title: Colon cancer 3M

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Library strategy: LoopSeq
Long-read were mapped to reference genome hg38 by Minimap2 aligner (version 2.11-r797)
Isoform and fusion transcripts were identified by SQANTI (version 1.2)
Differential gene/isoform expression were analyzed by R DEseq2 package
SNVs were called by SAMtools mpileup fusion (samtools version 1.9 and bcftools version 1.9-40)
SNVs were annotated by ANNOVAR tool (version 2018Apr16), dbSNP and Cosmic database
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using bam2wig (version 1.5)
Supplementary_files_format_and_content: Long-reads gene/isoform were annotate by SQANTI and shor-read counts were collected based on the annotation and read barcode

source_name: Colon

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, CA) and RNeasy column methods.
LoopSeq sequencing libraries were prepared using LoopSeq Transcriptome Kit according to manufacturer’s protocol except when specified. 200 ng of total RNA extracted from cancer patient tissues was reverse transcribed and barcoded using LoopSeq Transcriptome Kit, and an enrichment step using Twist Biosciences probes targeting selected genes annotated to be of significance in cancer development was applied prior to Barcode Amplification in LoopSeq library prep. Specifically, the barcoding reaction was purified using 0.6X SPRISelect ratio and then eluted into 20 μL of Hybridization Mix per manufacturer’s pre-capture concentration protocol. The hybridization reactions contain 20 μL of Hybridization Mix, 5 μL of  Blocker Solution, 9 μL of LG Adaptor Blocker (Loop Genomics), 4 μL of Twist Custom Enrichment Panel, 2 μL of Buffer EB (Qiagen), and 30 μL of Hybridization Enhancer. All probe hybridization and washes were conducted per manufacturer’s protocol. All target enrichment reagents are from Twist Biosciences except when specified. The captured barcoded cDNA was amplified following the LoopSeq Transcriptome protocol starting from Barcode Amplification.

value: Colon

tag: patient

value: Patient 3

tag: sample

value: metastasis sample


title: Nl5_3: Organoid Bulk RNA-seq Day 0 - replicate 3

status: Public on May 05 2021

type: SRA

city: Davis

first: Stefan

last: Siebert

address: One Shields Avenue

country: USA

institute: University of California, Davis

description: human iPSC

library_source: transcriptomic

data_processing:
Raw reads were trimmed for adapters and low-quality bases using Cutadapt 1.18 (-j 8 -b file:adapters.fa -B file:adapters.fa --trim-n -m 20 -o trimmed_R1.fq -p trimmed_R2.fq input_R1.fq input_R2.fq) prior to alignment to the reference genome (Human genome – hg38, annotation Gencode_v24) using STAR 2.6.1. Gene expression quantification analysis was performed using RSEM 1.2.31.
genome build: hg38
processed data files format and content: tab-delimited text file of RSEM gene level raw expression estimates

molecule: total RNA

organism: Homo sapiens

source_name: GFP-labeled human iPSC (NL5-GFP)

extract_protocol:
RNeasy Mini Kit (QIAGEN)
TruSeq Stranded Total RNA

tag: tissue

value: human iPSC


title: MED1 control

city: Richmond

first: Jiong

last: Li

state: Virginia

address: 800 E Leigh Street, suite 212

institute: VCU

description: MED1 control

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.2.0.
The unique mapped reads was used for peak calling by MACS2 with default setting
Supplementary_files_format_and_content: bedGraph files and big wig files

molecule: genomic DNA

source_name: Head and neck squamous cell carcinoma cells

growth_protocol: 10% FBS in DMEM

extract_protocol:
ChIP was performed uing EZ-Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (Sigma, Cat#17-10086). 10–50 ng of ChIP DNA for each sample was sonicated and used for the ligation of barcoded Kapa adapters.
Sequencing libraries were generated using a KAPA Hyper DNA Kit (KAPA Biosystems, Cat# KK8503)

treatment_protocol: SCC1 cells were treated with 500nM JQ1 or with control for 24 hours.

tag: agent

value: control

tag: cell line

tag: chip antibody

value: MED1 rabbit antibody (Bethyl, cat#A300-793A)


title: Older sedentary adult, O3

city: Boulder

first: Thomas

last: LaRocca

state: CO

address: 1725 Pleasant St

institute: University of Colorado Boulder

data_processing:
QC and adapters trimmed using fastp.
Reads aligned and counted using STAR.
Repetitive element transcripts counted using TEtranscripts.
Genome_build: hg19
Supplementary_files_format_and_content: Raw gene and repetitive element counts for each sample.

source_name: Peripheral blood mononuclear cells

extract_protocol:
RNA for polyA RNA-seq extracted using Trizol and Zymo spin columns.
Total RNA libraries were prepared according to manufacturer's instructions using the Illumina TruSeq kit with Ribo-Zero Depletion.

tag: Sex

value: Male

tag: age

tag: exercise status

value: sedentary

tag: cell type

value: Peripheral blood mononuclear cells


title: Input JQ1 treatment

description: Input JQ1 treatment


title: Older sedentary adult, O1

value: Female


title: Input control

description: Input control


title: Colon cancer 2M

state: PA

value: Patient 2


title: Wild-type retina #2

city: Lethbridge

first: Yaroslav

last: Ilnytskyy

state: AB

address: 4401, University Drive W

department: Biology

country: Canada

institute: University of Lethbridge

data_processing:
Basecalling and demultiplexing: CASAVA1.9
Initial quality controls: FastQC
Adapter trimming: TrimGalore! v.0.6.4
Mapping: bowtie v.2.3.5.1 with –very-sensitive option
SAM to BAM conversion, sorting and indexing: samtools v.0.1.19
Removal of mitochondrial reads using samtools idxstats
Creation of normalized coverage file in bigwig format using Deeptools 3.3.0 bamCoverage with RPGC normalization
Peak calling was done using MACS v.2.2.7.1 with -f BAMPE and –broad options specified
Differentially accessible peaks were called with DiffBind v.3.013 with TMM normalization and library sizes determined based in background method
Genome_build: GRCm38
Supplementary_files_format_and_content: bigwig, broadPeak

organism: Mus musculus

source_name: Wild-type retina

extract_protocol: Active Motif ATAC-seq kit was used for libraries construction

tag: developmental stage

value: Post-natal stage (P)7

tag: strain

tag: genotype

value: Wild-type

value: retina


title: Colon cancer 3N

value: benign colon tissue adjacent to cancer sample


title: Colon cancer 2T

value: tumor sample


title: Older sedentary adult, O2


title: Colon cancer 1M

value: Patient 1


title: HSPC CD49fLow

city: Shanghai

first: Aining

last: Xu

address: 197 Rui Jin Er Road

country: China

institute: State Key Laboratory Of Medical Genomics, Rui-jin Hospital

data_processing:
Alignment using STAR (version 2.5.2b)
Generate count files using HTseq (version 0.6.1)
Genome_build: hg19
Supplementary_files_format_and_content: count files generated from Htseq

source_name: Hematopoietic stem and progenitor cells

growth_protocol: hESCs were sequentially induced into mesodermal cells, hemogenic endothelial cells and HSPCs in a feeder-free and serum-free monolayer culture system.

extract_protocol:
Sorted CD49fHigh and CD49fLow HE at day 6 and CD49fHigh and CD49fLow HSPCs at day 8 were respectively harvested for RNA extraction with TRIzol Reagent (Invitrogen).
Libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina #RS-122-2001) and sequenced with Illumina NovaSeq 6000.

value: hESCs-derived hematopoietic stem and progenitor cells


title: Older habitually exercising adult, T1

value: habitually exercising


title: S-C_S4: Chronic LCMV scRNA-seq

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

description: Chronic

data_processing:
Reads were aligned to mouse reference genome mm10 using Cell Ranger (10x Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files were generated using Cell Ranger (10x Genomics)

source_name: Myeloid cells

extract_protocol:
Splenic myeloid cells were FACS-sorted from LCMV-infected mice on day 7 post-infection and were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Libraries were loaded onto an Illumina NextSeq with the NextSeq 500/550 High Output Kit v2 (150 cycles)
10x Genomics standard protocol

treatment_protocol: Mice were infected with 200 or 2,000,000 PFU LCMV Clone 13 to establish acute and chronic infection, respectively

tag: infection

value: LCMV Clone 13 (chronic infection)

value: Spleen

value: Myeloid cells


title: HSPC CD49fHigh


title: S-A_S3: Acute LCMV scRNA-seq

description: Acute

value: LCMV Clone 13 (acute infection)


title: single-cell RNA-seq_Ctrl

first: Ting

last: Wu

address: 320 Yue-Yang Road

institute: Institute of Biochemistry and Cell Biology, Chinese Acadamy of Sciences

data_processing:
Filtering, alignment to the mm10 transcriptome and unique molecular identifier (UMI)-collapsing were performed using the Cell Ranger (v2) pipeline with default mapping arguments (10X Genomics).
Genome_build: mm10
Supplementary_files_format_and_content: Format: tsv; Content: barcodes, features and matrix for every sample

source_name: mammary cells

extract_protocol:
Single cells were partitioned into gel beads in emulsion in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing, and 5’ adaptor and sample index attachment
Single cells were loaded onto 3’ library chips for the Chromium Single Cell 3’ Library (v2) according to the manufacturer’s recommendations (10X Genomics). Libraries were sequenced on an Illumina Hiseq PE150

treatment_protocol: 8-10 weeks old mice were injected with tamoxifen. After 4 weeks, mammary glands were harvested and digested into single cells, mammary cells were enriched by FACS.

value: primary mammary cells

value: 8-weeks old

tag: treatment

value: 4-weeks after tamoxifen administration


title: Colon cancer 1T

value: Colon


title: HE CD49fLow

source_name: Hemogenic endothelium

value: hESCs-derived hemogenic endothelium


title: Colon cancer 3T

value: Patient 3


title: Wild-type retina #3

value: Post-natal stage (P)7

value: Wild-type


title: Wild-type retina #1

value: retina


title: miRNA_LPS+TET Replicate Replicate 3

type: RNA

city: Durham

first: Jian-Liang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description: miRNA Expression Profile

hyb_protocol: Each labeled sample was hybridized for 16 hours at 48°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000 and data was obtained using Transcriptome Analysis Console 4.0 Software.

data_processing: The raw microRNA data were pre-processing and normalized using Affymetrix Expression Console (Build 1.4.1.46, Thermo Fisher Affymetrix, Santa Clara, CA). Only mouse microRNAs were retained for the downstream analysis.

label: biotin

source_name: Murine bone marrow derived macrophages

label_protocol: miRNA analysis was conducted on 3 biological replicates using Affymetrix GeneChipTM Version 4 miRNA arrays (Affymerix, Santa Clara, CA) following the Affymetrix hybridization protocols.  Affymetrix FlashTagTMBiotin HSR labeling was used to label 110 ng of total RNA according to the manufacturer’s protocol.

growth_protocol: C57BL6 mice (6-12-weeks-old) were euthanized under CO2, the femur excised, bone marrow extruded, and primary BMDMs cultured. Isolated cells were plated 1,000,000 cells/well/12-well plate in 3 mL DMEM supplemented with 10% FBS, 100 U/mL penicillin/streptomycin, and 10% L929 conditioned-media.  On days-in-vitro (DIV)4, cells underwent a half-media change.  On DIV5, media was changed to DMEM without L929 conditioned medium.  Cells were used in experiments on DIV6.

extract_protocol: Total RNA was isolated from BMDMs using TRIzol® (Invitrogen).  Resuspended pellets were treated with 2.5L DNase I and 10L Buffer RDD for 10 min at RT followed by column separation (RNeasy mini prep, Qiagen).

treatment_protocol: On DIV6, cells were treated with 33 ng/mL ultrapure LPS for 3 hours prior to the addition of either TMT OH (1.25M), TET Br (10M), or sterile saline for 6 hours.

