title: AGO7_CMV_bioreplicate_1

description: smallRNA IP

value: Rosette leaves

value: wild type

tag: ecotype

value: Columbia 0

tag: molecule subtype

value: sRNA

tag: rip target


title: eluturation-arrest-release-exp191107_medium-40min_bio-rep2

status: Public on Dec 01 2021

type: SRA

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

country: USA

institute: STANFORD UNIVERSITY

library_source: transcriptomic

data_processing:
read alignment, ChIP-seq Bowtie 1.0.1
read alignment, RNA-seq STAR-2.5.3a
custom code
Genome_build: custom
Supplementary_files_format_and_content: bedGraph of read coverage, normalized to RPM

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: cells

extract_protocol:
cell pellets were lysed in 300 µL TRI Reagent (Zymo Research) by bead beating using a Fastprep 24 (4°C, settings: 5.0 m/s, 1 x 30 seconds). Cell debris was pelleted (13 krpm, 5 minutes) and the supernatant recovered. RNA was then extracted using the direct-zol RNA microprep kit (Zymo Research).
mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and NEBNext Ultra II RNA Library Prep Kit for Illumina® (NEB, #E7775) was then used to prepare libraries for paired-end (2x150 bp) Illumina sequencing

tag: strain

tag: treatment

value: eluturation-arrest-release

tag: cell size

value: medium

tag: time point

value: 40 min


title: NERD4

city: Shanghai

first: Ye

last: Zhao

address: 197 Ruijin Er Road

country: China

institute: Ruijin Hospital

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: excel file includes FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Human esophagus biopsy from patients with NERD

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer’s instructions. RNA integrity was assessed on the Agilent Bioanalyzer 2100 system. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: esophagus

tag: disease

value: NERD

tag: gender

value: Male

tag: age (yrs)

tag: bmi

tag: regurgitation

value: present

tag: heartburn

tag: hiatus hernia

value: absent

tag: smoking history

value: smoker

tag: drinking hisotry

value: drinker


title: AGO7_Mock_bioreplicate_2

city: Uppsala

first: German

last: Martinez

state: Uppsala

address: Almas Allé 8

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

description: smallRNA IP

data_processing:
sRNAs were trimmed using Trim Galore.
All libraries were mapped to the Arabidopsis thaliana chromosome sequences from the TAIR10 genome version. sRNAs were mapped with bowtie allowing 2 mismatches (-t -v2).
Genome_build: TAIR10
Supplementary_files_format_and_content: Tabular files were generated using Galaxy. For sRNA seq experiments reads were aligned with bowtie with the parameters -t -v2.

organism: Arabidopsis thaliana

source_name: Rosette leaves

growth_protocol: Plants were grown under standard long day conditions at 22 °C, long day and 45% humidity

extract_protocol:
Total RNA was extracted using TRIzol reagent (Life Technologies) following the manufacturer instructions. Total RNA was directly used for sRNA library preparation. PARE sequencing was obtained by purification with the NEB mRNA isolation kit (New England Biolabs).
sRNA libraries were produced using the TruSeq Small RNA Sample Preparation Kit (Illumina). PARE libraries were constructed according to Zhai et al (2014).

treatment_protocol:
Two leaves per Col-0 plant in the 4 rosettes leaves stage, 1.04 stage from Boyes et. al 2001, were rub-inoculated with 0.1 M Na2HPO4 containing the three RNAs that constitutes CMV (strain FNY) genome. These RNAs were previously obtained by in vitro transcription using the MAXIscript T7 Transcription Kit (ThermoFisher) and plasmids containing the individual genomic RNA sequences as the template for the transcription. Mock plants were rub-inoculated with Na2HPO4 buffer. Rosettes leaves from these Col-0 plants were taken at 30 dpi to perform sRNA-seq and PARE-seq. At the same time, Nicotiana benthamiana plants were infected with the same in vitro transcription products to obtain a reservoir of infected tissue, which was used to infect the ago mutants for RT-qPCR analysis and the Col-0 and ago7-HA for IP-sRNA-seq. For all the different analysis, samples were taken 30 dpi and plants were grown in the same chamber under the same conditions (long day, 22oC and 45% humidity).
sRNA IPs were performed using AGO1, AGO2, AGO5, HA and 2b antibodies from Agrisera (references: AS09 527, AS13 2682, AS10 671, AS12 2220 and AS16 3981, respectively) and following the protocol described in McCue et al. 2016.

tag: genotype

tag: ecotype


title: eluturation-arrest-release-exp191107_medium-30min_bio-rep2

value: 30 min


title: NERD7

value: Female

value: non-smoker

value: non-drinker


title: 1715 WT 2h

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with HISAT (v0.1.5-beta) against themm10 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.0.2) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10.
Genome_build: mm10
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference genome

organism: Mus musculus

source_name: brain

growth_protocol: Primary microglial cell cultures were prepared from mouse brains. After 5–8 days of primary cultivation, microglial cells were harvested by shake off.

extract_protocol:
Cells were  lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 100-500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultivated for 2 or 8 hours with Amyloid-beta containing conditioned-medium.

value: WT

tag: time

value: 2 h

value: no


title: NERD2


title: 1713 WT 2h


title: NERD3


title: eluturation-arrest-release-exp191107_medium-10min_bio-rep2

tag: strain

value: eluturation-arrest-release

value: 10 min


title: NERD1


title: 1714 WT 2h

tag: treatment


title: AGO7_Mock_Input_bioreplicate_2

value: Rosette leaves

value: wild type

value: Columbia 0

tag: molecule subtype

value: sRNA

tag: rip target

value: none (input)


title: 1711 PD1 0h

value: PD-1 KO

value: 0 h


title: eluturation-arrest-release-exp191107_large-70min_bio-rep2

tag: cell size

value: large

tag: time point

value: 70 min


title: Hashed PBMCs loaded at 64k cells [HTO]

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

data_processing:
Demultiplexing: bcl2fastq vv2.20.0.422 (Illumina); Parameters: --use-bases-mask=Y28,I8,Y91 --create-fastq-for-index-reads --minimum-trimmed-read-length=8 --mask-short-adapter-reads=8 --ignore-missing-positions --ignore-missing-controls --ignore-missing-filter --ignore-missing-bcls -r 18 -w 18 -p 50 --barcode-mismatches=0
Alignment: cellranger count v4.0.0 (10x Genomics); reference: refdata-gex-GRCh38-2020-A (10x Genomics); Default parameters
Hash Tag Oligo Counting: BarCounter v1.0 ; Default Parameters
Genome_build: hg38
Supplementary_files_format_and_content: HDF5
Supplementary_files_format_and_content: barcodes, molecule-info

source_name: peripheral blood mononuclear cells

extract_protocol:
PBMCs were fluorescence activated cell sorted (FACS) into naïve T-cells (CD45+ CD3+ CD45RA+ CD27+), memory T-cells (CD45+ CD3+, excluding CD45RA+ CD27+) and a non-T-cell bulk population (CD45+ CD3-). Briefly, cells were incubated with TruStain FcX (BioLegend, 422302) for 10 minutes on ice, followed by staining with antibodies (Supplementary Table 6) for 20 minutes on ice. Cells were washed with AIM V medium plus 25mM HEPES and sorted on a BD FACSAria Fusion. An aliquot of each post-sort population was used to collect 2,000 events to assess post-sort purity. FACS sorted cells were stained according to the New York Genome Center published protocol  (Version: 2019-02-13). Briefly, 1 million cells of each population were resuspended in 100 μl of staining buffer: DPBS without calcium and magnesium (Corning 21-031-CM) supplemented with 0.2% w/v BSA (Sigma-Aldrich A2934, “PBS+BSA”). 10 μl TruStain FcX (BioLegend, 422302) was added and cells were incubated on ice for 10 minutes, after which they were stained with 0.5 μg of a TotalSeq-A hashing antibody (Supplementary Table 6) on ice for 30 minutes. Stained cells were washed three times with 1 mL of PBS+BSA. Cells from each population were pooled together in equal numbers, and passed through a 35 μm Falcon Cell Strainer (Corning, 352235). All cell counts were performed using a Cellometer Spectrum Cell Counter (Nexcelom) using ViaStain Acridine Orange/Propidium Iodide solution (Nexcelom, C52-0106-5).
Libraries were prepared using the Chromium Single Cell 3’ v3 reagent kit (10x Genomics, 1000075) following the 10x Genomics User Guide (CG000183 Rev A), with the only modification being cell overloading.

tag: cell type

value: PBMCs


title: AGO7_Mock_Input_bioreplicate_1

tag: tissue


title: AGO5_CMV_bioreplicate_2

description: smallRNA IP


title: AGO7_Mock_bioreplicate_1

description: smallRNA IP


title: 1710 PD1 0h


title: eluturation-arrest-release-exp191107_medium-20min_bio-rep2

value: medium

value: 20 min


title: 1709 WT 0h

value: WT


title: AGO7_CMV_Input_bioreplicate_2


title: 201119L01_exp201103_MK918_SCD_DMSO_AB107

library_source: genomic

data_processing:
read alignment, ChIP-seq data: Bowtie 1.0.1
bigWig file generation: custom code
Genome_build: custom
Supplementary_files_format_and_content: bedGraph of read coverage, normalized to RPM

molecule: genomic DNA

extract_protocol:
Cells were fixed with 1% formaldehyde (30 minutes), quenched with 0.125 M glycine (5 minutes), washed twice in cold PBS, pelleted, snap-frozen and stored at −80°C. Pellets were lysed in 300 µL FA lysis buffer (50 mM HEPES–KOH pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF, Roche protease inhibitor) with ∼1 mL ceramic beads using a Fastprep-24 (MP Biomedicals). The lysate was then collected and sonication to ~200bp fragments. Cell debris was then pelleted and the supernatant retained for ChIP. For each ChIP reaction, 30 µL Protein G Dynabeads (Invitrogen) were blocked (PBS + 0.5% BSA), prebound with 5-10 µL anti-V5 antibody (SV5-Pk1, BioRad Cat# MCA1360G) or  anti-FLAG antibody (M2, SIGMA Cat# F1804) and washed once with PBS before incubation with supernatant (4°C, overnight). Dynabeads were then washed (5 minutes per wash) twice in FA lysis buffer, twice in high-salt (500 mM NaCl) FA lysis buffer, twice in ChIP wash buffer (10 mM TrisHCl pH 7.5, 0.25 M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA, 1 mM PMSF) and once in TE wash buffer (10 mM TrisHCl pH 7.5, 1 mM EDTA, 50 mM NaCl). DNA was eluted in ChIP elution buffer (50 mM TrisHCl pH 7.5, 10 mM EDTA, 1% SDS) at 65°C for 15-20 minutes. Eluted DNA was incubated to reverse crosslinks (65°C, 5 hours), before treatment with RNAse A (37°C, 1 hour) and then Proteinase K (65°C, 2 hours). DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research).
Indexed sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep kit (NEB, # E7645) and pooled before paired-end (2x150 bp) Illumina sequencing

tag: tagged protein

tag: chip antibody


title: 1708 WT 0h


title: 1707 WT 0h


title: Hashed PBMCs loaded at 24k cells [HTO]


