title: Day 13, KO, rep2

city: Clayton

first: Kim

last: Good-Jacobson

state: Victoria

address: Gr Fl Reception (Bldg 77) 23 Innovation Walk

country: Australia

institute: Monash University

data_processing:
Raw data quality was assessed with FastQC. After this adaptors were removed with Cutadapt (v1.9.1).
Adaptor-trimmed paired end reads were alligned with Hisat2 (v2.01) to the mm39 mouse genome.
Aligned reads were assigned to genes with HTSeq (v0.6.1) using the gff annotation file downloaded from ENSEMBLE.
Due to their high expression, Ig genes were excluded from further analysis.
Differential expression analysis was done using Bioconductor package DESeq2 (V1.6.3).
Assembly: A gene was deemed Differentially Expressed (DE) if its Fold Change (FC) was > 2 and (BH) adjusted p-value < 0.05

source_name: Mesenteric lymph node

extract_protocol:
RNA extraction was performed on cell pellets using the RNeasy Plus MicroKit (Qiagen #74034). 1 μg total RNA was used for library preparation.
poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

value: Mesenteric lymph node

value: Germinal centre B cells  (CD19+IgDloCD95hiCD38lo)

value: MLL conditional KO (in CD23+ B cells)

value: Trichuris muris infection


title: LSK_PPM1Bfl/fl_1

status: Public on Jul 31 2024

type: SRA

city: Jinan

first: Zhiyuan

last: Lu

state: Shandong Province

address: No.6699, Qingdao Road, Huaiyin District

country: China

institute: Shandong First Medical University

library_source: transcriptomic

data_processing:
Raw sequencing data were processed employing the TrimGalore toolkit(0.6.7) to cleanse low-quality reads and eliminate Illumina sequencing adapters.
Reads were mapped to mouse reference genome files using the Hisat2(2.2.0) alignment tool.
FeatureCounts(2.0.1 ) computed the number of reads attributed to genomic features (exons), generating the original count matrix for subsequent analyses.
Assembly: mm10
Supplementary files format and content: CountMatrix text file includes gene id,chromosome and counts value for each sample

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
Total RNA from pre-sorted cells was extracted following TRIzol™ Reagent (ThermoFisher).
Library preparation was performed using the TruseqTM RNA sample prep Kit (Illumina) according to the manufacturer’s protocol.

tag: tissue

value: Bone marrow

tag: cell type

value: Lsk cells

tag: genotype


title: C3

city: Hamburg

first: Sydney

last: Gies

state: Hamburg

address: Martinistraße 52

department: III. Medizinische Klinik und Poliklinik

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger  CellRanger software suite (version 6.1.1, 10x Genomics, Pleasanton, CA) including intronic counts
SoupX (v1.6.1) was applied with default parameters to remove ambient RNA contamination
Doublets were removed using Scrublet (default parameters, v0.2.2)
Assembly: Sscrofa11.1 (GCA_000003025.6)
Supplementary files format and content: matrix files

organism: Sus scrofa

source_name: kidney

extract_protocol:
Lysis solution was prepared with Nuclei PURE lysis buffer, 1 mM dithiothreitol and 0.1 % Triton X-100 according to manufacturer protocol and an RNAse inhibitor mix was added. The single nuclei suspension was filtered through a 30 µm strainer  and centrifuged at 500g for 5 min at 4 °C. The pellet was resuspended and incubated for 2 min in 1ml red blood cell lysis buffer hybri-max™ , filtered through a 5 µm strainer and washed with 4 ml of ice -cold 0,01% BSA in DPBS with 0.04 U/µl SUPERaseIN RNAse Inhibitor and 0.04 U/µl RNAsin Plus RNAse Inhibitor at 500 g for 5 min at 4 °C. The pellet was resuspended in 1% BSA in DPBS with 0.04 U/µl SUPERaseIN RNAse Inhibitor and 0.04 U/µl RNAsin Plus RNAse Inhibitor.
Nuclei number was counted and samples were diluted prior to loading to the Chromium 10X device to capture ~ 6,000 nuclei of one snap frozen, one RNAlater and the CellCover stored sample and to capture ~ 10,000 nuclei of two snap frozen and one RNAlater stored sample The nuclei were separated into Gel Bead Emulsion droplets and libraries were prepared with the Chromium NEXT GEM Single Cell 3’ Reagent kits v3.1 according to manufacturer's protocol. The libraries were sequenced on an Illumina Novaseq6000 platform as symmetric paired end runs (150 bases) with 200 million raw sequencing reads per sample (pig)

value: kidney

tag: treatment

value: SnapFrozen


title: ATAC_H1048

city: North Chicago

first: Josh

last: Plotnik

state: IL

address: 1 North Waukegan Rd, AP10/210A

country: USA

institute: AbbVie Inc.

library_source: genomic

data_processing:
Sequence quality for ATAC-seq and ChIP-seq samples was assessed by FastQC method. The sequences were aligned to human reference genome hg19 using BWA aligner, and alignment metrics were calculated using Picard and samtools.
Narrow peaks, e.g. the transcription factor binding peaks, were detected using macs2 with default cutoff parameters. Processed ChIP-seq datasets by MACS were further analyzed using the USeq platform for Intersecting Regions and Neighboring Gene identifications (http://useq.sourceforge.net/).
Further analysis of aligned bam files was done using NGSPlot (https://github.com/shenlab-sinai/ngsplot) to visualize heatmaps and generate average profile plots.
For ATAC-seq, in brief, 50K viable cells were flow sorted (FACS AriaII) on ice and transposase reactions were carried out using Tn5 transposase as previously described (Buenrostro et al, Curr Protoc Mol Biol, 2015).
Assembly: hg19
Supplementary files format and content: bedgraph

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
For ChIP-seq, cells were fixed for ten minutes with direct addition of 1% formaldehyde (ThermoFisher, Waltham, MA). The fixation was stopped with 0.125 mM glycine (Sigma-Aldrich, St. Louis, MO) for five minutes, followed by wash and collection in cold PBS and subsequent lysis (1% SDS, 10 uM EDTA, 50 uM TrisCl pH 8.0, 5 mM sodium butyrate, cOmpleteTM protease inhibitor cocktail tablets) (Sigma-Aldrich, St. Louis, MO). Chromatin was sheared to 300-500 kb using the Bioruptor (Diagenode, Denville, NJ). Lysates were mixed 1:4 with dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 uM EDTA, 16.7 uM Tris-Cl pH 8.0, 167 uM NaCl, 5mM sodium butyrate, protease inhibitor cocktail tablet). Immunoprecipitation was completed for four hours using antibodies directed against H3K27ac, MYC, MYCL1, and MYCN with M280 Sheep Anti-Rabbit IgG Dynabeads (ThermoFisher, 11203D). ChIPs were washed 1x with TE and 3x with Wash Buffer (100 mM Tris-Cl pH 8.0, 500 mM LiCl, 15 Igepal, 1% deoxycholic acid) supplemented with PMSF. Beads were resuspended in Elution Buffer (20 mM NaHCO3, 1% SDS, 150 mM NaCl) and cross-links were reversed overnight at 65C, followed by 1 hr RNase A and proteinase K digestion at 45 C. DNA was purified using ChIP DNA Clean & Concentrator (Zymo). For ATAC-seq samples, cells were harvested by centrifugation and 50,000 viable cells were flow sorted on ice (FACS AriaII). Cells were then washed with cold PBS and resuspended in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Lysates were then incubated with Tn5 transposase at 37°C for 30 minutes. Following transposition, DNA was purified using the Qiagen MinElute PCR Purification Kit.
ChIP-seq and ATAC-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB).

tag: cell line

value: small cell lung cancer

tag: chip antibody


title: 54_SF__Rad_3

city: Bethesda

last: Stone

state: MD

address: 9000 Rockville Pike

department: CCR

institute: National Cancer Institue

data_processing:
The sequencing quality of each sample was assessed using FastQC.
Read- and alignment-level quality were assessed using FastQ Screen, Preseq, Picard tools, RSeQC and QualiMap.
Reads were trimmed for adapter sequences and low-quality bases using Cutadapt prior to alignment against the human reference genome, hg38, using STAR in two-pass mode with GENCODE v19 annotation
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including raw counts for each samples

molecule: polyA RNA

growth_protocol: All cells were cultured at 37°C, 5% CO2 in DMEM supplemented with 10% FBS, 1% L-Glutamine and 1% penicillin/streptomycin

extract_protocol:
mRNAs were extracted using the Qiagen Rneasy Plus kit according to the manufacturer’s instructions
Library was prepared with the Illumina® Stranded mRNA Ligation Kit according to the manufacturer’s instructions

treatment_protocol: Cells were transduced with lentiviral particles containing FLAG-Δ133p53α Wild-Type, FLAG-Δ133p53α R273H or control-RFP and selected with 1μg/ml Blasticidin. Cells were exposed to 50μM temozolomide (TMZ) for 5 days or were irradiated with 10 Grays X-rays and used for downstream experiments 5 days after treatment. Dimethyl-Sulfoxide (DMSO) was used as a control.

value: Glioblastoma

value: Radiations


title: Day 13, KO, rep1


title: 53_SF__Rad_2


title: MYCN_H69

value: MYCN


title: Day 13, wild type, rep2

value: WT


title: 52_SF__Rad_1


title: SG25

value: RNAlater


title: 57_SNR_DMSO_3

value: control

value: DMSO


title: MYCN_H526


title: Adult murine lung epithelial cells treated with influenza PR8

city: Shanghai

first: Guilin

last: Yang

address: Yueyang road 320

institute: Center for Excellence in Molecular Cell Science

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Lung

extract_protocol:
Left lung lobes from wild type adult mice infected influenza PR8 14 days were digested by gentle shaking at 37℃ in lysis buffer containing Dispase II and Collagenase type I. Tissue were dissociated to single cells and the following antibodies were used to sort epithelial cells: Rat anti-FITC CD45, Rat anti-FITC CD31, Rat anti-APC Epcam. Then the cells were subjected to Magnetic bead sorting (MACS) to remove CD31+ and CD45+ cells. The rest of cells were subjected to fluorescence activated cell sorting (FACS) to select all Epcam+CD31-CD45-cells. Sorted epithelial Dissociated cells were washed with 1× DPBS containing 2% FBS. Cells were stained with AO/PI, and viability was assessed using a Countstar Fluorescence Cell Analyzer (Aber Instruments).
Exposure cells to lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3. 1). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina), and 150 bp paired-end reads were generated. The sequencing was performed by Majorbio Co., Ltd (Shanghai, China).

