title: Infnar_mm__P7_HSC_Y5 ATAC-seq

description:
Y5
Processed data file: Infnar_mm__P7_HSC.fc.signal.bigwig
Processed data file: Infnar_mm__P7_HSC.optimal_peak.narrowPeak.gz

data_processing:
Sequencing reads were demultiplexed and aligned to mouse genome (mm10) by bowtie2 (versoin 2.2.6)
Signal strength relative to the control samples were generated using MACS2.
Optimal set of peaks were generated using the Kundaje lab ATAC-seq and DNase-seq processing pipeline (https://github.com/kundajelab/atac_dnase_pipelines, version 0.33)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwig, narrowPeak

source_name: Hematopoietic stem cell

extract_protocol:
per Corces et al., Nature Methods 14:959
tagmentation with Tn5 transposase

value: Hematopoietic stem cell


title: sRNA -SL15_CG - Rep1

status: Public on Aug 20 2020

type: SRA

city: Urrbrae

first: Haipei

last: Liu

state: South Australia

address: PMB1 Waite Building, School AFW

country: Australia

institute: The University of Adelaide

description:
DL73
sRNA-seq processed data.xlsx

library_source: transcriptomic

data_processing:
sRNA-Seq: Small RNA sequencing analysis was performed using the in-house ACGT101-miR program (LC Sciences, TX, USA). Raw reads were first processed by removing low-quality reads and adapter sequences to obtain clean sequences. Reads with a nucleotide (nt) length <18 nt or >25 nt were removed. Non-coding (nc) RNA families (rRNA, tRNA, snRNA and snoRNA), repeats and mRNA sequences were discarded using RFam, Repbase and durum wheat NCBI mRNA entries as references. Unique sRNA sequences were then obtained for each library. Conserved mature miRNAs and 5p- or 3p-derived miRNA variants were identified using BLAST search against the plant miRBase (Release 22.1). MIR (microRNA gene locus) and miRNA sequences from common plant species in the miRBase were used as references. Sequences mapped to the mature miRNA in the hairpin were identified as conserved mature miRNAs. Sequences mapped to the opposite arm of mature miRNA in the hairpin were identified as 5p- or 3p-derived variants. Single mismatch within the sequence and length variation at both 5p and 3p were allowed in the alignment. All the mapped miRNAs were aligned to the durum wheat genome (NCBI UID 3439611, assembly Svevo.v1) to determine their genomic location. The remaining unmatched sRNA sequences were used to identify novel durum miRNAs. Sequences were BLASTed to the durum wheat genome. To identify miRNA precursors, secondary hairpin structures containing matched sequences were predicted using RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi) from 120nt of flanking genome sequences.
mRNA-Seq: Prior to sequence assembly, low quality reads (those containing primer or adaptor sequence, and those with a sequencing quality score < 20) were removed. Clean reads were aligned to the durum reference genome using the HISAT package (V2.0). Aligned reads of each library were assembled and the transcript abundance were obtained using StringTie (V1.3.0). Normalised relative abundance was expressed in FPKM (Fragments Per Kilobase Million).
Degradome-Seq: Raw sequencing reads were processed using the ACGT101-DEG program (V4.1, LC Sciences) to remove low-quality reads, reads with adaptor and primer contamination, and reads that can be annotated as non-coding RNA families. The remaining clean reads were used to identify the degraded fragments of mRNAs that are targets of known and novel durum miRNAs with the CleaveLand package V4.0  and the ACGT101-DEG program (LC Sciences, TX, USA). The mRNA cleavage sites at the 10th position of miRNA alignment with P value < 0.05 were considered as significant.
Genome_build: Durum wheat genome (NCBI UID 3439611, assembly Svevo.v1)
Supplementary_files_format_and_content: Matrix table with abundance measurements of microRNAs (sRNA-seq), mRNAs (mRNA-seq) and mRNA targets (degradome-seq)

molecule: total RNA

organism: Triticum turgidum subsp. durum

source_name: Flag leaf tissue

growth_protocol: Stress-tolerant genotype DBA Aurora and stress-sensitive genotype L6 (University of Adelaide breeding line, UAD1301020-8) were grown in controlled glasshouse conditions as previously described (Liu et al., 2019). Briefly, the standard growing conditions were 22°C/12°C (day/night) with a 12h photoperiod.

extract_protocol:
Total RNA was extracted from a total of 120 samples (2 genotypes × 4 treatments × 5 time-points × 3 biological replicates) using the Tri reagent (Sigma-Aldrich) and treated with TURBO DNase (ThermoFisher Scientific). RNA concentration, quality and integrity was assessed by NanoDrop, gel electrophoresis and Bioanalyzer.
The 120 sRNA libraries were constructed using the NEBNext® Multiplex Small RNA Library Prep Kit. Eight transcriptome libraries were constructed using the Illumina mRNA-Seq sample preparation kit. For degradome-seq, mRNA was enriched using oligo-d(T) magnetic beads. The enriched mRNA was mixed with biotinylated random primers and were ligated to 5' adaptors. First-strand cDNA was reverse-transcribed from ligated mRNA products and then amplified with PCR.

treatment_protocol: Four treatment groups were: control group (CG), pre-anthesis water-deficit stress group (WS), post-anthesis heat stress group (HS) and water-deficit plus heat stress group (WH). All plants were well-watered from germination to booting. Water-deficit stress was applied to WS and WH by maintaining the soil water content at 6% (half of the field capacity) from booting until harvest (Liu et al., 2019). Heat stress was applied by placing plants in a growth chamber at 37°C/27°C with a 12h photoperiod. HS and WH plants were treated with heat for 24h at multiple reproductive time-points consecutively [5, 15, 25, 35, and 45 days post anthesis (DPA)] (Liu et al., 2019). After 24h, plants were moved back to the standard conditions and remained there between each treatment time-point. Flag leaf samples were collected at each DPA.

tag: genotype

value: L6 (Stres-sensitive)

tag: treatment group

value: Control group (CG)

tag: time-point (dpa, days post anthesis)


title: sRNA -SL5_HS - Rep1

description:
DL67
sRNA-seq processed data.xlsx

value: Heat stress (HS)


title: S4_MGAS_DLPFC

city: New York

first: Panos

last: Roussos

state: NY

address: 1470 Madison Ave

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: genomic

data_processing:
Reads from each sample were aligned on gender specific hg19 reference genome (pseudoautosomal region was masked on the chromosome Y for males) using the STAR aligner (v2.5.0) with the following parameters: --alignIntronMax 1, --outFilterMismatchNmax 100, --alignEndsType EndToEnd, --outFilterScoreMinOverLread 0.3, --outFilterMatchNminOverLread 0.3. For each sample, this produced a coordinate-sorted BAM file of mapped paired-end reads. We excluded reads that: (1) mapped to more than one locus; (2) were duplicated; and (3) mapped to the mitochondrial genome. For each sample, this produced a coordinate-sorted BAM file of mapped paired-end reads.
Genome_build: hg19

molecule: genomic DNA

organism: Homo sapiens

source_name: dorsolateral prefrontal cortex

extract_protocol:
50mg of frozen brain tissue was homogenized in cold lysis buffer (0.32M Sucrose, 5 mM CaCl2, 3 mM Magnesium acetate, 0.1 mM, EDTA, 10mM Tris-HCl, pH8, 1 mM DTT, 0.1% Triton X-100) and filtered through a 40µm cell strainer. The flow-through was underlaid with sucrose solution (1.8 M Sucrose, 3 mM Magnesium acetate, 1 mM DTT, 10 mM Tris-HCl, pH8) and subjected to ultracentrifugation at 24,000 rpm for 1 hour at 4°C. Pellets were resuspended in 500µl DPBS and incubated in BSA (final concentration 0.1%) and anti-NeuN antibody (1:1000, Alexa488 conjugated, Millipore Cat #MAB377X), anti-SOX67 and anti-SOX108 as previously described4 Prior to FANS sorting, DAPI (Thermoscientific) was added to a final concentration of 1µg/ml. GABAergic neurons (DAPI+ NeuN+ SOX6+), Glutamatergic neurons (DAPI+ NeuN+ SOX6-), oligodendrocytes (DAPI+ NeuN- SOX10+) and microglia/astrocytes (DAPI+ NeuN- SOX10-) nuclei were sorted into individual tubes (pre-coated with 5% BSA) using a FACSAria flow cytometer (BD Biosciences).
ATAC-seq reactions were performed on the 48 samples using an established protocol51 with minor modifications. In brief, 75,000 sorted nuclei were centrifuged at 500 g
for 10 min at 4°C. Pellets were re-suspended in transposase reaction mix (25 μL 2x TD Buffer (Illumina Cat #FC-121-1030) 2.5 μL Tn5 Transposase (Illumina Cat #FC-121-1030) and 22.5 μL Nuclease Free H2O) on ice. Reactions were incubated at 37°C for 30 min and then purified using the MinElute Reaction Cleanup kit (Qiagen Cat #28204), eluting in 10µL of buffer EB. Following purification, library fragments were amplified using the Nextera index kit (Illumina Cat #FC-121-1011) under the following cycling conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermocycling at 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute for a total of 5 cycles. To prevent saturation due to over-amplification, a 5 µl aliquot was then removed and subjected to qPCR for 20 cycles to calculate the optimal number of cycles needed for the remaining 45 µL reaction. The additional number of cycles was determined by first plotting linear Rn vs. Cycle
 and secondly calculating the cycle number corresponding to 1⁄4 of maximum fluorescence intensity. In general, adding 2-4 cycles to this estimate was found to yield optimal libraries, as evidenced by analysis on Tapestation D5000 ScreenTapes (Agilent technologies Cat# 5067-5588). Following amplification, libraries were resolved on 2% agarose gels and fragments ranging in size from 100-1000bp were excised and purified (Qiagen Minelute Gel Extraction Kit – Qiagen Cat#28604). Prior to sequencing, libraries were quantified with the Qubit dsDNA HS assay kit (Invitrogen Cat#Q32851) and by quantitative PCR (KAPA Biosystems Cat#KK4873). Fragment sizes were estimated using Tapestation D5000 ScreenTapes (Agilent technologies Cat# 5067-5588) and libraries were sequenced on Hi-Seq2500 (Illumina) obtaining 2x50 paired-end reads.

tag: tissue

value: dorsolateral prefrontal cortex

tag: cell type

value: microglia and astrocytes

tag: gender

value: Female

tag: age of death

tag: postmortem interval (hours)

tag: heart weight (grams)

tag: alcohol toxicology

value: negative

tag: Cause of death

value: sudden cardiac death


title: sRNA -SL5_WH - Rep3

description:
DL72
sRNA-seq processed data.xlsx

value: Water-deficit plus heat stress (WH)


title: sosi-1_small_RNA_3

city: Arlington

first: Alicia

middle: Kathryn

last: Rogers

state: Texas

address: 1225 W Mitchell Street

department: Department of Biology

institute: University of Texas at Arlington

data_processing:
Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform.
Bioinformatic analysis. Sequences were parsed from adapters using Cutadapt(Martin, 2011) and mapped to the C. elegans genome, WS258, using HISAT2(Kim, Langmead, & Salzberg, 2015) and the transcriptome using Salmon(Patro, Duggal, Love, Irizarry, & Kingsford, 2017). Data analysis was done using R, Excel, and custom Python scripts. Reads per million were plotted along the WS258 genome using Integrative Genomics Viewer 2.3.68(Robinson et al., 2011). Gene ontology analysis was performed using the Enrichment Analysis Tool on WormBase(Angeles-Albores, RY, Chan, & Sternberg, 2016). Gene enrichment analysis was performed using reference gene lists from WormExp(Yang et al., 2016).
Genome_build: WS258
Supplementary_files_format_and_content: tab-delimited text files including total reads mapping to each gene

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Synchronized L1s of ergo-1(tm1860) and prg-1(n4357) worms were plated on enriched peptone plates and cultured at 20°C.

