title: unc_CPAR0_4

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

data_processing:
Following sequencing, Illumina NextSeq Real Time Analysis version 2.4.11 and bcl2fastq2 version 2.20 were run to demultiplex reads and generate FASTQ files.
FASTQ files were then aligned to the smed_dd_g4 genome using STAR with parameters: --outFilterMultimapNmax 2 --alignIntronMax 5000 --quantMode GeneCounts, along with the Smes_hv_v1 gene models from the Max Plank Institute, obtained via Planmine, to generate read counts to genes.
TPM values were calculated from read counts to genes and gene length.
Genome_build: smed_dd_g4
Genome_build: http://planmine.mpi-cbg.de/planmine/
Supplementary_files_format_and_content: tpm.txt contains tab-delimited TPM values for each sample.

organism: Schmidtea mediterranea

source_name: asexual CIW4 adult

extract_protocol:
RNA was extracted using Trizol Reagent and TREATED WITH DNase.
Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded mRNA Prep Kit (Illumina).

treatment_protocol: Ctl or Hox gene RNAi animals (7x purified dsRNA feedings) animals were starved 5 days and snap frozen for RNA collection (4 samples with 3 animals each).

tag: wormid

tag: RNAi

value: unc

tag: replicate


title: P468_CRTH2-CD161-

status: Public on Aug 13 2021

type: SRA

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

state: MA

address: 500 Main St

department: Koch Institute

country: USA

institute: MIT

library_source: transcriptomic

data_processing:
Reads were aligned to the hg38 reference genome and collapsed by cell barcode and unique molecular identifier, and tabulated as described in Macosko et al.
Cells with fewer than 900 unique genes detected and genes detected in fewer than 5 cells were filtered out
Genome_build: hg38
Supplementary_files_format_and_content: barcodes.tsv.gz: single-cell barcodes from sample. Genes.txv: gene names from sample. Matrix.mtx.gz: single-cell gene/cell counts matrix in 10x sparse format.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
Cryopreserved PBMC from 8 of the 10 patients included in the tissue-resident single-cell analysis were thawed, and memory CD4+ T cells were isolated with the EasySep human memory CD4+ T cell enrichment kit (Stemcell Technologies, Vancouver, BC, Canada). T cells were cultured in AIM V medium (Gibco, Waltham, MA) for 6 hours at a density of 2 x 10e6 in 0.5 ml medium per well in 48-well plates, with human T-Activator CD3/CD28 beads (Thermo Fisher, Waltham, MA) in a 1:3 ratio of beads to T cells. After harvesting, the cells were labeled with BUV395-conjugated anti-CD3 (clone UCHT1), APC-Cy7-conjugated anti-CD4 (RPA-T4), PE-Cy7-conjugated anti-CD45RA (HI100), PerCP-Cy5.5-conjugated anti-CRTH2 (BM16) (all from BD Biosciences, San Jose, CA), eFluor450-conjugated anti-CD161 (HP-3G10), and Live/Dead Fixable Blue stain (L23105) (both from Thermo Fisher). Live CD3+CD4+CD45RA- CRTH2+CD161+, CRTH2+CD161-, and CRTH2-CD161- T cells were sorted with a FACSAria Fusion instrument (BD Biosciences).
Seq-Well

tag: diagnosis

value: Eosinophilic esophagitis (EoE)

tag: patient

tag: tissue

value: Peripheral blood

tag: sort fraction


title: d6_2

city: Qingdao

first: Wencheng

last: Wang

state: Shandong province

address: 700,Changcheng Road, Chengyang District

department: College of Horticulture

country: China

institute: Qingdao Agricultural University

data_processing:
Illumina software used for Base Calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Pyrus bretschneideri Rehd whole genome using HISAT.
Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Pyrus bretschneideri Rehd genome
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

organism: Pyrus ussuriensis

source_name: adventitious roots

growth_protocol: The adventitious buds of Pyrus ussuriensis Maxim were preserved in Qingdao Agricultural University, and the roots were induced by the adventitious buds with consistent growth and subculture for 25 days.

extract_protocol:
The adventitious roots of the four developmental stages were sampled, flash frozen on Liquid nitrogen, and RNA was harvested using EASYspin reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The medium induced by adventitious roots of Pyrus ussuriensis Maxim was: 1/2 MS + 0.5 mg/L IBA + 30.0 g/L sucrose + 7.5 g agar, pH = 6.0.

value: adventitious roots

tag: development stage

value: Day 6


title: 12-0732-MRCS

city: Philadelphia

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

data_processing:
RNA-seq data was aligned to the hg38 reference genome using GSNAP (v.   ) with default options. Required a mapping quality scofe of ≥30 for each read. Quality control analysis of the aligned data was performed using program RNA-SeQC.
Transcripts were assembled using Cufflinks (v.  ). A gene was considered differentially expressed if the false discovery rate (FDR) -adjusted p-value is <0.05.
Genome_build: hg38

source_name: Macula Choroid

extract_protocol:
Donor eyes were obtained from non-diabetic Caucasians at a death-to-preservation interval of <6h. Eyes were stored in RNA later before extraction of RNA. For each eye we dissected macula and periphery from retina and RPE/choroid/sclera resulting in 4 samples per eye. RNA was extracted using the ALLPrep DNA/RNA Mini Kit (Qiagen). All RNA had an RNA integrity number of ≥8.
Strand specific RNA library was prepared from 100 ng total RNA using the Encore Complete RNA-Seq library kit (Nugen Technologies, San Carlos, CA).
RNA-Seq on the Illumina HiSeq 2000.

tag: disease state

value: Normal


title: unc_CPAR0_3

molecule: polyA RNA


title: unc_CPAR0_2


title: d6_1


title: d12_1

value: Day 12


title: P468_CRTH2+CD161-


title: unc_CPAR0_1


title: P468_CRTH2+CD161+


title: P451_CRTH2+CD161-


title: d6_3


title: 12-0538-PR

source_name: Periphral Retina


title: P392_CRTH2+CD161-


title: P392_CRTH2+CD161+


title: post2b_CPAR104_24


title: post2b_CPAR104_21


title: 12-0538-MRCS


title: 12-0538-PRCS

source_name: Peripheral Choroid


title: lox5b_CPAR100_20


title: 12-0530-PRCS


title: d0_3

value: Day 0


title: 12-0538-MR

source_name: Macula Retina


title: P392_CRTH2-CD161-


title: post2b_CPAR104_23


title: P451_CRTH2+CD161+


title: d3_3

value: Day 3


title: post2b_CPAR104_22


title: 12-0530-MRCS


title: d3_1


title: lox5b_CPAR100_19


title: d3_2


title: lox5b_CPAR100_18


title: P355_CRTH2+CD161-


title: P354_CRTH2-CD161-


title: P355_CRTH2-CD161-


title: 12-0408-PRCS


title: d0_2


title: d0_1


title: 12-0408-MRCS


title: hox3b_CPAR97_15


title: 12-0530-MR


title: P292_CRTH2-CD161-


title: P292_CRTH2+CD161-


title: P354_CRTH2+CD161+


title: hox3b_CPAR97_14


title: 12-0396-PRCS


title: P355_CRTH2+CD161+


title: HSPCs, MPP4 KO3

city: illkirch

first: giovanni

last: cova

address: 1 Rue Laurent Fries

country: France

institute: igbmc

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Genome_build: mm10
Supplementary_files_format_and_content: table with raw, normalized data and Deseq analysis

organism: Mus musculus

source_name: primary hematopoietic stem and progenitor cells

extract_protocol:
Total RNA were extracted from 10.000 to 40.000 LT-HSC, MPP3 and MPP4 purified cells from WT and Helios KO bone marrow cells using the RNeasy Plus Micro Kit (Qiagen 74034).
Full length cDNAs were generated from 1000 pg of total RNA using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 12 cycles of cDNA amplification by Seq-Amp PCR. 600 pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation with the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoresis.

tag: cell type

value: Lin-Sca1+ckit+CD48+CD150-Flt3+ purified bone marrow cells

tag: genotype

value: Helios null

tag: age

value: 10 weeks


title: hox3b_CPAR97_13


title: 12-0530-PR


title: 12-0408-MR


title: lox5b_CPAR100_17


title: TS159_01_Fox_C1_KD

city: Manchester

first: Tim

middle: C

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

country: United Kingdom

institute: Cancer Research UK

description: Cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10% fetal bovine serum (Sigma Aldrich).

library_source: genomic

data_processing:
Reads were aligned to the human genome (hg38) using BWA-MEM v0.7.15 (5). Read duplicates were removed using Picard v2.1.0. Reads were further filtered using Bedtools v2.25.0 to keep only paired reads that mapped to standard chromosomes and to remove reads with a mapping quality of less than 10. Reads mapped to blacklisted regions defined by ENCODE were then removed using Bedtools (http://mitra.stanford.edu/kundaje).
Genome_build: GRCh38

molecule: genomic DNA

source_name: Fujioka cells

extract_protocol:
10^8 cells were used for each precipitation using the method described by Lee et al. (2006). Briefly, cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature before the reaction was quenched with 0.125M glycine. Cell pellets were washed twice with PBS and nuclear lysates sonicated for 6 cycles using a Bioruptor® Pico (Diagenode, Liege, Belgium). 10μg of antibody bound to 100μl of magnetic beads (Dynabeads Protein G, Invitrogen, Carlsbad, CA) was added to each sample and immunoprecipitation performed overnight on a rotator at 4°C and 20rpm. After five washes with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCl), chromatin IP-bound fractions were extracted by incubating for 15 min at 65°C with elution buffer (50mM TrisHCl pH8, 10mM EDTA, 1% SDS). Crosslinking was then reversed by incubation at 65°C for 6 hours. RNaseA (1mg/ml) and proteinase K (20mg/ml) were added to eliminate RNA and protein from the samples. DNA was extracted using phenol:chloroform:isoamyl alcohol and precipitated by adding 2 volumes of ice-cold 100% ethanol, glycogen (20μg/μl), 200mM NaCl and freezing at -80°C for at least 1hr. Pellets were washed with 70% ethanol and eluted in 50μl 10mM TrisHCl pH8.0.
Libraries were prepared for sequencing using a Microplex Library Preparation Kit (Diagenode). 200-800bp fragments were selected using AMPure beads (Beckman Coulter, Brea, CA) and quantified by qPCR with a KAPA Library Quantification Kit (Kapa Biosystems, Basel, Switzerland). Sequencing was performed using a NextSeq desktop sequencing system (Illumina) with 75bp, paired-end high output generating 65-80M reads per sample.

