title: g5, umbilical cord blood sample 17

description:
g5 umbilical cord blood sample
3111

tag: pregnancy complication

tag: batch


title: Patient_ENDPOP03_Control

status: Public on May 26 2022

type: RNA

city: Bialystok

first: Iwona

last: Sidorkiewicz

address: Sklodowska-Curie Street 24a

department: Clinical Research Centre

country: Poland

institute: Medical University of Bialystok

hyb_protocol: The samples were prepared for nCounter miRNA expression profiling according to the manufacturer’s recommendations (NanoString Technologies, USA). Briefly, 3 ng miRNA samples were prepared by ligating a specific miR-tag onto 3′ end of each mature miRNA followed by an overnight hybridization (65 °C) to nCounter Reporter and Capture probes. Subsequently, samples were placed into the nCounter Prep Station for automated sample purification and subsequent reporter capture.

scan_protocol: Each sample was scanned on the nCounter Digital Analyzer for data collection.

data_processing: nSolver 4.0 Analysis software (NanoString) was used for data analysis including normalization using the average geometric mean of the top 100 probes detected. The p-values were adjusted using the False Discovery Rate (FDR) correction for multiple comparisons, which was limited to 0.05

molecule: total RNA

organism: Homo sapiens

source_name: FFPE

label_protocol: Specific oligonucleotide probe pairs that are bound to barcoded tags (nanostring technologies inc.) were conducted according to the manufacturer's protocol.

growth_protocol: not applicable

extract_protocol: miRNeasy FFPE kit (Qiagen, Germany) according to the manufacturer’s instructions

treatment_protocol: not applicable

tag: disease state

value: Control

tag: tissue

value: control (normal thyroid)


title: Patient_ENDPOP04_FTC

value: FTC

tag: tnm staging system

tag: tumor size

tag: multifocalization

tag: angioinvasion

tag: lymph node metastasis


title: g5, umbilical cord blood sample 15

type: genomic

city: Maastricht

first: Rebekka

middle: Maria

last: Koeck

address: Maastricht UMC+

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Centre

description:
g5 umbilical cord blood sample
3152

hyb_protocol: bisulphite converted DNA (EpiTect - Qiagen) was hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: The raw data were processed in R using the RnBeads package. SWAN normalisation was carried out before greedycut (p-value threshold 0.05) filtering was applied to remove poor quality sites and samples. Further filtering was carried out to remove sites (i) on the sex chromosomes, (iii) near single nucleotide polymorphisms, (iii) with missing values in 5% or more of the samples, (iv) sites not in a CpG context. Samples were also excluded if their predicted sex, predicted using the sEst package, did not match the recorded sex. The values presented are methylation beta values.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: umbilical cord blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from umbilical cord blood samples using the Gentra Puregene DNA purification kit (Qiagen Hilden, Germany) according to the manufacturer's instructions with modifications to the red blood cell lysis solution (8.5mL) and the centrifugation time 4 or 8 minutes instead of 2 and 5, respectively).

tag: culture medium

tag: Sex

value: F

tag: maternal age

tag: gestational age

value: no

tag: birthweight


title: Patient_ENDPOP02_PTC

value: PTC


title: htf, umbilical cord blood sample 14

description:
htf umbilical cord blood sample
3160

value: htf

value: M


title: in vitro TEX day 0 replicate 2

type: SRA

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

country: USA

institute: Stanford University

library_source: genomic

data_processing:
Reads were trimmed and quality filtered using fastp.
Reads were aligned to mm10 or hg38 using hisat2
Aligned reads were de-duplicated using Picard
Mitochondrial reads and Y chromosome reads were removed
Peaks were called for each sample using MACS2, merged into a union peak set, and the peak by count matrix was loaded into DESeq2 for differential analysis
Assembly: mm10 or hg38
Supplementary files format and content: Genome tracks files were created by using the deduplicated reads, normalizing each sample using counts in TSS, and exported from R as bigwig files.

organism: Mus

source_name: primary CD8 T cells

growth_protocol: Primary T cells were isolated from mouse spleen or human blood and cultured in media containing IL-2

extract_protocol:
Live CD8+ T cells were isolated by FACS and subjected to ATAC-seq
Omni ATAC-seq was performed as previously described (Corces et al Nature Methods 2017)

treatment_protocol: After activation, T cells were plated on chronic stimulation (anti-CD3 coated) plates to induce exhaustion

tag: cell type

value: primary CD8 T cells

tag: days of_anti-cd3_stim

tag: sgrna

tag: sgrna delivery


title: in vitro TEX day 0 replicate 1


title: g5, umbilical cord blood sample 36

description:
g5 umbilical cord blood sample
2068

tag: pregnancy complication

tag: batch


title: in vitro TEX day 0 replicate 3


title: human TEX ARID1A sg60 donor 3

value: ARID1A sg60

value: Cas9 RNP


title: human TEX ARID1A sg60 donor 7


title: g5, umbilical cord blood sample 32

description:
g5 umbilical cord blood sample
5121

value: hyp


title: NE_Isha_R3

city: Bethesda

first: Elissa

last: Lei

state: MD

address: 50 South Drive

department: Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics

institute: NIDDK/NIH

library_source: transcriptomic

data_processing:
removing adapter sequences with cutadapt v2.9 with parameters “–q 20 -minimum-length 25 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA” to remove low quality reads and adaptors.
Resulting reads were mapped to the FlyBase r6-35 reference genome using HISAT2 v2.2.1. Duplicated reads are marked by picard v2.22.2 .
Aligned reads were counted using subread featureCounts (subread v2.0.0) with “-t gene -s1” for this sense-stranded library.
Differential expression analysis was done between the IP and input samples with DESeq2 v1.32.0 in R v4.1.0.
Assembly: dm6
Supplementary files format and content: featurecounts output  and fastq files

organism: Drosophila melanogaster

source_name: 0-24h mixed staged embryos

growth_protocol: Embryos aged 0–24 h were collected from wild-type Oregon R raised at RT in population cages fed with yeast and molasses. Embryos were dechorionated with 50% bleach, washed and stored at –80 °C to produce nuclear extracts (Caravaca, 2016).

extract_protocol:
Drosophila nuclear extract was prepared from 30 g of mixed stage (0–24 h) embryos as described previously (Bag et al., 2021) and nuclei were lysed with HBSMT buffer, supplemented with 1 U/μl RNasin (Promega). 12 mg nuclear extract was used per IP. Nuclear extracts were incubated with 600 μl Protein A conjugated sepharose (cytiva) prebound to 300 μl preimmune rabbit serum on rotator for 1 h at 4°C. Then precleared extracts were then transferred to 600 μl Protein A sepharose prebound to 300 μl rabbit anti-serum against Isha and incubated rotating for 1 h at 4°C. Next, beads were washed in HBSMT three times and HBSM twice. Bound RNA was isolated directly from Protein A beads by acid Phenol:Chloroform (Thermo Fisher Scientific) extraction followed by ethanol precipitated with 3 M NaOAc. RNA was DNase I (Roche) treated and purified further using acid Phenol:Chloroform extraction and ethanol precipitation. Then RNA was chemically fragmented using RNA Fragmentation Reagents (Thermo Fisher Scientific) and purified by ethanol precipitation with 3 M NaOAc.
100 ng of RNA was used for each RNA-seq library preparation using Ovation RNA-seq Systems 1–16 for Model Organisms (Nugen) according to manufacturer’s instruction. Then samples were sequenced on HiSeq3000 (Illumina) using 50 bp single-end sequencing at the NIDDK Genomics Core Facility.

treatment_protocol: Nuclear extract (NE) was preapared from 30 g of mixed stage (0–24 h) embryos as described previously (Bag et al., 2021).

tag: developmental stage

value: embryo

tag: age

value: 0-24h mixed staged

tag: treatment

value: Isha-RIP

tag: rip antibody


title: Gill tissue - 14d normoxia

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Raw sequencing data were processed using the CellRanger (v5.0.0, 10X Genomics) software with default paramters and a custom reference built from the Ensembl release 101 Danio rerio annotation (built on the GRCz11 assembly), plus an EGFP sequence.
FASTQ files were generated using the Cell Ranger mkfastq function, and cells were counted using Cell Ranger count.
MULTIseq barcodes were processed using the deMULTIplex pipeline to associate cells with their sample of origin
Filtered count matrices (filtered_feature_bc_matrix) were loaded into R as a sparse matrix with the Seurat::Read10X() function. Sample barcodes were demultipliexed using the standard deMULTIplex workflow (https://github.com/chris-mcginnis-ucsf/MULTI-seq).
Data were processed with Seurat to count the percentage of mitochondrial UMIs per cell, and data were filtered to retain only cells with <45% mitochondrial UMIs and >100 detected genes. Cell doublets were removed with DoubletFinder, assuming a 7.5% doublet formation rate.
Raw counts were normalized to depth per 10,000 reads and log normalized. Variable genes were identified and their values Z-scaled. The three libraries were merged into a single Seurat object. Dimensional reduction was performed with PCA, and cells were projected into UMAP space for visualization; cell clusters were identified with the Seurat FindClusters() function.
Fastq files from two NextSeq 500 runs were concatenated into a single file for each read for each library. Fastq files are included for both single cell GEX data (_SC_ files) and MULTI-seq barcodes (_barcode_ files)
Genome_build: GRCz11
Supplementary_files_format_and_content: RDS (serialized R object) containing data processed with seurat for all three libraries.

organism: Danio rerio

source_name: Distal gill filament

extract_protocol:
Distal filaments of gills were trimmed off, trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell 3’ Assay.
cDNA synthesis and library construction were carried out according to the manufacturer’s protocol and the resulting cDNA libraries were amplified using PCR.
Single cell samples were sequenced on a NextSeq 500 sequencing system.

tag: genotype

value: 14 days of normoxia


title: Gill tissue - 14d hypoxia

value: 14 days of hypoxia


title: human TEX ARID1A sg58 donor 5

value: ARID1A sg58


title: single_cell_TCRb

city: New York

first: Roham

last: Parsa

state: NY

address: 1230 York Avenue

institute: Rockefeller University

description: single cell RNA

data_processing:
Library strategy: TCR-seq
Fastq files were de-multiplexed and paired-end reads were assembled at their overlapping region using the PANDASEQ (Masella et al., 2012) and FASTAX toolkit. Demultiplexed and collapsed reads were assigned to wells according to barcodes.
Fasta files from MiSeq sequences were then aligned and analyzed on IMGT (http://imgt.org/HighV-QUEST) (Brochet et al., 2008). Cells with identical TCRb CDR3 nucleotide sequences were considered as the same clones
Supplementary_files_format_and_content: tab-delimited csv file

organism: Mus musculus

source_name: Small intestine epithelium

extract_protocol:
For single cell TCRseq: Single cells were index-sorted using a FACS Aria into 96-well plates containing 5µL of lysis buffer (TCL buffer, QIAGEN 1031576) supplemented with 1% b-mercaptoethanol) and frozen at -80 C prior to RT-PCR.
PCR products for TCRb were multiplexed with barcodes and submitted for MiSeq sequencing (Han et al., 2014) using True Seq Nano kit (Illumina). sequences were considered as the same clones.

tag: strain

tag: tissue

value: Small intestine epithelium

tag: time

value: multiplexed sample:10 and 30 days post treatment

tag: infection status

value: multiplexed sample:mAdV-2 infection and PBS control


title: NE_Isha_R1


title: NE_input_R3

value: input


title: human TEX ARID1A sg60 donor 5


title: NE_Isha_R2


title: human TEX ARID1A sg58 donor 7


title: Patient_ENDPOP01_PTC

tag: disease state

value: PTC

tag: tnm staging system

tag: tumor size

tag: multifocalization

tag: angioinvasion

tag: lymph node metastasis


title: H48

city: Qingdao

first: Zhen

last: Sun

address: Room 808, Block D, Haike Business Center Qingdao Oceantec Valley Jimo

country: China

institute: QINGDAO SINO-CELL BIOMED CO., LTD.

data_processing:
Read quality was checked for each sample using FastQC.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified  software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the  secondary structures.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean  datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without  3’adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time,  Q20, Q30, and GC-content of the raw dataswere calculated. Then, chose a certain range of length from clean reads to  do all the downstream analyses.
Predicting the target gene of miRNA was performed by psRobot_tar in psRobot (Wu et al, 2012) for plants or miRanda  (Enright et al, 2003) for animals.
Genome_build: miRBase20.0 was used as reference, modified  software mirdeep2(Friedlander et al., 2011)
Supplementary_files_format_and_content: TPM.txt:  Tab-delimited text file includes TPM for sample.