value: bone marrow derived macrophages

value: LPS prime+TET


title: HE CD49fHigh


title: B. subtilis PS533_Spores_b

city: Farmington

first: Peter

last: Setlow

state: CT

address: 263 Farmington Ave

department: Molecular Biology and Biophysics

institute: UConn Health

data_processing:
Files were concatenated.
Quality was assessed using FASTQC v011.8
Files trimmed Sickle single end V. 133
RPKM files were generated with EDGE_pro v1.3.1
Genome_build: ASM1506v1; ASM2582v1; ASM224349v1; ASM230013v1; ASM904v1; ASM208006v1
Supplementary_files_format_and_content: Coverage, #reads, RPKM

organism: Bacillus subtilis

source_name: B. subtilis PS533

growth_protocol: Spores of B. subtilis PS533  B. atrophaeus ATCC 9372 and B. thuringiensis Al Hakam were prepared as previously described on double strength Schaeffer's glucose agar plates(1,2) which were incubated for ~48 hours at 37 ˚C.   1. Nicholson WL, Setlow P. 1990. Sporulation, germination and outgrowth, p 391-450. In Harwood CR, Cutting SM (ed.), Molecular biological methods for Bacillus. John Wiley and Sons, Chichester, UK.  2. Paidhungat M, Setlow B, Driks A, Setlow P. 2000. Characterization of spores of Bacillus subtilis which lack dipicolinic acid. J Bacteriol 182:5505-5512.

extract_protocol:
1 ml of each strain of dormant spores at an OD600 of 25 was pelleted by centrifugation. Prior to pelleting, to get a more accurate quantitation of the number of spores present, spore samples were diluted 1 to 25 in water, to give an OD600 of ~1.0, and the numbers of spores were counted in a Petroff-Hausser chamber to determine spores per ml. Spores were disrupted by shaking with glass beads in a Mini-Bead-beater (Biospec Products, Bartlesville, OK) for 1 min, followed by 1 min on ice with a total of two disruption periods, and giving >98% spore breakage (9). RNA was extracted using the RiboPure – Bacteria kit (Thermo Fisher Scientific, Waltham, MA) as previously described (9). Total RNA was quantitated using the Qubit RNA HS (High Sensitivity) Assay Kit (Thermo Fisher Scientific) (10) with the Qubit Fluorometer, using appropriate dilutions to get measurements that fell within the standard curve (500 ng/mL maximum concentration). Generally, a dilution range of 1:500 to 1:1000 of the purified initial total RNA gave quantifiable values. From this obtained concentration and the previously counted spore value, values of total RNA per spore were determined.     9. Korza G, Setlow B, Li Q, Rao L, Setlow P. 2016. Changes in Bacillus small molecules, rRNA, germination and outgrowth after extended sublethal exposure to various temperatures: evidence that protein synthesis is not essential for spore germination. J Bacteriol 198:3254-3264.  10. Garcia-Elias A, Alloza L, Puigdecanet E, Nonell L, Tajes M, Curado J, Enjuanes C, Diaz O, Bruguera J, Martí-Almor J, Comin-Colet J, Benito B. 2017. Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs. Sci Rep 7:7725.
Total RNA extracted and purified from spores of various species was submitted to University of Connecticut’s Center for Genome Innovation for ribosomal RNA depletion, RNA-seq library synthesis, and next-generation sequencing. Briefly, total RNA was ribo-depleted to remove most rRNA, the quality of the ribo-depleted RNA examined using the Agilent TapeStation 4200 D1000 high-sensitivity assay, and RNA-seq on RNA from all species was carried out on duplicate samples using an Illumina Next-Seq 500/550, all as described previously (11,12). Sequencing read depth was targeted at > 4 x 106 reads per sample. RNA-seq data were processed and analyzed as described previously (14) and levels of mRNA nt in an individual spore in populations were calculated using values for total RNA nt per individual spore determined as described above, and assuming that spore mRNA comprised 3% of total RNA (11).      11. Korza G, Camilleri E, Green J, Robinson J, Nagler K, Moeller R, Caimano MJ, Setlow P. 2019. Analysis of messenger RNAs in spores of Bacillus subtilis. J Bacteriol 201:e-00007-19.  12. Camilleri E, Korza G, Green J, Hui J, Li YQ, Caimano MJ, Setlow P. 2019. Properties of aged spores of Bacillus subtilis. J Bacteriol 201:e00231-19.

treatment_protocol: Spores of all species were scraped from plates into 4 ˚C water and highly purified over ~7 d as described previously(6,7,8), including a final purification by centrifugation through a very high density (Histodenz) medium to remove spore associated debris as much as possible. Final spore preparations were >98% free from growing or sporulating cells and germinated spores as determined by phase contrast microscopy and spores pelleted by centrifugation had no obvious debris on the pellet surface. Spores were stored in water at 4 ˚C protected from light.    6. Crawshaw AD, Serrano M, Stanley WA, Henriques AO, Salgado PS. 2014. A mother cell-to-forespore channel: current understanding and future challenges. FEMS Microbiol Lett 358:129-136.

value: Spores


title: single-cell RNA-seq_cKO


title: B. subtilis PS533_Spores_a

value: pUB110 (encoding kanamycin resistance)

tag: derivation

value: derived from 168


title: ERCC synthetic RNA/Hela Total RNA 2

data_processing:
Library strategy: LoopSeq
Long reads were mapped to refseq RNA with human gene annotation or ERCC reference sequences by LoopSeq pipeline
Full-length sequences were extracted and compared with reference sequences to determine TSS and TTS using custom script
Full-length sequences were extracted, and the end sequences were compared to the reference mapping of the contig and with each other for chimera determination
Full-length sequences of contigs mapping to ERCC-0002 were extracted and aligned against the reference sequence to generate a variance table using Sequencher 5.4.6.
Genome_build: hg38
Supplementary_files_format_and_content: csv or xlsx files for analysis summary

organism:
Homo sapiens
synthetic construct

source_name: Synthetic/Cell line

extract_protocol:
RNA was obtained from ThermoFisher Scientific
LoopSeq sequencing libraries were prepared using LoopSeq Transcriptome Kit according to manufacturer’s protocol except when specified. 10 ng of total RNA from Hela Total RNA, 0.5ng of ERCC synthetic RNA, or a mixture of the two RNA sources were reverse transcribed and barcoded using LoopSeq Transcriptome Kit.

value: Synthetic/Cell line


title: miRNA_LPS+TET Replicate Replicate 2

description: miRNA Expression Profile


title: miRNA_LPS+TET Replicate Replicate 1

description: miRNA Expression Profile


title: ERCC synthetic RNA/Hela Total RNA 1


title: StAgo1-GFP H2O 1

city: Uppsala

first: Kristian

middle: Erik

last: Persson Hodén

address: Almas allé 5

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

data_processing:
smallRNA processing: The function SamToFastq, included in the Picard tool package, was used to convert the original BAM format to FASTQ format (for the raw data which was not already in FASTQ format), on which a quality control was performed, using FastQC
smallRNA processing: Cutadapt, quality trimming (20), read length filtration 18 - 38 nt
smallRNA processing: Bowtie2 in combination with SAMtools view were used for tRNA and rRNA trimming and potato and P. infestans sRNA filtering to exclude the reads from the other genome for the different datasets, using 0 mismatches allowed per seed against each Fasta filter
smallRNA processing:  SamToFastq converted the files to fastq
smallRNA processing: Seqtk was applied to convert the FASTQ files to FASTA.
Degradome processing: Raw RNA reads from degradome libraries were adaptor- and quality trimmed with Cutadapt
Degradome processing: Seqtk was applied to convert the FASTQ files to FASTA.
The sRNA and degradome fasta files and  were analyzed in PAREsnip2.
PAREsnip output data was imported in R where PAREsnip2 replicates were merged and duplicated targets were discarded.
Resulting datasets were analyzed in our machine learning script (https://github.com/kristianHoden/degradome). False positives were discarded
The datsets were sorted in list according to their Normalized Fragment Abundance (NFA) and targeting transcriptome
Solanom tuberosum genome v4.04, Phytophthora infestans genome (ASM14294v1)
fasta format of small RNA and degradome libraries
Genome_build: Solanom tuberosum genome v4.04, Phytophthora infestans genome (ASM14294v1)
Supplementary_files_format_and_content: pinfDown - contain the datasets with targets in P. infestans with decreased NFA of the targets upon infection
Supplementary_files_format_and_content: pinfUp - - contain the datasets with targets in P. infestans with increased NFA of the targets upon infection
Supplementary_files_format_and_content: potDown - contain the datasets with targets in potato with decreased NFA of the targets upon infection
Supplementary_files_format_and_content: potUp - - contain the datasets with targets in potato with increased NFA of the targets upon infection
Supplementary_files_format_and_content: rDown - contain the datasets with targets in resistance (R) genes in potato with decreased NFA of the targets upon infection
Supplementary_files_format_and_content: rUp - contain the datasets with targets in resistance (R) genes in potato with increased NFA of the targets upon infection

organism: Solanum tuberosum

source_name: Leaves

growth_protocol: Potato plants were grown in-vitro at 22°C with a 16-h photoperiod on Murashige-Skoog (MS) medium (Duchefa Biochemie B.V., Amsterdam, Netherlands), supplemented with 2% (w/v) sucrose and 0.3% (w/v) gelrite (Duchefa). After 3 weeks plants were transferred to pots with soil in a growth chamber with the same light and temperature regime. P. infestans were maintained at 20 °C on rye agar medium supplemented with 2 % sucrose (Caten & Jinks 1968), rifampicin (10 μg ml−1), and pimaricin (10 μg ml−1). Transgenic lines of P. infestans isolate 88069 were maintained as above, but with the addition of the antibiotic geneticin (G418; 10 μg ml−1) to the medium.

extract_protocol:
Inoculated leaves were harvested and flash frozen in liquid nitrogen. StAGO1a-GFP and control Pi-GFP immunoprecipitations were performed with anti-GFP antibody (Chromotek, gtm-100).
Barcoded sequencing libraries were constructed using the Ion Total RNA-Seq Kit v2 and Ion Xpress barcode primers. Sequencing was performed on the Ion Proton platform using the Ion PI™ Hi-Q™ Sequencing 200 Kit (Thermo Fisher Scientific).

treatment_protocol: H2O inoculations were added to the leaves 4 weeks post transfer to soil from in-vitro conditions.

tag: potato cultivar

value: StAgo1a-GFP (Sarpo Mira)

tag: dpi

value: Leaves

tag: ip antibody

value: GFP (Chromotek, gtm-100)


title: miRNA_LPS+TMT Replicate Replicate 2

description: miRNA Expression Profile

value: LPS prime+TMT


title: miRNA_LPS+TMT Replicate Replicate 3

description: miRNA Expression Profile


title: Mut5vsPCL1606_2

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

country: Spain

institute: UMA

data_processing:
We used Edge-Pro for mapping and quantification and qualimap for quality control
Noiseq was used for data normalization
Genome_build: CP011110.1 and NZ_CP011937.1
Supplementary_files_format_and_content: tab-delimited excel files include Log2FC of the comparison of interactions, with p-value

organism:
Bacillus amyloliquefaciens
Pseudomonas chlororaphis

source_name: Interaction Mut

extract_protocol:
Single colonies of PCL1606 and FZB42 WT and the GlpK mutant were grown overnight in LB medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 2 µl were spotted on King B plates alone and in interaction between PCL1606 and the Bacillus strains. Cultures were grown for 24h at 30°C. After that, colonies were recovered and stored at -80C. The collected cells were resuspended and homogenized by passing through a 25 5/8 G needle in BirnBoim A (20% sucrose, 10mM tris-HCl pH 8, 10mM EDTA and 50mM NaCl). Lysozyme (10 mg/ml) was added and incubated 30 min at 37C. After disruption, suspensions were centrifuged, and pellets were resuspended in Trizol reagent (Invitrogen). Total RNA extraction was performed as indicated by the manufacturer. Removal of DNA was carried out by in-column treatment with the rDNAse included in the Nucleo-Spin RNA Plant (Macherey-Nagel) following instructions from the manufacturer. Integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies) and by gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: P. chlororaphis PCL1606 and B. amyloliquefaciens FZB42

tag: genotype/variation

value: Interaction Mut


title: miRNA_LPS+TMT Replicate Replicate 1

description: miRNA Expression Profile


title: C.difficile 630 Δerm_Spores_a

description: Obtained from A. Shen

organism: Clostridioides difficile 630

source_name: C.difficile 630 Δerm

growth_protocol: C. difficile spores were prepared on 70:30 sporulation media agar plates in an anaerobic chamber as described previously (5).  5. Wang S, Shen A, Setlow P, Li YQ. 2015. Characterization of the dynamic germination of individual Clostridium difficile spores using Raman spectroscopy and differential interference contrast microscopy. J Bacteriol 197:2361-2373

tag: tissue


title: StAgo1-GFP H2O 2

extract_protocol:
Inoculated leaves were harvested and flash frozen in liquid nitrogen. StAGO1a-GFP co-IP were performed with anti-GFP antibody (Chromotek, gtm-100).
Barcoded sequencing libraries were constructed using the Ion Total RNA-Seq Kit v2 and Ion Xpress barcode primers. Sequencing was performed on the Ion Proton platform using the Ion PI™ Hi-Q™ Sequencing 200 Kit (Thermo Fisher Scientific).