tag: cell line

value: Fujioka


title: HSPCs, MPP3 KO3

value: Lin-Sca1+ckit+CD48+CD150-Flt3- purified bone marrow cells


title: OMN0013_S2: human ocular motor neurons in SOD1

city: Baltimore

first: Hojae

last: Lee

address: 733 north broadway

institute: Johns hopkins medicine

description: SOD1A4V ALS

data_processing:
The raw data was processed with the STAR aligner (version 2.5.2b). Reads were aligned to the Homo sapiens genome.
Sequenced reads were aligned to the mouse reference genome hg19
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab separated values of expression matrix; rows are genes; columns are cells

source_name: SOD1A4V PHOX2B::GFP+

growth_protocol: human ES/iPS cells were cultured using hES media and seeding for differentiation. After seeding,  LDN193189, SB431542, Purmorphamine, Retinoic acid were used for spinal motor neuron differentiation and LDN193189, SB431542, CHIR, FGF8, Purmorphamine, SHH were used for ocular motor neurons.

extract_protocol:
Total RNA was extracted using miRNeasy mini kit (Qiagen) as per manufacturer’s instructions. RNA concentration and purity were assessed by Nanodrop (Thermo Fisher), and RNA integrity was assessed using the Agilent Bioanalyzer.
cDNA Libraries were prepared for mRNA-enriched sequencing using TruSeq Stranded mRNA kit (Illumina). This was followed by normalization to 6 nM and pooling of libraries, followed by single end 75 bp sequencing on the Illumina HighSeq 4000.

treatment_protocol: Each compounds were treated at culture day 11 with 4 different concentrations

value: human ocular motor neurons

value: amyotrophic lateral sclerosis (ALS)


title: P354_CRTH2+CD161-


title: 12-0408-PR


title: hox3b_CPAR97_16


title: 12-0396-MRCS


title: hox3a_CPAR96_12


title: P292_CRTH2+CD161+


title: HSPCs, MPP4 WT3

value: WT


title: 12-0396-PR


title: hox3a_CPAR96_9


title: P355_Duodenum

data_processing:
Reads were aligned to the hg38 reference genome and collapsed by cell barcode and unique molecular identifier, and tabulated as described in Macosko et al.
Cells with less than 500 unique genes detected and genes detected in fewer than 5 cells were filtered out
Ambient RNA correction was performed using SoupX v0.3.0 as described in Young et al with minor modifications. Cell contamination fractions were estimated using the genes KRT4, KRT5, KRT13, KRT15, and KRT6A in non-esophagus epithelium cells for samples from the esophagus and the genes IGHA1, IGHA2, IGHM, IGJ, and IGKC in non-plasma cells for samples from the duodenum
Genome_build: hg38
Supplementary_files_format_and_content: barcodes.tsv: single-cell barcodes from sample. Genes.txv: gene names from sample. Matrix.mtx: single-cell gene/cell counts matrix in 10x sparse format.

source_name: Duodenal biopsy

extract_protocol:
Up to six biopsies in total from the proximal, mid, and distal esophagus or duodenum were collected from each patient. Biopsies were minced with scalpels into fragments of ~1 mm2 and processed into a single-cell suspension by performing two subsequent digestions with Collagenase A (2 mg/mL) and DNase I (100 µg/mL) (both from Millipore-Sigma, St. Louis, MO) in RPMI medium for 40 minutes at 37ºC. Remaining fragments of tissue were removed by centrifugation (100g for 2 minutes), and the supernatant cell suspension was filtered through a 70-micron cell strainer and washed twice with cold staining buffer (PBS + 0.5% BSA + 2mM EDTA) before further use. Single-cell suspensions from esophagus tissue and duodenum tissue were processed for single-cell RNA sequencing using the Seq-Well platform.
Seq-Well

value: Duodenum

value: Remission


title: 12-0396-MR


title: HSPCs, LT-HSC KO3

value: Lin-Sca1+ckit+CD48-CD150+ purified bone marrow cells


title: P292_Duodenum

value: Active Disease


title: HSPCs, LT-HSC WT3


title: P355_Esophagus

source_name: Esophageal biopsy

value: Esophagus


title: 12-0276-PRCS

value: Normal


title: hox3a_CPAR96_11


title: P292_Esophagus


title: hox1_CPAR95_6


title: hox1_CPAR95_7


title: HSPCs, LT-HSC KO2


title: hox1_CPAR95_5


title: hox3a_CPAR96_10


title: P392_Esophagus


title: HSPCs, MPP3 WT3


title: P249_Duodenum


title: HSPCs, MPP4 WT2


title: 12-0276-MRCS


title: 12-0276-PR


title: HSPCs, MPP4 KO2


title: 12-0276-MR


title: HSPCs, LT-HSC WT2


title: hox1_CPAR95_8


title: 12-0046-PR


title: 11-2154-PRCS

value: Neovascular


title: P392_Duodenum


title: HSPCs, MPP3 KO1


title: HSPCs, MPP3 WT2


title: P474_Duodenum


title: 12-0210-PRCS


title: P474_Esophagus


title: P475_Duodenum


title: DD/CM/ID 11

type: genomic

city: Jeddah

first: Sajjad

last: Karim

state: Makka

address: Sulemania, CEGMR-80216

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

description: Developmental delay and Delayed Speech

hyb_protocol: Probe mixture of Cy3-labelled sample DNA, Cy5-labelled reference DNA, 50 μl of 1.0mg/ ml of human Cot-1 DNA (Invitrogen, USA), 52 μl of Agilent 10X Blocking Agent and 260 μl of Agilent 2X Hybridization Buffer (Part/Cat No of human reference DNA Male and Female: 5190-3796 and 5190-3797, Agilent Technologies, Inc.) was denatured at 100C for 1 minute 30 seconds and incubated at 37C for 30 minutes. The probe was applied to the array using an Agilent microarray hybridization chamber, and hybridized for 40 hours at 65C in a rotating oven (Robbins Scientific, Sunnyvale, USA) at 20 rpm. Arrays were washed according to the manufacturer’s recommendation and air dried.

scan_protocol: Arrays were scanned using an Agilent 2565AA DNA microarray scanner (Agilent Technologies, Inc).

data_processing: Data were processed using Agilent’s Feature Extraction software protocol for array-CGH data. To analyze genomic imbalance tumour samples (2 arrays each) the processed R signal and processed G signal columns from the Agilent Feature Extraction-generated a-CGH .txt files were imported into PGS. The tumour-specific signal across all probes was normalized as a ratio to baseline using Normalise to Baseline Tool in PGS, where baseline data corresponded to the normal human DNA. The data was then log2 transformed using the PGS Normalization and Scaling Tool. In order to detect regions of genomic gain and loss we applied the Genomic Segmentation tool with segmentation parameters set at: min. probes: 10, p-value threshold: 0.01, and signal to noise: 0.1. Region report was set at values bellow -.5/+.5 (log2) and p-value threshold of 0.05 for 2/2 (replicate) arrays in individual analysis or at 40% cut-off in cumulative analysis (i.e. 4/10 tumour samples). Regions of significant gain or loss were annotated to the corresponding genes present on the Affymetrix Gene 1.0 Array using the HuGene-1_0-st-v1.na24.hg18.transcript.csv file. Visualizations and VENN analysis were performed in PGS.

source_name: Peripheral Blood

label_protocol: Labelling was performed using the Agilent Genomic DNA Labeling Kit PLUS (Agilent Technologies, Inc., Palo Alto, USA) according to the manufacturer’s directions. Briefly, DNA was labelled with 1.5 - 3 mM Cy3-dUTP (Agilent Technologies, Inc., Palo Alto, USA), and purified using a Centricon YM-30 filter (Millipore, Billerica, USA).

growth_protocol: Not Applicable

extract_protocol: DNA was extracted after harvesting the cells by Trypsin (Invitrogen) followed by phenol-chloroform extraction and subsequent precipitation in 100% ethanol. DNA precipitate was washed with 70% ethanol then eluted in DNAse free water.

treatment_protocol: Not Applicable

value: 7 years

tag: gender

value: Male

value: Peripheral Blood

tag: phenotype

value: Developmental delay and Delayed Speech

source_name: Agilent Euro reference DNA

tag: sample type

value: reference sample


title: H2AK115RK116R_R2

city: Uppsala

first: Shujing

last: Liu

state: Uppsala

address: Torgny Segerstedts Alle 20

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

description: 15 days old plants

data_processing:
RNA-seq: Untrimmed reads were mapped to the Marchantia polymorpha MpTak1 v5.1 reference genome (Montgomery et al., 2020) using STAR (v2.5.3.a, (Dobin et al., 2013)). Read numbers of mapping statistics are reported in Supplementary Table S2. Expression counts were generated using the R function summarizeOverlaps from the package HTSeq in union mode on exons from the reference transcriptome MpTak1v5.1_r1. Differential expression analyses were performed using the R package DESeq2 (v1.20.0, (Love et al., 2014)).
Genome_build: MpTak1v5.1
Supplementary_files_format_and_content: Tables with the values of the differential expression analysis for genes and TEs are presented in text files

organism: Marchantia polymorpha

source_name: Thallus

growth_protocol: Plants were grown on vented 9 by 2.5 cm petri dishes containing Gamborg’s B5 medium solified with 1.4% plant agar, pH 5.5, under 16/8 h photoperiod at 22°C with light intensity at 60-70 umol m-2 s-1. Plate lids were taped to prevent loss of water.

extract_protocol:
50 mg 15d thalli of WT, Mpbmi1/1l, Mph2a;H2AK115R/K116R and Mph2a;H2AK119R mutants were used for RNA extraction. RNA was extracted using the MagMAX™ Plant RNA Isolation Kit (Thermo Fisher Scientific) in biological triplicates.
Libraries were generated using DNA-free RNA with the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina according to manufacturer’s instructions. Sequencing was performed on an Illumina HiSeqX in 150-bp pair-end mode at Novogene (Hong Kong).