title: eluturation-arrest-release-exp191107_large-30min_bio-rep2

value: 30 min


title: AGO7_CMV_Input_bioreplicate_1


title: Hashed PBMCs loaded at 16k cells [HTO]


title: eluturation-arrest-release-exp191107_large-20min_bio-rep2


title: eluturation-arrest-release-exp191107_large-50min_bio-rep2

value: 50 min


title: eluturation-arrest-release-exp191107_large-60min_bio-rep2

value: eluturation-arrest-release

value: 60 min


title: Hashed PBMCs loaded at 48k cells [HTO]


title: 1712 PD1 0h

value: no


title: Hashed PBMCs loaded at 32k cells [HTO]


title: Hashed PBMCs loaded at 80k cells [HTO]


title: 001-050

city: Newton

first: Christopher

last: Walker

state: MA

address: 85 Wells Ave

institute: Karyopharm Therapeutics, Inc

description: ribodepleted RNA

data_processing:
RNAseq reads were aligned with HiSAT2.
Gene-level expressions were determined with featurecounts.
Gene expression normalization and comparison were performed with DESeq2.
RNAseq data were used to infer the activities of 6,203 regulatory proteins, including proteins annotated as Transcription Factors (GO:0003700, or GO:0004677 and GO:0030528 or GO:0045449), co-Transcription Factors (GO:0003712 or GO:0030528 or GO:0045449), and signaling proteins (GO:0007165 and GO:0005622 or GO:0005886) in Gene Ontology. Protein activity was measured by Virtual Inference of Protein-activity by Enriched Regulon analysis (VIPER), which converts tumor sample gene-expression profiles into accurate protein activity profiles, using a GBM context-specific model of transcriptional regulation (interactome) available from Bioconductor (https://www.bioconductor.org/packages/release/data/experiment/html/aracne.networks.html).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: gbm_rawcounts.tsv: Raw counts for each gene in each Sample.
Supplementary_files_format_and_content: gbm_vpmat.tsv: Protein activities.

source_name: glioblastoma tumor

extract_protocol: TruSeq™ Stranded Total RNA With Ribo-Zero™ Plus rRNA Depletion protocol (Illumina).

treatment_protocol:
NCT01986348
Experimental: Arm A: Selinexor 60 mg and Surgery
Participants who required surgery received up to 3 doses of oral selinexor tablets 60 milligrams (mg) twice weekly (BIW) on Day 1, Day 3 and between 2 and 48 hours prior to surgery, subsequently underwent surgery for resection of their tumor and resumed selinexor tablets 60 mg BIW after recovery, during Week 1 to 4 of each 4-week cycle, until progression of disease (PD) or development of unacceptable toxicities.
Drug: Selinexor
One cycle is 28 days (4 weeks).
Other Name: KPT-330
Experimental: Arm B: Selinexor 50 mg/m^2
Participants who were not eligible for surgery received selinexor tablets 50 mg per square meter (mg/m^2) BIW during Week 1 to 4 of each 4-week cycle until PD or development of unacceptable toxicities.
Drug: Selinexor
One cycle is 28 days (4 weeks).
Other Name: KPT-330
Experimental: Arm C: Selinexor 60 mg
Participants who were not eligible for surgery received selinexor tablets 60 mg BIW during Week 1 to 4 of each 4-week cycle until PD or development of unacceptable toxicities.
Drug: Selinexor
One cycle is 28 days (4 weeks).
Other Name: KPT-330
Experimental: Arm D: Selinexor 80 mg
Participants who were not eligible for surgery received selinexor tablets 80 mg once weekly (QW) during Week 1 to 4 of each 4-week cycle until PD or development of unacceptable toxicities.
Drug: Selinexor
One cycle is 28 days (4 weeks).
Other Name: KPT-330

value: glioblastoma tumor

tag: trial arm

value: A

tag: experimental set

value: Validation

tag: patient response

value: Responder


title: AGO5_CMV_bioreplicate_1

description: smallRNA IP

value: Rosette leaves

value: wild type

value: Columbia 0

value: sRNA


title: eluturation-arrest-release-exp191107_medium-00min_bio-rep2

value: 00 min


title: A3: pre-cDC_rep3

city: Planegg

first: Anne

middle: Barbara

last: Krug

state: Bavaria

address: Großhaderner Str. 9

department: Institute for Immunology

institute: LMU Munich

description: GTTTAT

data_processing:
Illumina RTA 1.18.66.3 was used for basecalling
Sequence reads were processed using the zUMIs pipeline (version 0.0.1, Parekh et al. 2018). Within zUMIs, barcode and UMI sequences were quality filtered, allowing 4 bases with Phred score below 20. Remaining reads were mapped to the mouse genome (build mm10) using STAR (version 2.5.2b72). Gene identities were obtained from Ensembl annotations (GRCm38 release 84). Count matrices were collapsed by UMI.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including UMI counts for each gene and each sample

source_name: Bone marrow

extract_protocol:
cells were FAC-sorted, total RNA extracted by means of silica spin columns and frozen.
modified bulk SCRB-seq (Parekh et al. 2016)

value: bone marrow

value: pre-cDC

tag: well


title: eluturation-arrest-release-exp191107_large-10min_bio-rep2

value: large

value: 10 min


title: AGO5_Mock_bioreplicate_2

description: smallRNA IP

tag: genotype


title: eluturation-arrest-release-exp191107_large-40min_bio-rep2

value: 40 min


title: AGO5_Mock_bioreplicate_1

description: smallRNA IP

tag: ecotype


title: B1_8

city: Calgary

first: Matthew

last: Workentine

state: Alberta

address: 3280 Hospital Drive NW

country: Canada

institute: University of Calgary

data_processing:
The reads were mapped to the GRCm38 mouse reference genome (Ensembl Release 84) using HISAT2 v2.0.2 with options “—ss” and “—exon”
 Read counts were created using the software featureCounts v1.4.6
Analysis of the read counts was performed in R with DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: DESeq2 normalized gene counts

source_name: Paired 14-day old proximal tibia epiphyses

extract_protocol:
After euthanasia, tibiae from both hindlimbs of the mice were dissected, measured and weighed. Then, we collected the proximal epiphysis of each tibia (consisting of the growth plate, metaphysis, articular cartilage and secondary ossification center), which were snap-frozen in liquid nitrogen. Before total RNA extraction, the frozen epiphyses were homogenized using a ball mill (Braun Mikro-Dismembrator S) at 2600rpm for 60 seconds. Total RNA-Seq Kit (Life Technologies) were used to obtain Poly-adenylated mRNAs only from the total RNA.
PolyA RNA was converted into bar-coded cDNA libraries and size selected using Agencourt AMPure XP beads and then amplified using PCR to obtain around 50ng of 240-270 base pairs length cDNAs
Equal amounts of each library were pooled together. Using the EZ-Bead system (Life Technologies) magnetic sequencing beads were added to the libraries. A yield of 2.2 billion beads was obtained. The samples were then sequenced on a 5500xl Genetic Analyzer (Life Technologies) to generate 35-50 base paired-end reads

value: Longshanks 1

value: Bone, cartilage, marrow

tag: age

value: 14 days postnatal


title: AGO2_CMV_bioreplicate_2

description: smallRNA IP


title: PBMCs with a single hash antibody [HTO]

value: PBMCs


title: A1_2

tag: strain


title: C1_2


title: AGO2_CMV_bioreplicate_1

description: smallRNA IP


title: AGO2_Mock_bioreplicate_1

description: smallRNA IP


title: Hashed PBMCs loaded at 80k cells

tag: n hashes

tag: n cells loaded


title: eluturation-arrest-release-exp190911_small-50min_bio-rep1

tag: treatment

value: eluturation-arrest-release

value: small

value: 50 min


title: Hashed PBMCs loaded at 48k cells


title: eluturation-arrest-release-exp191107_small-10min_bio-rep2

tag: cell size


title: eluturation-arrest-release-exp190911_small-60min_bio-rep1

tag: time point

value: 60 min


title: eluturation-arrest-release-exp190911_small-40min_bio-rep1


title: CC_16

value: Control (ICR)


title: eluturation-arrest-release-exp191107_large-00min_bio-rep2


title: Hashed PBMCs loaded at 64k cells

tag: cell type


title: cKDmix_2 ncRNA-seq

city: Qingdao

first: Yong

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

description:
The group information is prefixed with  cKDmix_2 in the column of processed data file
Allsamples.exp.xls

data_processing:
The 50nt sequence tags from HiSeq sequencing went through the data cleaning first,
which included getting rid of the low quality tags and several kinds of contaminants from the
50nt tags. Length distribution of clean tags was then summarized. Afterwards, the standard
bioinformatics analysis was used to annotate the clean tags into different categories and to take
those which cannot be annotated to any category to predict the novel miRNA and base edit of potential known miRNA
Genome_build: ARS1

organism: Capra hircus

extract_protocol:
goat mamamary gland cells were isolated for small RNA. Then small RNA samples were sequenced.
small RNA was used for the library.

value: Lanshan dairy goat

tag: tissue

value: mammary gland


title: AGO2_Mock_bioreplicate_2

description: smallRNA IP

value: Rosette leaves

value: wild type

value: Columbia 0

tag: molecule subtype

value: sRNA

tag: rip target


title: BC_8


title: eluturation-arrest-release-exp190911_small-70min_bio-rep1

value: 70 min


title: AGO1_Mock_bioreplicate_2

description: smallRNA IP


title: Hashed PBMCs loaded at 32k cells


title: AGO1_CMV_bioreplicate_2

description: smallRNA IP


title: AC_3


title: PBMCs with a single hash antibody


title: Hashed PBMCs loaded at 24k cells


title: AGO_CMV_Input_bioreplicate_2

value: none (input)


title: eluturation-arrest-release-exp190911_small-30min_bio-rep1

value: 30 min


title: AGO1_Mock_bioreplicate_1

description: smallRNA IP


title: PBMCs without hash antibody


title: eluturation-arrest-release-exp190911_small-10min_bio-rep1

value: 10 min


title: cRNA28250_2 ncRNA-seq

description:
The group information is prefixed with cRNA28250_2 in the column of processed data file
Allsamples.exp.xls


title: U87MG cells, NVPU87_3

city: Edinburg

first: Megan

middle: Erin

last: Keniry

state: TX

address: 1201 W. University Dr.

department: Biology

institute: UTRGV

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human whole genome Homo Sapiens(GRCh38/hg38) using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: U87MG cells

growth_protocol: 27000 U87MG cells were plated onto 10cm dishes.

extract_protocol:
RNA was extracted using Rneasy Qiagen kit as per manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated the next day with either DMSO control or 50nM NVP-BEZ235 for four days.