value: Lung

value: Epithelial cells (Epcam+CD31-CD45-)

tag: age

value: Adult

value: Influenza PR8


title: ATAC_COLO668


title: Day 13, wild type, rep1

value: Mesenteric lymph node

value: Germinal centre B cells  (CD19+IgDloCD95hiCD38lo)

value: Trichuris muris infection


title: 51_SFR_Rad_3


title: 50_SFR_Rad_2


title: 290_D9

city: Brisbane

first: Kylie

last: Alexander

address: Translational Research Institute, 37 Kent St Woolloongabba

institute: Mater Research Institute

data_processing:
RNAseq data was uploaded to Galaxy Australia (usegalaxy.org.au) for analysis
Allignment: HISTA2(Galaxy Version 2.2.1+galaxy0)
Read count: featureCounts (Galaxy Version 2.0.1+galaxy2)
Annotation:annotateMyIDs (Galaxy Version 3.12.0+galaxy1)
Differential expression analysis: limma-voom (Galaxy Version 3.50.1+galaxy0).
Low expression filter: Gene expression less than  CPM 0.5 or in less than 2 samples were filtered out
Assembly: mm10
Supplementary files format and content: tab-delimited text files include log2CPM values

source_name: Muscle

extract_protocol:
At day 4, post cardiotoxin injections, whole hamstring muscle were sampled and homogenized in 4 ml of Trizol (Invitrogen) IKA T10 basic homogenizer on ice for 30 seconds for 3 times with 10 second intervals followed by incubation at RT for 30 minutes. Tissue debris were removed by centrifuging at 12,000xg and supernatants were mixed with 1/5 volume of chloroform. After spinning down at 12,000xg, 4°C for 15 mins, aqueous phases containing RNA were transferred to fresh tubes for RNA precipitation with isopropanol. The RNA pellets were further washed in 75% ethanol, air-dried and dissolved in RNAse/DNase free water.
RNA-Seq libraries were generated in using the Illumina Stranded mRNA Library Prep Ligation kit (illumina, 20040534) and IDT for Illumina RNA UD Indexes (illumina, 20040553) according to the standard manufacturer’s protocol (illumina, document # 1000000124518 v02, April 2021) described briefly as follows. 80 ng of total RNA was enriched for mRNA using an oligo-dT bead isolation method. The purified mRNA was then subjected to a heat fragmentation step and copied into first strand complimentary DNA (cDNA) using reverse transcriptase and random primers. The resulting cDNA was converted into dsDNA in the presence of dUTP to prevent subsequent amplification of the second strand and thus maintaining the strand orientation of the original mRNA. The 3’ ends of the cDNA were adenylated and pre-index anchors were ligated. The libraries were then amplified with 13 cycles of PCR incorporating unique indexes for each sample to produce libraries ready for sequencing. The libraries were quantified on the Perkin Elmer LabChip GX Touch with the DNA High Sensitivity Reagent kit (Perkin Elmer, CLS760672). Libraries were pooled in equimolar ratios.

treatment_protocol:
All mice were injected with cardiotoxin  (0.32mg/kg) in hamstring via intramuscular injection
After cardiotoxin ntramuscular injections, C1-5 were treated with saline via  once daily; D1-9 were treated with dexamethasone (10mg/kg) once daily via intraperitoneal injection

tag: strain

tag: Sex

value: Female

value: Muscle

tag: surgery

value: CDTX (0.32mg/kg, i.m)

value: Dexamethasone 10mg/kg (ip once daily, day0-4)

tag: time point

value: Day 4


title: 49_SFR_Rad_1

value: Glioblastoma

value: Radiations


title: MYCL1_H889

value: small cell lung cancer


title: C2

value: kidney

value: SnapFrozen


title: 48_SF__TMZ_3

value: Temozolomide


title: 290_D8


title: MYC_SHP77

value: MYC


title: MYCL1_COLO668


title: MYC_H847


title: 47_SF__TMZ_2


title: 46_SF__TMZ_1


title: MYC_H211


title: 45_SFR_TMZ_3

value: control


title: 290_D5


title: MYC_H1048


title: 290_D4


title: 44_SFR_TMZ_2


title: 290_D3


title: 2B2.2020.HIV+METH-

type: RNA

city: San Diego

first: Maria

middle: Cecilia

last: Marcondes

state: CA

address: 3525 John Hopkins Ct. #200

institute: San Diego Biomedical Research Institute

description: Transcriptional profile of peripheral blood monocytes

hyb_protocol: The nCounter gene expression assays (NanoString Technologies, Seattle, WA) were performed using a custom-made combination of Neuropathology and Neuroinflammation NanoString panels.  Briefly, panel code-set probes were hybridized with 150ng of total RNA per specimen or total cell pellets over 18hr at 65oC in a SimplyAmp Thermocycler (Applied Biosystems, Waltham, MA).

scan_protocol: Hybridized RNA was diluted in water and loaded into nCounter SPRINT cartridge (NanoString) in nCounter SPRINT Profiler, and then RNA-conjugated probes were counted via NanoString Sprint Profiler technology, following manufacturer’s protocols.

data_processing: Results from each panel were merged into a data file. Normalization was performed for each sample by dividing each sample’s raw count profiles by the geometric mean of 8 reference genes in nSolver.

source_name: Total blood

growth_protocol: Specimens were cryopreserved peripheral blood leukocytes isolated from participants that included adults enrolled by the University of California San Diego’s HIV Neurobehavioral Research Program (HNRP) and Translational Methamphetamine Research Center (TMARC) under informed consent and approved protocols.

extract_protocol: For assays, archived specimens were thawed in fetal bovine serum, washed and viability was counted using disposable hemocytometers (Bulldog Bio, Portsmouth, NH). Cell numbers were adjusted for flow cytometry and for digital transcriptome.The RNA purification from pellets was performed using Nucleospin RNA Mini kit with DNA separation column (Macherey-Nagel, Bethlehem, PA). RNA quality and levels were monitored in a NanoDrop spectrophotometer ND-2000 (Thermo Scientific, Waltham, MA), and used to adjust concentrations for subsequent assays.

treatment_protocol: The subset of PWH and PWoH selected for this study were by design males, between 35 – 44 years old, due to cohort characteristics and to increase statistical power. The participants were divided based on HIV serostatus (HIV+/-) and Meth use (METH+/-). METH+ was defined as meeting lifetime DSM-IV criteria for methamphetamine use or dependence, and METH dependence or abuse within 18 months (LT Methamphetamine Dx), with 8.2% urine toxicology positive/current METH users. A cross-sectional design assembled the following groups: HIV-METH- (n=47), HIV+METH- (n=62), HIV-METH+ (n=39), and HIV+METH+ (n=54). Exclusion criteria were a history of non-HIV-related neurological, medical, or psychiatric disorders that affect brain function (e.g., schizophrenia, traumatic brain injury, epilepsy), learning disabilities, or dementia. Inclusion of major depressive disorder (MDD) and polysubstance use occurred in the cohort due to the high prevalence among Meth users and accounted for in the analysis models.

value: Peripheral blood cells


title: 290_D7


title: 2A9.2020.HIV-METH+


title: 2B1.2020.HIV+METH-


title: 2B8.2020.HIV+METH-


title: 2B4.2020.HIV+METH+


title: 2B7.2020.HIV+METH-


title: 2B6.2020.HIV+METH+


title: 2B3.2020.HIV+METH-


title: 43_SFR_TMZ_1


title: 42_SF__DMSO_3

value: DMSO


title: H3K27Ac_H889


title: 290_D1


title: 290_D6


title: 290_D2


title: MYC_H524


title: H3K27Ac_H847


title: 2B5.2020.HIV+METH-


title: 41_SF__DMSO_2


title: 2A8.2020.HIV-METH-


title: 290_C5

value: Saline (ip once daily, day0-4)


title: H3K27Ac_H69


title: 40_SF__DMSO_1


title: H3K27Ac_SHP77


title: 2A6.2020.HIV+METH-


title: 290_C3


title: 2A7.2020.HIV+METH+


title: H3K27Ac_H526


title: 39_SFR_DMSO_3


title: 37_SFR_DMSO_1


title: 290_C2


title: H3K27Ac_H524


title: 290_C1


title: 38_SFR_DMSO_2


title: H3K27Ac_H211


title: H3K27Ac_H196


title: 36_A__Rad_3


title: Intestinal crypts, Arid3a cKO, 2

city: London

first: Vivian

last: Li

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Samples were analyzed with nfcore/atacseq v1.2.1 (https://nf-co.re/atacseq/1.2.1)
normalized coverage track generation was done with BEDtools
peak calling was carried out with MACS2
Assembly: GRCm38/release-95
Supplementary files format and content: bigWig, narrowPeak

source_name: Intestinal crypts

extract_protocol:
For nuclei isolation, single cells were incubated in RSB buffer for 30min. Isolated nuclei were  treated with Tn5 transposase (Illumina, 20034197) for 30min at 37oC with agitation for DNA tagmentation
Purified DNA was used for library preparation using NEBNext® High-Fidelity 2X PCR Master Mix (NEB, M0541S) using primers with Nextera dual indexes

treatment_protocol: WT and Arid3a conditional KO animals were injected with tamoxifen for 3 consecutive days and animals were culled by S1K at 1 month after the first tamoxifen injection. Intestinal crypts were collected as previously described (Baulies et al., 2020)

value: Arid3a KO

tag: time

value: Intestinal crypts


title: H3K27Ac_H1048


title: 2A3.2020.HIV+METH+


title: 2A1.2020.HIV-METH-


title: Intestinal crypts, Arid3a cKO, 3


title: 35_A__Rad_2


title: 2A4.2020.HIV-METH-


title: 2A2.2020.HIV+METH+


title: 34_A__Rad_1


title: H3K27Ac_COLO668


title: I9.2020.HIV+METH-


title: Intestinal crypts, WT, 3

value: Arid3a WT


title: 33_AR_Rad_3


title: MOLM13, CLICKonCUT&TAG with DB2750 [CLICK3]

city: Bronx

first: Samuel

middle: John

last: Taylor

state: NY

address: 1300 Morris Park Ave, Chanin building 601

institute: Albert Einstein College of Medicine

data_processing:
library strategy: CUT&Tag (ChIP Seq)
Cleaned and trimmed reads were analyzed by FastQC for base sequence quality, GC content, N content, and sequence duplication levels.
Sequencing reads passing quality control criteria were aligned to the Homo Sapiens transcriptome (hg38) using bowtie2 aligner using the options --end-to-end --very-sensitive --no-mixed --no-discordant --phred -I 10 -X 700.
Normalized bedgraphs were generated using genomecov with a normalization factor of 1,000,000/ number of total reads.
Assembly: hg38
Supplementary files format and content: Bedgraph of each sample

source_name: hematopoietic

growth_protocol: MOLM13, MV411 and THP1 cells were maintained in 10% FBS, 1% Pen Strep, RPMI media. HL60 cells were maintained in IMDM media with 20% FBS and 1% Pen Strep.

extract_protocol:
CUT&Tag was performed as follows, 5 × 10^5 cells per cell line were harvested and lightly fixed with 2% formaldehyde for 2 minutes. The cells were bound to Concavalin A-coated beads (Bangs laboratories) and incubated with the primary antibody (anti-PU.1 (Santa Cruz, sc-352, or anti-Cas9 (Cell signaling, 14697S) or IgG control (Santa Cruz, sc-3888) at 4°C overnight. Samples were then incubated with a secondary antibody (guinea pig α-rabbit (Antibodies Online, ABIN101961)) followed by adding pre-loaded pA-Tn5 adapter complex (generated in house). Tagmentation buffer with magnesium was used to induce transposase fragmentation. And PCR based library preparation was conducted (see below).  For CLICKonCUT&Tag samples, PU.1 vehicle treated CUT&Tag fragments were incubated with DB2115-conjugated magnetic beads (by using a alkyne linker tagged version of DB2115 known as DB2750) and pulldown performed. Purified fragments were amplified via PCR and sequenced to identify DB2115 binding sites within the PU.1 cistrome.
DNA was extracted by phenol/chloroform/isoamyl alcohol and fragments were amplified with NEBNext HiFi 2x PCR Master mix and universal i5 and barcoded i7 primers for 13 cycles. AMPure XP beads (#A63880) were used for post-PCR clean-up of the libraries. Libraries were subject to 35 bp paired-end sequencing using Illumina NextSeq 500 platform with 35bp paired end reads on high output mode at the Einstein Epigenomics core. Fastq files were generated using Picard tools v2.17.1 with adapter trimming by TrimGalore v0.3.7 and QC assessment using FASTQC v0.11.4.

treatment_protocol: Cells were maintained at 1mill/ml before treatment with 5uM DB compound, or Vehicle (0.001% DMSO) for 12hrs

value: hematopoietic

value: Acute myeloid leukemia

value: DB2750 pulldown


title: 2A5.2020.HIV-METH+


title: Intestinal crypts, WT, 2


title: MOLM13, CLICKonCUT&TAG with DB2750 [CLICK2]


title: I8.2020.HIV+METH+


title: 32_AR_Rad_2

value: Glioblastoma


title: MOLM13, CLICKonCUT&TAG with DB2750 [CLICK1]


title: 31_AR_Rad_1

value: Radiations


title: Intestinal crypts, WT, 1


title: I7.2020.HIV+METH+


title: MOLM13, CRISPRd targeting STRAP upstream region [sgSTRAP_PU1_2]

value: PU.1 antibody


title: 30_A__TMZ_3


title: Dmp1Cre-Mfn2flox/flox-Brains, replicate 1, scRNA-seq

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: 10X Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 40%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: GRCm38Ensembl92
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: brain