tag: ecotype

value: Upp

tag: biological replicate

value: thallus


title: 12-0046-PRCS


title: HSPCs, MPP3 WT1

value: Lin-Sca1+ckit+CD48+CD150-Flt3- purified bone marrow cells

value: 10 weeks


title: DD/CM/ID 9

description: Developmental delay and dysmorphic feature

value: 4 months


title: 12-0884-MRCS

tag: Sex

value: F

value: early


title: 12-0210-PR


title: HSPCs, MPP3 KO2

value: Helios null


title: P468_Esophagus

value: Remission


title: HSPCs, MPP4 KO1

value: Lin-Sca1+ckit+CD48+CD150-Flt3+ purified bone marrow cells


title: HPC7 cells, Ikzf2-ChIP seq

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: HPC7 cell line

growth_protocol: HPC-7 cells were grown in 10% conditioned mSCF and IL-6 media and were routinely counted and split every 2-3 days to be kept between 80.000 -1.00.000 cells/ml.

extract_protocol:
Lysed nuclei from 50 000 000 HPC7 cells were sonicated with a Diagenode Bioruptor sonicator for 6 cycles (one cycle is 5’ HIGH 15’’ON / 15’’OFF).  Sheared from 200-500 pb chromatin was immunoprecipitated with anti-Helios antibody (#D8W4X, Cell Signaling technology), purified and sequenced using Illumina sequencer as recommended by the manufacturer.
Libray were prepared following the Diagenode MicroPlex Libray Preparation Kit (C05010014) using the manufacturer instructions.

value: HPC7 (Early haematopoietic cell line derived from ES cells)

tag: chip antibody


title: DD/CM/ID 4

value: 6 years

value: Female

value: Developmental delay and dysmorphic feature


title: 12-0094-PRCS

value: geographic atrophy


title: P354_Duodenum

value: Duodenum

tag: diagnosis

value: Active Disease


title: P249_Esophagus

tag: patient

value: Esophagus


title: DD/CM/ID 5

description: Developmental delay and Hypogonadism, Microcephaly

value: 9 years

value: Male

tag: tissue

value: Peripheral Blood

value: reference sample


title: DD/CM/ID 10

description: Developmental delay and Dysmorphic, Brain Atrophy, Muscle Dystrophy

value: 1.6 years


title: 12-0094-MRCS

value: F


title: 11-2154-MRCS

value: Neovascular


title: 11-2253-PRCS

value: early


title: 12-0884-PRCS


title: P471_Duodenum


title: 11-2154-PR


title: HSPCs, KO1

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Raw reads were aligned with bowtie2 v2.3.4.3 using the ENCODE ATAC-seq pipeline v1.5.1. Normalized BigWig files were generated using Homer make UCSC file v4.11.1 with the following parameters ’-norm 3e7 -style dnase’.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx table (Raw data, chromosome annotation and DEseq analysis) and bigwig files

extract_protocol:
5x104 Lin-Sca1+ckit+ bone marrow cells purified by cytometry flow from 2 WT and 2 helios deficient mice were processed using the fast-ATAC-seq protocol as described in M. Ryan Corces et al., 2016.
Libraries were prepared as described in J. Buenrostro et al., 2013.

value: Lin-Sca1+ckit+ bone marrow cells

value: 10 weeks

value: Helios null


title: P451_Esophagus


title: HSPCs, LT-HSC KO1

value: Lin-Sca1+ckit+CD48-CD150+ purified bone marrow cells


title: P471_Esophagus


title: DD/CM/ID 1

description: Developmental delay and Delayed Speech

value: 5 years

value: Female

value: Developmental delay and Delayed Speech


title: P451_Duodenum

value: Duodenum

value: Active Disease


title: P475_Esophagus

value: Esophagus


title: 11-2104-PRCS

value: M

value: geographic atrophy


title: HSPCs, MPP4 WT1

value: Lin-Sca1+ckit+CD48+CD150-Flt3+ purified bone marrow cells

value: WT


title: P468_Duodenum

value: Remission


title: HSPCs, LT-HSC WT1


title: SMN_iPS_3

city: Suwon

first: Su Bin

last: Lim

state: Gyeonggi-do

address: Worldcup-Ro 164, Yeongtong-Gu

country: South Korea

institute: Ajou University School of Medicine

description:
SMN_iPS
processed_data.txt

data_processing:
A pooled library of 12 samples was subjected to Illumina platform (NovaSeq6000 S4) in 150 bp paired-end mode.
Raw data (FASTQ files) were imported into Altanalyze v2.1.4 software, which uses the embedded software Kallisto and Ensembl 72 annotations
Genome_build: hg19
Supplementary_files_format_and_content: Processed read counts are available as "processed_data.txt".

tag: line

value: iPS

value: spinal motor neuron


title: 2 - treatment

city: Cologne

first: Malte

last: Stockebrand

address: Kerpener Str. 62

country: Germany

institute: DZNE e.V.

data_processing:
base calling on illumina
cell ranger (10X Genomics) 3.0.2 Pipeline
cell ranger mkfastq for demultiplexing and BCL to fastq conversion
cell ranger count for alignment, filtering, barcode counting, and UMI counting to generate feature barcode matrices
cell ranger (10X Genomics) 3.0.2 was used for dataset aggregation
Genome_build: rnor6.0
Supplementary_files_format_and_content: aggregated UMI count matrix of cell barcodes (sample index 1 = ctrl, 2 = treated) and features (genes), format: MEX

organism: Rattus norvegicus

source_name: primary cortical neuronal stem cells

growth_protocol: NSCs isolated from cortex of E14.5 Sprague-Dawley rats (R&D sytems, #NSC001) were cultured according to the manufacturer's protocol.

extract_protocol:
Cells were harvested according to the manufacturer's protocol and processed in the 10X chromium system according to manufacturer's protocol
Chromium Single Cell 3' Library & Gel Bead kit v2 and i7 Multiplex kit (10X Genomics)

treatment_protocol: Cells were treated with 30µM ZD7288 in vehicle (DMSO to a final concentration of 0.2%) or vehicle only in complete medium (in the presence of differentiation inhibitor FGF2) for 48h with complete replacement of medium and blockers after 24h.

tag: treatment


title: DD/CM/ID 8

description: Developmental delay and Delayed Speech

value: 2 years

value: Male

value: Peripheral Blood

value: reference sample


title: 11-2154-MR

tag: disease state

value: Neovascular


title: DD/CM/ID 6

description: Developmental delay and Congenital Heart Disease

value: 8 days

value: Female


title: HSPCs, KO2

tag: cell type

value: Lin-Sca1+ckit+ bone marrow cells

value: 10 weeks

value: Helios null


title: DD/CM/ID 7

value: 5 years

value: Developmental delay and dysmorphic feature


title: HPC7 cells, Input DNA

value: HPC7 (Early haematopoietic cell line derived from ES cells)


title: 11-1732-PRCS

value: M

value: early


title: DD/CM/ID 3

description: Developmental delay and Fragile X Syndrome, Autism

value: 7.9 years


title: HSPCs, WT1

tag: genotype

value: Wild Type


title: P354_Esophagus

value: Esophagus

value: Active Disease


title: 11-2033-MRCS

tag: age

value: F


title: 11-2033-PRCS


title: 11-2253-MRCS


title: SMN_iPS_1

description:
SMN_iPS
processed_data.txt

value: iPS

value: spinal motor neuron


title: SMN_iPS_2

description:
SMN_iPS
processed_data.txt


title: NSC_ZD7288_treatment_I

description: total of 500 cells from 2 treatment groups (each 4 replicates) and additional controls (5 positive bulk RNA, 5 negative empty wells)

data_processing:
base calling on Illumina
QC with FastQC
read trimming with cutadapt
Read Alignment with STAR aligner
Feature Assignment with featureCounts module of Subread package
Genome_build: rnor6.0
Supplementary_files_format_and_content: csv, raw gene count matrix of cell barcodes (columns) and features (genes in rows)
Supplementary_files_format_and_content: csv, barcode sample treatment assignment

extract_protocol:
Cells were pipetted into a 5,184 well chip (Icell8 platform, Wafergen / Takara), and after life/dead staining 500 wells containing single living cells (and 10 control wells) were selected for in well cDNA synthesis and cDNA was collected with collection kit (WaferGen / Takara).
WaferGen / Takara protocol: SMARTScribe RT cDNA synthesis, SeqAmp cDNA amplification, concentrated with DNA Clean & Concentrator Kit (Zymo Research) and purified with 0.6X AMpure XP beads (Beckman). After QC on Tape 12 Station (Agilent) cDNA was tagmented (Nextera XT transposome) and adaptor sequences added. Library purification was performed with AMpure XP beads, followed by dual SPRI treatment.

treatment_protocol: Cells were treated with 30µM ZD7288 in or non-treated in complete medium (in the presence of differentiation inhibitor FGF2) for 48h with complete replacement of medium and blocker after 24h.

value: ZD7288 OR non-treated


title: cholinium chloride_rep3 - CholCl_R3

city: Aveiro

first: Guilherme

middle: de Abreu

last: Jeremias

address: Campus Universitário de Santiago

department: Biology Department

country: Portugal

institute: University of Aveiro

data_processing:
Reads were trimmed with Trimmomatic (version 0.39)
Cleaned reads were mapped against the reference transcriptome of D. magna using the STAR aligner (version 2.7.3a)
HTseq-count in the intersection-nonempty mode was used for reads counting
Genome_build: Reference transcriptome of D. magna from Orsini et al. 2016: Orsini L, Gilbert D, Podicheti R, et al (2016) Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors. Sci Data 3:. doi: 10.1038/sdata.2016.30
Supplementary_files_format_and_content: Reads counting text files

organism: Daphnia magna

source_name: Whole-body

growth_protocol: Dedicated bulk cultures were established for a synchronised yield of the 3rd brood neonates needed (1440), all strictly ageing less than 10 h old. These neonates were then randomly assigned to 12 glass vessels comprising 3 replicates for each of the four treatments, i.e. control (blank ASTM medium) and EC20 of [Chol]Cl, [C2mim]Cl and [C12mim]Cl.

