH1-/- HSCs

growth_protocol: Mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.

extract_protocol:
Bone marrow cells isolated from tibiae, femurs and hip bones and red cells were lysed. For cell sorting, samples where additionally enriched for hematopoietic progenitor cells by depleting the lineage positive fraction using the biotin-conjugated lineage cocktail with antibodies against CD3e, CD11b/Mac-1, CD45R/B220, Ly-6/Ly6C, and TER-119. The lineage negative fraction was then washed and resuspended in staining buffer at a concentration of 10x106 cells per ml, and were then stained with FITC or PE-conjugated lineage cocktail antibodies, CD117/c-kit, Sca-1, CD48, CD150, CD135/Flk2, CD34. We used CD150+CD48- LSK cells for the scRNA-seq experiments.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: No treatmenat was performed on the isolated HSCs.

tag: strain background

tag: genotype/variation

tag: age

value: 8 weeks

value: bone marrow

value: hematopoietic stem cells (HSCs)


title: IFIH1KO_P3_12

tag: tissue


title: LTi cells, Ctrl_rep1

value: Ctrl


title: IFIH1KO_P3_10


title: IFIH1KO_P2_16


title: IFIH1KO_P3_11


title: IFIH1KO_P2_15


title: IFIH1KO_P2_14


title: IFIH1KO_P2_13


title: IFIH1WT_P3_9

source_name: library of 96 IFIH1+/+ HSCs


title: IFIH1KO_P1_8


title: IFIH1KO_P1_5


title: IFIH1WT_P3_11


title: IFIH1KO_P1_6


title: IFIH1WT_P2_5


title: IFIH1WT_P2_7


title: IFIH1KO_P1_7


title: IFIH1WT_P3_12


title: IFIH1WT_P2_6


title: IFIH1WT_P2_8


title: IFIH1WT_P3_10


title: IFIH1WT_P1_1


title: IFIH1WT_P1_3


title: IFIH1WT_P1_4


title: IFIH1WT_P1_2


title: O11_31954_29

city: Minneapolis

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

data_processing:
Quality of mRNA-seq reads were assessed using FastQC version 0.11.3 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Both rhesus globin and ribosomal sequences were filtered via alignments with Bowtie v2.1.0.
Adapters were digitally removed using cutadapt, version 1.8.3.
Mapping was performed using STAR v2.4.0h1 .
Gene counts were generated using HTSeq-count v0.6.1p1.
Genome_build: Macaque mulatta genome Mmul1 (https://support.illumina.com/sequencing/sequencing
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Macaca mulatta

source_name: Whole blood

extract_protocol:
Whole blood was collected from RM in PAXgene RNA tubes (PreAnalytiX) following the manufacturer's procedures. (PreAnalytiX). RNA was isolated using PAXgene Blood miRNA  kits (Qiagen) following the protocol provided with the kit that included an on-column DNase treatment.
Illumina TruSeq® Stranded mRNA HT kit

treatment_protocol: Doses of 5, 10 and 15ug/kg were given at D1, D3 and D8, respectively.


title: O11_34100_29


title: O11_34024_29


title: O11_31954_21


title: O11_33047_29


title: O11_34024_21


title: O11_32062_29


title: O11_33047_21


title: O11_34100_21


title: O11_32062_21


title: O11_34100_17


title: O11_33047_17


title: O11_32062_17


title: O11_34024_17


title: O11_31954_17


title: O11_34100_14


title: O11_33047_14


title: SBMA_iPSC_EtOH_Bioreplicate_3

source_name: iPSC

value: iPSC

tag: culture condition

value: EtOH

tag: biological replicate

tag: sample group

value: SBMA

tag: donor

tag: gender

value: Male

tag: race

value: Caucasian

tag: author sample id

tag: author reference id


title: O11_32062_14


title: O11_34100_10


title: O11_31954_14


title: O11_32062_10


title: O11_34024_8


title: O11_31954_8


title: O11_34024_10


title: O11_33047_10


title: O11_33047_8


title: O11_34100_8


title: O11_32062_8


title: O11_31954_7


title: O11_34100_7


title: O11_33047_7


title: O11_34024_7


title: O11_32062_7


title: O11_31954_4


title: O11_34100_4


title: O11_34024_4


title: O11_34024_14


title: O11_31954_3


title: O11_31954_10


title: O11_34100_3


title: O11_34024_3


title: O11_34100_1


title: O11_34024_1


title: O11_31954_1


title: O11_32062_1


title: O11_33047_1


title: O11_33047_3


title: O11_34024_0


title: O11_32062_0


title: O11_31954_0


title: O11_34100_neg13


title: O11_31954_neg13


title: O11_33047_neg13


title: O11_32062_4


title: O11_33047_4


title: O11_32062_neg13


title: O11_32062_3


title: X_W0D0_X15_Protected

data_processing:
Quality of mRNA-seq reads were assessed using FastQC version 0.11.3 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Both rhesus globin and ribosomal sequences were filtered via alignments with Bowtie v2.1.0.
Adapters were digitally removed using cutadapt, version 1.8.3.
Mapping was performed using STAR v2.4.0h1 .
Cene counts were generated using HTSeq-count v0.6.1p1.
Genome_build: Macaque mulatta genome Mmul1 (https://support.illumina.com/sequencing/sequencingsoftware/igenome.html )
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