source_name: Exosome

extract_protocol:
Exosomes were collected, and RNA was harvested using exoRNeasy Maxi Kit.
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Small RNA libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina®. The libraries were sequenced on an Illumina platform by Novogene corporation.

tag: sample type

value: cell culture supernatant


title: htf, umbilical cord blood sample 12

description:
htf umbilical cord blood sample
3087

tag: culture medium

value: htf

tag: Sex

value: M

tag: maternal age

tag: gestational age

tag: pregnancy complication

value: no

tag: birthweight

tag: batch


title: htf, umbilical cord blood sample 31

description:
htf umbilical cord blood sample
3083


title: Murine MC3T3 cell strain derived exosome, 3

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: Excel, normalized expression profiles

source_name: MC3T3 osteoblast precursor cell

growth_protocol: 1%FBS low-glucose DMEM were used as culture medium for osteoclast and osteoblast cell culture. When cells reach 70% confluent, the cells were ready to perform exosome collection. For exosome collection, the medium were collected at a 3-days interval for exosome collection.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA libraries according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

tag: cell type

value: MC3T3 osteoblast precursor cell

value: small extracellular vesicles

tag: treatment

value: untreated


title: human TEX AAVS sg1 donor 5

value: primary CD8 T cells

tag: days of_anti-cd3_stim

tag: sgrna

value: AAVS sg1

tag: sgrna delivery

value: Cas9 RNP


title: human TEX ARID1A sg58 donor 3


title: NE_input_R1

tag: developmental stage

value: embryo

tag: age

value: 0-24h mixed staged

tag: rip antibody


title: htf, umbilical cord blood sample 8

description:
htf umbilical cord blood sample
3168


title: Murine MC3T3 cell strain derived exosome, 1


title: g5, umbilical cord blood sample 10

description:
g5 umbilical cord blood sample
3187


title: human TEX AAVS sg1 donor 3


title: IL-1b treated Murine Osteoclast derived exosome, rep3

source_name: Osteoclast

value: Osteoclast


title: NE_input_R2


title: g5, umbilical cord blood sample 7

description:
g5 umbilical cord blood sample
5117

value: F


title: human TEX AAVS sg1 donor 7


title: Gill tissue - combined normoxia and hypoxia

tag: genotype

value: normoxia and hypoxia samples combined


title: Murine MC3T3 cell strain derived exosome, 2

tag: sample type


title: Kc167_IshaKD_CP190_R2

data_processing:
ChIP-seq reads were aligned to the Flybase r6-35 genome assembly  using Bowtie2 v2.4.1
Multimapping reads removed with samtools v1.9 using “view” subcommand and the additional argument “-q 20”, duplicated reads were removed with Picard v2.22.2
SPP (http://compbio.med.harvard.edu/Supplements/ChIP-seq/) was used to call peaks based on IP and input BAMs using arguments “-FDR 0.05”.
For Isha, we used additional parameter “srange = (50, 500)”. For CP190, Su(hw) and Mod(mdg4)67.2, we used “srange = (50, 300)” in SPP.
Peaks present in two replicates are overlapped by using subsetByOverlaps() in R package IRanges v2.26.0.
Assembly: dm6
Supplementary files format and content: bed and bigWig

growth_protocol: Kc167 cells-derived from Drosophila embryo, were routingly maintained in CCM3 (Thermo Scientific HyClone, Logan, UT). The cells were maintained in monolayer at 25°C.

extract_protocol:
Total of 2–3 × 107 cells were fixed with 1% formaldehyde and chromatin was prepared as described previously (Bag et al., 2021). 300 µg of chromatin was diluted to 1:5 with IP dilution buffer and incubated with rabbit normal serum for 1h on rotator at 4 °C. Then precleared chromatin was collected by centrifugation at 2000g for 5 min at 4 °C. Chromatin was added to 100 µl prewashed Protein A Sepharose beads (cytiva) and 50 µL of rabbit anti-serum against Isha and rotated overnight at 4°C. The next day beads were washed with the following wash buffers: two times with low-salt wash buffer (20 mM Tris-HCl pH 8, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.1% SDS), two times with high-salt wash buffer (20 mM Tris-HCl pH 8, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS), and once with LiCl wash buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% deoxycholate). Chromatin was eluted two times with 200 μl of elution buffer (0.1 M NaHCO3, 1% SDS) for 30 min at 65°C each in a thermomixer at 800 rpm. Then chromatin was de-crosslinked with solution (20 μl of 5 M NaCl, 8 μl of 0.5 M EDTA, 10 μl of 1 M Tris-HCl pH 8) by incubating overnight at 65°C. After de-crosslinking, elutes were treated with 4 µl of proteinase K (20 mg/ml) for 2 h at 50°C and further purified using phenol-chloroform followed by ethanol precipitation with 0.1 vol of 3 M NaOAc pH 5.2 and 2.5 vol of 100% ethanol supplemented with 2 μl of Glycoblue (Ambion) and incubated overnight at −80°C. Next day, samples were centrifuged at 10,000 g for 20 min at 4°C and pellets were washed with 70% ethanol. Pellets were air-dried at room temperature and then resuspended with 10 μl of nuclease-free water. For Chromatin immunoprecipitation with guinea pig anti-serum against Su(Hw), rabbit anti-serum against CP190, rabbit anti-serum against Mod(mdg4)67.2 followed the same methods as mentioned earlier (Bag et al., 2021).
ChIP-seq library was performed as described previously (Bag et al., 2021). All samples were sequenced with HiSeq3000 (Illumina) using 50 bp single-end sequencing.

treatment_protocol: 10 million Kc167 cells were transfected with 12 µg of dsRNA against Isha by using Amexa cell line Nucleofector kit V (Lonza) and incubated 5 days at 25°C to obtain significant knockdown of Isha.

tag: cell line

value: Kc167 cells

value: female

value: IshaKD

tag: chip antibody


title: Kc167_IshaKD_CP190_R1

tag: Sex


title: IL-1b treated Murine Osteoclast derived exosome, rep1


title: Kc167_IshaKD_SuHw_R2

value: SuHw


title: g5, umbilical cord blood sample 9

description:
g5 umbilical cord blood sample
3089

tag: culture medium

value: M

tag: maternal age

tag: gestational age

value: hyp


title: Kc167_IshaKD_SuHw_R1


title: HCC1143 ReA

city: Gyeonggi-do

first: Hyonchol

last: Jang

address: 323, Ilsan-ro, Ilsandong-gu, Goyang-si

country: South Korea

institute: National Cancer Center

data_processing:
Sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Homo sapiens (hg19) using HISAT v2.1.0
HISAT utilizes two types of indexes for alignment (a global, whole-genome index and tens of thousands of small local indexes). These two types’ indexes are constructed using the same BWT (Burrows–Wheeler transform)/ a graph FM index (GFM) as Bowtie2.
The reference genome sequence of Homo sapiens (hg19) and annotation data were downloaded from the UCSC. Transcript assembly and abundance estimation using StringTie
After alignment, StringTie v1.3.4d was used to assemble aligned reads into transcripts and to estimate their abundance. It provides the relative abundance estimates as Read Count values of transcript and gene expressed in each sample. Also transcript assembly of known transcripts, novel transcripts, and alternative splicing transcripts was processed by StringTie v1.3.4d.
expression abundance of transcript and gene were calculated as read count or FPKM value (Fragments Per Kilobase of exon per Million fragments mapped) per sample
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

source_name: breast

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using Illumina TruSeq mRNA Sample Prep kit, according to the manufacturer's protocol.

value: breast

value: breast cancer cell lines

value: reattached tumor sphere cells under the same conditions as the parental cells


title: HCC1143 parental

value: control


title: Murine Osteoclast derived exosome, rep3

value: small extracellular vesicles

value: untreated


title: Kc167_mock_MOD_R2

value: embryo

value: mock

value: MOD


title: Kc167_IshaKD_input_R1


title: Murine Osteoclast derived exosome, rep1

value: Osteoclast


title: IL-1b treated Murine Osteoblast derived exosome, rep3

source_name: Osteoblast

value: Osteoblast


title: Murine Osteoclast derived exosome, rep2


title: Kc167_IshaKD_input_R2

value: Kc167 cells


title: htf, umbilical cord blood sample 6

description:
htf umbilical cord blood sample
4048

value: htf

value: F

tag: pregnancy complication

value: no

tag: birthweight

tag: batch


title: IL-1b treated Murine Osteoblast derived exosome, rep2

tag: cell type

tag: treatment


title: g5, umbilical cord blood sample 1

description:
g5 umbilical cord blood sample
5053

value: M


title: Murine Osteoblast derived exosome, rep3


title: Murine Osteoblast derived exosome, rep2


title: IL-1b treated Murine Osteoclast derived exosome, rep2


title: IL-1b treated Murine Osteoblast derived exosome, rep1


title: Kc167_mock_SuHw_R2

value: female

value: SuHw


title: Kc167_mock_input_R2


title: htf, umbilical cord blood sample 13

description:
htf umbilical cord blood sample
3074


title: Kc167_IshaKD_Isha_R2

value: IshaKD


title: g5, umbilical cord blood sample 5

description:
g5 umbilical cord blood sample
3171

value: hyp


title: htf, umbilical cord blood sample 3

description:
htf umbilical cord blood sample
5135


title: htf, umbilical cord blood sample 16

description:
htf umbilical cord blood sample
3055


title: BaP 10hpf, 2 (RNA-seq)

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

data_processing:
DNA methylation analysis was carried out following Bisulfite Analysis Toolkit (BAT). The details are provided in this website: https://www.bioinf.uni-leipzig.de/Software/BAT/. This contains 4 different modules - Mapping,  Calling, Analysis and DMRs
RNAseq - pre-processing using FASTQC
RNAseq - mapping the reads to the genome using Salmon
RNAseq - statistical analysis using DESeq2
Assembly: GRCz11
Supplementary files format and content: Text format - RNAseq data files contains read counts ; bigWig - DNA methylation calls of differentially methylated regions. (DMRs).

extract_protocol:
Both RNA and DNA were extracted using a Quick-DNA/RNA Miniprep Plus Kit (Zymo, Cat # D7005) following the manufacturer’s instructions
RNAseq libraries were prepared using the Zymo-Seq RiboFree Total RNA Library Prep Kit (Cat # R3000) according to the manufacturer’s instructions. RNA-Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs (150 bp paired-end sequencing) per sample.
DNA methylation profiling - Starting input genomic DNA (100 ng) was digested with 30 units of MspI (NEB). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines. Adaptor-ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™-5 (Cat#: D4003). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (Cat#: D5030). Preparative-scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™-5 (Cat#: D4003) for sequencing on an Illumina platform.