title: B. atrophaeus ATCC 9372_Spores_b

organism: Bacillus atrophaeus ATCC 9372

source_name: B. atrophaeus ATCC 9372

value: ATCC 9372


title: Mut5vsPCL1606_1


title: B. atrophaeus ATCC 9372_Spores_a


title: IC_24h_3

status: Public on May 04 2021

city: Salt Lake City

first: Ian

last: Boys

state: Utah

department: Human Genetics

institute: University of Utah

data_processing:
fastp was used to clean reads
HISAT2 was used to map reads
Stringtie was used to predict novel transcripts
Featurecounts was used to quantify mapped reads and convert to RPKM
DEseq2 was used to perform differential expression analysis
Genome_build: xenLae2
Supplementary_files_format_and_content: BAM containing mapped reads
Supplementary_files_format_and_content: BAI containing index for BAM files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Xenopus laevis

source_name: A6 Kidney Cells

growth_protocol: 28°C at 5% CO2 in NCTC 109 media supplemented with 1x L-Glutamine, 15% ddH2O, and 10% FBS

extract_protocol:
Cells were washed once with PBS and RNA was extracted using trizol and Zymo direct-zol columns
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)

treatment_protocol: Cells on a subconfluent 6-well dish were transfected with 2μg poly(I:C) (or mock) using lipofectamine 3000

value: 24 hours poly(I:C)


title: miRNA_LPS Replicate Replicate 2

description: miRNA Expression Profile

value: LPS prime


title: IC_24h_2


title: IC_24h_1


title: IC_12h_2

value: 12 hours poly(I:C)


title: StAgo1-GFP H2O 3


title: miRNA_LPS Replicate Replicate 1

description: miRNA Expression Profile


title: C.difficile 630 Δerm_Spores_b

description: Obtained from A. Shen


title: IC_12h_1


title: IC_6h_3

value: 6 hours poly(I:C)


title: IC_12h_3


title: Mock_2

value: Mock Transfection


title: IC_6h_2


title: Mock_3


title: IC_6h_1


title: Mock_1


title: miRNA_LPS Replicate Replicate 3

description: miRNA Expression Profile

value: bone marrow derived macrophages


title: E13.5_MS116_162

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: Single cell transcriptome of amplified cDNA from mouse embryo at E13.5

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the mouse genome, mm10, or cynomolgus monkey genome, macFas5.0,  and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels (RPM) by cufflinks-2.2.0 using the “—compatible-hits-norm”,  “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and GRC38.p2 reference gene annotations with extended TTSs. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Expression levels (read counts per gene) were also estimated with HTSeq v0.9.1.
Genome_build: mm10
Genome_build: macFas5.0
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include gene name, entrez_id and read count for each Sample

source_name: Mouse fetal ovaies E13.5

extract_protocol: RNA preparation, cDNA synthesis and amplification from single cells were perfomed essentially as reported in [Nakamura et al., Nucleic Acids Res. 2015 43(9):e60]. Library constructions for Illumina System were performed as reported in [Ishikura et.al., Cell Rep. 2016 17(10):3789-2804].

value: fetal ovaries

value: mST


title: E13.5_MS132_246


title: E13.5_MS116_127


title: E13.5_MS132_253


title: E13.5_MS132_255


title: E13.5_MS132_242


title: E11.5_MS116_61

description: Single cell transcriptome of amplified cDNA from mouse embryo at E11.5

source_name: Mouse fetal ovaies E11.5


title: E13.5_MS116_148


title: E11.5_MS127_217


title: E11.5_MS116_45


title: E13.5_MS116_163


title: E11.5_MS132_266


title: E10.5_MS134_100

description: Single cell transcriptome of amplified cDNA from mouse embryo at E10.5

source_name: Mouse female genital ridge E10.5

value: genital ridge


title: E10.5_MS134_84


title: E10.5_MS134_88


title: E9.5_MS133_125

description: Single cell transcriptome of amplified cDNA from mouse embryo at E9.5

source_name: Mouse embryo Wt1+ E9.5

value: embryo

value: mPIM


title: E10.5_MS155_2


title: E9.5_MS133_116


title: E13.5_MS116_143


title: E10.5_MS134_89


title: E10.5_MS155_14


title: E10.5_MS134_104


title: E9.5_MS152_19


title: E9.5_MS134_112


title: E9.5_MS152_13


title: E9.5_MS133_140


title: E9.5_MS152_3


title: E10.5_MS134_101


title: E9.5_MS151_64


title: E9.5_MS133_134


title: E9.5_MS134_105


title: E9.5_MS151_61


title: E9.5_MS152_7


title: E9.5_MS152_6


title: E9.5_MS133_120


title: E9.5_MS133_126


title: E9.5_MS151_63


title: E9.5_MS133_119


title: E9.5_MS133_122


title: E9.5_MS133_114


title: E9.5_MS152_8


title: E9.5_MS134_111


title: E13.5_MS130_215

value: mpGrL


title: E11.5_MS116_72


title: E13.5_MS116_134


title: E11.5_MS116_32


title: E11.5_MS116_60


title: E11.5_MS115_191


title: E9.5_MS152_18


title: E11.5_MS116_31


title: E11.5_MS117_239


title: E9.5_MS133_124


title: E11.5_MS117_237


title: E11.5_MS152_28


title: E11.5_MS127_47


title: E11.5_MS132_209


title: E11.5_MS116_69


title: E11.5_MS116_33


title: E11.5_MS116_49


title: E11.5_MS116_36


title: E11.5_MS116_42


title: E11.5_MS132_268


title: E11.5_MS127_34


title: E11.5_MS127_63


title: E11.5_MS127_40


title: E11.5_MS116_41


title: E11.5_MS132_269


title: E11.5_MS116_66


title: E11.5_MS127_39


title: E11.5_MS115_192


title: E11.5_MS116_57


title: E11.5_MS116_53


title: E11.5_MS116_43

value: mpGrE


title: E11.5_MS152_33


title: E11.5_MS115_184


title: E11.5_MS116_44


title: E11.5_MS130_52


title: E11.5_MS127_51


title: E11.5_MS132_265


title: E11.5_MS115_187


title: E11.5_MS117_240


title: E11.5_MS127_59


title: E11.5_MS116_38


title: E11.5_MS116_35


title: E11.5_MS116_62


title: E11.5_MS116_48


title: E11.5_MS155_52


title: E11.5_MS155_44


title: E11.5_MS155_43


title: E11.5_MS155_39


title: E11.5_MS130_54


title: E11.5_MS116_70


title: E11.5_MS152_25


title: E11.5_MS152_24


title: E11.5_MS155_47


title: E11.5_MS132_208


title: E11.5_MS127_71


title: E11.5_MS152_30


title: E11.5_MS152_31


title: E11.5_MS152_23


title: E11.5_MS155_54


title: E11.5_MS152_34


title: E10.5_MS134_103


title: E10.5_MS134_102


title: E11.5_MS152_35


title: E10.5_MS134_86


title: E10.5_MS134_99


title: E10.5_MS134_90


title: E10.5_MS134_97


title: E10.5_MS134_93


title: E10.5_MS134_85


title: E10.5_MS134_96


title: E10.5_MS134_98


title: E10.5_MS134_95


title: E10.5_MS134_91


title: E9.5_MS133_121

value: mGPCs


title: E11.5_MS155_55


title: E10.5_MS134_94


title: Colon cancer 1N

source_name: Colon

value: Colon

tag: patient

value: Patient 1

tag: sample

value: benign colon tissue adjacent to cancer sample


title: E10.5_MS155_1


title: E10.5_MS134_87


title: E10.5_MS134_81


title: E10.5_MS155_10


title: E10.5_MS134_83


title: E10.5_MS134_82


title: AB6711

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
read2 used to read cell and molecule barcodes only; Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Meta data file associating each single cell with its amplification batch and index sorting readouts

molecule: polyA RNA

source_name: Blood

growth_protocol: 6 to 8 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
Mice were euthanized and auricular LNs were disected. Lymph nodes were digested in IMDM containing 100µg/mL Liberase TL and 100µg/mL DNase I for 20 minutes at 37°C. In the last 5 minutes of incubation, EDTA was added at a final concentration of 10mM. Cells were collected, filtered through a 70µm cell strainer, washed with IMDM and maintained strictly at 4°C. Cells were stained with FACS antibodies, then sorted into 384-well plates
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}
single cell RNA-seq for gene expression quantitation

treatment_protocol:
treatment protocol (1):  Mice were anesthetized and the indicated inactivated pathogens were administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals.
treatment protocol (2):  mice were treated with depleting or neutralizing antibodies or their isotype controls: Anti-NK1.1 (200 µg/dose), anti-IFNγ (500 µg/dose), Mouse IgG2a Isotype control and Rat IgG1 Isotype control were injected 24 hours prior to immunization and on the day of immunization

value: Blood

value: NK/Ilc1 cells

tag: selection marker

tag: time point

value: 8 Weeks

tag: mouse age

value: 8 weeks


title: E10.5_MS155_9

tag: cell type


title: E10.5_MS155_8

tag: developmental stage


title: AB6710

tag: strain


title: AB6709


title: AB6708


title: AB6706


title: AB6705


title: E9.5_MS152_1


title: AB6703


title: E10.5_MS134_92


title: AB6704


title: AB6702


title: AB6662


title: AB6660


title: AB6661


title: AB6115


title: AB6113


title: AB6112


title: AB6111


title: AB6110


title: AB6109


title: AB6023


title: AB6108


title: AB6021

value: CpG


title: AB6107


title: AB6022


title: AB5991

source_name: LP

value: LP


title: AB5992


title: AB5990


title: AB6707


title: AB5989


title: AB5988


title: AB5986


title: AB5983


title: AB5985


title: AB5918


title: AB5984


title: AB6020


title: AB6114


title: AB5917


title: AB5915


title: AB5914


title: AB5913


title: AB5891


title: AB5889


title: AB5887


title: AB5886


title: AB5987


title: AB5883


title: AB5884


title: AB5881


title: AB5890


title: AB5885


title: AB5882


title: AB5879


title: AB5836

source_name: Lymph node

value: Lymph node


title: AB5835


title: AB5916


title: AB5834


title: AB5833


title: AB5827

source_name: SG

value: SG


title: AB5832


title: AB5824


title: AB5825


title: AB5820

source_name: IEL

value: IEL


title: AB5821


title: AB5823


title: AB5818


title: AB5819


title: AB5822


title: AB5888


title: AB5724

source_name: uterus

value: uterus


title: AB5880


title: AB5721


title: AB5720


title: AB5718

source_name: Spleen

value: Spleen


title: AB5716


title: AB5678

source_name: VAT

value: VAT


title: AB5715


title: AB5677


title: AB5826


title: AB5676


title: AB5675


title: AB5673

source_name: Liver

value: Liver


title: AB5672


title: AB5817


title: AB5671


title: AB5674


title: AB5670


title: AB5669


title: AB5723


title: AB5243


title: AB5241


title: AB5242


title: AB5722


title: AB4984

source_name: LN

value: LN


title: AB4985


title: AB4983


title: AB4982


title: AB5719


title: AB5717


title: AB4981


title: AB4980

source_name: LPL

value: LPL


title: AB4978

source_name: Uterus

value: Uterus


title: AB4906


title: AB4903


title: AB4904


title: AB5668


title: AB4803


title: AB4902


title: AB4801


title: AB4800


title: AB4799


title: AB4986


title: AB4802


title: AB4796


title: AB4797


title: AB4798


title: AB4795


title: AB4528


title: AB4527


title: AB4517


title: AB3911


title: AB4720


title: AB4526


title: AB4977


title: AB4518


title: AB3912


title: AB4979


title: AB4905


title: AB3876


title: AB3875


title: RH4 - H3K9ac ChIP

city: Colum bus

first: Stephanie

middle: D

last: LaHaye

state: OH

address: 575 Children's Crossroads

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description:
paired-end, 150 bp
SEG0126