value: glioblastoma cancer cell line

tag: cell line


title: c5NC_2 ncRNA-seq

description:
The group information is prefixed with c5NC_2 in the column of processed data file
Allsamples.exp.xls


title: U87MG cells, NVPU87_2


title: AGO1_CMV_bioreplicate_1

description: smallRNA IP


title: cRNA28250_1 ncRNA-seq

description:
The group information is prefixed with cRNA28250_1 in the column of processed data file
Allsamples.exp.xls


title: AGO_CMV_Input_bioreplicate_1


title: AGO_Mock_Input_bioreplicate_2


title: eluturation-arrest-release-exp190911_small-00min_bio-rep1

value: 00 min


title: c5NC_1 ncRNA-seq

description:
The group information is prefixed with c5NC_1 in the column of processed data file
Allsamples.exp.xls


title: U87MG cells, NVPU87_1


title: eluturation-arrest-release-exp190911_medium-70min_bio-rep1

value: eluturation-arrest-release

value: medium


title: cKDmix_1 ncRNA-seq

description:
The group information is prefixed with  cKDmix_1 in the column of processed data file
Allsamples.exp.xls


title: AGO_Mock_Input_bioreplicate_1


title: Hashed PBMCs loaded at 16k cells

value: PBMCs


title: c3NC_1 ncRNA-seq

description:
The group information is prefixed with c3NC_1 in the column of processed data file
Allsamples.exp.xls


title: U87MG cells, DU87_3

value: DMSO


title: eluturation-arrest-release-exp190911_medium-60min_bio-rep1

value: 60 min


title: eluturation-arrest-release-exp190911_small-20min_bio-rep1

value: small

value: 20 min


title: U87MG cells, DU87_2


title: U87MG cells, DU87_1


title: cRNA28250_1 RNA-seq

description: The group information is prefixed with  cRNA28250_1 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: ARS1

extract_protocol:
goat mamamary gland cells were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

value: Lanshan dairy goat

value: mammary gland


title: CMV_bioreplicate_1_PARE

value: Rosette leaves

value: wild type

value: Columbia 0

value: 5'P RNA


title: cRNA28250_2 RNA-seq

description: The group information is prefixed with  cRNA28250_2 in the column of processed data file


title: eluturation-arrest-release-exp190911_medium-40min_bio-rep1

value: 40 min


title: CMV_bioreplicate_2

value: sRNA


title: CMV_bioreplicate_2_PARE


title: eluturation-arrest-release-exp190911_medium-30min_bio-rep1

value: 30 min


title: cKDmix_2 RNA-seq

description: The group information is prefixed with  cKDmix_2 in the column of processed data file

value: cKDmix


title: eluturation-arrest-release-exp190911_medium-20min_bio-rep1

value: eluturation-arrest-release


title: Mock_bioreplicate_2


title: TREM2-KO-D

city: London

first: Jacqueline

last: Mitchell

address: 5 Cutcombe Road

department: Department of Basic & Clinical Neuroscience

country: United Kingdom

institute: King's College London

data_processing:
Adapter trimming and poor quality reads were removed using Trimmomatic v.0.36
The trimmed reads were mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2.
The Analysis was carried out in R (v4.0.2), Differential expression analysis was conducted using DESeq2 package (v1.28.1)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts

source_name: Bini10 iPSC_KO

growth_protocol: Microglia were generated following Haenseler et al. (Haenseler et al., 2017). In short, embryonic bodies (EBs) was generated from iPSCs using an AggreWell 800 (34850, StemCell Technologies) in E8-Flex medium supplemented with 50 ng/ml BMP4 (120-05ET, Peprotech), 50 ng/ml VEGF (PHC9394, ThermoFisher), and 20 ng/ml SCF (300-07, PeproTech) for 3 days with 75% medium change each day. Following incubation, EBs were transferred onto a T75 flask and maintained in X-VIVO15 (BE02-060F, Lonza) medium supplemented with 100 ng/ml M-CSF (300-25, PeproTech), 25 ng/ml IL-3 (PHC0031, ThermoFisher), 2 mM Glutamax (35050061, ThermoFisher) and 0.055 mM β-mercaptoethanol (31350-010, ThermoFisher). After 4 weeks, precursor cells started to emerge. Precursor cells were collected and differentiated to microglia over 7-days in 50/50 DMEM F:12, Neuronal basal medium plus supplemented with 100 ng/ml M-CSF, 100 ng/ml IL-34, and 10 ng/ml GM-CSF.

extract_protocol:
For the iPSC, approximately 2x105 cells were harvested using TRIzol reagent (Ambion Life Technologies 15596018) for total RNA isolation. Total RNA was isolated using Direct-ZolTM RNA microprep columns (Zymo research R2062) according to the manufacturer’s protocol. RNA quantity was assayed using UV spectrophotometry on Nanodrop One (Thermo Scientific). Optical density absorption ratios A260/A280 & A260/A230 of the iPSC microglia samples were 2.0 (±0.1 SD) and 2.1 (±0.1 SD) respectively. Furthermore, RNA integrity was verified using Agilent bioanalyzer at the King’s College London Genomic Centre.
RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with RNA Kit on Agilent 5600 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing library preparation was prepared using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, rRNA was depleted with NEBNext rRNA Depletion Kit (Human/Mouse/Rat). rRNA depleted RNAs were fragmented. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3’ends, and indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library amplification. The dUTP incorporated into the cDNA of the second strand enabled its specific degradation to maintain strand specificity. Sequencing libraries were validated using DNA Kit on the Agilent 5600 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA). The sequencing libraries were multiplexed and clustered on the flowcell. After clustering, the flowcell was loaded on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software v1.6 on the NovaSeq instrument. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.

value: Bini10 iPSC

value: TREM2 -/-


title: Mock_bioreplicate_1


title: eluturation-arrest-release-exp190911_medium-10min_bio-rep1

value: medium

value: 10 min


title: TREM2-KO-C


title: c5NC_2 RNA-seq

description: The group information is prefixed with c5NC_2 in the column of processed data file


title: cKDmix_1 RNA-seq

description: The group information is prefixed with  cKDmix_1 in the column of processed data file


title: TREM2-KO-B


title: eluturation-arrest-release-exp190911_medium-00min_bio-rep1

value: 00 min


title: TREM2-KO-A


title: c3NC_2 ncRNA-seq

description:
The group information is prefixed with c3NC_2 in the column of processed data file
Allsamples.exp.xls


title: c3NC_2 RNA-seq

description: The group information is prefixed with  c3NC_2 in the column of processed data file


title: eluturation-arrest-release-exp190911_large-70min_bio-rep1

value: large

value: 70 min


title: eluturation-arrest-release-exp190911_medium-50min_bio-rep1

value: 50 min


title: c3NC_1 RNA-seq

description: The group information is prefixed with c3NC_1 in the column of processed data file

value: Lanshan dairy goat

value: mammary gland


title: eluturation-arrest-release-exp190911_large-60min_bio-rep1

value: 60 min


title: scRNA_seq_LGC, Granulosa cells

description: The group information is prefixed with LGC in the column of processed data file

data_processing:
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
We used CellRanger count pipeline 2.2.0 to analyze the sequencing data and generated the single cell information. To generate same number of total cells for downstream analysis, we used augments ‘--force-cells=5000 \’.
Genome_build: ARS1
Supplementary_files_format_and_content: tab-delimited text file stores normalized and log-transformed single cell expression value

source_name: LGC_Granulosa cells

extract_protocol:
Ovarian granulosa cells were isolated and washed with PBS solution supplemented with 0.04% bovine serum albumin. Then, the cellss were digested with 1X TrypLE™ Express (Cat# 12605010) for 3 min to obtain single cell pellets. The single-cell Gel-Bead in Emulsions (GEMs) were then generated with Chromium 10x Genomics single-cell system by using single-cell 3’ Library and Gel Bead Kit V2 (10x Genomics, Cat#120237). Captured cells were then lysed and the released RNA were barcoded through reverse transcription in individual GEMs.
Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V2 (10x Genomics, 120237) following the manufacture’s introduction.

tag: breed

value: Ji'ning grey goat

value: Ovarian granulosa cells

tag: fertility

value: Low fertility


title: TREM2-WT-C

source_name: Bini10 iPSC_WT

value: WT


title: TREM2-WT-D


title: eluturation-arrest-release-exp190911_large-50min_bio-rep1


title: eluturation-arrest-release-exp190911_large-40min_bio-rep1

value: 40 min


title: CMV_bioreplicate_1

value: Rosette leaves

value: wild type

value: Columbia 0

value: sRNA


title: TREM2-WT-A

value: Bini10 iPSC


title: HN215 HNSCC (Oral cavity)

type: RNA

city: Mexico City

first: Patricia

middle: Piña

last: Sánchez

state: CDMX

address: Cuauhtémoc Avenue

department: Medical Research Unit in Oncological Diseases

country: Mexico

institute: IMSS

description: HNSCC (Oral cavity)

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Sample were hybridized using Affymetrix hybridization kits

data_processing:
Gene expression was evaluated using the Human Transcriptome Array 2.0 microarray (HTA 2.0, Affymetrix). Data were normalized by the RMA (Robust Multichip Average) method and analyzed using the Affymetrix Transcriptome and Expression Analysis Console (TAC 4.0, Applied biosystems) to compare gene expression between HPV+/p16+ and HNSCC HPV-/p16- HNSCC samples. In order to obtain high-quality gene annotation and to identify non-Affymetrix-annotated transcripts, the Bioconductor biomaRt package and the Integrative Genomics Viewer (IGV) were used to enrich biological data.
probe group file: HTA-2_0.r3.pgf
meta-probeset file: HTA-2_0.r3.Psrs.mps

label: biotin

source_name: HNSCC (HPV- / p16-)

label_protocol: Sample were labeled with the SensationPlus FFPE Amplification and 3´ IVT Labeling kit, following the instruction of manufacturer.

extract_protocol: Sample RNAs were isolated with the RNAeasy FFPE kit Qiagen, following the instruction of manufacturer.

tag: gender

value: men

tag: disease status

value: Negative


title: HN213 HNSCC (Oral cavity)

description: HNSCC (Oral cavity)

value: woman


title: eluturation-arrest-release-exp190911_large-30min_bio-rep1

value: eluturation-arrest-release

value: large

value: 30 min


title: eluturation-arrest-release-exp190911_large-20min_bio-rep1

value: 20 min


title: Overlap Hypoxia Rep3

city: La Jolla

first: Omar

middle: A

last: Mesarwi

address: 9500 Gilman Drive, MTF 240

institute: University of California San Diego

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using bowtie v1.3.0
read quantification and gene count matrix was generated with RSEM v1.3.023 and GENCODE annotation (Mus_musculus.GRCm38.68.gtf)
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