tag: strain

tag: tissue

value: 10hpf embryos

value: Benzo[a]Pyrene


title: Kc167_mock_SuHw_R1

tag: developmental stage


title: Murine Osteoblast derived exosome, rep1

value: small extracellular vesicles

value: untreated


title: Kc167_IshaKD_input_for_Isha_R1

value: embryo


title: Kc167_mock_input_R1

value: mock


title: Kc167_IshaKD_MOD_R2

value: MOD


title: htf, umbilical cord blood sample 4

description:
htf umbilical cord blood sample
3017


title: BaP 10hpf, 3 (RNA-seq)


title: Kc167_IshaKD_input_for_Isha_R2


title: Kc167_IshaKD_Isha_R1


title: BaP eggs, 3 (RNA-seq)

source_name: BaP eggs

value: Eggs


title: BaP 10hpf, 1 (RNA-seq)


title: g5, umbilical cord blood sample 2

description:
g5 umbilical cord blood sample
3059


title: BaP eggs, 2 (RNA-seq)


title: Kc167_mock_MOD_R1

value: Kc167 cells


title: BaP 10hpf, 4 (RNA-seq)


title: Kc167_mock_CP190_R1


title: Kc167_mock_Isha_R1


title: Kc167_mock_CP190_R2


title: Kc167_mock_Isha_R2


title: BaP eggs, 4 (RNA-seq)


title: iAT2 wild-type and DSP-kd (hashed)

city: Boston

first: Feiya

last: Wang

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

data_processing:
The sample was processed using the standard Cellranger v.2 pipeline
Reads were mapped to GRCh38 with TdTomato reporter
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Genome_build: GRCh38 with TdTomato reporter
Supplementary_files_format_and_content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5  format

source_name: BU3 NGST CRISPRi line

growth_protocol: To generate iAEC2s, we performed PSC directed differentiation via definitive endoderm into NKX2-1 lung progenitors using methods we have previously described (Hawkins et al., JCI 2017; Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019). In brief, cells maintained in mTeSR1 media were differentiated into definitive endoderm using the STEMdiff Definitive Endoderm Kit (StemCell Technologies) for 3 days (day 0-3) and after the endoderm-induction stage, cells were dissociated with gentle cell dissociation reagent and passaged into 6-well dishes pre-coated with growth factor reduced Matrigel in ‘‘DS/SB’’ anteriorization media, consisting of complete serum-free differentiation media (cSFDM) base as previously described (Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019), supplemented with 2 µM Dorsomorphin (‘‘DS’’; Stemgent) and 10 µM SB431542 (‘‘SB’’; Tocris). For the first 24 hour after passaging, 10 µM Y-27632 was added to the media. After anteriorization in DS/SB media for 3 days (day 3-6), cells were cultured in ‘‘CBRa’’ lung progenitor-induction media until day 15, as we have previously published (Jacob et al., Cell Stem Cell 2017). ‘‘CBRa’’ media consists of cSFDM base supplemented with 3 µM CHIR99021 (Tocris), 10 ng/ml recombinant human BMP4 (rhBMP4, R&D Systems), and 100 nM retinoic acid (RA, Sigma). On day 15 of differentiation, live cells were sorted on a high-speed cell sorter (MoFlo Legacy or MoFlo Astrios EQ) to isolate NKX2-1+ lung progenitors based on CD47hi/CD26neg gating (Hawkins et al., JCI 2017). Sorted lung progenitors were resuspended in undiluted growth factor reduced 3D Matrigel (Corning) at a concentration of approximately 400 cells/µl and distal/alveolar differentiation of cells was performed in CK+DCI media, consisting of cSFDM base supplemented with 3 µM CHIR99021, 10 ng/mL rhKGF (CK), and 50 nM dexamethasone (Sigma), 0.1 mM 8-Bromoadenosine 30,50-cyclic monophosphate sodium salt (Sigma) and 0.1 mM 3-Isobutyl-1-methylxanthine (IBMX; Sigma) (DCI). On day 30, live SFTPCtdTomato+ positive cells were sorted and encapsulated for scRNA-seq using the 10X Chromium System.

extract_protocol: 10X Chromium system

tag: culture

value: directed differentiation of iPSC-derived type 2 alveolar epithelial cells

value: CK+DCI media +/- doxycyline


title: Kc167_mock_input_for_Isha_R1


title: BaP eggs, 1 (RNA-seq)


title: Kc167_mock_input_for_Isha_R2


title: Kc167_IshaKD_MOD_R1


title: ST WT PRV siYTHDC1 2

status: Public on May 25 2022

city: Merelbeke

first: Robert

last: Jansens

address: Salisburylaan 133

department: Department of Translational Physiology, Infectiology and Public Health

country: Belgium

institute: Ghent University

description: DF.csv

data_processing:
Alignment and counting were performed using STAR. The resulting read count tables were used as input for all downstream RNA-seq analysis.
Assembly: Ss11 and Hg38
Supplementary files format and content: read count tables

organism: Sus scrofa

source_name: ST

extract_protocol:
RNA was extracted using the RNeasy mini kit (QIAgen)
RNA libraries for RNA-seq were prepared using  the QuantSeq 3' mRNA library prep FWD kit (Lexogen) following manufacturer's protocols.

value: ST

value: Swine Testicle

tag: infection

value: PRV NIA3

value: YTHDC1 siRNA, infected

tag: time

value: 48 hours knockdown + 16 hpi


title: ST WT PRV siYTHDC1 1

description: DF.csv

tag: cell line


title: ST WT PRV siYTHDC2 1

description: DF.csv

value: YTHDF2 siRNA, infected


title: ST WT PRV siYTHDC2 2

description: DF.csv


title: ST WT PRV scrambled 1

description: DF.csv

value: scrambled siRNA, infected


title: ST mock siYTHDC2 2

description: DF.csv

value: uninfected

value: YTHDF2 siRNA, uninfected


title: ST WT PRV siYTHDF123 2

description: DF.csv

value: YTHDF123 siRNA, infected


title: g5, umbilical cord blood sample 11

description:
g5 umbilical cord blood sample
4500

value: F


title: ST mock siYTHDC2 1

description: DF.csv


title: ST WT PRV scrambled 2

description: DF.csv


title: ST mock siYTHDC1 2

description: DF.csv

value: YTHDC1 siRNA, uninfected


title: ST mock scrambled 2

description: DF.csv

value: scrambled siRNA, uninfected


title: ST UL41null PRV 1

description: PRV.csv

value: infected

value: 16 hpi


title: ST mock scrambled 1

description: DF.csv


title: ST UL13null PRV 1

description: PRV.csv


title: ST UL13null PRV 2

description: PRV.csv


title: ST UL41null PRV 2

description: PRV.csv


title: ST US3null PRV 1

description: PRV.csv


title: ST US3null PRV 2

description: PRV.csv


title: ST mock siYTHDC1 1

description: DF.csv


title: ST WT PRV 2

description: PRV.csv


title: ST mock 1

description: PRV.csv


title: ST WT PRV 1

description: PRV.csv


title: ST WT PRV siYTHDF123 1

description: DF.csv


title: ST mock 2

description: PRV.csv


title: ST mock siYTHDF123 1

description: DF.csv

value: YTHDF123 siRNA, uninfected


title: ST mock siYTHDF123 2

description: DF.csv


title: THP-1 cGAS KO + cGAS WT

city: Berlin

last: Kazmierski

address: Charitéplatz 1

country: Germany

institute: Charité Universitätsmedizin Berlin

data_processing:
Data generated from individual samples were mapped separately against the hg38 human reference genome.
Gene expression was calculated for individual transcripts as reads per kilobase per million bases mapped (RPKM).
All transcriptomic analyses were performed using Geneious Prime Version 2020.0.4
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: cGAS KO THP-1 cells were reconstituted with with individual cGAS-GFP variants by lentiviral transduction and cultured in RPMI 1640 medium supplemented with 10% fetal calf serum (FCS), 100 U/ml penicillin, 100 µg/ml streptomycin, 2 mM L-glutamine, 1x MEM non-essential amino acids solution and 1 mM sodium pyruvate. Cells were selected using 1 µg/ml puromycin.

extract_protocol:
Total RNA from cells was extracted using the Rnease Mini Kit (Qiagen) and residual DNA contaminations were removed with the RNase-free Dnase set (Qiagen).
The RNA sequencing libraries were generated using TruSeq Stranded mRNA Library Prep Kits (Illumina)

tag: genotype

value: cGAS KO + cGAS WT

value: No


title: THP-1 cGAS KO + cGAS P261H

value: cGAS KO + cGAS P261H


title: A549 cells, t-3

city: Shenzhen

first: Rihong

last: Zhai

state: Guangdong

address: 1066 Xueyuan Ave.

institute: Shenzhen University School of Medicine

data_processing:
Base-calls were performed using Solexa pipeline version 1.8
Data were filtered using the following specifications:1) reads with 5’ adapter; 2) reads without 3’ adapter or insert sequence; 3) removes ≤20bp fragments. All the downstream analyses were based on the clean data with high quality.
Clean reads were mapped to human genome database (GRCh37) using the HISAT2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Genome_build: GRCh37
Supplementary_files_format_and_content: Processed data_tRF-induced transcriptome profiles_1.xlsx

source_name: tRF-overexpression cells

growth_protocol: Cells were cultured in DEME medium containing 10% FBS in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from cells using the TRIzol Reagent.
RNA-seq libraries were prepared using the Illumina KAPA Stranded RNA-Seq Library Prep Kit.Sequencing was performed on an Illumina HiSeq 4000.

treatment_protocol: tRF plasmid or empty vector were transfected into A549 cells using Lipofectamine 3000 transfection reagent.

value: Human adenocarcinoma tissue-derived cells

value: transfected tRF to A549 cells


title: THP-1 cGAS KO + cGAS G212A/S213A

value: cGAS KO + cGAS G212A/S213A


title: A549 cells, t-2


title: A549 cells, t-NC2

source_name: Control cells

value: untreated

value: control


title: A549 cells, t-1


title: A549 cells, t-NC3


title: FPwIFNgwIL17a_36

city: Columbus

first: Rodney

last: Britt

state: Oh

address: 575 Childrens Crossroad

department: Center for Perinatal Research

institute: Nationwide Children's Hospital

data_processing:
Data was trimmed of adaptors and low quality content with bbtools, and aligned to the HG38 geneome with Hisat2
Features were counted with HTSeq (-rpos -t exon -I gene_id -s no -m intersection-strict)
Differential Expression analysis was performed using EdgeR
Genome_build: GrCH38
Supplementary_files_format_and_content: counts

source_name: Airway Smooth Muscle primary cells

growth_protocol: Human ASM were cultured in DMEM/F12 media supplemented with 10% fetal bovine serum and 1% antibiotic/antimytotic at 37⁰C and 5% CO2. Cells were grown to 80-90% confluency and then serum starved for 48 h.

extract_protocol:
Cells cultures were trypsonized, harvested in TriReagent (Molecular Research Center; Part # TR118), purified with DNAse I (Epicentre; Part # D9905K) and purified with RNClean XP beads (Agencourt; Part # A63987).
200ng of total RNA using the Universal Plus mRNA-Seq Library Prep Kit (NuGEN Technologies, Inc.; Part # 0508-96).

treatment_protocol: Cells were treated with 10 ng/mL TNFα, IFNγ, IL-17A, TNFα/IFNγ, or IFNγ/IL-17A in the presence of vehicle (0.01% DMSO) or 10 nM fluticasone propionate (FP).

value: Airway Smooth Muscle

value: Primary

value: FP + IFNg + IL17a


title: A549 cells, t-NC1


title: FPwIFNgwIL17a_48


title: Cf.Bm.10hpf, 1 (RNA-seq)

value: 10hpf embryos

value: Control female x BaP male


title: IL17a_9


title: FPwTNFwIFNg_20

value: FP + TNF + IFNg


title: FPwIFNgwIL17a_24


title: IL17a_21


title: FPwTNFwIFNg_8


title: FPwIFNgwIL17a_12


title: FPwIL17a_34

value: FP + IL17a


title: FPwTNFwIFNg_32


title: FPwIL17a_10


title: IFNgwIL17a_11

value: IFNg + IL17a


title: FPwTNFwIFNg_44


title: IL17a_45


title: FPwIL17a_22


title: IFNgwIL17a_35


title: FPwIL17a_46


title: IFNgwIL17a_47


title: IFNgwIL17a_23


title: FPwIFNg_42

value: FP + IFNg


title: IL17a_33


title: FPwIFNg_30


title: FPwIFNg_18


title: FPwTNFa_16

value: FP + TNFa


title: FPwTNFa_28


title: FPwIFNg_6


title: FP_38

value: FP


title: TNFa_39

value: TNFa


title: FP_26


title: FPwTNFa_4


title: TNFawIFNg_19

value: TNFa + IFNg


title: IFNg_5

value: IFNg


title: TNFawIFNg_31


title: TNFawIFNg_7


title: Control_37

value: Control


title: TNFa_15


title: IFNg_17


title: IFNg_41


title: SAS miR-NC RIP_2

city: Tokyo

first: Jun

last: Inoue

address: Yushima 1-5-45, Bunkyo-ku

department: Molecular Cytogenetics

country: Japan

institute: Tokyo Medical & dental univ.

description: miR-NC-RIP

hyb_protocol: 0,6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K (G4851C) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61 x 21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-107) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: miR-NC-RIP