extract_protocol:
8,000 animals per sample were harvested as adults (~64hrs at 20°C) for RNA extraction. Worms were washed off plates using water and then settled on ice to form a pellet. Water was aspirated off and worm pellets were resuspended in 1mL TRIzol reagent (Life Technologies) and freeze-thawed on dry ice followed by vortexing. Worm carcasses were pelleted using centrifugation and the supernatant containing RNA was collected. 0.2 volume chloroform was add to supernatant, vortexed, centrifuged, and then the aqueous phase was transferred to a new tube. Samples were precipitated using isopropanol and rehydrated in 50μL nuclease-free H2O.
mRNA-seq library preparation. Nuclease-free H2O was added to 7.5μg of each RNA sample, extracted from whole animals, to a final volume of 100μL. Samples were incubated at 65°C for 2 minutes then incubated on ice. The Dynabeads mRNA Purification Kit (ThermoFisher 61006) was used according to the manufacturer’s protocol. 20μL of Dynabeads was used for each sample. 100ng of each mRNA sample was used to prepare libraries with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760S) according to the manual, using NEBNext multiplex oligos for Illumina (NEB E7335S). Library quality was assessed (Agilent BioAnalyzer Chip) and concentration was determined using the Qubit 1X dsDNA HS Assay kit (ThermoFisher Q33231). Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform. Three biological replicates were generated for wild-type (N2) and mut-16 mutants cultured at 20°C and 25°C.Small RNA library preparation. Small RNAs (18- to 30- nt) were size selected on denaturing 15% polyacrylamide gels (Criterion 3450091) from total RNA samples. Libraries were prepared as previously described(Montgomery et al., 2012). Library quality was assessed (Agilent BioAnalyzer Chip) and concentration was determined using the Qubit 1X dsDNA HS Assay kit. Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform. Three biological replicates were generated for wild-type (N2) and mut-16 mutants cultured at 20°C and 25°C.

tag: strain

value: USC1335 - sosi-1{delta}(cmp262) I

tag: Stage

value: Day 1 Adult

tag: molecule subtype

value: size selected RNA from total RNA


title: Infnar_mm__P7_HSC_Y4 ATAC-seq

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine - Cardiovascular Division

institute: Washington University School of Medicine

description:
Y4
Processed data file: Infnar_mm__P7_HSC.fc.signal.bigwig
Processed data file: Infnar_mm__P7_HSC.optimal_peak.narrowPeak.gz

organism: Mus musculus

tag: age


title: sosi-1_small_RNA_2


title: Infnar_mm__P7_48+LSK_U3 ATAC-seq

description:
Y3
Processed data file: Infnar_mm__P7_48+LSK.fc.signal.bigwig
Processed data file: Infnar_mm__P7_48+LSK.optimal_peak.narrowPeak.gz

source_name: Hematopoietic progenitor cell

value: Hematopoietic progenitor cell


title: S4_MGAS_ACC

source_name: anterior cingulate cortex

value: anterior cingulate cortex


title: sRNA -SL5_WS - Rep2

description:
DL65
sRNA-seq processed data.xlsx

value: Water-deficit stress (WS)


title: S2_MGAS_ACC

value: Male


title: sRNA -SL5_WH - Rep1

description:
DL70
sRNA-seq processed data.xlsx


title: Infnar_mm__P7_48+LSK_Y2 ATAC-seq

description:
Y2
Processed data file: Infnar_mm__P7_48+LSK.fc.signal.bigwig
Processed data file: Infnar_mm__P7_48+LSK.optimal_peak.narrowPeak.gz


title: sosi-1_small_RNA_1


title: sRNA -SL5_WS - Rep1

description:
DL64
sRNA-seq processed data.xlsx


title: eri-6[e-f]_mut-16-small-RNA-3


title: Infnar_mm__P7_48+LSK_Y1 ATAC-seq

description:
Y1
Processed data file: Infnar_mm__P7_48+LSK.fc.signal.bigwig
Processed data file: Infnar_mm__P7_48+LSK.optimal_peak.narrowPeak.gz


title: S3_MGAS_ACC


title: sRNA -SL5_CG - Rep3

description:
DL63
sRNA-seq processed data.xlsx


title: S1_MGAS_DLPFC


title: BA_P7_HSC_U6 ATAC-seq

description:
U6
Processed data file: BA_P7_HSC.fc.signal.bigwig
Processed data file: BA_P7_HSC.optimal_peak.narrowPeak.gz

value: Wildtype

value: Hematopoietic stem cell


title: S1_MGAS_ACC


title: eri-6[e-f]_mut-16-small-RNA-2


title: sRNA -SL5_CG - Rep2

description:
DL62
sRNA-seq processed data.xlsx

value: L6 (Stres-sensitive)

value: Control group (CG)


title: sosi-1_mut-16-small-RNA-1


title: eri-6[e-f]_mut-16-small-RNA-1


title: BA_P7_HSC_U5 ATAC-seq

description:
U5
Processed data file: BA_P7_HSC.fc.signal.bigwig
Processed data file: BA_P7_HSC.optimal_peak.narrowPeak.gz


title: sRNA -SL5_CG - Rep1

description:
DL61
sRNA-seq processed data.xlsx


title: S2_OLIG_PVC

source_name: primary visual cortex

value: primary visual cortex

value: oligodendrocytes


title: S4_OLIG_PVC

value: Female


title: eri-6[e-f]_small_RNA_3

value: USC1332 - eri-6[e-f]{delta}(cmp261) I


title: BA_P7_HSC_U4 ATAC-seq

description:
U4
Processed data file: BA_P7_HSC.fc.signal.bigwig
Processed data file: BA_P7_HSC.optimal_peak.narrowPeak.gz


title: sRNA -TL45_WH - Rep3

description:
DL60
sRNA-seq processed data.xlsx

value: DBA Aurora (Stress-tolerant)


title: sRNA -SL5_WS - Rep3

description:
DL66
sRNA-seq processed data.xlsx


title: BA_P7_48+LSK_U3 ATAC-seq

description:
U3
Processed data file: BA_P7_48+LSK.fc.signal.bigwig
Processed data file: BA_P7_48+LSK.optimal_peak.narrowPeak.gz


title: sRNA -TL45_WH - Rep2

description:
DL59
sRNA-seq processed data.xlsx

value: Water-deficit plus heat stress (WH)


title: eri-6[e-f]_small_RNA_2


title: S3_OLIG_PVC

value: negative

value: sudden cardiac death


title: S1_OLIG_PVC


title: BA_P7_48+LSK_U2 ATAC-seq

description:
U2
Processed data file: BA_P7_48+LSK.fc.signal.bigwig
Processed data file: BA_P7_48+LSK.optimal_peak.narrowPeak.gz


title: eri-6[e-f]_small_RNA_1

value: Day 1 Adult

value: size selected RNA from total RNA


title: sRNA -TL45_WH - Rep1

description:
DL58
sRNA-seq processed data.xlsx


title: sRNA -TL45_HS - Rep3

description:
DL57
sRNA-seq processed data.xlsx

value: Heat stress (HS)


title: S4_OLIG_DLPFC

value: dorsolateral prefrontal cortex


title: S3_OLIG_DLPFC

value: Male


title: S1_OLIG_DLPFC


title: Adult rep3

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2fastq v1.8.4
The reads were mapped to the mouse reference genome (GRCm38) with the Ensembl gene annotation (release 92) with TopHat2 v2.1.0 (parameters: --no-coverage-search -x 1 -g 1).
All reads mapped to an Ensembl gene were counted using FeatureCounts v1.5.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file containing reads counts, RPMs and RPKMs per gene over all samples

source_name: cortical plate

extract_protocol:
Half (E14.5) or a piece (~100mg, adult)  of cortical plate was collected in RNA later and total RNA was isolated by using Tri Reagent (T9424, Sigma-Aldrich, Munich, Germany).
Preparation of libraries was done using TruSeq RNA v2 (E14.5 samples) or TruSeq stranded mRNA (10.5m samples) according the manufacturer‘s description

value: cortical plate

tag: Sex

value: female

value: 10. 5 months

value: Atr fl/+;CamK II-Cre tg

tag: date of birth

tag: date of death


title: Adult rep2

tag: genotype

value: Atr +/+;CamK II-Cre tg


title: sRNA -TL45_HS - Rep2

description:
DL56
sRNA-seq processed data.xlsx

tag: treatment group

tag: time-point (dpa, days post anthesis)


title: S2_OLIG_DLPFC

tag: tissue

tag: cell type

value: oligodendrocytes


title: sRNA -TL45_HS - Rep1

description:
DL55
sRNA-seq processed data.xlsx


title: Adult rep1


title: E14.5 rep4

value: male

value: Embryonic day 14.5

value: Nbs1 fl/+; Nestin-Cre tg

value: Mother had plug at 27/11/2014

value: brain isolation at 9/12/2014


title: sRNA -TL45_WS - Rep3

description:
DL54
sRNA-seq processed data.xlsx

value: DBA Aurora (Stress-tolerant)

value: Water-deficit stress (WS)


title: sRNA -TL45_WS - Rep2

description:
DL53
sRNA-seq processed data.xlsx


title: BA_P7_48+LSK_U1 ATAC-seq

description:
U1
Processed data file: BA_P7_48+LSK.fc.signal.bigwig
Processed data file: BA_P7_48+LSK.optimal_peak.narrowPeak.gz

value: Wildtype

value: Hematopoietic progenitor cell


title: E14.5 rep3


title: E14.5 rep2


title: S3_OLIG_ACC

value: anterior cingulate cortex

tag: gender

tag: age of death

value: negative

value: sudden cardiac death


title: S4_OLIG_ACC

value: Female

tag: postmortem interval (hours)

tag: heart weight (grams)


title: S1_OLIG_ACC

value: Male

tag: alcohol toxicology

tag: Cause of death


title: S2_OLIG_ACC


title: sRNA -TL45_CG - Rep3

description:
DL51
sRNA-seq processed data.xlsx

value: Control group (CG)


title: sRNA -TL45_CG - Rep2

description:
DL50
sRNA-seq processed data.xlsx


title: E14.5 rep1

tag: strain

value: cortical plate

value: Mother had plug at 22/11/2014

value: brain isolation at 4/12/2014


title: JM121: Input 2 ChIP-seq

data_processing:
Sequencing reads were demultiplexed and aligned to mouse genome (mm10) by novoalign (versoin 3.04.06)
Signal strength relative to the control samples were generated using MACS2.
Optimal set of peaks were generated using the Kundaje lab AQUAS TF and histone ChIP-seq pipeline (https://github.com/kundajelab/chipseq_pipeline version 0.33)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwig, narrowPeak

source_name: Hematopoietic Progenitor Cell

extract_protocol:
HSCs and HPCs were soted and then fixed for chromatin isolation per Schmidl et l., Nature Methods 10:963.
Chipmentation - Chromatin isolation with the indicated antibody followed by tagmentation with Tn5 as per Schmidl et l., Nature Methods 10:963.

value: Hematopoietic Progenitor Cell


title: S1_GABA_PVC

value: primary visual cortex

value: GABAergic neurons


title: S2_GABA_PVC


title: sRNA -TL45_CG - Rep1

description:
DL49
sRNA-seq processed data.xlsx


title: MBD3_ChIPSeq

city: shanghai

first: yin

middle: Chuan

last: Li

address: 320 Yue-yang Road

country: China

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences.

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: hg19
Supplementary_files_format_and_content: Bed file and excel file contain peaks,BedGraph contain aligement  sequanence

source_name: HEK293T cells

growth_protocol: HEK293T cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM),supplemented with 10% fetal bovine serum (FBS), 50 units/ml  penicillin and 50 μg/ml streptomycin.