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

value: Liver

value: 12 weeks

tag: genotype

value: Overlap hypoxia


title: Overlap Hypoxia Rep2

tag: age


title: HN211 HNSCC (Oral cavity)

description: HNSCC (Oral cavity)


title: eluturation-arrest-release-exp190911_large-00min_bio-rep1

tag: strain

value: 00 min


title: HN210 HNSCC (Larynx)

description: HNSCC (Larynx)


title: Overlap Hypoxia Rep4


title: Overlap Hypoxia Rep1


title: 191113L05_MS537c1_3xFLAG-WHI5_WIQ-ChIP

extract_protocol:
Cells were fixed with 1% formaldehyde (30 minutes), quenched with 0.125 M glycine (5 minutes), washed twice in cold PBS, pelleted, snap-frozen and stored at −80°C. Pellets were lysed in 300 µL FA lysis buffer (50 mM HEPES–KOH pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF, Roche protease inhibitor) with ∼1 mL ceramic beads using a Fastprep-24 (MP Biomedicals). The lysate was then collected and sonication to ~200bp fragments. Cell debris was then pelleted and the supernatant retained for ChIP. For each ChIP reaction, 30 µL Protein G Dynabeads (Invitrogen) were blocked (PBS + 0.5% BSA), prebound with 10 µL anti-V5 antibody (SV5-Pk1, BioRad Cat# MCA1360G) or 10 µL anti-FLAG antibody (M2, SIGMA Cat# F1804) and washed once with PBS before incubation with supernatant (4°C, overnight). Dynabeads were then washed (5 minutes per wash) twice in FA lysis buffer, twice in high-salt (500 mM NaCl) FA lysis buffer, twice in ChIP wash buffer (10 mM TrisHCl pH 7.5, 0.25 M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA, 1 mM PMSF) and once in TE wash buffer (10 mM TrisHCl pH 7.5, 1 mM EDTA, 50 mM NaCl). DNA was eluted in ChIP elution buffer (50 mM TrisHCl pH 7.5, 10 mM EDTA, 1% SDS) at 65°C for 15-20 minutes. Eluted DNA was incubated to reverse crosslinks (65°C, 5 hours), before treatment with RNAse A (37°C, 1 hour) and then Proteinase K (65°C, 2 hours). DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research).
Indexed sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep kit (NEB, # E7645) and pooled before paired-end (2x150 bp) Illumina sequencing

tag: chip-antibody


title: 191113L06_MS537c2_3xFLAG-WHI5_WIQ-ChIP

value: anti-FLAG antibody (M2, SIGMA Cat# F1804)


title: Intermittent Hypoxia Rep4

value: Intermittent hypoxia


title: TREM2-WT-B

value: WT


title: Intermittent Hypoxia Rep2

value: wild type


title: Intermittent Hypoxia Rep3


title: scRNA_seq_HGC, Granulosa cells

description: The group information is prefixed with HGC in the column of processed data file

source_name: HGC_Granulosa cells

value: Ji'ning grey goat

value: Ovarian granulosa cells

value: High fertility


title: Intermittent Hypoxia Rep1


title: 191113L04_MS536c2_3xFLAG-WHI5-ChIP


title: 191113L03_MS536c1_3xFLAG-WHI5-ChIP


title: HN207 HNSCC (Larynx)

description: HNSCC (Larynx)

value: Negative


title: HN203 HNSCC (Oral cavity)

description: HNSCC (Oral cavity)

source_name: HNSCC (HPV+ / p16+)

value: woman


title: HN202 HNSCC (Pharynx)

description: HNSCC (Pharynx)

value: men


title: HN201 HNSCC (Pharynx)

description: HNSCC (Pharynx)


title: 191113L02_MS535_LacI-GFP-NLS-5xFLAG-ChIP


title: Sustain Hypoxia Rep3

value: Sustained hypoxia


title: Sustain Hypoxia Rep2


title: 190722L69_MS524_SWI6-V5-ChIP

value: anti-V5 antibody (SV5-Pk1, BioRad Cat# MCA1360G)


title: 191113L01_MS534_GFP-NLS-5xFLAG-ChIP


title: Sustain Hypoxia Rep1


title: HN206 HNSCC (Oral cavity)

description: HNSCC (Oral cavity)


title: 190722L68_MS522_SWI4-V5-ChIP


title: Room Air Rep4

value: Room air


title: CsEVs

city: Xuzhou

first: Chao

last: Yan

state: Jiangsu

address: 209 of Tongshan Road

institute: Xuzhou Medical University

description: CsEVs.expr.xlsx

data_processing:
Small RNA libraries were constructed and sequenced by BGISEQ-500 sequencing technology at the BGI
The obtained raw sequence reads were processed following a standard bioinformatics protocol.
Mapping sequence reads to the reference genome
Predicted novel miRNAs and piRNAs
GO, KEGG pathway analysis and target prediction
Genome_build: Clonorchis sinensis

organism: Clonorchis sinensis

source_name: extracellular vesicles secreted by adult of Clonorchis sinensis

extract_protocol:
Total RNAs from adult worms and CsEVs were extracted using Trizol (Invitrogen, USA) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: adult worms

tag: sample type

value: EV (extracellular vesicle)


title: Room Air Rep3

value: Liver

value: 12 weeks

tag: treatment


title: CsMet

data_processing:
Small RNA libraries were constructed and sequenced by BGISEQ-500 sequencing technology at the BGI
The obtained raw sequence reads were processed following a standard bioinformatics protocol.
Mapping sequence reads to the reference genome
Predicted novel miRNAs and piRNAs
GO, KEGG pathway analysis and target prediction

source_name: metacercaria

extract_protocol:
Total RNAs from metacercaria, adult worms and eggs were extracted using Trizol (Invitrogen, USA) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: metacercaria


title: Room Air Rep2


title: HN200 HNSCC (Larynx)

description: HNSCC (Larynx)


title: Room Air Rep1


title: HN209 HNSCC (Larynx)

description: HNSCC (Larynx)


title: HN194 HNSCC (Larynx)

description: HNSCC (Larynx)


title: eluturation-arrest-release-exp190911_large-10min_bio-rep1

data_processing:
read alignment, ChIP-seq Bowtie 1.0.1
read alignment, RNA-seq STAR-2.5.3a
custom code
Genome_build: custom
Supplementary_files_format_and_content: bedGraph of read coverage, normalized to RPM

source_name: cells

extract_protocol:
cell pellets were lysed in 300 µL TRI Reagent (Zymo Research) by bead beating using a Fastprep 24 (4°C, settings: 5.0 m/s, 1 x 30 seconds). Cell debris was pelleted (13 krpm, 5 minutes) and the supernatant recovered. RNA was then extracted using the direct-zol RNA microprep kit (Zymo Research).
mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and NEBNext Ultra II RNA Library Prep Kit for Illumina® (NEB, #E7775) was then used to prepare libraries for paired-end (2x150 bp) Illumina sequencing

value: eluturation-arrest-release

tag: cell size

value: large

tag: time point

value: 10 min


title: HN189 HNSCC (Larynx)

description: HNSCC (Larynx)


title: HN195 HNSCC (Oral cavity)

description: HNSCC (Oral cavity)


title: Sustain Hypoxia Rep4

tag: tissue

value: wild type


title: HN187 HNSCC (Pharynx)

description: HNSCC (Pharynx)


title: HN188 HNSCC (Oral cavity)

description: HNSCC (Oral cavity)


title: HN186 HNSCC (Larynx)

description: HNSCC (Larynx)


title: CsAd

source_name: adult worms


title: HN185 HNSCC (Larynx)

description: HNSCC (Larynx)


title: s2nTS2_RRA120113-V

city: Tianjin

first: Ling

last: Shuai

address: 38 Tong Yan Road, Jinnan district

department: State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy

institute: Nankai University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: trophoblast stem cells

extract_protocol:
Cell samples were collected and RNA was harvested using Trizol reagent. NEB Next® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: strain background

tag: cell type

value: trophoblast stem cells

tag: genotype/variation

value: WT-TSCs


title: s2nTS3_RRA120114-V


title: s2nTS1_RRA120112-V


title: ControlM4

city: New Orleans

first: Robert

middle: f

last: Garry

state: LA

address: Dept Mic/Imm, 1430 Tulane Avenue

institute: Tulane

description: Liigated ileal loop instilled with 0.025% acetic acid and resected at  9 hours after surgery

data_processing:
Abundance measurments were calculated using kallisto quant v0.46.0 with parameters -b 100 --rf-stranded --single -l 200 -s 30
Differential expression was performed using Sleuth.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with gene counts (abundance measurements) for every gene and every sample
Supplementary_files_format_and_content: tab delimited files include TPM values for genes in every sample
Supplementary_files_format_and_content: Matrix table with gene counts (abundance measurements) for every gene and every sample plus results of differential expression testing with statistics

source_name: vehicle 4 - 9 hrs

growth_protocol: Ligated ileal loops instilled with either 0.025% acetic acid or 100 μM E23ox and resected at 6 and 9 hours after surgery were collected for RNA-Seq analysis.

extract_protocol:
RNA quality (RIN) was determined on an Agilent 2100 Bioanalyzer using an Agilent RNA 6000 Nano kit.
One microgram of each sample was used to generate mRNA libraries following the Illumina TruSeq Stranded mRNA Sample Preparation Guide following the low sample protocol
Final cDNA libraries were quantitated using Qubit dsDNA BR assay kit.
The quality of the libraries was determined by running each on an Agilent 2100 Bioanalyzer using the DNA 1000 kit.
Smear analysis was performed using Agilent 2100 Expert Software (Version B.02.09.SI725 (SR1)) with a range of 200-600bp to determine average size of each library.
Size and concentration were then used to calculate the molarity of each library.
All libraries were pooled and denatured following the standard normalization method in the Illumina Denature and Dilute Libraries Guide for the NextSeq System.
Denatured libraries were loaded onto an Illumina NextSeq 550 v2 High output reagent cartridge at a final concentration of 1.8pM in HT1 buffer. Illumina Denatured PhiX control library v3 was also included at 1% concentration
Single end 75bp single index sequencing was performed on an Illumina High flow cell v2.5 (#20024907) yielding approximately 15M SE reads per sample.

treatment_protocol: Prior to Illumina mRNA library construction, DNase treated RNA was quantitated using the Qubit RNA BR assay kit.

value: ileum

value: BALB/C

value: 0.025% acetic acid

value: resection at 9 hrs


title: HN184 HNSCC (Pharynx)

description: HNSCC (Pharynx)

value: men


title: ControlM2

source_name: vehicle 3 - 9 hrs


title: s2nES3_RRA120108-V

source_name: embryonic stem cells

value: embryonic stem cells

value: WT-ESCs


title: Control-9hr-M2

source_name: vehicle 1 - 9 hrs


title: s2nES2_RRA120107-V


title: E23ox-9hr-M8

description: Ligated ileal loop instilled with 100 μM E23ox and resected at  9 hours after surgery

source_name: E23ox 8 - 9 hrs

value: E23ox 100uM


title: s2nES1_RRA120106-V


title: E23ox-9hr-M7

source_name: E23ox 7 - 9 hrs


title: HN070 HNSCC (Oral cavity)

description: HNSCC (Oral cavity)

value: woman

value: Negative


title: HN087 HNSCC (Oral cavity)

description: HNSCC (Oral cavity)


title: Rif1_TS3

source_name: induced trophoblast stem cells

value: induced trophoblast stem cells

value: Rif1-KO iTSCs


title: Rif1_ES3

value: Rif1-KO heterozygote


title: Rif1_TS1


title: Control-9hr-M3

source_name: vehicle 2 - 9 hrs


title: HN182 HNSCC (Larynx)

description: HNSCC (Larynx)

source_name: HNSCC (HPV- / p16-)


title: E23ox-9hr-M5

source_name: E23ox 5 - 9 hrs


title: HN183 HNSCC (Oral cavity)

description: HNSCC (Oral cavity)


title: siR386_5

city: Neustadt-Mußbach

first: Veli Vural

last: Uslu

state: DEUTSCHLAND

address: Epigenetics, Breitenweg 71

department: Epigenetics

institute: AgroScience GmbH AlPlanta-Institute for Plant Research

description:
only silenced areas are collected
22-nt-siRNA
samples are all sRNA enriched

data_processing:
performed by GeneXPro GmbH-Frankfurt
The fastq files are aligned solely to the 16C-GFP sequence using bowtie2.
Genome_build: 16C-GFP_ the sRNA reads were mapped only to 16C-GFP sequence described by Philips et al 2017 (Plos One)
Supplementary_files_format_and_content: These data contains the number of reads at each position of the GFP (from 1-792) for each treatment and one additional processed data file is given for normalized read counts for each position of the GFP in a sliding window of 10 nucleotides.