tag: group

value: X

value: Subcuraneous

tag: phase

value: Prime

tag: outcome

value: Protected


title: X_W0D7_X15_Protected


title: X_W18D7_X15_Protected

value: Boost


title: X_W88D0_X14_Unprotected

value: Unprotected


title: X_W18D1_X15_Protected


title: X_W0D1_X15_Protected


title: X_W18D0_X15_Protected


title: X_W88D0_X15_Protected


title: O11_33047_0


title: O11_34024_neg13


title: ChIP WT

source_name: Bacterial cells grown to OD ∼0.5

tag: genotype

value: 854 wild-type

tag: media

value: THY broth

tag: chip antibody

value: anti-FLAG magnetic beads (Sigma)


title: X_W0D7_X14_Unprotected


title: X_W18D3_X14_Unprotected


title: X_W18D0_X14_Unprotected


title: X_W0D1_X14_Unprotected


title: X_W0D0_X14_Unprotected


title: X_W18D7_X13_Unprotected


title: X_W18D3_X13_Unprotected


title: X_W18D3_X15_Protected


title: X_W18D1_X13_Unprotected


title: O11_34100_0


title: X_W0D3_X15_Protected


title: X_W0D7_X13_Unprotected


title: X_W18D0_X13_Unprotected


title: X_W0D3_X13_Unprotected


title: X_W0D1_X13_Unprotected


title: X_W88D0_X12_Unprotected


title: X_W18D1_X14_Unprotected


title: X_W18D0_X12_Unprotected


title: X_W18D1_X12_Unprotected


title: X_W0D0_X13_Unprotected


title: X_W0D3_X14_Unprotected


title: X_W18D7_X14_Unprotected


title: X_W18D3_X12_Unprotected


title: X_W0D7_X12_Unprotected


title: X_W18D7_X12_Unprotected


title: X_W0D0_X12_Unprotected


title: X_W88D0_X13_Unprotected


title: X_W0D1_X12_Unprotected


title: X_W18D3_X11_Unprotected


title: X_W88D0_X11_Unprotected


title: X_W18D1_X11_Unprotected


title: X_W18D0_X11_Unprotected


title: X_W0D7_X11_Unprotected


title: X_W0D3_X11_Unprotected


title: X_W0D0_X11_Unprotected


title: X_W88D0_X10_Unprotected


title: X_W18D7_X10_Unprotected


title: X_W18D3_X10_Unprotected


title: X_W18D0_X10_Unprotected


title: X_W18D1_X10_Unprotected


title: X_W0D3_X12_Unprotected


title: X_W0D3_X10_Unprotected


title: X_W88D0_X9_Protected


title: X_W0D0_X10_Unprotected


title: X_W0D1_X10_Unprotected


title: X_W18D7_X9_Protected


title: X_W18D3_X9_Protected


title: X_W18D1_X9_Protected


title: X_W18D7_X11_Unprotected


title: X_W18D0_X9_Protected


title: X_W0D7_X9_Protected


title: X_W0D1_X11_Unprotected


title: X_W0D3_X9_Protected


title: X_W88D0_X8_Unprotected


title: X_W0D1_X8_Unprotected


title: X_W18D3_X8_Unprotected


title: X_W0D1_X9_Protected


title: X_W0D0_X9_Protected


title: X_W18D0_X8_Unprotected


title: X_W0D3_X8_Unprotected


title: X_W18D7_X8_Unprotected


title: X_W0D0_X8_Unprotected


title: X_W18D1_X8_Unprotected


title: X_W18D7_X7_Protected


title: X_W18D3_X7_Protected


title: X_W18D1_X7_Protected


title: X_W18D0_X7_Protected


title: X_W0D7_X10_Unprotected


title: X_W0D7_X7_Protected


title: X_W0D3_X7_Protected


title: X_W0D1_X7_Protected


title: X_W0D0_X7_Protected


title: X_W18D3_X6_Protected


title: X_W18D0_X6_Protected


title: X_W18D1_X6_Protected


title: X_W18D7_X6_Protected


title: X_W0D7_X8_Unprotected


title: X_W88D0_X6_Protected


title: X_W0D7_X6_Protected


title: X_W0D3_X6_Protected


title: X_W88D0_X7_Protected


title: X_W0D0_X6_Protected


title: X_W0D1_X6_Protected


title: X_W18D1_X5_Unprotected


title: X_W88D0_X5_Unprotected


title: X_W18D0_X5_Unprotected


title: X_W0D3_X5_Unprotected


title: X_W18D3_X5_Unprotected


title: X_W0D7_X5_Unprotected


title: X_W0D1_X5_Unprotected


title: X_W18D7_X5_Unprotected


title: X_W18D7_X4_Unprotected


title: X_W88D0_X4_Unprotected


title: X_W0D0_X5_Unprotected


title: X_W18D1_X4_Unprotected


title: X_W18D0_X4_Unprotected


title: X_W0D7_X4_Unprotected


title: X_W18D3_X4_Unprotected


title: X_W0D1_X4_Unprotected


title: X_W0D3_X4_Unprotected


title: X_W88D0_X3_Protected


title: X_W0D0_X4_Unprotected


title: X_W18D0_X3_Protected


title: X_W18D7_X3_Protected


title: X_W18D3_X3_Protected


title: X_W0D3_X3_Protected


title: X_W18D1_X3_Protected


title: X_W0D1_X3_Protected


title: X_W0D7_X3_Protected


title: X_W88D0_X2_Unprotected


title: X_W0D0_X3_Protected


title: X_W18D3_X2_Unprotected


title: X_W18D7_X2_Unprotected


title: X_W0D7_X2_Unprotected


title: X_W0D1_X2_Unprotected


title: X_W88D0_X1_Protected


title: X_W18D7_X1_Protected


title: X_W18D0_X2_Unprotected