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

tag: chip antibody

value: MBD3 ( Abcam,ab157464)


title: JM120: Input 1 ChIP-seq

source_name: Hematopoietic Stem Cell

value: Hematopoietic Stem Cell

tag: age


title: sRNA -TL35_WH - Rep3

description:
DL48
sRNA-seq processed data.xlsx

value: DBA Aurora (Stress-tolerant)

value: Water-deficit plus heat stress (WH)


title: sRNA -TL35_WH - Rep2

description:
DL47
sRNA-seq processed data.xlsx


title: S3_GABA_PVC


title: sRNA -TL45_WS - Rep1

description:
DL52
sRNA-seq processed data.xlsx

value: Water-deficit stress (WS)


title: 4T1-T2 primary tumor from mouse 3

type: RNA

city: Fribourg

first: Girieca

last: Lorusso

state: Fribourg

address: Route A. Gockel, 1

department: Medicine, Pathology

country: Switzerland

institute: University of Fribourg

description: Gene expression data from cell line

hyb_protocol: According to manufacturer's instruction at Lausanne Genomic Technologies Facility

data_processing: RMA

label: biotin

source_name: GL_T60 Primary tumor cell line

extract_protocol: RNAeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

tag: cell line

tag: origin

value: primary tumor


title: S4_GABA_PVC

value: negative


title: 4T1-T2 primary tumor from mouse 1

description: Gene expression data from cell line

scan_protocol: According to manufacturer's instruction at Lausanne Genomic Technologies Facility

source_name: GL_T58 Primary tumor cell line


title: JM117: Adult HPC H3K4me1-2 ChIP-seq

description:
Adult_HPC_H3K4me1
processed data in series file Adult_HPC_H3K4me1.pooled.fc.signal.bigwig
processed data in series file Adult_HPC_H3K4me1.filt.narrowPeak.gz

value: 8 week old


title: JM119: Adult HPC H3K4me1-3 ChIP-seq


title: JM118: Adult HPC H3K27ac -3 ChIP-seq

description:
Adult_HPC_H3K27ac
processed data in series file Adult_HPC_H3K27ac.pooled.fc.signal.bigwig
processed data in series file Adult_HPC_H3K27ac.filt.narrowPeak.gz


title: 4T1-T2 primary tumor from mouse 2

description: Gene expression data from cell line

source_name: GL_T59 Primary tumor cell line

label_protocol: According to manufacturer's instruction at Lausanne Genomic Technologies Facility


title: 4T1-LM2 lung met from mouse 3

description: Gene expression data from cell line

source_name: GL_L66 Lung metastasis cell line

value: lung metastasis


title: sRNA -TL35_WH - Rep1

description:
DL46
sRNA-seq processed data.xlsx


title: 4T1-LM2 lung met from mouse 2

description: Gene expression data from cell line

source_name: GL_L65 Lung metastasis cell line


title: sRNA -TL35_HS - Rep2

description:
DL44
sRNA-seq processed data.xlsx

value: Heat stress (HS)


title: 4T1-BM2 brain met from mouse 3

description: Gene expression data from cell line

source_name: GL_B96 Brain metastasis cell line

value: brain metastasis


title: 4T1-BM2 brain met from mouse 2

description: Gene expression data from cell line

source_name: GL_B77 Brain metastasis cell line


title: 4T1-LM2 lung met from mouse 1

description: Gene expression data from cell line

source_name: GL_L64 Lung metastasis cell line


title: JM116: Adult HPC H3K27ac -2 ChIP-seq


title: 4T1-BM2 brain met from mouse 1

description: Gene expression data from cell line

source_name: GL_B74 Brain metastasis cell line


title: S2_GABA_DLPFC

source_name: dorsolateral prefrontal cortex

value: dorsolateral prefrontal cortex

value: Male

value: sudden cardiac death


title: JM115: Adult HPC H3K4me1-1 ChIP-seq

value: Hematopoietic Progenitor Cell


title: H838 H838 24h scratched Rep2

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays were normalized together using quantile normalization algorithm using R Bioconductor packages beadarray and lumi.

source_name: Lung

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: The human NSCLC cell line H838 and the primary human endothelial cell line HPAEC were purchased from Promocell. H838 was propagated in DMEM (Lonza) with 10% fetal calf serum (Invitrogen) and 50,000 U/ml Penicillin/Streptomycin (Biochrom AG). HPAEC was propagated in Endothelial cell growth medium 2 (Promocell) including 2% fetal calf serum with supplements EGF 5ng/ml, bFGF 10ng/ml, Long R3 IGF 20ng/ml, VEGF 0.5ng/ml, ascorbic acid 1μg/ml, heparin 22.5μg/ml and hydrocortisone 0.2μ/ml (all Promocell). Cells were passaged at a split ratio of to 1:10

extract_protocol: RNA was extracted with the QIAGEN RNeasy Plus Mini Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Monocultures of H838 cells were applied in 6-well plates at a density of 2.5 × 105 cells/well. Next, H838 and HPAEC cells were applied to polycarbonate transwell culture inserts (35.5mm diameter with 0.4μm pore size, Greiner bio-one), at densities of 2.0 × 105 and 4.5 × 105 cells/filter, respectively. Six hours after cell seeding, the filters were placed to the corresponding well plates and allowed to propagate until confluence was reached. The whole procedure was performed in the medium as specified for the HPAEC cells

tag: treatment

value: scratched

tag: cell line 1

tag: time

tag: cell line 2

tag: co-culture

value: H838 with H838

value: Lung


title: S4_GABA_DLPFC

tag: tissue

tag: cell type

value: GABAergic neurons

value: Female


title: sRNA -TL35_HS - Rep1

description:
DL43
sRNA-seq processed data.xlsx

source_name: Flag leaf tissue

tag: genotype

value: DBA Aurora (Stress-tolerant)

tag: treatment group

tag: time-point (dpa, days post anthesis)


title: H838 H838 0h unscratched Rep2

value: unscratched


title: H838 HPAEC 0h unscratched Rep2

value: H838 with HPAEC


title: sRNA -TL35_WS - Rep3

description:
DL42
sRNA-seq processed data.xlsx

value: Water-deficit stress (WS)


title: JM114: Adult HPC H3K27ac -1 ChIP-seq

value: 8 week old


title: S1_GABA_DLPFC

tag: gender

tag: age of death

tag: postmortem interval (hours)

tag: heart weight (grams)

tag: alcohol toxicology

value: negative


title: JM113: Fetal HPC H3K4me1-3 ChIP-seq

description:
Fetal_HPC_H3K4me1
processed data in series file Fetal_HPC_H3K4me1.pooled.fc.signal.bigwig
processed data in series file Fetal_HPC_H3K4me1.filt.narrowPeak.gz

tag: age


title: sRNA -TL35_HS - Rep3

description:
DL45
sRNA-seq processed data.xlsx

value: Heat stress (HS)


title: S3_GABA_DLPFC

tag: Cause of death


title: sRNA -TL35_WS - Rep2

description:
DL41
sRNA-seq processed data.xlsx


title: S1_GABA_ACC

source_name: anterior cingulate cortex

value: anterior cingulate cortex


title: S4_GABA_ACC


title: JM111: Fetal HPC H3K4me1-2 ChIP-seq


title: S3_GABA_ACC


title: JM112: Fetal HPC H3K27ac -3 ChIP-seq

description:
Fetal_HPC_H3K27ac
processed data in series file Fetal_HPC_H3K27ac.pooled.fc.signal.bigwig
processed data in series file Fetal_HPC_H3K27ac.filt.narrowPeak.gz


title: sRNA -TL35_WS - Rep1

description:
DL40
sRNA-seq processed data.xlsx


title: sRNA -TL35_CG - Rep3

description:
DL39
sRNA-seq processed data.xlsx

value: Control group (CG)


title: S1_GLU_PVC

source_name: primary visual cortex

value: primary visual cortex

value: glutamatergic neurons

value: Male


title: H838 H838 24h scratched Rep1

tag: treatment

value: scratched


title: S4_GLU_PVC

value: sudden cardiac death


title: JM110: Fetal HPC H3K27ac -2 ChIP-seq

source_name: Hematopoietic Progenitor Cell

value: Hematopoietic Progenitor Cell


title: sRNA -TL35_CG - Rep2

description:
DL38
sRNA-seq processed data.xlsx


title: H838 HPAEC 24h scratched Rep2

tag: cell line 1

value: Lung


title: H838 H838 4h scratched

tag: time

value: H838 with H838


title: H838 H838 15h scratched

tag: cell line 2


title: H838 H838 5h scratched

tag: co-culture


title: JM109: Fetal HPC H3K4me1-1 ChIP-seq

tag: tissue


title: H838 H838 10h scratched


title: S2_GLU_PVC

tag: cell type


title: H838 H838 3h scratched


title: sRNA -TL35_CG - Rep1

description:
DL37
sRNA-seq processed data.xlsx

tag: genotype

value: DBA Aurora (Stress-tolerant)


title: S3_GLU_PVC


title: JM105: Adult HSC H3K4me1-2 ChIP-seq

description:
Adult_HSC_H3K4me1
processed data in series file Adult_HSC_H3K4me1.pooled.fc.signal.bigwig
processed data in series file Adult_HSC_H3K4me1.filt.narrowPeak.gz

value: Hematopoietic Stem Cell


title: S1_GLU_DLPFC

value: dorsolateral prefrontal cortex


title: sRNA -TL25_WH - Rep1

description:
DL34
sRNA-seq processed data.xlsx

tag: treatment group

value: Water-deficit plus heat stress (WH)


title: JM104: Adult HSC H3K4me1-1 ChIP-seq

value: 8 week old


title: sRNA -TL25_HS - Rep2

description:
DL32
sRNA-seq processed data.xlsx

tag: time-point (dpa, days post anthesis)


title: S2_GLU_DLPFC

tag: gender

value: negative


title: JM103: Fetal HSC H3K4me1-3 ChIP-seq

description:
Fetal_HSC_H3K4me1
processed data in series file Fetal_HSC_H3K4me1.pooled.fc.signal.bigwig
processed data in series file Fetal_HSC_H3K4me1.filt.narrowPeak.gz


title: sRNA -TL25_HS - Rep1

description:
DL31
sRNA-seq processed data.xlsx

value: Heat stress (HS)


title: S3_GLU_ACC

value: anterior cingulate cortex

tag: age of death


title: JM102: Fetal HSC H3K4me1-2 ChIP-seq


title: sRNA -TL25_WS - Rep3

description:
DL30
sRNA-seq processed data.xlsx

value: Water-deficit stress (WS)


title: S1_GLU_ACC

tag: postmortem interval (hours)


title: JM101: Fetal HSC H3K4me1-1 ChIP-seq


title: sRNA -TL25_WS - Rep2

description:
DL29
sRNA-seq processed data.xlsx


title: S4_GLU_ACC

value: Female

tag: heart weight (grams)


title: sRNA -TL25_HS - Rep3

description:
DL33
sRNA-seq processed data.xlsx


title: S4_GLU_DLPFC

value: glutamatergic neurons

tag: alcohol toxicology


title: Adult_HPC_WT-3 ATAC-seq

description:
HPC9
processed data in series file adult_HPC.pooled.fc.signal.bigwig
processed data in series file adult_HPC.filt.narrowPeak.gz

source_name: Hematopoietic progenitor cell

value: Hematopoietic progenitor cell

tag: age

value: 8 weeks old


title: JM108: Fetal HPC H3K27ac -1 ChIP-seq


title: H838 H838 0h unscratched Rep1

value: unscratched


title: JM106: Adult HSC H3K4me1-3 ChIP-seq

source_name: Hematopoietic Stem Cell


title: S3_GLU_DLPFC

value: Male

tag: Cause of death

value: sudden cardiac death


title: sRNA -TL25_WH - Rep3

description:
DL36
sRNA-seq processed data.xlsx


title: H838 H838 30min scratched

tag: treatment

value: scratched

value: H838 with H838

value: Lung


title: H838 H838 2h scratched

tag: cell line 1


title: S2_GLU_ACC


title: H838 HPAEC 24h scratched Rep1

tag: time

value: HPAEC

value: H838 with HPAEC


title: H838 HPAEC 10h scratched

tag: cell line 2


title: H838 HPAEC 5h scratched

tag: co-culture


title: Adult_HPC_WT-2 ATAC-seq

description:
HPC5
processed data in series file adult_HPC.pooled.fc.signal.bigwig
processed data in series file adult_HPC.filt.narrowPeak.gz


title: Adult_HPC_WT-1 ATAC-seq

description:
HPC1
processed data in series file adult_HPC.pooled.fc.signal.bigwig
processed data in series file adult_HPC.filt.narrowPeak.gz


title: H838 HPAEC 15h scratched

tag: tissue


title: sRNA -TL25_WH - Rep2

description:
DL35
sRNA-seq processed data.xlsx

value: DBA Aurora (Stress-tolerant)

value: Water-deficit plus heat stress (WH)


title: sRNA -TL25_CG - Rep3

description:
DL27
sRNA-seq processed data.xlsx

value: Control group (CG)


title: sRNA -TL25_WS - Rep1

description:
DL28
sRNA-seq processed data.xlsx


title: P21_HPC-2 ATAC-seq

description:
P21_wt_2
processed data in series file P14_HSC.pooled.fc.signal.bigwig
processed data in series file P14_HSC.filt.narrowPeak.gz

tag: cell type


title: sRNA -TL25_CG - Rep1

description:
DL25
sRNA-seq processed data.xlsx

tag: genotype


title: sRNA -TL15_WH - Rep3

description:
DL24
sRNA-seq processed data.xlsx

tag: treatment group


title: P21_HPC-1 ATAC-seq

description:
P21_wt_1
processed data in series file P14_HSC.pooled.fc.signal.bigwig
processed data in series file P14_HSC.filt.narrowPeak.gz


title: kali443

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

data_processing:
Illumina Casava1.8.2 software was used for basecalling
Reads were processed using fastx toolkit to trim for adapter and low quality bases and filter for low quality reads.
Processed reads were mapped to the Plasmodium falciparum genome using Hisat2 version 2.0.4
Reads mapping to genes were counted using htseq-count
Gene normalization and differential expression analysis were performed using Deseq2
Genome_build: ASM276v1
Supplementary_files_format_and_content: tab delimited text file containing deseq2 normalized values in a single matrix format.