data_processing:
Initial ChIP-seq Alignment: bowtie2 was used to align reads separately to hg38 and mm10.
ChIP-seq Normalization: For PAX3-FOXO1/FOXO1 ChIP and Input samples, sequencing depth was normalized by first using samtools to determine the number of reads aligning to mm10. A scaling factor (f) was determined for each sample by defining the minimum number of mouse reads across all samples (m), and dividing this by the number of mouse reads in a given sample (s), f=m/s. Scaling factors for each sample were used to normalize hg38 aligned BAM files through subsampling with samtools. Picard SamToFastq converted the resulting SAM files to normalized paired-end fastq files.
All ChIP data were subsequently processed with ENCODE ChIP-seq pipeline with chip.xcor_exclusion_range_max set at 30
ENCODE ChIP-seq alignment: normalized paired-end fastqs were aligned with bowtie2 aligner (version 2.3.4.3) to human genome UCSC hg38, with parameters bowtie2 -X2000 --mm
ENCODE ChIP-seq read filtering: black listed region, unmapped, mate unmapped, not primary alignment, multi-mapped, low mapping quality (MAPQ<30), duplicate reads and PCR duplicate were removed
ENCODE ChIP-seq peak calling: Peaks were called with MACS2 (version 2.2.4), with parameters -p 1e-2 --nomodel --shift 0 --extsize ${FRAGLEN} --keep-dup all -B –SPMR. IDR analyses were performed on peaks from replicate samples, with threshold 0.05
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: bigwig files, signals represent fold change over Input

growth_protocol: RH4 and C2C12 were grown in DMEM supplemented with 10% FBS. Parental Dbt and Dbt/iP3F cells were grown in Ham’s/F-10 supplemented with 15% FBS, glutamine, sodium pyruvate, creatine monohydrate, and uridine.

extract_protocol:
For spike-in normalized ChIP-seq, human RMS cells and mouse C2C12 cells were fixed in 1% formaldehyde for 10 minutes before quenching with 125 mM glycine. Cells were combined in a ratio of 3 human:1 mouse cell equivalents for each experiment prior to sonication. Sonicated chromatin was immunoprecipitated with antibodies against FOXO1 (Cell Signaling #2880), H3K27ac (Active Motif #39133), H3K27me3 (Active Motif #39155), BRD9 (Abcam ab137245), or DPF2 (Abcam ab134942). Input and ChIP-enriched DNA was decrosslinked and purified using Qiagen MinElute PCR Purification columns prior to library preparation. For ATAC-seq, 5x10^4 cells per experiment were first washed with RSB buffer and gently permeabilized with RSB lysis buffer on ice. Cells were suspended in 50 uL of tagmentation master mix prepared from Illumina Tagment DNA TDE1 Enzyme and Buffer Kit components (#20034197), and transposition was performed for 30 minutes at 37°C. Tagmented DNA fragments were isolated using Qiagen MinElute PCR Purification columns prior to library preparation.
H3K9ac ChIP and Input DNA libraries were prepared by blunt end repair using the Lucigen End-It DNA End-Repair Kit, 3’ A-tailing by Klenow fragment (3’-5’ exo-) (NEB), adaptor ligation by T4 DNA ligase (NEB), and size selection on an E-Gel 2% EX agarose gel. For H3K9me3 ChIP and Input libraries, decrosslinked and purified DNA samples were sonicated for 3 minutes prior to library construction/amplification, and no size-selection was performed. Libraries were amplified with barcoded primers for 14 cycles and isolated from unreacted primers by gel purification. Libraries were sequenced on the HiSeq4000 platform running in PEx150bp mode.

value: FP-RMS

tag: antibody


title: RH4 - Input - rep4

description:
paired-end, 150 bp
Input sample for H3K9ac ChIP
SEG0125


title: HsD2-2

city: Redwood City

first: Xu

last: Shi

state: CA

address: 1500 Seaport Blvd

institute: AbbVie Inc.

description: CITE-Seq

data_processing:
Cellranger for data preprocessing
Genome_build: GRCh38

source_name: PBMC

growth_protocol: Peripheral whole blood was harvested in K2 EDTA tubes.  PBMC were separated from whole blood by density gradient centrifugation using Ficoll-Paque (GE Healthcare) and Leucosep tubes (Greiner Bio-One GmbH) according to manufacturer’s protocol (MACS Miltenyi Biotec GmbH).  After PBMC isolation, cells were either stimulated with antibodies or rested overnight prior to COMP fusion protein/FACS staining.  For antibody stimulations, fresh PBMC were incubated with 20ug/mL of antibody overnight prior to harvest and FACS staining.  THP-1 cells were cultured in RPM-based media at a density ~2.5x105/mL prior to 5ng/mL PMA stimulation where indicated.  After 48 hours, cells were detached with enzyme-free dissociation buffer prior to FACS staining protocol.

extract_protocol: none provided by the submitter

treatment_protocol:
anti-VISTA treatment
CITE-Seq

value: immune cells

value: untreated


title: HsD3-1

description: CITE-Seq


title: HsD3-2

description: CITE-Seq


title: HsD2-3

description: CITE-Seq

value: treated with anti-VISTA


title: AB4721

value: NK/Ilc1 cells

value: 8 Weeks

value: 8 weeks


title: HsD2-4

description: CITE-Seq


title: HsD2-1

description: CITE-Seq


title: RH4 - H3K9me3 ChIP

description:
paired-end, 150 bp
SEG0117

value: Active Motif #39062


title: HsD1-3

description: CITE-Seq


title: HsD1-4

description: CITE-Seq


title: HsD1-2

description: CITE-Seq


title: RH4 - Input - rep3

description:
paired-end, 150 bp
Input sample for H3K9me3 ChIP
SEG0116


title: HsD3-4

description: CITE-Seq


title: Sorted cells-Rep1

city: Dallas

first: Nicholas

middle: K

last: Conrad

state: TX

address: 6000 Harry Hines Blvd

department: Microbiology

institute: UT Southwestern Medical Center

description:
Lentiviral sgRNA sequencing
sort2

data_processing:
Library strategy: CRISPR screen
Three independent biological replicates were sequenced on an Illumina NextSeq 500 with read configuration as 75bp, single end
The fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen), and adapters trimmed using an in-house script.
The trimmed fastq files were mapped to Brunello library sequence (Doench et al. 2016; Addgene #73179) with mismatch option as 0 using MAGeCK (Li et al., 2014)
Further, read counts for each sgRNA were generated and median normalization was performed to adjust for library sizes. Positively and negatively selected sgRNA and genes were identified using the default parameters of MAGeCK.
Genome_build: n/a; seqences aligned to Brunello (Doench et al. 2016; Addgene #73179)
Supplementary_files_format_and_content: The processed files for the analysis performed using the three combined biological replicates (called "triplicate" in Scarborough et al). These are found in two .txt output files from MAGeCK; one file is the gene summary and the other is the sgRNA summary.

source_name: Brunello Lentiviral library

growth_protocol: An HCT116-derived clonal line that expressses the GFP-MAT2A detained intron reporter was infected with 100X coverage of the Brunello library. After two days puromycin was added and cells were selected for an additional 7 days. Thus, cells were sorted 9 days after transduction. The day prior to sorting/harvesting, cells were placed in methionine-free media to induce GFP expression.

extract_protocol:
DNA was extracted using phenol:chloroform:iso-amyl alcohol method. See Scarborough et al 2021 for details.
Library amplification was completed following a two-step variation of the BROAD institute protocol (BROAD Institute PCR of sgRNAs for Illumina sequencing). The two step variation of the BROAD institute protocol consists of an initial amplification step using primers flanking the P5 and P7 primers used for sequencing.

treatment_protocol: Cells were sorted using FACS and the lowest 1%GFP expressing cells were selected as the "sort" samples. Inputs were not subject to sorting.

tag: gfp sorting

value: These were sequenced from cells that were sorted for low GFP signal after 9 days of lentiviral infection and selection with puromycin


title: Sorted cells-Rep3

description:
Lentiviral sgRNA sequencing
sort4


title: HsD3-3

description: CITE-Seq

tag: treatment


title: Unselected cells-Rep2

description:
Lentiviral sgRNA sequencing
input3

value: These were sequenced from cells without GFP sorting cells after 9 days of lentiviral infection and selection with puromycin


title: RNA_CD3Tcells_48

city: Atlanta

first: Rafick-Pierre

last: Sekaly

state: GA

address: 1750 Haygood Drive

institute: Emory University

description:
RNASeq
Uganda_Longitudinal_Normalized_Corrected_expression_counts.xlsx

data_processing:
sorted cells/plasma: Raw sequencing reads were trimmed off adapter sequence contaminants using Trimmomatic v. 0.36
sorted cells/plasma: Mapped onto the Refseq Grch38 of the human genome using the STAR RNA-Seq aligner (version 2.5.3a)
sorted cells: Gene abundance was then estimated by counting using HTSeq (version 0.9.1)
sorted cells: Transcript counts were then normalized by TMM (Trimmed Mean of M-values by correcting for the library size
plasma: Unaligned paired-end reads were then assembled into contigs using Trinity
plasma: Trinity contigs were then aligned against HG38 again to further remove host-derived sequences with BLAST+. Trinity contigs that aligned to non-reference human sequences in the NCBI nucleotide database were also removed
plasma: Remaining contigs were then aligned against the NCBI nucleotide database and quantified with Salmon
plasma: Taxonomic information was assigned for each contig and transcripts per million (TPM) values were collapsed at the species level for each sample. TPM are normalized for sequencing read depth and length for each sample, allowing for a more accurate comparisons between proportion of reads mapping to the same gene in various samples
Genome_build: Human (Refseq Grch38) and Non-human (NCBI nucleotide database and quantified with Salmon)
Supplementary_files_format_and_content: xlsx data matrix files with normalized read counts (sorted cells; sample by transcript) or TPM (plasma; sample by species abundance)

source_name: Sorted Tcells

extract_protocol:
sorted cells: RNA was extracted from sorted cells lysed in RNAzol RT (MRC Inc., OH, USA), according to the manufacturer’s instructions. Briefly, 0.4 volume of sterile water was added to each lysate to allow aqueous and organic phase separation. Total RNA was then extracted from the aqueous phase by isopropanol precipitation. RNA pellets were washed with 70% ethanol and resuspended in sterile water. Extracted RNA was stored at -80°C until preparation of mRNA libraries. RNA yield and integrity were verified by microelectrophoresis using the High Sensitivity RNA ScreenTape Kit (Agilent) on the 2200 TapeStation system (Agilent).
plasma: Circulating total RNA and DNA were isolated from frozen plasma using RNAzolBD (MRC) according to the manufacturer’s recommendations.
sorted cells: mRNA libraries were constructed as described previously (Sandler et al., 2014) using the NEBNext Ultra RNA library preparation kit. Polyadenylated transcripts were purified with oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers and incorporated into barcoded cDNA libraries based on the Illumina TruSeq platform. Libraries were validated by microelectrophoresis on a 2100 Bioanalyzer system (Agilent), quantified with Kapa Library Quantification Kits (Roche), pooled and clustered on Illumina TruSeq v2 flow cells. Clustered flow cells were sequenced in 2x75 base paired-end runs on Illumina HiSeq 2000 and HiSeq 4000.
plasma: RNA fragmentation and reverse transcription using random hexamers, the obtained transcripts, as well as the isolated plasma DNA, were individually incorporated into barcoded cDNA libraries on the basis of the Illumina TruSeq platform. Libraries were validated by microelectrophoresis on a 2100 Bioanalyzer system (Agilent), quantified using Kapa Library Quantification Kits (Roche), pooled and clustered on Illumina patterned flow cells. Clustered flow cells were sequenced on an Illumina HiSeq 4000 in 75-base paired reads. To control for contamination, four water samples were processed along with plasma samples from nucleic acids extraction through sequencing.