title: X_W18D1_X2_Unprotected


title: X_W0D3_X2_Unprotected


title: X_W0D0_X2_Unprotected


title: X_W0D7_X1_Protected


title: X_W18D1_X1_Protected


title: X_W18D3_X1_Protected


title: X_W18D0_X1_Protected


title: X_W0D0_X1_Protected


title: X_W0D3_X1_Protected


title: S_W18D7_S15_Unprotected

value: S


title: S_W88D0_S15_Unprotected


title: S_W18D3_S15_Unprotected


title: X_W0D1_X1_Protected


title: S_W0D1_S15_Unprotected 2


title: S_W18D3_S14_Unprotected


title: S_W0D7_S14_Unprotected


title: S_W0D3_S15_Unprotected


title: S_W0D0_S15_Unprotected


title: S_W18D1_S15_Unprotected


title: S_W0D3_S14_Unprotected


title: S_W18D7_S14_Unprotected


title: S_W88D0_S14_Unprotected


title: S_W0D0_S14_Unprotected


title: S_W18D3_S13_Protected


title: S_W0D1_S15_Unprotected


title: S_W0D7_S1_Protected


title: S_W88D0_S13_Protected


title: S_W18D1_S14_Unprotected


title: S_W0D1_S14_Protected


title: S_W0D0_S13_Protected


title: S_W18D3_S12_Protected


title: S_W18D0_S13_Protected


title: S_W18D0_S15_Unprotected


title: S_W88D0_S12_Protected


title: S_W18D1_S12_Protected


title: S_W18D0_S12_Protected


title: S_W0D3_S13_Protected


title: S_W18D7_S12_Protected


title: S_W0D7_S12_Protected


title: S_W18D0_S14_Unprotected


title: S_W0D3_S14_Protected


title: S_W88D0_S11_Protected


title: S_W0D1_S12_Protected


title: S_W0D0_S12_Protected


title: S_W0D3_S11_Protected


title: S_W18D7_S11_Protected


title: S_W18D3_S11_Protected


title: S_W18D7_S13_Protected


title: S_W18D1_S11_Protected


title: S_W18D3_S10_Unprotected


title: S_W0D0_S11_Protected


title: S_W0D7_S11_Protected


title: S_W18D1_S13_Protected


title: S_W88D0_S10_Unprotected


title: S_W18D0_S10_Unprotected


title: S_W18D1_S10_Unprotected


title: S_W0D0_S10_Unprotected


title: S_W18D7_S9_Protected


title: S_W0D3_S10_Unprotected


title: S_W0D7_S10_Unprotected


title: S_W88D0_S9_Protected


title: S_W18D1_S9_Protected


title: S_W18D3_S9_Protected


title: S_W0D7_S9_Protected


title: S_W18D0_S9_Protected


title: S_W0D3_S9_Protected


title: S_W18D0_S11_Protected


title: S_W18D7_S8_Unprotected


title: S_W88D0_S8_Unprotected


title: S_W0D0_S9_Protected


title: S_W0D1_S11_Protected


title: S_W0D1_S10_Protected


title: S_W18D7_S10_Unprotected


title: S_W18D3_S8_Unprotected


title: S_W18D0_S8_Unprotected


title: S_W0D3_S8_Unprotected


title: S_W0D1_S9_Unprotected


title: S_W88D0_S7_Unprotected


title: S_W18D7_S7_Unprotected


title: S_W0D0_S8_Unprotected


title: S_W0D7_S8_Unprotected


title: S_W18D3_S7_Unprotected


title: S_W18D0_S7_Unprotected


title: S_W0D7_S7_Unprotected


title: S_W18D1_S7_Unprotected


title: S_W0D3_S7_Unprotected


title: S_W0D1_S11_Unprotected


title: S_W88D0_S6_Protected


title: S_W0D1_S7_Unprotected


title: S_W18D7_S6_Protected


title: S_W18D1_S6_Protected


title: S_W18D3_S6_Protected


title: S_W18D0_S6_Protected


title: S_W0D7_S6_Protected


title: S_W18D1_S8_Unprotected


title: S_W0D1_S6_Protected


title: S_W18D3_S5_Protected


title: S_W88D0_S5_Protected


title: S_W0D0_S6_Protected


title: S_W18D1_S5_Protected


title: S_W0D3_S6_Protected


title: S_W18D7_S5_Protected


title: S_W0D3_S5_Protected


title: S_W0D7_S5_Protected


title: S_W18D0_S5_Protected


title: S_W0D0_S5_Protected


title: S_W88D0_S4_Protected


title: S_W18D7_S4_Protected


title: S_W18D3_S4_Protected


title: S_W0D1_S5_Protected


title: S_W0D0_S7_Unprotected


title: S_W18D0_S4_Protected


title: S_W18D1_S4_Protected


title: S_W0D1_S4_Protected


title: S_W88D0_S3_Protected


title: S_W0D0_S4_Protected


title: S_W18D7_S3_Protected


title: S_W0D7_S4_Protected


title: S_W18D3_S3_Protected


title: S_W18D1_S3_Protected


title: S_W18D0_S3_Protected


title: LH M2-rep1

city: Chengdu

first: Miao

last: Xu

address: 37#,Guoxue alley, Wuhou district

department: Clinical Nutrition

institute: West China hospital of Sichuan university

data_processing:
Illumina HiSeq sequencer and software used for sequencing and basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome of hg19 using HISTA2. Transcript assembly were performed using Cufflink. DEG analyses were performed using DESeq2.
Genome_build: UCSC_hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: in vitro induced cells