organism: Plasmodium falciparum

source_name: blood

extract_protocol:
Total RNA was prepared directly from the frozen pellets of parasitized erythrocytes, where approximately 1 ml of cell pellet was lysed in 7.5 ml Trizol (GIBCO) and RNA was extracted according to the manufacturer's instructions.
The RNA input going into NGS sample preparation ranged from 100 pg up to 100 ng. The samples were prepared for transcriptome analysis following a previously described protocol (Broadbent, et.al., 2015) with minor modifications. Initially, samples were treated with TURBO DNase as described. Following DNase treatment, the Agencourt RNAclean SPRI beads (Beckman Coulter) were resuspended in 19 μL to modify the protocol for a low input ribosomal RNA depletion step. Ribosomal RNA was depleted following the Clontech Modified Protocol for Removal of rRNA from Small Amounts of Total RNA (100 ng) using Human/Mouse/Rat Ribo-Zero Magnetic Kit (Epicentre). The purification beads were resuspended in 21 μL to proceed with the fragmentation step as described12. The first and second strand cDNA synthesis steps were followed without modification except for the final bead purification was eluted in 55 μL. Aliquots from the DNase, Ribo-zero treatment, and fragmentation were analysed on Agilent BioAnalyzer Pico RNA chips, along with the final cDNA constructs. The purified cDNA was below detectable levels of the BioAnalyzer Pico chips. 50 μL of purified cDNA were prepared for NGS sequencing using the KAPA Hyper Prep Kit (KAPA Biosystems). The adaptor stock concentration was 300 nM for the ligation with 4 h incubation at 20°C. The USER digestion step was omitted as the Hi-Fi polymerase does not amplify uracil containing products. The number of amplification cycles for PCR was determined to be 14 based on quantification of the amount of post-ligation product with a KAPA Quant Kit for Illumina Sequencing (KAPA Biosystems). The purified amplified libraries were visualized on Agilent DNA 1000 chips. Libraries were quantified using the KAPA Quant Kit for Illumina Sequencing (KAPA Biosystems) and normalized to 2 nM.

tag: condition

value: wet season


title: P14_HPC-2 ATAC-seq

description:
wt_HPC2
processed data in series file P14_HSC.pooled.fc.signal.bigwig
processed data in series file P14_HSC.filt.narrowPeak.gz


title: kali459


title: kali400


title: sRNA -TL15_WH - Rep2

description:
DL23
sRNA-seq processed data.xlsx

tag: time-point (dpa, days post anthesis)


title: H838 HPAEC 1h scratched


title: H838 HPAEC 2h scratched


title: kali383


title: Adult_KO

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to mm10 genome build via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Lin- c-Kit+ Hematopoietic cells

extract_protocol: 10x Genomcis Chromium single cell preparation

tag: strain background

tag: genotype/variation

value: Ifnar KO

value: Lin- c-Kit+ Hematopoietic cells


title: H838 HPAEC 4h scratched


title: Adult_WT

value: WT


title: P14_HPC-1 ATAC-seq

description:
wt_HPC1
processed data in series file P7_HPC.pooled.fc.signal.bigwig
processed data in series file P7_HPC.filt.narrowPeak.gz

value: Hematopoietic progenitor cell


title: sRNA -TL15_WH - Rep1

description:
DL22
sRNA-seq processed data.xlsx


title: H838 HPAEC 3h scratched


title: P14_WT


title: kali224


title: P7_HPC-3 ATAC-seq

description:
P7_HPC3
processed data in series file P7_HPC.pooled.fc.signal.bigwig
processed data in series file P7_HPC.filt.narrowPeak.gz


title: P14_KO


title: sRNA -TL15_HS - Rep3

description:
DL21
sRNA-seq processed data.xlsx

value: Heat stress (HS)


title: P7_HPC-2 ATAC-seq

description:
P7_HPC2
processed data in series file P7_HPC.pooled.fc.signal.bigwig
processed data in series file P7_HPC.filt.narrowPeak.gz


title: kali170


title: sRNA -TL15_HS - Rep2

description:
DL20
sRNA-seq processed data.xlsx


title: P7_HPC-1 ATAC-seq

description:
P7_HPC1
processed data in series file fetal_HPC.pooled.fc.signal.bigwig
processed data in series file fetal_HPC.filt.narrowPeak.gz


title: Fetal_HPC-3 ATAC-seq

description:
E16_wt_3
processed data in series file fetal_HPC.pooled.fc.signal.bigwig
processed data in series file fetal_HPC.filt.narrowPeak.gz


title: kali371


title: P0_WT


title: P0_KO


title: kali262


title: sRNA -TL15_WS - Rep3

description:
DL18
sRNA-seq processed data.xlsx

value: Water-deficit stress (WS)


title: kali148


title: kali189


title: sRNA -TL15_HS - Rep1

description:
DL19
sRNA-seq processed data.xlsx


title: Fetal_HPC-2 ATAC-seq

description:
E16_wt_2
processed data in series file fetal_HPC.pooled.fc.signal.bigwig
processed data in series file fetal_HPC.filt.narrowPeak.gz


title: E16_5_KO


title: sRNA -TL15_WS - Rep1

description:
DL16
sRNA-seq processed data.xlsx


title: kali391


title: Fetal_HPC-1 ATAC-seq

description:
E16_wt_1
processed data in series file P21_HPC.pooled.fc.signal.bigwig
processed data in series file P21_HPC.filt.narrowPeak.gz


title: P7_HSC_BM

source_name: Hematopoietic stem cell

value: Hematopoietic stem cell


title: H838 H838 1h scratched


title: kali322


title: JM107: Adult HSC H3K4me1-4 ChIP-seq

value: Hematopoietic Stem Cell

value: 8 week old


title: sRNA -TL15_CG - Rep3

description:
DL15
sRNA-seq processed data.xlsx


title: H838 HPAEC 0h unscratched Rep1

value: unscratched


title: H838 HPAEC 30min scratched

value: scratched

value: Lung


title: kali448

value: dry season


title: P0_HSC_BM


title: adult_HSC_WT-4 ATAC-seq

description:
HSC3
processed data in series file P14_HPC.pooled.fc.signal.bigwig
processed data in series file P14_HPC.filt.narrowPeak.gz

value: 8 weeks old


title: sRNA -TL15_CG - Rep2

description:
DL14
sRNA-seq processed data.xlsx

value: DBA Aurora (Stress-tolerant)


title: E16_5_WT


title: adult_HSC_WT-3 ATAC-seq

description:
HSC1
processed data in series file P14_HPC.pooled.fc.signal.bigwig
processed data in series file P14_HPC.filt.narrowPeak.gz


title: P0_HSC_Liver


title: kali308


title: sRNA -TL15_WS - Rep2

description:
DL17
sRNA-seq processed data.xlsx


title: E16_5_HSC_Liver


title: MYD88_HPC scRNA-seq

description: scRNA-seq


title: kali373


title: kali334


title: adult_HSC_WT-1 ATAC-seq

description:
Ad2.3
processed data in series file adult_HSC.pooled.fc.signal.bigwig
processed data in series file adult_HSC.filt.narrowPeak.gz


title: P14_HSC-3 ATAC-seq

description:
P14_HSC3
processed data in series file adult_HSC.pooled.fc.signal.bigwig
processed data in series file adult_HSC.filt.narrowPeak.gz


title: IFNAR_HPC scRNA-seq

description: scRNA-seq


title: kali326


title: sRNA -TL5_WH - Rep1

description:
DL10
sRNA-seq processed data.xlsx

value: Water-deficit plus heat stress (WH)


title: sRNA -TL15_CG - Rep1

description:
DL13
sRNA-seq processed data.xlsx

value: Control group (CG)


title: sRNA -TL5_WH - Rep2

description:
DL11
sRNA-seq processed data.xlsx


title: P14_HSC-2 ATAC-seq

description:
P14_HSC2
processed data in series file adult_HSC.pooled.fc.signal.bigwig
processed data in series file adult_HSC.filt.narrowPeak.gz


title: sRNA -TL5_HS - Rep3

description:
DL9
sRNA-seq processed data.xlsx


title: WT_HPC scRNA-seq

description: scRNA-seq


title: P7_WT_HPC scRNA-seq

description: scRNA-seq


title: kali244


title: P14_HSC-1 ATAC-seq

description:
P14_HSC1
processed data in series file adult_HSC.pooled.fc.signal.bigwig
processed data in series file adult_HSC.filt.narrowPeak.gz


title: sRNA -TL5_HS - Rep2

description:
DL8
sRNA-seq processed data.xlsx


title: kali388


title: kali357


title: P0_HPC_Liver scRNA-seq

description: scRNA-seq


title: adult_HSC_WT-5 ATAC-seq

description:
HSC5
processed data in series file P21_HPC.pooled.fc.signal.bigwig
processed data in series file P21_HPC.filt.narrowPeak.gz


title: fetal_HSC-3 ATAC-seq

description:
Ad2.2
processed data in series file fetal_HSC.pooled.fc.signal.bigwig
processed data in series file fetal_HSC.filt.narrowPeak.gz


title: adult_HSC_WT-2 ATAC-seq

description:
Ad2.4
processed data in series file adult_HSC.pooled.fc.signal.bigwig
processed data in series file adult_HSC.filt.narrowPeak.gz


title: sRNA -TL5_WH - Rep3

description:
DL12
sRNA-seq processed data.xlsx


title: kali351


title: fetal_HSC-2 ATAC-seq

description:
Ad2.1
processed data in series file fetal_HSC.pooled.fc.signal.bigwig
processed data in series file fetal_HSC.filt.narrowPeak.gz


title: sRNA -TL5_WS - Rep3

description:
DL6
sRNA-seq processed data.xlsx


title: sRNA -TL5_HS - Rep1

description:
DL7
sRNA-seq processed data.xlsx


title: P0_HPC_BM scRNA-seq

description: scRNA-seq


title: kali355


title: E16_5_WT_HPC scRNA-seq

description: scRNA-seq


title: fetal_HSC-1 ATAC-seq

description:
wt_fetal_HSC2479
processed data in series file fetal_HSC.pooled.fc.signal.bigwig
processed data in series file fetal_HSC.filt.narrowPeak.gz


title: kali310


title: sRNA -TL5_WS - Rep2

description:
DL5
sRNA-seq processed data.xlsx


title: HPC_Adult scRNA-seq

description: scRNA-seq


title: kali320


title: HPC_P14 scRNA-seq

description: scRNA-seq


title: sRNA -TL5_CG - Rep3

description:
DL3
sRNA-seq processed data.xlsx


title: HPC_P7 scRNA-seq

description: scRNA-seq


title: Col-0 open flower RNA-Seq_S_61

city: Athens

first: Zhihua

last: Hua

state: Ohio

address: 22 Richland Ave

department: Department of Environmental and Plant Biology

institute: Ohio University

description: Pair end 150-mer RNA-Seq

data_processing: Adapter and low-quality sequences in the raw FASTQ sequencing data were removed to produce valid sequences using Trimmomatic (phred=33, minimum length=36; (Bolger et al., 2014)), which were further aligned to the A. thaliana Col-0 reference genome (TAIR10; www.arabidopsis.org) via TOPHAT2 (Kim et al., 2013a) to identify accepted hits of each locus.  HTSeq was then used to calculate an absolute expression level (counts) of each locus based on the accepted hits (Anders et al., 2015).

organism: Arabidopsis thaliana

source_name: Open flower

growth_protocol: The plants were grown under long-day photoperiod with 16-h light (150 μmol/m2/s)/ 8-h darkness at 21°C and 19°C, respectively.

extract_protocol: Total RNA was extracted from 10-50 mg of floral buds or open flowers from both WT and ask1 primary inflorescences five hours after dawn using the NucleoSpin® RNA kit (Macherey-Nagel).