value: Sorted Tcells

value: Uganda

tag: cd4 count

tag: cd8 count

value: cd8 t cell ratio:Data_in_Manuscript

value: Yes

value: Post_ART_HIV_subject (24months on ART)


title: RNA_CD3Tcells_40


title: RNA_CD3Tcells_64


title: RNA_CD3Tcells_96

value: No


title: RNA_CD3Tcells_80


title: RNA_CD3Tcells_88


title: RNA_CD3Tcells_72


title: RNA_CD3Tcells_56


title: Unselected cells-Rep3

description:
Lentiviral sgRNA sequencing
input4


title: Sorted cells-Rep2

description:
Lentiviral sgRNA sequencing
sort3


title: Unselected cells-Rep1

description:
Lentiviral sgRNA sequencing
input2


title: FLAG_PFDN5_input_rep2

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

institute: CABIMER

description: Replicate 2

data_processing:
Two biological replicates of the ChIP-seq data for each condition were primarily filtered using the FASTQ Toolkit program. Data were aligned using align function from Rsubread package, to map reads to the hg19 human reference genome using type = 1, TH1 = 2 and unique = TRUE parameters.
The downstream analysis was performed on bamfiles with duplicates removed using the samtools rmdup command
Bigwig files were created on Flag-PFDN5 over Flag for each replicate using bamCompare from deeptools package (v3.1.3) with --scaleFactorsMethod readCount --operation log2 parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

growth_protocol: Human HCT166 cells were maintained in McCoy's 5A modified medium supplemented with 10 % foetal bovine serum, 60 mg/l penicillin, and 100 mg/l streptomycin

extract_protocol: Human chromatin immunoprecipitation was carried out by fixation (10 minutes, 1 % formaldehyde, 37 ºC) and quenching (5 minutes, 2 % glycine), cells were lysed in lysis buffer (50 mM Tris-HCl, 10 mM EDTA, 1% SDS, pH 8.1 and protease inhibitors). Samples were then sonicated (Bioruptor, Diagenode) with cycles of 30 seconds for 15 minutes and the extracts of 300 bp obtained were cleared by centrifugation. Sonicated chromatin were incubated with 50 µl of magnetic dynabeads protein A o G (Life technology) coupled to anti-FLAG (Sigma, F3165, ChIP) antibody-.  Immunoprecipitated material was washed with three different wash buffers (wash buffer 1: 0.1 % (w/v) SDS; 1 % (v/v) Triton-X100; 2 mM EDTA; 20 mM Tris-HCl pH 8; 150 mM NaCl. Wash buffer 2: 0.1 % (w/v) SDS; 1 % (v/v) Triton-X100; 2 mM EDTA; 20 mM Tris-HCl pH 8; 500 mM NaCl. Wash buffer 3: 0.25 M LiCl; 1 % (v/v) NP-40; 1 % (w/v) Sodium deoxicholate; 1 mM EDTA; 10 mM Tris-HCl pH 8) and TE (10 mM Tris-HCl pH 8; 1 mM EDTA). DNA was eluted using elution buffer (1 % (w/v) SDS; 0.1 M NaHCO3) and, treated with 5 µl proteinase K (20 mg/ml) for 1 hour at 37 ºC. The resultant DNA was fenol-chloroform extracted, and precipitated.

tag: cell line

tag: expression

tag: condition

value: input


title: FLAG_input_rep2

description: Replicate 2

value: Flag


title: FLAG_PFDN5_rep2

description:
Replicate 2
flag_pfdn5_flag_log2_readCount_r2.bw

value: ChIP


title: RNA_CD3Tcells_16

tag: tissue


title: FLAG_rep2

description: Replicate 2


title: RNA_CD3T_RAL16_Mo3

value: Post_ART_HIV_subject (3months on ART)


title: RNA_CD3T_RAL15_Mo3


title: RNA_CD3Tcells_8


title: U20S_siDDX41_RNA-seq_5

city: Mainz

first: Petra

last: Beli

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology (IMB)

data_processing:
Basecalling was done using RTA v 2.4.11. Demultiplexing was done using bcl2fastq v. 2.19.
Samples were mapped using STAR (v2.7) against hg38 with the Gencode annotation (v25) as gene reference.
Reads per gene were counted using Subread/featureCounts ( v.1.6).
Sequencing depth normalised tracks were created using Deeptools (v3.4.1).
Genome_build: hg38
Supplementary_files_format_and_content: sequencing depth normalised bigwig files; read counts per gene (tab separated value file)

source_name: U20S_DDX41 knockdown

growth_protocol: U2OS cells were cultured in DMEM containing 10% FBS, Pen-Strep,1% Glutamine

extract_protocol:
RNA extraction was performed using Qiagen Rneasy Plus mini kit.
NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following TruSeq Stranded mRNA Reference Guide (Oct.2017) (Document # 1000000040498v00). Libraries were prepared with a starting amount of 1000 ng and amplified in 10 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer (Agilent Technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life Technologies).

treatment_protocol: Knockdowns were induced for 48 hourse using pool siRNAs.

value: DDX41 knockdown

tag: replicate


title: U20S_siDDX41_RNA-seq_4


title: U20S_siDDX41_RNA-seq_3


title: RNA_CD3T_RAL15_D0


title: RNA_CD3T_RAL14_D0


title: U20S_siDDX41_RNA-seq_2


title: U20S_siDDX41_RNA-seq_1


title: RNA_CD3T_RAL14_Mo3


title: RNA_CD3T_RAL11_D0


title: RNA_CD3T_RAL11_Mo3


title: RNA_CD3T_RAL13_Mo3


title: RNA_CD3T_RAL12_Mo3


title: RNA_CD3T_RAL13_D0


title: RNA_CD3Tcells_32


title: U20S_siCtrl_RNA-seq_3

source_name: U20S_control knockdown

value: control knockdown


title: U20S_siCtrl_RNA-seq_5


title: RNA_CD3Tcells_24


title: RNA_CD3T_RAL10_D0


title: U20S_siCtrl_RNA-seq_4


title: RNA_CD3T_RAL10_Mo3


title: U20S_siCtrl_RNA-seq_2


title: RNA_CD3T_RAL08_Mo3


title: U20S_siCtrl_RNA-seq_1


title: RNA_CD3T_RAL08_D0


title: RNA_CD3T_RAL07_D0


title: RNA_CD3T_RAL12_D0


title: RNA_CD3T_RAL03_Mo3


title: RNA_CD3T_RAL16_Mo12

value: Post_ART_HIV_subject (12months on ART)


title: RNA_CD3T_RAL15_Mo12


title: RNA_CD3T_RAL03_D0


title: RNA_CD3T_RAL13_Mo12


title: RNA_CD3T_RAL12_Mo12


title: RNA_CD3T_RAL14_Mo12


title: Cells from Smoker COPD transduced with non-targeting sequence, biological rep3

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description: Gene expression data from  Smoker COPD transduced with non-targeting sequence

hyb_protocol: 2.5μg of labelled cDNA were used to prepare an hybridization cocktail to perform Affymetrix human Gene 2.1 ST hybridization. All steps including microarray 4C robotics, as recommended by the manufacturer.hybridization, washes, staining and scanning were achieved using the Affymetrix GeneTitan 4C robotics, as recommended by the manufacturer.

scan_protocol: raw data were collected using the GeneTitan 4C system.

data_processing: raw data were process with the Affymetrix Expression Console software to control and normalize data. A GC-RMA normalization war carried out based on Affymetrix settings (Plier algorithm taking into account GC content).

source_name: Basal epithelial Cells  from Smoker COPD control knockdown

label_protocol: 100ng of total RNA were amplified according to Affymetrix WT Target preparation kit. 5.5μg of Sens DNA were labelled according to the manufacturer recommendations.

growth_protocol: Primary bronchial epithelial cells were transduced with lentiviral particules containing shRNA with SNAI2 specific or non-targetting sequence on Transwell cell culture inserts  with a polyethylene (PET) membrane and 0.4 μm pores.

extract_protocol: Extraction of total RNA was performed using the NucleoSpin RNA Kit (Macherey-Nagel) according to the manufacturer's instructions.

treatment_protocol: After 4 days,Transduced cells were put in ALI condition (by removing the medium at the top of the culture)  and further cultured for 2 days.

tag: patient diagnosis

value: COPD

value: Primary bronchial epithelial basal cells

tag: passage

tag: genotype


title: Cells from Smoker non-COPD transduced with non-targeting sequence, biological rep2

description: Gene expression data from  Smoker non-COPD transduced with non-targeting sequence

source_name: Basal epithelial Cells  from Smoker non-COPD control knockdown

value: non-COPD


title: Cells from Smoker COPD transduced with non-targeting sequence, biological rep2


title: Cells from Smoker COPD transduced with SNAI2 specific sequence, biological rep2

description: Gene expression data from  Smoker COPD transduced with SNAI2 specific sequence

source_name: Basal epithelial Cells  from Smoker COPD SNAI2 knockdown

value: SNAI2 knockdown


title: RNA_CD3T_RAL10_Mo12

value: Sorted Tcells


title: Cells from Smoker non-COPD transduced with non-targeting sequence, biological rep3


title: Cells from Smoker non-COPD transduced with non-targeting sequence, biological rep1


title: RNA_CD3T_RAL11_Mo12

value: Uganda


title: Cells from Smoker COPD transduced with SNAI2 specific sequence, biological rep1


title: Cells from Smoker non-COPD transduced with SNAI2 specific sequence, biological rep1

description: Gene expression data from  Smoker non-COPD transduced with SNAI2 specific sequence

source_name: Basal epithelial Cells  from Smoker non-COPD SNAI2 knockdown


title: RNA_CD3T_RAL08_Mo12

value: cd8 t cell ratio:Data_in_Manuscript


title: Cells from Smoker COPD transduced with non-targeting sequence, biological rep1


title: Cells from Smoker non-COPD transduced with SNAI2 specific sequence, biological rep2


title: RNA_CD3T_RAL07_Mo12

value: Yes


title: RNA_CD3T_RAL04_Mo12


title: RNA_CD3T_RAL03_Mo12


title: dd-2_r1

city: Austin

first: Wei

last: Zong

state: Texas

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Raw reads wer mapped to the TAIR10 Arabidopsis genome using HISAT2 with default parameters
Featurecount was used to count read numbers of each gene
edgeR was used to identify differentially expressed genes
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values  of each gene for each sample

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: For seed germination, seeds were sterilized and then stratified for 3 days at 4 ℃ under dark condition; seeds were germinated on 1/2 Murashige and Skoog (MS) plates containing 0.8% Phytagel. Seedlings were grown in growth chamber with 16-h light/8-h dark cycles at 22℃.

extract_protocol:
Total RNA was isolaed from 7-day-old seedlings using Purelink Plant RNA Regent (Invitrogen) according to manufacturer's instructions.
RNA-Seq libraries were prepared by NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (E7420) according to the manufacturer’s instructions.

value: dek3-2 dek4-2 double mutant

tag: age

value: 7 days old

value: whole seedling


title: dek4-2_r2

value: dek4-2 mutant


title: PC9DR wth Dacomitinib 3

first: Yosef

last: Yarden

address: Herzl St 234

department: Biological Regulation

description: Treated with increasing concentration of dacomitinib (from 1 pM to 100 nM) for 6 months

data_processing:
Data filtering: cutadapt
Read alignment software: STAR
Abundance measurement: HTSeq-count
Genome_build: Homo sapiens (human) genome assembly GRCh38 (hg38)
Quantification: DESeq2
Supplementary_files_format_and_content: DESEq2 output file

source_name: PC9 ATCC cell line

growth_protocol: Cell were grown in a 37 degree incubator under 5% CO2.