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

value: brain

value: All digested single cells from brains

value: male

value: 6 weeks old


title: Intestinal crypts, Arid3a cKO, 1


title: WT-Brains, replicate 1, scRNA-seq

description: 10X Genomics

value: WT


title: I6.2020.HIV-METH+

value: Peripheral blood cells


title: 29_A__TMZ_2

value: Temozolomide


title: MOLM13, CRISPRd targeting STRAP upstream region [sgSTRAP_dCas9]

value: dCas9 antibody


title: bEnd.3 cells, Mito_T, 2

data_processing:
FastQC(v0.11.5)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using skewer(v0.2.2)
Clean reads were aligned to the Mouse genome mm10 using STAR(2.5.3a).
Read count extraction and normalization were performed using StringTie(v1.3.1c).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: bEnd.3 endothelial cells were maintained in high-glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using RNeasy Mini kit ( Qiagen, Germany).RNA quality was examined by gel electrophoresis and with Qubit (Thermo, Waltham, MA, USA).
RNA libraries for RNA-seq were prepared using Stranded mRNA-seq Library Prep Kit (Vazyme)following manufacturer's protocols.

treatment_protocol: Experimental (Mito-T) samples were co-incubated with isolated mitochondria reconstituted by 100ul of culture medium; Control (Ctrl) samples were treated with equal amount of culture medium alone.

value: endothelial cells

value: Mitochondrial transplantation


title: I5.2020.HIV+METH-


title: I4.2020.HIV-METH+


title: MOLM13, CRISPRd sgNon-targeting [sgNT_dCas9]


title: bEnd.3 cells, Mito_T, 3


title: MOLM13, CRISPRd targeting STRAP upstream region [sgSTRAP_PU1_1]


title: 27_AR_TMZ_3

value: control


title: I3.2020.HIV+METH-


title: I2.2020.HIV-METH+


title: bEnd.3 cells, Mito_T, 1


title: MOLM13, CRISPRd sgNon-targeting [sgNT_PU1_2]

value: hematopoietic


title: I1.2020.HIV+METH-


title: 26_AR_TMZ_2


title: MOLM13, CRISPRd sgNon-targeting [sgNT_PU1_1]

value: Acute myeloid leukemia


title: bEnd.3 cells, Ctrl, 3

value: Control


title: 25_AR_TMZ_1

value: Glioblastoma


title: MOLM13, VEH, 12hr [MOLM_VEH_timecourse]

value: VEH


title: H9.2020.HIV-METH-


title: bEnd.3 cells, Ctrl, 1


title: 28_A__TMZ_1


title: H8.2020.HIV-METH-


title: MOLM13, 5uM DB2115, 12hr [MOLM_12hr_DB]

value: PU.1 antibody


title: 23_A__DMSO_2

value: DMSO


title: MOLM13, 5uM DB2115, 4hr [MOLM_4hr_DB_2]


title: H7.2020.HIV+METH+


title: Brain-Dendra2+, replicate 2, scRNA-seq

description: 10x Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: GRCm38Ensembl92
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Brain

value: All enriched primary brain single cells

value: Brain

value: Male

value: 4-6 weeks old


title: 22_A__DMSO_1


title: 21_AR_DMSO_3


title: liver-high fat diet plus NAC-4

city: Hangzhou

first: Wenwen

address: No.548 Binwen Road, Binjiang District

department: School of Life Science

institute: Zhejiang Chinese Medical University

description:
Mice were fed for 14 weeks and gave water with 2g NAC/L water every day
NAC_HFD4

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
The expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: liver

value: post natal day 8 weeks

value: high fat diet plus NAC


title: H6.2020.HIV+METH+

value: Peripheral blood cells


title: H4.2020.HIV+METH-


title: MOLM13, 5uM DB2115, 4hr [MOLM_4hr_DB_1]


title: Brain-Dendra2+, replicate 1, scRNA-seq

description: 10x Genomics


title: MOLM13, 5uM DB2115, 1hr [MOLM_1hr_DB_2]


title: liver-high fat diet plus NAC-3

description:
Mice were fed for 14 weeks and gave water with 2g NAC/L water every day
NAC_HFD3


title: H5.2020.HIV-METH-


title: 20_AR_DMSO_2


title: bEnd.3 cells, Ctrl, 2

value: endothelial cells

value: WT


title: liver-high fat diet plus NAC-2

description:
Mice were fed for 14 weeks and gave water with 2g NAC/L water every day
NAC_HFD2


title: MOLM13, 5uM DB2115, 1hr [MOLM_1hr_DB_1]

value: hematopoietic


title: 24_A__DMSO_3


title: H3.2020.HIV-METH+


title: 19_AR_DMSO_1

value: control


title: liver-high fat diet plus NAC-1

description:
Mice were fed for 14 weeks and gave water with 2g NAC/L water every day
NAC_HFD1


title: 17_U__Rad_2

value: Radiations


title: H2.2020.HIV-METH-


title: MOLM13, VEH, 12hr [MOLM_VEH_DaunAraC]

value: Acute myeloid leukemia


title: 18_U__Rad_3

value: Glioblastoma


title: MOLM13, 200nM Daun, 12hr [MOLM_Daun_IgG]

value: IgG antibody

value: 200nM Daun


title: liver-high fat diet-4

description:
Mice were fed for 14 weeks
HFD4

value: high fat diet


title: H1.2020.HIV+METH+


title: liver-high fat diet-3

description:
Mice were fed for 14 weeks
HFD3


title: MOLM13, 400nM Cytarabine, 12hr [MOLM_AraC]

value: PU.1 antibody

value: 400nM Cytarabine


title: 16_U__Rad_1


title: G9.2020.HIV+METH+


title: MOLM13, 200nM Daunorubicin, 12hr [MOLM_Daun]

value: 200nM Daunorubicin


title: 15_UR_Rad_3


title: G8.2020.HIV+METH-


title: MOLM13, 5uM DB2750, 12hr [MOLM_DB2750]


title: MOLM13, 5uM DB2826, 12hr [MOLM_DB2826]


title: 13_UR_Rad_1


title: 14_UR_Rad_2


title: liver-high fat diet-1

description:
Mice were fed for 14 weeks
HFD1

value: liver


title: 12_U__TMZ_3

value: Temozolomide


title: MOLM13, 5uM DB2313, 12hr [MOLM_DB2313]


title: liver-normal fat diet-4

description:
Mice were fed for 14 weeks
NFD4

value: post natal day 8 weeks

value: normal fat diet


title: G7.2020.HIV-METH+

value: Peripheral blood cells


title: liver-normal fat diet-3

description:
Mice were fed for 14 weeks
NFD3


title: MOLM13, 5uM DB2373, 12hr [MOLM_DB2373]


title: 11_U__TMZ_2


title: G5.2020.HIV-METH-


title: liver-normal fat diet-2

description:
Mice were fed for 14 weeks
NFD2


title: HL60, VEH, 12hr [HL60_IgG]

value: VEH


title: 10_U__TMZ_1


title: liver-normal fat diet-1

description:
Mice were fed for 14 weeks
NFD1


title: liver-high fat diet-2

description:
Mice were fed for 14 weeks
HFD2


title: 9_UR_TMZ_3


title: THP1, VEH, 12hr [THP1_IgG]

value: hematopoietic


title: G3.2020.HIV-METH-


title: G2.2020.HIV+METH+


title: DC2.4 cells, Vdbp overexpressed group-3

city: Wuhan

first: Wenying

last: Zhong

address: Shizi Street No.1

institute: Huazhong Agricultural University

data_processing:
Illumina PE150/SE50  software used for basecalling.
Compare the clean reads to the reference sequence useing Hisat2 software
Use Stringtie software to splice the reads into transcripts and quantify them
Quantitative expression levels of all detected and predicted samples
Supplementary_files_format_and_content: gene_count.txt, gene_fpkm.txt

growth_protocol: The immature murine dendritic cell line (DC2.4) was obtained from Procell (Wuhan, China) and cultured in RPMI1640 medium (Gibco; Thermo Fisher Scientific, Inc., Waltham, MA, USA), supplemented with 100 U/ml penicillin, 100mg/lLstreptomycin, 2 mmol/l L-glutamine, and 10% fetal bovine serum (Hangzhou Evergreen Biological Engineering Materials Co., Ltd., Hangzhou, China) at 37˚C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from DCs using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), accordance with the instructions of the kits used.
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were transfected with empty vector and Vdbp overexpressing vector, respectively. The cells were passaged at 1:10 with fresh growth medium 48 h after transfection, and then selected by adding selective medium in the next day. The expression levels of Vdbp were assessed by RT-qPCR.

value: bone marrow derived dendritic cells

value: Vdbp overexpressing cells

tag: vector


title: MV411, VEH, 12hr [MV411_IgG]

value: Acute myeloid leukemia


title: G6.2020.HIV+METH+


title: G1.2020.HIV-METH+


title: DC2.4 cells, Vdbp overexpressed group-2


title: DC2.4 cells, Vdbp overexpressed group-1


title: 6_U__DMSO_3

value: Glioblastoma

value: DMSO


title: F9.2020.HIV+METH-


title: MV411, 5uM DB2115, 12hr [MV411_DB1]


title: F8.2020.HIV-METH+


title: F7.2020.HIV+METH+


title: 5_U__DMSO_2


title: DC2.4 cells, normal control-2

value: empty vector transduced cells


title: MV411, VEH, 12hr [MV411_VEH2]


title: DC2.4 cells, normal control-3


title: DC2.4 cells, normal control-1


title: No-epitope ChIP-seq on a WT 3D7 parasite line at 40hpi IP

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

data_processing:
Fastq files were trimmed for low quality reads and adator sequence removal using Trimmomatic (v 0.38.0). Single-end options were "SE ILLUMINACLIP:TrueSeq3-SE:2:30:10 SLIDINGWINDOW:4:30". Paired-end options were "PE ILLUMINACLIP:TrueSeq3-PE:2:30:10 SLIDINGWINDOW:4:30". Trimmed reads were aligned to the Plasmodium falciparum genome (strain 3D7; version 3; release 38) using BWA-MEM (v0.7.17.2) with simple illumina mode. Then filtered for multiple mapped reads using SamTools (v1.1.2) with option "-q 1". The output file format being BAM.
Aligned BAM files were displayed using DeepTools BAMCoverage (v3.5.1.0.0) with options "--binSize 20 --smoothLength 60". The output file format being BIGWIG.
Aligned BAM files were displayed using DeepTools BAMCompare (v3.3.2.0.0) with options "--binSize 20 --scaleFactorsMethod readCount --operation log2 --pseudocount 1 --smoothLength 60". The output file format being BIGWIG.
Paired IP and Input BAM files were used to call peaks with significant enrichment in IP samples compared to the input using MACS2 (v2.1.1.20160309.6) with options "--gsize 20000000 --keep-dup 1 --qvalue 0.01 --nomodel --extsize 200 --shift 0". The narrow peaks output file format being BED.
Paired IP and Input BAM files were used to call peaks with significant enrichment in IP samples compared to the input using MACS2 (v2.1.1.20160309.6) with options "--gsize 20000000 --keep-dup 1 --qvalue 0.01 --nomodel --extsize 200 --shift 0". The peak summits output file format being BED.
Assembly: Plasmodium falciparum genome (strain 3D7; version 3; release 38)
Supplementary files format and content: BAM: BWA-MEM output files with mulltiple mapped reads filtered out
Supplementary files format and content: BIGWIG: DeepTools BAMCompare output files for Log2(IP/Input) sample display
Supplementary files format and content: BED: MACS2 outfile of narrow genomic regions ("ChIP-seq peak") significantly enriched in paired IP samples compared to Input samples
Supplementary files format and content: BED: MACS2 outfile of ChIP-seq peak summits

organism: Plasmodium falciparum

source_name: Schizont (40hpi) Parasitized Erythrocyte Cells

growth_protocol: Wild type and AP2-LT+3xHA modified parasites (3D7 strain) were cultured under standard P. falciparum culturing conditions (5% O2, 7% CO2, 37°C, RPMI 1640 media with 0.5% AlbumaxII and hypoaxanthine). No additional drug selection added to AP2-LT+3xHA modified parasites after transfection.