growth_protocol: THP-1 derived macrophage were routinely generated by incubating THP-1(at 2*10e6/well) with PMA (in growth medium) for 48h.Then remove PMA and repace with growth medium without PMA and rest for 24h, collect cells for M0.

extract_protocol:
After treatment, cells were collected and flash frozen liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For M1 activation, add LPS(100ng/ml) and IFNγ(25ng/ml) to M0 cells.For M2 activation, add IL-4(20ng/ml)and IL-13(20ng/ml)to M0 cells.For extra lipid, add lipid mixture (Sigma Aldrich,0.25%) to growth medium during LPS+IFNγ or IL-4+IL-13 treating.

tag: cell type

value: THP-1 derived macrophage

tag: treatment

value: Maintained in growth medium with extra lipid mixture (0.25%)and treated with IL-4 20ng/ml+IL-13 20ng/ml


title: LH M2-rep3


title: LH M2-rep2


title: S_W0D7_S3_Protected


title: S_W0D3_S3_Protected


title: S_W0D1_S3_Protected


title: LH M1-rep3

value: Maintained in growth medium with extra lipid mixture (0.25%) and treated with LPS 100ng/ml+IFNγ 25ng/ml


title: LH M1-rep1


title: S_W88D0_S2_Unprotected


title: S_W0D0_S3_Protected


title: LH M0-rep3

value: Maintained in growth medium with extra lipid mixture (0.25%)


title: LH M1-rep2


title: LH M0-rep2


title: S_W18D1_S2_Unprotected


title: S_W0D3_S4_Protected


title: LH M0-rep1


title: LN M2-rep3

value: Maintained in normal growth medium and treated with IL-4 20ng/ml+IL-13 20ng/ml


title: S_W18D3_S2_Unprotected


title: LN M2-rep2


title: S_W18D0_S2_Unprotected


title: S_W0D7_S2_Unprotected


title: S_W0D3_S2_Unprotected


title: LN M1-rep3

value: Maintained in normal growth medium and treated with LPS 100ng/ml+IFNγ 25ng/ml


title: LN M1-rep2


title: LN M2-rep1


title: S_W0D1_S2_Unprotected


title: S_W0D0_S2_Unprotected


title: LN M1-rep1


title: S_W88D0_S1_Unprotected


title: S_W18D7_S1_Unprotected


title: LN M0-rep3

value: maintained in normal growth medium without treatment.


title: LN M0-rep2


title: S_W18D1_S1_Unprotected


title: S_W18D3_S1_Unprotected


title: S_W18D0_S1_Unprotected


title: LN M0-rep1


title: Homozygous rep1

city: Münster

first: Anke

last: Hermann

address: Albert-Schweitzer-Campus 1

department: Internal Medicine D

institute: University Hospital Münster

data_processing:
Using a molecular barcode, the samples were demultiplexed (bcl2fastq2) to fastq data and quality controlled (FastQC)
Trimmomatic (Version 0.33) was used for adapter trimming and read filtering
Reads were aligned to the mouse reference genome (mm10) using Hisat2 and SAMtools (Kim et al., 2015 and Li et al., 2011).
The sorted and aligned reads were counted into genes using HTSeq-counts and differential expression was performed using the r-package deseq2 (Anders et al., 2015 and Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing basemeans, log2(FC) and padj values of all determined genes from comparison of wildtype versus homozygous or wildtype versus heterozygous.

source_name: embryo

extract_protocol:
Embryos were isolated and washed with PBS at 4°C. Embryos were homogenized and RNA was isolated using the GenEluteTM Mammalian total RNA Miniprep Kit according to the manufacturer’s instructions.
After determination of the concentration and RNA integrity number, the library was constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina and the NEBNext Poly(A) mRNA Magnetic Isolation Module.

tag: strain

tag: tissue

value: embryo

tag: age

value: embryonic day 11.5 (E11.5)