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

extract_protocol: total RNA

value: SAS

value: miR-NC

tag: rip antibody


title: SAS miR-634 Input_2

value: normal rabbit IgG


title: SAS miR-NC Input_1

description: miR-NC-Input

source_name: miR-NC-Input


title: SAS miR-634 Input_1


title: SAS miR-NC RIP_1

description: miR-NC-RIP


title: SAS miR-634 RIP_1


title: SAS miR-NC Input_2

description: miR-NC-Input


title: SAS miR-634 RIP_2


title: TNFa_3

value: Airway Smooth Muscle

value: Primary


title: FP_14


title: Control_25


title: TNFawIFNg_43


title: FP_2


title: Control_13


title: FPwTNFa_40


title: Fish_Oil_rep2

city: los angeles

first: Shubhamoy

last: Ghosh

state: CA

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

data_processing:
Demultiplexed fastq.gz files were aligned using STAR aligner against the mm10 referece, to obtain uniquly aligned reads.
Output from featureCounts has been used as an input for differential expression analysis by DESEq2 package from R
ggplot2 was used for visulazation of RNAseq data
Genome_build: mm10
Supplementary_files_format_and_content: Expression Matrix

source_name: Placental cell at Gestational D19

growth_protocol: C57BL/6J mouse were obtained from Jackson Laboratories housed under dark: light 12:12(h) conditions with free access to water and chow in the University of California Animal Facility

extract_protocol:
RNA was extracted from D19 placenta of  CON or Air Pollution particle exposed mice with Dirct Zol RNA MiniPrep kit from Zymo following manufacturer's protocol.
Libraries were prepared according to Illumina's instructions accompanying the KAPA Stranded mRNA sequencing kit (# KK8420; Kapa Biosystem, Cape Town, South Africa). Briefly,100ng of total RNA from each sample was used as the starting material with quadruplicate biological replicate from each group. mRNA was captured using magnetic oligo-dT, fragmented by heat and Mg and reverse transcribed to cDNA using random primers. After 2nd strand synthesis, cDNA was then end-repaired, index adapter-ligated and PCR amplified. SPRIselect beads (# B23318, Beckman Coulter, Indianapolis, IN, USA) were used to purify nucleic acids after each step of the library preparation. RNA sequencing libraries were sequenced by the HiSeq-4000 (Illumina Inc.; San Diego, CA, USA).

treatment_protocol: Female mice were exposed  with SRM1649b particle (resuspend in sterile PBS and sonicated to obtain a concentration of 15μg/µl) intranasally either starting from 2months prior to gestation followed by 18th day of gestation.

tag: tag

value: Placenta

tag: agent

value: Fis Oil


title: Air_Pollution_rep4

value: Air Pollution


title: Air_Pol+Fish_Oil_rep3

value: Fish Oil + Air Polution


title: Air_Pollution_rep3


title: Air_Pol+Fish_Oil_rep1


title: Fish_Oil_rep1


title: Air_Pol+Fish_Oil_rep2


title: Control_1


title: CONTROL_rep4


title: Air_Pollution_rep1


title: CONTROL_rep3


title: Wild-type ECs 30dynes/cm2_2

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCm38.89
Supplementary_files_format_and_content: Raw counts measurements

growth_protocol: Embryonic aortic endothelial cells from wild-type and Tg737orpk/orpk mice were grown in dishes coated with 0.1% gelatin (Sigma-Aldrich) at 37◦C in a humidified atmosphere containing 5% CO2. Cells were cultured in advanced-DMEM (Gibco 12491-015) supplemented with 2% fetal bovine serum (Sigma), 10000U/mL penicillin-streptomycin (Gibco 15140-122), 1% glutamax (Gibco 35050-038), 1% insulin-transferrin-selenium (Gibco 41400-045).

extract_protocol:
Total RNA was isolated using NucleoSpin RNA II (Macherey-Nagel) according to the manufacturers’ instructions. The Quality of the all samples per condition was verified using the Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Nano Kit (Agilent Technologies).
100 ng cDNA libraries were prepared using the Illumina TruSeq mRNA Stranded Kit according to the manufacturer's protocol.
Libraries were sequenced using single-end reads (50 nt-long) on an Illumina HiSeq4000.

value: endothelial cells

tag: protocol

value: 30 dynes/cm2


title: Air_Pollution_rep2


title: Wild-type ECs 30dynes/cm2_3


title: CONTROL_rep2


title: Wild-typek ECs 30dynes/cm2_1


title: Tg737orpk/orpk ECs 30dynes/cm2_3

value: Insertion mutation in IFT88


title: Wild-type ECs static_2

value: Static


title: Wild-type ECs static_1


title: Wild-types 2dynes/cm2_2

value: 2 dynes/cm2


title: Fish_Oil_rep3


title: Tg737orpk/orpk ECs 30dynes/cm2_2


title: Wild-type ECs 2dynes/cm2_3


title: Tg737orpk/orpk ECs 30dynes/cm2_1


title: Fish_Oil_rep5


title: Wild-typek ECs static_3


title: Tg737orpk/orpk ECs static_2


title: Tg737orpk/orpk ECs static_1


title: CONTROL_rep1


title: Tg737orpk/orpk ECs 2dynes/cm2_3


title: Tg737orpk/orpk ECs 2dynes/cm2_1


title: Tg737orpk/orpk ECs 2dynes/cm2_2


title: Wild-type ECs 2dynes/cm2_1


title: scc2_IAA_tc_3

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description:
scc2_IAA_tc_avg_rpm.bw
scc2_IAA_3_peaks.narrowPeak

data_processing:
Following sequencing, Illumina Primary Analysis version RTA v2.4.11 was run to demultiplex reads for all libraries and generate FASTQ files.
Reads were aligned to version sacCer3 of the yeast genome from UC Santa Cruz using bowtie2 v2.4.2
Peaks of enrichment were called using MACS2 version 2.1.1.20160309.
RPM tracks were generated in R using GenomicRanges from Bioconductor. RPM coverage was calculated separately for each replicate, and the average of each group was used to create the average RPM bigWig track.
Assembly: sacCer3
Supplementary files format and content: bigWig files containing average RPM, and narowPeak files containing MACS2 peak calls

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: cultures of 250 ml per replicate were grown in YPD to OD600 ~ 0.2 and arrested 1.5 hrs with alpha-factor.

extract_protocol:
Cells were fixed in 1% formaldehyde for 30 min at room temperature, then quenched with glycine (final concentration 0.125 M) for 5 min. Cells were washed twice with cold PBS, frozen in liquid nitrogen, and stored in −80°C until used. Cells were lysed by bead beating at 4°C in FA-Lysis SDS buffer (50 mM Hepes (pH7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.2% SDS, protease inhibitors). The lysate was sonicated using a Covaris SS20 sonicator for 25 min and centrifuged to remove cell debris. 10% of the total chromatin was processed for input and chromatin shearing was verified on a bioanalyzer. Chromatin extract was used to set up three IPs and one no antibody control per replicate and incubated with MYC antibody (BioLegend 626802) at 4°C overnight followed by 4hrs at 4°C with Protein G Dynabeads (Invitrogen 100-04D) pre-washed in FA-Lysis buffer. Beads were washed at room temperature with the following sequence of buffers; FA-Lysis buffer, two washes in FA-Lysis buffer with 500 mM NaCl, TEL buffer (0.25M LiCl, 10 mM Tris–HCl pH 8.0, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate), twice with 1XTE. Dynabeads from the three IPs per replicate and three no antibody controls (one from each replicate) were combined during the final wash. Chromatin fragments were eluted using 200 μl of Elution Buffer (TE + 1% SDS) at 65°C 20 min with agitation. NaCl was added to a final concentration of 250mM, and crosslinks were reversed overnight at 65°C. Elutions were treated with RNAse 1hr at 37°C and proteinase K for 2hr at 55°C. DNA was purified by running the elutions through a Qiagen PCR purification column.
Libraries were prepared with a Sciclone liquid-handling robot using the KAPA HTP Library Prep Kit for Illumina (Roche KK8234) and Bio Scientific NEXTflex DNA barcodes (PerkinElmer). NEXTflex DNA barcode adapters were used at a dilution of 1:125 with 15 cycles of PCR. The resulting libraries were then quantified using a Bioanalyzer (Agilent Technologies) and a Qubit fluorometer (Life Technologies). Libraries were pooled and sequenced on an Illumina NextSeq 500 instrument as High Output 75 bp single read runs.

treatment_protocol: IAA was added to 1mM and cultures were held in alpha-factor arrest for an additional 1.5 hrs before release into YPD containing IAA and nocodazole for 2 hrs until mitotic arrest was reached. 50ml of culture was removed to verify Med14 depletion by Western blot. Mis4-Myc tagged S. pombe cells were added as a spike-in control at a 1:4 ratio.

value: yeast cells

tag: calibration organism

value: Saccharomyces pombe

tag: replicate

tag: chip antibody

value: MATa ura3-1::ADH1-OsTIR1(pMK200,URA3) MED14-AID*-6FLAG::HYG SCC2-13MYC::NAT

value: auxin

tag: lims ids

value: MOLNG-3238, mma7


title: scc2_noIAA_tc_2

description:
scc2_noIAA_tc_avg_rpm.bw
scc2_noIAA_2_peaks.narrowPeak

tag: cell type

tag: treatment


title: scc2_noIAA_ip_1

description:
scc2_noIAA_ip_avg_rpm.bw
scc2_noIAA_1_peaks.narrowPeak

tag: strain

value: myc 9E10 (Biolegends)


title: scc2_IAA_tc_1

description:
scc2_IAA_tc_avg_rpm.bw
scc2_IAA_1_peaks.narrowPeak


title: scc2_IAA_ip_3

description:
scc2_IAA_ip_avg_rpm.bw
scc2_IAA_3_peaks.narrowPeak


title: WM164, S (RNA-seq)

first: Hensin

last: Tsao

address: 50 Blossom St

institute: Massachusetts General Hospital

data_processing:
fastqc to QC fastq file
StringTie was used to assemble RNA-Seq alignments into potential transcripts.
Using STAR aligner, read counts were converted to FPKM (Fragments per kilobase of transcript per million read pairs). FPKMs are calculated from the number of reads mapped to each particular gene sequence taking into account the gene length and the sequencing depth.
Assembly: hg38
Supplementary files format and content: comma-separated text files include FPKM fold change values for each sensitive-resistant pair.

source_name: melanoma cell line

growth_protocol: Cells were grown in DMEM with 10% FBS.

extract_protocol:
Total cell RNA was extracted using TRIzol Reagent (Invitrogen; Thermo Fisher Scientific, Waltham, MA) and RNeasy Mini kit (Qiagen, Hilden, Germany). RNA quality was examined by Qubit 3 (Thermo Fisher Scientific) and Fragment Analysis (Whitehead Institute Genome Technology Core, Massachusetts Institute of Technology, Cambridge, MA).
Sequencing libraries were prepared following the NEBNext Ultra II RNA Library Prep kit (New England Biolabs, MA) protocol and sequenced at Admera Health (South Plainfield, NJ) using the Illumina platform.

treatment_protocol: Cells were treated with vemurafenib to gain acquired resistance.

value: melanoma

value: untreated

tag: phenotype

value: vemurafenib-sensitive


title: ChIP-Seq G1E-ER4 cells hHIC2-OE HA ChIP-seq rep1

city: Guangzhou

first: Peng

last: Huang

address: Xinzao, Panyu District

department: GMU-GIBH Joint School of Life Sciences

institute: Guangzhou Medical University

data_processing:
Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1
Reads were mapped to reference genome mm10 with Bowtie 1.3.0 using parameters --best --sam --chunkmbs 256 -X 800.  Peaks were called using MACS2. Peaks overlapped with blacklist were further filtered out.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files with read coverage; bed files of peaks

source_name: G1E-ER4 cells

growth_protocol:
HUDEP1 and HUDEP2 cells were cultured with StemSpan SFEM (Stem Cell Technologies) supplemented with 1 μg/ml doxycycline, 1 μM dexamethasone, 100 ng/ml human SCF, 3 units/ml erythropoietin and 1% penicillin/streptomycin.
G1E-ER4 cells were cultured with IMDM supplemented with 15% FBS, 2% penicillin/streptomycin, 0.6% Kit ligand conditioned medium, 0.15 mM monothioglycerol and 2 units/ml erythropoietin

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Fixed cells were lysised in 1mL Cell Lysis Buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP-40/Igepal). Nuclei were collected and lysised in 1mL Nuclear Lysis Buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS). Chromatin was sonicated at 4 degrees C (Epishear, Active Motif). Chromatin was incubated with antibody and then decrosslink at 65C overnight.
Samples were processed for library construction for Illumina sequencing using Illumina’s TruSeq ChIP Sample Preparation Kit (Illumina cat# IP-202-1012) according to Illumina's instructions..