extract_protocol:
QIAGEN miRNeasy Mini Kit
Libraries for RNA-seq were prepared using a modified version of TranSeq, as described (Jaitin et al., 2014). Briefly, RNA was reversed transcribed with MARS-seq barcoded RT primers in a 10 µl volume with the Affinity Script kit (Agilent). Reverse transcription was analyzed by qRT-PCR and samples with a similar CT were pooled (up to eight samples per pool). Each pool was treated with Exonuclease I (NEB) for 30 min at 37°C and cleaned by 1.2× volumes of SPRI beads (Beckman Coulter). Next, the cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20 ml reaction, incubating for 2 h at 16 °C. The product was purified with 1.4× volumes of SPRI beads, eluted in 8 µl and in vitro transcribed (with the beads) at 37 °C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37 °C and the amplified RNA (aRNA) purified with 1.2 volumes of SPRI beads. The aRNA was fragmented by incubating min at 70 °C in Zn 621 2+ RNA fragmentation reagents (Ambion) and purified with 2× volumes of SPRI beads. The aRNA was ligated to the MARS-seq ligation adapter with T4 RNA Ligase I (NEB).  The reaction was incubated at 22 °C for 2 h. After 1.5× SPRI cleanup, the ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent) and a primer complementary to the ligated adapter. The reaction was  incubated for 2 min at 42°C, 45 min at 50°C, and 5 min at 85°C. The cDNA was purified with 1.5× volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5 mM of P5_Rd1 and P7_Rd2 primers and PCR ready mix  (Kappa Biosystems). The amplified pooled library was purified with 0.7× volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a TapeStation instrument. RNA-seq libraries were sequenced using the Illumina NextSeq® 500 High Output v2 Kit (75 cycles).

treatment_protocol: Parental PC9 cells were treated with increasing concentration of dacomitinib (from 1 pM to 100 nM) for 6 months.

tag: cell type

value: Dacomitinib (100 nM)

value: non-small cell lung cancer

tag: phenotype

value: Dacomitinib resistant


title: dek4-2_r1


title: PC9DR wth Dacomitinib 2


title: dd-2_r2


title: dek3-2_r2

value: dek3-2 mutant


title: d6_T2-C6: Cells from Smoker COPD at d6 with TGFb, biological rep3

description: Gene expression data from Smoker COPD at d6 ALI with TGFb, on-set of differentiation

source_name: Basal epithelial Cells from Smoker COPD at d6 with TGFb

growth_protocol: Primary bronchial epithelial cells were plated at a density of 1.5 x 105 / cm2 on Transwell cell culture inserts  with a polyethylene (PET) membrane and 0.4 μm pores and cultured for 3 days (d0 ALI)

treatment_protocol: For on-set of differentiation condition, cells were put in ALI condition by removing the medium at the top of the culture and further cultured for 6 days in absence or presence of TGFb at 1ng/ml.

tag: status

value: Cells at d6 ALI with TGFb, on-set of differentiation


title: RNA_C306L3I9

source_name: Sorted NK

value: Sorted NK

value: Post_ART_HIV_subject (3months on ART)


title: RNA_C306L2I9


title: RNA_C306L3I8


title: dek3-2_r1


title: PC9DR wth Dacomitinib 1


title: Col-0_r2

value: wild type


title: Col-0_r1


title: Parental PC9 3

description: Parental PC9 cells

value: Untreated


title: d6_T2-C2: Cells from Smoker COPD at d6 with TGFb, biological rep2

value: Primary bronchial epithelial basal cells


title: Cells from Smoker non-COPD transduced with SNAI2 specific sequence, biological rep3

value: non-COPD

value: SNAI2 knockdown


title: d6_T2-B6: Cells from Smoker non-COPD at d6 with TGFb, biological rep3

description: Gene expression data from Smoker non-COPD at d6 ALI with TGFb, on-set of differentiation

source_name: Basal epithelial Cells from Smoker non-COPD at d6 with TGFb


title: Cells from Smoker COPD transduced with SNAI2 specific sequence, biological rep3

value: COPD


title: RNA_C306L2I27

value: Uganda

value: cd8 t cell ratio:Data_in_Manuscript

value: Yes


title: d6_T2-B4: Cells from Smoker non-COPD at d6 with TGFb, biological rep2


title: d6_T1-C1: Cells from Smoker COPD at d6, biological rep1

description: Gene expression data from Smoker COPD at d6 ALI, on-set of differentiation

source_name: Basal epithelial Cells from Smoker COPD at d6

value: Cells at d6 ALI, on-set of differentiation


title: d0_T1-B2: Cells from Smoker non-COPD at d0, biological rep1

description: Gene expression data from Smoker non-COPD at d0 ALI, undifferentiated

source_name: Basal epithelial Cells from Smoker non-COPD at d0

value: Cells at d0 ALI, undifferentiated


title: d6_T2-B2: Cells from Smoker non-COPD at d6 with TGFb, biological rep1


title: d0_T1-B4: Cells from Smoker non-COPD at d0, biological rep2


title: RNA_C306L2I25


title: d6_T1-B2: Cells from Smoker non-COPD at d6, biological rep1

description: Gene expression data from Smoker non-COPD at d6 ALI, on-set of differentiation

source_name: Basal epithelial Cells from Smoker non-COPD at d6


title: Parental PC9 2

description: Parental PC9 cells

value: non-small cell lung cancer


title: d6_T1-C2: Cells from Smoker COPD at d6, biological rep2


title: d6_T1-C6: Cells from Smoker COPD at d6, biological rep3


title: d0_T1-C1: Cells from Smoker COPD at d0, biological rep1

description: Gene expression data from Smoker COPD at d0 ALI, undifferentiated

source_name: Basal epithelial Cells from Smoker COPD at d0


title: d6_T2-C1: Cells from Smoker COPD at d6 with TGFb, biological rep1


title: d6_T1-B4: Cells from Smoker non-COPD at d6, biological rep2


title: d6_T1-B6: Cells from Smoker non-COPD at d6, biological rep3


title: d0_T1-B6: Cells from Smoker non-COPD at d0, biological rep3


title: d0_T1-C6: Cells from Smoker COPD at d0, biological rep3


title: RNA_C306L2I23


title: Glu_JG207-1

city: Tianjin

first: Jingen

last: Li

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Myceliophthora thermophila ATCC 42464 genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p2).
Genome_build: Myceliophthora thermophila ATCC 42464(https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html)
Supplementary_files_format_and_content: tab-delimited text files including Reads count for each sample.

organism: Thermothelomyces thermophilus

source_name: Myceliophthora thermophila JG207

growth_protocol: Mycelia for RNA isolation were harvested from malate production medium after 2 of cultivation.

extract_protocol:
Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The culture (50 mL) was filter with vacuum filtration and transferred into 100 mL RNAlater in 250 mL Erlenmeyer flask. After mixed, mycelia were collected by filtration, immediately homogenized in liquid nitrogen and stored at −80 °C until used for RNA extraction.

tag: strain

value: strain

tag: growth condition

value: Glucose condition


title: Glu_JG207-2


title: Glu_WT-2

source_name: Myceliophthora thermophila ATCC 42464


title: d0_T1-C2: Cells from Smoker COPD at d0, biological rep2


title: Parental PC9 1

description: Parental PC9 cells

tag: treatment


title: Glu_WT-1


title: Avi_JG336-2

source_name: Myceliophthora thermophila JG336

value: Avicel condition


title: HsD1-1

description: CITE-Seq

source_name: PBMC

value: immune cells

value: untreated


title: Sub-screen_Set3_GFP_positive

first: Travis

last: Hinson

state: Connecticut

address: 10 Discovery Dr

institute: JAX-GM

data_processing:
Library strategy: CRISPR screen
alignment to gRNA library and count generation
normalization to non-targeting
Mageck gRNA enrichment analysis
Genome_build: hg38
Supplementary_files_format_and_content: Excel file from Mageck output

source_name: iPSC-CMs (cardiomyocytes)

extract_protocol:
Qiagen DNeasy
Broad Institute’s Genetic Perturbation Platform

value: Day 25

tag: background

value: iPSC-CMs (cardiomyocytes)

tag: ploidy


title: Sub-screen_Set3_4n_plus


title: RNA_C306L2I12

value: Sorted NK

tag: cd4 count

tag: cd8 count

value: Post_ART_HIV_subject (3months on ART)


title: Avi_JG207-3


title: Avi_JG207Ncclr2-2

source_name: Myceliophthora thermophila JG207Ncclr2


title: Avi_JG207Ncclr2-1


title: Sub-screen_Set3_4n_C


title: RNA_C306L2I11


title: Avi_JG207-1


title: RNA_C306L2I10


title: Sub-screen_Set3_4n_B


title: Avi_JG207-2


title: Avi_JG141-1

source_name: Myceliophthora thermophila JG141


title: Avi_WT-2


title: RNA_NK_61

value: Post_ART_HIV_subject (24months on ART)


title: Avi_WT-1


title: RNA_NK_69


title: Avi_JG141-2


title: Sub-screen_Set3_4n_A


title: Sub-screen_Set3_2n_C


title: P. inhibens, eDNA treatment, Replicate C

city: Oldenburg

first: Laura

last: Wolter

state: Deutschland

address: Carl-von-Ossietzky str. 9-11

department: Institute for Chemistry and Biology of the Marine Environment

institute: Carl-von-Ossietzky University Oldenburg

data_processing:
The demultiplexed raw fastq-files were quality-controlled using the FASTQ-mcf suite (https://github.com/ExpressionAnalysis/ea-utils). Low quality bases (Phred-score < 30) and Illumina adaptors were clipped. Reads were mapped to the reference genome using bowtie2 (Langmead et al., 2012) with default parameters for single end reads. Ambiguously mapping reads were randomly distributed between all regions to which they could be assigned. The resulting sam-files were converted to indexed binary format and pile-up format using samtools (Li et al., 2009). The program featureCounts (Liao et al., 2014) was used to count the reads mapping to genes.
Genome_build: NC_018290.1, NC_018291.1 NC_018288.1, NC_018287.1
Supplementary_files_format_and_content: tab-delimited text file contains reads per gene

organism: Phaeobacter inhibens DSM 17395

source_name: P. inhibens_eDNA treatment

growth_protocol: P. inhibens cultivated in chemotaxis medium

extract_protocol:
For isolation and purification the RNeasy-kit (Qiagen) was used according to the manufacturer’s manual. Modifications are listed below. Cells lysis was performed enzymatically using 15 mg/mL lysozyme in Tris-EDTA-buffer (ph 8.0) and mechanically by vortexing for 3 min with acid washed glass beads. A first digestion of genomic DNA was performed on the column, using RNase-free DNase I (Qiagen) according to the manufacturer’s protocol. Total RNA was eluted in 88 µL RNase-free H2O and a second DNase I-digestion of genomic DNA was performed in solution, followed by a second RNeasy purification step. In this second purification an additional washing step with 80 % ethanol was performed prior to elution with 30µl RNase-free water. The concentration of the RNA was quantified using a NanoDrop spectrophotometer (Peqlab, Erlangen, Germany) and the RNA integrity was assessed using Bioanalyzer 2100 (Agilent, Santa Clara, USA). Ribosomal RNA depletion:  The Ribo-Zero (gram-negative) kit to remove the prokaryotic rRNA, according to the manufacturer’s instructions.
Single end, strand specific cDNA libraries were prepared using the Scriptseq v2 RNA-Seq Library Preparation Kit (Illumina, San Diego, CA, USA) following the manufacturers protocol. For sequencing equal volumes of libraries (12 pM) were multiplexed on a single lane. Sequencing was done on the HiSeq 2500 (Illumina, San Diego, CA, USA) using TruSeq SBS Kit v3 - HS (Illumina, San Diego, CA, USA) for 50 cycles resulting in 50 bp reads. Image analysis and base calling were performed using the Illumina pipeline v 1.8 (Illumina, San Diego, CA, USA).

