title: WT_Hc_M8: Wild-type Hippocampi, rep 6

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8)
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1)
Remaining reads were further filtered for low complexity with reaper (v. 15-065)
Reads were aligned to the Mus musculus.GRCm38.92 genome using STAR (v. 2.5.3a)
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7)
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1)
Genome_build: Mus musculus GRCm38.92
Supplementary_files_format_and_content: Tab-separated .txt files with gene-level read count estimates, computed by the htseq-count software package

source_name: Murine hippocampi

growth_protocol: Atria, ventricles, cerebellum, hippocampi, and cerebral cortex were excised from 18weeks-old male mice with ad-libitum access to food and water

extract_protocol:
Tissues were dissociated in QIAzol Lysis Reagent (Qiagen) using the gentleMACS™ Dissociator (Miltenyi Biotec). Cell suspension was used to obtain total RNA. Genomic DNA contamination was removed by digestion with RNase-free Deoxyribonuclease I (DNase I) (Qiagen). RNA concentration and purity were measured by ND-1000 spectrophotometer (Thermo Scientific, Wilmington, NC, USA) and RNA integrity was verified by fragment analyzer automated CE system (Advanced Analytical Technologies, Inc).
Libraries were prepared with 350 ng total RNA using Illumina TruSeq Stranded Total RNA Library Prep.

treatment_protocol: Wild-type, Heterzygous and knock-out mice (n = 6 per genotype)

value: Murine hippocampi

tag: genotype

value: Gnb5 Wild-type


title: WT_Hc_M7: Wild-type Hippocampi, rep 5

status: Public on Nov 30 2020

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue


title: WT_Co_M18: Wild-type Cerebral cortex, rep 4

source_name: Murine cerebral cortex

value: Murine cerebral cortex


title: WT_Hc_M18: Wild-type Hippocampi, rep 4


title: msLung_Male/Intact_nuc

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

country: USA

institute: University of Michigan

data_processing:
Read alignment and quantification were conducted with Cellranger (3.1.0) and pre-mRNA reference built from mm10-2.1.0 with mkref function
Genome_build: mm10
Supplementary_files_format_and_content: h5

growth_protocol: Eight-week old male C57BL/6 mice were purchased from the Jackson Laboratory. Four mice were surgically castrated and monitored for post-surgical health condition.

extract_protocol:
All buffers used were pre-chilled to 4oC and all steps were performed on ice or at 4oC, unless otherwise mentioned. Perfused mouse lungs, transported in RPMI (phenol-red free) at 4oC, were washed 2x with 1x PBS. Excess buffer from the lungs were wicked away, lungs were transferred to individual tubes and then the tubes were flash frozen in liquid nitrogen and used immediately or stored at -80oC. Tissues were then minced with a fresh, RNase free scalpel and added to a tube congaing chilled nuclei isolation buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.16% Nonidet™ P40 and 0.2 U/µL RNase inhibitor) at a tissue : buffer ratio of 0.1g : 100 µL. After incubating at 4oC with rotation for 10 min, tubes were incubated at 4oC for 2 min to let the debris settle down, and the supernatant containing the nuclei were collected. The supernatant was centrifuge at 500xg, 4oC for 5 min to pellet the nuclei. The supernatant was discarded and the pellet was resuspended in 500 µL resuspension buffer (1x PBS, 0.4% BSA and 0.2 U/µl of RNase inhibitor) and passed through a 70 µm filter. The above step was repeated, but the resuspended nuclei were passed through a 40 µm filter, and this step was repeated one more time. The nuclei suspension was centrifuged at 500xg, 4oC for 5 min to pellet the nuclei and the nuclei were resuspended in 100 µL of resuspension buffer. After counting (tryphan blue staining of ~10 µL of the sample), the nuclei suspension was diluted to a concentration of 1 million nuclei/mL and immediately used for 10x barcoding.
Approximately 5,000 nuclei from each sample were captured in Gel Bead-In-EMulsions (GEMs) containing ~ 750,000 unique molecular Indexes (UMIs) using the 10X Chromium Controller module. The GEMs were generated in a chip, containing Master Mix/cells mixture, Gel Beads and partitioning oil (placed in distinct compartments). Subsequent to dissolution of the Single Cell 3’ Gel Bead in a GEM, primers containing an Illumina P7 and R2 sequence (read 2 sequencing primer), a 14 bp 10x barcode, a 10 bp randomer and a poly-dT sequence werere released and mixed with cell lysate and reaction master mix. Reverse transcription produced barcoded, full-length cDNA. After GEMs were broken and cDNA cleaned using Solid Phase Reversible Immobilization (SPRI) beads the contents were subject to PCR. The sheared (Covaris) amplified cDNA were subjected to end repair, A-tailing, adaptor ligation, and PCR.
Samples were sequenced on Illumina HiSeq.

treatment_protocol: Twelve days post castration, four castrated male mice, together with four age-matched intact male mice, were sacrificed and lungs were perfused through the right ventricle with 10-20 ml PBS. After perfusion, the entire lung was washed twice with PBS and flash frozen in liquid nitrogen for use immediately or stored at -80 oC for single nuclei isolation.

tag: strain

value: C57BL/6 mice

value: Lung

tag: Sex

value: Male

tag: status

value: Intact

tag: age


title: WT_Co_M7: Wild-type Cerebral cortex, rep 5


title: WT_Hc_M17: Wild-type Hippocampi, rep 3


title: WT_Hc_M16: Wild-type Hippocampi, rep 2


title: WT_Co_M17: Wild-type Cerebral cortex, rep 3


title: WT_Hc_M15: Wild-type Hippocampi, rep 1


title: WT_Co_M8: Wild-type Cerebral cortex, rep 6


title: msLung_4Male/Castrated_12wks_nuc

value: Castrated


title: msLung_Male/Castrated_nuc


title: WT_Co_M16: Wild-type Cerebral cortex, rep 2


title: WT_Co_M15: Wild-type Cerebral cortex, rep 1


title: msLung_4Male/Intact_12wks_nuc


title: msLung_4Male/Intact_16wks_nuc


title: WT_Cb_M7: Wild-type Cerebellum, rep 5

source_name: Murine cerebellum

value: Murine cerebellum


title: WT_Cb_M8: Wild-type Cerebellum, rep 6


title: WT_BMDM_LPS_rep1

type: RNA

city: Dublin 2

first: Claire

middle: E

last: McCoy

address: 123 St Stephen's Green

country: Ireland

institute: Royal College of Surgeons in Ireland

hyb_protocol: cDNA was hybridised onto the Affymetrix mouse 430 2.0 array in accordance with the NuGEN guidelines for hybrdisation onto Affymetrix GeneChip arrays

scan_protocol: The array was scanned using probe level intensity measurements (CEL files), background corrected, normalised and summarised as expression measurement

data_processing: The data were processed with R/Bioconductor using the affy package and the rma function with default settings. Subsequent statistical analyses were performed using the limma package.

label: biotin

source_name: Wild-type bone marrow derived macrophages treated with LPS

label_protocol: RNA was amplified using NUGEN ovation RNA amplification system. cDNA was fragmented, labelled and hysridised using the NuGEN encore biotin Module

growth_protocol: bone marrow was extracted from the femurs of C57Bl/6 wild-type (n=2) and miR-155 KO animals (n=2) and stored in liquid nitrogen until later use. Cells were thawed and differentiated into BMDM using L929 (15%) conditioned media for 7 days.

extract_protocol: RNA was extracted using Applied Biosystems Rneasy kit

treatment_protocol: BMDM were stimulated with LPS (100 ng/ml) alone for 24 hours or pre-treated with IL-10 (20 ng/ml) for 5 minutes prior to the addition of LPS

tag: cell type

value: bone marrow derived macrophages

tag: genotype/variation

value: Wild-type

tag: treatment

value: LPS

tag: replicate

tag: gender

value: female


title: WT_BMDM_LPS_IL10_rep1

source_name: Wild-type bone marrow derived macrophages treated with LPS and IL10


title: WT_Cb_M17: Wild-type Cerebellum, rep 3


title: WT_Cb_M16: Wild-type Cerebellum, rep 2


title: WT_BMDM_LPS_rep2


title: hAstroStim2: Human Astrocytes 13 days IL1beta stimulation, replicate 2

city: Uppsala

first: Bo

last: Segerman

address: Dag Hammarskjolds v 20

country: Sweden

institute: Uppsala University

hyb_protocol: GeneChip® Human Transcriptome Array 2.0 were hybridized for 16 hours in a 45°C incubator. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev. 3, Affymetrix Inc., Santa Clara, CA) the arrays were washed and stained using the Fluidics Station 450

scan_protocol: scanned using the GeneChip® Scanner 3000 7G

data_processing:
The data were analyzed with Affymetrix® Expression Console™ Software using Affymetrix default analysis settings with the Robust Multiarray Averaging (RMA) algorithm.
probe group file: HTA-2_0.r3.pgf
meta-probeset file: HTA-2_0.r3.Psrs.mps

organism: Homo sapiens

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

growth_protocol: Astrocyte media (AM) supplemented with 2% fetal calf serum and 1% astrocyte growth supplement (ScienCell)

extract_protocol: RNeasy Plus Mini Kit, QIAGEN

treatment_protocol: 10 ng/ml IL1beta (Peprotech)