extract_protocol:
After exposure, active organisms were randomly collected from each replicate into RNAlater® for further storage at -80 °C. Pools of 90 individuals collected from each replicate were used for extraction. Organisms were homogenized with a disposable pestle before RNA extraction with the RNeasy kit and Qiashredder by Qiagen (Venlo, Netherlands) following the manufacturer's protocol.
The library construction of cDNA molecules was carried out using the Kapa Stranded mRNA Library Preparation Kit (Kapa Biosystems) and the generated DNA fragments were sequenced in an lllumina HiSeq 4000 platform, using 150 bp paired-end sequencing reads

treatment_protocol: Each replicate contained a total of 120 neonates in 500 mL of test solution, and the exposure lasted for exactly 48 h with no food addition.

tag: development stage

value: 48 hours

value: whole-body

value: EC20 of cholinium chloride

tag: number of organisms

value: pool of 90 individuals


title: HSPCs, WT2

value: Lin-Sca1+ckit+ bone marrow cells

value: 10 weeks


title: DD/CM/ID 2

description: Developmental delay and Delayed Speech

value: 6 years

tag: gender

value: Male

value: Peripheral Blood

tag: phenotype

value: Developmental delay and Delayed Speech

value: reference sample


title: 11-2104-MRCS

value: M

value: geographic atrophy


title: SMN_ES_2

description:
SMN_ES
processed_data.txt

value: ES


title: OMN_iPS_3

description:
OMN_iPS
processed_data.txt

value: iPS

value: ocular motor neuron


title: 11-1732-MRCS

value: early


title: SMN_ES_3

description:
SMN_ES
processed_data.txt

value: spinal motor neuron


title: SMN_ES_1

description:
SMN_ES
processed_data.txt


title: 1-dodecyl chloride-3-methylimidazolium_rep3 - C12mimCl_R3

value: 48 hours

value: whole-body

value: EC20 of 1-dodecyl chloride-3-methylimidazolium


title: Bmncs2

city: Beijing

first: Xianda

last: Hu

address: 218 Anwaixiaoguanbeili St

institute: Beijing Tibetan Hospital, CTRC

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Trimmed reads were used for de novo assembly using Trinity v2.5.1 with parameters --min_contig_length 150  --CPU 8 --min_kmer_cov 3 --min_glue 3 --bfly_opts '-V 5 --edge-thr=0.1 --stderr'
All contig sequences assembled were annotated using Blast2GO pipeline. The RNA-seq reads were mapped to the built reference transcriptome using Bowtie2 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed -- no-discordant -p 1 -k 200,  and fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using RSEM software..

organism: Byasa mencius

source_name: fatbody

extract_protocol:
The fatbody tissue of Papilio clytia and Atrophaneura mencius with or without LPS were collected and total RNAs were extracted with Trizol reagent, from which mRNAs were purified by poly-T oligo-attached magnetic beads.
Libraries were constructed for sequencing using a Superscript Double-Stranded cDNA Synthesis kit according to manufacturer's specifications.

value: fatbody

value: lipopolysaccharide challenge

tag: developmental stage

value: final instar


title: M14-input-UVB2

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
High-quality reads were then mapped to hg19 reference genome by HISAT2 with uniquely mapped reads retained for the following analyses.
Normalization were performed by Deeptools.
Differential expression analysis was performed by DESeq2.
Peak calling was performed with exomePeak.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig normalized signal

source_name: Skin

extract_protocol:
At 48-h post-transfection, total RNA was isolated from transfected cells with TRIZOL reagent. Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen).
RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols.

value: skin

tag: technology

value: RNA-Seq

tag: condition

value: UVB irradiation


title: Bmncs1

value: control


title: OMN_iPS_1

description:
OMN_iPS
processed_data.txt


title: M14-input-UVB1


title: cholinium chloride_rep1 - CholCl_R1

value: EC20 of cholinium chloride

value: pool of 90 individuals


title: OMN_ES_3

description:
OMN_ES
processed_data.txt

value: ES


title: M14-ip-UVB1


title: M14-ip-UVB2


title: OMN_ES_1

description:
OMN_ES
processed_data.txt


title: shMETTL14-IP-2

value: METTL14 knockdown


title: cholinium chloride_rep2 - CholCl_R2


title: OMN_iPS_2

description:
OMN_iPS
processed_data.txt

value: iPS

value: ocular motor neuron


title: 1-dodecyl chloride-3-methylimidazolium_rep2 - C12mimCl_R2


title: 1 - control

value: vehicle-treated


title: 1-ethyl-3-methylimidazolium chloride_rep1 - C2mimCl_R1

value: 48 hours

value: EC20 of 1-ethyl-3-methylimidazolium chloride


title: shNC-IP-1

value: Control


title: SYSMH3

city: guangzhou

first: peng

last: yu

address: Department of Oral and Maxillofacial Surgery

institute: Sun Yat-sen Memorial Hospital of Sun Yat-sen University

description: single cell RNA

data_processing:
Reads were processed using the Cell Ranger 3.0.1 pipeline with the default and recommended parameters. FASTQ files generated from Illumina sequencing output were aligned to the human genome, version GRCh38, using the STAR algorithm
gene barcode matrices were generated for each individual sample by counting UMIs and filtering noncell-associated barcodes.
we generated a gene-barcode matrix containing the barcoded cells and gene expression counts. This output was then imported into the Seurat R toolkit for quality control and downstream analysis of our single-cell RNA-seq data. All functions were run with default parameters unless specified otherwise. We excluded cells with fewer than 200 or more than 6000 detected genes (where each gene had to have at least one UMI aligned in at least three cells. The expression of mitochondrial genes was calculated using the PercentageFeatureSet function of the Seurat package
To remove low-activity cells, cells with more than 10% expression of mitochondrial genes were excluded. The normalized data (NormalizeData function in the Seurat package) were used to extract a subset of variable genes. Variable genes were identified while controlling for the strong relationship between variability and average expression. Next, we integrated data from different samples after identifying ‘anchors’ between datasets using FindIntegrationAnchors and IntegrateData in the Seurat package. Then, we performed principal component analysis (PCA) and reduced the data to the top 30 PCA components after scaling the data. We visualized the clusters on a 2D map produced with t-distributed stochastic neighbor embedding (t-SNE).
Cells were clustered using graph-based clustering of the PCA reduced data with the Louvain method. after computing a shared nearest neighbor graph. For subclustering, we applied the same procedure of scaling, dimensionality reduction, and clustering to the specific set of data (usually restricted to one type of cell. For each cluster, we used the Wilcoxon rank-sum test to find significant differentially expressed genes comparing the remaining clusters. SingleR and known marker genes were used to identify cell types.
Genome_build: mm9
Supplementary_files_format_and_content: peak text files

source_name: OSCC cells

growth_protocol: Tumor tissue was obtained immediately after surgery, and then surgical resection and cell separation began.

extract_protocol:
According to the manufacturer's protocol, the Chromium Single Cell 3'Reagent v3 Kit (10X Genomics, USA) was used to prepare a barcoded scRNA-seq library. The single-cell suspension was loaded onto a chromium single-cell controller instrument (10×genomics, USA) to produce single-cell gel beads in the emulsion. After generating Gel Beads-in-emulsion (GEM), reverse transcription was performed to generate full-length barcode genes.
The purified cDNA was amplified by PCR using a Qubit to detect the concentration, and an Agilent 2100 was used to detect the fragment size. Each library was sequenced on the HiSeqXTen platform (Illumina).

treatment_protocol: Each sample was cut into small pieces (1-2 mm diameter) and incubated with collagenase digestion solution on a shaker at 37°C for 1 hour. Subsequently, 5 ml of DMEM was added to dilute the suspension, and the suspension was filtered through a 70-micron cell mesh. After centrifugation at 400 rcf for 10 minutes, the supernatant was discarded, and the cells were washed twice with PBS. Then, the cell pellet was resuspended in 1 ml of prechilled red blood cell lysis buffer and incubated at room temperature for 3 minutes. Next, 5 ml of ice-cold PBS was added to the test tube and centrifuged at 300 rcf for 5 minutes. After decanting the supernatant, the pellet was resuspended in 5 ml of calcium magnesium phosphate buffer containing 2% (weight/volume) bovine serum albumin. Finally, the cells were counted under an inverted microscope with a hemocytometer. Trypan blue was used to quantify living cells.

value: OSCC TUMOR

value: untreated


title: shNC-input-1


title: Control_rep1

value: whole-body

value: Control:blank ASTM medium


title: SYSMH2

description: single cell RNA


title: SYSMH6

description: single cell RNA


title: SYSMH4

description: single cell RNA


title: shNC-IP-2

value: skin


title: 35min_after_FeCl2_addition_rep2

status: Public on Aug 12 2021

city: Newark

first: Clara

last: Chan

state: DE

institute: University of Delaware

data_processing:
Sequnce reads were quanlity controled using FASTQC and trimed using Trim Galore! v0.6.4 with a cutoff Q score of 28
Trimmed reads were mapped to S.lithotrophicus genome using bowtie2 v2.3.5.1
Raw counts were counted using Htseq-count
Genome_build: S.lithotrophicus genome
Supplementary_files_format_and_content: raw counts from all samples

organism: Sideroxydans lithotrophicus

extract_protocol:
Samples were collected and extracted using Qiagen Micro RNeasy kit. Genomic DNA was removed using Turbo Dnase kit and ribosomal rRNA was removed using MICROBExpress kit. rRNA-depleted RNA 1 ng was used for library prep and sequenced on Illumina NextSeq 550 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: stage/treatment