title: Homozygous rep2


title: Heterozygous rep3


title: Homozygous rep3


title: Homozygous rep4


title: Heterozygous rep2


title: S_W0D1_S1_Unprotected

value: Subcuraneous

value: Prime


title: O_W88D0_O15_Protected

value: O

value: Oral

value: Protected


title: Heterozygous rep1


title: S_W0D0_S1_Unprotected

value: Unprotected


title: WT rep3

value: wild type


title: WT rep2


title: O_W18D3_O15_Protected

value: Boost


title: O_W18D7_O15_Protected


title: O_W18D0_O15_Protected


title: O_W18D1_O15_Protected


title: O_W0D7_O15_Protected


title: Sample_NF5T RNA-seq

city: Cambridge

first: Ayush

middle: T

last: Raman

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

description: mRNA seq

data_processing:
The quality of raw reads was assessed using FastQC (Andrews, 2010). The average per base quality score across all the files were greater than 32 and had passed all the major tests.
The raw reads were aligned to the Homo sapiens genome (hg19) using STAR v2.4.2a (Dobin et al., 2013). The mappability of unique reads on average was ~82%. The raw counts were computed using quantMode function in STAR.
The obtained read counts are analogous to the expression level of each gene across all the samples. The differential expression analysis was done using DESeq2 (Love et al., 2014a). Genes with raw mean reads greater than 10 were used for normalization and differential gene expression analysis using DESeq2 package in R. Wald test defined in the DESeq function of the package was used for differential expression analysis and shrunken log fold-changes (i.e., obtaining reliable variance estimates by pooling information across all the genes) were used for further analysis. Principal Component Analysis (PCA), hierarchical clustering plots (hclust) and XY plots between replicates of same genotypes were used to examine for nominal amounts of non-technical variation and other latent factors. PCA, hclust and bar plots were generated using ggplot2 (Wickham). All the heatmaps of differentially expressed genes were generated using pheatmap package (Kolde, 2012) in R environment.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files; raw counts file output from STAR and Diff Expressed Genes using DESeq2.

source_name: Neurofibroma

extract_protocol:
RNA was isolated from fresh frozen surgical specimens using TRIzol (Cat# 10296010 Invitrogen) and purified using the RNeasy Mini Kit (Cat# 74106 Qiagen, Valencia, CA, USA) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Neurofibroma


title: Sample_31T RNA-seq

description: mRNA seq


title: S_W0D3_S1_Unprotected

first: Michael

value: S


title: S_W0D7_S1_Unprotected


title: O_W88D0_O14_Unprotected


title: O_W0D0_O15_Protected


title: O_W0D1_O15_Protected


title: Sample_T3 RNA-seq

data_processing:
The quality of raw reads was assessed using FastQC (Andrews, 2010). The average per base quality score across all the files were greater than 32 and had passed all the major tests.
The raw reads were aligned to the Homo sapiens genome (hg19) using STAR v2.4.2a (Dobin et al., 2013). The mappability of unique reads on average was ~82%. The raw counts were computed using quantMode function in STAR.
The obtained read counts are analogous to the expression level of each gene across all the samples. The differential expression analysis was done using DESeq2 (Love et al., 2014a). Genes with raw mean reads greater than 10 were used for normalization and differential gene expression analysis using DESeq2 package in R. Wald test defined in the DESeq function of the package was used for differential expression analysis and shrunken log fold-changes (i.e., obtaining reliable variance estimates by pooling information across all the genes) were used for further analysis. Principal Component Analysis (PCA), hierarchical clustering plots (hclust) and XY plots between replicates of same genotypes were used to examine for nominal amounts of non-technical variation and other latent factors. PCA, hclust and bar plots were generated using ggplot2 (Wickham). All the heatmaps of differentially expressed genes were generated using pheatmap package (Kolde, 2012) in R environment.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files; raw counts file output from STAR and Diff Expressed Genes using DESeq2

source_name: Tumor

extract_protocol:
RNA was isolated from fresh frozen surgical specimens using TRIzol (Cat# 10296010 Invitrogen) and purified using the RNeasy Mini Kit (Cat# 74106 Qiagen, Valencia, CA, USA) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MPNST

value: PRC2 mutant

tag: patient diagnosis


title: O_W18D7_O14_Unprotected


title: Sample_T6 RNA-seq


title: Sample_T9 RNA-seq


title: Sample_T27 RNA-seq


title: Sample_T26 RNA-seq


title: O_W18D0_O14_Unprotected


title: O_W18D3_O14_Unprotected


title: O_W18D1_O14_Unprotected


title: Sample_7BT RNA-seq


title: Sample_32T RNA-seq


title: O_W0D7_O14_Unprotected


title: Sample_N6 RNA-seq

source_name: Adjacent Normal

value: Muscle


title: Sample_NF4T RNA-seq

description: mRNA seq


title: Sample_N9 RNA-seq


title: Sample_N3 RNA-seq


title: O_W0D1_O14_Unprotected


title: WT rep1


title: O_W0D3_O15_Protected


title: Sample_N26 RNA-seq

value: Fat


title: O_W88D0_O13_Unprotected


title: O_W18D7_O13_Unprotected


title: Sample_7BN RNA-seq


title: O_W18D1_O13_Unprotected


title: O_W18D3_O13_Unprotected


title: T265  Cell line Input ChIP

description: PRC2 mutant

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the hg19 reference genome using Bowtie version 1.1.2 with the following criteria: -m 1 --best --strata. Duplicate reads were marked using SAMBLASTER before compression to BAM files. To directly compare FED and FASTED ChIP-seq samples, uniquely mapped reads for each mark were normalized by total reads per condition, sorted and indexed using samtools version 1.9
Model based analysis of ChIP-seq (MACS) version 1.4.2 and macs2  peak calling algorithm with a p-value threshold of 1e-5 to identify histone mark enrichment over “input” background
deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bed peak file, bigwig

source_name: Patient derived

growth_protocol: Cells were cultured in DMEM, 10% Fetal Bovine Serum (FBS), 1% Penicillin/Streptomycin at 37c, 5% CO2.