value: Astrocytes


title: KO_Hc_M5: Knock-out Hippocampi, rep 6

value: Gnb5 Knock-out


title: KO_Hc_M3: Knock-out Hippocampi, rep 5


title: KO_Hc_M1: Knock-out Hippocampi, rep 4


title: KO_Hc_M10: Knock-out Hippocampi, rep 1


title: KO_Co_M3: Knock-out Cerebral cortex, rep 5


title: KO_Hc_M14: Knock-out Hippocampi, rep 3


title: KO_Co_M5: Knock-out Cerebral cortex, rep 6


title: KO_Cb_M3: Knock-out Cerebellum, rep 5


title: KO_Co_M1: Knock-out Cerebral cortex, rep 4


title: KO_Cb_M10: Knock-out Cerebellum, rep 1


title: KO_Cb_M12: Knock-out Cerebellum, rep 2


title: WT_Cb_M18: Wild-type Cerebellum, rep 4


title: WT_Vt_M8: Wild-type Ventricles, rep 6

source_name: Right and left murine ventricles

value: Right and left murine ventricles


title: KO_Cb_M5: Knock-out Cerebellum, rep 6


title: KO_Co_M12: Knock-out Cerebral cortex, rep 2


title: KO_Co_M10: Knock-out Cerebral cortex, rep 1


title: KO_Cb_M14: Knock-out Cerebellum, rep 3


title: WT_Vt_M17: Wild-type Ventricles, rep 3


title: KO_Cb_M1: Knock-out Cerebellum, rep 4


title: WT_Vt_M18: Wild-type Ventricles, rep 4


title: WT_Vt_M7: Wild-type Ventricles, rep 5


title: WT_Vt_M16: Wild-type Ventricles, rep 2


title: WT_At_M18: Wild-type Atria, rep 4

source_name: Right and left murine atria

value: Right and left murine atria


title: KO_Hc_M12: Knock-out Hippocampi, rep 2

value: Murine hippocampi


title: WT_At_M7: Wild-type Atria, rep 5

value: Gnb5 Wild-type


title: WT_At_M8: Wild-type Atria, rep 6


title: WT_At_M17: Wild-type Atria, rep 3


title: WT_At_M16: Wild-type Atria, rep 2


title: WT_At_M15: Wild-type Atria, rep 1


title: KO_Vt_M5: Knock-out Ventricles, rep 6


title: KO_Co_M14: Knock-out Cerebral cortex, rep 3

value: Murine cerebral cortex


title: KO_Vt_M3: Knock-out Ventricles, rep 5


title: KO_Vt_M1: Knock-out Ventricles, rep 4


title: KO_Vt_M12: Knock-out Ventricles, rep 2


title: KO_Vt_M14: Knock-out Ventricles, rep 3


title: WT_Cb_M15: Wild-type Cerebellum, rep 1


title: KO_Vt_M10: Knock-out Ventricles, rep 1


title: KO_At_M5: Knock-out Atria, rep 6


title: WT_Vt_M15: Wild-type Ventricles, rep 1


title: KO_At_M3: Knock-out Atria, rep 5


title: KO_At_M14: Knock-out Atria, rep 3


title: KO_At_M1: Knock-out Atria, rep 4


title: HET_Vt_M4: Herozygous Ventricles, rep 4

value: Gnb5 Herozygous


title: HET_Vt_M9: Herozygous Ventricles, rep 6


title: HET_Vt_M6: Herozygous Ventricles, rep 5


title: KO_At_M10: Knock-out Atria, rep 1


title: HET_Vt_M13: Herozygous Ventricles, rep 2


title: HET_At_M9: Herozygous Atria, rep 6


title: HET_Vt_M11: Herozygous Ventricles, rep 1


title: HET_At_M6: Herozygous Atria, rep 5


title: HET_Vt_M2: Herozygous Ventricles, rep 3


title: HET_At_M4: Herozygous Atria, rep 4


title: HET_At_M13: Herozygous Atria, rep 2


title: HET_At_M2: Herozygous Atria, rep 3


title: HET_At_M11: Herozygous Atria, rep 1


title: WT_repeat2

city: Shanghai

first: Liufan

last: Yin

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

country: China

institute: Fudan University

data_processing:
Initial quality-control analysis for sequencing reads was performed using FastQC (Andrews S et al, 2013) . Raw sequencing reads were trimmed to remove the adapters and bases with low quality score (< 20) using Cutadapt (Martin 2011) . The trimmed reads were aligned to the Arabidopsis thaliana genome (TAIR10) with HISAT2 (Kim, Langmead et al. 2015) with parameter "--rna-strandness RF". SAMtools (Li, Handsaker et al. 2009) was used to gain high quality mapped reads (samtools view -q 20), sort reads (samtools sort), add index (samtools index) and estimate the number of uniquely mapped reads (samtools view -F 4 -c). FeatureCounts (Liao, Smyth et al. 2014) was empolyed to assign aligned reads to genes with parameters "-p -s 2 -t exon -g gene_id ". Differentially expressed genes (DEGs) were called with DESeq2 (Love, Huber et al. 2014) filtering the genes without expression in all samples. Genes were considered to be significantly differentially expressed between mutant and wild-type when |log2foldchange| ≥ log2(1.5) and the P value ≤ 0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files generated using DeepTools with binsize of 10. The matrix including log2Foldchange and pvalue gernerated by DESeq2

organism: Arabidopsis thaliana

source_name: 14-day-old seddlings grown up under long-day condition (16h light and 8h dark)

growth_protocol: Seeds were surface-sterilized by treatment with 75% alcohol for 20 min and washed with absolute ethanol. After sterilization seeds  were sown onto MS nutrient medium containing 1% agar and were incubated at 4°C in darkness for more than 3 days, followed by long-day condition (16h light and 8h dark in 22℃) for 14 days.

extract_protocol:
Total RNA was extracted from the snap-frozen tissues using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen).  PolyA+ RNA was enriched by selection with two rounds of oligo(dT) Dynabeads (Invitrogen).
Stranded RNA-seq library was constructed as previously described (Liu, Wei et al. 2016) according to a dUTP-based protocol (Zhong, Joung et al. 2011)

value: seedling

tag: development stage

value: wild-type

tag: growth protocol

value: long-day condition


title: WT_repeat1


title: atino80_repeat2


title: atino80_input_repeat1

library_source: genomic

data_processing:
Sequenced reads were aligned to the Arabidopsis thaliana genome (TAIR10). Bowtie2 v2.3.4.1 was used to map sequenced reads with default parameters to the Arabidopsis thaliana genome (TAIR10). Samtools v1.9 was used to get high quality (>20) mapped reads and remove potential PCR duplicates. Bed format files were generated by BEDTools v2.17.0. SICER v1.1 was used to identify H3 and H2A.Z enriched regions (peaks) by comparing ChIP library with the input library (parameters: W=200, G=200). Significant peaks are selected with the FDR <=0.05 criteria. The BigWig format files were generated by DeepTools v3.1.3 with the parameter “--binSize 10 --normalizeUsing RPKM”.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files were generated using DeepTools with binsize of 10.

molecule: genomic DNA

growth_protocol: Seeds were surface-sterilized by treatment with 75% alcohol for 20 min and washed with absolute ethanol, after sterilization, seeds were sown onto 1/ 2MS nutrient medium containing 1% agar and were incubated at 4°C in darkness for more than 3 days, followed by long-day condition (16h light and 8h dark in 22℃) for 14 days.

extract_protocol:
ChIP was performed as previously described (Johnson et al., 2002).
ChIP-seq libraries were prepared using the method previously described (Barski, Cuddapah et al. 2007).

tag: chip antibody


title: atino80_input_repeat2


title: atino80_H2AZ_repeat2

value: H2A.Z (Abmart)


title: atino80_H3_repeat1

value: H3 (Abcam, ab179)


title: atino80_H2AZ_repeat1


title: WT_input_repeat2

value: WT


title: KO_At_M12: Knock-out Atria, rep 2


title: atino80_H3_repeat2


title: WT_input_repeat1


title: WT_H3_repeat1


title: WT_H3_repeat2


title: WT_H2AZ_repeat1

source_name: 14-day-old seddlings grown up under long-day condition (16h light and 8h dark in 22℃)


title: data2_H820_E14

city: Seoul

first: AHYOUNG

last: CHOI

address: 52, Ewhayeodae-gil

country: South Korea

institute: Ewha womans university

description:
data2
sgRNA

data_processing:
Raw read data was first run through quality control metrics using FastQC.
Sequenced reads were filtered low quality sequence using fastx tool kit.
Resulting reads were trimmed to remove the constant portion of the sgRNA sequences with CRISPR.sgRNA_read_trimmer in the GenePattern Module Archive, then aligned to the GeCKO v2 sgRNA library using bowtie 1 (v1.1.1) under default settings.
After alignment, the number of uniquely aligned reads for each library sequence was calculated by CRISPR.single_sgRNA_count in GParc.
The raw read counts were normalized as follows: normalized reads per sgRNA = (reads per sgRNA / total reads for all sgRNAs in sample) x 10^6 + 1.
Genome_build: hg19
Supplementary_files_format_and_content: csv file include raw read count

source_name: CRISPR Screening

growth_protocol: Freshly prepared NCI-H820 cells (~2 × 107 cells) containing GeCKO libraries were split into three plates with each portion containing a minimum of 3 x 106 cells. The first portion were frozen down for genomic DNA analysis to profile the sgRNA diversity after transfection (D0) and  the second portion cultured in DMSO without erlotinib for 7 (D7) or 14 days (D14) as control samples.

extract_protocol:
Frozen cell pellets were thawed and genomic DNA was extracted with a Blood & Cell Culture Midi kit (Qiagen).
The amplification of sgRNA target sequences for deep sequencing was performed as described (http://genome-engineering.org/gecko) with minor modifications. All PCR products obtained from each sample were run on an agarose gel, gel-extracted, and purified according to manufacturer’s recommendations.
sgRNA (RNA-seq)

treatment_protocol: The third portion cultured with erlotinib for 7 (E7) or 14 days (E14). Erlotinib treated cells and control cells were passaged in fresh media with and without erlotinib, respectively (media changed in every 2-3 days). The screening experiment was performed in duplicate. All samples were subjected to sgRNA sequencing as follows.

tag: genotype/treatment

value: Erlotinib treated (day 14)

tag: cell line


title: atino80_repeat1


title: data1_H820_E14

description:
data1
sgRNA


title: data2_H820_D0

description:
data2
sgRNA

value: Wild type (day 0)


title: data1_H820_E7

description:
data1
sgRNA

value: Erlotinib treated (day 7)


title: data1_H820_D14

description:
data1
sgRNA

value: Wild type (day 14)


title: data2_H820_D14

description:
data2
sgRNA


title: data2_H820_D7

description:
data2
sgRNA

value: Wild type (day 7)


title: data1_H820_D7

description:
data1
sgRNA


title: Input

city: Fukuoka

first: TOMONORI

last: KAMEDA

address: 3-1-1, Maidashi, Higashi-ku, Fukuoka-shi

country: Japan

institute: Kyushu-University

description: Treatment: non

data_processing:
ChIP-seq; ChIP-seq was performed with 50-bp single-end sequencing by an Illumina Hiseq 3000. Obtained reads were processed with FASTX tool kit to remove short (<20bp) and low quality (quality score<20) reads, followed by trimming of the adaptor sequence.  Processed reads were aligned to the mouse genome (UCSC mm10) using Bowtie v2.2.4. All redundant reads were removed from further analysis. SAM files were converted to the BAM format using SAMtools (v0.1.19).  Peak calling for H3K27ac and H3K4me1 was performed using MACS version 1.4.1 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq; tab-delimited text files include peak region for each samples.
Supplementary_files_format_and_content: bw

source_name: Cultured hippocampal neurons (10DIV)

extract_protocol:
ChIP-seq; Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq; Sequencing libraries were made using the NEBNext ultraⅡ DNA Library Prep kit for Illumina (New England Biolabs).

value: ICR

value: E17 hippocampus

value: no antibody


title: data1_H820_D0

description:
data1
sgRNA


title: H3K4me1_non_treat_rep2

description: Treatment: non

value: mouse monoclonal anti-H3K4me1; MBL


title: H3K27ac_Bic/4AP_rep

description: Treatment: bicuculline/4-aminopyridine 3hrs

value: mouse monoclonal anti-H3K27ac; MBL


title: H3K27ac_non_treat_rep

description: Treatment: non


title: DIPG6_S1_Hi-C

city: Montreal

first: Carol

last: Chen

state: QC

address: 1001 Decarie Boulevard, Rm E01.4380

department: Human Genetics

country: Canada

institute: Research Institute of McGill University Hospital Centre

data_processing:
Trimming using TrimGalore v0.6.5
alignement using HiCUP v0.7.2
Compartment and Loop calls using Juicer and associated Juicer Tools v1.22.01
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: Compartments and loops are in bed format

source_name: patient-derived glioma cell line

growth_protocol: Tumor-derived cell lines Su-DIPG-VI, G477, and pcGBM2 were cultured in NeuroCult NS-A proliferation media (StemCell Technologies) supplemented with bFGF (10 ng/mL), rhEGF (20 ng/mL), and heparin (0.0002%) (StemCell Technologies) and on plates coated with poly-L-ornithine (0.01%) (Sigma) and laminin (0.01 mg/mL) (Sigma). All lines were tested monthly for mycoplasma contamination (MycoAlert Mycoplasma Detection kit by Lonza), and STR fingerprinting was regularly performed.

extract_protocol: For Hi-C, libraries were generated from 5 million cultured glioblastoma cell lines and disassociated mouse embryonic tissue as described in (Rao et al., 2014) with minor modifications. Briefly, in situ Hi-C consists of 7 steps: (1) crosslinking cells with formaldehyde, (2) digesting the DNA using a 4-cutter restriction enzyme (e.g., DpnII) within intact permeabilized nuclei, (3) filling in, biotinylating the resulting 5′-overhangs and ligating the blunt ends, (4) shearing the DNA, (5) pulling down the biotinylated ligation junctions with streptavidin beads, (6) library amplification and (7) analyzing these fragments using paired end sequencing. As quality control (QC) steps, we checked for efficient sonication with an agarose DNA gel and for appropriate size selection using the Agilent Bioanalyzer on final amplified libraries. For the final QC, we performed superficial sequencing on the Illumina Hiseq 2500 (~30M reads/sample) to assess quality of the libraries using percent of reads passing filter, percent of chimeric reads, and percent of forward-reverse pairs.  125bp paired-end sequencing was performed on the Illumina HiSeq 4000.