organism: Nicotiana benthamiana

source_name: 3 silenced leaves are pooled in a single tube

extract_protocol:
mirVANA-thermoFisher
performed by GeneXPro GmbH-Frankfurt
TrueQuant SmallRNA Seq Kit for library preparation

treatment_protocol: 140ng/ul sRNA

value: samples collected 6 dps

tag: line

value: 16C-GFP line is used


title: siR739_8

value: 3 silenced leaves are pooled in a single tube


title: siR739_9


title: siR386_4


title: siR386_6


title: Rif1_ES2


title: Rif1_ES1


title: HN199 HNSCC (Larynx)

description: HNSCC (Larynx)


title: siR739_7


title: siR164_3


title: siR164_2


title: E23ox-9hr-M1

source_name: E23ox 1 - 9 hrs


title: E23ox-9hr-M2

source_name: E23ox 2 - 9 hrs


title: Rif1_8

value: Rif1-KO homozygote


title: HN193 HNSCC (Larynx)

description: HNSCC (Larynx)


title: E23ox-9hr-M6

source_name: E23ox 6 - 9 hrs

value: ileum


title: Rif1_TS4


title: Control-6hr-M3

description: Liigated ileal loop instilled with 0.025% acetic acid and resected at  6 hours after surgery

source_name: vehicle 2 - 6 hrs

value: BALB/C

value: resection at 6 hrs


title: siR164_1


title: E23ox-9hr-M4

source_name: E23ox 4 - 9 hrs

value: resection at 9 hrs


title: Control-6hr-M1

description: Ligated ileal loop instilled with 0.025% acetic acid and resected at  6 hours after surgery

source_name: vehicle 1 - 6 hrs

value: 0.025% acetic acid


title: HeLa_5Kcells_One-pot universal NicE-seq_rep1

city: Ipswich

first: Sriharsa

last: Pradhan

address: 240 County Road

institute: New England Biolabs

description:
Technical replicate1
HeLa_5K.bw

data_processing:
Library strategy: NicE-seq
Adaptor and low-quality sequences were trimmed from paired-end sequencing reads using Trim Galore v 0.5.0
Trimmed read pairs were mapped to the reference genome (human: hg38) using Bowtie2 v. 2.3.4.3. PCR duplicates and mitochondrial reads were removed using Picard tools and samtools.
Peak calling was done with MACS2 v. 2.1.2
Genome_build: hg38
Supplementary_files_format_and_content: Bigwigs were generated using 100bp bins using deeptools bamCoverage with the following parameters: --normalizeUsing RPKM

source_name: HeLa

growth_protocol: HCT116, HeLa, HEK293 and GM12878 cells were grown according to ATCC ‘s recommendations.

extract_protocol: One-tube NicE-seq

treatment_protocol: For DNA damage study, HCT116 cells were cultured on micro cover glass (VWR #48366067) in a 6 well plate format and fixed for 10 min at RT with different percentage of formaldehyde added in PBS. After formaldehyde removal, PBS with 0.125M Glycine was added for 5 min at RT to quench the crosslinking reaction. Cells were then washed once with PBS and incubated with 5% BSA (Sigma #A7906) for 1h at RT in 0.1% Tween-PBS (T-PBS). Anti-phospho-histone H2A.X (Ser139) and anti-ADPribose antibodies (Cell Signaling Technology #9718S and Santa Cruz Biotechnology #sc-56198 respectively) were added overnight at 4C at the recommended manufacturer’s dilutions. After 3 T-PBS washes for 5 min at RT, anti-rabbit IgG Alexa 488 or anti-mouse IgG Alexa 594 were added at 1/500 dilution in 5% BSA+T-PBS for 1h at RT for phospho-histone H2AX (Ser139) or ADPribose detection respectively. After 3 T-PBS washes for 5 min at RT, micro cover glass was mounted on microscope slides (VWR Vista Vision #16004-368) using Prolong gold antifade reagent with DAPI (Thermo Fisher Scientific #P36935). Immunofluorescence (DNA damage detection and NicEview labelling) was visualized using a LSM880 confocal microscope (Zeiss) and mean pixel intensity per channel was quantified on at least 80 individual cells for every formaldehyde fixation conditions

value: Cervical cancer cells

tag: cell line

value: HeLa


title: E23ox-6hr-M9

description: Ligated ileal loop instilled with 100 μM E23ox and resected at  6 hours after surgery

source_name: E23ox 9 - 6 hrs

value: E23ox 100uM


title: E23ox-6hr-M8

source_name: E23ox 8 - 6 hrs


title: HeLa_500cells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
HeLa_500.bw


title: Prostate tumor, HF+PFOS_5

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

description:
DE-results-hf-plus-pfos.csv; rnaseq_featurecounts.txt
81

data_processing:
Reads were processed and analyzed through a series of steps. Base calling and de-multiplexing of samples within each lane were done with Casava 1.8.2.
STAR (version 2.7.6a) was employed to map RNA-Seq reads to version mm39 of the Mus musculus reference genome, GRCm39, from NCBI Genome Reference Consortium Mouse Build 39.
Gene expression values (raw read counts) from BAM files were calculated using FeatureCounts function from the Subread module (version 2.0.0).
DESeq normalization algorithm with DESeq2 module in R using default values was used.  Differentially expressed genes were then determined by fold-change and p-value for each gene for each treatment relative to the vehicle control.
Genome_build: mm39
Supplementary_files_format_and_content: Genome mapping feature count file.  Differential expression results csv file.

source_name: Prostate tumor, HF+PFOS

growth_protocol: RWPE-kRAS (tumorigenic, derived from RWPE-1 with K-ras oncogene transfection) cells were purchased from ATCC (RWPE-1, #CRL-11609; RWPE-kRAS, #CRL-11610) and maintained in Gibco Keratinocyte SFM 1X growth media with glutamine (Gibco 17005042, Fisher Scientific, Waltham, MA, USA).

extract_protocol:
RNA extraction: For gene expression analysis, total RNA was extracted from at least 3 biological replicates for each ligand treatment using Trizol reagent and further cleaned using the RNAeasy kit from QIAGEN.
Once the sample quality and replicate reproducibility was verified at least 2 samples from each group were subjected to sequencing. RNA at a concentration of 100 ng/µL in nuclease-free water was used for library construction.The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNAseq Sample Prep kit.  The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a HiSeq2000  using a TruSeq SBS sequencing kit version 3. Fastq files were generated with the software Casava 1.8.2 (Illumina). Briefly, the poly-A containing mRNA was purified from total RNA, RNA was fragmented, double-stranded cDNA was generated from fragmented RNA, and adapters were ligated to the ends.

treatment_protocol: Mouse experiments and protocols were approved by the University of Illinois at Urbana-Champaign (IACUC Protocol #20159), and National Institutes of Health standards for the use and care of animals were followed. RWPE-KR prostate cancer epithelial cell lines was used for the tumor xenograft study. Four-week-old athymic nude male mice (RRID:RGD_5508395) were obtained from Jackson Laboratory (stock no. 007850; Bar Harbor, ME, USA). After a week of acclimatization, to test synergy between PFAS and a high-fat diet (HFD), we compared carcinogenesis in mice fed a HFD to mice fed a control diet. Mice were fed ad libitum. Because standard diets contain isoflavones with estrogenic activity that interferes with metabolic effects, we used F4031 diet (Bio-Serv, USA) as control diet. Purified HFDs (F3282 diet, Bio-Serv, USA) for our studies, meant to mimic the “Western diet”, are high in butterfat (~60% Kcal from fat) and polysaccharides, with a modest level of cholesterol (0.2%).  Ten days after diets were initiated, 2 x 106 RWPE-kRAS cells suspended in 50ul 1x PBS (Corning, NY, USA) and mixed in 50ul Matrigel (Matrix High Concentration (HC), Phenol-Red Free, LDEV-free Corning, NY, USA) were injected to the left and right flanks of mice (N=8 mice/group) with 255/8  𝐺 needle under anesthesia. In addition, silastic tubes packed with testosterone were implanted to provide continuous testosterone needed for xenograft establishment and growth. Mice were administered PFOS by oral gavage seven days per week at 10 mg/kg. Food consumption and animal weights were monitored twice weekly. Tumor size measurements were obtained three times per week using digital calipers. Animals were euthanized five weeks after the initial cancer cell line injection. Tumors, livers, prostates, and blood were harvested and flash frozen or in RNAlater.

tag: Sex

value: female

value: High fat diet + Perfluorooctane sulfonate

value: Prostate tumor

value: Athymic nude male mice (RRID:RGD_5508395)


title: Prostate tumor, HF+PFOS_4

description:
DE-results-hf-plus-pfos.csv; rnaseq_featurecounts.txt
79


title: E23ox-9hr-M3

source_name: E23ox 3 - 9 hrs


title: E23ox-6hr-M6

source_name: E23ox 6 - 6 hrs


title: HeLa_25cells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
HeLa_25.bw


title: HeLa_500cells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
HeLa_500.bw


title: HeLa_25cells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
HeLa_25.bw


title: Prostate tumor, HF+PFOS_3

description:
DE-results-hf-plus-pfos.csv; rnaseq_featurecounts.txt
78


title: E23ox-6hr-M7

source_name: E23ox 7 - 6 hrs


title: HeLa_1Kcells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
HeLa_1K.bw


title: E23ox-6hr-M5

source_name: E23ox 5 - 6 hrs


title: HeLa_1Kcells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
HeLa_1K.bw


title: Prostate tumor, HF+PFOS_2

description:
DE-results-hf-plus-pfos.csv; rnaseq_featurecounts.txt
77


title: Prostate tumor, HF+PFOS_1

description:
DE-results-hf-plus-pfos.csv; rnaseq_featurecounts.txt
76


title: E23ox-6hr-M4

source_name: E23ox 4 - 6 hrs


title: Prostate tumor, PFOS_6

description:
DE-results-pfos.csv; rnaseq_featurecounts.txt
73

source_name: Prostate tumor, PFOS

value: Perfluorooctane sulfonate


title: Prostate tumor, PFOS_7

description:
DE-results-pfos.csv; rnaseq_featurecounts.txt
74


title: E23ox-6hr-M3

source_name: E23ox 3 - 6 hrs


title: HeLa_100cells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
HeLa_100.bw