extract_protocol:
Cells were crosslinked with both 0.75% formaldehyde and glycine. Chromatin was sheared to 200-700 bp using a Diagenode Bioruptor.
DNA were end-repaired, adapter-ligated using NEBNext Ultra II DNA library prep kit from Illumina and sequenced by Illumina HiSeq2000 at SR-36.

treatment_protocol: Cells did not undergo any treatment.

value: Peripheral nerve


title: Sample_32N RNA-seq


title: O_W18D0_O13_Unprotected


title: T265   Cell line H3K27me3 ChIP

description: PRC2 mutant

tag: chip-antibody

value: H3K27me3 Abcam ab6002


title: O_W0D3_O13_Unprotected


title: T265   Cell line H3K79me2 ChIP

description: PRC2 mutant

value: H3K79me2 Abcam ab3594


title: O_W0D3_O14_Unprotected


title: T265  Cell line H3K9me3 ChIP

description: PRC2 mutant

value: H3K9me3 Abcam ab8898


title: O_W0D0_O13_Unprotected

value: Prime


title: Sample_N27 RNA-seq


title: O_W0D0_O14_Unprotected

value: O


title: O_W88D0_O12_Protected

value: Oral


title: ST88 Cell line Input ChIP

description: PRC2 mutant


title: O_W18D3_O12_Protected

value: Protected


title: O_W18D1_O12_Protected


title: ST88  Cell line H3K4me3 ChIP

description: PRC2 mutant

value: H3K4me3 Abcam ab8580


title: O_W18D0_O12_Protected


title: O_W0D7_O12_Protected


title: ST88  Cell line H3K79me2 ChIP

description: PRC2 mutant


title: ST88  Cell line H3K27Ac ChIP

description: PRC2 mutant

value: H3K27ac Abcam ab4729


title: ST88 Cell line H3K4me1 ChIP

description: PRC2 mutant

value: H3K4me1 Abcam ab8895


title: O_W0D3_O12_Protected


title: O_W0D1_O12_Protected


title: O_W0D7_O13_Unprotected

value: Unprotected


title: T265   Cell line H3K4me3 ChIP

description: PRC2 mutant


title: ST88  Cell line H3K27me3 ChIP

description: PRC2 mutant


title: O_W0D1_O13_Unprotected


title: T265   Cell line H3K27Ac ChIP

description: PRC2 mutant


title: O_W0D0_O12_Protected


title: STS26T Cell line Input ChIP

description: PRC2 WT

value: PRC2 WT


title: O_W18D7_O11_Protected

value: Boost


title: STS26T  Cell line H3K27me3 ChIP

description: PRC2 WT


title: T265 Cell line H3K4me1 ChIP

description: PRC2 mutant

value: PRC2 mutant


title: O_W18D7_O12_Protected


title: O_W18D3_O11_Protected


title: O_W18D1_O11_Protected


title: STS26T  Cell line H3K4me3 ChIP

description: PRC2 WT


title: O_W18D0_O11_Protected


title: STS26T  Cell line H3K79me2 ChIP

description: PRC2 WT


title: O_W0D7_O11_Protected


title: STS26T  Cell line H3K27Ac ChIP

description: PRC2 WT


title: STS26T  Cell line H3K9me3 ChIP

description: PRC2 WT


title: STS26T Cell line H3K4me1 ChIP

description: PRC2 WT


title: SNF02.2  Cell line Input ChIP

description: PRC2 WT

source_name: ATCC


title: O_W0D3_O11_Protected


title: O_W0D1_O11_Protected


title: SNF02.2  Cell line H3K27me3 ChIP

description: PRC2 WT


title: O_W0D0_O11_Protected


title: ST88  Cell line H3K9me3 ChIP

description: PRC2 mutant


title: O_W88D0_O10_Unprotected


title: SNF02.2  Cell line H3K4me3 ChIP

description: PRC2 WT


title: O_W18D7_O10_Unprotected


title: O_W18D3_O10_Unprotected


title: O_W88D0_O11_Protected


title: SNF02.2  Cell line H3K79me2 ChIP

description: PRC2 WT


title: SNF02.2  Cell line H3K9me3 ChIP

description: PRC2 WT


title: O_W18D1_O10_Unprotected


title: SNF02.2  Cell line H3K27Ac ChIP

description: PRC2 WT


title: S462 Cell line Input ChIP

description: PRC2 mutant


title: S462 Cell line H3K27me3 ChIP

description: PRC2 mutant


title: S462 Cell line H3K4me3 ChIP

description: PRC2 mutant


title: O_W0D3_O10_Unprotected


title: O_W0D0_O10_Unprotected


title: O_W0D1_O10_Unprotected


title: O_W0D7_O10_Unprotected


title: S462 Cell line H3K79me2 ChIP

description: PRC2 mutant


title: S462 Cell line H3K27Ac ChIP

description: PRC2 mutant


title: O_W18D7_O9_Protected


title: O_W88D0_O9_Protected


title: S462 Cell line H3K9me3 ChIP

description: PRC2 mutant


title: NSC Cell line Input ChIP

description: PRC2 WT

source_name: Normal Schwann cell