value: patient-derived glioma cell line

tag: cell line name

value: Su-DIPG-VI

tag: clone name

tag: passage

tag: media

value: stem

tag: library type

value: Hi-C


title: data2_H820_E7

description:
data2
sgRNA


title: PCGBM2_S1_Hi-C

tag: tissue

tag: genotype

value: H3 WT


title: G477_S1_Hi-C


title: H3K4me1_non_treat_rep1

description: Treatment: non

tag: strain


title: Spleen_3_d15

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

country: Germany

institute: German Center for Cancer Research

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: Trimmomatic
Preprocessing, quality filtering:Trimmomatic
BS-mapping: bsmap 2.74
computation of methylation ratios: methratio.py (part of bsmap package)
Genome_build: galGal5
Supplementary_files_format_and_content: bedgraph format containing coverage and methylation ratio information

organism: Gallus gallus

source_name: spleen tissue

extract_protocol:
For epithelial cell preparation from colon, colon was flushed with ice-cold PBS, cut open longitudinally. Distal and proximal colon region were processed separately. Each part was minced into small pieces in cold PBS. Enterocytes were mechanically isolated by shaking in PBS with 30 mM EDTA, at 37oC. Crypts were recovered and then stored at -80°C for DNA extraction. Only samples from distal colon were used in our study.
5 µg of high molecular weight DNA were used for fragmentation using the Covaris S2 AFA System in a total volume of 100 µl. Fragmentation-run parameters: Duty cycle 10%; Intensity: 5; Cycles/burst: 200; Time: 3 min; number of cycles: 3, resulting in a total fragmentation-time of 180 s. Fragmentation was confirmed with a 2100 Bioanalyzer (Agilent Technologies) using a DNA1000 chip. The fragmented DNAs were concentrated to a final volume of 75 µl using a DNA Speed Vac. End repair of fragmented DNA was carried out in a total volume of 100 µl using the Paired End DNA Sample Prep Kit (Illumina) as recommended by the manufacturer. For the ligation of the adaptors, the Illumina Early Access Methylation Adaptor Oligo Kit and the Paired End DNA Sample Prep Kit (Illumina) were used, as recommended by the manufacturer. For the size selection of the adaptor-ligated fragments, we used the E-Gel Electrophoresis System (Invitrogen) and a Size Select 2% precast agarose gel (Invitrogen). Each fragmented DNA was loaded on two lanes of the E-gel. Electrophoresis was carried out using the “Size Select” program for 16 min. According to the standard loaded (50 bp DNA Ladder, Invitrogen), 240 bp fragments were extracted from the gel, pooled, and directly transferred to bisulfite treatment without further purification. For the bisulfite treatment we used the EZ-DNA Methylation Kit (Zymo) as recommended by the manufacturer with the exception of a modified thermal profile for the bisulfite conversion reaction. The conversion was carried out in a thermal cycler using the following thermal profile: 95°C for 15 s, 50°C for 1 h, repeat from step 1, 15×, 4°C for at least 10 min. The libraries were subsequently amplified, using the Fast Start High Fidelity PCR System (Roche) with buffer 2, and Illuminas PE1.1 and PE2.1 amplification primers. PCR thermal profile: 95°C for 2 min, 95°C for 30 s, 65°C for 20 s, 72°C for 30 s, then repeat from step 2, 11×, 72°C for 7min, hold at 4°C. PCR reactions were purified on PCR purification columns (MinElute, Qiagen) and eluted in 20 µl elution buffer (Qiagen).

value: No treatment

tag: disease state

value: healthy

tag: age

value: 15 days after birth

value: spleen tissue


title: Spleen_3_d34

tag: treatment

value: 34 days after birth


title: WT_H2AZ_repeat2

value: seedling

tag: genotype/variation

value: WT

value: H2A.Z (Abmart)


title: Spleen_2_d15


title: Spleen_2_d3

value: 3 days after birth


title: Spleen_1_d34


title: Spleen_1_d15


title: Jejunum_3_d35_infl

source_name: jejunum tissue

value: inflamed

value: 35 days after birth

value: jejunum tissue


title: Jejunum_3_d35_cont


title: Spleen_1_d3


title: Spleen_3_d3


title: Jejunum_3_d16_infl

value: 16 days after birth


title: Jejunum_3_d16_cont


title: Spleen_2_d34


title: Jejunum_3_d14_cont

value: 14 days after birth


title: Jejunum_2_d16_infl


title: Jejunum_2_d14_cont


title: Jejunum_2_d35_infl


title: Jejunum_1_d35_infl


title: Jejunum_2_d14_infl


title: Jejunum_2_d35_cont


title: Ile_3_d34

source_name: ileum tissue

value: ileum tissue


title: Jejunum_1_d14_cont


title: Jejunum_1_d16_infl


title: Jejunum_1_d16_cont


title: Jejunum_2_d16_cont


title: Ile_3_d15


title: Jejunum_1_d35_cont


title: Jejunum_1_d14_infl


title: Ile_3_d3


title: Ile_2_d34


title: Ile_2_d3


title: Ile_1_d15


title: Breast_10_d14

source_name: breast tissue

value: breast tissue


title: Breast_8_d14


title: Ile_1_d3


title: Ile_2_d15


title: Breast_3_d34


title: Breast_3_d28

value: 28 days after birth


title: Breast_4_d28

value: No treatment


title: Breast_3_d15

value: healthy


title: Breast_3_d3


title: Breast_2_d34


title: Breast_1_d34


title: Breast_2_d15

value: 15 days after birth


title: Breast_1_d28


title: Breast_2_d3


title: Breast_1_d15


title: Breast_1_d3


title: Breast_7_d14


title: Jejunum_3_d14_infl


title: iPSC-EC 3

city: Hannover

first: Monika

last: Szepes

address: Carl-Neuberg Str. 1

department: Department of Cardiac, Thoracic, Transplantation and Vascular Surgery

institute: Hannover Medical School

description: ECs differentiated in suspension culture (Olmer et al. 2018 Stem Cell Reports)

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol V6.7’, except that 1000ng of labeled cRNA were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’.  Measurements of on-chip replicates (quintuplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  Averaged gPS values were normalized by quantile normalization followed by global linear scaling. For the latter approach, all quantile normalized gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array i’ in the formula shown below). Accordingly, finally normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   Finally normalized gPSArray i = quantile normalized gPSArray i  x (1500 / 75th PercentileArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 10 finally normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 10.

source_name: iPSC-EC (hCBiPSC2-eGFP)

label_protocol: 375ng of total RNA were used for synthesis of aminoallyl-UTP-modified (aaUTP) cRNA with the ‘Quick Amp Labeling kit, no dye’ (#5190-0447, Agilent Technologies) according to the manufacturer’s recommendations, except that reaction volumes were quartered and contained NTP-mix was exchanged by NTP Set (ATP, CTP, GTP, UTP) and aminoallyl-UTP (Fermentas, Thermo Scientific; order numbers R1091, R0481, respectively). Final NTP concentrations used for in-vitro transcription were 2.5mM (ATP, CTP, GTP), 1.88mM UTP, and 0.62mM aaUTP. The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; LifeTechnologies) as described in the Amino Allyl MessageAmp™ II Kit Manual (#AM1753; Life Technologies) except that reaction volumes were quartered.

growth_protocol: See at sample description

extract_protocol: Total RNA was isolated with the RNeasy Kit (Macherey-Nagel).

treatment_protocol: See at sample description

tag: passage number


title: iPSC-EC 1


title: hESC-CM 2

description: CMs differentiated in suspension culture (Dahlman et al. 2013 Biomaterials)

source_name: hESC-CM (hESC-αMHCneo)

value: Differentiation day 18


title: iPSC-EC 2


title: hESC-CM 3


title: HFF 2

description: ATCC; SCRC-1041

source_name: human foreskin fibroblast


title: hPSC 3

description: Kensah et al. Eur Heart J. 2013

source_name: undifferentiated hESC-αMHCneo

value: 36 (Feeder) + 11 (Geltrex)


title: hPSC 1

description: Hartung et al. Stem Cells Dev. 2013; Kropp et al. Stem Cells Transl Med. 2016

source_name: undifferentiated HSC1285_T-iPS2

value: 47 (Feeder) + 7 (Geltrex)


title: hPSC 2

description: Haase at al. Cell Stem Cell 2009; Merkert et al. Stem Cell Reports 2014

source_name: undifferentiated hCBiPSC2-eGFP

value: 76 (Feeder) + 4 (Geltrex)


title: RA4_271_CTL_27d: Malignant glioma clone U3065MG-C271 27 days control, replicate serie 2

type: genomic

hyb_protocol: bisulphite converted DNA, by using the EZ-96 DNA Methylation Gold Kit from Zymo Research, was hybridised to Illumina Infinium Human Methylation Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing: Illumina GenomeStudio

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: adherent cultures on laminin-coated dishes using neural stem cell media

extract_protocol: Dneasy blood and tissue kit (Qiagen)

tag: cell type

value: Malignant glioma clone

value: Untreated


title: iPSC-PC 2

description: PCs differentiated from iPSC (based on Orlova et al. Arterioscler Thromb Vasc Biol. 2014)

source_name: iPSC-PC (HSC1285_T-iPS2)


title: iPSC-PC 1


title: mGE_rep2_Hi-C

source_name: embryonic ganglionic eminence

value: embryonic ganglionic eminence

value: WT

value: Hi-C


title: hESC-CM 1

value: Differentiation day 21


title: RA2_271_IL1b_28d: Malignant glioma clone U3065MG-C271 28 days IL1beta stimulation, replicate serie 1


title: RA4_271_IL1b_13d: Malignant glioma clone U3065MG-C271 13 days IL1beta stimulation, replicate serie 2


title: hPC-PL 2

description: PromoCell, lot#3051403

source_name: placental pericyte


title: mCORTEX_rep2_Hi-C

source_name: embryonic forebrain cortex

value: embryonic forebrain cortex


title: iPSC-PC 3


title: hPC-PL 1

description: PromoCell, lot#4021804


title: Human_PBMCs_HSP #3917

city: Koga-City

first: Takashi

last: Imai

state: Fukuoka

address: 1-1-1 Chidori

department: Pediatrics

institute: FUKUOKA HIGASHI MEDICAL CENTER

hyb_protocol: not provided

scan_protocol: The arrays were scanned by FLA-8000 (Fuji Photo Film,Tokyo, Japan). Images were quantified using ArrayVision (Amersham Biosciences).

data_processing: The numerical data were normalized using LOWESS method without baseline transformation.

source_name: human PBMCs, HSP patient

label_protocol: Double-strand cDNA was synthesized from total RNA using oligo dT primer with a T7 RNA polymerase promoter site added to the 3’ end. Then, in vitro transcription was performed in the presence of amino allyl UTP to produce multiple copies of amino allyl labelled cRNA. Amino allyl labelled cRNA was purified, and then reacted with N-hydroxy succinimide esters of Cy3 (Amersham Pharmacia Biotech, Piscataway, NJ, USA) for cRNA from PBMCs of HSP patient.

extract_protocol: Total RNA was extracted using an RNA extraction kit Isogen (Nippon Gene, Tokyo, Japan), according to the manufacturer's instruction.

tag: diagnosis

value: HSP

value: PBMCs

tag: gender

value: female

source_name: human PBMCs, healthy controls

label_protocol: Double-strand cDNA was synthesized from total RNA using oligo dT primer with a T7 RNA polymerase promoter site added to the 3’ end. Then, in vitro transcription was performed in the presence of amino allyl UTP to produce multiple copies of amino allyl labelled cRNA. Amino allyl labelled cRNA was purified, and then reacted with N-hydroxy succinimide esters of Cy5 (Amersham Pharmacia Biotech, Piscataway, NJ, USA) for cRNA from PBMCs of healthy controls.