tag: treatment (concentration)

value: eDNA (5 µg/ml)

value: C


title: P. inhibens, eDNA treatment, Replicate B

value: B


title: P. inhibens, eDNA treatment, Replicate A

value: A


title: P. inhibens, TDA treatment, Replicate C

source_name: P. inhibens_TDA treatment

value: TDA (10µM)


title: Avi_JG336-1


title: P. inhibens, TDA treatment, Replicate B


title: Sub-screen_Set3_2n_B


title: Sub-screen_Set3_2n_A


title: RNA_NK_37

tag: tissue

value: Uganda

value: cd8 t cell ratio:Data_in_Manuscript

value: Yes


title: RNA_NK_45


title: Sub-screen_Set2_GFP_positive


title: P. inhibens, DMSP treatment, Replicate B

source_name: P. inhibens_DMSP treatment

value: DMSP (500 µM)

tag: replicate


title: P. inhibens, DMSP treatment, Replicate C


title: P. inhibens, TDA treatment, Replicate A


title: Sub-screen_Set2_4n_plus


title: P. inhibens, DMSP treatment, Replicate A


title: RNA_NK_29


title: P. inhibens, C18 1 treatment, Replicate C

source_name: P. inhibens_C18 1 treatment


title: RNA_NK_21

source_name: Sorted NK


title: Sub-screen_Set2_4n_C


title: P. inhibens, C18 1 treatment, Replicate B


title: RNA_NK_53


title: P. inhibens, C14 1 treatment, Replicate C

source_name: P. inhibens_C14 1 treatment


title: RNA_NK_13


title: Sub-screen_Set2_4n_B


title: P. inhibens, C18 1 treatment, Replicate A


title: RNA_NK_5


title: Sub-screen_Set2_4n_A


title: Sub-screen_Set2_2n_C


title: RNA_NK_RAL16_Mo12

value: Post_ART_HIV_subject (12months on ART)


title: P. inhibens, 3OH C10 treatment, Replicate B

source_name: P. inhibens_3OH C10 treatment

value: 3OH C10 AHL (1 µM)


title: P. inhibens, 3OH C10 treatment, Replicate C


title: P. inhibens, DMSO treatment, Replicate C

source_name: P. inhibens_DMSO treatment

value: DMSO (14 mM)


title: P. inhibens, C14 1 treatment, Replicate B


title: P. inhibens, 3OH C10 treatment, Replicate A


title: Sub-screen_Set2_2n_B

value: Day 25


title: P. inhibens, DMSO treatment, Replicate A


title: RNA_NK_RAL15_Mo12


title: RNA_NK_RAL14_Mo12


title: P. inhibens, DMSO treatment, Replicate B


title: RNA_NK_RAL13_Mo12


title: Sub-screen_Set1_GFP_positive

value: iPSC-CMs (cardiomyocytes)


title: P. inhibens without treatment, Replicate C

source_name: P. inhibens without treatment


title: Sub-screen_Set2_2n_A


title: P. inhibens without treatment, Replicate A


title: P. inhibens without treatment, Replicate B


title: RNA_NK_RAL12_Mo12

value: Sorted NK


title: DNA_YD1417

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

data_processing:
Library strategy: PathSeq metagenome
sorted cells/plasma: Raw sequencing reads were trimmed off adapter sequence contaminants using Trimmomatic v. 0.36
sorted cells/plasma: Mapped onto the Refseq Grch38 of the human genome using the STAR RNA-Seq aligner (version 2.5.3a)
sorted cells: Gene abundance was then estimated by counting using HTSeq (version 0.9.1)
sorted cells: Transcript counts were then normalized by TMM (Trimmed Mean of M-values by correcting for the library size
plasma: Unaligned paired-end reads were then assembled into contigs using Trinity
plasma: Trinity contigs were then aligned against HG38 again to further remove host-derived sequences with BLAST+. Trinity contigs that aligned to non-reference human sequences in the NCBI nucleotide database were also removed
plasma: Remaining contigs were then aligned against the NCBI nucleotide database and quantified with Salmon
plasma: Taxonomic information was assigned for each contig and transcripts per million (TPM) values were collapsed at the species level for each sample. TPM are normalized for sequencing read depth and length for each sample, allowing for a more accurate comparisons between proportion of reads mapping to the same gene in various samples
Genome_build: Human (Refseq Grch38) and Non-human (NCBI nucleotide database and quantified with Salmon)
Supplementary_files_format_and_content: xlsx data matrix files with normalized read counts (sorted cells; sample by transcript) or TPM (plasma; sample by species abundance)

organism: human blood metagenome

source_name: Plasma

value: Plasma

value: No

value: HD


title: P. inhibens, C14 1 treatment, Replicate A


title: Sub-screen_Set1_4n_plus


title: Sub-screen_Set1_4n_C


title: RNA_NK_RAL11_Mo12


title: DNA_SV1296

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: RNA_NK_RAL10_Mo12


title: DNA_VB115_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: Sub-screen_Set1_4n_B


title: DNA_RD1214

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.21627907


title: DNA_OB1249

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: DNA_SM1408_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: Post_ART_HIV_subject (~0-2yrs on ART)


title: Sub-screen_Set1_4n_A


title: RNA_NK_RAL07_Mo12


title: RNA_NK_RAL04_Mo12


title: Sub-screen_Set1_2n_C


title: DNA_OB1249_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: DNA_NB1518

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.3109375


title: DNA_NB1518_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: cd8 t cell ratio:1.14953271


title: Sub-screen_Set1_2n_A


title: RNA_NK_RAL03_Mo12

value: Uganda


title: DNA_JPR1150

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: DNA_KBC1196_3

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: DNA_JL1235_3

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: RNA_NK_93

value: cd8 t cell ratio:Data_in_Manuscript


title: Genome-wide_Set3_GFP_positive


title: DNA_JL_1235

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: Yes


title: DNA_GTJ1321

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: DNA_GL1587_3

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: Genome-wide_Set3_4n_plus


title: DNA_GC1587_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: DNA_SV_1296_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: RNA_NK_77


title: RNA_NK_RAL08_Mo12


title: RNA_NK_85


title: DNA_FM1317_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: DNA_EC1124EC

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: DNA_MIPAV1_06_015

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: DNA_EG1148_3

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: Sub-screen_Set1_2n_B


title: Genome-wide_Set3_4n_B


title: DNA_DPL1241

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: Genome-wide_Set3_2n_C


title: DNA_CMD1177

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: DNA_CM1811

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: DNA_CMG2049

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: DNA_CH1476_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: Genome-wide_Set3_2n_B


title: RNA_C306L2I22

value: Post_ART_HIV_subject (3months on ART)


title: RNA_C306L2I8


title: RNA_C306L3I7


title: RNA_C306L3I6


title: DNA_CH_1476

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: RNA_C306L2I7


title: DNA_CBD1256

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: Genome-wide_Set3_2n_A


title: Genome-wide_Set3_4n_C


title: DNA_AM1408

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: DNA_AM1325

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: DNA_AS1152

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: Genome-wide_Set2_GFP_positive


title: DNA_ABG1178A

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: RNA_C306L2I5


title: Genome-wide_Set2_4n_plus


title: Genome-wide_Set3_4n_A


title: DNA_RAL8-Mo9

description:
PathSeq
Uganda_Longitudinal_B2_PathSeq_TPM.xlsx

value: Post_ART_HIV_subject (9months on ART)


title: Genome-wide_Set2_4n_C


title: DNA_106_106

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: RNA_C306L2I20


title: RNA_C306L2I21


title: RNA_C306L2I6


title: DNA_RAL7-Mo9


title: Genome-wide_Set2_4n_B


title: RNA_C306L2I2


title: DNA_RAL7-Mo12

value: Post_ART_HIV_subject (12months on ART)


title: Genome-wide_Set2_4n_A


title: DNA_RAL4-Mo9


title: Genome-wide_Set2_2n_C


title: RNA_C306L2I19


title: DNA_RAL3-Mo12


title: RNA_H5GYL1I1

source_name: Sorted Monocytes

value: Sorted Monocytes


title: Genome-wide_Set2_2n_B

value: Day 25


title: DNA_RAL16-Mo12


title: RNA_C306L4I4


title: DNA_RAL12-Mo12_1


title: DNA_RAL14-Mo12


title: DNA_RAL13-Mo12


title: Genome-wide_Set2_2n_A

value: iPSC-CMs (cardiomyocytes)


title: DNA_ABG_1178A_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: DNA_RAL11-Mo12


title: Genome-wide_Set1_GFP_positive


title: RNA_C306L4I3


title: RNA_C306L4I27


title: DNA_RAL10-Mo12


title: DNA_181030_RAL16-Mo9


title: Genome-wide_Set1_4n_plus


title: DNA_181030_RAL15-Mo9


title: DNA_RAL8-Mo12


title: RNA_C306L2I18

value: Sorted NK


title: DNA_RAL3-Mo9

value: Plasma


title: Genome-wide_Set1_4n_C


title: DNA_181030_RAL14-Mo9


title: RNA_C306L4I2


title: DNA_RAL4-Mo12


title: DNA_181030_RAL11-Mo9


title: RNA_C306L4I15


title: RNA_C306L4I14


title: DNA_181030_RAL10-Mo9


title: DNA_RAL16-Mo4

description:
PathSeq
Uganda_Longitudinal_B1_PathSeq_TPM.xlsx

value: Post_ART_HIV_subject (4months on ART)


title: DNA_RAL16-D0

value: No


title: DNA_RAL16-Mo24

value: Post_ART_HIV_subject (24months on ART)


title: Genome-wide_Set1_2n_C


title: DNA_RAL16-Mo3


title: RNA_C306L4I1


title: RNA_Monocytes_70


title: Genome-wide_Set1_2n_B


title: DNA_RAL15-Mo9


title: Genome-wide_Set1_2n_A


title: DNA_RAL15-Mo3


title: RNA_Monocytes_62


title: DNA_RAL15-Mo4


title: DNA_181030_RAL13-Mo9


title: GFP_positive_R1/R2

data_processing:
paired-end FASTQ files were converted to SAM files using FastqToSam 4.0.5.1 from the Broad’s Genome Analysis Toolkit (GATK)
SAM files were aligned to the hg19 human genome using Drop-seq_tools-1.0 and Spliced Transcripts Alignment to a Reference (STAR) 2.5.3
BAM files were converted to a unique molecular identifiers (UMI) read count matrix using DigitalExpression in Drop-seq_tools-1.0
Analysis of single cell gene expression was performed by following the Monocle 2 documentation
Genome_build: hg19
Supplementary_files_format_and_content: unique molecular identifiers (UMI) read count matrix

source_name: iPSC-CMs

extract_protocol:
All RT reagents were dispensed using an Echo 525 acoustic liquid handler for a final total reaction volume of 1 ul
First and second strand synthesis was performed using Maxima H Minus reverse transcriptase
Reactions from each well were subsequently pooled into a siube assisted by a Caliper liquid handler. The pooled libraries were treated with ExoI (NEB M0293L) at 37oC for 45 min to trim single-stranded ends and then cleaned up with AMPure beads (Beckman Coulter A63881). Amplification of libraries was for 12 cycles using KAPA HiFi-based (Kapa Biosystems KM2602) PCR followed by AMPure bead clean up with quantity and quality evaluated on Agilent Bioanalyzer. cDNA (1 ng) was fragmented and indexed through Nextera XT Library Prep Kit (tagmentation) (Illumina 15032354), followed by PCR with indexing primers for sequencing with a final AMPure bead clean up and bioanalyzer analysis prior to sequencing

value: CCNB1-eGFP reporter cardiomyocytes (CMs)

value: GFP+


title: DNA_RAL15-Mo24


title: Genome-wide_Set1_4n_B


title: DNA_RAL15-D0


title: 4n_R1/R2


title: DNA_RAL16-Mo9


title: DNA_RAL14-Mo4


title: DNA_RAL14-Mo9


title: RNA_Monocytes_54


title: RNA_Monocytes_46


title: RNA_C306L4I13


title: DNA_RAL14-Mo3


title: DNA_RAL14-Mo24


title: Genome-wide_Set1_4n_A


title: 2n_R1/R2


title: RNA_Monocytes_38


title: DNA_RAL13-Mo9


title: DNA_RAL14-D0


title: RNA_Monocytes_30


title: 2834: Ovarian cancer metastatic cells

first: Bingqing

last: Xie

address: 6001 Forest Park Rd

department: Internal medicine

institute: University of Texas Southwestern medical center

data_processing:
Barcode and umi were extracted by umi_tools 0.5.1
Allows for proportion of 0.1 mismatches (e.g. 10*0.1=1 mismatch in 10bp adaptor match, bp below zero are rounded to 0) and sequences to match are poly at the 3 prime end (at least 6) and TSO oligo on the 5 prime end via cutadapt
Alignment with STAR(2.1.6) using defaults
Assign reads to genes using featureCounts
Sort gene reads and index using samtools 1.7.0
Generate gene DGE matrix using umi_tools
Filter DGE matrix using genes per cell 700 using Seurat V3.1.0
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: Ovarian cancer metastatic cells

extract_protocol:
Tumors were dissociated using collagenase IV, Dnase I and hyaluronidase at 370C. Recovered single cells were run using the Drop-seq protocol; cells were lysed in droplet and mRNA was captured using barcode beads.
Libraries were prepared using Nextera XT DNA library preparation kit (FC-131-1096) following Illumina's instructions.