extract_protocol:
The ChIP-seq protocol had 5 major steps including: (1) Chemically crosslinking the all protein-protein and chromatin-protein interactions, (2) Isolation of parasite nuclei, (3) Parasite nuclei lysis with chromatin sonication, (4) Chromatin-protein complex immunoprecipitation, and (5) DNA purification. The crosslinking step included: (a) Chemical crosslinking suspended PfAP2-LTHA (or WT culture for negative control experiment) parasite culture (At least 108 40hpi (hours post invasion) schizont-stage parasites synchronized with 10% Sorbitol more than one cycle prior) with 1% formaldehyde for 10 minutes at 37°C, (b) Quench the crosslinking with 125mM Glycine on ice for 5 minutes, (c) Pellet the cells by centrifugation and lyse the red blood cells with 0.1% Saponin in 1xPBS, and (d) Wash the cells by repeated centrifugation with 1xPBS to remove the red blood cell debris. The nuclei isolation step included: (a) Resuspend parasite pellet with 109 schizonts/2mL Lysis Buffer (10mM HEPES [pH 7.9], 10mM KCl, 0.1mM EDTA [pH 8.0], 0.1mM EGTA [pH 8.0], 1mM DTT (added just before using), and 1x protease inhibitors) and incubate on ice for 30 minutes, (b) Add a final concentration of 0.25% NP-40 and incubate for 1 minute, (c) Lyse parasite membranes with pre-chilled glass dounce homogenizer for 100 strokes per 109 schizonts/2mL Lysis Buffer, and (d) Pellet the nuclei and freeze pellet at -80°C overnight. The sonication step included: (a) Resuspend parasite nuclei pellet in 500μL of Shearing Buffer (0.1% SDS, 10mM Tris [pH 8.0], 1mM EDTA, and 1x protease inhibitors) per 5x108 parasites and (b) Sonicate the chromatin until sufficiently sheared (5% duty cycle, 75W peak incident power, 200 cycles per burst, 7°C, for 5 minutes using Covaris Focus-Ultrasonicator M220). The immunoprecipitation step included: (a) Dilute the sample 1:5 with Dilution Buffer (0.01% SDS, 1.1% TritonX-100, 1.2mM EDTA, 16.7mM Tris-HCl [pH 8.1], and 150mM NaCl), (b) Reduce background signal by pre-clearing with 20μL of Protein A/G magnetic beads (Millipore 16-663) per 1mL of sample for 2 hours at 4°C with rotation, (c) Aliquot and store 1/10 of the sample for the control Input sample until after DNA elution step, (d) Remaining 9/10 of sample is immunoprecipitated with 1:1000 anti-HA antibody (0.1mg/mL Roche Rat Anti-HA High Affinity [11867423001]) overnight at 4°C with rotation, (e) Collect the immune complexes with 20μL of Protein A/G magnetic beads per 1mL of sample for 2 hours at 4°C with rotation, (f) Wash (5 minutes each) immune complexes on magnet once with Low Salt Immune Complex Wash Buffer (0.1% SDS, 1% TritonX-100, 2mM EDTA, 20mM Tris-HCl [pH 8.1], and 150mM NaCl) at 4°C with rotation, once with High Salt Immune Complex Wash Buffer (0.1% SDS, 1% TritonX-100, 2mM EDTA, 20mM Tris-HCl [pH 8.1], and 500mM NaCl) at 4°C with rotation, once with LiCl Immune Complex Wash Buffer (0.25M LiCl, 1% NP-40, 1% Deoxycholate, 1mM EDTA, and 10mM Tris-HCl [pH 8.1]) at 4°C with rotation, and twice with 1xTE at room temperature with rotation, and (g) Elution from beads with 200μL fresh Elution Buffer (0.01% SDS and 100mM NaHCO3) per 1mL of sample for 15 minutes at room temperature with rotation (also added to Input sample). The DNA purification step included: (a) Reverse-crosslink Input and IP samples with 0.2M NaCl and incubate overnight at 45°C with shaking, (b) 0.4v/v% RNaseA treat from 30 minutes at 37°C with shaking, (c) 0.3mg/mL Proteinase K treatment for 2 hours at 45°C with shaking, and (d) Purify DNA using MinElute column (Qiagen) as directed.
DNA sequencing libraries were prepared for high-throughput Illumina sequencing on the HiSeq 2500 single-end or NextSeq 2000 paired-end mode. The library prep protocol includes 6 major steps: (1) end repair of DNA fragments, (2) addition of A-tail for adaptor ligation, (3) ligation of Illumina adaptors, (4) DNA sequence size selection, (5) DNA sequence amplification by PCR, and (6) DNA sequence clean up. The 6-nt single indexed adaptors used were diluted 1:10 prior to ligation. DNA library was size selected for 250-bp sequences. Due to the A/T-richness of the P. falciparum genome, KAPA HiFi polymerase was used for amplification during PCR steps. Only 12 rounds of amplification was used for AP2-LT ChIP-seq samples (both for input and IP libraries), and 16 rounds for the no-epitope negative control. After DNA sequence clean up, completed libraries were quantified using the Qubit fluorometer for high-sensitivity DNA and library sequence length by the Agilent Bioanalyzer 1000 or Agilent TapeStation 4150.

value: 3D7 strain (WT line)

tag: chip target

value: HA

value: anti-HA (Roche 3F10)

value: 40 hours post invasion parasites

value: Parasitized Erythrocyte Cells


title: 8_UR_TMZ_2

value: control

value: Temozolomide


title: HL60, 5uM DB2115, 12hr [HL60_DB2]

value: PU.1 antibody


title: 3_UR_DMSO_3


title: F5.2020.HIV+METH-

value: Peripheral blood cells


title: 2_UR_DMSO_2


title: No-epitope ChIP-seq on a WT 3D7 parasite line at 40hpi Input

treatment_protocol: At least 108 40hpi (hours post invasion) schizont-stage parasites synchronized with 10% Sorbitol more than one cycle prior

value: Input

value: No Antibody Control


title: HL60, 5uM DB2115, 12hr [HL60_DB1]

value: hematopoietic


title: 7_UR_TMZ_1


title: MV411, 5uM DB2115, 12hr [MV411_DB2]


title: F3.2020.HIV+METH-


title: HL60, VEH, 12hr [HL60_VEH2]

value: VEH


title: F4.2020.HIV-METH+


title: aggregates_co-culture_3

city: Beijing

first: Yifei

last: Zhang

address: Haidian

institute: Peking University

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean data was generated by quality control and then mapped to the reference genome (Mus musculus, GRCm38_release95) using Hisat2.
Quantification of gene expression levels were measured by fragments per kilobase of transcript per million fragments mapped (FPKM) from Florea L,. F1000Res. 2013.
In the equation, cDNA Fragments represents the number of PE reads mapped to the specific transcript;  Mapped Fragments (Millions) is the number of all mapped reads, which is counted as 10^6;  Transcript Length(kb) is the length of transcript in unit of 10^3 b.
Assembly: Mus musculus, GRCm38_release95
Supplementary files format and content: tab-delimited list files include FPKM values for each Sample

source_name: mESC 129w2

growth_protocol: The mESC line (129w2, passages 13–16) used in our experiments was kindly provided by the Tang Fuchou Laboratory at Peking University. Cells were cultured in 6-well plates coated with 0.1% gelatin.

extract_protocol:
For RNA sequencing (RNA-seq), total RNA was extracted from aggregates using the RNeasy Mini Kit (Qiagen).
Sequencing libraries were prepared using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: To initiate differentiation, colonies of mESCs were detached from the culture dish using Accutase, collected as a single-cell suspension in base differentiation medium SFEBq (serum-free floating culture of embryoid body like aggregates with quick reaggregation, GMEM medium (Gibco) supplemented with 1% glutamine, 1% penicillin/streptomycin, 0.1 mM NEAA, 1% sodium pyruvate, 2% KO serum replacement, and 0.1 mM β-mercaptoethanol). On day 0, cells were counted using a cell counter and distributed at a density of 3,000 cells in 150 μl per well into 96-well U-bottom ultra-low attachment plates (Corning). Cell aggregation was facilitated by centrifugation at 900 rpm for 5 min. These cell aggregates were then incubated at 37 °C incubator under 5% CO2 for 1 day. After this incubation period, half of the medium was changed by removing 75 μl of spent medium and adding 75 μl of fresh medium containing 4% growth factor reduced Matrigel (BD). On day 3 of differentiation, 37.5 μl of fresh differentiation medium containing 2% Matrigel and 2 ng/ml BMP4 was added, increasing the final volume to 187.5 μl. On day 4, 2% Matrigel, 25 ng/ml bFGF, and 1 μM RA were added in a volume of 25 μl per well, bringing the final volume to 212.5 μl per well. On day 5, the aggregates were transferred to individual wells of 24-well low-attachment plates (Corning) containing base differentiation medium with 1% Matrigel.

value: mESC 129w2

value: co-culture with mSMGs at D5-7


title: eIF4G2 overexpression bio rep 2

city: Rochester

first: feng

last: jiang

state: New York

address: 601 Elmwood Ave box CVRI

department: Biochemistry and Biophysics

institute: University of Rochester

data_processing:
Raw reads were demultiplexed using bcl2fastq version 2.19.0.
Quality filtering and adapter removal were performed using Trimmomatic version 0.36
Processed/cleaned reads were then mapped to the Homo sapien reference genome (GRCh38, hg38) with Hisat version 2.1.0
RIPSeeker was used to detect eIF4G2 targets following the default settings
Assembly: GRCh38, hg38
Supplementary files format and content: comma-delimited table include genomic regions detected in RIP

source_name: IHCF

growth_protocol: Human IHCF cells were propagated in Dulbecco's modified Eagle's medium (DMEM; Gibco) supplemented with 10% fetal bovine serum, 1% non-essential amino acid (NEAA; Gibco) and 5 µg/ml human insulin (Abm).

extract_protocol:
For RNA isolation, TRIzol reagent was added directly to the tube containing beads resuspended with RIP lysis buffer, followed by the conventional precipitation method. The RNA pellet was then treated with DNase I and EDTA to remove any DNA contamination, before being repurified using phenol/chloroform/isoamyl alcohol (25:24:1, pH 6.7) to obtain pure RNA samples.
Sequencing libraries were constructed using the NEBNext® UltraTM II RNA Library Prep Set following the manufacturer’s instructions.

treatment_protocol: Human IHCF cells were infected with lentiviral-based eIF4G2 overexpression vector or a scramble control overexpression vector. Then, these cells were lysed and immunoprecipitated using eIF4G2 antibody.