tag: cell types


title: RA4_271_IL1b_27d: Malignant glioma clone U3065MG-C271 27 days IL1beta stimulation, replicate serie 2


title: mCORTEX_rep1_Hi-C

tag: cell line name


title: RA4_271_CTL_13d: Malignant glioma clone U3065MG-C271 13 days control, replicate serie 2


title: R2 PIK3D transfected

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

country: France

institute: university Paris Sud11

description: Gene expression from liver cell line

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip human Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: the data were RMA normalized with Affymetrix expression console software

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

growth_protocol: liquid culture in triplicate

extract_protocol: Extraction of total RNA with RNeasy Mini kit with DNase I digestion according to the manufacturer's instructions.

treatment_protocol: transfection of PIK3D in R condition versus scramble in C condition

tag: cell line

tag: transfection


title: R3 PIK3D transfected

description: Gene expression from liver cell line


title: RA2_271_CTL_11d: Malignant glioma clone U3065MG-C271 11 days control, replicate serie 1


title: RA2_271_IL1b_21d: Malignant glioma clone U3065MG-C271 21 days IL1beta stimulation, replicate serie 1


title: mGE_rep1_Hi-C

tag: clone name

tag: passage

tag: media


title: liver_MMI_rep1

first: Dandan

last: Zhang

address: Dongan Road

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
log(MMI+T3/MMI)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were rendered hypothyroid by the addition of 0.1% methimazole (MMI) and 1% NaClO4 in their drinking water for two weeks . To identify hepatic miRNAs that have maximal T3 responsiveness, hypothyroid mice were injected intraperitoneally with a single dose of T3 (5μg/20g body weight).

extract_protocol: RNA was prepared using TRIZOL following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tissue

value: liver


title: RA2_271_IL1b_34d: Malignant glioma clone U3065MG-C271 34 days IL1beta stimulation, replicate serie 1


title: RA4_271_IL1b_42d: Malignant glioma clone U3065MG-C271 42 days IL1beta stimulation, replicate serie 2


title: RA2_271_IL1b_11d: Malignant glioma clone U3065MG-C271 11 days IL1beta stimulation, replicate serie 1


title: RA2_271_CTL_34d: Malignant glioma clone U3065MG-C271 34 days control, replicate serie 1


title: R1 PIK3D transfected

description: Gene expression from liver cell line


title: RA4_271_CTL_42d: Malignant glioma clone U3065MG-C271 42 days control, replicate serie 2


title: Rimo-Pf

city: Yokohama

first: Hiroko

last: Asahi

state: Kanagawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN Center for Biosystems Dynamics Research

description: Pf with RIMO

hyb_protocol: cRNA was hybridized to Affymetrix GeneChip® Plasmodium/Anopheles Genome Array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner..

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix Power Tools 1.15.0 software, and obtained normalized intensity values.

organism: Plasmodium falciparum

source_name: Pf exposed to RIMO

label_protocol: The cRNA was amplified, labeled usingGeneChip 3'IVT PLUS Kit according to the manufacturer's instructions.

growth_protocol: Erythrocytic Plasmodium falciparum was maintained in vitro in serum-free culture medium (GFSRPMI) in a humidified atomosphere of 5% oxygen at 37C.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: P. falciparum synchronized at the ring stage was cultured in the presence of dihydroartemisinin, 7-benzylidenenaltrexon, or rimonaband hydrochloride for 12 h. Parasites were isolated at the end of the incubation period, and preserved in RNAprotect Cell reagent (Qiagen).

tag: Stage

value: ring

value: rimonaband hydrochloride


title: Ile_1_d34

value: No treatment

tag: disease state

value: healthy

value: 34 days after birth

value: ileum tissue


title: MEF cells, CP_KO_rep2

city: Taichung

first: Yi-Ying

last: Chiou

address: No.145, Xingda Rd., South Dist.

department: Graduate Institute of Biochemistry

country: Taiwan

institute: National Chung Hsing University

data_processing:
Reads were aligned to the mm10 genome assembly using RNA STAR (Galaxy 2.6.0b-1)
The numbers of mapped reads of each gene were counts using FeatureCounts (Galaxy 1.6.0.6)
Raw gene counts were analyzed by Deseq2 (1.22.2)
Genome_build: mm10
Supplementary_files_format_and_content: Tabular files are raw gene counts (2nd column) for each gene (1st column) for each sample
Supplementary_files_format_and_content: Csv files are the output of Deseq2 analysis

source_name: immortalized MEF cell line

growth_protocol: Cells were maintained in the high glucose-DMEM (Gibco) medium supplemented with 10% FBS at 37 oC in a humidified incubator containing 5% CO2

extract_protocol: After removal of medium, cells were lysed with Trizol reagent. After phase separation, total RNA was purified by RNA mini kit (Invitrogen)  Purified RNA was poly-A enriched and the libraries were constructed using TruSeq stranded RNA preparation kit

tag: strain

value: immortalized MEF cell line

tag: genotype


title: MEF cells, PN_KO_rep1


title: RA2_271_CTL_21d: Malignant glioma clone U3065MG-C271 21 days control, replicate serie 1

value: Malignant glioma clone

tag: treatment

value: Untreated


title: DHART-Pf

description: Pf with DHART

source_name: Pf exposed to DHART

value: dihydroartemisinin


title: SARS-CoV-2 infected HUH-7_CNBP_eCLIP_input

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
library strategy: eCLIP-seq
Raw sequencing reads were trimmed using a custom python script.
Trimmed reads were aligned to a modified hg38 reference genome with the SARS-CoV2 contig appended.
Peaks and fold change signal were computed via macs2 'callpeak'
Genome_build: hg38 combined with NC_045512.2
Supplementary_files_format_and_content: Treatment over control binding peaks and overall signal (bigwig)

source_name: SARS-CoV-2 infected HUH-7 cell line

growth_protocol: We maintained HuH-7 cells in DMEM media (Thermo Fisher Scientific) supplemented with 10% heat-inactivated FBS (Thermo Fisher Scientific), and 100 units/ml streptomycin and 100 mg/ml penicillin. Cells were grown at 37°C and 5% CO2 atmosphere.

extract_protocol:
Following UV crosslinking, frozen lysates were combined with an equal amount of nuclease free water to adjust the lysis buffer to a 1x concentration. Subsequent steps were performed as described in the eCLIP protocol, with the following modifications. Immunoprecipitates were washed two times in 1 ml CLIP lysis buffer, two times in IP wash buffer (50 mM Tris-HCl pH 7.4, 300 mM NaCl, 1 mM EDTA, 1% (v/v) NP40, 0.5% sodium deoxycholate, 0.25 mM DTT), followed by two washes in 50 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.5% (v/v) NP40. All other steps were carried out as described in the eCLIP method (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016)). We used the following antibodies for immunoprecipitation reactions: CNBP antibody (Proteintech, 67109-1-Ig), LARP1 (Bethyl, A302-087A)
eCLIP-seq (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016))

treatment_protocol: For eCLIP experiments, we grew 8xe6 Huh7 cells and infected them with SARS-CoV-2 at MOI 5 PFU/cell. 24 hours after infection, culture media was removed, cells were briefly rinsed with PBS and subjected to UV-irradiation with a total dose of 0.8 J/cm2. Cells were scraped in PBS using a rubber policeman, pelleted at 200x g for 5 min and lysed by adding 2x CLIP lysis buffer (100 mM Tris-HCl pH 7.4, 300 mM NaCl, 2 mM EDTA, 2% (v/v) NP40, 1% sodium deoxycholate, 0.5 mM DTT). Following a 30 min incubation at room temperature, lysates were stored at -80°C.

value: SARS-CoV-2 at MOI 5 PFU/cell

tag: antibody


title: BNTX-Pf

description: Pf with BNTX

source_name: Pf exposed to BNTX


title: Human_PBMCs_HSPN #3983

source_name: human PBMCs, HSPN patient

label_protocol: Double-strand cDNA was synthesized from total RNA using oligo dT primer with a T7 RNA polymerase promoter site added to the 3’ end. Then, in vitro transcription was performed in the presence of amino allyl UTP to produce multiple copies of amino allyl labelled cRNA. Amino allyl labelled cRNA was purified, and then reacted with N-hydroxy succinimide esters of Cy3 (Amersham Pharmacia Biotech, Piscataway, NJ, USA) for cRNA from PBMCs of HSPN patient.

value: HSPN

tag: cell type

tag: age


title: C3 control

description: Gene expression from liver cell line

value: scramble control


title: MEF cells, PN_KO_rep2


title: Human_PBMCs_HSPN #3942

tag: diagnosis

tag: gender


title: SARS-CoV-2 infected HUH-7_CNBP_eCLIP

value: CNBP


title: GFSRPMI-Pf

description: Pf in GFSRPMI

source_name: Pf normally developed


title: Human_PBMCs_HSP #3843

value: HSP

value: PBMCs

value: male

tag: cell types


title: C2 control

description: Gene expression from liver cell line

tag: cell line


title: E17.5-SC

city: Suita

first: Tokuichi

last: Iguchi

state: Osaka

address: 2-2 Yamada-oka

institute: Osaka University

description: Gene expression data from superior colliculus dissected from the E17.5 mouse brain, pooled from 16 mice.

hyb_protocol: Sense strand cDNA was hybridized to an Affymetrix GeneChip Mouse Gene 1.0 ST Array (Affymetrix, PN 901169) in the Hybridization Oven 645 (Affymetrix) according to the manufacturer’s instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings and global scaling as normalization method.

source_name: embryonic day 17.5 superior colliculus

label_protocol: Generation of sense strand cDNA from total RNA was performed using the Ambion WT Expression Kit (Applied Biosystems). Sense strand cDNA was labeled using the Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix, PN 900671).

growth_protocol: Mice were maintained on 12 hour light/dark cycle.

extract_protocol: Total RNA was extracted using Trizol (Thermo) followed by column purification using RNeasy Mini kit (QIAGEN).

tag: strain/background

value: ICR

value: superior colliculus

value: embryonic day 17.5


title: RA2_271_CTL_28d: Malignant glioma clone U3065MG-C271 28 days control, replicate serie 1


title: E17.5-OB

description: Gene expression data from olfactory bulb dissected from the E17.5 mouse brain, pooled from 14 mice.

source_name: embryonic day 17.5 olfactory bulb

value: olfactory bulb


title: C1 control

description: Gene expression from liver cell line

tag: transfection


title: MEF cells, CP_KO_rep1


title: Postnatal day 5 Pontine nucleus

description: Gene expression data from pontine nucleus dissected from the P5 mouse brain, pooled from 13 mice.

source_name: postnatal day 5 pontine nucleus

value: pontine nucleus

value: postnatal day 5


title: Postnatal day 1 Pontine nucleus

description: Gene expression data from pontine nucleus dissected from the P1 mouse brain, pooled from 16 mice.

source_name: postnatal day 1 pontine nucleus

value: postnatal day 1


title: Postnatal day 14 Pontine nucleus

description: Gene expression data from pontine nucleus dissected from the P14 mouse brain, pooled from 12 mice.

source_name: postnatal day 14 pontine nucleus

value: postnatal day 14


title: HFF 1

description: ATCC; SCRC-1041

source_name: human foreskin fibroblast

tag: passage number


title: MEF cells, CMEF cells, PN_KO_rep2

value: immortalized MEF cell line


title: E17.5-Pons

description: Gene expression data from pontine nucleus dissected from the E17.5 mouse brain, pooled from 15 mice.

source_name: embryonic day 17.5 pontine nucleus


title: SARS-CoV-2 infected HUH-7_LARP1_eCLIP_input


title: Embryonic day 17.5 pontine nucleus

description: Gene expression data from pontine nucleus dissected from the E17.5 mouse brain, pooled from 27 mice.


title: SARS-CoV-2 infected HUH-7_LARP1_eCLIP


title: E17.5-cerebellum

description: Gene expression data from cerebellum dissected from the E17.5 mouse brain, pooled from 13 mice.