value: Erythroid cells

value: hHIC2 OE

value: HA (Bethyl Laboratories, A190-108A, lot 10)


title: Tg737orpk/orpk ECs static_3

value: endothelial cells


title: MGH-CH-1, S (RNA-seq)


title: MGH-CH-1, P (RNA-seq)

value: vemurafenib

value: vemurafenib-resistant


title: scc2_noIAA_tc_3

description:
scc2_noIAA_tc_avg_rpm.bw
scc2_noIAA_3_peaks.narrowPeak


title: WM1205, S (RNA-seq)


title: scc2_noIAA_ip_2

description:
scc2_noIAA_ip_avg_rpm.bw
scc2_noIAA_2_peaks.narrowPeak


title: ChIP-Seq G1E-ER4 cells hHIC2-OE input 2


title: scc2_noIAA_tc_1

description:
scc2_noIAA_tc_avg_rpm.bw
scc2_noIAA_1_peaks.narrowPeak


title: scc2_IAA_ip_2

description:
scc2_IAA_ip_avg_rpm.bw
scc2_IAA_2_peaks.narrowPeak


title: scc2_IAA_ip_1

description:
scc2_IAA_ip_avg_rpm.bw
scc2_IAA_1_peaks.narrowPeak


title: ChIP-Seq G1E-ER4 cells hHIC2-OE GATA1 ChIP-seq rep1

value: GATA1 (Santa Cruz, SC-265X, lot L1020)

value: Induced with 10 nM estradiol for 24 hours


title: scc2_noIAA_ip_3

description:
scc2_noIAA_ip_avg_rpm.bw
scc2_noIAA_3_peaks.narrowPeak

value: yeast cells


title: ChIP-Seq G1E-ER4 cells hHIC2-OE HA ChIP-seq rep2


title: ChIP-Seq G1E-ER4 cells hHIC2-OE input 1


title: scc2_IAA_tc_2

description:
scc2_IAA_tc_avg_rpm.bw
scc2_IAA_2_peaks.narrowPeak

value: Saccharomyces pombe


title: WM164, P (RNA-seq)


title: UACC903, S (RNA-seq)


title: UACC903, P (RNA-seq)


title: SK-MEL-37, S (RNA-seq)


title: SK-MEL-37, P (RNA-seq)


title: K4, P (RNA-seq)


title: K4, S (RNA-seq)


title: SK-MEL-28, P (RNA-seq)


title: ChIP-Seq G1E-ER4 cells hHIC2-OE GATA1 ChIP-seq rep2


title: A375, S (RNA-seq)


title: RNA-Seq Primary newborn erythroblasts HIC2 KO rep2

data_processing:
Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1
Reads were mapped to reference genome hg38 with ENCODE RNA-seq pipeline.
Genome_build: hg38
Supplementary_files_format_and_content: tsv files with FPKM and TPM values for each gene

source_name: Cord blood erythroblasts

growth_protocol: Human CD34+ HSPCs were cultured using a three-phase protocol. For phase 1 medium, IMDM was supplemented with 100 ng/mL of human stem cell factor, 1 ng/mL of interleukin-3, 3 units/mL of erythropoietin, 2% penicillin/streptomycin, 200 μg/mL of holotransferrin, 10 μg/mL of insulin, 5% human male A/B plasma, and 10 mg/mL of heparin. For phase 2 medium, the interleukin-3 was withdrawn after 9 days of culture. For phase 3, the cells were cultured with IMDM supplemented with 3 units/mL of erythropoietin, 2% penicillin/streptomycin, 1 mg/mL of holotransferrin, 10 μg/mL of insulin, 5% human A/B plasma, and 10 μg/mL of heparin.

extract_protocol:
Cells were homogenized using TRIzol (Life Technologies). RNA was extracted using RNeasy Mini Kit (Qiagen).
Sequencing libraries were constructed from 500 ng of DNase-treated, total RNA using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB cat# 6310) for rRNA depletion, followed by the TruSeq Stranded Total kit (Illumina cat# 20020598) for cDNA synthesis and library preparation according to manufacturer’s specifications.

tag: tissue

value: CD34+ cells derived from cord blood

tag: developmental stage

value: Day 13

value: HIC2 sgRNA#2


title: WM1205, P (RNA-seq)


title: MGH-CH-1, S, Input (ChIP-seq)

data_processing:
fastqc to QC fastq file
Fastq files were aligned to the human reference genome hg38 using bowtie2 and samtools.
Peak calling on all ChIP-Seq data was performed using MACS2 and using input genomic DNA as background control.
Super-enhancers were identified using the rank ordering of super-enhancers (ROSE) algorithm developed by Richard Youngs group (Whyte et al., 2013).
Assembly: hg38
Supplementary files format and content: bigwig files

extract_protocol:
H3K27Ac ChIP-seq was done using a protocol modified from previous publications (Eliades et al., 2018, Kang et al., 2016). In brief, cells were cross-linked with 1% formaldehyde for 10 min, the reaction was quenched with 125 mM glycine for 10 min on ice, and chromatin pelleted by centrifugation at 2,000×g for 10 min. Cross-linked cells were lysed with lysis buffer 1 (50 mmol/L HEPES, pH 7.5; 140 mmol/L NaCl; 1 mmol/L EDTA; 10% glycerol; 0.5% NP-40; and 0.25% Triton X-100), pelleted, and resuspended in lysis buffer 2 (10 mmol/L Tris-HCl, pH 8.0; 200 mmol/L NaCl; 1 mmol/L EDTA; 0.5 mmol/L EGTA). The subsequent pellet was resuspended in and sonicated in sonication buffer (50 mmol/L HEPES, pH 7.5; 140 mmol/L NaCl; 1 mmol/L EDTA, pH 8.0; 1 mmol/L EGTA; 0.1% Na-deoxycholate; 0.1% SDS; 1% Triton X-100). Cells were sonicated for ten cycles at 30 seconds each on ice (18–21 W) with 60 seconds on ice between cycles. 50 μl of Dynal magnetic beads (Sigma-Aldrich, St. Louis, MO) were blocked with 0.5% bovine serum albumin (weight/volume) in phosphate-buffered saline. Magnetic beads were bound with 5 ug of H3K27ac (Abcam, Cambridge, UK; catalog no. AB4729A). Sonicated lysates were cleared and incubated overnight at 4°C with magnetic beads bound with antibodies to enrich for DNA fragments bound by the indicated factor. Beads were washed two times with sonication buffer, one time with sonication buffer with 500 mmol/L NaCl, one time with LiCl wash buffer (10 mmol/L Tris-HCl, pH 8.0; 1 mmol/L EDTA; 250 mmol/L LiCl; 0.5% NP-40; 0.5% Na-deoxycholate), and one time with Tris-EDTA. DNA was eluted in elution buffer (50 mmol/L Tris-HCl, pH 8.0; 10 mmol/L EDTA; 1% SDS). Cross-links were reversed overnight. RNA and protein were digested using RNase A and Proteinase K, respectively, and DNA was purified with phenol-chloroform extraction and ethanol precipitation.
Sequencing libraries were prepared following the Illumina TruSeq DNA Sample Preparation v2 kit protocol and sequenced at Admera Health (South Plainfield, NJ) using the Illumina platform.


title: RNA-Seq Primary newborn erythroblasts control rep2

value: Control sgRNA


title: A375, P (RNA-seq)

value: melanoma


title: RNA-Seq Primary newborn erythroblasts control rep1


title: WM164, S, Input (ChIP-seq)

value: untreated

value: H3K27ac (Abcam, Cambridge, UK; catalog no. AB4729A)


title: Adult_GATA1_r2

data_processing:
library strategy: CUT&RUN
Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1
Reads were mapped to reference genome hg38 with Bowtie 1.3.0 using parameters --best --sam --chunkmbs 256 -X 800. Peaks were called using MACS2. Peaks overlapped with blacklist were further filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files with read coverage; bed files of peaks

source_name: Adult erythroblasts

extract_protocol:
500-800k cells were collected for CUT&RUN. CUT&RUN were performed using the CUT&RUN Assay Kit (Cell Signaling, #86652S) according to the manufacturer’s instructions.
Samples were processed for library construction for Illumina sequencing using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645S) according to NEB's instructions..

tag: tissue/cell type

value: CD34+ cells derived from adult peripheral blood

value: Erythroid cells

tag: differentiation

value: Differentiated day11


title: WM164, P, Input (ChIP-seq)

tag: cell line


title: MGH-CH-1, P, Input (ChIP-seq)


title: WM1205, P, Input (ChIP-seq)


title: Fetal_GATA1_r1

source_name: Fetal erythroblasts

value: CD34+ cells derived from fetal liver


title: Fetal_GATA1_r2


title: UACC903, S, Input (ChIP-seq)

value: vemurafenib-sensitive


title: SK-MEL-28, S (RNA-seq)


title: SK-MEL-37, S, Input (ChIP-seq)


title: WM1205, S, Input (ChIP-seq)


title: Fetal_H3K27ac_r2


title: SK-MEL-37, P, Input (ChIP-seq)

value: vemurafenib

value: vemurafenib-resistant


title: Fetal_H3K27ac_r1


title: K4, S, Input (ChIP-seq)


title: K4, P, Input (ChIP-seq)


title: Adult_H3K27ac_r2


title: Adult erythroblasts rep2

data_processing:
Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1
Mapping to reference genome hg38 with Bowtie 1.3.0 using parameters --best --sam --chunkmbs 256 -X 800
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files with read coverage

growth_protocol: HUDEP1 and HUDEP2 cells were cultured with StemSpan SFEM (Stem Cell Technologies) supplemented with 1 μg/ml doxycycline, 1 μM dexamethasone, 100 ng/ml human SCF, 3 units/ml erythropoietin and 1% penicillin/streptomycin. Human CD34+ HSPCs were cultured using a three-phase protocol. For phase 1 medium, IMDM was supplemented with 100 ng/mL of human stem cell factor, 1 ng/mL of interleukin-3, 3 units/mL of erythropoietin, 2% penicillin/streptomycin, 200 μg/mL of holotransferrin, 10 μg/mL of insulin, 5% human male A/B plasma, and 10 mg/mL of heparin. For phase 2 medium, the interleukin-3 was withdrawn after 9 days of culture. For phase 3, the cells were cultured with IMDM supplemented with 3 units/mL of erythropoietin, 2% penicillin/streptomycin, 1 mg/mL of holotransferrin, 10 μg/mL of insulin, 5% human A/B plasma, and 10 μg/mL of heparin.

extract_protocol:
50-100k cells were lysised with 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin, then incubated with Tagment DNA Enzyme (Illumina) for 30 minutes at 37C. DNA was purified with Qiagen MinElute Reaction Cleanup Kit.
Library fragments were amplified using Phusion High-Fidelity PCR Master Mix with HF Buffer (ThermoFisher cat#F531S) and custom v2_Ad1 and v2_Ad2 unique dual indexes (Mezger, et al., 2018, Nat Commun).


title: Adult erythroblasts rep1


title: Fetal erythroblasts rep2


title: RNA-Seq Primary newborn erythroblasts HIC2 KO rep1

tag: genotype

value: HIC2 sgRNA#1


title: SK-MEL-28, P, Input (ChIP-seq)


title: RNA-Seq HUDEP2 cells HIC2 OE rep1

source_name: HUDEP2 cells

growth_protocol:
Human CD34+ HSPCs were cultured using a three-phase protocol. For Phase I medium, IMDM was supplemented with 100 ng/mL human SCF, 50 ng/mL IL3, 3 units/ml erythropoietin, 1% penicillin/streptomycin, 330 μg/ml holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 2 units/ml heparin. For Phase II medium, the IL3 was withdrawn after 9 days of culture. For Phase III medium, the cells were cultured with IMDM supplemented with 3 units/ml erythropoietin, 1% penicillin/streptomycin, 330 μg/ml holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 2 units/ml heparin.
HUDEP2 cells were cultured with StemSpan SFEM (Stem Cell Technologies) supplemented with 1 μg/ml doxycycline, 1 μM dexamethasone, 100 ng/ml human SCF, 3 units/ml erythropoietin and 1% penicillin/streptomycin.