tag: strain


title: sRNA -TL5_CG - Rep2

description:
DL2
sRNA-seq processed data.xlsx


title: HPC_E16_5 scRNA-seq

description: scRNA-seq


title: Col-0 open flower RNA-Seq_S_221

description: Pair end 150-mer RNA-Seq


title: sRNA -TL5_CG - Rep1

description:
DL1
sRNA-seq processed data.xlsx


title: Col-0 flower bud RNA-Seq_S_91

description: Pair end 150-mer RNA-Seq

source_name: Flower bud


title: Col-0 flower bud RNA-Seq_S_281

description: Pair end 150-mer RNA-Seq


title: SL5_WH_mRNA

description: mRNA-seq processed data

value: L6 (Stres-sensitive)


title: ASK1 WT open flower RNA-Seq_S_131

description: Pair end 150-mer RNA-Seq


title: SL5_WS_mRNA

description: mRNA-seq processed data


title: HSC_Adult scRNA-seq

description: scRNA-seq


title: HSC_P7 scRNA-seq

description: scRNA-seq


title: sRNA -TL5_WS - Rep1

description:
DL4
sRNA-seq processed data.xlsx


title: V6.5_shGFP_rep3

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description:
Mouse embryonic stem (ES) cells cultured in defined medium with MEK and GSK3 inhibitors (2i)
Fang_bcat_FPKM.csv

data_processing:
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
RNA-seq was aligned to genome mm10 from UCSC using tophat 2.0.13.
FPKM was generated using Cufflinks v2.2.1
ChIP-seq was aligned to genome mm10 using bowtie2
Bigwig files are normalized and extended to fragment length for IP samples
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq FPKM in excel file, ChIP-seq in bigwig files

source_name: shRNA mock control

extract_protocol:
RNA-Seq: RNA was isolated by first homogenizing cells in 1ml TRIzol reagent (Invitrogen 15596026) through triturating the cell lysate through a 27-gauge needle a minimum of 7 times. Homogenized samples were mixed with 200µ l chloroform and vigorously shaken by hand for 30sec. Samples were then incubated at RT for 10min before centrifuging at 12,000g for 10min at RT. The aqueous phase containing RNA was transferred to a new tube, mixed with 100µ l chloroform, and subjected to a second round of shaking, incubation and centrifuging.  The aqueous phase was transferred to a new tube containing 1.5µ l 20mg/ml glycogen, and mixed with 450µ l isopropanol to pre- cipitate RNA. Samples were gently mixed and incubated at RT for 10min before centrifuging at 4 °C for 15min. The supernatant was discarded and the pellet was washed by 1ml 75% ethanol. After the wash the RNA pellet was dried at RT for 20min and resuspended in RNase-free water. Yield and purity of RNA was determined by spectrophotometry with Nano drop (Thermo Scien- tific). The RNA was treated with DNase (Promega M6101)
ChIP-Seq: A total of 2×10^7 ES cells were used per ChIP assay. Cells were washed with 1 x PBS and crosslinked with 1% paraformaldehyde for 10 min at RT and quenched with 1ml 2.5M glycine. Cells were washed with cold PBS three times and resuspended in 300μl lysis buffer. The cell suspension was sonicated in Bioruptor Pico sonication device with the setting of 30 sec on, 30 sec off for 16 cycles followed with centrifuga- tion at maximum speed for 10 min. The supernatant was saved and mixed with antibody coated protein G dynabeads(Invitrogen 10003D) at a ratio of 5μl per 1μg antibody for immunoprecip- itation overnight at 4°C . The next day the protein G dynabeads were washed with 800μl RIPA buffer three times. After the elution, 4μ l RNase A(10μ g/ml) was then added with the beads being incubated at 37°C for 2 hours, after which 2μl Protease K(Invitrogen 20mg/ml) was added and the beads were incubated at 55 °C for 2 hours. After the RNase A and Protease K treatment, the beads were incubated at 55 °C overnight for decrosslinking. The next day the DNA on beads was extracted by 300 μl phenol chloroform isoamyl alcohol(25:24:1) with centrifugation at 12,000 rpm for 5 min at RT. The supernatant was transferred to a new 1.5ml tube with 12μl of 5M NaCl and 2μl glycogen (20mg/ml). The DNA was precipitated by 750μl cold 100% ethanol with at least 30 min incubation at - 80 °C . The sample was centrifuged for 30 min in 4 °C at maximum speed and the ethanol was decanted. The pellet was washed with 800 μ l cold 70% ethanol, centrifuged and air dried. The DNA was resuspended in 55μl nuclease-free water.
RNA-seq and ChIP-seq libraries were prepared using the TruSeq RNA kit for sequencing,

value: shRNA mock control

tag: cell line

value: Embryonic stem cells


title: V6.5_shHP1r_rep_2

source_name: HP1r knock down

value: HP1r knock down


title: V6.5_shGFP_rep6


title: V6.5_shGFP_rep5


title: HSC_E16_5 scRNA-seq

description: scRNA-seq

tag: age


title: V6.5_shHP1r_rep_1


title: WCE_ctnnb1BF_covaris

description: Mouse embryonic stem (ES) cells cultured in defined medium with MEK and GSK3 inhibitors (2i)

source_name: Whole cell extract

tag: antibody

value: input:Whole cell extract


title: HSC_P14 scRNA-seq

description: scRNA-seq


title: ASK1 WT flower bud RNA-Seq_S_141

description: Pair end 150-mer RNA-Seq


title: n1: Adult HSC-4 RNA-seq

data_processing:
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR version 3.0.4.b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Sailfish version 0.6.3. was used to produce isoform estimated counts.
Genome_build: Ensemble R76
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

extract_protocol:
Qiagen RNAeasy micro plus
Clontech SMRTr


title: V6.5_shGFP_rep2


title: V6.5_shGFP_rep1


title: ASK1 WT flower bud RNA-Seq_S_101

description: Pair end 150-mer RNA-Seq


title: n2: Adult HSC-3 RNA-seq


title: n3: Adult HSC-2 RNA-seq


title: ask1 Ds open flower RNA-Seq_S_201

description: Pair end 150-mer RNA-Seq


title: ask1 Ds open flower RNA-Seq_S_311

description: Pair end 150-mer RNA-Seq


title: n4: Adult HSC-1 RNA-seq


title: V6.5_shGFP_Hp1r_StaphSeq_rep1

source_name: HP1r antibody

value: HP1r antibody


title: V6.5_shGFP_rep4


title: ASK1 WT open flower RNA-Seq_S_121

description: Pair end 150-mer RNA-Seq


title: V6.5_shGFP_E2f6_StaphSeq_rep2

source_name: E2F6 antibody

value: E2F6 antibody


title: n5: P0 HSC-4 RNA-seq

value: Hematopoietic stem cell


title: n6: P0 HSC-3 RNA-seq


title: V6.5_shGFP_E2f6_StaphSeq_rep1


title: ask1 Ds flower bud RNA-Seq_S_181

description: Pair end 150-mer RNA-Seq


title: n7: P0 HSC-2 RNA-seq


title: V6.5_shE2F6_rep1

source_name: E2F6 knock down

value: E2F6 knock down


title: V6.5_shE2F6_rep2


title: n8: P0 HSC-1 RNA-seq


title: na1: P14 HSC-4 RNA-seq


title: D0172Mut

city: Lubbock

first: Petar

last: Grozdanov

address: 3601 4th Street

department: Cell Biology and Biochemistry

institute: Texas Tech University Health Sciences Center

data_processing:
Raw image data was converted to sequence reads (base calling) by using Illumina CASAVA v1.8 software and the data was stored as fastq files. Base Quality and Phred score were also calculated in CASAVA v1.8 software. These steps were performed by Novogene Corporation.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence greater than 10%, then mapped to mm10 whole genome using STAR v2.5 with parameters mismatch=2. Gene expression is estimated by counting the number of reads aligning on a feature (FPKM) and normalized for the length of the gene and sequencing depth of the sample using HTSeq v0.6.1 (-m union). These steps were perfomed by Novogene Corporation.
FPKM values were used to perform differential gene expression analysis between Cstf2D50A mutant and control (wild type) mice using an R package of DESeq2 software (V2_1.6.3). Difference in gene expression with P values, which were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate, smaller than 0.05 were considered statistically significant. These steps were performed by Novogene Corporation.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

molecule: polyA RNA

growth_protocol: Mice were housed in the vivarium, fed normal mouse chow ad libitim, and sacrificed at 50 days postpartum; Mutants and wild type littermates were maintained as a congenic strain by backcrossing four generations to C57BL/6NCrl (Charles River) and subsequently breeding exclusively within the colony.

extract_protocol:
Total brain tissue was removed from the animal and collected in Trizol reagent. Tissue was homogenized and an aliquot of the homogenate was sent to Novogene corporation. Novogene corporation isolated the total RNA, selected for poly(A)+ RNA using oligo dT magnetic beads, and prepared the sample libraries. Quality of the total RNA was monitored by absorbance at 260/280 ratio, agarose gel electrophoresis and Agilent 2100 Bioanalyzer obtaining RIN. The concentrations of the RNAs was derived from the A260 and Agilent 2100 bioanalyzer.
Libraries were prepared by Novogene corporartion using NEBNext® UltraTM RNA Library Prep Kit

treatment_protocol: No treatments

value: post natal day 50

value: total brain

tag: molecule subtype

value: Poly(A)+ selected RNA derived from total RNA


title: V6.5_shBcat_rep_2

source_name: β-catenin knock down

value: beta-catenin knock down


title: V6.5_shGFP_Hp1r_StaphSeq_rep2


title: V6.5_shBcat_rep_1


title: D0170Mut


title: D0169Mut


title: na2: P14 HSC-3 RNA-seq


title: na3: P14 HSC-2 RNA-seq


title: ask1 Ds flower bud RNA-Seq_S_191

description: Pair end 150-mer RNA-Seq


title: V6.5_2i_shGFP_TCF3_rep2

source_name: Tcf3 antibody

value: Tcf3 antibody


title: V6.5_2i_shGFP_TCF3_rep1


title: D0167WT

source_name: wild type_brain

value: wild type


title: D0171WT


title: na4: P14 HSC-1 RNA-seq


title: K562 CALR INS_2

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: Gene expression data from K562 cells transduced with INS5 CALR

hyb_protocol: Following fragmentation,  cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U219 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station

scan_protocol: GeneChips were scanned using Affymetrix GeneChio Scanner 3000 7G

data_processing: Data were analyzed using Partek GS and RMA normalization

source_name: K562 cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: K562 cells were seeded at 3×105 cells/mL in Roswell Park Memorial Institute medium (RPMI-1640; Euroclone) supplemented with 10% FBS (Sigma-Aldrich).

extract_protocol: Total cellular RNA was harvested from 1×105 cells from each sample using the miRNeasy Micro RNA isolation kit (QIAGEN)

treatment_protocol: Transduction of K562 cells was performed by four cycles of infection (one every 12h) with viral supernatant with the addition of polybrene (8 μg/ml), and 20% FBS (Sigma-Aldrich) in retronectin-coated plates. Untreated 24-wells plates were coated with retronectin (10μg/cm2) (Takara Bio Inc, Japan) following the manufacturer’s protocol. To achieve optimal expansion and infection of K562 cells, the retronectin-coated plates were pre-incubated with retroviral supernatant for 4h, then K562 cells were seeded in 24-wells plate at 3x105 cells/ml (1ml/well) in fresh viral supernatant. After transduction, K562 cells were maintained in Roswell Park Memorial Institute medium (RPMI-1640; Euroclone) supplemented with 20% FBS for additional 36h. Transduced K562 cells were subsequently purified by means of immunomagnetic selection (EasySep “Do-It-Yourself” Selection Kit; StemCell Technologies) using the anti-human p75-NGFR mouse monoclonal antibody (BD Biosciences). Purity of the NGFR+ cell fraction was assessed by flow cytometry after labeling with PE-conjugated anti-NGFR monoclonal antibody (Miltenyi) 48h post-purification and was always >90%.