title: O_W18D0_O9_Protected


title: O_W18D1_O9_Protected


title: NSC Cell line H3K27me3 ChIP

description: PRC2 WT


title: O_W0D7_O9_Protected


title: NSC Cell line H3K4me3 ChIP

description: PRC2 WT


title: O_W0D3_O9_Protected


title: O_W18D0_O10_Unprotected


title: O_W0D1_O9_Protected


title: SNF02.2 Cell line H3K4me1 ChIP

description: PRC2 WT


title: O_W0D0_O9_Protected


title: O_W18D3_O9_Protected


title: MPNST724 Cell line Input ChIP

description: PRC2 WT


title: NSC Cell line H3K27Ac ChIP

description: PRC2 WT


title: NSC Cell line H3K4me1 ChIP

description: PRC2 WT


title: NSC Cell line H3K9me3 ChIP

description: PRC2 WT


title: O_W18D7_O8_Protected


title: MPNST724 Cell line H3K27me3 ChIP

description: PRC2 WT


title: S462 Cell line H3K4me1 ChIP

description: PRC2 mutant


title: MPNST724 Cell line H3K79me2 ChIP

description: PRC2 WT


title: O_W0D3_O8_Protected


title: O_W18D0_O8_Protected


title: O_W18D3_O8_Protected


title: O_W18D1_O8_Protected


title: MPNST724 Cell line H3K4me3 ChIP

description: PRC2 WT


title: MPNST724 Cell line H3K9me3 ChIP

description: PRC2 WT


title: O_W0D7_O8_Protected


title: MPNST724 Cell line H3K27Ac ChIP

description: PRC2 WT


title: MPNST724 Cell line H3K4me1 ChIP

description: PRC2 WT


title: O_W0D1_O8_Protected


title: O_W0D0_O8_Protected


title: MPNST642 Cell line Input ChIP

description: PRC2 mutant


title: MPNST642 Cell line H3K27me3 ChIP

description: PRC2 mutant


title: O_W88D0_O7_Unprotected


title: MPNST642 Cell line H3K4me3 ChIP

description: PRC2 mutant


title: O_W18D1_O7_Unprotected


title: O_W18D7_O7_Unprotected


title: MPNST642 Cell line H3K27Ac ChIP

description: PRC2 mutant


title: O_W18D3_O7_Unprotected


title: MPNST642 Cell line H3K9me3 ChIP

description: PRC2 mutant


title: MPNST642 Cell line H3K79me2 ChIP

description: PRC2 mutant


title: O_W18D0_O7_Unprotected


title: MPNST642 Cell line H3K4me1 ChIP

description: PRC2 mutant


title: MPNST3813E Cell line Input ChIP

description: PRC2 mutant


title: MPNST3813ECell line H3K4me3 ChIP

description: PRC2 mutant


title: O_W0D3_O7_Unprotected


title: 3D+0.1%gel_1

city: Hangzhou

first: Wei

last: Shan

state: Zhejiang

address: Bone Marrow Transplantation Center, The First Afﬁliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, Zhejiang, PR China.

institute: Zhejiang University

description: D5_ gel_1

data_processing:
Library sequencing was performed on an Illumina HiSeq X Ten platform (Illumina) to generate 150-bp paired-end reads.
The paired-end reads were processed and aligned to the reference genome (GRCm38) using HISAT2 (v.2.0.5).
Mapped reads for each sample were assembled into transcriptome data using StringTie (v.1.3.3) with a reference-based approach. The normalized expression value was represented by fragments per kilobase of transcript per million mapped reads (FPKMs).
Cuffdiff (v1.3.0) was used to calculate the differential expression genes for each sample. Only comparisons with q-values < 0.05 and absolute log2 (fold change) values ≥1 were considered as significantly differentially expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: mouse pluripotent stem cells derived  total cells

growth_protocol: 3D inducment derived hematopoietic like colonies were seeded on OP9 stromal and 0.1% gelatin

extract_protocol:
Total RNA was extracted from sorted cell samples using TRIzol Reagent (Life Technologies) following the manufacturer’s instructions.
cDNA libraries were constructed using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina (Vazyme) according to the manufacturer’s protocol

treatment_protocol: using FACS to sort total cells from 3D+OP9 and3D+0.1%gelatin. In the 3D+OP9 hematopoietic differentiation system, we sorted D5-LSKCD201+ and D5-LSKCD201- cells, at the same time, we used  PE-anti-mouse-SSEA-1 to  sort mESC and sorted bone marrow derived  D5-LSKCD201+ and fetal liver derived  D5-LSKCD201+