title: Prostate tumor, PFOS_5

description:
DE-results-pfos.csv; rnaseq_featurecounts.txt
72


title: E23ox-6hr-M2

source_name: E23ox 2 - 6 hrs


title: HeLa_100cells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
HeLa_100.bw


title: Prostate tumor, HF+PFOS_6

description:
DE-results-hf-plus-pfos.csv; rnaseq_featurecounts.txt
82


title: Prostate tumor, PFOS_4

description:
DE-results-pfos.csv; rnaseq_featurecounts.txt
71


title: E23ox-6hr-M1

source_name: E23ox 1 - 6 hrs


title: NC-5

city: Bengbu

first: Biao

last: Ding

state: Anhui

address: No.287 Changhuai Road

department: Reproductive Medicine Center

institute: The First Affiliated Hospital of Bengbu Medical College

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Sus scrofa (susScr11).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak). HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: susScr11

organism: Sus scrofa

source_name: preimplantation embryo

extract_protocol:
The RNA was extracted using a RNeasy Mini Kit (74034, Qiagen, Germany). A cDNA library was constructed using a TruSeq Nano DNA LT Library Preparation Kit (Illumina, FC-121-4001, USA). The cDNA was fragmented by dsDNA Fragmentase (NEB, M0348S, USA) by incubating at 37 °C for 30 min. The library construction began with the fragmented cDNA. Paired-end sequencing was performed on an Illumina 6000 sequence platform
The libraries were prepared according to the transcriptome differential expression analysis of the NC group and the DDB1_KD group

treatment_protocol: Porcine matured oocytes were injected the non-specific siRNA  (NC) and the DDB1-siRNA (DDB1-KD). Injected oocytes were perfomed parthenogenetic activate and cultured to morula.

tag: development stage

value: morula

value: non-specific-siRNA injected  (Negative control, NC)


title: HEK293_5Kcells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
HEK293_5K.bw

value: Embryonic Kidney cells


title: NC-3


title: HEK293_5Kcells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
HEK293_5K.bw


title: NC_2


title: NC-4


title: Prostate tumor, PFOS_3

description:
DE-results-pfos.csv; rnaseq_featurecounts.txt
70


title: HEK293_500cells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
HEK293_500.bw


title: Prostate tumor, PFOS_2

description:
DE-results-pfos.csv; rnaseq_featurecounts.txt
69


title: Prostate tumor, HF_6

description:
DE-results-hf.csv; rnaseq_featurecounts.txt
66

source_name: Prostate tumor, HF

value: High fat diet


title: HEK293_500cells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
HEK293_500.bw


title: Prostate tumor, PFOS_1

description:
DE-results-pfos.csv; rnaseq_featurecounts.txt
67


title: NC_1


title: Prostate tumor, HF_5

description:
DE-results-hf.csv; rnaseq_featurecounts.txt
65


title: Prostate tumor, HF_4

description:
DE-results-hf.csv; rnaseq_featurecounts.txt
63


title: HEK293_25cells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
HEK293_25.bw


title: DDB1_KD_4

value: DDB1-siRNA injected (DDB1-knockdown, DDB1-kD)


title: HEK293_25cells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
HEK293_25.bw


title: DDB1_KD_5


title: HEK293_1Kcells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
HEK293_1K.bw


title: DDB1_KD_3


title: Prostate tumor, HF_2

description:
DE-results-hf.csv; rnaseq_featurecounts.txt
60


title: Prostate tumor, Ctrl_4

description:
rnaseq_featurecounts.txt
54

source_name: Prostate tumor, Ctrl

value: Control


title: HEK293_100cells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
HEK293_100.bw


title: HEK293_1Kcells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
HEK293_1K.bw


title: HEK293_5Kcells_One-pot universal NicE-seq_rep3

description:
Technical replicate3
HEK293_5K.bw


title: DDB1_KD_2


title: DDB1_KD_1


title: Prostate tumor, HF_1

description:
DE-results-hf.csv; rnaseq_featurecounts.txt
59


title: HEK293_100cells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
HEK293_100.bw


title: Prostate tumor, Ctrl_3

description:
rnaseq_featurecounts.txt
53


title: PAM-CD2v-rep3

city: Minhang District

first: Min

last: Zhang

state: Shanghai

address: 518 Ziyue RD

department: The viruses and Swine diseases of reproductive failures

institute: Shanghai Veterinary Research Institute, CAAS

description: Stable expression of ASFV-CD2v protein

data_processing:
Quality of FASTQ file were evaluated by FastQC software
Raw reads were filtered with Cutadapt sofware with parameters of 10 bp overlap, 20% base mismatch
Reas were mapped to sus scrofa genome Sus_scrofa.Sscrofa11.1.dna.toplevel.fa with Bowtie2 with default parameter
Raw counts were generated using Htseq with Sus_scrofa.Sscrofa11.1.dna.toplevel.fa annotation file
Gene differential expression was analyzed by Deseq2 software using genes raw counts
Genome_build: Sus_scrofa.Sscrofa11.1.dna.toplevel.fa
Supplementary_files_format_and_content: PAM_CD2v_GFP_Expression.csv (includes raw reads counts and FPKM values for each Sample)

growth_protocol: iPAM-GFP and iPAM-CD2v cell line were incubated at 37°C in 5% CO2 and grown in 1640 medium with 10% FBS.

extract_protocol:
Total RNA were isolated with miRNeasy MiniKit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: untreated

value: iPAM

value: immortalized pulmonary alveolar macrophage cell

tag: stable expression of

value: ASFV-CD2v protein


title: Prostate tumor, Ctrl_2

description:
rnaseq_featurecounts.txt
52


title: HCT116_5Kcells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
HCT116_5K.bw

value: Colorectal cancer cells


title: PAM-GFP-rep3

description: Stable expression of GFP protein

source_name: PAM-GFP


title: Prostate tumor, Ctrl_1

description:
rnaseq_featurecounts.txt
51


title: PAM-CD2v-rep1

description: Stable expression of ASFV-CD2v protein


title: PAM-GFP-rep1

description: Stable expression of GFP protein


title: HOMO4

city: Charleston

first: Carol

last: Feghali-Bostwick

state: SC

address: 96 Johnathan Lucas St Suite 816 MSC 637

department: Medicine - Rheumatology

institute: Medical University of South Carolina

data_processing:
Novogene: Original image data file from HTS platforms is transformed to sequenced reads ( Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
STAR software is used to accomplish the mapping. The alignment by STAR precisely and effectively performs positioning junction reads for RNA sequencing data analysis.
Gene expression level is calculated by the number of mapped reads with FeatureCounts. Read counts is proportional to gene expression level, gene length and sequencing depth, and is used for DE analysis.
DE analysis of two conditions/groups was performed using the DESeq2 R package (Anders et al., 2010). Significance criteria q-value<0.1, log2FC> |0.6|
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison …

source_name: primary lung fibroblasts_hIGFBP5

growth_protocol: lung fibroblasts were maintained in complete media

extract_protocol:
total RNA was extracted with trizol method
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA library prep kit for Illumina (NEB, USA).

tag: genotype

value: primary lung fibroblasts


title: PAM-CD2v-rep2

description: Stable expression of ASFV-CD2v protein


title: HCT116_25cells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
HCT116_25.bw


title: HCT116_500cells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
HCT116_500.bw


title: HCT116_500cells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
HCT116_500.bw


title: HOMO2


title: HCT116_5Kcells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
HCT116_5K.bw


title: Prostate tumor, HF_3

description:
DE-results-hf.csv; rnaseq_featurecounts.txt
61

tag: strain


title: HCT116_25cells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
HCT116_25.bw


title: HOMO1


title: HOMO3


title: CsEgg

source_name: eggs

value: eggs


title: HCT116_1Kcells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
HCT116_1K.bw


title: pESC2

city: Hohhot

first: manling

last: zhang

address: university west road

institute: Inner Mongolia University

data_processing:
Reads were aligned to the reference genome using Hisat2 v2.0.5 and paired-end clean  reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5).
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: gene_fpkm text file includes FPKM values for each Sample .
Supplementary_files_format_and_content: gene_count.txt file includes raw gene counts for every gene and every sample.

source_name: primed embryonic stem cells

extract_protocol:
RNA was harvested using Trizol reagent.A total amount of 1 μg RNA per sample was used as input material for the  the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primed embryonic stem cells converted from naive like embryonic stem cells

tag: cell passage number

value: passage 20


title: pESC1


title: WT4

source_name: primary lung fibroblasts_WT

value: wild type


title: HCT116_1Kcells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
HCT116_1K.bw


title: WT3


title: HCT116_100cells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
HCT116_100.bw


title: WT2


title: nESC2

source_name: naïve like embryonic stem cells

value: ICM derived naive like embryonic stem cells

value: passage 22


title: HCT116_100cells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
HCT116_100.bw


title: WT1


title: XEN3

source_name: extra-embryonic endoderm cells

value: ICM derived extra-embryonic endoderm cells

value: passage 23


title: PAM-GFP-rep2

description: Stable expression of GFP protein


title: GM12878_5Kcells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
GM12878_5K.bw

value: Lymphoblastoid cells


title: BO112+DMXAA treated tumors biological replicate 3

city: Pamplona

first: Jose

last: Gonzalez

state: Navarra

address: C/PIO XII s/n

country: Spain

institute: FIMA

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm39 whole genome using STAR
Counts were first normalized using the TMM (trimmed mean of M-values) normalization using edgeR package, then the log2CPM values were calculated using voom from limma package and the normalized expression matrix was used for the statistical analysis with limma (Ritchie et.al, 2015).
Genome_build: mm39
Supplementary_files_format_and_content: tab-delimited text files include log2CPM values for every gene and every Sample ...
Supplementary_files_format_and_content: tab-delimited text files with raw gene counts for every gene and every sample

growth_protocol: 4x105 MC38 tumor cells were subcutaneously injected in the right flank of C57BL/6 mice. When tumos reached aproximately 5mm, mice were treated intratumorally

extract_protocol:
Treated tumors were collected 24h after intratumoral treatment and storage in RNAlater (Sigma Aldrich) at -20C. Total RNA was isolated using the Rneasy Mini Kit (Qiagen) following manufacture's instructions.
TruSeq Stranded mRNA preparation Guide. Part
RNAseq with NovaSeq6000 150PE (150 x 2bp) 40 M reads/sample (6 Gb/sample)

treatment_protocol: Control groups received 100μL of vehiche control (PBS containing 5% DMSO and 5% glucose). BO-112 groups were treated with 50μg/100μL of BO-112 (Highlight Therapeutics). DMXAA groups were treated with 100μg/100μL of DMXAA. BO-112+DMXAA groups were treated with 50μg of BO-112 and 100μg of DMXAA in 100μL.