value: Immortalized Human Erythroid Progenitor

value: Differentiated for 5 days

value: HIC2 OE


title: A375, S, Input (ChIP-seq)


title: A375, P, Input (ChIP-seq)


title: RNA-Seq HUDEP2 cells GFP control rep2

value: GFP OE


title: Fetal erythroblasts rep1


title: RNA-Seq HUDEP2 cells HIC2 OE rep2


title: RNA-Seq Primary erythroblasts HIC2 OE

source_name: Human erythroblasts

value: Adult peripheral blood

value: CD34+ derived erythroblasts

value: Day 13


title: RNA-Seq Primary erythroblasts GFP control


title: ChIP-Seq HUDEP1 cells HIC2 KO GATA1 ChIP-seq rep2

data_processing:
Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1
Reads were mapped to reference genome hg38 with Bowtie 1.3.0 using parameters --best --sam --chunkmbs 256 -X 800. Peaks were called using MACS2. Peaks overlapped with blacklist were further filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files with read coverage; bed files of peaks

source_name: HUDEP1 cells

value: Undifferentiated

value: HIC2 KO


title: SK-MEL-28, S, Input (ChIP-seq)

value: melanoma

value: untreated

value: H3K27ac (Abcam, Cambridge, UK; catalog no. AB4729A)


title: ChIP-Seq Newborn erythroblasts HIC2

growth_protocol: Human CD34+ HSPCs were cultured using a three-phase protocol. For Phase I medium, IMDM was supplemented with 100 ng/mL human SCF, 50 ng/mL IL3, 3 units/ml erythropoietin, 1% penicillin/streptomycin, 330 μg/ml holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 2 units/ml heparin. For Phase II medium, the IL3 was withdrawn after 9 days of culture. For Phase III medium, the cells were cultured with IMDM supplemented with 3 units/ml erythropoietin, 1% penicillin/streptomycin, 330 μg/ml holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 2 units/ml heparin.

value: CD34+ cells derived from cord blood

value: Erythroid cells

value: Differentiated day12

value: WT

value: HIC2 (Proteintech, 22788-1-AP)


title: MGH-CH-1, P (ChIP-seq)

value: vemurafenib

value: vemurafenib-resistant


title: MGH-CH-1, S (ChIP-seq)

value: vemurafenib-sensitive


title: WM164, S (ChIP-seq)


title: ChIP-Seq HUDEP1 cells WT GATA1 ChIP-seq rep2

value: Immortalized Human Erythroid Progenitor


title: WM1205, S (ChIP-seq)


title: WM1205, P (ChIP-seq)


title: WM164, P (ChIP-seq)


title: ChIP-Seq HUDEP1 cells WT GATA1 ChIP-seq rep1


title: ChIP-Seq HUDEP1 cells HIC2 KO GATA1 ChIP-seq rep1


title: SK-MEL-37, P (ChIP-seq)


title: K4, S (ChIP-seq)


title: ChIP-Seq HUDEP2 cells HIC2-ER induced HA ChIP-seq rep2

value: HIC2-ER OE

value: HA (Bethyl Laboratories, A190-108A, lot 10)

value: Induced with 10 nM tamoxifen for 24hrs


title: SK-MEL-28, S (ChIP-seq)


title: RNA-Seq HUDEP2 cells GFP control rep1

value: Differentiated for 5 days

value: GFP OE


title: ChIP-Seq HUDEP2 cells HIC2-ER induced input

value: Undifferentiated


title: A375, S (ChIP-seq)

value: melanoma

value: untreated


title: K4, P (ChIP-seq)

value: H3K27ac (Abcam, Cambridge, UK; catalog no. AB4729A)


title: SK-MEL-37, S (ChIP-seq)


title: ChIP-Seq HUDEP1 cells HIC2 KO input

value: Erythroid cells

value: HIC2 KO


title: UACC903, S (ChIP-seq)


title: ChIP-Seq HUDEP2 cells HIC2-ER induced HA ChIP-seq rep1


title: ChIP-Seq HUDEP2 cells HIC2-ER uninduced input


title: Air_Pol+Fish_Oil_rep5

tag: tag

value: Placenta

value: Fish Oil + Air Polution


title: ChIP-Seq HUDEP1 cells WT input

value: WT


title: A375, P (ChIP-seq)

value: vemurafenib

value: vemurafenib-resistant


title: ChIP-Seq HUDEP2 cells HIC2-OE GATA1 ChIP-seq rep2

value: Immortalized Human Erythroid Progenitor

value: HIC2 OE


title: P409_Control_BL_Normal [sam1116261]

first: James

last: Krueger

department: Center for Clinical and Translational Science

institute: The Rockefeller University

data_processing:
STAR 2.4.2a for alignment
subread 1.5.0.post3 (featureCount) for quantification of genes
Assembly: GRCh37
Supplementary files format and content: Tab delimited gene expression data of each sample

source_name: Skin

extract_protocol:
Qiagen miRNeasy micro kit (not performed by Regeneron)
KAPA Stranded mRNA-Seq Kit for Illumina® Platforms with 100ng input and 12 PCR cycles.

tag: subjectid

tag: condition

value: Control

tag: timepoint

value: BL

value: Normal


title: ChIP-Seq HUDEP2 cells HIC2-OE GATA1 ChIP-seq rep1


title: P410_Control_BL_Normal [sam1116262]


title: P406_Control_BL_Normal [sam1116258]


title: ChIP-Seq HUDEP2 cells HIC2-OE input


title: P407_Control_BL_Normal [sam1116259]


title: ChIP-Seq HUDEP2 cells WT H3K27ac ChIP-seq


title: ChIP-Seq HUDEP2 cells WT GATA1 ChIP-seq rep1


title: ChIP-Seq HUDEP2 cells HIC2-ER uninduced HA ChIP-seq rep2

value: HIC2-ER OE

value: HA (Bethyl Laboratories, A190-108A, lot 10)


title: ChIP-Seq HUDEP2 cells HIC2-ER uninduced HA ChIP-seq rep1

value: Undifferentiated


title: ChIP-Seq HUDEP2 cells HIC2-OE H3K27ac ChIP-seq


title: P402_Control_BL_Normal [sam1116254]


title: Adult_GATA1_r1

value: CD34+ cells derived from adult peripheral blood

value: Differentiated day11


title: Capture-C HUDEP2 cells HIC2 OE rep4

description:
BCL_3100_3103_HIC2_OE_nor.bigwig
HS3_3100_3103_HIC2_OE_nor.bigwig

data_processing:
Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1
Reads were processed using the published pipeline (https://github.com/telenius/captureC/releases).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files with the normalized Capture-C interaction signals

growth_protocol: HUDEP2 cells were cultured with StemSpan SFEM (Stem Cell Technologies) supplemented with 1 μg/ml doxycycline, 1 μM dexamethasone, 100 ng/ml human SCF, 3 units/ml erythropoietin and 1% penicillin/streptomycin.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Fixed cells were lysised in 1mL Cell Lysis Buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP-40/Igepal).
Capture-C libraries were generated as described (Davies et al. 2016 Nature Methods).

treatment_protocol: HUDEP2 cells were differentiated for 5 days in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 330 μg/ml holo-transferrin, 10 μg/ml insulin, 2 units/ml heparin, 5% FBS, 3 units/ml erythropoietin, 1 μg/ml doxycycline and 1% penicillin/streptomycin.

value: Erythroid cells

value: Differentiated for 5 days


title: ChIP-Seq HUDEP2 cells WT input


title: Capture-C HUDEP2 cells HIC2 OE rep2


title: P408_Control_BL_Normal [sam1116260]


title: P311_PS_BL_LS [sam1116252]

value: PS

value: LS


title: P405_Control_BL_Normal [sam1116257]


title: P404_Control_BL_Normal [sam1116256]


title: P403_Control_BL_Normal [sam1116255]


title: Capture-C HUDEP2 cells WT rep4

description:
BCL_3096_3099_WT_nor.bigwig
HS3_3096_3099_WT_nor.bigwig

value: WT


title: SK-MEL-28, P (ChIP-seq)

value: melanoma

value: vemurafenib

value: H3K27ac (Abcam, Cambridge, UK; catalog no. AB4729A)


title: P401_Control_BL_Normal [sam1116253]


title: P309_PS_BL_LS [sam1116248]


title: UACC903, P (ChIP-seq)

value: vemurafenib-resistant


title: Capture-C HUDEP2 cells HIC2 OE rep3

value: Immortalized Human Erythroid Progenitor

value: HIC2 OE


title: P308_PS_BL_NL [sam1116245]

value: BL

value: NL


title: P307_PS_BL_LS [sam1116244]


title: P311_PS_BL_NL [sam1116251]


title: Capture-C HUDEP2 cells WT rep1


title: Capture-C HUDEP2 cells HIC2 OE rep1


title: ChIP-Seq HUDEP2 cells WT GATA1 ChIP-seq rep2


title: P310_PS_BL_LS [sam1116250]


title: Capture-C HUDEP2 cells WT rep3


title: P310_PS_BL_NL [sam1116249]


title: Capture-C HUDEP2 cells WT rep2


title: ATAC-Seq HUDEP1 cells WT rep1

growth_protocol: HUDEP1 and HUDEP2 cells were cultured with StemSpan SFEM (Stem Cell Technologies) supplemented with 1 μg/ml doxycycline, 1 μM dexamethasone, 100 ng/ml human SCF, 3 units/ml erythropoietin and 1% penicillin/streptomycin.


title: ATAC-Seq HUDEP2 cells HIC2 OE rep1


title: ATAC-Seq HUDEP1 cells HIC2 KO rep1

value: HIC2 KO


title: P306_PS_BL_NL [sam1116241]


title: ATAC-Seq HUDEP1 cells WT rep2

value: Undifferentiated


title: P305_PS_BL_NL [sam1116239]


title: ATAC-Seq HUDEP2 cells HIC2 OE rep2


title: P307_PS_BL_NL [sam1116243]


title: ATAC-Seq HUDEP1 cells HIC2 KO rep2


title: P304_PS_BL_NL [sam1116237]


title: P308_PS_BL_LS [sam1116246]


title: Adult_H3K27ac_r1

value: CD34+ cells derived from adult peripheral blood


title: P306_PS_BL_LS [sam1116242]


title: P304_PS_BL_LS [sam1116238]


title: P303_PS_BL_NL [sam1116235]


title: P305_PS_BL_LS [sam1116240]


title: UACC903, P, Input (ChIP-seq)


title: ATAC-Seq HUDEP2 cells WT rep2


title: P303_PS_BL_LS [sam1116236]


title: P301_PS_BL_NL [sam1116233]


title: P214_NPPP_BL_LS [sam1116232]

value: NPPP


title: P309_PS_BL_NL [sam1116247]


title: ATAC-Seq HUDEP2 cells WT rep1

value: Erythroid cells


title: oxsR untreated batch 1 rep1

city: Seoul

first: Sungmin

last: Hwang

address: Hwarangno 14-gil 5, Seongbuk-gu

institute: Korea Institute of Science and Technology

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis).
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Adapters are not trimmed away from the reads.
The sequencing artifacts and contamination of raw sequencing reads were assessed by FastQC v.0.11.9 and further adapter, poor-quality or short reads (< 10 bp) were trimmed by Cutadapt v.1.18.
The number of reads mapped to each transcript was counted by HTSeq v.0.11.0
Assembly: The preprocessed reads were aligned to the reference genome of GCF_000025685.1_ASM2568v1_genomic.gff by Bowtie2 v.2.3.4.3, followed by sorting and indexing by Samtools v.1.9.
Supplementary files format and content: DESeq2 v.1.32.0 was used to normalize the read counts and the resulting count matrix contains the raw gene counts for every gene except rRNAs and every sample.