source_name: embryonic day 17.5 cerebellum

value: cerebellum


title: MEF cells, CMEF cells, PN_KO_rep1


title: HNES1_PXGL_MEF_rep2

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

country: United Kingdom

institute: Cerevance ltd

data_processing:
Trim Galore!
STAR alignment
XenofilteR
GATK for RNAseq
HTSeq
Genome_build: hg38/mm10
Supplementary_files_format_and_content: raw count

growth_protocol: Naïve hPSCs were cultured in 5% O2, 7% CO2 in a humidified incubator at 37°C. Cell lines were maintained without antibiotics and confirmed free of mycoplasma contamination by periodic in-house PCR assay.     Chemically reset (cR), embryo-derived (HNES1) naïve stem cells and naïve iPSC were propagated in N2B27 with PXGL [1 µM PD0325901 (P), 2 µM XAV939 (X), 2 µM Gö6983 (G) and 10 ng/mL human LIF (L)] on irradiated MEF feeders as described (Bredenkamp et al., 2019). ROCK inhibitor (Y-27632) and Geltrex (0.5µL per cm2 surface area; hESC-Qualified, Thermo Fisher Scientific, A1413302,) were added to media during replating. Cultures were passaged by dissociation with Accutase (Biolegend, 423201) every 3-5 days.     Human adullt dermal fibroblast (HDF) and endothelial progenitor cells(EPC) derived naïve iPSCs were generated with StemRNA 3rd Gen Reprogramming Kit as described (Bredenkamp et al., 2019).

extract_protocol:
Total RNA was extracted from two biological replicate cultures of each cell line and time point using TRIzol/chloroform (Thermo Fisher Scientific, 15596018), and RNA integrity assessed by Qubit measurement and RNA.Ribosomal RNA was depleted from 1 µg of total RNA using Ribozero (Illumina kit). nanochip Bioanalyzer.
Sequencing libraries were prepared using the TruSeq RNA Sample Prep Kit (RS-122-2001, Illumina).
Sequencing was performed on the Novaseq S1 or S2 platform (Illumina), according to the manufacturer’s instructions.

value: embryo derived naive hESC

tag: original tissue

value: epiblst/blastocyst


title: EPC_niPSC_PXGL_MEF_rep1

value: naive iPSC

value: peripheral blood-derived endothelial progenitor cells


title: EPC_niPSC_PXGL_MEF_rep2


title: HDF16_niPSC_PXGL_MEF_rep1

value: adult dermal fibroblast


title: cR_H9_PXGL_MEF_rep1

value: chemically reset naive hESC

value: hESC


title: cR_H9_PXGL_MEF_rep2


title: HDF16_niPSC_PXGL_MEF_rep2


title: HNES1_PXGL_MEF_rep1


title: AK58_leaf_HiC_rep1

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

data_processing:
Sequencing reads were cleaned with the Trim Galore (version 0.4.4), Trimmomatic (version 0.36) , and Sickle programs, which eliminated bases with low-quality scores (< 25), irregular GC contents, sequencing adapters, and short reads.
The cleaned reads were mapped to AK58 genome using  Bismark_v0.19.0 for bisulfite-sequencing data, HISAT2(v2.1.0)for RNA-sequencing data, HiC-Pro(v2.11.1) for HiC-sequencing data.For smRNA-seq, cleaned reads of 24-nt were mapped to AK58 genome using Shortstack(v3.8.5)
Genome_build: AK58 genome
Supplementary_files_format_and_content: In RNA-seq, read counts for genes were provided;In smRNA-seq ,24nt-sRNA cluster files were provided; In Bisulfite-seq ,tdf files with position and  methylation ratio were provided.

organism: Triticum aestivum

growth_protocol: Seeds were germinated and cultured with water in Petri dishes for 1 week, then transferred into nutrient solution cultured for another 2 weeks till three-leaf stage, in a growth chamber with 20 °C/18 °C (day/night), 16 h/8 h (light/dark). Leaves were harvested at 11:00 AM-12:00 PM

extract_protocol:
Bisulfite and RNA sequencing samples were prepared with 2.2 μg DNA and 2μg total RNA (rRNA depleted) extracted from the harvested leaves respectively.
The library were constructed and the subsequent deep sequencing was completed by Novogene Co Ltd. For in situ HiC library, rep1 used HindIII enzyme  and rep2 used DpnII enzyme.

treatment_protocol: No treatment applied

tag: tissue

value: leaf

tag: cultivar


title: AK58_leaf_RNA_seq_rep3


title: AK58_leaf_RNA_seq_rep2


title: AK58_leaf_HiC_rep2


title: AK58_leaf__sRNA_seq_rep2

data_processing:
Sequencing reads were cleaned with the Trim Galore (version 0.4.4), Trimmomatic (version 0.36) , and Sickle programs, which eliminated bases with low-quality scores (< 25), irregular GC contents, sequencing adapters, and short reads.
The cleaned reads were mapped to AK58 genome using  Bismark_v0.19.0 for bisulfite-sequencing data, HISAT2(v2.1.0)for RNA-sequencing data, HiC-Pro(v2.11.1) for HiC-sequencing data.For smRNA-seq, cleaned reads of 24-nt were mapped to AK58 genome using Shortstack(v3.8.5)
Genome_build: AK58 genome
Supplementary_files_format_and_content: In RNA-seq, read counts for genes (IWGSC RefSeq v1.0) were provided;In smRNA-seq ,24nt-sRNA cluster files were provided; In Bisulfite-seq ,tdf files with position and  methylation ratio were provided.

extract_protocol:
Bisulfite and RNA sequencing samples were prepared with 2.2 μg DNA and 2μg total RNA (rRNA depleted) extracted from the harvested leaves respectively.
The library were constructed and the subsequent deep sequencing was completed by Novogene Co Ltd.
Bisulfite-seq, smRNA-seq


title: D_atino80_repeat2

data_processing:
Initial quality-control analysis for sequencing reads was performed using FastQC (Andrews S et al, 2013) . Raw sequencing reads were trimmed to remove the adapters and bases with low quality score (< 20) using Cutadapt (Martin, 2011) . The trimmed reads were aligned to the Arabidopsis thaliana genome (TAIR10) with HISAT2 (Kim, Langmead et al. 2015) with default parameters. SAMtools (Li, Handsaker et al. 2009) was used to gain high quality mapped reads (samtools view -q 20), sort reads (samtools sort), add index (samtools index) and estimate the number of uniquely mapped reads (samtools view -F 4 -c). FeatureCounts (Liao, Smyth et al. 2014) was empolyed to assign aligned reads to genes with parameters “-p -s 0 -t exon -g gene_id”. Differentially expressed genes (DEGs) were called with DESeq2 (Love, Huber et al. 2014) filtering the genes without expression in all samples. Genes were considered to be significantly differentially expressed between mutant and wild-type when |log2foldchange| ≥ log2(1.5) and the P value ≤ 0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files generated using DeepTools with binsize of 10. The matrix including log2Foldchange and pvalue gernerated by DESeq2

source_name: 4-day-old seddlings grown up under continuous dark

growth_protocol: Seeds were surface-sterilized by treatment with 75% alcohol for 20 min and washed with absolute ethanol.after sterilization seeds  were sown onto 1/2 MS nutrient medium containing 1% agar and were incubated in darkness in 4°C  for more than 3 days and then transferred to 22℃  at continuous dark for 4 days .

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara)
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA)

value: seedling

tag: development stage

value: atino80-6 mutant

tag: growth protocol

value: dark condition


title: D_atino80_repeat3

tag: genotype


title: D_WT_repeat3

value: wild-type


title: D_atino80_repeat1


title: D_WT_repeat1


title: AK58_leaf__Bisulfite_seq_rep2


title: AK58_leaf__sRNA_seq_rep1


title: D_WT_repeat2


title: AK58_leaf__Bisulfite_seq_rep1

extract_protocol:
Bisulfite and RNA sequencing samples were prepared with 2.2 μg DNA and 2μg total RNA (rRNA depleted) extracted from the harvested leaves respectively.
The library were constructed and the subsequent deep sequencing was completed by Novogene Co Ltd.


title: MuSCs, Post-injury Day 21, Sestrin1,2 Knockout [d21_SestrinKO_Rep1]

status: Public on Nov 26 2020

city: Ann Arbor

first: Carlos

middle: Andres

last: Aguilar

state: MI

address: 2800 Plymouth Rd

department: Biomedical Engineering

description:
d21_SestrinKO_Rep1
76bp SE RNA-Seq
MuSC-d-21-KO-R1
bulkRNAseq.TPM.tsv
bulkRNAseq.estimated_counts.tsv
bulkRNAseq.batchCorrected.rlogTransformed.tsv

data_processing:
Read pseudo-alignment and estimated transcript abundance using Kallisto (v.0.46.1) with the following parameters: kallisto quant -b 100 --single -l 300 -s 30 -i [mm10.idx] -t 45 -o [output folder] [trimmed FASTQ]
Gene-level count matrices using tximport (v.1.14.0).
Technical replicates with pearson correlation < 0.9 across gene TPM values were excluded from analysis.
Genome_build: mm10 (GRCm38.p6)
Supplementary_files_format_and_content: bulkRNAseq.TPM.tsv: Tab-delimited text file including abundance measurements (TPM) for each mm10 gene.
Supplementary_files_format_and_content: bulkRNAseq.estimated_counts.tsv: Tab-delimited text file including estimated counts for each mm10 gene.
Supplementary_files_format_and_content: bulkRNAseq.batchCorrected.rlogTransformed.tsv: Tab-delimited text file including surrogate variable analysis (SVA) batch corrected and regularized log (rlog) transformed TPM for each mm10 gene.

source_name: Tibialis anterior, gastrocnemius, and quadriceps

extract_protocol:
Hind limb muscles (tibialis anterior, gastrocnemius, and quadriceps) of wild type and Sestrin1,2 knockout mice were dissected using sterile surgical tools at 0, 7, and 21 days after injury. Tissues were minced and transferred into 50 mL conical tubes containing 20 mL of digest solution. Cell sorting was done using a BD FACSAria III Cell Sorter.
MuSCs were FACS sorted directly into Trizol and snap frozen. Samples were subsequently thawed, and RNA was extracted using a Qiagen miRNeasy Micro Kit as per manufacturer’s instructions. The integrity of the isolated RNA was verified with a Bioanalyzer (Agilent 2100) and 1-10 ng of high-quality RNA (RIN>8) was used to produce cDNA libraries using the SmartSeq v4 protocol (Clontech) as per the manufacturer’s instructions. cDNAs were prepared into sequencing libraries using 150 pg of full-length cDNA amplicons (Nextera XT DNA Library Preparation Kit, Illumina) with dual index barcodes. Barcoded cDNA libraries were pooled into a single tube and sequenced on a NextSeq (Illumina) using 76-bp single-ended reads.