value: IHCF

value: Immortalized human cardiac fibroblasts

value: eIF4G2 overexpression

tag: rip antibody

value: eIF4G2 antibody


title: F6.2020.HIV+METH+


title: F2.2020.HIV-METH-


title: G4.2020.HIV-METH-


title: HL60, VEH, 12hr [HL60_VEH1]

value: Acute myeloid leukemia


title: 4_U__DMSO_1

value: Glioblastoma

value: DMSO


title: eIF4G2 overexpression bio rep 1


title: ChIP-seq on AP2-LT in a AP2-LT+3xHA 3D7 parasite line at 40hpi replicate 1 Input

value: 3D7 strain (AP2-LT+3xHA line)

value: 40 hours post invasion parasites

value: Parasitized Erythrocyte Cells


title: MV411, VEH, 12hr [MV411_VEH1]

value: PU.1 antibody


title: E9.2020.HIV+METH-

value: Peripheral blood cells


title: 1_UR_DMSO_1

value: control


title: ChIP-seq on AP2-LT in a AP2-LT+3xHA 3D7 parasite line at 40hpi replicate 1 IP

value: HA

value: anti-HA (Roche 3F10)


title: eIF4G2 overexpression total bio rep 2


title: THP1, 5uM DB2115, 12hr [THP1_DB2]

value: hematopoietic


title: THP1, VEH, 12hr [THP1_VEH1]

value: VEH


title: F1.2020.HIV+METH+


title: THP1, 5uM DB2115, 12hr [THP1_DB1]


title: E8.2020.HIV-METH-


title: repl.2_ChmA-KD_20minpi

city: Würzburg

first: Jörg

last: Vogel

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

institute: Würzburg University

description: 20 min pi chmA-KD replicate 2

data_processing:
The library was sequenced on the NextSeq2000 (Illumina) with a P1-seq kit (single-end 1x100 bp, Illumina). RNA-seq analysis for the ChmA knockdown and the screen was conducted with READemption 0.4.3 (Förstner et al. 2014). Reads were aligned for PAO1 and ΦKZ to NC_002516 and NC_004629, respectively. Enrichment of transcripts was calculated with the DeSeq2 module in READemption. Read-coverage was illustrated with the Integrated Genomics Viewer (IGV, Robinson et al. 2011).
Assembly: NC_002516, NC_004629
Supplementary files format and content: reads (fq.gz)
Supplementary files format and content: coverage files (wig)
Supplementary files format and content: counts table (csv)

organism:
Pseudomonas aeruginosa
Pseudomonas phage phiKZ

source_name: bacterial culture

growth_protocol: PAO1 was grown o/n in LB at 37 °C 220 rpm. Cells were inoculated 1:100 in MH media at 37 °C and grown until OD600 0.3.

extract_protocol:
RNA was isolated from 200 µl of cells using the RNAsnap procedure (Stead et al. 2012). Two volumes of RNAprotect (Qiagen) were added and cells were incubated for 5 min. Cells were pelleted at full-speed for 20 min at 4 °C and the supernatant was removed. The pellet was resuspended in 100 µl SNAP buffer (0.025% SDS, 18 mM EDTA, 1% β-mercaptoethanol, 95% formamide (RNA-grade)). Samples were incubated for 7 min at 95 °C, cell debris was pelleted at full-speed for 5 min at room-temperature, and the supernatant was transferred to a new tube. 1.5 volumes of ethanol was added to the supernatant and the sample was mixed by pipetting. The sample was loaded onto a miRNeasy mini column (Qiagen) two times and spun at full-speed for 20 s at room-temperature. Columns were washed two times with 500 µl RPE buffer (Qiagen) and spun at 8k×g for one minute at room-temperature. One final spin was used to dry the column in an empty tube. 30 µl RNase-free water was added to the column and the RNA eluted at 8k×g for one minute at room-temperature. The elution was repeated with the flow-through to recover more RNA. The RNA concentration was determined by absorption at 260 nm. RNA was stored at -80 °C.
RNA-sequencing was performed at the CoreUnit SysMed at the University of Würzburg. DNA was digested with DNaseI and the rRNA was depleted with the Lexogen RiboCOP META depletion kit. RNA library was prepared with the CORALL Total RNA-Seq Library Prep Kit V1 (Lexogen).

treatment_protocol: 4 µM AS molecules were added to 1.6 ml of cell culture and incubated for 30 min at 37 °C 220 rpm. Cells were infected  with ΦKZ at an MOI of 5. At indicated time points, 250 µl were removed and put on ice. Infection efficiency was independently validated by confocal microscopy and CFU spotting with 50 µl of cells.

value: bacterial culture

value: bacteria

value: wt

value: chmA-KD anti-sense molucule


title: repl.2_ChmA-KD_10minpi

description: 10 min pi chmA-KD replicate 2


title: repl.2_ChmA-KD_35minpi

description: 35 min pi chmA-KD replicate 2


title: repl.2_ChmA-KD_25minpi

description: 25 min pi chmA-KD replicate 2


title: THP1, VEH, 12hr [THP1_VEH2]

value: Acute myeloid leukemia


title: control bio rep 1

value: IHCF

value: Immortalized human cardiac fibroblasts

value: control overexpression

value: eIF4G2 antibody


title: control total bio rep 1


title: repl.1_ChmA-KD_25minpi

description: 25 min pi chmA-KD replicate 1


title: repl.1_ChmA-KD_35minpi

description: 35 min pi chmA-KD replicate 1


title: E7.2020.HIV-METH+


title: E6.2020.HIV-METH+


title: control total bio rep 2


title: eIF4G2 overexpression total bio rep 1

value: eIF4G2 overexpression


title: eIF4G2 Knockdown polysome bio rep 2

data_processing:
Raw reads were demultiplexed using bcl2fastq version 2.19.0.
Quality filtering and adapter removal were performed using Trimmomatic version 0.36
Processed/cleaned reads were then mapped to the Homo sapien reference genome (GRCh38, hg38) with Hisat version 2.1.0
The subread-2.0.1(57) package (featureCounts) was used to derive gene counts based on utilizing the gencode.v38 gene annotations
Normalizing raw counts and identifying significantly changed genes were performed by DESeq2 within an R-4.1.2 environment.
Assembly: GRCh38, hg38
Supplementary files format and content: comma-delimited table include raw counts for each sample

extract_protocol:
For RNA isolation, purification was carried out using a mixture of phenol/chloroform/isoamyl alcohol (25:24:1, pH 6.7) (Fisher, BP1752I-100) and vortexed for 30 sec. The samples were then centrifuged at 14,000 rpm for 10 min at 4C. The top aqueous phase was transferred to a new tube containing 3 M sodium acetate, 2 µg of glycogen and 250 µl of absolute ethanol, and was then left for overnight precipitation at -80C. The resulting pellet was washed with prechilled 70% ethanol before centrifuging at the same speed. DNase I (NEB, Cat #M0303L) was added to the RNA pellet and incubated at 37oC for 10 min, followed by treatment with 50 mM EDTA (Bioworld, Cat #40520000-1) to eliminate DNA contamination. The RNA pellet was then purified as described above one more time to obtain pure RNA samples.
RNA libraries for RNA-seq were prepared using NGS Library Prep Kit following manufacturer's protocols.

treatment_protocol: Human IHCF cells were infected with lentiviral-based shRNA targeting eIF4G2 or a scramble control shRNA without any targeting. Both cells were serum-starved for at least 6 hours before TGFb for another 24 hours.

value: Immortalized human cardiac fibroblast

value: eIF4G2 shRNA


title: control bio rep 2


title: MOLM13, VEH, 12hr [MOLM_IgGV1]

value: IgG antibody


title: MOLM13, 5uM DB2115, 12hr [MOLM_DB2]

value: PU.1 antibody


title: E5.2020.HIV-METH+

value: Peripheral blood cells


title: repl.1_ChmA-KD_20minpi

description: 20 min pi chmA-KD replicate 1


title: MOLM13, 5uM DB2115, 12hr [MOLM_DB3]

value: hematopoietic


title: repl.2_ChmA-KD_15minpi

description: 15 min pi chmA-KD replicate 2


title: Scramble Knockdown polysome bio rep 2

value: scramble shRNA


title: MOLM13, VEH, 12hr [MOLM_VEH2]

value: VEH


title: Scramble Knockdown polysome bio rep 1


title: E4.2020.HIV-METH+


title: eIF4G2 Knockdown polysome bio rep 1


title: D9.2020.HIV-METH+


title: MOLM13, 5uM DB2115, 12hr [MOLM_DB1]


title: MOLM13, VEH, 12hr [MOLM_VEH3]


title: E2.2020.HIV-METH-


title: MOLM13, 5uM DB2115, 12hr [MOLM_IgGDB1]


title: D8.2020.HIV+METH-


title: MOLM13, VEH, 12hr [MOLM_VEH1]


title: repl.1_ChmA-KD_10minpi

description: 10 min pi chmA-KD replicate 1

value: bacterial culture

value: bacteria


title: D6.2020.HIV+METH+


title: Scramble Knockdown total bio rep 2


title: E3.2020.HIV+METH+


title: repl.2_control_15minpi

description: 15 min pi control replicate 2

value: wt

value: control anti-sense molucule


title: repl.2_control_35minpi

description: 35 min pi control replicate 2


title: D5.2020.HIV+METH-


title: eIF4G2 Knockdown total bio rep 2

value: IHCF


title: repl.2_control_25minpi

description: 25 min pi control replicate 2


title: repl.1_ChmA-KD_15minpi

description: 15 min pi chmA-KD replicate 1

value: chmA-KD anti-sense molucule


title: circSOD2-sh treated-4

city: guangzhou

first: Gaosheng

last: Yao

state: Guangdong

address: Zhongshan second road

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
Illumina Casava1.8 software used for base-calling. FastQC version 0.11.2 was used to visually evaluate the sequencing data quality of the samples.
Trimmomatic 0.36 were used for data processing. Bowtie 1.1.1 and RepeatMasker 4.1.0 was used to compare reads of each samples with the reference genome.
The sequences of known miRNAs were obtained from miRBase database, and identified using mirDeep2 software version 2.0.0.8 for subsequent analysis.
For samples with no biological duplicates, TMM was used to standardize the Read count data
Principal Component Analysis, Hierarchical cluatering and so on are implemented
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every miRNAs of every sample
Supplementary files format and content: Counts is normalized to reads Count per million (CPM)
Supplementary files format and content: Differential expression matrix

source_name: kidney cancer 786O cells

growth_protocol: 786O cells are cultured in RPMI 1640 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. The cells were cultured in a humidified environment at 37°C with 5% CO2, and regularly checked to ensure that they were free of mycoplasma.

extract_protocol:
According to the structure characteristics of small RNA with 3' -end hydroxyl group and 5' -end phosphoric acid group, the 8 RNA samples of this project were processed by 3' -end connection, reverse transcription primer hybridization, 5' -end connector connection, cDNA single-strand synthesis and library amplification using the catalytic reaction characteristics of related enzymes and molecular biology techniques.After quality inspection and purification, libraries that meet Illumina platform sequencing were finally obtained.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: circSOD2-sh and control plasmid were transfected into 786O cells with Lipofectamine 3000. After 48 hours transfection, total RNA was extracted for further RNA sequencing.

value: Human ccRCC cells

value: circSOD2-sh treated


title: circSOD2-sh treated-1


title: E1.2020.HIV+METH+


title: circSOD2-sh treated-3


title: eIF4G2 Knockdown total bio rep 1


title: D7.2020.HIV-METH+


title: repl.1_control_35minpi

description: 35 min pi control replicate 1


title: circSOD2-sh treated-2


title: repl.2_control_20minpi

description: 20 min pi control replicate 2


title: Scramble Knockdown total bio rep 1


title: 2_m14K_empty_2

city: Portland

first: Peter

last: Ryabinin

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

data_processing:
all paired end reads were trimmed using Trimmomatic 0.39 and the "TruSeq3.fa" adapter file with the following parameters: "2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36"
trimmed files were cleaned using fastqc
molm13 and ociaml3 derived samples were aligned to GRCh38.89 using STAR 2.5.3a with setting outFilterMismatchNmax = 2
molm14 derived samples were aligned to GRCh37.75 using kallisto 0.46.2 and the following parameters: --bias --rf-stranded --plaintext --bootstrap-samples=50
Assembly: GRCh38.89 and GRCh37.75 (see processing details)
Supplementary files format and content: molm13o3_gene_level_raw_counts.csv contains gene level counts for molm13 and ociaml3 derived samples in CSV file format
Supplementary files format and content: molm14_transcript_level_raw_counts.csv contains transcript level counts for molm14 derived samples in CSV format
Supplementary files format and content: molm14_transcript_level_abundance.csv contains transcript level abundances (TPM) for molm14 derived samples in CSV format
Supplementary files format and content: molm14_transcript_level_length.csv contains transcript level feature lengths for molm14 derived samples in CSV format
Supplementary files format and content: molm14_gene_level_raw_counts.csv contains gene level counts for molm14 derived samples in CSV format
Supplementary files format and content: molm14_gene_level_abundance.csv contains gene level abundances (TPM) for molm14 derived samples in CSV format
Supplementary files format and content: molm14_gene_level_length.csv contains gene level feature lengths for molm14 derived samples in CSV format

growth_protocol: Molm14, Molm13, and OCIAML3 cells were maintained in RPMI 1640 supplemented with 10% FBS, L-glutamine, and penicillin/streptomycin.