tag: calr status

value: INS

tag: replicate


title: K562 CALR WT_3

description: Gene expression data from K562 cells transduced with WT CALR

value: WT


title: K562 CALR WT_2


title: sRNA -TL25_CG - Rep2

description:
DL26
sRNA-seq processed data.xlsx

source_name: Flag leaf tissue

value: DBA Aurora (Stress-tolerant)

value: Control group (CG)


title: D0166WT


title: na6: P7 HSC-3 RNA-seq


title: K562 CALR INS_3


title: D0165Mut


title: V6.5_2i_shGFP_input

value: Embryonic stem cells


title: Cov_Flag_ctnnb1

source_name: Flag M2 monoclonal antibody

value: Flag M2 monoclonal antibody


title: na7: P7 HSC-2 RNA-seq


title: D0168Mut


title: 11-VC-12-7: K562 cells Vector Control #5

city: Gainesville

first: William

middle: Bradley

last: Barbazuk

state: Florida

address: UF-CGRC Room 407 2033 Mowry Rd

department: Biology

institute: University of Florida

data_processing:
Basecalls perfromed with BCL2FastQ v 2.18.0.12
Raw sequence reads were adapter trimmed with Cutadapt v1.1 with the following parameters: --error-rate=0.1 --times=1 --overlap=5 --minimumlength=0 --adapter=GATCGGAAGAGCACACGTCT --quality-base=33.
Adapter trimmed sequences were quality filtered/trimmed with Trimmomatic v0.22 using parameters (HEADCROP:0, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:40) to truncate reads for base quality
Adapter and quality trimmed reads were aligned with Hisat2 v 2.0.4 with the following parameters: --max-intronlen 100000 -q --pen-noncansplice 6 --no-discordant --rna-strandness RF
Raw counts collected with HTSeq_count v 10.0.0 with the following parameters: -t exon -f sam -i gene_id -m intersection-nonempty -s reverse -t exon using Homo_sapiens.GRCh38.87.gtf
Genome_build: Homo_sapiens.GRCh38.dna.primary_assembly.fa

source_name: K562 Cells

growth_protocol: The K-562 cells (ATCC® CCL-243TM) were incubated at 37° C with 5% CO2 and cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) (Thermo Fisher, cat# 12440053) supplemented with L-glutamine, Phenol Red, and 10% (v/v) HycloneTM fetal bovine serum (FBS) (Fisher Scientific, cat# SH3007103).

extract_protocol:
Approximately 1 x 106 cells from each samples was resuspended in Trizol reagent. Homogenized cells were subjected to chloroform/isopropanol extraction. Following DNase treatment, the samples were further purified using the RNeasy MinElute Cleanup Kit.
The NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, cat# E7530S) was used to generate paired-end 100 bp  stranded RNA-Seq libraries.

treatment_protocol: K-562 cells were co-transfected with 0.5 µg of pX459 expressing TAG sgRNA and 0.5 µg HDR donor template containing the Myc-tag.  The cells were transfected using 0.75 µL of Lipofectamine 3000 diluted in Opti-MEMTM I Reduced Serum Medium, and cultured for 24 hours following manufacturer’s instructions.  Transfected colonies were isolated by incubating the cells for an additional 48 hours with 3 µg/mL of puromycin.  The cells were then selected for single cell isolation and subjected to immediate expansion to generate homogenous population of RBM48 Myc-tagged cells.

value: Vector Control


title: na8: P7 HSC-1 RNA-seq


title: 12-VC-13-8: K562 cells Vector Control #6


title: Donor 1 D6 H3K27ac ChIP-seq

city: Los Angeles

first: Daniel

middle: James

last: Mullen

state: CA

address: 1441 Eastlake Ave., Room NTT 6420

department: Biochemistry and Molecular Medicine, Surgery

institute: University of Southern California

description: H3K27ac ChIP-seq in Donor 1 differentiated AT1-like cells (D6)

data_processing:
ChIP-seq reads were aligned to the human reference genome hg38 following standards used by the ENCODE3 consortium outlined in Landt SG et al. 2012 and detailed in the ENCODE3 ChIP-seq pipeline (https://www.encodeproject.org/chip-seq/). In brief, bwa v.0.7.17 was used to align the reads, trimming the first 5 base pairs of each read, allowing for two mismatches. Duplicate reads were marked using Picard MarkDuplicates v.2.12.0, and the duplicated reads and reads with mapping quality lower than 30 were removed using samtools v.1.9. Peaks and signal tracks were generated using the Macs2 v.2.1.2 peak caller. For peak calling, the callpeak function was used with a p-value cutoff set to 0.01, no shift selected, an extension size equal to the value calculated by for the ChIP files from cross correlation, with all duplicate tags kept, and a pileup signal file created.
ATAC-seq reads were aligned to the human reference genome hg38 using the same methods performed for ChIP-seq, using the ENCODE3 pipeline for paired end files.
RNA-seq reads were aligned to the human reference genome hg38 using the Genomic Data Commons Bioinformatics mRNA analysis pipeline (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/). In brief, the two-pass alignment method was performed using STAR v2.6.0a using settings as specified by the pipeline. Read counts were generated for GENCODE v22 genes using the htseq-count function from HTSeq v0.11.1
Genome_build: hg38
Supplementary_files_format_and_content: For ChIP-seq and ATAC-seq, tab-delimited narrowPeak files contain locations of peaks and bigwig files contain read pileup information
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files contain read counts for GENCODE v22-annotated genes

source_name: Differentiated AT2-like alveolar epithelial cells

growth_protocol: Human lung adenocarcinoma A549 cells (ATCC # CRL-185) were grown at 37oC with 5% CO2 in RPMI 1640 (#10-040-CV, Corning, NY, USA) supplemented with 10% FBS (#FBS-500, X&Y Cell Culture, MI, USA) and 100 units/ml of penicillin/streptomycin (formulated by Norris Comprehensive Cancer Center Media Core, CA, USA). Human alveolar epithelial cells (AECs) were isolated from remnant transplant lung from de-identified non-smoking donors as previously described by Marconett CN et al. 2013. AECs were isolated from the samples and plated, after which they differentiated from AT2-like cells to AT1-like cells. Cells used here included freshly isolated AEC (AT2 - D0) cells plated for 4 days (D4) representing cells in an AT2-to-AT1-transitional state, and cells plated for six days (D6), representing AT1-like cells as described by Marconett CN et al. 2013 and Yang C et al. 2018.

extract_protocol:
ChIP sequencing was performed on D0, D4, and D6 alveolar epithelial cells originally isolated from Donor 1 using antibodies for H3K27ac (catalog #39133, Active Motif, CA, USA) as described previously by Yang C et al. 2018.
ATAC sequencing was performed on D0 alveolar epithelial cells originally isolated from Donor 2 using the protocol from Buenrostro et al. 2015. Briefly, intact nuclei were isolated and incubated with Tn5 transposase (#FC-121-1030, Illumina, CA, USA). The transposed DNA was extracted and was amplified with PCR using NEBNExt High-Fidelity PCR Master Mix (#M0541S, New England Biolabs, MA, USA) and the resulting library was purified using a bead clean with AMPure XP Magnetic Beads (#A63880, Beckman Coulter, CA, USA) and quality control was performed using a BioAnalyzer High-Sensitivity DNA Analysis kit (#5067-4626, Agilent, CA, USA).
For RNA sequencing, RNA was extracted using the Aurum Total RNA Mini Kit (# 7326820, Bio-Rad, CA, USA). cDNA was synthesized using an iScript cDNA Synthesis Kit (# 1708891, Bio-Rad, CA, USA).
ChIP-seq libraries were made was performed at the USC Epigenome center and sequenced using 50bp single-end reads on an Illumina HiSeq 2000 according to the manufacturer’s instructions after performing QC as previously described by Yang C et al. 2018.
ATAC-seq library construction was performed at the USC Epigenome center and sequenced using 75bp paired end reads on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
RNA-seq was performed after siRNA knockdown using libraries created by GENEWIZ (NJ, USA), and sequenced using 150bp paired-end reads on Illumina HiSeq 4000 by GENEWIZ (NJ, USA).

treatment_protocol: siRNA knockdown was performed in quadruplicate on A549 cells using 100 nM of ON-TARGETplus siRNA oglionucleotides for human MYBL2 (# L-010444-00-005, Dharmacon - Horizon Discovery, UK), FOXM1 (# L-009762-00-005, Dharmacon - Horizon Discovery, UK) , or non-targeting control (# D-001810-10-05, Dharmacon - Horizon Discovery, UK) mixed with 5X siRNA buffer (# B-002000-UB-100, Horizon Discovery, UK) and transfected using DharmaFECT 1 Transfection reagent (# T-2001-01, Horizon Discovery, UK). Cells were transfected, cultured for 24 hours, and transfected again with the same concentration of siRNA, then were incubated for an additional 24 hours


title: K562 CALR WT_1


title: K562 CALR INS_1


title: ZFF-16: MNNG/HOS cells

city: Hefei,

first: Youguang

last: Pu

state: Anhui

address: No. 96 Jinzhai Road, Hefei City, Anhui Province

institute: University of Science and Technology of China

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

source_name: Osteosarcoma cells

growth_protocol: Cells were added 10% fetal bovine serum (PAN biotechnology), 100 U/ml penicillin and 100 mg/ml streptomycin (WISTENC) to DMEM or RPMI1640 (biological industry) medium, and 5% CO2 was added to humidified air at 37°C.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Osteosarcoma cells

value: overexpressed DICER1-AS1 in  multi-drugresistant Osteosarcoma MNNG/HOS cells


title: Donor 1 D4 H3K27ac ChIP-seq

description: H3K27ac ChIP-seq in Donor 1 AT2-to-AT1 cells (D4)

source_name: Transitional AT2-to-AT1 alveolar epithelial cells


title: Donor 2 D0 ATAC-seq

description: ATAC-seq in Donor 2 purified AT2 cells (D0)

source_name: Purified AT2 alveolar epithelial cells

value: Purified AT2 alveolar epithelial cells


title: K562 CALR DEL_3

description: Gene expression data from K562 cells transduced with DEL52 CALR

value: DEL


title: ZFF-15: MNNG/HOS cells


title: K562 CALR DEL_2


title: 10-VC-11-6: K562 cells Vector Control #4


title: K562 CALR DEL_1


title: ZFF-14: SJSA-1 cells

value: overexpressed DICER1-AS1 in  multi-drugresistant Osteosarcoma SJSA-1 cells


title: nb1: E14 HSC-3 RNA-seq

source_name: Hematopoietic stem cell

value: Hematopoietic stem cell


title: na5: P7 HSC-4 RNA-seq


title: 9-VC-10-5: K562 cells Vector Control #3


title: ZFF-13: SJSA-1 cells


title: Donor 1 D0 H3K27ac ChIP-seq

description: H3K27ac ChIP-seq in Donor 1 purified AT2 cells (D0)


title: C4-2-ENZ-Rep3

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Reads aligned to human reference genome (hg19) using Tophat (v2.0.6) with default parameters
Raw count and RPKM were calcualted using RSeQC (v2.3.6) on hg19.refseq.bed12
Genome_build: hg19
Supplementary_files_format_and_content: raw count and FPKM

source_name: prostate

growth_protocol: Cells were maintained at 37°C and 5% CO2 in RPMI 1640 containing 10% fetal bovine serum (FBS) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).

extract_protocol:
RNAs were extracted using RNeasy Mini Kit.
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit.

treatment_protocol: C4-2-ENZ cells through long-term (> two months) treatment with enzalutamide (ENZ) were maintained by continuous treatment of ENZ. Control cells C4-2-CON were generated in parallel by treating cells with vehicle (DMSO).

value: prostate cancer

tag: passages


title: nb2: E14 HSC-2 RNA-seq


title: nb3: E14 HSC-1 RNA-seq


title: 8-VC-9-4: K562 cells Vector Control #2


title: C4-2-ENZ-Rep2


title: ZFF-1: SJSA-1 cells

value: multi-drugresistant Osteosarcoma cells


title: ZFF-2: G-292 cells

value: multi-drugresistant multi-drugsensitive Osteosarcoma cells


title: C4-2-ENZ-Rep1


title: 7-VC-8-3: K562 cells Vector Control #1


title: nb4: E16 HSC-4 RNA-seq


title: nb5: E16 HSC-3 RNA-seq


title: sh2_6hR_rep2

city: Urbana

first: Prasanth Kumar

middle: Vijayan

last: Kannanganattu

state: Illinois

address: 601S, Goodwin Avenue

department: Cell and Developmental Biology

institute: University of Illinois at Urbana-Champaign

data_processing:
Reads of the samples were trimmed for adapters using Flexbar
RNA-seq reads were aligned to human reference genome GRCh38 assembly using HISAT2
raw gene counts were first analyzed by HTSEQ-Count
Genome_build: GRCh38
Supplementary_files_format_and_content: Individual files include gene count information are presented in txt format

source_name: WI-38 cells

growth_protocol: WI-38 cells are cultured in 10% FBS+MEM with essential amino acid and sodium pyruvate.

extract_protocol:
Total RNA was extracted using RNeasy minikit from Qiagen
12 mRNA-Seq samples were pooled and sequenced on HiSeq4000 using Illumina TruSeq Stranded mRNA Library Prep and paired-end sequencing.

treatment_protocol: Lentivirus was added in WI-38 cells for MIR222HG depletion. The following day, lentivirus-transfected cells were induced to quiescence by changing the medium with MEM+0.1% FBS and 2.5ug/uL puromycin and inducabted for 3 days. Then, serum stimulation was performed by changing back to 10% FBS contained medium. Control and MIR222HG-depleted cells in quiescence or at serum release time points 6 hour were collected for RNA extraction.