title: 90min_after_FeCl2_addition_rep2


title: 1-ethyl-3-methylimidazolium chloride_rep2 - C2mimCl_R2


title: 35min_after_FeCl2_addition_rep3


title: shMETTL14-input-1

value: RNA-Seq


title: 90min_after_FeCl2_addition_rep1


title: shNC-input-2


title: 1-dodecyl chloride-3-methylimidazolium_rep1 - C12mimCl_R1

value: EC20 of 1-dodecyl chloride-3-methylimidazolium


title: OMN_ES_2

description:
OMN_ES
processed_data.txt


title: Stationary_thiosulfate_rep2


title: Stationary_thiosulfate_rep3


title: Control_rep3


title: Latelog_thiosulfate_rep1


title: shMETTL14-IP-1


title: Midlog_thiosulfate_rep3


title: SYSMH1

description: single cell RNA


title: Midlog_thiosulfate_rep1


title: Latelog_Fe(II)-citrate_rep2


title: 15min_after_FeCl2_addition_rep1


title: 1-ethyl-3-methylimidazolium chloride_rep3 - C2mimCl_R3


title: SYSMH5

description: single cell RNA


title: shMETTL14-input-2


title: Stationary_Fe(II)-citrate_rep1


title: Midlog_Fe(II)-citrate_rep3


title: 90min_after_FeCl2_addition_rep3


title: Midlog_Fe(II)-citrate_rep1


title: Latelog_thiosulfate_rep2


title: Latelog_thiosulfate_rep3


title: Control_rep2


title: 35min_after_FeCl2_addition_rep1


title: Stationary_thiosulfate_rep1


title: Midlog_thiosulfate_rep2


title: PC-3 shCONTROL rep2

city: Boston

first: Marie-Anne

last: Goyette

address: 450 Brookline avenue

institute: DFCI

data_processing:
Quality of the raw reads was assessed with FastQC 0.11.5
Reads were aligned to the GRCh38 genome with Star 2.5.1b
Raw alignment counts were calculated with featureCounts 1.4.6
Differential expression measurements were performed with DESeq2 1.12.3
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file with raw alignment counts of each sample
Excel file of Deseq analysis including raw counts normalized relative to the total number of reads

source_name: PC-3 prostate cancer cells

extract_protocol:
Total RNA was extracted using RNeasy columns (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: shRNA

tag: cell line

value: PC-3 prostate cancer cells

value: shCONTROL


title: PC-3 shCONTROL rep3


title: Midlog_Fe(II)-citrate_rep2


title: 15min_after_FeCl2_addition_rep3


title: 15min_after_FeCl2_addition_rep2


title: PC-3 shCDGAP rep 2

value: shCDGAP


title: PC-3 shCONTROL rep1


title: Latelog_Fe(II)-citrate_rep3


title: Latelog_Fe(II)-citrate_rep1


title: p53 knockout, PDGFRA knock-in 4

city: New York

first: Oren

middle: Josh

last: Becher

state: NY

address: 1468 Madison Avenue, A21-02

department: Pediatrics

institute: Mount Sinai

description: Control_vs_Mut_Differential_Expression.xlxs

data_processing:
FASTQ files were aligned to the mm10 genome using RNA-STAR 2.7 .
Aligned reads were counted using HTSeq-count with the Ensembl mm10 transcriptome GTF file as the feature with the following HTSeq-count parameters: stranded = no, mode = union, minimum alignment quality = 10, map nonunique or ambiguous reads = none.
HTSeq-count files were imported into R (https://www.r-project.org/https://www.r-project.org/), genes with < 10 reads base mean were removed, and differential expression analysis was performed with the DESeq2 package using the DESeqDataSetFromHTSeqCount function with default settings. DESeq2 analyses were run comparing hPDGFRA KI and control mice.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table in Excel format containing DESeq2 output and DESeq2 normalized abundance measurements for each sample

source_name: Mut 13

growth_protocol: Nestin Tv-a; p53 fl/fl; Olig2-Tv-a/Cre mice and Nestin tv-a; p53 fl/fl; hPDGFRA fl/+; Olig2-Tv-a/Cre mice were allowed to reach P19, then euthanized and brain stem was collected.

extract_protocol:
Purified RNA was obtained by using Qiagen Rneasy extraction kit and protocol
TruSeq mRNA-Seq Library Prep

treatment_protocol: No treatments were given

value: brain stem


title: p53 knockout, PDGFRA knock-in 3

source_name: Mut 3


title: Stationary_Fe(II)-citrate_rep2


title: p53 knockout 4

source_name: Control 12C


title: 12823_380_IF_SR_2.2_3

city: Stanford

first: Magdalena

last: Matusiak

state: California

address: 300 Pasteur Dr

department: Pathology

institute: Stanford University

data_processing:
Base calls from the NextSeq were de-multiplexed and converted to FASTQ format with bcl2fastq (Illumina)
The five-base unique molecular identifier (UMI) sequence and the G-overhang were extracted from FASTQ data, and A-tails were removed with umi_homopolymer.py (github.com/jwfoley/3SEQtools)
Reads were aligned and further processed to remove duplicates using STAR (github.com/alexdobin/STAR)
Genome_build: hg38
Supplementary_files_format_and_content: TPM (transcript per milion)

source_name: Invasive Front, Stroma, Colon Cancer

extract_protocol:
For each patient 3 serial sections of the FFPE tissue were taken at 7 µm thickness and mounted onto frame slides with polyethylene naphthalate membranes (Thermo Fisher Scientific, #LCM0521). Slides were immersed for 20 s each in xylene (three times), 100% ethanol (three times), 95% ethanol (two times), 70% ethanol (two times), water, hematoxylin (Dako, #S3309), water, bluing reagent (Thermo Fisher Scientific, #7301), water, 70% ethanol (two times), 95% ethanol (two times), 100% ethanol (three times), and xylene (three times). Immediately after staining, regions containing arround 500 cells were dissected on an ArcturusXT LCM System (Thermo Fisher Scientific) using the ultraviolet laser to cut out the desired region and the infrared laser to adhere the membrane to a CapSure HS LCM Cap (Thermo Fisher Scientific, #LCM0215). Cell numbers were determined based on density estimates by cell counting in an adjacent H&E-stained section. After microdissection, the caps were sealed using 0.5-ml tubes (Thermo Fisher Scientific, #N8010611) and stored at -80 °C until cDNA library preparation.
Sequencing libraries were prepared according to the Smart-3SEQ protocol for LCM HS caps as previously described with slight modifications21. Briefly, 10 µl of lysis mix consisting of 40% (v/v) 5 M trimethylglycine solution (Sigma, #B0300), 20% (v/v) 10 mM nuclease-free dNTP mix (Thermo Fisher Scientific, #R0192), 10% (v/v) 20 µM first-strand primer in TE buffer (1S, /5Biosg/GT GAC TGG AGT TCA GAC GTG TGC TCT TCC GAT CTT TTT TTT TTT TTT TTT TTT TTT TTT TTT TV; Integrated DNA Technologies), 10% (v/v) Triton-X 100 (Sigma #T8787; diluted to 0.5% v/v in molecular biology-grade water), and 20% (v/v) Proteinase K (New England Biolabs, #P8107S; diluted to 0.125 mg/ml in in molecular biology-grade water) was added to the center of each LCM cap. Caps were sealed with 0.2 ml low-retention PCR tubes (Corning, #PCR-02-L-C) and incubated on a pre-warmed metal CapSure incubation block (Thermo Fisher Scientific, #LCM0505) at 60 °C in an incubator. Then, tubes were briefly centrifuged, and 10 µl of template-switching reverse-transcription (TS-RT) FFPE LCM mix consisting of 40% (v/v) 5x SMARTScribe first-strand reaction buffer (Clontech, #639537), 20% (v/v) 20 mM DTT (Clontech, #639537), 10% (v/v) 20x RNase inhibitor (Thermo Fisher Scientific, #AM2694), 4% (v/v) 50 µM second-strand primer in TE buffer (2S, /5Biosg/CT ACA CGA CGC TCT TCC GAT CTN NNN NrGrG rG; Integrated DNA Technologies), 4% (v/v) 200 mM MgCl2 (Sigma, #63069), 2% 5 mM proteinase K inhibitor (EMD Millipore, #539470), and 20% (v/v) 100 U/µl SMARTScribe reverse transcriptase (Clontech, #639537) was added. Samples were incubated in a programmable thermal cycler (42 °C for 30 min, 70 °C for 10 min, 4 °C hold), and 1.25 µl of a unique P5 primer and 1.25 µl of a universal P7 primer (2 µM in TE buffer each; Integrated DNA Technologies; sequences available upon request) and HiFi HotStart ReadyMix (Kapa, #KK2601) were then added, followed by 22 cycles of PCR amplification (98 °C for 45 s; 22 cycles at 98 °C for 15 s, 60 °C for 30 s, 72 °C for 10 s; then 72 °C for 60 s, and 4 °C hold). Amplified cDNA was next purified with SPRI bead mix (Beckman Coulter, #B23317) and a magnetic separation block (V&P Scientific, #VP772F4). Finally, the samples were washed with 80% ethanol and resuspended in TE buffer to yield the sequencing-ready library.