extract_protocol:
RNA was harvested using Qiagen Rneasy mini kit. 1ug RNAs were used for RNA library preparation.
The RNA library was prepared using the Illumina Stranded mRNA Preparation kit, following the manufacturer's protocol.

treatment_protocol: Molm14, Molm13, and OCIAML3 cells were transduced with lentivirus encoding sWT1 transcripts or HOXA3, followed by sorting of the transduced cells using flow cytometry. Sorted cells were cultured in RPMI 1640 supplemented with 10% FBS, L-glutamine, and penicillin/streptomycin (HOXA3 expressing cells were cultured in the presence or absence of doxycycline).

value: control


title: D3.2020.HIV+METH+


title: repl.1_control_25minpi

description: 25 min pi control replicate 1


title: repl.2_control_10minpi

description: 10 min pi control replicate 2


title: 1_m14K_empty_1


title: D4.2020.HIV+METH-


title: repl.1_control_15minpi

description: 15 min pi control replicate 1


title: negative control-3

value: negative control


title: D1.2020.HIV+METH+


title: 4_m14_2_S

value: transduced sWT1--


title: negative control-1


title: negative control-4


title: C9.2020.HIV-METH+


title: p2-14dpi

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

institute: Stowers Institute for Medical Research

description:
L46088
RSEM_TPM_table.txt

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl-convert (v 3.10.5). Reads were aligned to UCSC genome astMex_2.0 with STAR aligner (v 2.7.3a ), using Ensembl 102 gene models. TPM values were generated using RSEM (v 1.3.0)
Assembly: Astyanax mexicanus 2.0
Supplementary files format and content: TPM gene expression in text file

organism: Astyanax mexicanus

source_name: Skeletal Muscle

extract_protocol:
RNA from skeletal muscle was extracted using standard phenol/chloroform extraction. The subsequent RNA pellet was cleaned with the RNeasy Mini Kit (Qiagen #74104) with on-column DNAse digestion (Qiagen #79256).
Libraries were prepared according to the manufacturer’s instructions using the TruSeq Stranded mRNA Prep Kit (Illumina #20020594)
The resulting libraries were quantified using a Bioanalyzer (Agilent Technologies) and Qubit fluorometer (Life Technologies). Libraries were normalized, pooled, multiplexed, and sequenced on an Illumina NextSeq-75-HO instrument as v2 Chemistry High Output 75bp single read runs.

treatment_protocol: Free Running Darkness

value: Skeletal Muscle

tag: group

value: troglobitic cavefish

value: cardiotoxin injection


title: 5_m14_S_Plus

value: transduced sWT1-+


title: 3_m14_S


title: repl.1_control_10minpi

description: 10 min pi control replicate 1


title: 8_m14_2_S_Plus

value: transduced sWT1+-


title: D2.2020.HIV+METH-

value: Peripheral blood cells


title: repl.1_control_20minpi

description: 20 min pi control replicate 1

value: bacterial culture


title: C8.2020.HIV+METH+


title: 6_m14_2_S_Plus


title: p1-14dpi

description:
L46087
RSEM_TPM_table.txt


title: C7.2020.HIV-METH+


title: CD3+ depleted, IFNg stimulated, Nanostring GEX, D60, S14

city: Rixensart

first: Viviane

middle: Jeanne

last: Bechtold

state: Brabant Wallon

address: rue de l'Institut 89

department: Molecular Biology

country: Belgium

institute: GSK

hyb_protocol: RNA samples were diluted in Rnase-free water at the concentration of 25ng/5µl. Then hybridization reaction was performed by mixing 10 µl of master mix (containing 3 μL of custom Reporter CodeSet, 2 μL of Reporter Plus and 5 μL of hybridization buffer for each sample) with 5µl of RNA samples. Next capture reagents (2 μL of Capture ProbeSet, and 1 μL of Capture Plus for each samples) were added to the samples and incubated at 65°C for 16h.

scan_protocol: After hybridization, samples were loaded onto the nCounter Prep Station, (NanoString) to be immobilized on NanoString panel cartridge according to the instrument’s protocol. The scan for barcode counting was performed on the nCounter Analysis System (all from NanoString).  RCC files containing raw counts were generated.

data_processing: Analysis was performed by first adjusting the background and normalizing the samples’ value with the housekeeping genes (GUSB, HPRT1, MRPS7, NMT1, OAZ1, PGK1, SDHA, TBP) in NanoString panel. This selection was determined with a nSolver Advanced analysis and its underlying geNorm algorithm.

label: fluorophore

source_name: CD3-depleted PBMCs

label_protocol: labelling performed accorfing to manufacturer's protocol (11_nCounter_XT_Assay)

extract_protocol: RNA was extracted according to the Qiagen RNA extraction kit.

treatment_protocol: CD3+- depleted PBMCs were stimulated in vitro with IFN-γ (100ug, 2h).

tag: individual

tag: age interval

value: adults (18-49 year old)

value: IFNg stimulated

tag: vaccination

value: 2 doses of HBS/AS01

value: CD3-depleted PBMCs


title: CD3+ depleted, non stimulated, Nanostring GEX, D44, S14

value: non stimulated

tag: cell type


title: C6.2020.HIV+METH-

data_processing: Results from each panel were merged into a data file. Normalization was performed for each sample by dividing each sample’s raw count profiles by the geometric mean of 8 reference genes in nSolver.

tag: tissue


title: s2-14dpi

description:
L46086
RSEM_TPM_table.txt

value: river-dwelling surface fish

tag: treatment


title: CD3+ depleted, non stimulated, Nanostring GEX, D60, S14


title: 7_m14_S_Plus

tag: cell line

tag: genotype


title: negative control-2

value: Human ccRCC cells


title: C5.2020.HIV-METH-


title: s1-14dpi

description:
L46085
RSEM_TPM_table.txt


title: 10_m14_2_S_Plus_Plus

value: transduced sWT1++


title: p2-7dpi

description:
L46084
RSEM_TPM_table.txt


title: 9_m14_S_Plus_Plus


title: p1-7dpi

description:
L46083
RSEM_TPM_table.txt


title: o3_hoxa3_dox

value: dox-inducible WT1


title: C3.2020.HIV-METH-


title: C4.2020.HIV-METH+


title: CD3+ depleted, IFNg stimulated, Nanostring GEX, D32, S14


title: CD3+ depleted, IFNg stimulated, Nanostring GEX, D44, S14


title: CD3+ depleted, non stimulated, Nanostring GEX, D32, S14


title: o3_hoxa3_no_dox

value: control


title: C2.2020.HIV-METH+


title: B9.2020.HIV-METH+


title: p2-1dpi

description:
L46079
RSEM_TPM_table.txt

value: Skeletal Muscle


title: HepG2_BLM_H3K27me3

first: Xiaoguang

last: Ren

address: 130 Dong-An Road

department: Department of Biochemistry and Molecular Biology

institute: Fudan University

data_processing:
library strategy: CUT&Tag-seq
Remove the adapter sequence that may exist at the 5’ end of the sequencing data, then use DynamicsTrim to dynamically cut the R1 and R2 sequencing files separately, and save the cleaned raw data.
Using bowtie2 to align the cleaned data to the genome, using the hg38 version of the reference genome for analysis. Remove PCR-duplicated reads from the alignment results, and then perform various data format conversions on the alignment results.
Using macs2 to perform enrichment analysis on the aligned data and extract the enrichment fold change for each enriched region.
Screen for enriched regions between the drug treatment group and the control group, and normalize the enrichment fold change within the treatment and control groups. Then use the ratio of the normalized enrichment fold change scores as the fold change of differential enrichment between the experimental and treatment groups.
Intersect the differential enrichment regions from step 4 with the genome gene annotation file to obtain the gene sets of differential enrichment regions in the drug treatment group compared to the control group.
Using DAVID to perform Gene Ontology and KEGG functional enrichment analysis on different gene sets, and extract the top 10 functions for graphical annotation of functional enrichment results.
Assembly: hg38
Supplementary files format and content: Bedgraph

source_name: HepG2 bleomycin treat 24h

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Cells were harvested and incubated with ConA-beads, cells were binded to the beads, 200 μL antibody buffer was incubated with beads for 1h at room tempreature, then the transposome was added into the beads and incubated for 1h at room tempreature, tagmentation buffer was added to the beads for 1h at 37℃, the reaction was stopped by adding EDTA and proteinase K, cell total genomic DNA was extracetd by phenol-chloroform.
DNA library was constructed by NEB Next HiFi 2×PCR Mix, the PCR products were purified by VAHTS DNA clean beads (Vazyme).

treatment_protocol: Cells were treated with 10 mg/ml (Sellect) of bleomycin for 24 hours.

value: Hepatoma cell

tag: chip antibody

value: bleomycin for 24h


title: m13_hoxa3_dox


title: C1.2020.HIV-METH-

extract_protocol: For assays, archived specimens were thawed in fetal bovine serum, washed and viability was counted using disposable hemocytometers (Bulldog Bio, Portsmouth, NH). Cell numbers were adjusted for flow cytometry and for digital transcriptome.The RNA purification from pellets was performed using Nucleospin RNA Mini kit with DNA separation column (Macherey-Nagel, Bethlehem, PA). RNA quality and levels were monitored in a NanoDrop spectrophotometer ND-2000 (Thermo Scientific, Waltham, MA), and used to adjust concentrations for subsequent assays.