tag: treatment

value: MIR222HG shRNA2

tag: stimulation

value: 6-hour serum released WI-38 cells


title: C4-2-CON-Rep3

tag: cell type


title: 5-2B-12-7: K562 cells RBM48 KO #5

tag: genotype

value: RBM48 KO


title: sh1_6hR_rep2

value: MIR222HG shRNA1


title: nb6: E16 HSC-2 RNA-seq

tag: tissue


title: C4-2-CON-Rep2


title: 4-2B-11-6: K562 cells RBM48 KO #4


title: Ctr_6hR_rep2

value: Control shRNA


title: nb7: E16 HSC-1 RNA-seq


title: C4-2-CON-Rep1


title: sh2_Q_rep2

value: Serum starved quiescent WI-38 cells


title: 3-2B-10-5: K562 cells RBM48 KO #3


title: nb8: E18 HSC-3 RNA-seq


title: C4-2-CON-H3K27ac-Rep3

data_processing:
Basecalls performed using CASAVA version 1.4
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using bowtie2 with defautl parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated by deeptools 2.5.4, and peaks were called by Macs2

growth_protocol: Cells were maintained at 37°C and 5% CO2 in RPMI 1640 containing 10% fetal bovine serum (FBS) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).FGF-2 (NS expansion medium).

tag: chip antibody

value: anti-H3K27ac #ab4729, Abcam


title: 2-2B-9-4: K562 cells RBM48 KO #2


title: nb9: E18 HSC-2 RNA-seq


title: C4-2-CON-H3K27ac-Rep2


title: nb10: E18 HSC-1 RNA-seq


title: Ctr_Q_rep2


title: C4-2-CON-H3K27ac-Rep1


title: D0172Mut [19075-01PG-08]

data_processing:
library strategy: 3'-seq
Raw image data was converted to sequence reads (base calling) by using Illumina RTA v2.7.7 software and the data was stored as fastq files. Base Quality and Phred score were calculated in FastQC (version 0.11.3) software. These steps were performed by Admera Health.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence greater than 10%, then mapped to mm9 whole genome using STAR v2.5. Gene expression is estimated by counting the number of reads aligning on a feature (TPM) using HTSeq v0.6.0. These steps were performed by Admera Health.
TPM values were used to perform differential alternative polyadenylation analysis between mutant and control (wild type) mice using a proprietary software based on work performed in the laboratory of Dr. Tian (most recently described in Bioinformatics. 2020 Apr 22;btaa266.  doi: 10.1093/bioinformatics/btaa266). Difference in polyadenylation were calculated using Fisher’s exact test. P value smaller than 0.05 was considered statistically significant event. These steps were performed by Admera Health.
Genome_build: mm9
Supplementary_files_format_and_content: raw counts

extract_protocol:
Total brain tissue was removed from the animal and collected in Trizol reagent. Tissue was homogenized and an aliquot of the homogenate was sent to Ademra Health. Quality of the total RNA was monitored by absorbance at 260/280 ratio, agarose gel electrophoresis and Agilent 2100 Bioanalyzer obtaining RIN. The concentrations of the RNAs was derived from the A260 and Agilent 2100 bioanalyzer.
Admera Health isolated the total RNA and prepared the libraries using QuantSeq 3’ mRNA-Seq Library Prep Kit REV for Illumina.

value: post natal day 50

value: total brain

value: 3' end of polyadenylated mRNA


title: a1: P14 HPC-5 RNA-seq

source_name: Hematopoietic progenitor cell

value: Hematopoietic progenitor cell


title: 6-2B-13-8: K562 cells RBM48 KO #6


title: D0171WT [19075-01PG-07]

value: wild type


title: C4-2-CON-FOXA1-Rep3

value: anti-FOXA1 #ab23738, Abcam


title: sh1_6hR_rep1


title: 1-2B-8-3: K562 cells RBM48 KO #1


title: a4: P14 HPC-4 RNA-seq


title: C4-2-CON-FOXA1-Rep2


title: D0170Mut [19075-01PG-06]


title: sh2_Q_rep1


title: D0169Mut [19075-01PG-05]


title: C4-2-CON-FOXA1-Rep1


title: D0168Mut [19075-01PG-04]


title: a7: P14 HPC-2 RNA-seq


title: sh1_Q_rep2


title: a8: P14 HPC-1 RNA-seq


title: C4-2-CON-AR-Rep3

value: anti-AR #sc-816, Santa Cruz Biotechnology


title: Ctr_6hR_rep1


title: D0167WT [19075-01PG-03]


title: sh1_Q_rep1


title: Ctr_Q_rep1


title: e1: P0 HPC-4 RNA-seq


title: C4-2-CON-AR-Rep1

value: prostate cancer


title: sh2_6hR_rep1


title: A549 siFOXM1 rep4 RNA-seq

description: RNA-seq in A549 cells after FOXM1 siRNA treatment rep4

source_name: A549 lung adenocarcinoma cell line

value: A549 lung adenocarcinoma cell line


title: e2: P0 HPC-3 RNA-seq


title: D0165Mut [19075-01PG-01]


title: e3: P0 HPC-2 RNA-seq


title: A549 siFOXM1 rep3 RNA-seq

description: RNA-seq in A549 cells after FOXM1 siRNA treatment rep3


title: D0166WT [19075-01PG-02]


title: C4-2-ENZ-H3K27ac-Rep2


title: a5: P14 HPC-3 RNA-seq


title: e4: P0 HPC-1 RNA-seq


title: A549 siFOXM1 rep2 RNA-seq

description: RNA-seq in A549 cells after FOXM1 siRNA treatment rep2


title: C4-2-ENZ-H3K27ac-Rep1


title: C4-2-ENZ-FOXA1-Rep3


title: Sigma_70

city: Waltham

first: Jeff

last: Gelles

state: MA

address: 415 South Street

department: Biochemistry

institute: Brandeis University

description: sigma.wig

data_processing:
ChIP-seq reads were trimmed with trimgalore
Trimmed reads were mapped to the E. coli genome with bowtie2 using default parameters
Data were filtered to have quality score > 10 using samtools
Biological replicates were merged with samtools merge
.wig files were generated with igvtools count with settings -w 1 -e 250. Scores represent the number of mapped reads at each basepair position in the genome.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: .wig files contain the number of mapped reads at each basepair position in the genome.

organism: Escherichia coli

source_name: Escherichia coli RL3000 cells

growth_protocol: E. coli RL300 cells were grown by inoculating 5 ml MOPS +0.2% carbon source with a single colony, and grown overnight at 37C. Cell cutures were inoculated to OD 0.01, and then grown to OD 0.3-0.4 (as close to 0.4 as possible) in 50 ml MOPS Minimal Media + 0.2% glucose at 250 rpm on an orbital shaking table at 37C for 5-6 hours.

extract_protocol:
Cell lysates were clarified from sonicated cells and histone-DNA complexes were isolated with an antibody.
Purified immunoprecipitated and input DNA was submitted to the University of Wisconsin-Madison Biotechnology Center.  DNA concentration and sizing were verified using the Qubit® dsDNA HS Assay Kit (Invitrogen, Carlsbad, California, USA) and Agilent DNA HS chip (Agilent Technologies, Inc., Santa Clara, CA, USA), respectively.  Samples were prepared according the TruSeq® ChIP Sample Preparation kit (Illumina Inc., San Diego, California, USA) with minor modifications. Libraries were size selected for an average insert size of 350 bp using SPRI-based bead selection. Quality and quantity of the finished libraries were assessed using an Agilent DNA1000 chip and Qubit® dsDNA HS Assay Kit, respectively. Libraries were standardized to 2nM.  Cluster generation was performed using standard Cluster Kits (v3) and the Illumina Cluster Station.  Single 100bp sequencing was performed, using standard SBS chemistry (v3) on an Illumina HiSeq2000 sequencer.  Images were analyzed using the standard Illumina Pipeline, version 1.8.2.

value: K-12 substr. MG1655

value: (Sigma 70) 2G10, Neoclone:cat# W0004

tag: strain description

value: F-, λ-, ilvG468+, rfb-50, rph+ ybhJ(L54->I) yebN(G25xxx->D)


title: A549 siFOXM1 rep1 RNA-seq

description: RNA-seq in A549 cells after FOXM1 siRNA treatment rep1


title: RNAP_68

description: rnap.wig

value: Beta NT63, Neoclone:cat# W0002


title: f2: P7 HPC-3 RNA-seq


title: C4-2-ENZ-FOXA1-Rep2

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


title: C4-2-CON-AR-Rep2


title: f3: P7 HPC-2 RNA-seq


title: RNAP_76

description: rnap.wig


title: A549 siMYBL2 rep3 RNA-seq

description: RNA-seq in A549 cells after MYBL2 siRNA treatment rep3


title: A549 siMYBL2 rep4 RNA-seq

description: RNA-seq in A549 cells after MYBL2 siRNA treatment rep4


title: C4-2-ENZ-FOXA1-Rep1


title: C4-2-ENZ-H3K27ac-Rep3


title: A549 siMYBL2 rep2 RNA-seq

description: RNA-seq in A549 cells after MYBL2 siRNA treatment rep2


title: f4: P7 HPC-1 RNA-seq


title: Sigma_77

description: sigma.wig


title: 25_RPF_RAPA

city: Beijing

first: Hua

last: Jin

state: Choose a State or Province

address: Rm 225-1, Bldg Qiushilou, Beijing Institute of Technology,

institute: Beijing Institute of Technology

description:
RPF from Ribo-seq
Ribosome protected fragment (RPF)

data_processing:
Library strategy: Ribo-seq
Trimmomatic-0.30/trimmomatic-0.30.jar SE -phred33 CROP:70 HEADCROP:6 LEADING:25 TRAILING:25 AVGQUAL:$avgquality MINLEN:19
Genome_build: Drosophila dm3 (BDGP Release 5); Human hg38 (GRCh38)
Supplementary_files_format_and_content: *.threshold.txt: Edited sites
Supplementary_files_format_and_content: *bw: bigWig files

organism: Drosophila melanogaster

source_name: late stage embryo-derived S2 cells

growth_protocol: S2 cells were grown in Hyclone SFX-insect media with 10% of FBS. PC3 cells were grown in F-12K Medium (ATCC) with 10% of FBS.

extract_protocol:
GFP-positive cells were sorted and collected with a BD FACSAria II machine. Total RNA was extracted with TRIzol LS reagent.
TRIBE: Standard Illumina TruSeq RNA Library Kit.

tag: transfected plasmids

value: 100nM of Rapamycin for 2 hrs


title: C4-2-ENZ-AR-Rep3


title: 26_RPF_Torin

value: 100nM of Torin-1 for 2 hrs


title: C4-2-ENZ-AR-Rep2


title: A549 siMYBL2 rep1 RNA-seq

description: RNA-seq in A549 cells after MYBL2 siRNA treatment rep1


title: 24_RPF_DMSO

value: DMSO for 2 hrs


title: h1: E16 HPC-3 RNA-seq

city: St Louis

first: Jeffery

last: Magee

institute: Washington University School of Medicine


title: h3: E16 HPC-2 RNA-seq


title: C4-2-ENZ-AR-Rep1


title: f1: P7 HPC-4 RNA-seq


title: 23_Input_Torin

description:
Input from Ribo-seq
Input RNA, rRNA depleted


title: A549 siControl rep3 RNA-seq

description: RNA-seq in A549 cells after control siRNA treatment rep3


title: h4: E16 HPC-1 RNA-seq


title: 22_Input_RAPA


title: A549 siControl rep2 RNA-seq

description: RNA-seq in A549 cells after control siRNA treatment rep2


title: C4-2-ENZ-AR-shCXXC5-Rep1


title: k3: Adult HPC -2 RNA-seq

value: 8 week old


title: k2: Adult HPC -3 RNA-seq


title: C4-2-ENZ-IgG-Rep2

value: Rabbit IgG #ab171870, Abcam


title: 9_RPF_Torin


title: 21_Input_DMSO


title: A549 siControl rep1 RNA-seq

description: RNA-seq in A549 cells after control siRNA treatment rep1


title: C4-2-ENZ-IgG-Rep1


title: k4: Adult HPC -1 RNA-seq


title: 8_RPF_RAPA


title: RNAseq-Cbx2-1

first: Claudia

last: Baumann

state: GA

address: 501 DW Brooks Drive

department: Physiology and Pharmacology

institute: University of Georgia

description: targeted deletion of Chromobox domain protein 2

data_processing:
Data retrieved from RNA-Seq on DNBseq platform was filtered by removing reads mapped to rRNA and low-quality, adaptor-polluted and high content of unknown base (N) reads
Mapped clean reads to reference genome using HISAT2, using  paramters --phred33 --sensitive --no-discordant --no-mixed -I 1 -X1000
DEseq2 algorithm was used to identify differentially-expressed genes, which are defined by genes with log2(fold change) >= 1.00 and adjusted p value <= 0.05, these were then recorded in excel
Novel coding transcripts were merged with reference transcripts to obtain the complete reference, and then Bowtie2 was used to map clean reads to this reference (Bowtie2 parameter: -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X1000 --nomixed --no-discordant -p 1 -k 200)
Gene expression level was calculated for each sample by the RSEM software with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: DEG table files

source_name: MEF Cbx2-KO rep1

growth_protocol: Primary mouse embryonic fibroblasts were collected from E18 control and Cbx2-/- mouse embryos and cultured for 2 passages under standard conditions before collection of cells and subsequent analysis.