tag: tumor


title: BO112+DMXAA treated tumors biological replicate 4


title: DMXAA treated tumors biological replicate 4

value: DMXAA


title: GM12878_500cells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
GM12878_500.bw


title: IWR2

city: Seattle

first: Jeet

middle: H

last: Patel

state: WA

address: HSB J-Wing, J405

department: Biochemistry

institute: University of Washington

data_processing:
TrimGalore-0.6.5 was used to remove low quality reads (Phred33),  remove read pairs where either read was less than 35 bp, and trim adapter sequences
Pseudoalignment and count quantification was performed by Kallisto using an index built from the Xenopus tropicalis 9.1 transcriptome
Kallisto adjusted counts were converted to raw counts in order to process using edgeR
The counts table was made into a DGEList object and filtered for transcripts with low counts and scaled with the calcNormFactors command
Differential expression between 0hpa and DMSO (24hpa), and DMSO and each treatment group – 2ME, Ech, and IWR – were performed using glmQLFTest. To determine significance, p-values for each gene generated for the DMSO vs 2ME, Ech, and IWR conditions were ordered and corrected using the Benjamini-Hochberg procedure to identify false discovery rate (FDR).
Genome_build: Xentr9.1
Supplementary_files_format_and_content: tsv files contain Kallisto adjusted counts, edgeRCPMs.csv contains the normalized CPMs derived via edgeR

organism: Xenopus tropicalis

growth_protocol: Xenopus tadpoles were reared in 1/9 Modified Ringers solution at 23C

extract_protocol:
For 0hpa, ~250 um of tissue was collected anterior to the amputation plane. For 24hpa, the tadpoles were anestetized and ~250 microns of tissue was collected. RNA was extracted via phenol:chloroform extraction following by ethanol precipitation and DNAseI treatment.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions.

treatment_protocol: Tadpoles were anestetized at NF Stage 41 and the posterior third of the tail was amputated. For 24hpa, tadpoles were allowed to recover and reared at 23C in Modified Ringers containing the indicated treatments.

value: wild-type

tag: stage amputated

value: NF Stage 41 (3dpf)

tag: timepoint

value: 10 uM IWR-2


title: IWR3

tag: treatment

value: 10 uM IWR-3


title: IWR1

value: 10 uM IWR-1


title: BO112+DMXAA treated tumors biological replicate 2


title: XEN1

value: passage 26


title: GM12878_25cells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
GM12878_25.bw


title: GM12878_25cells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
GM12878_25.bw


title: DMXAA treated tumors biological replicate 3


title: DMXAA treated tumors biological replicate 2


title: GM12878_1Kcells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
GM12878_1K.bw


title: Ech3

value: 0.5 uM Echinomycin


title: Ech2


title: BO-112 treated tumors biological replicate 4


title: nESC1

value: passage 21


title: GM12878_100cells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
GM12878_100.bw


title: DMXAA treated tumors biological replicate 1


title: GM12878_1Kcells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
GM12878_1K.bw


title: 2ME3

value: 5 uM 2methoxyestradiol


title: Ech1


title: GM12878_100cells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
GM12878_100.bw


title: GM12878_5Kcells_One-pot universal NicE-seq_rep2

description:
Technical replicate2
GM12878_5K.bw


title: BO-112 treated tumors biological replicate 3


title: XEN2


title: 2ME2


title: BO112+DMXAA treated tumors biological replicate 1


title: 4%_formaldehyde_One-pot universal NicE-seq_rep2

description:
Technical replicate2
4percent_formaldehyde.bw

value: Colorectal cancer cells


title: GM12878_500cells_One-pot universal NicE-seq_rep1

description:
Technical replicate1
GM12878_500.bw


title: 2ME1


title: BO-112 treated tumors biological replicate 2


title: DMSO3

value: 0.1% DMSO control


title: DMSO2


title: 1%_formaldehyde_One-pot universal NicE-seq_rep1

description:
Technical replicate1
1percent_formaldehyde.bw


title: Vehicle control treated tumors biological replicate 2

value: Vehicle control


title: BO-112 treated tumors biological replicate 1


title: 0.2%_formaldehyde_One-pot universal NicE-seq_rep2

description:
Technical replicate2
0.2percent_formaldehyde.bw


title: 0.2%_formaldehyde_One-pot universal NicE-seq_rep1

description:
Technical replicate1
0.2percent_formaldehyde.bw


title: 0hpa3

value: untreated


title: Vehicle control treated tumors biological replicate 1


title: 0hpa2


title: 0hpa1


title: Oocytes XY rep2

city: Montreal

first: Dunarel

last: Badescu

address: 740 Dr Penfield Ave

department: Human Genetics

institute: McGill University

description:
Oocytes of 50-60 µm in diameter
XY-2_2-646658_S7_L001

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 SP Paired-end 150bp lane.
The primary reads were aligned to the GRCm38/mm10 mouse genome and transcriptome from Gencode, using Hisat2, in stranded and paired-end mode
Reads from the 5' exons, were demultiplexed, and UMIs counted, using regular expressions, according to the 5' end sequencing patterns
The read counts, corresponding to 5' UMIs, were normalized using ERCC spike-ins
Batch effects were assessed using Surrogate Variable Analysis sva, log-voom transformed using lv2Transformer, provided by the countTransformers R package, and regressed-out, using cleaningY function of the jaffelab R package
Genome_build: mm10
Supplementary_files_format_and_content: Raw matrix 5prime umi counts per million for every gene and every sample
Supplementary_files_format_and_content: Normalized matrix using ERCC, normalization of the 5prime umi matrix
Supplementary_files_format_and_content: Normalized matrix, log-voom transformed and with batch effects regressed out for every gene and every sample
Supplementary_files_format_and_content: Full length-coverage tracks in bigwig format for each sample

source_name: Oocytes XY

extract_protocol:
Total 30 oocytes (10 oocytes of 50-55 µm and 20 oocytes of 55-60 µm diameter) per sample were pooled in 10 µl lysis buffer (12 µM polyT primer, 0.4% Triton-X 100, 10 mM each dNTP, RNase inhibitor and ERCC) in biological triplicate for each genotype. Lysis was carried out in a thermocycler at 72C for 3 min, 4C for 10 min, and 25C for 1min, and the lysed samples were stored at -80C.
RNA libraries were prepared using an in-house Smartseq3 protocol, with modified oligo-dTVN: 5'-AGATGTGTATAAGAGACAGN12ACT30VN-3' and Template Switching Oligo (TSO): 5'-AGATGTGTATAAGAGACAGN12ACGCrGrGrG-3'

treatment_protocol: Ovaries were dissociated into single cells in phsophase buffer saline after treatment with collaganase and trypsin.

value: oocytes of growth phase

tag: age

value: 18 days post partum

value: XY


title: Oocytes XY rep3

description:
Oocytes of 50-60 µm in diameter
XY-3_2-646661_S10_L001

tag: tissue


title: Oocytes XY rep1

description:
Oocytes of 50-60 µm in diameter
XY-1_2-646655_S4_L001


title: Oocytes XO rep3

description:
Oocytes of 50-60 µm in diameter
XO-3_2-646664_S13_L001

source_name: Oocytes XO

value: XO


title: Oocytes XO rep2

description:
Oocytes of 50-60 µm in diameter
XO-2_2-646663_S12_L001


title: Oocytes XX rep3

description:
Oocytes of 50-60 µm in diameter
XX-3_2-646660_S9_L001

source_name: Oocytes XX

value: XX


title: Oocytes XO rep1

description:
Oocytes of 50-60 µm in diameter
XO_2-646652_S1_L001


title: 4%_formaldehyde_One-pot universal NicE-seq_rep1

description:
Technical replicate1
4percent_formaldehyde.bw


title: Primary CFs p4

first: Adam

middle: Jeffrey

last: Engler

state: CA

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: UC San Diego

description:
From Age 46 Male Donor, from Cell Biologics, cat #: H-6049, Lot #: M072117Y46IIAM, cryopreserved: 7/21/2017
Primary.cardiac.fibroblasts..passage.4..late.

data_processing:
All data processing was performed by UCSD Center for Epigenomics using the following pipeline: https://github.com/epigen-UCSD/atac_seq_pipeline
Additional details can be found: https://biomystery.gitbooks.io/ataq_seq/content/pipeline/overall_steps.html
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files, show peak locations across the genome, easy format to visualize on genome browsers quickly

source_name: Primary Cardiac Fibroblasts

growth_protocol: Based on Bao et al protcol, varies by developmental stage, see publication

extract_protocol:
Extraction was perfomed by the UCSD Center for Epigenomics using the following protocl: https://medschool.ucsd.edu/som/cmm/research/epigenomics/Partnerships/Documents/EPIGEN_ATACseq_cells%20protocol_05102019.pdf
Libraries were constructed using a protocol adapted from Buenrostro et. al (doi: 10.1002/0471142727.mb2129s109) by the UCSD Center for Epigenomics (https://medschool.ucsd.edu/som/cmm/research/epigenomics/Partnerships/Documents/EPIGEN_ATACseq_cells%20protocol_05102019.pdf)

tag: source/clone id

value: Primary Cardiac Fibroblasts, passage 4

value: CF

tag: assay

value: Tn5 ATAC-Seq


title: Primary CFs p1

description:
From Age 46 Male Donor, from Cell Biologics, cat #: H-6049, Lot #: M072117Y46IIAM, cryopreserved: 7/21/2017
Primary.cardiac.fibroblasts..passage.1..early.

value: Primary Cardiac Fibroblasts, passage 1

tag: cell type


title: C512 TAL1-9 CF p4

source_name: iPSC-Derived Cardiac Fibroblasts

value: Cardiac Fibroblasts from Clone 2


title: Vehicle control treated tumors biological replicate 3


title: Oocytes XX rep2

description:
Oocytes of 50-60 µm in diameter
XX-2_2-646657_S6_L001


title: 1%_formaldehyde_One-pot universal NicE-seq_rep2

description:
Technical replicate2
1percent_formaldehyde.bw


title: C512 TAL1-9 CPC p1

source_name: iPSC-Derived Cardiac Progenitor Cells

value: Cardiac Progenitor Cells from Clone 2

value: CPC


title: DMSO1

value: wild-type

value: NF Stage 41 (3dpf)


title: C2C12_D5_myotubes_rep3

city: New York

first: Lydia

last: Finley

state: NY

address: 430 E 67th St

department: Cell Biology Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Quality control and filtering of raw fastq files was performed using fastp.
Sequencing reads were aligned to mm10 using STAR.
Raw counts were generated using featurecounts.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files include raw counts for each sample in CSV format.

growth_protocol: C2C12 cells were maintained as myoblasts at sub-confluence unless otherwise noted. Myoblasts were cultured in high glucose DMEM supplemented with 10% FBS and 4 mM L-glutamine. For differentiation into myotubes, C2C12 cells were grown to 100% confluence for three days and then washed with PBS and changed into differentiation medium composed of high glucose DMEM supplemented with 2% horse serum (Gibco), 4 mM L-glutamine and 100X insulin-transferrin-selenium-ethanolamine (ITS-X; Gibco) for the 5 days.