title: CD3+ depleted, IFNg stimulated, Nanostring GEX, D180, S14


title: m13_hoxa3_no_dox


title: CD3+ depleted, non stimulated, Nanostring GEX, D180, S14


title: s2-7dpi

description:
L46082
RSEM_TPM_table.txt

value: cardiotoxin injection


title: s1-7dpi

description:
L46081
RSEM_TPM_table.txt


title: p1-1dpi

description:
L46078
RSEM_TPM_table.txt

value: troglobitic cavefish


title: B7.2020.HIV+METH+

value: Peripheral blood cells


title: CD3+ depleted, IFNg stimulated, Nanostring GEX, D0, S14


title: B8.2020.HIV+METH+


title: s2-1dpi

description:
L46076
RSEM_TPM_table.txt


title: HepG2_BLM_H3R26me2a

value: H3R26me2a (Abclonal, #A2375)


title: HepG2_BLM_H3R26me2s

value: H3R26me2s (Abclonal, #A3153)


title: CD3+ depleted, IFNg stimulated, Nanostring GEX, D60, S12

value: adults (18-49 year old)

value: IFNg stimulated


title: CD3+ depleted, non stimulated, Nanostring GEX, D60, S12

value: 2 doses of HBS/AS01

value: CD3-depleted PBMCs


title: s3-1dpi

description:
L46077
RSEM_TPM_table.txt

value: river-dwelling surface fish


title: B5.2020.HIV-METH-


title: B6.2020.HIV+METH+


title: p3-control

description:
L46074
RSEM_TPM_table.txt

value: pbs injection


title: HepG2_BLM_IgG

value: Control IgG (Abclonal, #AC005)


title: CD3+ depleted, non stimulated, Nanostring GEX, D44, S12

value: non stimulated


title: CD3+ depleted, non stimulated, Nanostring GEX, D0, S14


title: B4.2020.HIV-METH-


title: CD3+ depleted, IFNg stimulated, Nanostring GEX, D44, S12


title: p1-control

description:
L46072
RSEM_TPM_table.txt


title: HepG2_BLM_γH2AX

value: γH2AX (Abclonal, #A11412)


title: s3-control

description:
L46071
RSEM_TPM_table.txt

value: Skeletal Muscle


title: CD3+ depleted, IFNg stimulated, Nanostring GEX, D32, S12


title: B1.2020.HIV+METH-


title: HepG2_Ctrl_H3K27me3

source_name: HepG2 untreat

value: Hepatoma cell

value: none; untreated


title: B3.2020.HIV-METH-


title: CD3+ depleted, non stimulated, Nanostring GEX, D32, S12


title: HepG2_Ctrl_H3K27ac


title: A9.2020.HIV-METH+


title: p2-control

description:
L46073
RSEM_TPM_table.txt


title: HepG2_Ctrl_H3R26me2s


title: B2.2020.HIV+METH-


title: s2-control

description:
L46070
RSEM_TPM_table.txt


title: CD3+ depleted, non stimulated, Nanostring GEX, D180, S12


title: CD3+ depleted, IFNg stimulated, Nanostring GEX, D180, S12


title: CD3+ depleted, non stimulated, Nanostring GEX, D0, S12


title: A8.2020.HIV-METH+


title: HepG2_Ctrl_H3R26me2a


title: s1-control

description:
L46069
RSEM_TPM_table.txt


title: Set1, D5, 3

city: Baltimore

first: Velinda

last: Vidaurre

state: Maryland

address: 3400 N Charles St

institute: Johns Hopkins

data_processing:
The sequencing reads were examined using the FastQC quality software (Galaxy Version 0.73+galaxy0)
Reads that passed the quality filter were then mapped to the Drosophila genome (D. melanogaster Aug 2014 (BDGP Release 6 + ISO11 MT/dm6)) using Bowtie 2 version 2.5.1
For gene mapping, the gene model (Drosophila_melanogaster.BDGP6.87.gtf) was utilized, and we followed an RNA-seq data analysis tutorial using Galaxy
Assembly: dm6
Supplementary files format and content: DESeq

organism: Drosophila melanogaster

source_name: testis

growth_protocol: Fly stocks were maintained in bottles containing a standard molassas recipe from the Bloomington Stock Center. Crosses to combine the nanos driver with the mCherry or Set1 RNAi transgenes were prepared in vials and maintained at 18°C. Upon eclosion, male progenies of the appropriate genotype were allowed to age for 0, 1, 3, or 5 days prior to sample preparation at 25°C.

extract_protocol:
Total RNA was purified following the manufacturers instruction of the Quick-RNA Microprep Kit (R1050, Zymo Research corporation).
The libraries were generated using the reagents provided in NEBNext Ultra II Directional RNA library Prep Kit for Illumina (E7760S, New England Biolabs Inc) and NEB Next Poly(A) mRNA Magnetic Isolation Module (E7490, New England Biolabs inc).

treatment_protocol: Male flies of the correct genotype were dissected in freshly prepared and filter sterilized Schneider's media containing 10% FBS. The biological replicates for each genotype and timepoint contain ~ 15 number of testis pairs. Following dissection, testes were digested in 200-300uL tissue digestion buffer composed of 2mg/mL collagenase disolved in TrypLE Express. The tissue was digested to completion in a 37°C water bath for 10-15 with agitation every 2-3 minutes. The suspended cells were next filtered with a 40um nylon mesh cell stainer. Cells were pelleted in 10 minute intervals at 1,200rpm until all digestion buffer was removed. The cells were washed with 200 ul of PBS and pelleted again for 5 min at 1,200 rpm.

value: testis

value: germ cell

value: Set1 knockdown

value: Day 5


title: HepG2_Ctrl_γH2AX


title: A7.2020.HIV-METH-

value: Peripheral blood cells


title: HepG2_BLM_H3K27ac

value: bleomycin for 24h


title: CD3+ depleted, IFNg stimulated, Nanostring GEX, D0, S12

value: adults (18-49 year old)

value: IFNg stimulated


title: A6.2020.HIV+METH-


title: s1-1dpi

description:
L46075
RSEM_TPM_table.txt

value: cardiotoxin injection


title: Set1, D5, 2


title: CD3+ depleted, non stimulated, Nanostring GEX, D60, S8

value: 2 doses of HBS/AS01

value: CD3-depleted PBMCs


title: A3

city: Nanjing

first: Xuedan

last: Han

address: School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road. Nanjing , China.

institute: China Pharmaceutical University

data_processing:
Illumina casav2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm9
Supplementary files format and content: raw counts for each Sample

growth_protocol: A549 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: A549 cells were treated with 5uM Anlotinib for 48h

value: Non-small cell lung cancer cells

value: Anlotinib


title: A5.2020.HIV-METH+

first: Maria

institute: San Diego Biomedical Research Institute

treatment_protocol: The subset of PWH and PWoH selected for this study were by design males, between 35 – 44 years old, due to cohort characteristics and to increase statistical power. The participants were divided based on HIV serostatus (HIV+/-) and Meth use (METH+/-). METH+ was defined as meeting lifetime DSM-IV criteria for methamphetamine use or dependence, and METH dependence or abuse within 18 months (LT Methamphetamine Dx), with 8.2% urine toxicology positive/current METH users. A cross-sectional design assembled the following groups: HIV-METH- (n=47), HIV+METH- (n=62), HIV-METH+ (n=39), and HIV+METH+ (n=54). Exclusion criteria were a history of non-HIV-related neurological, medical, or psychiatric disorders that affect brain function (e.g., schizophrenia, traumatic brain injury, epilepsy), learning disabilities, or dementia. Inclusion of major depressive disorder (MDD) and polysubstance use occurred in the cohort due to the high prevalence among Meth users and accounted for in the analysis models.


title: A2


title: Set1, D5, 1


title: CD3+ depleted, IFNg stimulated, Nanostring GEX, D60, S8


title: A4.2020.HIV-METH-


title: A3.2020.HIV+METH+


title: A1


title: Set1, D3, 3

value: Day 3


title: Set1, D3, 2


title: HepG2_Ctrl_IgG

city: Shanghai

value: Control IgG (Abclonal, #AC005)


title: C3

value: DMSO


title: CD3+ depleted, non stimulated, Nanostring GEX, D44, S8

value: non stimulated


title: Set1, D3, 1

value: testis


title: C2


title: A2.2020.HIV-METH+


title: C1


title: CD3+ depleted, IFNg stimulated, Nanostring GEX, D44, S8


title: CD3+ depleted, IFNg stimulated, Nanostring GEX, D32, S8


title: A0.2020.HIV-METH-


title: CD3+ depleted, non stimulated, Nanostring GEX, D32, S8


title: AGY1612_Day28_R3

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

library_source: other

data_processing:
Read counts generated using a script to identify samples from fastq files that are associated with each 10bp index tag
Assembly: YPS1009
Supplementary files format and content: Raw Count data
Library strategy: BAR-seq

molecule: other

organism: Saccharomyces cerevisiae YPS1009

growth_protocol: Strains used in the study are all haploids of the YPS1009 background. 1 mL frozen glycerol stocks of librarytransformed cells were thawed into 100 mL of liquid YPD + G418 (G418 to ensure maintenance of plasmids) at a starting OD600of 0.05, then grown in shake flasks at 30°C with shaking. The remaining cells from the frozen stocks were pelleted by centrifugation and represented the starting pool (Time 0) for each strain. At day 1 and day 28, an aliquot of each culture was plated and spread on solid YPD + G418 to select for viable cells. Cell lawns were allowed to grow for 48 hours then scraped into tubes and flash frozen. Cell pellets were stored at −80°C.

extract_protocol:
Plasmids were recovered from each pool using Zymoprep Yeast Plasmid Miniprep II (Zymo Research D2004-A) with the following modifications: samples were incubated with 15 units zymolyase at 37°C for 1 hour, with inversion every 15 minutes; incubation in cell lysis buffer was extended to 10 minutes; 500uM glass beads were added with lysis buffer and samples were vortexed for 1 minute 3 times during the 10 lysis incubation; after neutralization, samples were put on ice for 30 minutes, then centrifuged at 4°C.
Plasmid barcodes were amplified using primers containing Illumina multiplex adaptors as described in (Piotrowski et al. 2015), with number of PCR cycles reduced to 20. Barcode amplicons were pooled and purified using AxyPrep Mag beads (1.8X volume beads per sample volume) according to the manufacturer’s instructions (Axygen).

tag: strain

tag: genetic lineage

value: North American

value: Day 28

tag: media

tag: stress

value: stationary phase


title: A1.2020.HIV-METH-

city: San Diego

last: Marcondes

address: 3525 John Hopkins Ct. #200

value: Peripheral blood cells


title: Med_211_ic_huv

city: Toronto

first: Vikas

last: Patil

state: Ontario

address: 610 University Ave.

country: Canada

institute: Princess Margaret Cancer Center

data_processing:
Quality of reads assessed by FastQC tool.
The reads were aligned to the human reference genome using Star aligner.
RNA-Seq reads were counted using HtSeq and differnetial expression was analysed by DEseq2.
Assembly: GRCh38
Supplementary files format and content: count matrix (txt.file)

source_name: PDX line

extract_protocol:
The total RNA was extracted with RNeasy kit (Qiagen, 74004) as per manufacturers instructions.
RNA converted into cDNA library using TruSeq Stranded Total RNA kit (Illumina) using manufacturers instructions.

value: PDX line

value: Medulloblastoma

value: co-cultured with huvec


title: CD3+ depleted, IFNg stimulated, Nanostring GEX, D180, S8

value: adults (18-49 year old)

value: IFNg stimulated

tag: time


title: AGY1612_Day1_R3

value: Day 1


title: AGY1612_T0_R3

value: start


title: Set1, D1, 1

value: germ cell

value: Set1 knockdown


title: Med_425_ic_huv

source_name: Cell line

value: Cell line


title: Set1, D1, 3


title: CD3+ depleted, non stimulated, Nanostring GEX, D180, S8

value: 2 doses of HBS/AS01

value: CD3-depleted PBMCs


title: Set1, D1, 2

value: testis


title: AGY1611_Day28_R3

value: North American


title: Med_411_ic_huv


title: CD3+ depleted, non stimulated, Nanostring GEX, D0, S8

value: non stimulated


title: Set1, D0, 2

value: Day 0


title: AGY1611_Day1_R3

value: stationary phase


title: Set1, D0, 1


title: Med_MB2_ic_huv


title: siUFBP1-3

city: hefei

first: Meng

middle: hao

state: An hui

address: An hui Agricultural

department: College of life

institute: An hui Agricultural

data_processing:
Bomo_genome_assembly
raw data for splice removal and removal of low quality sequences, The parameter is ~fastp -i sample.R1.fastq -I sample.R2.fastq -o out.R1.fastq -p sample.R2.fastq -q 20-l 100-n 10
The clean reads were mapped to the reference genome  using HISAT2
Read count extraction and normalization were performed using Bomo_genome_assembly
Assembly: Bomo_genome_assembly
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Bombyx mori

source_name: Fat body

growth_protocol: In a nutshell, the B. mori P50 strain was grown in Anhui Province Key Laboratory of Resource Insect Biology and Innovative Utilization, School of Life Sciences, Anhui Agricultural University, Hefei, China. Mulberry leaves were given to the larvae at 26°C and 75% relative humidity.