value: Flow sorted muscle stem cells

tag: strain

value: Sestrin1,2 Knockout

value: 2-3 months

tag: timecourse

value: Post-injury Day 21


title: MuSCs, Post-injury Day 21, Wild type [d21_WT_Rep2]

description:
d21_WT_Rep2
76bp SE RNA-Seq
MuSC-d-21-WT-R2
bulkRNAseq.TPM.tsv
bulkRNAseq.estimated_counts.tsv
bulkRNAseq.batchCorrected.rlogTransformed.tsv

tag: cell type

value: Sestrin1,2 Wild type


title: MuSCs, Post-injury Day 21, Wild type [d21_WT_Rep1]

description:
d21_WT_Rep1
76bp SE RNA-Seq
MuSC-d-21-WT-R1
bulkRNAseq.TPM.tsv
bulkRNAseq.estimated_counts.tsv
bulkRNAseq.batchCorrected.rlogTransformed.tsv

tag: age


title: MuSCs, Post-injury Day 21, Sestrin1,2 Knockout [d21_SestrinKO_Rep2]

description:
d21_SestrinKO_Rep2
76bp SE RNA-Seq
MuSC-d-21-KO-R2
bulkRNAseq.TPM.tsv
bulkRNAseq.estimated_counts.tsv
bulkRNAseq.batchCorrected.rlogTransformed.tsv


title: MuSCs, Post-injury Day 7, Wild type [d7_WT_Rep1]

description:
d7_WT_Rep1
76bp SE RNA-Seq
MuSC-d-7-WT-R1
bulkRNAseq.TPM.tsv
bulkRNAseq.estimated_counts.tsv
bulkRNAseq.batchCorrected.rlogTransformed.tsv

value: Post-injury Day 7


title: MuSCs, Pre-injury, Wild type [d0_WT_Rep1]

description:
d0_WT_Rep1
76bp SE RNA-Seq
MuSC-d-0-WT-R1
bulkRNAseq.TPM.tsv
bulkRNAseq.estimated_counts.tsv
bulkRNAseq.batchCorrected.rlogTransformed.tsv

value: Pre-Injury


title: MuSCs, Pre-injury, Wild type [d0_WT_Rep2]

description:
d0_WT_Rep2
76bp SE RNA-Seq
MuSC-d-0-WT-R2
bulkRNAseq.TPM.tsv
bulkRNAseq.estimated_counts.tsv
bulkRNAseq.batchCorrected.rlogTransformed.tsv


title: MuSCs, Post-injury Day 7, Sestrin1,2 Knockout [d7_SestrinKO_Rep1]

description:
d7_SestrinKO_Rep1
76bp SE RNA-Seq
MuSC-d-7-KO-R1
bulkRNAseq.TPM.tsv
bulkRNAseq.estimated_counts.tsv
bulkRNAseq.batchCorrected.rlogTransformed.tsv


title: AK58_leaf_RNA_seq_rep1


title: LPS-stimulated naive RAW264.7 cells

city: fukuoka

first: naoya

last: matsunaga

address: maidashi 3-1-1, higashi-ku

institute: kyushu university

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: naive RAW264.7 cells, LPS-stimulated

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using ReliaPrep TM  RNA Cell Miniprep System (Promega) according to the manufacturer's instructions.

tag: genotype/variation

value: wild type

tag: lps stimulated

value: yes


title: LPS-stimulated Mfp2-/- RAW264.7 cell

source_name: Mfp2-/-  RAW264.7 cells,  LPS-stimulated


title: MuSCs, Pre-injury, Sestrin1,2 Knockout [d0_SestrinKO_Rep1]

institute: University of Michigan

description:
d0_SestrinKO_Rep1
76bp SE RNA-Seq
MuSC-d-0-KO-R1
bulkRNAseq.TPM.tsv
bulkRNAseq.estimated_counts.tsv
bulkRNAseq.batchCorrected.rlogTransformed.tsv


title: naive RAW264.7 cells

source_name: naive RAW264.7 cells

value: no


title: paternal vehicle injection offspring [KG7.9]

status: Public on Nov 25 2020

first: Eric

last: Miska

address: Gurdon Institute, Tennis Court Rd

department: Cambridge University

institute: Cambridge University

description:
KG7.9
small RNA seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using Star.
Reads matching mirRBase annotations (v21) were quantified using feature counts.
Countmatrix obtained was normalized using DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: HS639_counts.csv: Comma-separated text file with DESeq2 normalized readcounts.

source_name: 2-cell embryo

growth_protocol: Thawed sperm was preincubated for 30 minutes in TYH (with Methyl-b-cyclodextrin, Sigma C4555) medium at 37 deg C, 5% CO2 in air, before being added to the COC complexes for fertilisation. 4 hours after insemination, the presumptive zygotes were washed through several drops of KSOM (Millipore, MR-121-D) and incubated overnight in KSOM.

extract_protocol:
7-10 2-cell Embryos resulting from IVF were frozen in Trizol. After thawing, samples were subjected to standard Trizol RNA extraction.
TruSeq small RNA library preparation using 1:4 diluted adapters, 22 PCR cycles, starting amount: RNA from 7-10 embryos.

treatment_protocol: Paternal intraperitoneal injection of Dexamethasone 2mg/kg in 10% DMSO and saline in males followed by sperm cryopreservation. This sperm was used to generate offspring via in vitro fertilization.

value: 2-cell embryo

value: WT

tag: treatment

value: Paternal vehicle control


title: paternal vehicle injection offspring [KG7.8]

description:
KG7.8
small RNA seq


title: paternal vehicle injection offspring [KG7.7]

description:
KG7.7
small RNA seq


title: paternal vehicle injection offspring [KG7.6]

description:
KG7.6
small RNA seq


title: paternal vehicle injection offspring [KG7.5]

description:
KG7.5
small RNA seq


title: paternal dexamethasone injection offspring  [KG7.4]

description:
KG7.4
small RNA seq

value: Paternal dexamethasone


title: paternal dexamethasone injection offspring  [KG7.2]

description:
KG7.2
small RNA seq


title: paternal dexamethasone injection offspring  [KG7.3]

description:
KG7.3
small RNA seq


title: MuSCs, Post-injury Day 7, Wild type [d7_WT_Rep2]

description:
d7_WT_Rep2
76bp SE RNA-Seq
MuSC-d-7-WT-R2
bulkRNAseq.TPM.tsv
bulkRNAseq.estimated_counts.tsv
bulkRNAseq.batchCorrected.rlogTransformed.tsv


title: Vehicle 15 [F15]

description:
F15
small RNA seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, next reads of the same sequence containing the identical unique identifier barcode were collapsed, then mapped to mm10 whole genome using Star.
Reads matching miRBase annotations (v21) were quantified using feature counts.
Countmatrix obtained was normalized using DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: FGCZ6510_counts.csv: Comma-separated text file with DESeq2 normalized readcounts.

source_name: Sperm cells

growth_protocol: Alive mice.

extract_protocol:
Mature sperm was extracted from cauda epididymis and placed in M2 medium. After passage through a filter, sperm was subjected to somatic lysis and 2 washes. RNA was extracted using Directzol (Zymo R2080).
Nextflex small RNA library preparation using indexed barcodes and 1:4 diluted adapters, 22 PCR cycles, starting amount: 100ng RNA.

treatment_protocol: Intraperitoneal injection of Dexamethasone 2mg/kg in 10% DMSO and saline.

value: Sperm

value: 13 weeks

value: Vehicle control


title: Vehicle 18 [F18]

description:
F18
small RNA seq


title: paternal dexamethasone injection offspring  [KG7.1]

description:
KG7.1
small RNA seq


title: Mfp2-/-  RAW264.7 cells

source_name: Mfp2-/-  RAW264.7 cells

tag: cell line


title: MuSCs, Pre-injury, Sestrin1,2 Knockout [d0_SestrinKO_Rep2]

description:
d0_SestrinKO_Rep2
76bp SE RNA-Seq
MuSC-d-0-KO-R2
bulkRNAseq.TPM.tsv
bulkRNAseq.estimated_counts.tsv
bulkRNAseq.batchCorrected.rlogTransformed.tsv

value: Flow sorted muscle stem cells


title: Vehicle 14 [F14]

description:
F14
small RNA seq


title: Vehicle 13 [F13]

description:
F13
small RNA seq


title: MuSCs, Post-injury Day 7, Sestrin1,2 Knockout [d7_SestrinKO_Rep2]

description:
d7_SestrinKO_Rep2
76bp SE RNA-Seq
MuSC-d-7-KO-R2
bulkRNAseq.TPM.tsv
bulkRNAseq.estimated_counts.tsv
bulkRNAseq.batchCorrected.rlogTransformed.tsv

value: Sestrin1,2 Knockout


title: Vehicle 12 [F12]

description:
F12
small RNA seq


title: dexa 10 [F10]

description:
F10
small RNA seq

value: Dexamethasone


title: Vehicle 11 [F11]

description:
F11
small RNA seq


title: dexa 8 [F8]

description:
F8
small RNA seq


title: dexa 5 [F5]

description:
F5
small RNA seq


title: dexa 6 [F6]

description:
F6
small RNA seq


title: 3 hours in vivo dexa [KG10.15]

description:
KG10.15
3 hours post in vivo dex treated
small RNA seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, next reads of the same sequence containing the identical unique identifier barcode were collapsed, then mapped to mm10 whole genome using Star.
Reads matching miRBase annotations (v21) were quantified using feature counts.
Countmatrix obtained was normalized using DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: HS692_counts.csv: Comma-separated text file with DESeq2 normalized readcounts.

extract_protocol:
Mature sperm was extracted from cauda epididymis and placed in M2 medium. Sperm was subjected to somatic lysis and 2 washes. RNA was extracted using Trizol.
TruSeq small RNA library preparation using 1:4 diluted adapters, 22 PCR cycles, starting amount: 100ng RNA.

value: 9 weeks

tag: time point

value: 3 hours


title: dexa 7 [F7]

description:
F7
small RNA seq


title: 3 hours in vivo dexa [KG10.13]

description:
KG10.13
3 hours post in vivo dex treated
small RNA seq


title: dexa 3 [F3]

description:
F3
small RNA seq


title: 3 hours in vivo veh [KG10.11]

description:
KG10.11
3 hours post in vivo vehicle treated
small RNA seq

value: Vehicle


title: 3 hours in vivo veh [KG10.10]

description:
KG10.10
3 hours post in vivo vehicle treated
small RNA seq


title: dexa 9 [F9]

description:
F9
small RNA seq


title: dexa 1 week exposed sperm collected in 3 ml only 2 ml taken and only cauda  [KG10.8]

description:
KG10.8
1 week post dex treated
small RNA seq

value: 11 weeks

value: 1 week


title: dexa 1 week exposed sperm collected in 3 ml only 2 ml taken and only cauda  [KG10.7]

description:
KG10.7
1 week post dex treated
small RNA seq

value: wild type


title: 3 hours in vivo veh [KG10.12]

description:
KG10.12
3 hours post in vivo vehicle treated
small RNA seq


title: 3 hours in vivo dexa [KG10.14]

description:
KG10.14
3 hours post in vivo dex treated
small RNA seq


title: Vehicle 16 [F16]

description:
F16
small RNA seq


title: dexa 1 week exposed sperm collected in 3 ml only 2 ml taken and only cauda  [KG10.6]

description:
KG10.6
1 week post dex treated
small RNA seq


title: dexa 1 week exposed sperm collected in 3 ml only 2 ml taken and only cauda  [KG10.5]

description:
KG10.5
1 week post dex treated
small RNA seq


title: veh 1 week exposed sperm collected in 3 ml only 2 ml taken and only cauda  [KG10.3]

description:
KG10.3
1 week post Vehicle treated
small RNA seq


title: veh 1 week exposed sperm collected in 3 ml only 2 ml taken and only cauda  [KG10.4]

description:
KG10.4
1 week post Vehicle treated
small RNA seq


title: dexa 4 [F4]

description:
F4
small RNA seq


title: veh 1 week exposed sperm collected in 3 ml only 2 ml taken and only cauda box 21 [KG10.1]