extract_protocol:
RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

tag: cell line background

value: myotubes


title: C2C12_D5_myotubes_rep2


title: S47 Healthy controls

city: Karachi

first: Asghar

last: Nasir

state: Sindh

address: Stadium Road

department: Pathology and Laboratory Medicine

country: Pakistan

institute: Aga Khan University

description: gene expression data

hyb_protocol: Clariom S Array Type gene expression, Affymetrix

scan_protocol: GeneChipTM Scanner 3000 7G

data_processing: CEL files were analysed using the TCAS Transcriptome Analysis Software Suite (version 2) using the Summarization Method: Gene Level - SST-RMA Pos vs Neg AUC Threshold: 0.7 against Genome Version: hg38 (Homosapiens)

source_name: blood

growth_protocol: RNA was extracted from whole blood collected in Plasma/EDTA tube.

extract_protocol: Qiagen RNA Blood Mini Kit (Qiagen, GmbH, Germany)

treatment_protocol: no treatment

tag: disease state

value: healthy control

tag: symptons

value: Healthy controls


title: C2C12_D5_myotubes_rep1


title: C512 TAL1-5 CF p5

value: Cardiac Fibroblasts from Clone 1


title: S46 Healthy controls

description: gene expression data

label_protocol: Clariom S Array Type gene expression, Affymetrix


title: S44 Healthy controls

description: gene expression data


title: S45 Healthy controls

description: gene expression data


title: S43 Healthy controls

description: gene expression data


title: C2C12_myoblasts_rep3

value: myoblasts


title: S42 Healthy controls

description: gene expression data


title: S40 Healthy controls

description: gene expression data


title: S41 Healthy controls

description: gene expression data


title: S39 Healthy controls

description: gene expression data


title: C2C12_myoblasts_rep2


title: C512 TAL1-9 EpiC p5

source_name: iPSC-Derived Epicardal Cells

value: Epicardial Cells from Clone 2

value: EpiC


title: MUT2

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: Illimuna next-generation sequencing (2x150bp, paired-end)

data_processing:
RNA-Seq data was analyzed using a Salmon-tximport-DEseq2 pipeline. Raw sequence reads (FASTQ format) were mapped to the reference human genome assembly (GRCh38/hg38, GENCODE release 36) and quantified with Salmon (DOI: 10.1038/nmeth.4197). Gene-level counts were imported with tximport (DOI: 10.12688/f1000research.7563.2) into DESeq2 (DOI: 10.1186/s13059-014-0550-8) and normalized.
Processed data is a data matrix of normalized read counts generated from the output of Salmon, imported wih tximport, and normalized with DESeq2. GENCODE release 36 was used for annotation. The file contains the Ensembl ID and normalized gene-level read count data for each sample.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Data matrix in tab-delimited text format. The file contains the Ensembl ID and normalized, gene-level counts for each sample.

source_name: human primary effusion lymphoma

growth_protocol: BCBL-1 xenogrft tumors were established and grown by intraperitoneal (i.p.) injection of BCBL-1 cells (2 x 10^7 cells in 200 uL PBS) into eight-week-old male NRG (NOD.Cg-Rag1tm1Mom Il2rgtm1Wjl/SzJ).

extract_protocol:
Total RNA was isolated using the TRIzol Reagent (Invitrogen).
Indexed, stranded mRNA-seq libraries were prepared from total RNA (100 ng) using the KAPA Stranded mRNA-Seq (Roche) according to the manufacturer’s standard protocol.

treatment_protocol: On day 2 (i.e., 24 hours after injection of BCBL-1 cells), mice were randomly assigned to PBS control, MBK50 (10 mg/kg), or mutant control peptide (10 mg/kg) groups. Treatments were administered by daily i.p. injection for 10 days.

tag: xenograft tumor

value: mutant type peptide (10 mg/kg, i.p. injection, daily) for 10 days

tag: mouse strain for xenograft growth

value: NRG (NOD.Cg-Rag1tm1Mom Il2rgtm1Wjl/SzJ)


title: S38 Healthy controls

description: gene expression data


title: C2C12_myoblasts_rep1


title: all_cells_tcr

city: Baltimore

first: Christopher

last: Cherry

state: MD

address: 1800 Orleans St

institute: Johns Hopkins University

description:
RNA
TCR VDJ for all samples

data_processing:
CellRanger with default parameters
Genome_build: CellRanger premade references; mm10
Supplementary_files_format_and_content: ZIP file containing filtered CellRanger output for hashing, BCR, TCR library

source_name: All samples pooled with hashing

extract_protocol:
Murine tissue samples (quadriceps femoris muscle and inguinal lymph nodes) were obtained for single cell flow cytometry and/or fluorescence activated cell-sorting. Quad tissue samples were finely diced and digested with 1.67 Wünsch U/mL Liberase TL (Roche Diagnostics) and deoxyribonuclease I (0.2 mg/ml; Roche Diagnostics) in RPMI-1640 medium (Gibco) for 45 min at 37°C. The digested quad tissues were ground through 70-µm cell strainers (Thermo Fisher Scientific), rinsed with RPMI-1640 + 5% fetal bovine serum. Percoll (GE Healthcare) density gradient centrifugation was used to remove debris from quad digestions and enrich the leukocyte fraction. Inguinal lymph node samples were ground through 70-µm cell strainers with excess RPMI-1640 + 10 mM HEPES buffer solution. The enriched single-cell suspensions were washed and stained following antibody panels, respective to the intended application. No differences in single-cell isolation from different material environments were observed.
According to 10X protocol
All samples were pooled into one after hashing. The library was split appropriately into sequencing lanes as needed for sequencing depth.


title: Oocytes XX rep1

description:
Oocytes of 50-60 µm in diameter
XX-1_2-646654_S3_L001

value: oocytes of growth phase

value: 18 days post partum

tag: genotype

value: XX


title: C512 TAL1-9 iPSC p52

city: La Jolla

source_name: Induced Pluripotent Stem Cells

value: iPSC Clone 2

value: iPSC

value: Tn5 ATAC-Seq


title: MUT1


title: all_cells_bcr

description:
RNA
BCR VDJ for all samples

tag: strain


title: S35 Healthy controls

description: gene expression data


title: C512 TAL1-5 CPC p1

value: Cardiac Progenitor Cells from Clone 1

value: CPC


title: S37 Healthy controls

description: gene expression data


title: A549_HDACi_timecourse_DEX

first: Hyeon-Jin

last: Kim

address: 3720 15th Ave NE

department: Genome Sciences

description: sci-RNA-seq profiles and hash ladder calibration lines of A549 cells exposed to 10 uM of Abexinostat or Pracinostat for increasing amounts of time or DMSO control (HDACi timecourse) or varying dose and time of Abexinostat, Pracinostat or DMSO control in combination with 100 nM of dexamethasone or EtOH control (HDACi and DEX co-treatment).

data_processing:
Illumina RTA software used for basecalling.
The sci-RNA-seq libraries were processed according to the protocol described in Srivatsan et al. First, Illumina reads were demultiplexed using bcl2fastq (v2.20). Custom scripts were used to extract barcodes that match reverse transcription (RT) indices within Levenstein distance cutoff of 2. After RT barcode matching, poly(A) sequences were trimmed using trim-galore, and the trimmed reads were aligned to  hg38  using STAR aligner (v2.5.2b) with default settings. The aligned reads were filtered with MAPQ >= 30, deduplicated, and collapsed by unique molecular identifiers (UMIs). The deduplicated reads were then assigned to genes using bedtools intersect function with an annotated human gene model. Knee plots were then generated from UMI counts per cell barcode to filter out true cell barcodes from debris. Thresholds were selected on a per-experiment basis and gene expression profiles from cell barcodes with total UMI counts greater than the knee threshold were used to generate a CDS object for downstream analysis.
The hash IDs were assigned sample labels as described in Srivatsan et al. In summary, reads from hash oligos were extracted from the demultiplexed read files by matching the first 10 bp of read 2 to the hash barcodes with the Levenstein distance of 2 and looking for trailing poly(A) sequences from position 12-16 bp. These reads were deduplicated and collapsed by UMIs, which were then used for sample assignment and hash ladder calibration line construction.
Genome_build: GRCh38
Supplementary_files_format_and_content: _UMI.count.matrix: single cell gene expression data in a sparse matrix format (gene_index | cell_index | gene_count).
Supplementary_files_format_and_content: _cell.annotations: Cell annotation file (cell_barcode | experiment name).
Supplementary_files_format_and_content: _gene.annotations: Gene annotation file (gene_id | gene_short_name).
Supplementary_files_format_and_content: _hashLadderSampleSheet.txt: Sample sheet for hash oligos used for calibration.
Supplementary_files_format_and_content: _hashIDSampleSheet.txt: Sample sheet for hash oligos used for labeling different treatment conditions.
Supplementary_files_format_and_content: _hash-ladder-exp.txt: Sample sheet for hash oligos used for labeling different treatment conditions.
Supplementary_files_format_and_content: _hashID-annotation.txt: Sample sheet for hash oligos used for labeling different treatment conditions.
Supplementary_files_format_and_content: _hashTable.out: Table that contains hash ladder oligo counts for each cell in the experiment.
Supplementary_files_format_and_content: _hashTable-labels-filtered.out: Table that contains hash ID oligo counts for each cell in the experiment.
Supplementary_files_format_and_content: _hashTable_unique_filtered.txt: Table that summarizes hash ladder calibration lines in each cell
Supplementary_files_format_and_content: _cds_conv.rds: Monocle3 cds object constructed with conventional size factor normalization.
Supplementary_files_format_and_content: _cds_hash_ladder.rds: Monocle3 cds object constructed with hash ladder based size factor normalization.

source_name: Cell line

growth_protocol: A549 and HEK293T cells were cultured in DMEM (Gibco) media containing 10% fetal bovine serum (Invitrogen) and 1% penicillin and streptomycin (Gibco) at 37°C with 5% CO2.

extract_protocol:
After drug treatment, cells were harvested via trypLE incubation and lysed with ice cold cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Extracted nuclei were then labeled with hash oligos by paraformaldehyde fixation with appropriate hash oligos and subjected to sci-RNA-seq (Cao et al. 2017). Detailed protocol is described in the method section of the manuscript.
sci-RNA-seq libraries were prepared by following the protocol described in Cao et al. 2017 and Srivatsan et al. 2020.

treatment_protocol: For the proof of concept experiment, HEK293T cells were grown in a T-75 flask. For the flavopiridol time course experiment, HEK293T cells were seeded onto a 6-well culture plate at a density of 400,000 cells per well in 2 mL of media. For the HDAC inhibitor time course and HDAC inhibitor and dexamethasone co-treatment experiments, A549 cells were seeded onto a 96-well culture plate at a density of 25,000 cells per well in 100 μL of media.

tag: cell line

value: mixed sample (non-demultiplexed):HDACi timecourse:10 uM of Abexinstat or Pracinostat for 0(DMSO),0.5,1,3,6,12,24 hours. HDACi and DEX co-treatment:1 or 10 uM of Abexinstat or Pracinostat for 0(DMSO),4,24 hours. 100 nM of dexamethasone for 0 or 2 hours prior to harvest


title: HEK293T_proof-of-concept

description: sci-RNA-seq profiles and hash ladder calibration lines of HEK293T cells


title: WT2

value: MBP50 wild type peptide (10 mg/kg, i.p. injection, daily) for 10 days