tag: tissue

value: colon

tag: type of macrophages present

value: spindly

tag: patient number


title: 12791_406_CT_SR_22

source_name: Center of the Tumor, Stroma, Colon Cancer


title: Stationary_Fe(II)-citrate_rep3


title: PC-3 shCDGAP rep 3

tag: treatment


title: 12669_393_IF_MO_high_SR1_24

value: foamy


title: 12728_393_IF_MO_high_SR2_24


title: PC-3 shCDGAP rep 1


title: p53 knockout, PDGFRA knock-in 2

source_name: Mut 2

tag: cell type


title: p53 knockout 3

source_name: Control 11C


title: 12742_380_IF_SR_2.1_3


title: p53 knockout, PDGFRA knock-in 1

source_name: Mut 1


title: p53 knockout 2

source_name: Control 10C


title: zt00066

city: Lebanon

first: Caitlin

middle: G

last: Howe

state: NH

address: 1 Medical Center Dr

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

data_processing:
Alignment using HISAT2 aligner
Gene-level quantification using Featurecounts
Genome_build: hg38
Supplementary_files_format_and_content: Text file of raw read counts for each sample
Supplementary_files_format_and_content: Text file of RPKM values for each sample
Supplementary_files_format_and_content: Text file of TPM values for each sample

source_name: Trimester 1 Maternal Blood Leukocytes

extract_protocol:
Buffy coat was homogenized using the QIAshredder (Qiagen 79654) before extraction with the Allprep Universal Kit for DNA/RNA/miRNA Extraction (Qiagen 80224)
RNA quality was determined on a fragment analyzer instrument and quantity measured by qubit. 500ng of high quality RNA was used as input into the Kapa RNA HyperPrep with RiboErase plus globin kit. 12 PCR cycles were used for final library amplification. All samples were pooled and sequenced on a NextSeq500 instrument to generate 25M, 75bp single-end reads per sample. Basecalling was performed on instrument using RTA v2.4.11 and converted to fastqs using bcl2fastq v2.20.0.422

value: First trimester maternal blood leukocytes


title: zj05762


title: wf00978


title: zp06755


title: 12833_393_IF_MO_high_SR3_24


title: ws09552


title: wc08450


title: p53 knockout 1

source_name: Control 5C


title: Microglia TNF/Smac/zVAD/Nec-1s rep4

city: Framingham

first: Dimitry

last: Ofengeim

address: 49 New York Avenue

institute: Sanofi

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD24-6D_001

data_processing:
The raw RNA-seq data were uploaded, processed and analyzed with the RNA-seq process pipeline in OmicSoft Array Studio software (version 10.1.1.3), including data quality control, alignment, quantification, normalization and log2 transformation to obtain the expression values (log2 FPKM) for each sample
Genome_build: MouseB38
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text file including gene annoation

source_name: Microglia

growth_protocol: Brains from 2-4 day old C57BL/6 mice were harvested and pooled in DMEM/F12-Glutamax media with 10% FBS transferred into warm 0.25% trypsin (2mL/brain) and incubated at 37ºC while rotating for 30 minutes.  The tissues were dissociated and filtered through a 70µM cell strainer.  The single-cell suspension was plated in T150 tissue culture flasks (1 flask/mouse) and the mixed gilal cells were cultured and fed for 12 days. On day 12 mixed glial cells were trypsinized and the single cell suspensions were counted. To isolate primary murine microglia, the EasySep Mouse CD11b Positive Selection Kit (StemCell #18970) was used with EasySep Magnets (StemCell #18000) according to manufacturer’s instructions. Primary murine astrocytes were isolated from the microglia negative fraction, with the EasySep Mouse APC Positive Selection Kit (StemCell #18452) and plated in DMEM high glucose with 10% FBS and N2 supplement (1:100 dilution; Thermo Fisher Scientific #17502-048). Isolated microglia were seeded at 2x10^6 cells/well and astrocytes at 1x10^6 cells/well in 6-well plates and rested for 24-48 hours prior to treatment

extract_protocol:
Cells were lysed in 350uL RLT Plus Lysis Buffer and RNA was extracted with the Qiagen Rneasy Plus Mini Kit according to manufacturer's instructions
Microglia (Genewiz): RNAseq library preparation consists of (A) mRNA enrichment, mRNA fragmentation and random priming; (B) first and second strand cDNA synthesis; (C) end repaire, 5'phophorylation and dA-tailing and (D) adaptor ligation and PCR enrichment and sequencing. Astrocytes (BGI): we captured mRNA with oligo dT and  constructed mRNA-seq library by strand-specific protocol. Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA were fragmented into small pieces (200-350bp) with fragment buffer at appropriate temperature. Then First-strand cDNA is generated in First Strand reaction system by random hexamer-primed reverse transcription, and the second-strand cDNA was generated with dNTP (dTTP replaced by dUTP). Adapters were added by incubating to end repair. After degradation of  the second-strand cDNA, the first Strand were amplified by PCR. Products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on DNBseq platform

treatment_protocol: Microglia and astrocytes were treated with (1) DMSO, (2) Nec-1s, (3) TNF/5z-7 (microglia only), (4) TNF/Smac/zVAD, (5) TNF/5z-7/Nec-1s (microglia only), and (6) TNF/Smac/zVAD/Nec-1s for 4 hours prior to lysis and RNA extraction

value: Microglia


title: Microglia TNF/Smac/zVAD/Nec-1s rep3

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD18-6C_001


title: Microglia TNF/Smac/zVAD rep4

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD23-5D_001

value: TNF/Smac/zVAD


title: up04513


title: vj05882


title: ul01308


title: yc09610


title: vl04509


title: Microglia TNF/Smac/zVAD rep1

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD05-5A_001


title: Microglia TNF/Smac/zVAD/Nec-1s rep2

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD12-6B_001


title: zg00030


title: Microglia TNF/5z-7/Nec-1s rep2

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD10-4B_001


title: Microglia TNF/5z-7/Nec-1s rep3

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD16-4C_001


title: Microglia TNF/Smac/zVAD rep3

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD17-5C_001


title: tp04076


title: Microglia TNF/Smac/zVAD/Nec-1s rep1

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD06-6A_001


title: wm05009


title: ri02200


title: Microglia TNF/5z-7/Nec-1s rep4

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD22-4D_001


title: qo05187


title: sz01638


title: Microglia DMSO rep2

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD07-1B_001

value: DMSO


title: Microglia DMSO rep3

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD13-1C_001


title: Microglia TNF/5z-7/Nec-1s rep1

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD04-4A_001


title: tf06738


title: sl00765


title: Microglia TNF/5z-7 rep2

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD09-3B_001


title: Microglia TNF/5z-7 rep4

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD21-3D_001


title: Microglia Nec-1s rep4

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD20-2D_001


title: Microglia TNF/Smac/zVAD rep2

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD11-5B_001


title: sf03295


title: Microglia TNF/5z-7 rep1

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD03-3A_001


title: Microglia Nec-1s rep2

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD08-2B_001


title: qy04712


title: pa09915


title: tp04704


title: na08228


title: pl04872


title: Microglia DMSO rep4

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD19-1D_001


title: rw08819


title: Microglia DMSO rep1

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD01-1A_001


title: Microglia TNF/5z-7 rep3

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD15-3C_001


title: lr04577


title: Microglia Nec-1s rep3

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD14-2C_001


title: sb03953


title: rb06824


title: qf04849


title: Microglia Nec-1s rep1

description:
mouse_microglia_24_samples_gene_exp_norm_log.txt
MD02-2A_001


title: ox06988


title: mc09212


title: jm00238


title: CTR.no_PlaB.repl2.Total

city: St Louis

first: Sabine

last: Dietmann

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

description:
CTR_no_PlaB_2.RNA
RNA.CTR.no.2
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt

data_processing:
Trim Galore! was used to quality trim the reads and remove sequencing adapters.
TopHat2 with parameters "--max-multihits 1 --read-mismatch 2 --b2-sensitive" was used to align the reads to the hg38 reference genome.
FeatureCounts with parameters "-p -B -C -s 2 --primary -Q 20" was used to calculate gene counts using either "exon" or "intron" regions as gene models.
The R Bioconductor DESeq2 package was used to calculate differentially expressed genes.
Genome_build: hg38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files containing counts for each gene and sample.

source_name: human primary keratinocytes

growth_protocol: Cells were grown in KBM gold (Lonza).

extract_protocol:
RNA was extracted using TRIZOL reagent (Thermo Fisher Scientific) following manufacturer instructions and quantified using a Nanodrop. For isolation of 4SU labelled RNA, 80 μg of RNA were used per replicate. The incorporated 4SU was biotinylated by incubating 1h 30 minutes at room temperature with EZ-link biotin-HPDP (Pierce) in biotinylation buffer (10mM Tris Ph 7.4, 1mM EDTA). Biotinylated RNA was then purified by phenol-chloroform extraction and loaded onto micro-MACS streptavidin columns (Miltenyi biotech). After 3 washes with warm (65°C) and 3 with room temperature washing buffer (100mM Tris pH 7.4, 10mM EDTA, 1M NaCl, 0.1% Tween 20), 4SU labelled RNA was then eluted directly into RLT buffer (Qiagen) by adding twice 100μl of 100mM DTT (Sigma Aldrich) and processed using the kit RNeasy MinElute (Qiagen), following manufacturer instructions.
Libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit, Pico Input Mammalian kit (Takara biotech), following manufacturer instructions. Four replicates per sample were sequenced on an Illumina HiSeq 4000 platform.

treatment_protocol: Cells were transfected with either control or Rn7sk siRNAs for 24h and treated with 1 μM Pladienolide B (Santa Cruz Biotech) or an equivalent volume of DMSO for the last 1 or 4 hours. 4SU was added at a concentration of 583μM for the last 10 minutes prior collection, where appropriate.

value: Keratinocytes

tag: sirna

value: Control

tag: time point

value: no


title: ma02224


title: CTR.4h_PlaB.repl3.Total

description:
CTR_4h_PlaB_3.RNA
RNA.CTR.4h.3
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt

value: Pladienolide B


title: ir07471


title: CTR.4h_PlaB.repl1.Total

description:
CTR_4h_PlaB_1.RNA
RNA.CTR.4h.1
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: lh01569


title: CTR.no_PlaB.repl1.Total

description:
CTR_no_PlaB_1.RNA
RNA.CTR.no.1
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: ly04595


title: CTR.4h_PlaB.repl4.Total

description:
CTR_4h_PlaB_4.RNA
RNA.CTR.4h.4
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: CTR.no_PlaB.repl4.Total

description:
CTR_no_PlaB_4.RNA
RNA.CTR.no.4
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: io05883


title: CTR.1h_PlaB.repl2.Total

description:
CTR_1h_PlaB_2.RNA
RNA.CTR.1h.2
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: gz03095


title: 7SK.no_PlaB.repl4.Total

description:
7SK_no_PlaB_4.RNA
RNA.7SK.no.4
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: ji04434


title: fl04721


title: CTR.4h_PlaB.repl2.Total

description:
CTR_4h_PlaB_2.RNA
RNA.CTR.4h.2
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: CTR.no_PlaB.repl3.Total

description:
CTR_no_PlaB_3.RNA
RNA.CTR.no.3
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: 7SK.no_PlaB.repl1.Total

description:
7SK_no_PlaB_1.RNA
RNA.7SK.no.1
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: eq01118


title: gp06952


title: 7SK.4h_PlaB.repl4.Total

description:
7SK_4h_PlaB_4.RNA
RNA.7SK.4h.4
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: en09652