value: Ovarian cancer metastatic cells

tag: site

value: Omentum

tag: origin

value: Fallopian

tag: histologic type

value: Malignant mixed Mullerian tumor

tag: histological grade

value: High grade

tag: neoadjuvant therapy

tag: stage (pmn/figo)

value: ypT3c Nx/  IIIc

tag: race

value: Asian


title: DNA_RAL13-Mo4

value: Uganda

value: cd8 t cell ratio:Data_in_Manuscript

value: Yes


title: 3401: Ovarian cancer metastatic cells

tag: cell type

value: Left ovary

value: High grade serous carcinoma

value: pT3c Nx Mx/  IIIc

value: White

tag: age


title: DNA_RAL13-Mo3

value: Plasma

value: Post_ART_HIV_subject (3months on ART)


title: RNA_Monocytes_22

value: Sorted Monocytes

value: Post_ART_HIV_subject (24months on ART)


title: DNA_RAL13-D0

value: No


title: DNA_RAL12-Mo9

value: Post_ART_HIV_subject (9months on ART)


title: 6885: Ovarian cancer metastatic cells

value: Ovarian cancer metastatic cells

value: Omentum

value: Left fallopian (STIC)

value: ypT3c N1a / IIIc

value: Black


title: 4806: Ovarian cancer metastatic cells

value: High grade

value: pT3c, N1, M1/ IIIc


title: RNA_Mono_RAL16_Mo12

value: Uganda

value: cd8 t cell ratio:Data_in_Manuscript

value: Yes

value: Post_ART_HIV_subject (12months on ART)


title: DNA_RAL12-Mo4

value: Plasma

value: Post_ART_HIV_subject (4months on ART)


title: DNA_RAL12-Mo3

value: Post_ART_HIV_subject (3months on ART)


title: 3232: Ovarian cancer metastatic cells

value: High grade serous carcinoma

value: pT3c Nx / IIIc

value: Asian


title: DNA_RAL12-D0

value: No


title: 5150: Ovarian cancer metastatic cells

value: Ovarian cancer metastatic cells

value: Omentum

value: undetermined

value: Serous

value: Not applicable

value: ypT3a Nx M1/ Ivb

value: White


title: RNA_Monocytes_6

value: Sorted Monocytes

value: Uganda

value: cd8 t cell ratio:Data_in_Manuscript

value: Post_ART_HIV_subject (24months on ART)


title: DNA_RAL11-Mo9

value: Plasma

value: Yes

value: Post_ART_HIV_subject (9months on ART)


title: RNA_Mono_RAL14_Mo12

value: Post_ART_HIV_subject (12months on ART)


title: DNA_RAL11-Mo4

value: Post_ART_HIV_subject (4months on ART)


title: RNA_Mono_RAL15_Mo12


title: RNA_Mono_RAL13_Mo12


title: DNA_RAL11-Mo3

value: Post_ART_HIV_subject (3months on ART)


title: DNA_RAL11-Mo24


title: RNA_Mono_RAL12_Mo12


title: DNA_RAL11-D0

value: No


title: DNA_RAL10-Mo9


title: DNA_RAL13-Mo24


title: LSD1-KD_input_ChIP-seq

city: Kumamoto

first: Kensaku

last: Kohrogi

state: Kumamoto

address: 2-2-1, Honjo, Chuo-ku

department: Department of Medical Cell Biology

institute: Kumamoto University

data_processing:
Basecalls and conversion to FASTQ files were performed using Basesapce online (Illumina)
Sequence data were alignmened onto the human reference genome hg19 using the BWA algorithm in Galaxy.
Duplicate reads and low read/mapping quality reads were trimmed out with Galaxy.
Enrichment of histone modification were detected based on the ChIP peaks significantly enriched over input peaks at a cutoff value of p=10^-5.
Genome_build: hg19
Supplementary_files_format_and_content: The BED files were generated using MACS algorithm in Galaxy.

source_name: human erythroleukemia

growth_protocol: HEL were grown in Roswell Park Memorial Institute 1640 medium (RPMI1640) (Sigma), supplemented with 10% heat inactivated fetal bovine serum (FBS) , 50 U/ml penicillin, and 50 mg/ml streptomycin in a 37℃ incubator equilibrated with 95% air, 5% CO2. The medium was changed every other day.

extract_protocol:
Cells were crosslinked with formaldehyde. Cell lysates were subjected to  DNA fragmentation by a  bath sonifier, and chromatin-DNA complexes were pulled down using the specific antibody.
Libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs) according to the manufacturer's instructions. Briefly, ChIP DNA was end-repaired using an end prep enzyme. After adapter ligation, DNA was PCR amplified with NEB Index primers for 8-10 cycles. The purified DNA was checked for quality on Agilent TapeStation instrument with an Agilent High Sensitivity D1000 kit. The library DNA was approximately 170–500 bp in length. Libraries ware quantified using quantitative real-time PCR with the Kapa Library Quantification Kit. Diluted library DNA was subjected NextSeq sequencers (Illumina) according to the manufacturer's protocols.

treatment_protocol: HEL cells were transduced with a lentivus vector containing either control or LSD1 shRNA. LSD1-KD was induced by the addition of doxycyclin, and cells were harvested after four days.

value: HEL (human erythroleukemia)

tag: chip antibody


title: LSD1_ChIP-seq

data_processing:
Basecalls and conversion to FASTQ files were performed using Basesapce online (Illumina)
Sequence data were alignmened onto the human reference genome hg19 using the BWA algorithm in Galaxy.
Duplicate reads and low read/mapping quality reads were trimmed out with Galaxy.
Duplicate samples which was separately mapped to the genome was merged before peak calling using MACS2 algorithm in Galaxy.
LSD1 binding sites were detected based on the LSD1 peaks significantly enriched over input peaks at a cutoff value of p=10^-5.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files for visualization, and the BED files were generated using MACS algorithm in Galaxy.

growth_protocol: HEL cells were grown in Roswell Park Memorial Institute 1640 medium (RPMI1640) (Sigma), supplemented with 10% heat inactivated fetal bovine serum (FBS) , 50 U/ml penicillin, and 50 mg/ml streptomycin in a 37ºC incubator equilibrated with 95% air, 5% CO2. 10% of the cells were passaged after being cultured for 4 days.

extract_protocol:
Cells were crosslinked with formaldehyde and disuccinimidyl glutarate. Cell lysates were subjected to two-step DNA fragmentation by a probe-type sonifier and a water bath sonifier, and chromatin-DNA complexes were pulled down using the specific antibody.
Libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs) according to the manufacturer's instructions. Briefly, ChIP DNA was end-repaired using an end prep enzyme. After adapter ligation, DNA was PCR amplified with NEB Index primers for 8-10 cycles. The purified DNA was checked for quality on Agilent TapeStation instrument with an Agilent High Sensitivity D1000 kit. The library DNA was approximately 170–500 bp in length. Libraries ware quantified using quantitative real-time PCR with the Kapa Library Quantification Kit. Diluted library DNA was subjected NextSeq sequencers (Illumina) according to the manufacturer's protocols.

value: anti-LSD1 (Abcam, ab17721)


title: DNA_RAL10-Mo4


title: RNA_Mono_RAL11_Mo12


title: DNA_RAL10-Mo3


title: LSD1-KD_panH3_ChIP-seq

value: panH3 (Abcam, ab1791)


title: DNA_RAL10-Mo24


title: DNA_RAL10-D0


title: LSD1-KD_H3K4me2_ChIP-seq

value: H3K4me2 (Millipore, 07-030)


title: DNA_RAL12-Mo24


title: DNA_RAL08-Mo9


title: RNA_Mono_RAL07_Mo12


title: input DNA


title: DNA_RAL08-Mo4


title: ctrl_input_ChIP-seq


title: RNA_Mono_RAL03_Mo12


title: DNA_RAL07-Mo9


title: DNA_RAL08-D0


title: RNA_Mono_RAL04_Mo12


title: DNA_RAL07-Mo4


title: ctrl_panH3_ChIP-seq


title: DNA_RAL07-Mo3


title: DNA_RAL07-Mo24


title: ctrl_H3K4me2_ChIP-seq


title: DNA_RAL07-D0


title: DNA_RAL04-Mo9


title: RNA_C306L4I25


title: ctrl_H3K4me1_ChIP-seq

value: H3K4me1 (Abcam, ab8895)


title: DNA_RAL04-Mo3


title: RNA_Mono_RAL10_Mo12


title: DNA_RAL04-Mo4


title: DNA_RAL08-Mo3


title: S2101_HEL

data_processing:
Resulting reads were aligned to the UCSC hg19 reference genome using TopHat.
Normalization, differential analysis, and gene ontology analysis was performed using Strand NGS (Strand Genomics).
Genome_build: hg19
Supplementary_files_format_and_content: Fold_change_by_LSD1_inhibition.xlsx  in spread sheet (Excel) format.

extract_protocol:
Total RNA from HEL cells was extracted using RNeasy Mini Kit (Qiagen). mRNA was purified using NEB Next Poly (A) mRNA Magnetic Isolation Module (NEB).
cDNA library for sequencing was synthesized using NEB Next Ultra DNA Library Prep Kit for Illumina (NEB) and was sequenced on NextSeq 500 sequencer (Illumina) with 75-bps single-end reads.

treatment_protocol: For induction of shRNA expression, doxycycline (DOX) was added in the medium at 500 ng/ml. Selective LSD1 inhibitior, S2101 was added in medium at 10μM. The samples were collected four days after Dox or S2101 treatment.

tag: treatment

value: LSD1 inhibitor S2101 10μM


title: DNA_RAL04-Mo24


title: ctrl_HEL

value: untreated


title: RNA_C306L4I12

value: Sorted Monocytes

value: Uganda


title: LSD1-KD_H3K4me1_ChIP-seq


title: RNA_C306L4I11

value: cd8 t cell ratio:Data_in_Manuscript


title: DNA_RAL03-Mo9

value: Plasma


title: DNA_RAL03-Mo4

value: Yes


title: DNA_RAL03-Mo3


title: DNA_RAL03-Mo24

value: Post_ART_HIV_subject (24months on ART)


title: LSD1-KD_HEL (shLSD1_HEL_DOX)

value: sh_LSD1_HEL (human erythroleukemia)

value: Doxycyclin induced LSD1_KD


title: ctrl_HEL (shLSD1_HEL_ctrl)


title: RNA_C306L4I10


title: RNA_C306L4I9


title: DNA_QA37

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:1.25


title: DNA_RAL03-D0

value: No


title: RNA_C306L4I23


title: RNA_C306L3I27


title: DNA_QA21

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:1.57

value: Healthy


title: DNA_QA22

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.67

value: Post_ART_HIV_subject (~0-2yrs on ART)


title: RNA_C306L3I25


title: RNA_C306L3I23


title: DNA_QA18

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.4


title: DNA_QA19

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:3.14


title: DNA_QA20

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:1.44