description:
KG10.1
1 week post Vehicle treated
small RNA seq


title: Nanog ChIP-nexus wild-type control for crispr experiments

status: Public on Nov 21 2020

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

data_processing:
ChIP-nexus data processing steps: Random barcodes and fixed barcodes were trimmed off the reads and reassigned to FASTQ labels using nimnexus (v0.1.1). The adapters were then trimmed using cutadapt (v1.8.1).
Reads were aligned with BWA (v0.7.13) using the command bwa aln -q 5 -l 32 -k to the mouse genome assembly mm10. Mapping stats were computed using SAMtools flagstat (v1.2). Mutant samples were aligned to a modified mm10 genome that accommodated the CRISPR changes.
Reads were filtered using SAMtools view to remove unmapped reads and mates, non-primary alignments, reads failing platform or vendor quality checks, and PCR or optical duplicates (-F 1804). Low quality reads (MAPQ < 30) were also removed. Reads aligned to the same position with the same barcode, CIGAR string and the SAM flag were de-duplicated using nimnexus dedup (v0.1.1).
The final filtered BAM file was converted to tagAlign format (BED 3+3) using bedtools `bamtobed` (v2.26) (126). Cross-correlation scores were obtained for each file using phantompeakqualtools (v1.2).
BigWig tracks containing the strand-specific number of aligned 5' read ends (pooled across all replicates) were generated using bedtools genomecov -5 -bg -strand <+/->, followed by bedGraph to BigWig conversion using UCSC bedGraphToBigWig.
Peaks were called using MACS2 (v2.1.1.20160309) by shifting and extending the reads to obtain coverage tracks similar to ChIP-seq (shift=-75, extsize=150). Peaks overlaping the blacklisted regions listed in  http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz were excluded. Peak calling was performed on different combinations of aligned reads from different replicate experiments as described in Landt et al. 2012 and as used in the ENCODE ChIP-seq pipeline. Finally, 1kb regions centered at peak summits from the "optimal set" of reproducible, ranked consistent peaks passing the Irreproducible Discovery Rate (IDR) threshold of 0.05 were used as the peak regions for the corresponding TF (i.e. peaks that are reproducible and rank consistently across replicates).
ChIP-seq datasets were processed using the ENCODE ChIP-seq pipeline https://github.com/ENCODE-DCC/chip-seq-pipeline2/releases/tag/v1.2.2. The ChIP-seq pipeline is identical to the ChIP-nexus pipeline described above except that it uses the SPP peak caller and doesn't use barcodes for read de-duplication.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig tracks containing the strand-specific number of aligned 5' read ends (pos=+ strand, neg=- strand) were generated using bedtools genomecov -5 -bg -strand <+/->, followed by bedGraph to BigWig conversion using UCSC bedGraphToBigWig.
Supplementary_files_format_and_content: Bed files contain the "optimal'' peaks passing the IDR threshold of 0.05 as described above.

source_name: embryonic stem cells

growth_protocol: Mouse R1 ESCs were cultured on 0.1% gelatin-coated plates without feeder cells. Mouse ESC medium was prepared by supplementing N2B27 medium (1:1 mix of DMEM/F12 with GlutaMax supplemented with N2 and Neurobasal medium supplemented with B27, Invitrogen) with 2 mM L-Glutamine (Stemcell Technologies), 1x 2‑Mercaptoethanol (Millipore), 1x NEAA (Stemcell Technologies), 3 µM CHIR99021 (Stemcell Technologies), 1 µM PD0325901 (Stemcell Technologies), 0.033% BSA solution (Invitrogen) and 107 U/ml LIF (Millipore).

extract_protocol:
For each ChIP experiment, 10^7 mouse ESCs were used. Cells were washed with PBS and cross-linked with 1% formaldehyde (Fisher Scientific) in PBS for 10 min at room temperature. The reaction was quenched with 125 mM glycine. Fixed cells were washed with cold PBS, scraped, centrifuged, resuspended in cold lysis buffer (15 mM HEPES (pH 7.5), 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.5% N‑lauroylsarcosine, 0.1% sodium deoxycholate, 0.1% SDS), incubated for 10 min on ice and sonicated with a Bioruptor Pico for four cycles of 30 s on and 30 s off.  ChIP-seq experiments were performed as previously described in Koenecke et al 2017 "Drosophila poised enhancers are generated during tissue patterning with the help of repression" with 10^7 mouse ESCs per ChIP. For each ChIP, 5 µg of the following antibodies were used: ɑ-Oct3/4 (Santa Cruz, sc-8628), ɑ-Sox2 (Santa Cruz, sc-17320), or ɑ-Nanog (Santa Cruz, sc-30328). At least two biological replicates were performed for each factor. Single-end sequencing was performed on either an Illumina HiSeq instrument (50 cycles) or NextSeq 500 instrument (75 cycles) according to manufacturer’s instructions.
Sequencing libraries were prepared for sequencing using standard Illumina protocols
The ChIP-nexus procedure and data processing were performed as previously described in Johnston et al 2015 except that the ChIP-nexus adaptor mix contained four fixed barcodes (ACTG, CTGA, GACT, TGAC). For each ChIP, 5 µg antibody was coupled to 50 µl of Dynabeads Protein A or Protein G (Invitrogen). The following antibodies were used: ɑ-Oct3/4 (Santa Cruz, sc-8628), ɑ-Sox2 (Santa Cruz, sc-17320), ɑ-Nanog (Santa Cruz, sc-30328), ɑ-Klf4 (R&D Systems, AF3158), ɑ-Klf4 (Abcam, ab106629), ɑ-Esrrb (Abcam, ab19331), ɑ-Pbx 1/2/3 (Santa Cruz, sc-888), and ɑ-Zic3 (Abcam, ab222124).

treatment_protocol: Using mouse R1 ES cells, the predicted Nanog motif on chr10: 85,539,756-85,539,765 (mm10) was mutated from CTGATGGCT (wildtype) to CGGCTGGCT (mutant). The predicted Sox2 motif on chr10: 85,539,634-85,539,643 (mm10) was mutated from CCTTTGTTCC (wildtype) to CCTAGGTTCC (mutant). GuideRNA target sites were designed using CCTop target predictor tool. The target sites were selected by evaluating the predicted on-target efficiency score and the off-target potential. To generate the specific point mutations, a single stranded DNA oligonucleotide (ssODN) donor was designed containing ~40 bases of homology from the targeted cut site. A ribonucleoprotein (RNP) complex was formed by combining 90 pmol of sgRNA (ordered as Alt-R sgRNA; IDT, USA) and 10 pmol of Cas9 HiFi protein (IDT) and hybridizing for 10 min at room temperature. The RNP was combined with 100 pmol of ssODN donor and delivered to cells by Neon electroporation (1500 V, 10 ms, 3 pulses; Neon Transfection System, Model MPK5000, Life Technologies). Single cells were screened for the expected mutations through paired-end sequencing on an Illumina MiSeq instrument (250 cycles). On-target indel frequency and expected mutations were analyzed using CRIS.py124. Only clones with the intentional mutation and sequence alignments above 90% were chosen for future experiments.

value: R1 ESCs

value: embryonic stem cells

tag: chip antibody

value: anti-Nanog (Abcam, ab214549)


title: Sox2 ChIP-nexus with CRISPR-knockout of Nanog binding site

value: anti-Sox2 (Active Motif, 39843)


title: Nanog ChIP-nexus with CRISPR-knockout of Sox2 binding site


title: Sox2 ChIP-nexus with CRISPR-knockout of Sox2 binding site


title: Nanog ChIP-nexus with CRISPR-knockout of Nanog binding site


title: RNASeq_PSEN1_A246E_iPSCNeuron_rep3

status: Public on Nov 13 2020

city: La Jolla

first: Shankar

last: Subramaniam

state: CA

address: 9500 Gilman Drive

department: Department of Bioengineering

institute: University of California, San Diego

description: RNASeq_DESeq2_DEGs_PSEN1A246E_iPSCNeuron.csv

data_processing:
RNA-Seq data preprocessing was performed using the BBDuk package (v37.95) in the BBTools suite, removing sequencing adaptors and selecting for all paired-end reads above a quality score threshold (Phred Q>10).
Trimmed RNA-Seq reads were mapped to the GRCh38.p12 human transcriptome using Salmon v0.9.12 with the options --gcBias --seqBias --biasSpeedSamp 5.
Transcript level summation to the gene level using the R package tximport v1.8.0.
Differential expression analysis was performed for psen1M146L and psen1A246E iPSC-derived neurons relative to NDC using the R package DESeq2 v1.20.0, selecting for genes with a q-value (FDR-adjusted p-value) of <0.01 and a log2 fold-change of >0.5.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Differentially expressed genes relative to NDC

source_name: hiPSC-derived neurons from human EOFAD patient, psen1 A246E mutation

growth_protocol: Non-Demented Control (NDC) and psen1M146L fibroblasts were derived from skin biopsies in accordance with UC San Diego IRB approval, whereas psen1A246E fibroblasts were obtained commercially (Coriell Cat. AG06840). The generation and characterization of the hiPSC lines were carried out as previously reported from fibroblasts by retroviral transduction using the reprogramming factors oct4, sox2, klf4, and c-myc. Neural stem cells (NSCs) were expanded in NSC growth medium (DMEM /F12, GlutamaxTM (Thermo Fisher Cat. 10565018), 1x B-27 (Thermo Fisher Cat. 17504044), 1x N-2 (Thermo Fisher Cat. 17502001), 1x Penicillin-Streptomycin (Thermo Fisher Cat. 15070063), and 20ng/mL human bFGF-2 (BioPioneer Cat. HRP-0011)). At 80% confluence, the medium was changed to neural differentiation medium (DMEM /F12, GlutamaxTM, 1x B-27, 1x N-2, and 1x Penicillin-Streptomycin) for 3 weeks of differentiation. After differentiation, the cultures were dissociated with Accutase (Sigma Cat. A6964). Cells were resuspended in 200μL of IMag buffer (1x neural differentiation medium, 0.5µM EDTA, 0.5% Bovine Serum Albumin) followed by incubation with PE Mouse Anti-Human CD184 and CD44 antibodies (BD Biosciences Cat. 561733 and 561858, respectively) for 15min on ice in the dark. The mixture was washed with IMag buffer and subsequently incubated with magnetic beads (BD Biosciences) for 30min at room temperature. Magnetic bead separation was carried out for 8min according to the manufacturer’s protocol (BD Biosciences). The supernatant containing purified CD184-/CD44- neurons was then removed and spun down for RNA-Seq.

extract_protocol:
Total RNA from magnetically purified human NDC, psen1M146L, and psen1A246E (biological replicates, n = 4) hiPSC-derived neurons was prepared using RNeasy Plus Micro Kit (Qiagen Cat. 74034) according to the manufacturer’s protocol. On-column DNAse digestion was subsequently performed on total RNA extracts according to the manufacturer’s recommendations to remove any genomic contamination (Qiagen Cat. 79254).
Libraries were prepared for RNA-Seq using the TruSeq Stranded Total RNA Library prep kit (Illumina, Cat. RS-122-2303) by the Ribo-Zero ribosomal RNA reduction method (Illumina, Cat. MRZG12324). Samples were sequenced at the UC San Diego Institute for Genomics Medicine (IGM) sequencing core on an Illumina HiSeq4000 generating Paired-End, 100bp reads with an average of 25 million reads per sample (Illumina, Cat. FC-410-1001).