extract_protocol:
Following the directions supplied by the manufacturer, RNAiMAX (Thermo Fisher SCIENTIFIC, USA) was used to transfect BmUFBP1 dsRNA or siRNA. For instance, in a 6-well plate, 5 μg of dsRNA was added to a 300 μL volume of serum-free TC100 culture medium for each well, and the mixture was added to an equal volume of RNAiMAX-containing TC100 culture medium, blended thoroughly, and allowed to stand for 15 minutes. The transfection complexes were then added to the BmN cells' supernatant to complete transfection.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: he small interfering RNA (siRNA) against BmUFBP1 and siNC (negative control) were designed and synthesized by the Sangon Biotech Company (Sangon, Shanghai, China); the siRNA sequences are shown in Table 1. Thirty larvae on the 3rd day of the 5th instar were used for RNA interference experiments. Each larva was injected with 2.5 µg siNC or siBmUFBP1, and all larvae were administered with 5 µL of BmNPV suspended in water (1 × 106 ODVs/mL) at 12 h post injection of siRNA. Fat body were obtained at 24 h, 48 h and 72 h post injection.

value: Fat body

value: BmN


title: CD3+ depleted, IFNg stimulated, Nanostring GEX, D0, S8


title: AGY1612_Day28_R2

value: Day 28


title: Med_411_con

value: PDX line

value: Medulloblastoma

value: control


title: Med_425_con


title: mCherry, D5, 2

value: WT

value: Day 5


title: siUFBP1-2


title: Set1, D0, 3

value: germ cell

value: Set1 knockdown


title: siUFBP1-1


title: siNC-2


title: AGY1612_Day1_R2

value: Day 1


title: Med_211hc_pos

value: Hoechst 33342


title: siNC-3


title: mCherry, D3, 3

value: testis

value: Day 3


title: Med_MB2_con

value: Cell line


title: Med_211_con


title: mCherry, D5, 1


title: mCherry, D3, 2


title: AGY1612_T0_R2

value: North American

value: start


title: mCherry, D3, 1


title: Med_051hc_pos_rep2


title: siNC-1

value: Fat body


title: AGY1611_Day28_R2

value: stationary phase


title: mCherry, D5, 3


title: Med_051hc_pos_rep1


title: AGY1611_T0_R2


title: mCherry, D1, 3


title: AGY1611_T0_R3


title: AGY1611_Day1_R2


title: KO CoV2 D3 rep3

city: Galveston

middle: De jesus

last: Gonzalez Orozco

state: Texas

address: 301 University Blvd

department: Microbiology and Immunology

institute: UTMB

description: KO CoV2 D3_3

data_processing:
Base calling was using Illumina's bcl2fastq2-v2.17.1 converter
A genome index was built with STAR (v2.5.1b) using the mouse mm39 genome.
Reads were aligned to the mm39 reference using the STAR software version 2.5.1b with the parameters recommended for the ENCODE consortium.
Read counts per gene were produced with the --quantMode GeneCounts function of STAR.
Differential gene expression was analyzed with the R (version 3.3.1) software DESeq2 (version 1.12.1)
Assembly: Genome_build: GRCm39
Supplementary files format and content: Tab delimited table of raw read counts per gene

source_name: KO CoV2 day 3

extract_protocol:
Total cellular RNA was extracted using Trizol Reagent (Life Technologies, CA) according to the manufacturer’s recommendations.
Poly-A plus RNA was enriched from ~0.1 ug of total RNA and used to generate libraries using the Illumina TruSeq kit.

value: Lung

value: TRIM7 KNOCKOUT

value: Infected SARS-coV-2 CMA3p20


title: KO CoV2 D3 rep2

description: KO CoV2 D3_2


title: AGY1612_Day28_R1

value: Day 28


title: AGY1612_Day1_R1


title: mCherry, D1, 1

value: WT


title: Med_411hc_pos_rep1

value: Medulloblastoma


title: AGY1612_T0_R1


title: Med_411hc_pos_rep2


title: WT CoV2 D3 rep2

description: WT CoV2 D3_2

source_name: WT CoV2 day 3


title: KO CoV2 D3 rep1

description: KO CoV2 D3_1


title: mCherry, D0, 2

value: germ cell

value: Day 0


title: Med_411hc_neg_rep1


title: Med_211hc_neg


title: Med_051hc_neg_rep2


title: Med_411hc_neg_rep2


title: WT CoV2 D3 rep1

description: WT CoV2 D3_1


title: AGY1611_Day28_R1


title: AGY1611_T0_R1


title: mCherry, D0, 1


title: WT CoV2 D3 rep3

description: WT CoV2 D3_3


title: UMUC3-circMGA

city: WuHan

first: Guosong

last: Jiang

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Illumina PE150  software used for basecalling.
Compare the clean reads to the reference sequence useing Hisat2 software
Use Stringtie software to splice the reads into transcripts and quantify them
Quantitative expression levels of all detected and predicted samples
Genome_build: hg38

source_name: human bladder cancer cells

growth_protocol: Cells were cultured  in Dulbecco’s modified Eagle medium (Gibco, United States), which supplemented with 10% fetal bovine serum (Gibco, United States), 100 U/ml penicillin, and 100 μg/ml streptomycin. Then, incubating the cells at 37 °C in a humidified atmosphere (Thermo Fisher Scientific, MA, USA) with 5 % CO2.

extract_protocol:
Total RNA was extracted from all cells using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), accordance with the instructions of the kits used.
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: EJ, T24T, and UMUC3 cells transfected with circMGA and compaired vector. Transfection was carried out using Lipofectamine 2000 (Life Technologies) according to the manufacturer’s instructions. The transfected cells were then selected with neomycin (Invitrogen)

value: circMGA-overexpressed UMUC3 cell

tag: vector


title: Mononuclear cells, relapse, TMR, 34

city: Old Al rayyan

first: Nisar

last: Ahmed

state: Doha

address: LAS Building, Education city

department: College of Health and Life Sciences

country: Qatar

institute: Hamad Bin Khalifa University

description: Omni-C

data_processing:
Omni-C libraries underwent in-house processing. Sequencing QC was conducted  using FastQC, followed by adapter trimming with TrimGalore. Alignment to the GRCh38 human genome was performed using BWA-MEM. Ligation junctions were identified using pairtools parse, filtering for MAPQ ≥ 40 and 5unique walks-policy. The resulting pairsam files were sorted and PCR duplicates removed using pairtools dedup, which also generated library statistics. Finally, deduplicated pairsam files were used to generate pairs and BAM files for downstream analysis.
Assembly: Hg38
Supplementary files format and content: Count table

source_name: Relapse

growth_protocol: Flash-frozen mononuclear cells from bone marrow and/or peripheral blood of adult AML diagnosis and relapse pair samples were maintained in IMDM supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
We have employed the Omni-C kit from Dovetail Genomics for DNase-based Hi-C. 1 x 10^6 MNCs were fixed in DSG, followed by formaldehyde and fixed cells were treated with DNaseI. Next, the chromatin ends were polished and biotin-tagged bridges were used to create chimeric molecules.
The library preparation kit used in the Dovetail Omni-C protocol is called the  "Dovetail Library Kit." This kit is specifically designed to prepare sequencing libraries from the DNA fragments generated during the Hi-C experiment using the Dovetail Omni-C technology. It includes steps such as end repair, adapter ligation, and PCR amplification to generate libraries.

treatment_protocol: Cryopreserved bone marrow samples were slowly thawed using IMDM supplemented with 10% FBS and DNAse. Viability was calculated under a hemocytometer with trypan blue – samples with a viability <80% were subjected to a dead cell sort using MACS dead cell removal kit (cat: 130-090-101)

value: Relapse

tag: disease

value: AML

value: Mononuclear cells


title: wt-3

city: Lincoln

first: Edgar

last: Cahoon

state: NE

address: 1901 Vine St

institute: University of Nebraska Lincoln

data_processing:
Parameters for data filtering raw data with adapter sequences or low-quality sequences was filtered. We first went through a series of data processing to remove contamination and obtain valid data. This step was completed by SOAPnuke software developed by BGI. SOAPnuke software filter parameters: " -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim", steps of filtering: 1. Filter adapter: if the sequencing read matches 25.0% or more of the adapter sequence (maximum 2 base mismatches are allowed), cut the adapter; 2. Filter low-quality data: if the bases with a quality value of less than 20 in the sequencing read account for 40.0% or more of the entire read, discard the entire read; 3. Remove N: if the N content in the sequencing read accounts for 0.1% or more of the entire read, discard the entire read; 4. Obtain Clean reads: the output read quality value system is set to Phred+33.
Assembly: N/A
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Sorghum bicolor

source_name: leaf

growth_protocol: Plants were grown in the field at the Eastern Nebraska Research, Extension, and Education center in the summer of 2022.

extract_protocol:
Total RNA was isolated from fully developed leaves of wild-type and transgenic sorghum plants using an RNeasy Plant Mini Kit according to the manufacturer’s protocol (Qiagen, Germantown, MD). RNA was cleaned from DNA contamination using TURBO DNA-free™ Kit (ThermoScientific, Waltham, MA). To determine expression level of transgenes, first-strand cDNA was synthesized from 1 µg of total RNA with a High-Capacity cDNA Reverse Transcription Kit (ThermoScientific)
DNBSEQ Eukaryotic Strand-specific mRNA library prepared by BGI Americas.

treatment_protocol: Comparing leaves of wild-type plants versus leaves from plants engineered to produce triacylglycerols (TAG).

value: leaf

value: Tx430 WT

value: no TAG production


title: Med_051hc_neg_rep1


title: mCherry, D0, 3

value: testis


title: wt-2


title: Mononuclear cells, diagnosis, TMD, 273

description: Omni-C

source_name: Diagnosis

value: Diagnosis


title: VYS_MEHP_POS_3

city: East Lansing

first: Karilyn

middle: E

last: Sant

state: MI

address: 1355 Bogue St., Life Science B440

department: Pharmacology & Toxicology

institute: Michigan State University

description: *** The raw data (CEL files) are not included because they were lost due to disk corruption ***

hyb_protocol: Samples were processed and scanned at the University of Michigan Microarray Core Facility (Ann Arbor, MI)

data_processing:
The affy, limma, and affyPLM packages of bioconductor were used in R (v2.15.1).
Background correction, normalization, and quantification of log2 expression was performed within-array using RMA, and quantile normalization was used across-arrays.

label: biotin - IVT Express Kit (Affymetrix)

source_name: mouse visceral yolk sacs exposed to 100 μg/ml MEHP for 24 hours in whole embryo culture, with a neural tube defect

label_protocol: RNA was processed using the IVT Express Kit (Affymetrix)

growth_protocol: Whole mouse conceptuses were manually extracted from untreated, pregnant dams on GD8. Conceptuses were transferred to whole embryo culture for 24 h, containing either 0.01% dimethyl sulfoxide (control) or 100 ug/ml mono-2-ethylhexyl phthalte. On GD9, conceptuses were removed from culture and manually dissected with watchmakers' forceps to yield embryos and visceral yolk sacs. Culture protocols were performed as described by Harris (2012; PMID: 22669667).

extract_protocol:
RNA extraction  was done immediately upon sampling using the RNeasy Mini Kit (Qiagen). RNA was stored at -80°C until use.
RNA purity and integrity were confirmed using the RNA 6000 Nano Kit for the Agilent 2100 Bioanalyzer. Other quality controls including PM chip density, RNA degradation, and standard error analyses were performed on the raw data.

value: visceral yolk sacs

tag: exposure

value: Mono-2-ethylhexyl phthalate (MEHP) - 100 μg/ml for 24 hours in whole embryo culture

tag: ntd status

value: positive

tag: age


title: UMUC3-vector control

value: UMUC3 cell in control group


title: Mononuclear cells, relapse, MBR, 293

description: Omni-C


title: T24T-circMGA

value: circMGA-overexpressed T24T cell


title: wt-1


title: AGY1611_Day1_R1

value: North American

value: Day 1

value: stationary phase


title: 1569-2

value: Tx430 transgenic

value: TAG producer


title: Mononuclear cells, diagnosis, MBD, LB

description: Omni-C

value: AML


title: 1569-3


title: 1569-1


title: EJ-circMGA

value: circMGA-overexpressed EJ cell