tag: strain background


title: 3D+OP9_3

description: D5_OP9 _3

value: pluripotent stem cells derived  total cells


title: O_W0D7_O7_Unprotected


title: O_W0D1_O7_Unprotected


title: 3D+0.1%gel_2

description: D5_ gel_2


title: MPNST3813E Cell line H3K27Ac ChIP

description: PRC2 mutant


title: MPNST3813E Cell line H3K9me3 ChIP

description: PRC2 mutant


title: MPNST3813E Cell line H3K4me1 ChIP

description: PRC2 mutant


title: 3D+OP9_2

description: D5_OP9 _2


title: MPNST007 Cell line Input ChIP

description: PRC2 WT


title: 3D+OP9_1

description: D5_OP9 _1


title: MPNST007 Cell line H3K27me3 ChIP

description: PRC2 WT


title: MPNST007 Cell line H3K4me3 ChIP

description: PRC2 WT


title: 3D+0.1%gel_3

description: D5_ gel_3


title: MPNST007 Cell line H3K79me2 ChIP

description: PRC2 WT


title: MPNST007 Cell line H3K27Ac ChIP

description: PRC2 WT


title: MPNST3813E Cell line H3K27me3 ChIP

description: PRC2 mutant


title: MPNST007 Cell line H3K9me3 ChIP

description: PRC2 WT


title: O_W18D7_O6_Protected


title: O_W88D0_O6_Protected


title: MPNST3813E Cell line H3K79me2 ChIP

description: PRC2 mutant


title: MPNST007 Cell line H3K4me1 ChIP

description: PRC2 WT


title: [3'-RACE] B. anthracis 34F2 ΔatxA #2

city: Sapporo

first: Yoshikazu

last: Furuta

state: Hokkaido

address: North 20 West 10, Kita-ku

department: International Institute for Zoonosis Control

institute: Hokkaido University

data_processing:
[ChIP-seq] Sequence reads were applied for adapter trimming and quality filtering using Trim Galore! version 0.6.4_dev with the option "-a GATCGGAAGAGCACACGT", followed by mapping to the genome sequence of B. anthracis Ames ancestor strain (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using BWA-mem 0.7.17. The mapping data was applied for R package csaw 1.22.1 with 158 bp of fragment length and 50 bp of window width.
[Cappable-seq] For the analysis of sequence reads, adapter sequence was removed using cutadapt 2.1 with the option "-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", followed by mapping to the genome sequence of B. anthracis Ames ancestor (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using Bowtie2 2.3.5 with the option "-L 16". Coverage of the first base of mapped reads was calculated for each position with considering strands.
[3´-RACE] Reads were mapped to B. anthracis Ames ancestor (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using BWA-backtrack 0.7.17.
[RNA-seq] Reads were trimmed using Trim Galore! 0.6.4_dev with the option "-a AGATCGGAAGAGA", mapped to B. anthracis Ames ancestor (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using BWA-mem 0.7.17, and tag counted with htseq-count.

organism: Bacillus anthracis

source_name: B. anthracis 34F2 ΔatxA

growth_protocol: A colony of the strain grew on BHI plate at 37°C for overnight was inoculated into NBY medium supplemented with 8% NaHCO3, followed by shaking at 37°C under 15% CO2 for 3 h. 100-fold diluted in NBY medium supplemented with NaHCO3 and cultured at 37°C under 15% CO2 for 3 h.

extract_protocol:
[ChIP-seq] Cells were pelleted and treated with 1% formaldehyde for for crosslinking. 250 mM glycine was added for quenching. After pelleting and resuspension in lysis buffer with cOmplete Mini Protease Inhibitor Cocktail, the samples were sonicated using Covaris S2. Supernatants were combined with Anti-FLAG M2 affinity gel for enrichment, followed by wash and protease K treatment at 65°C. [Cappable-seq] RNA was extracted using TRIzol after incubating the pellet with 2% SDS. After removing DNA with DNA-free DNA removal kit, RNA samples followed the protocol described before (Ettwiller et al, BMC Genomics 17:199, 2016) [3´-RACE] RNA was extracted using TRIzol after incubating the pellet with 2% SDS. DNA was removed with DNA-free DNA removal kit. [RNA-seq] RNA was extracted using TRIzol after incubating the pellet with 2% SDS. DNA was removed with DNA-free DNA removal kit. rRNA was depleted by the protocol described before (Culviner et al, mBio, 2020), followed by fragmentation with the treatment with a divalent cation and heat.
[ChIP-seq] Library was constructed with NEBNext Ultra II DNA Library Prep Kit for Illumina. [Cappable-seq, 3´-RACE, and RNA-seq] Library was constructed with NEBNext Multiplex Small RNA Library Prep Set for Illumina.

value: B. anthracis 34F2 {delta}atxA


title: [3'-RACE] B. anthracis 34F2 ΔatxA #1


title: O_W18D3_O6_Protected


title: [3'-RACE] B. anthracis 34F2 WT #2

source_name: B. anthracis 34F2 WT

value: B. anthracis 34F2 WT


title: O_W18D1_O6_Protected


title: [3'-RACE] B. anthracis 34F2 WT #1


title: [Cappable-seq] B. anthracis 34F2 ΔatxA #3 enriched

data_processing:
Library strategy: Cappable-seq
[ChIP-seq] Sequence reads were applied for adapter trimming and quality filtering using Trim Galore! version 0.6.4_dev with the option "-a GATCGGAAGAGCACACGT", followed by mapping to the genome sequence of B. anthracis Ames ancestor strain (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using BWA-mem 0.7.17. The mapping data was applied for R package csaw 1.22.1 with 158 bp of fragment length and 50 bp of window width.
[Cappable-seq] For the analysis of sequence reads, adapter sequence was removed using cutadapt 2.1 with the option "-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", followed by mapping to the genome sequence of B. anthracis Ames ancestor (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using Bowtie2 2.3.5 with the option "-L 16". Coverage of the first base of mapped reads was calculated for each position with considering strands.
[3´-RACE] Reads were mapped to B. anthracis Ames ancestor (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using BWA-backtrack 0.7.17.
[RNA-seq] Reads were trimmed using Trim Galore! 0.6.4_dev with the option "-a AGATCGGAAGAGA", mapped to B. anthracis Ames ancestor (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using BWA-mem 0.7.17, and tag counted with htseq-count.