value: hiPSC-derived neuron

value: psen1A246E fibroblasts


title: RNASeq_PSEN1_A246E_iPSCNeuron_rep1


title: 3 hours in vivo veh, box 21 [KG10.9]

description:
KG10.9
3 hours post in vivo vehicle treated
small RNA seq

value: Sperm


title: Vehicle 17 [F17]

description:
F17
small RNA seq

value: 13 weeks

value: Vehicle control


title: MED14-IAA7, MED17-FLAG, +IAA, DMSO Rep 2

status: Public on Nov 12 2020

city: Bloomington

first: Gabriel

last: Zentner

state: IN

address: 915 E 3rd St

department: Biology

institute: Indiana University

data_processing:
alignment with bowtie2, options: `-I 10 -X 700 --no-unal --dovetail --no-discordant --no-mixed’
CPM normalization with deepTools `bamCoverage -b [SAMPLE.BAM]" --normalizeUsing CPM  -bs 1 -p [#PROCS] -e -of bigwig -o [BIGWIG_OUT.bw]'
log2 fold change +IAA / DMSO calculation with deepTools `bamCompare -b1 [IAA.bam] -b2 [DMSO.bam] -e --scaleFactorsMethod SES -bs 1 -p [#PROCS] -of bigwig -o [LOG2_BIGWIG_OUT.bw]’
Genome_build: sacCer3
Supplementary_files_format_and_content: bigWig CPM normalization with deepTools

organism: Saccharomyces cerevisiae

growth_protocol: Grown at 30C in YPD

extract_protocol:
ChIP was performed as described (PMID 19378172) with minor modifications. A 100 mL culture was grown to an OD600 ≥ 0.8 and treated with 500 μM 3-IAA or an equal volume of DMSO for 15 min. After 15 min of 3-IAA or DMSO treatment, the culture was split into two flasks. One culture was treated with 6 μM 1-Napthyl PP1 (NAPP1, Cayman Chemicals) and the other was treated with an equal volume of DMSO for 15 min. Cells were crosslinked using 1% formaldehyde for 30 minutes at 30C and then quenched using Tris pH 8.0 (final concentration of 0.75 M). Crosslinked cells were lysed with bead beating using a Disruptor Genie for 8 cycles of 3 min at 2850 rpm and 1 min on ice. Then, lysate was transferred to a new tube and centrifuged as previously described. Lysate was sonicated using a Bioruptor Pico for 8 cycles of 30 sec on and 30 sec off. Soluble chromatin was immunoprecipitated using 30 μL of serum bovine albumin pre-blocked Sigma FLAG M2 magnetic beads (catalog number M8823) overnight at  4C. Beads were washed as described and and decrosslinked by resuspending the beads in 98 μL of TE/1% SDS and shaking (800 RPM) at 65C for 12 -16 hours. DNA was purified from the supernatant using a Qiagen PCR purification kit per the manufacturer’s protocol. Sequencing libraries were constructed by the Indiana University Center for Genomics and Bioinformatics (CGB) using the NEBNext Ultra II Library Prep Kit for Illumina and sequenced for 80 cycles in paired-end mode on the Illumina NextSeq 500 platform at the CGB.
NEB Next Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: 3-IAA in DMSO added to treatment samples at 0.5mM for 30m

tag: background

value: BY4741 RPB3-TAP kin28as pGPD1-OsTIR1

tag: degron tag

tag: chip tag

value: Sigma M2 anti-FLAG


title: MED14-IAA7, DMSO Rep 2

value: no Tag control


title: MED14-IAA7, +IAA, NAPP1 Rep 1

treatment_protocol: 3-IAA in DMSO added to treatment samples at 0.5mM for 15m; then 1-NA-PP1 in DMSO added to treatment samples at 6 uM for additional 15m


title: MED14-IAA7, +IAA, DMSO Rep 1


title: MED14-IAA7, DMSO Rep 1


title: MED14-IAA7, NAPP1 Rep 1

treatment_protocol: 1-NA-PP1 in DMSO added to treatment samples at 6 uM for 15m


title: MED14-IAA7, MED17-FLAG, +IAA, NAPP1 Rep 1


title: MED14-IAA7, MED17-FLAG, NAPP1 Rep 2


title: MED14-IAA7, MED17-FLAG, +IAA, NAPP1 Rep 2


title: MED14-IAA7, NAPP1 Rep 2


title: MED14-IAA7, +IAA, NAPP1 Rep 2


title: MED14-IAA7, +IAA, DMSO Rep 2


title: MED14-IAA7, MED17-FLAG, +IAA, DMSO Rep 1


title: MED14-IAA7, MED17-FLAG, NAPP1 Rep 1

extract_protocol: ChIP was performed as described (PMID 19378172) with minor modifications. A 100 mL culture was grown to an OD600 ≥ 0.8 and treated with 500 μM 3-IAA or an equal volume of DMSO for 15 min. After 15 min of 3-IAA or DMSO treatment, the culture was split into two flasks. One culture was treated with 6 μM 1-Napthyl PP1 (NAPP1, Cayman Chemicals) and the other was treated with an equal volume of DMSO for 15 min. Cells were crosslinked using 1% formaldehyde for 30 minutes at 30C and then quenched using Tris pH 8.0 (final concentration of 0.75 M). Crosslinked cells were lysed with bead beating using a Disruptor Genie for 8 cycles of 3 min at 2850 rpm and 1 min on ice. Then, lysate was transferred to a new tube and centrifuged as previously described. Lysate was sonicated using a Bioruptor Pico for 8 cycles of 30 sec on and 30 sec off. Soluble chromatin was immunoprecipitated using 30 μL of serum bovine albumin pre-blocked Sigma FLAG M2 magnetic beads (catalog number M8823) overnight at  4C. Beads were washed as described and and decrosslinked by resuspending the beads in 98 μL of TE/1% SDS and shaking (800 RPM) at 65C for 12 -16 hours. DNA was purified from the supernatant using a Qiagen PCR purification kit per the manufacturer’s protocol. Sequencing libraries were constructed by the Indiana University Center for Genomics and Bioinformatics (CGB) using the NEBNext Ultra II Library Prep Kit for Illumina and sequenced for 80 cycles in paired-end mode on the Illumina NextSeq 500 platform at the CGB.


title: RNASeq_PSEN1_A246E_iPSCNeuron_rep4

tag: tissue


title: Sox2 ChIP-nexus wild-type control for crispr experiments


title: veh 1 week exposed sperm collected in 3 ml only 2 ml taken and only cauda  [KG10.2]

description:
KG10.2
1 week post Vehicle treated
small RNA seq


title: RNASeq_PSEN1_A246E_iPSCNeuron_rep2


title: MED14-IAA7, MED17-FLAG, DMSO Rep 1

tag: degron


title: R02_S11_Adult_CD34Hi_WT

status: Public on Oct 29 2020

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

data_processing:
Convert from BCL and demultiplex using bcl2fastq 2.17.1
Adapter trimming of 50 and 61 base reads with Trimgalore
FastQ reads were mapped to mm10 using Tophat 2.1.1
Expression was quantitated to counts using HTCount or RPKM using Partek 7.0
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq counts or normalized RPKM values

source_name: skeletal muscle

growth_protocol: Cells were processed for RNA extraction right after sorting. No cell culture was performed.

extract_protocol:
Qiagen microkit or SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara)
0.2-0.4 ng of total RNA (or 400 cells) were used to amplify the cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). 1 ng of amplified cDNA was used to generate barcoded libraries using the Nextera XT DNA library preparation kit (Illumina). Basically, cDNA was fragmented, and adapters were added in a single reaction followed by amplification and clean up. The size of the libraries was checked using the Agilent 2100 Bioanalyzer High Sensitivity DNA chip and their concentration was determined using the Qubit® fluorometer (ThermoFisher Scientific).

treatment_protocol: Cells were isolated form resting non-injured muscles of young and geriatric WT mice without previous treatment

value: skeletal muscle

tag: mice age

value: Adult

value: WT


title: R02_S08_Adult_CD34Lo_WT

tag: genotype


title: R02_S16_Adult_CD34Lo_WT


title: R02_S12_Adult_CD34Lo_WT


title: R02_S07_Adult_CD34Hi_WT


title: MED14-IAA7, MED17-IAA7, SUA7-FLAG, +IAA Rep 2

value: MED17-3xV5-IAA7, MED14-3xHA-IAA7


title: MED14-IAA7, MED17-FLAG, DMSO Rep 2


title: R02_S04_Adult_CD34Lo_WT


title: WT Control 6

status: Public on Oct 22 2020

city: worcester

first: Eduardo

middle: M

last: Torres

state: MA

address: 364 Plantation Street, LRB-523

department: Department of Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

data_processing:
Paired-end reads were aligned to human primary genome hg38, with star_2.5.3a 1, annotated with GENECODE GRCh38.p12 annotation release 292.
Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts_1.5.2 3
Expression normalization was performed using the TPM (Transcripts Per Kilobase Million) method.
Genome_build: hg38
Supplementary_files_format_and_content: xlsx, normalized expression values

source_name: Coriell #GM03440

growth_protocol: Cells were grown for 48 hours and 2 x 10^5 cells were harvested between 50 to 70% confluency. Cells were maintained in Minimum Essential Media (MEM with NEAA; Gibco 10370088) supplemented with 15 % FBS and 2 mM L-glutamine.

extract_protocol:
The RNAeasy Kit from Qiagen (cat # 74104) was used to purify the RNA and a nanoDrop was used to measure concentration. Samples were shipped for on dried ice for transcriptome sequencing to BGI
BGI protocol

treatment_protocol: no treatment

value: Primary fibroblasts

value: euploid


title: WT Control 5

source_name: Coriell #GM03377


title: WT Control 4

source_name: Coriell #GM02036


title: Trisomy 21-7

source_name: Coriell #AG08941

value: trisomy 21


title: WT Control 1

source_name: Coriell #GM08447


title: Trisomy 21-6

source_name: Coriell #GM02767


title: Trisomy 21-1

source_name: Coriell #GM04616


title: Trisomy 21-4

source_name: Coriell #AG05397


title: Trisomy 18-2

source_name: Coriell #GM03538


title: WT Control 3

source_name: Coriell #GM00969


title: R02_S03_Adult_CD34Hi_WT


title: Trisomy 21-3

source_name: Coriell #GM04592


title: Trisomy 18-1

source_name: Coriell #GM00734


title: Trisomy 21-5

source_name: Coriell #AG06922


title: MED14-IAA7, MED17-IAA7, SUA7-FLAG, DMSO Rep 2


title: Trisomy 13-1

source_name: Coriell #GM00526


title: Trisomy 13-2

source_name: Coriell #GM02948


title: WT Control 2

source_name: Coriell #GM05659


title: Trisomy 21-8

source_name: Coriell #AG08942


title: H3K4me1-1K-1

status: Public on Sep 22 2020

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1
Trimmed reads were aligned using bowtie 1.1.2
Reads were extended to 250bp
Sample was normalized and input subtracted
Sample was converted to BigWig format
Genome_build: hg19
Supplementary_files_format_and_content: Normalized ChIP-seq signal in BigWig format

source_name: GM12878 cell line

growth_protocol: GM12878 was bought from Coriell Institute for Medical Research. Cells were cultured in RPMI 1640 media (30-2001, ATCC) supplemented with 15% FBS (16000044, Life Technologies Corporation), 100U/mL Penicillin-Streptomycin (15140122, Life Technologies Corporation) in an incubator maintaining 5% CO2 and 37 ℃. Mycoplasma contamination was tested every 6 months using Universal Mycoplasma Detection Kit (ATCC® 30-1012K™).

extract_protocol:
Cells were suspended in 10 µl PBS and mixed with 10 µl lysis buffer [4% Triton X-100, 100 mM Tris (pH 7.5), 100 mM NaCl, and 30 mM MgCl2] containing freshly added 1% PIC (0.1 µl) and 1 mM PMSF (0.1 µl of 100mM). After 10-min incubation at room temperature, 0.21 µl of 500 m0.1M CaCl2 and 0.2 µl of 100U/µl MNase were added followed by another 10-min incubation. The reaction wais stopped by adding 0.2.22 µl of 0.5M EDTA , and incubated on ice for 10 min. Samples containing more than 1,000 cells was centrifuged at 16,100 g at 4 ℃ for 5min, and supernatant was transferred to a new Eppendorf tube. Chromatin solution can be stored on ice for a few hours.
Adapters were added by tagmentation followed by PCR amplification. The use of microfluidic device and associated procedures are detailed in our paper.

tag: number of cells

value: H3K4me1 (Active Motif, 61634)


title: H3K4me1-1K-2


title: 19129

status: Public on Oct 05 2020

city: Boston

first: Sunita

last: Setlur

address: 221 Longwood Avenue

institute: Brigham and Women's Hospital

description: Normal EBV transformed lymphoblastoid cell line DNA

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software

source_name: LCL

label_protocol: Samples were labeled according to the standard Illumina protocol

extract_protocol: Genomic DNA was purchased from Coriell Cell Repository

tag: gender

value: Female

value: Lymphoblastoid cell lines

tag: disease state

value: Normal


title: 19240

tag: cell type


title: 18558

value: Male


title: 12890