title: CTR.1h_PlaB.repl1.Total

description:
CTR_1h_PlaB_1.RNA
RNA.CTR.1h.1
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: CTR.1h_PlaB.repl3.Total

description:
CTR_1h_PlaB_3.RNA
RNA.CTR.1h.3
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: kn05854


title: br02535


title: ca07040


title: 7SK.1h_PlaB.repl3.Total

description:
7SK_1h_PlaB_3.RNA
RNA.7SK.1h.3
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: cd01173


title: OX02514


title: ik09540


title: 7SK.no_PlaB.repl2.Total

description:
7SK_no_PlaB_2.RNA
RNA.7SK.no.2
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: 7SK.4h_PlaB.repl3.Total

description:
7SK_4h_PlaB_3.RNA
RNA.7SK.4h.3
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: 7SK.no_PlaB.repl3.Total

description:
7SK_no_PlaB_3.RNA
RNA.7SK.no.3
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: 7SK.4h_PlaB.repl2.Total

description:
7SK_4h_PlaB_2.RNA
RNA.7SK.4h.2
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: bi07249


title: CTR.no_PlaB.repl4.4SU

description:
CTR_no_PlaB_4.4SU
4SU.CTR.no.4
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: dv00351


title: aq04898


title: CTR.no_PlaB.repl2.4SU

description:
CTR_no_PlaB_2.4SU
4SU.CTR.no.2
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: au02019


title: 7SK.1h_PlaB.repl4.Total

description:
7SK_1h_PlaB_4.RNA
RNA.7SK.1h.4
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: ai09166


title: 7SK.4h_PlaB.repl1.Total

description:
7SK_4h_PlaB_1.RNA
RNA.7SK.4h.1
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: CTR.4h_PlaB.repl4.4SU

description:
CTR_4h_PlaB_4.4SU
4SU.CTR.4h.4
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: gc02452


title: CTR.1h_PlaB.repl4.Total

description:
CTR_1h_PlaB_4.RNA
RNA.CTR.1h.4
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: CTR.4h_PlaB.repl3.4SU

description:
CTR_4h_PlaB_3.4SU
4SU.CTR.4h.3
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: 7SK.1h_PlaB.repl2.Total

description:
7SK_1h_PlaB_2.RNA
RNA.7SK.1h.2
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: eh02957


title: 7SK.no_PlaB.repl2.4SU

description:
7SK_no_PlaB_2.4SU
4SU.7SK.no.2
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: bm09152


title: 7SK.no_PlaB.repl3.4SU

description:
7SK_no_PlaB_3.4SU
4SU.7SK.no.3
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: 7SK.4h_PlaB.repl1.4SU

description:
7SK_4h_PlaB_1.4SU
4SU.7SK.4h.1
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: 7SK.1h_PlaB.repl3.4SU

description:
7SK_1h_PlaB_3.4SU
4SU.7SK.1h.3
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: 7SK.4h_PlaB.repl3.4SU

description:
7SK_4h_PlaB_3.4SU
4SU.7SK.4h.3
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: CTR.no_PlaB.repl1.4SU

description:
CTR_no_PlaB_1.4SU
4SU.CTR.no.1
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: CTR.no_PlaB.repl3.4SU

description:
CTR_no_PlaB_3.4SU
4SU.CTR.no.3
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: 7SK.1h_PlaB.repl1.Total

description:
7SK_1h_PlaB_1.RNA
RNA.7SK.1h.1
Total RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: 7SK.1h_PlaB.repl4.4SU

description:
7SK_1h_PlaB_4.4SU
4SU.7SK.1h.4
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: bd09479


title: 7SK.4h_PlaB.repl2.4SU

description:
7SK_4h_PlaB_2.4SU
4SU.7SK.4h.2
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: CTR.4h_PlaB.repl1.4SU

description:
CTR_4h_PlaB_1.4SU
4SU.CTR.4h.1
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: CTR.1h_PlaB.repl2.4SU

description:
CTR_1h_PlaB_2.4SU
4SU.CTR.1h.2
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: CTR.4h_PlaB.repl2.4SU

description:
CTR_4h_PlaB_2.4SU
4SU.CTR.4h.2
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: bc07966


title: CTR.1h_PlaB.repl3.4SU

description:
CTR_1h_PlaB_3.4SU
4SU.CTR.1h.3
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: 7SK.no_PlaB.repl4.4SU

description:
7SK_no_PlaB_4.4SU
4SU.7SK.no.4
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: 7SK.no_PlaB.repl1.4SU

description:
7SK_no_PlaB_1.4SU
4SU.7SK.no.1
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: 7SK.4h_PlaB.repl4.4SU

description:
7SK_4h_PlaB_4.4SU
4SU.7SK.4h.4
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: 7SK.1h_PlaB.repl2.4SU

description:
7SK_1h_PlaB_2.4SU
4SU.7SK.1h.2
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: A549_RNA2_3

first: Haiqing

last: Bai

address: 5th floor, Center for Life Science, 3 Blackfan Circle

institute: Wyss Institute

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2 followed by differential expression analysis using DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: A549 cells

growth_protocol: A549 cells (ATCC CCL-185) were were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Life Technologies) supplemented with 10% fetal bovine serum (FBS) (Life Technologies) and penicillin-streptomycin (Life Technologies).

extract_protocol:
Total RNA was extracted from cells using RNeasy Plus Mini Kit (QiaGen, Cat#74134) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina HiSeq with 150-bp pair-ended reads

treatment_protocol: Cells were seeded into 6-well plate at 3 *10E5 cells/well and cultured for 24 h before transfection. Transfection was performed using TransIT-X2 Dynamic Delivery System (Mirus) according to the manufacturer’s instructions with some modifications. 6.8 μL of 10 μM RNA stock solution and 5 μL of transfection reagent were added in 200 μL Opti-MEM (Invitrogen) to make the transfection mixture. 200 μL of the transfection mixture was added to each well. At 48 hours after transfection, cell samples were collected and subjected to RNA-seq (Genewiz, lnc.)

value: human lung carcinoma epithelial cells

tag: transfection


title: A549_RNA1_3


title: A549_RNA2_1


title: A549_RNA2_2


title: A549_RNA1_2


title: 7SK.1h_PlaB.repl1.4SU

description:
7SK_1h_PlaB_1.4SU
4SU.7SK.1h.1
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: A549_control_3

value: scramble control


title: CTR.1h_PlaB.repl4.4SU

description:
CTR_1h_PlaB_4.4SU
4SU.CTR.1h.4
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: A549_control_2


title: A549_control_1


title: CTR.1h_PlaB.repl1.4SU

description:
CTR_1h_PlaB_1.4SU
4SU.CTR.1h.1
4SU RNA-seq
processed data file: counts.exon.txt
processed data file: counts.intron.txt


title: Sh-NC rep2

city: Guangzhou

first: Wen-Tao

last: Wang

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: sun yat sen university

data_processing:
Library strategy: Ribo-seq
Raw reads containing over 50% of low quality bases or over 10% of N bases were removed. Adapter   sequences were trimmed. Reads with length between 10-50bp were retained for subsequent analysis
Short reads alignment tool Bowtie2（version2.2.8） was used for mapping reads to ribosome RNA (rRNA) database. The   rRNA mapped reads will be removed. The remaining reads were further used in downstream analysis
The rRNA removed reads of each sample were mapped to reference genome by Bowtie2 allowing no   mismatches. RFs were assigned to different genomic features (5’UTR, CDS, 3’UTR and others) based on   the position of the 5’ end of the alignment,Reads number in the open reading frame of coding genes was calculated by software RiboTaper,and the   gene expression level was normalized by using FPKM
To identify differentially translated genes across sample groups, the edgeR package (http://www.r  project.org/ ) was used. Genes with a fold change ≥2 and a false discovery rate (FDR) <0.05 in a comparison   were considered as significant DTGs. DTGs were then subjected to enrichment analysis of GO functions   and KEGG pathways
Translational efficiency is the ratio of translating mRNAs to total mRNAs of a gene. The formula is shown   as follows: TE = (FPKM in Ribo-seq) / (FPKM in RNA-seq). TE of genes were calculated and compared   between samples and groups.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: acute myeloid leukemia cells

growth_protocol: To immobilize initiating ribosomes, harringtonine was added to cell culture medium to a final   concentration of 2 µg/ml. Cells were Incubated for 120 s with harringtonine in the incubator. Next, to block   translational elongation, cycloheximide was added to cell culture medium to a final concentration of 100   µg/ml. Cells were mixed well and proceeded immediately to cell lysis

extract_protocol:
Size exclusion columns (illustra MicroSpin S-400 HR Columns; GE Healthcare; catalog no. 27-5140-01) were   equilibrated with 3 mL of polysome buffer by gravity flow and centrifuged at 600g for 4 min at room   temperature. 100μL of digested RFs were added to the column and centrifuged at 600g for 2 min. Next,   10μL 10% (wt/vol) SDS was added to the elution, and RFs with a size greater than 17nt was isolated   according to the RNA Clean and Concentrator-25 kit (Zymo Research;R1017)
After obtaining ribosome footprints above, Ribo-seq libraries were constructed using NEBNext® Multiple   Small RNA Library Prep Set for Illumina® (catalog no.E7300S, E7300L). Briefly, adapters were added to both ends of RFs, followed by reverse transcription and PCR amplification. The 140-160bp size PCR products   were enriched to generate a cDNA library and sequenced using Illumina HiSeqTM 2500

value: sh-NC

tag: sample type

value: Ribosome profiling RNA


title: Sh-NC rep1


title: LXG_G

city: Tianjin

first: Jing

address: Huanhu West Road

institute: Tianjin Medical University Cancer Institute and Hospital

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perlscripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads on containing ploy_x0002_N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using Bowtie (Langmead, B.et al).
The circRNA were detected and identified using find_circ and CIRI2
The raw counts were first normalized using TPM.Normalized expression level = (readCount*1,000,000) / libsize (libsize is the sum of circRNA readcount) .
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files for each circRNA and each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Gastric cancer tissue