organism: Haloferax volcanii

source_name: Haloferax volcanii

growth_protocol: Strains H26 wild-type and mutant (ΔoxsR) were streaked on fresh ATCC974 medium plates from -80°C stock and grown for five days. Colonies were transferred to fresh ATCC974 liquid media in 13 ×100 mm culture tube and incubated at 42°C for 17 h (aeration by rotary shaking, 200 rpm) to log-phase (OD600nm of 0.3 to 0.7). Cells were transferred to fresh ATCC974 liquid medium in 13 ×100 mm culture tube and similarly incubated for 15 h until early log phase (OD600 nm of 0.3 to 0.5). The culture was transferred to a 125 mL Erlenmeyer flask in 50 mL of ATCC974 liquid medium and similarly incubated for 10 h to reach an early log phase. An aliquot (10 mL) of cell culture was transferred to 15 mL conical tubes for each strain and centrifuged for 5 min at 5,000 x g at room temperature to remove the complex medium. Cells were washed twice with GMM to remove any remaining ATCC974 medium. The cells were resuspended 50 mL of GMM and divided into two 125 mL Erlenmeyer flasks (25 mL per flask). Cells were exposed to 1.5 mM of HOCl or the mock only water for 1 h at 42°C with aeration at 200 rpm. After treatment, 10 mL cultures were transferred to 15 mL conical tubes and harvested by centrifugation (5 min at 5,000 x g, 22°C). The supernatant was removed, and the cell pellets were flash frozen on an ice bath with 100 % ethanol and NaCl. Cell pellets were stored at -80°C.

extract_protocol:
The RNA was extracted using TRI Reagent® (#T9424, Sigma-Aldrich). To verify RNA integrity, the samples were separated by 0.8 % (w/v) agarose gel electrophoresis (at 90 V for 20 min) in 1X TAE buffer using 2X RNA Loading Dye (#R0641, Thermo Fisher Scientific). The samples were then treated with TURBO DNase-free kit (AM1907, Invitrogen) to remove traces of DNA.
Only RNA samples with DNA below the limit of PCR detection were further processed. From each sample preparation, total RNA ≥ 6 μg in 50 μL with RIN value ≥ 6 was used to prepare a cDNA library and analyzed by high throughput sequencing (Novogene). The abundance of rRNA was reduced using the Ribo-ZeroTM Magnetic kit, and the cDNA was prepared using a 250 to 300 bp insert strand-specific library. The library was sequenced using the Illumina Platform PE150, Q30≥ 80% yielding 2G raw data / sample.

value: oxsR deletion

value: untreated


title: oxsR untreated batch 2 rep2


title: oxsR NaOCl batch 2 rep3

value: NaOCl treated


title: oxsR untreated batch 1 rep3


title: oxsR untreated batch 2 rep3


title: oxsR untreated batch 2 rep1


title: oxsR untreated batch 1 rep2


title: oxsR NaOCl batch 2 rep4


title: P214_NPPP_BL_NL [sam1116231]


title: P301_PS_BL_LS [sam1116234]

value: PS

value: LS


title: oxsR NaOCl batch 2 rep1


title: P211_NPPP_BL_LS [sam1116226]


title: P212_NPPP_BL_NL [sam1116229]


title: wt untreated batch 2 rep4

value: wt


title: P212_NPPP_BL_LS [sam1116230]


title: wt untreated batch 2 rep2


title: oxsR NaOCl batch 2 rep2


title: oxsR NaOCl batch 1 rep2


title: oxsR NaOCl batch 1 rep4


title: wt untreated batch 2 rep1


title: P211_NPPP_W3_NL [sam1116227]


title: oxsR NaOCl batch 1 rep1


title: oxsR NaOCl batch 1 rep3


title: wt untreated batch 1 rep4


title: P210_NPPP_BL_LS [sam1116224]


title: wt untreated batch 1 rep3


title: P208_NPPP_W3_LS [sam1116218]


title: P211_NPPP_W3_LS [sam1116228]


title: P208_NPPP_BL_NL [sam1116215]


title: wt untreated batch 1 rep2


title: P210_NPPP_BL_NL [sam1116223]


title: wt NaOCl batch 2 rep3


title: P209_NPPP_BL_LS [sam1116220]


title: wt NaOCl batch 2 rep2


title: P206_NPPP_BL_LS [sam1116212]


title: P209_NPPP_W3_NL [sam1116221]


title: P211_NPPP_BL_NL [sam1116225]


title: P208_NPPP_BL_LS [sam1116216]


title: P205_NPPP_W3_NL [sam1116209]


title: wt NaOCl batch 2 rep4


title: wt NaOCl batch 1 rep3


title: P208_NPPP_W3_NL [sam1116217]


title: wt NaOCl batch 1 rep2


title: wt untreated batch 1 rep1


title: P209_NPPP_BL_NL [sam1116219]


title: P205_NPPP_BL_LS [sam1116208]


title: P206_NPPP_BL_NL [sam1116211]


title: P204_NPPP_BL_LS [sam1116206]


title: P205_NPPP_BL_NL [sam1116207]


title: wt untreated batch 2 rep3


title: wt NaOCl batch 1 rep1


title: wt NaOCl batch 2 rep1


title: HEKT mock 2

description: HSV.csv

data_processing:
Alignment and counting were performed using STAR. The resulting read count tables were used as input for all downstream RNA-seq analysis.
Assembly: Ss11 and Hg38
Supplementary files format and content: read count tables

extract_protocol:
RNA was extracted using the RNeasy mini kit (QIAgen)
RNA libraries for RNA-seq were prepared using  the QuantSeq 3' mRNA library prep FWD kit (Lexogen) following manufacturer's protocols.

value: Human Embryonic Kidney

tag: infection

value: uninfected

tag: time

value: 16 hpi


title: wt NaOCl batch 1 rep4


title: HEKT mock 1

description: HSV.csv


title: P207_NPPP_BL_LS [sam1116214]


title: Rett 12B

city: Dublin 8

first: Daniela

last: Tropea

address: TRINITY SCIENCES CENTRE SAINT JAMES'S HOSPITAL JAMES'S STREET

department: Psychiatry

country: Ireland

institute: Trinity College Dublin

data_processing:
RNA was analysed by 3’-Digital Gene Expression (3’-DGE)
The sequencing read data was then combined with barcode information in a FASTQ format and mapped onto the Hg19 reference sequence using BWA. Per-gene count quantification was conducted with the End Sequence Analysis Toolkit (ESAT) for downstream differential gene expression analysis
Assembly: Hg19
Supplementary files format and content: File containing logCPM values

source_name: Whole Blood

extract_protocol:
RNA from whole blood samples was collected and extracted using PAXgene™ Blood RNA tubes (BD Biosciences, Radnor, PA, USA).
RNA libraries were prepared for sequencing using standard protocols

value: Whole Blood

tag: age

tag: patient id

value: Timepoint 1


title: Rett 12C

value: Timepoint 2


title: Rett 11C


title: P205_NPPP_W3_LS [sam1116210]

city: New York

address: 1230 York Avenue


title: P201_NPPP_BL_LS [sam1116198]

value: BL


title: Rett 11B


title: P207_NPPP_BL_NL [sam1116213]

value: NL


title: P203_NPPP_BL_LS [sam1116204]


title: Rett 10D

value: MRD

value: Timepoint 3


title: P110_PPPP_BL_NL [sam1116195]

value: PPPP


title: P204_NPPP_BL_NL [sam1116205]

value: NPPP


title: P108_PPPP_W3_LS [sam1116194]


title: P108_PPPP_W3_NL [sam1116193]


title: Rett 10A

value: Timepoint 0


title: P202_NPPP_W3_LS [sam1116202]


title: P202_NPPP_W3_NL [sam1116201]


title: P203_NPPP_BL_NL [sam1116203]


title: P108_PPPP_BL_LS [sam1116192]


title: HEKT WT HSV1 1

description: HSV.csv

tag: cell type

value: HSV1 KOS

tag: treatment

value: infected


title: P202_NPPP_BL_NL [sam1116199]


title: Rett 11D


title: P108_PPPP_BL_NL [sam1116191]


title: HEKT WT HSV1 2

description: HSV.csv


title: P202_NPPP_BL_LS [sam1116200]

value: LS


title: P201_NPPP_BL_NL [sam1116197]


title: Rett 8D


title: Rett 9A


title: Rett 11A


title: Rett 9D


title: Rett 12A


title: Rett 9C


title: P106_PPPP_BL_NL [sam1116187]


title: P110_PPPP_BL_LS [sam1116196]


title: Rett 10C


title: P106_PPPP_BL_LS [sam1116188]


title: P104_PPPP_BL_NL [sam1116183]


title: Rett 10B


title: P103_PPPP_W3_NL [sam1116181]


title: Rett 7A


title: Rett 8A


title: Rett 8C


title: P104_PPPP_BL_LS [sam1116184]


title: Rett 6D


title: Rett 6C


title: Rett 6B


title: P107_PPPP_BL_LS [sam1116190]


title: P101_PPPP_W3_LS [sam1116178]


title: Rett 6A


title: P101_PPPP_W3_NL [sam1116177]


title: Rett 7D


title: Rett 9B


title: Rett 7C


title: Rett 5B


title: P101_PPPP_BL_NL [sam1116175]


title: P107_PPPP_BL_NL [sam1116189]


title: P103_PPPP_BL_LS [sam1116180]


title: P104_PPPP_W3_LS [sam1116186]


title: P103_PPPP_W3_LS [sam1116182]


title: Rett 4D


title: Rett 7B


title: S_93: Slow to warm up Temperament_11

first: Jia

last: Liu

address: 85 Saint Nicholas Ter

department: Neuroscience

institute: CUNY Advanced Science Research Center

data_processing:
Bulk RNA sequencing data was processed with the trimmomatic tool to remove adaptor barcode
mapped to the hg38 reference genome by the subread aligner
Mapped reads were summarized with the featureCounts tool of the subread package against Ensembl’s human gene annotation
Differential expression analysis was performed by DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: raw counts of each gene in each sample

source_name: Plancenta

extract_protocol:
Briefly, placenta biopsies, free of maternal decidua, were excised from each placenta quadrant, snap frozen in liquid nitrogen for 24 hours and then stored at -80°C. RNA extraction was carried out by first grinding frozen tissue in a liquid nitrogen-cooled mortar. RNA was extracted with the Maxwell 16 automated DNA/RNA extraction equipment (Promega: Madison, WI) using the proprietary extraction kits following the manufacturer’s protocol.
Ribosomal RNA was removed using Ribo-Zero Kit. mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized using mRNA template and random hexamer primers, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. After a series of terminal repair, ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

value: Plancenta

tag: infant temperment

value: Slow to Warm Up Temperament


title: Rett 8B

tag: tissue


title: S_83: Slow to warm up Temperament_9


title: Rett 4C


title: Rett 5C


title: S_135: Slow to warm up Temperament_7


title: Rett 4A


title: S_136: Slow to warm up Temperament_8


title: S_115: Slow to warm up Temperament_5


title: Rett 2B


title: P101_PPPP_BL_LS [sam1116176]


title: S_114: Slow to warm up Temperament_4


title: P103_PPPP_BL_NL [sam1116179]


title: Rett 2A


title: Rett 1D


title: Rett 5A


title: Rett 3B


title: Rett 1C


title: S_107: Slow to warm up Temperament_2


title: S_100: Slow to warm up Temperament_1


title: Rett 4B


title: S_96: Easy Temperament_10

value: Easy Temperament


title: S_124: Slow to warm up Temperament_6


title: S_91: Slow to warm up Temperament_10


title: Rett 3A


title: Clone 596-7 NextSeq Replicate 4 Dox

city: Bethesda

first: Jonathan

last: Hernandez

address: Building 37

institute: NCI/NIH

description:
596-7-Dox-4_NextSeq
RSEM.genes.limmavoom_normalized.Nextseq.tsv

data_processing:
24 Total RNA-Seq samples were pooled and sequenced on NovaSeq 6000 and NextSeq 500 using Illumina TruSeq Stranded Total RNA Library Prep and paired-end sequencing.
Basecalling was performed by RTA (version 3.4.4).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.20) allowing 1 mismatch.
Reads were filtered with a base call quality >91% of bases with Q30 and and above.
Trimming of adapters and low-quality bases was performed using CutAdapt (v1.18).
STAR (version 2.7.6a) is run in twopass basic mode to align trimmed reads to custom hg38+shRNA reference genome
Gene-level expression quantificiation  was performed using RSEM (version 1.3.3) and the hg38 (Gencode v35) + custom shRNA gene annotation.
Quantile-normalization and differential expression was performed using limma-voom (version 3.48.3).
Genome_build: hg38+shRNA (custom)
Supplementary_files_format_and_content: Tab-delimited text file contains limma-voom normalized counts output.

source_name: HT-29 colon adenocarcinoma

growth_protocol: 596 clones were grown in McCoy's 5A medium with 10% tetracycline-free FBS, 1% penicillin-streptomycin and 3µg/ml of puromycin.