extract_protocol: The transcriptomes of wild type and Cbx2-/- fibroblasts at passage P2 were mapped and quantified by deep sequencing and quantifying the frequency of each gene represented in duplicate (RNA-Seq). 2×10^5 cells per replicate and genotype were used for RNA extraction and transcriptome analysis using a DNBseq platform, generating approximately 4.62 Gb bases per sample.

tag: passage

value: Passage 2

value: embryonic day 18

value: mouse embryonic fibroblasts


title: RNAseq-WT-2

description: wildtype litter mate

source_name: MEF WT rep2

value: wild type


title: 7_RPF_DMSO


title: RNAseq-WT-1

description: wildtype litter mate

source_name: MEF WT rep1


title: C4-2-CON-IgG-Rep2


title: A549 siControl rep4 RNA-seq

description: RNA-seq in A549 cells after control siRNA treatment rep4


title: RNA-seq in A549 cells after FOXM1 and MYBL2 siRNA double knockdown treatment rep3

data_processing:
RNA-seq reads were aligned to the human reference genome hg38 using the Genomic Data Commons Bioinformatics mRNA analysis pipeline (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/). In brief, the two-pass alignment method was performed using STAR v2.6.0a using settings as specified by the pipeline. Read counts were generated for GENCODE v22 genes using the htseq-count function from HTSeq v0.11.1
Genome_build: hg38
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files contain read counts for GENCODE v22-annotated genes

growth_protocol: Human lung adenocarcinoma A549 cells (ATCC # CRL-185) were grown at 37oC with 5% CO2 in RPMI 1640 (#10-040-CV, Corning, NY, USA) supplemented with 10% FBS (#FBS-500, X&Y Cell Culture, MI, USA) and 100 units/ml of penicillin/streptomycin (formulated by Norris Comprehensive Cancer Center Media Core, CA, USA).

extract_protocol:
For RNA sequencing, RNA was extracted using the Aurum Total RNA Mini Kit (# 7326820, Bio-Rad, CA, USA). cDNA was synthesized using an iScript cDNA Synthesis Kit (# 1708891, Bio-Rad, CA, USA).
RNA-seq was performed after siRNA knockdown using libraries created by MedGenome (Foster City, CA), and sequenced using 100bp paired-end reads on an Illumina NovaSeq 6000 by MedGenome (Foster City, CA).

treatment_protocol: siRNA knockdown was performed in triplicate on A549 cells using 100 nM of ON-TARGETplus siRNA oglionucleotides for human MYBL2 (# L-010444-00-005, Dharmacon - Horizon Discovery, UK) and FOXM1 (# L-009762-00-005, Dharmacon - Horizon Discovery, UK) , or non-targeting control (# D-001810-10-05, Dharmacon - Horizon Discovery, UK) mixed with 5X siRNA buffer (# B-002000-UB-100, Horizon Discovery, UK) and transfected using DharmaFECT 1 Transfection reagent (# T-2001-01, Horizon Discovery, UK). Cells were transfected, cultured for 24 hours, and transfected again with the same concentration of siRNA, then were incubated for an additional 24 hours

tag: sirna

value: siFOXM1 and siMYBL2


title: RNA-seq in A549 cells after FOXM1 and MYBL2 siRNA double knockdown treatment rep2

tag: cell line


title: C4-2-ENZ-AR-shTET2-Rep2

value: anti-AR #sc-816, Santa Cruz Biotechnology


title: 6_RPF_Torin


title: Arabidopsis npr1-1 with SA treatment rep3

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

institute: SUSTC (current, may different with previous institution )

data_processing:
Reads were mapped to the genome using TopHat2 (https://ccb.jhu.edu/software/tophat/index.shtml) software with two mismatches allowed. Cuffdiff (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/) was used for differential expression analysis. Differentially expressed genes were identified based on a fold change > 2 and q-value < 0.05 when comparing the test group sample to the control group sample. Data were summarized in file SA-NPR1-EIN3_GEO submission_processed data.xls
Genome_build: TAIR10
Supplementary_files_format_and_content: SA-NPR1-EIN3_GEO submission_processed data.xls (FPKMs)

source_name: Arabidopsis npr1-1 with SA treatment

growth_protocol: Etiolated seedlings were grown in the dark for 3.5 days after stratification at 4 degrees for 3 days.

extract_protocol:
RNeasy Plant Mini Kit
stander Illumina mRNA-seq protocol

treatment_protocol: Etiolated seedlings were treated with MS liquid supplemented with or without 500 μM SA for 4 hrs.

tag: age

value: etiolated seedlings

value: SA


title: 5_RPF_RAPA


title: C4-2-CON-IgG-Rep1

value: prostate cancer


title: C4-2-ENZ-AR-shTET2-Rep1


title: k1: Adult HPC -4 RNA-seq

address: 660 S Euclid Ave.

value: Hematopoietic progenitor cell


title: 4_RPF_DMSO


title: Arabidopsis npr1-1 with SA treatment rep2


title: RNA-seq in A549 cells after FOXM1 and MYBL2 siRNA double knockdown treatment rep1


title: RNAseq-Cbx2-2

source_name: MEF Cbx2-KO rep2


title: C4-2-ENZ-AR-shCXXC5-Rep2


title: RNA-seq in A549 cells after control siRNA treatment for double knockdown samples rep3

value: siControl


title: Arabidopsis npr1-1 with MS treatment rep3

source_name: Arabidopsis npr1-1 with MS treatment

value: MS


title: 3_Input_Torin


title: Arabidopsis npr1-1 with SA treatment rep1


title: C4-2-CON-TET2-Rep1

value: anti-TET2 #ab94580, Abcam


title: RNA-seq in A549 cells after control siRNA treatment for double knockdown samples rep2


title: RNA-seq in A549 cells after control siRNA treatment for double knockdown samples rep1


title: C4-2-CON-TET2-Rep2


title: C4-2-CON-CXXC5-Rep2

value: anti-CXXC5 #16513-1-AP, Proteintech


title: 1_Input_DMSO

value: DMSO for 2 hrs


title: Arabidopsis npr1-1 with MS treatment rep2


title: WI38_6hR_rep2

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina)
RNA-seq reads were aligned to human reference genome GRCh38 assembly using HISAT2
raw gene counts were first analyzed by HTSEQ-Count
Genome_build: GRCh38
Supplementary_files_format_and_content: Individual files include gene count information are presented in txt format

extract_protocol:
Total RNA was extracted using RNeasy minikit from Qiagen
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina), polyadenylated mRNAs were captured with oligodT beads.

treatment_protocol: To induce cellular quiescence, WI-38 cells are cultured in 0.1% serum for 72 hours. Then, serum re-activation is performed by adding back the regular 10% serum growth medium.

value: 6-hour serum released WI-38 cells


title: Arabidopsis npr1-1 with MS treatment rep1


title: C4-2-ENZ-TET2-Rep2


title: WI38_6hR_rep1


title: 13_Thor_Hyper_uninduced_replicate2

description:
TRIBE, RNA-seq
Poly(A) tailed RNA

data_processing:
Library strategy: TRIBE
Trimmomatic-0.30/trimmomatic-0.30.jar SE -phred33 CROP:70 HEADCROP:6 LEADING:25 TRAILING:25 AVGQUAL:$avgquality MINLEN:19
Genome_build: Drosophila dm3 (BDGP Release 5); Human hg38 (GRCh38)
Supplementary_files_format_and_content: *.threshold.txt: Edited sites
Supplementary_files_format_and_content: *bw: bigWig files

value: pAC5.1-eGFP and pMTA-thor-hyperADARcd

tag: expression of gene in pmta

value: Uninduced

value: DMSO for 5 hrs


title: 12_Thor_Hyper_uninduced_replicate1

description:
TRIBE, RNA-seq
Poly(A) tailed RNA


title: Arabidopsis ein3 eil1 with SA treatment rep3

source_name: Arabidopsis ein3 eil1 with SA treatment

value: ein3 eil1


title: C4-2-ENZ-TET2-Rep1


title: WI38_3hR_rep2

value: 3-hour serum released WI-38 cells


title: WI38_3hR_rep1


title: 11_Thor_Hyper_induced_+Torin 1_replicate2

description:
TRIBE, RNA-seq
Poly(A) tailed RNA

value: Induced the expression overnight

value: 50nM of Torin-1 for 5 hrs


title: C4-2-ENZ-CXXC5-Rep2


title: Arabidopsis ein3 eil1 with SA treatment rep1

value: etiolated seedlings


title: 2_Input_RAPA

value: 100nM of Rapamycin for 2 hrs


title: C4-2-ENZ-CXXC5-Rep1

value: prostate cancer


title: 9_Thor_Hyper_induced_+Rapa_replicate2

description:
TRIBE, RNA-seq
Poly(A) tailed RNA

value: 50nM of Rapamycin for 5 hrs


title: WI38_Q_rep2

value: Serum starved quiescent WI-38 cells


title: Arabidopsis ein3 eil1 with MS treatment rep3

source_name: Arabidopsis ein3 eil1 with MS treatment

value: MS


title: 8_Thor_Hyper_induced_+Rapa_replicate1

description:
TRIBE, RNA-seq
Poly(A) tailed RNA


title: Arabidopsis ein3 eil1 with MS treatment rep2


title: WI38_Q_rep1


title: Arabidopsis ein3 eil1 with SA treatment rep2

value: SA


title: WI38_A_rep2

value: Asynchronous WI-38 cells


title: C4-2-CON-CXXC5-Rep1

value: anti-CXXC5 #16513-1-AP, Proteintech


title: 7_Thor_Hyper_induced_-FBS_+Rapa_replicate2

description:
TRIBE, RNA-seq
Poly(A) tailed RNA

value: Serum depletion and 50nM of Rapamycin for 5 hrs


title: 10pg 150nM rep1

city: Atlanta

first: Chris

last: Scharer

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description:
100pg.600nM.rep_mate1.fastq.gz
100pg.600nM.rep_mate2.fastq.gz

data_processing:
Raw sequencing reads were mapped to the hg19 version of the human genome using Bowtie version1.1.1 with the default parameters
reads per million normalized bigWig files were generated using the GenomicRanges R/Bioconductor package and UCSC tool bedGraphToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: reads per million normalized bigWig

source_name: Raji cells

extract_protocol:
Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Scharer et al. Cancer Research, 69:709-717).  Briefly, 10^7 cells were fixed in 1% formaldehyde for 10 minutes, nuclei isolated, and sonicated to an average chromatin fragment size of 200-600 bp.  30 mg chromatin was immunoprecipitated with 3 μg anti-H3K4me3 antibody over night at 4 degrees.  Antibody-chromatin complexes were captured with Protein A magnetic beads (Invitrogen), cross-links reversed, and DNA purified.  ChIP DNA was quantitated by Qubit assay and diluted to the indicated starting amounts.
ChIP-seq libraries were generated using the indicated amount of input DNA with the KAPA Hyper Prep Kit according to the manufacturers instructions.

tag: library construction

value: Raji


title: Arabidopsis ein3 eil1 with MS treatment rep1


title: 10pg 150nM rep2

description:
100pg.600nM.rep.2cycles_mate1.fastq.gz
100pg.600nM.rep.2cycles_mate2.fastq.gz

value: KAPA Hyper Prep Kit according to the manufacturers instructions


title: 100pg 600nM rep3

description:
100pg.600nM_mate1.fastq.gz
100pg.600nM_mate2.fastq.gz