extract_protocol:
Total RNA, treated with Dnase I (Qiagen; 79254), was extracted using RNeasy kit (Qiagen; 74106).
Stranded total RNA library was prepared according to the Illumina library prep protocol (Illumina; Document # 1000000040499 v00).
Stranded Total RNAseq

treatment_protocol: Doxycycline (1μg/ml) was treated for 24 hours to induce shRNA expression.

value: HT-29-derived clone 596-7 cell

value: Doxycycline treated

value: ephrinB2 silencing


title: Clone 596-7 NextSeq Replicate 3 Dox

description:
596-7-Dox-3_NextSeq
RSEM.genes.limmavoom_normalized.Nextseq.tsv


title: S_84: Easy Temperament_8


title: S_64: Easy Temperament_6


title: S_108: Slow to warm up Temperament_3


title: Rett 1B

value: Whole Blood

value: Timepoint 1


title: Clone 596-7 NextSeq Replicate 4 No Dox

description:
596-7-4_NextSeq
RSEM.genes.limmavoom_normalized.Nextseq.tsv

value: Doxycycline untreated

value: control


title: S_98: Easy Temperament_11


title: Rett 1A


title: P104_PPPP_W3_NL [sam1116185]

value: NL


title: S_85: Easy Temperament_9


title: S_113: Easy Temperament_2


title: S_123: Easy Temperament_3


title: S_75: Easy Temperament_7


title: Clone 596-7 NextSeq Replicate 1 Dox

description:
596-7-Dox-1_NextSeq
RSEM.genes.limmavoom_normalized.Nextseq.tsv


title: case9-be

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
Sequencing quality was examined by FastQC software and trimmed reads (pass Illumina quality filter, trimmed 3’-adaptor bases by cutadapt) were aligned to mature-tRNA and pre-tRNA sequence getting from GtRNAdb using NovoAlign software (v2.07.11).
The remaining reads are aligned to. transcriptome sequences (mRNA/ rRNA /snRNA /snoRNA /piRNA /miRNA).
The expression profiling and differentially expressed tRFs & tiRNAs were then calculated (based on the normalized TPM values).
Genome_build: GtRNAdb
Supplementary_files_format_and_content: "Plasma tRF profiles in NSCLC.xlsx" represents TPMs and TagCounts

source_name: plasma

extract_protocol:
Total RNA was extracted using the TRIzol reagent. RNA sample was then pretreated to remove some RNA modifications that interfered with small library construction using the tRF&tiRNA Pretreatment Kit. The pretreated total RNA samples were then subjected to library preparation using the NEBNext Multiplex Small RNA Library Prep Set for Illumina kit. The completed libraries were then sequenced on Illumina NextSeq 500 system.
Sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter. The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2100.
tRF-seq

tag: individual

value: plasma

value: pre-operation


title: Clone 596-7 NextSeq Replicate 2 Dox

description:
596-7-Dox-2_NextSeq
RSEM.genes.limmavoom_normalized.Nextseq.tsv


title: S_238Q: Easy Temperament_5


title: Clone 596-7 NextSeq Replicate 1 No Dox

description:
596-7-1_NextSeq
RSEM.genes.limmavoom_normalized.Nextseq.tsv


title: S_126: Easy Temperament_4


title: case8-af

value: post-operation


title: S_106: Easy Temperament_1


title: case9-af


title: Clone 596-7 NextSeq Replicate 3 No Dox

description:
596-7-3_NextSeq
RSEM.genes.limmavoom_normalized.Nextseq.tsv


title: 0902 Macula Retina

city: Philadelphia

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

data_processing:
For each sample a cell by gene count matrix is provided
Genome_build: HG38
Supplementary_files_format_and_content: 10X Genomics sparse data matrix

source_name: Retina

extract_protocol:
The human eyeball was immediately removed within 6 hours after death, and placed in cold phosphate buffered saline (PBS). The retina and RPE /choroid was carefully removed under a dissecting microscope and both tissue layers were dissociated straightaway using the Papain dissociaton system (Worthington, Lakewood, NJ, USA) following the manufacturer's instructions.
To assess cell viability, cells were stained with 0.4% trypan blue (Mediatech, Inc., Manassas, VA, USA) and counted using a hemocytometer. Sc-RNA seq was carried out on the viable cells using Chromium 10x Genomics as per the manufacturer's recommendations.
single cell RNA-Seq

tag: Sex

value: Male

tag: race

value: Black or African American

tag: medhx

value: HTN, hypothyroid, gout, sepsis, PNA, alzheimers, left hip fx, UTI, hypoglycemia (glucose 52 on admission but not treated for DM after Dr. consult), hypotension, dementia

tag: phenotype

value: Early AMD

tag: sequenced estimated number of cells


title: 0902 Peripheral Choroid

source_name: Choroid


title: case7-be


title: 0828 Peripheral Choroid

value: White

value: NO hepatitis, but on tx list Hepatic Enceph. CAD, GERD, HTN,  Hypercholesterolemia, obst sleep apnea, cirrhosis, esoph varices, ascites, right hepatic lobe lesion w/ other lesions. HTN. Increased On August  08/26/20 20 WBC . was 8. NO DM / Lacitc acid :14.4, 15.0. 15.7 today & none drawn before.  Coronavirus Negative on August 19t h or 23rd.

value: Normal


title: 0902 Peripheral Retina


title: case7-af


title: 0902 Macula Choroid


title: Clone 596-7 NextSeq Replicate 2 No Dox

description:
596-7-2_NextSeq
RSEM.genes.limmavoom_normalized.Nextseq.tsv

value: HT-29-derived clone 596-7 cell

tag: genotype


title: 0828 Peripheral Retina


title: 0828 Macula Choroid

source_name: Chorod


title: 0828 Macula Retina


title: case6-af


title: 0715 Peripheral Retina

value: Female

value: glaucoma, AFlutter, MVP, SVT, COVID test NEG


title: case5-af


title: case5-be


title: case3-be


title: 0715 Macula Choroid


title: case2-be


title: 0715 Peripheral Choroid


title: case3-af


title: case2-af


title: 0715 Macula Retina


title: case8-be


title: case4-af


title: case1-af


title: case6-be


title: Th17_72h_LNA4_replicate3_LANE3

city: Turku

first: Riitta

last: Lahesmaa

address: Tykistökatu 6A

department: Turku Bioscience

country: Finland

institute: University of Turku

data_processing:
FastQC was used to check the quality of the raw sequencing reads (Andrews, 2010), and Trimmomatic (Bolger et al., 2014) was used to trim the adapters and low-quality bases. Tophat2 (Kim et al., 2013) was used to align the trimmed reads to the human reference genome GRCh37.75 (Ensembl release 75). HTseq-count (Anders et al., 2015) was used to calculate the summarized read counts for each gene.
Genome_build: hg19
Supplementary_files_format_and_content: csv

source_name: cord blood

growth_protocol: Ficoll (GE Healthcare, cat# 17-1440-03) was used to isolate PBMCs from human umbilical cord blood samples from Turku University Central Hospital, which was followed by CD4+ T cells were isolation (Invitrogen (cat# 11331D).  CD4+ T cells were activated using a plate coated anti-CD3 antibody (Beckman Coulter, cat# IM-1304) (3750 ng/well in a six-well culture plate), and anti-CD28 antibody (Beckman Coulter, cat# IM1376) was added in the medium in a concentration of 1 μg/mL. X-vivo 20 serum-free medium (Lonza, Bazel, Switzerland) containing 0.5 million cells/mL complemented with L-glutamine (2 mM, Sigma-Aldrich) and antibiotics (50 U/mL penicillin and 50 μg/mL streptomycin; Sigma-Aldrich) was used for the cultures. Cells were plated at a density of 2 million cells per well and cultured at 37° C in 5% CO2. For Th17 polarization of CD4+ cells, IL-6 (20 ng/mL; Roche, cat# 11138600 001), IL-1β (10 ng/mL, R&D Systems, cat# 201 LB) and TGFβ (10 ng/mL, R&D Systems, cat# 240) were used as the cytokine cocktail along with neutralizing antibodies against IFNγ (1 μg/mL, R&D Systems, cat# MAB-285) and IL4 (1 μg/mL, R&D Systems, cat# MAB204). Nonpolarizing control (Th0) cells were activated with anti-CD3 and anti-CD28 antibodies in the presence of the neutralizing antibodies without differentiating cytokines.

extract_protocol:
RNA was isolated (RNeasy Mini Kit, cat# 74106, QIAGEN) and treated in-column with DNase (RNase-Free DNase Set; QIAGEN) for 15 min. The removal of genomic DNA was ensured by an additional treatment of the samples with DNase I (Invitrogen). RNA quantification was performed using Nanodrop 2000 and quality control was performed using BioRad Experion or Agilent Bioanalyzer.
libraries for RNA-Seq were prepared using Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part #15031047). The quality of the libraries was confirmed with Advanced Analytical Fragment Analyzer, and the concentrations of the libraries were quantified with Qubit® Fluorometric Quantitation (Life Technologies).
24 samples pooled on one lane and sequence 3 lanes with 2x100bp read length (about 37 x _x000B_10^6 reads per sample). Sequencing was performed at the Finnish Functional Genomics Centre using the HiSeq2500 Next-Generation Sequencing platform.

treatment_protocol: For LNA transfections, 4 million cells mixed with 150 pmols of LNA, prepared in 100 μL volume of OptiMEM (Gibco by Life Technologies, cat # 31985-047), were used to transfect the cells using the Amaxa Nucleofector II system (Lonza). After transfection, cells were first rested at 37° C for 48 h in RPMI 1640 (Sigma-Aldrich) medium supplemented with 10% FCS, 50 U/mL penicillin, 50 μg/mL streptomycin, and 2 mM L-glutamine and then activated and cultured as described above. The following LNAs (provided by QIAGEN) were used:  LNA-NC (non-targeting control): 5´-AACACGTCTATACGC -3´;  LNA-1: 5'-ACTTTGGCATTCTAGG-3´;  LNA-4: 5'-AGGCTGGTAGGCTATG-3´.

value: In vitro differentiated Th17 cells

value: Nucleofected cells differentiated for 72 hour in Th17 media


title: Th17_72h_LNA2_replicate3_LANE3


title: Th17_72h_LNA4_replicate3_LANE2


title: Th17_72h_LNA4_replicate3_LANE1


title: IFNg_29

data_processing:
Data was trimmed of adaptors and low quality content with bbtools, and aligned to the HG38 geneome with Hisat2
Features were counted with HTSeq (-rpos -t exon -I gene_id -s no -m intersection-strict)
Differential Expression analysis was performed using EdgeR
Genome_build: GrCH38
Supplementary_files_format_and_content: counts

source_name: Airway Smooth Muscle primary cells

extract_protocol:
Cells cultures were trypsonized, harvested in TriReagent (Molecular Research Center; Part # TR118), purified with DNAse I (Epicentre; Part # D9905K) and purified with RNClean XP beads (Agencourt; Part # A63987).
200ng of total RNA using the Universal Plus mRNA-Seq Library Prep Kit (NuGEN Technologies, Inc.; Part # 0508-96).

value: Airway Smooth Muscle

value: Primary

value: IFNg


title: Th17_72h_LNA2_replicate3_LANE1


title: Th17_72h_LNA1_replicate3_LANE2


title: Th17_72h_LNA1_replicate3_LANE3


title: TNFa_27

value: TNFa


title: Th17_72h_LNA2_replicate3_LANE2


title: Th17_72h_LNANT_replicate3_LANE3


title: Th17_72h_LNANT_replicate3_LANE1


title: Th17_72h_LNA1_replicate3_LANE1


title: case4-be

value: plasma

value: pre-operation


title: Th17_72h_LNANT_replicate3_LANE2


title: Th17_24h_LNA4_replicate3_LANE3

value: Nucleofected cells differentiated for 24 hour in Th17 media


title: case1-be


title: Th17_24h_LNA2_replicate3_LANE2


title: Th17_24h_LNA2_replicate3_LANE1


title: Th17_24h_LNA4_replicate3_LANE1


title: Th17_24h_LNA1_replicate3_LANE2


title: Th17_24h_LNA1_replicate3_LANE3


title: Th17_24h_LNANT_replicate3_LANE3


title: Th17_24h_LNA4_replicate3_LANE2