extract_protocol:
Total RNA was extracted from GC tissues with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions
A total amount of 5 μg RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribozero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, the linear RNA was digested with 3 U of RNase R (Epicentre, USA) per μg of RNA. The sequencing libraries were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250-300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37° C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Gastric cancer tissue

tag: neoadjuvant chemotherapy

value: untreated

tag: Sex

value: male

tag: age

tag: rfs

tag: t stage

tag: n stage

tag: tnm stage


title: LBX_B


title: LWL_G


title: XXY_G

value: female


title: DQR_B


title: A549_RNA1_1


title: BZJ_B


title: LNCaP proL1+ 3

city: Bronx

first: Kelvin

middle: Paul

last: Davies

state: New York

address: 1300 Morris Park Avenue, Forchheimer 742

department: Urology

institute: Albert Einstein College of Medicine

description:
Transformed to overexpress proL1 via lentiviral transduction
DESeq2_normalized_count_matrix.txt

data_processing:
Reads were aligned with STAR (v 2.4.0c)
Genes were annotated in Gencode v18
Reads were quantified with featureCounts (v 1.4.3-p1)
Normalization and differential experession was performed with Bioconductor package DESeq2
Genome_build: GRCh37.p12
Supplementary_files_format_and_content: Tab-delimited text files include count matrix for counts per gene, normalized for library size using DESeq2 (*DESeq2_count_matrix.txt) and count data transformed to the log2 scale in a way which minimizes differences between samples for rows with small counts, and normalizes with respect to library size (*DESeq2_regularized_log_transformed.txt)

source_name: Prostate cancer cells

growth_protocol: LNCaP cells were routinely passaged every 7 days (typically 2-3 x 10^6 cells into a T75 flask) in RPMI 1640 supplemented with 10% FBS, 100 units/mL penicillin, and 0.1 mg/mL streptomycin

extract_protocol:
RNA was harvested using the Qiagen RNeasy Mini Kit and its quality was checked using an Agilent 2100 Bioanalyzer
Illumina TruSeq Stranded Total RNA Library Prep, with Ribosomal Depletion

tag: strain

value: LNCaP FGC

tag: genotype

value: proL1 overexpression


title: LNCaP wt 3

value: parental cell line


title: LNCaP wt 2


title: Sh-NC input rep2

data_processing:
Raw reads containing over 50% of low quality bases or over 10% of N bases were removed. Adapter   sequences were trimmed. Reads with length between 10-50bp were retained for subsequent analysis
Short reads alignment tool Bowtie2（version2.2.8） was used for mapping reads to ribosome RNA (rRNA) database. The   rRNA mapped reads will be removed. The remaining reads were further used in downstream analysis
The rRNA removed reads of each sample were mapped to reference genome by Bowtie2 allowing no   mismatches. RFs were assigned to different genomic features (5’UTR, CDS, 3’UTR and others) based on   the position of the 5’ end of the alignment,Reads number in the open reading frame of coding genes was calculated by software RiboTaper,and the   gene expression level was normalized by using FPKM
To identify differentially translated genes across sample groups, the edgeR package (http://www.r  project.org/ ) was used. Genes with a fold change ≥2 and a false discovery rate (FDR) <0.05 in a comparison   were considered as significant DTGs. DTGs were then subjected to enrichment analysis of GO functions   and KEGG pathways
Translational efficiency is the ratio of translating mRNAs to total mRNAs of a gene. The formula is shown   as follows: TE = (FPKM in Ribo-seq) / (FPKM in RNA-seq). TE of genes were calculated and compared   between samples and groups.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

tag: cell line

value: RNA-seq


title: LNCaP wt 1


title: Sh-Speptide rep1

value: Sh-Speptide


title: Total RNAseq 48h calcium high Rn7sk rep 3

description: Total RNA seq

data_processing:
Paired-end RNA-seq reads (for 4SU and total RNA) were quality-trimmed using Trim Galore!, and mapped to the human reference genome (GRCh37/hg19) using TopHat2 with the parameters “--max-multihits 1 --read-mismatch 2 --b2-sensitive”. ENSEMBL (release 74) gene models were used to guide alignments with the “–GTF” option. Read counts for genes or first exons were obtained using featureCounts with the parameters “-p –s 1 –O --minOverlap 10 –B –C”. Read counts were normalized, and the statistical significance of differential expression between Rn7SK and WT was assessed using the R Bioconductor DESeq2 package. Gene counts - normalized by DESeq2 size factors - were subsequently normalized by their effective transcript length/1000, and log2-transformed. Effective transcript lengths were obtained with featureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: Files with read counts per ENSEMBL transcript obtained by 'featureCounts'

source_name: Human primary keratinocytes

growth_protocol: Human keratinocytes were grown in KGM gold with 0.06mM Calcium, without antibiotics

extract_protocol:
Total RNA was extracted with TRIZOL, following manufacturer protocol and DNAse treated. For 4SU labelled RNA isolation,  80 μg of total RNA were used per replicate. The incorporated 4SU was biothinylated by incubating 1h 30 minutes at room temperature with EZ-link biothin-HPDP (Pierce) in biothinylation buffer (10mM Tris Ph 7.4, 1mM EDTA). Biothinylated RNA was then purified by phenol-chloroform extraction and loaded onto micro-MACS streptavidin columns (Miltenyi biotech). After 3 washes with warm (65°C) and 3 with room temperature washing buffer (100mM Tris pH 7.4, 10mM EDTA, 1M NaCl, 0.1% Tween 20), 4SU labelled RNA was then eluted directly into RLT buffer (Qiagen) by adding twice 100μl of 100mM DTT (Sigma Aldrich) and processed using the kit RNeasy MinElute (Qiagen), following manufacturer instructions.
For 4SU RNA sequencing (sample 9 to 16) and total RNA sequencing at 24h (samples 1 to 8) libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit, Pico Input Mammalian kit (Takara biotech), following manufacturer instructions. For total RNA sequencing at 48h (samples 17 to 24) ribosomal RNA was depleted using the Ribo-Zero kit (Cambio), following manufacturer instruction. Ribo-depleted RNA was then processed with NEXTflex directionl RNA-seq Kit (dUTP-Based) v2 (bioo Scientific), following manufacturer instructions.

treatment_protocol: Cells were transfected with siRNAs, control or agains Rn7SK, using Lipofectamine RNAi and collected 24h or 48h later. 4SU was added at a concentration of 583μM for the last 10 minutes prior collection, where appropriate.

tag: developmental stage

value: Neonatal

tag: time point after transfection


title: LBC_B

last: Liu

tag: tissue


title: Total RNAseq 48h calcium high Rn7sk rep 4

description: Total RNA seq


title: Total RNAseq 48h calcium high Rn7sk rep 2

description: Total RNA seq


title: Total RNAseq 48h calcium high control rep 4

description: Total RNA seq


title: Sh-NC input rep1

tag: treatment


title: YBQ_G


title: Sh-Speptide input rep1


title: Sh-Speptide input rep2


title: Total RNAseq 48h calcium high control rep 1

description: Total RNA seq


title: Total RNAseq 48h calcium low Rn7sk rep 2

description: Total RNA seq


title: Total RNAseq 48h calcium low Rn7sk rep 4

description: Total RNA seq


title: SLZ_B


title: Total RNAseq 48h calcium low control rep 1

description: Total RNA seq


title: Total RNAseq 48h calcium low control rep 3

description: Total RNA seq


title: Total RNAseq 48h calcium low control rep 2

description: Total RNA seq


title: YU2 HIV infected monocyte-derived macrophages, replicate 2

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
MDM.Y.2
MDM_CD4_HIV_data.txt

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and hg19 genome with Ensembl transcriptome information.
DESeq2 was used for differential expression analysis.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: MDM_CD4_HIV_data.txt: Processed data file contains the raw counts for each gene.

source_name: monocyte-derived macrophages

extract_protocol:
RNA samples were extracted from MDM or CD4 T cells derived from 3 independent donors, infected or uninfected with HIV YU2 virus, then further treated with DNase I by using DNase treatment and removal kit (Ambion). RNA quality was determined using the Bioanalyzer (Agilent). All samples used for analysis had RIN numbers >7.5.
The total RNA-seq libraries were made with KAPA Hyper-Prep with rRNA removal by using Qiagen FastSelect kit, then subjected to 2 x 75 bp high output sequencing on Illumina NextSeq 500 platform.

tag: cell type

value: MDM

tag: infection

value: YU2 HIV infected

tag: replicate


title: YU2 HIV infected monocyte-derived macrophages, replicate 1

description:
MDM.Y.1
MDM_CD4_HIV_data.txt


title: 4SU RNAseq 24h control rep 4

description: Newly synthesised RNA seq


title: Total RNAseq 48h calcium low Rn7sk rep 3

description: Total RNA seq


title: YU2 HIV infected monocyte-derived macrophages, replicate 3

description:
MDM.Y.3
MDM_CD4_HIV_data.txt


title: Uninfected monocyte-derived macrophages, replicate 2

description:
MDM.u.2
MDM_CD4_HIV_data.txt

value: Uninfected


title: LNCaP proL1+ 2


title: 4SU RNAseq 24h Rn7sk rep 1

description: Newly synthesised RNA seq


title: Uninfected monocyte-derived macrophages, replicate 3

description:
MDM.u.3
MDM_CD4_HIV_data.txt


title: YU2 HIV infected CD4 T cells, replicate 3

description:
CD4.Y.3
MDM_CD4_HIV_data.txt

source_name: CD4 T cells

value: CD4 T cells


title: 4SU RNAseq 24h control rep 1

description: Newly synthesised RNA seq


title: Total RNAseq 48h calcium high control rep 3

description: Total RNA seq


title: CXW_G

tag: neoadjuvant chemotherapy


title: 4SU RNAseq 24h Rn7sk rep 4

description: Newly synthesised RNA seq


title: LNCaP proL1+ 1


title: Total RNAseq 48h calcium high Rn7sk rep 1

description: Total RNA seq


title: Uninfected CD4 T cells, replicate 3

description:
CD4.u.3
MDM_CD4_HIV_data.txt


title: Sh-Speptide rep2

tag: sample type


title: Total RNAseq 48h calcium low Rn7sk rep 1

description: Total RNA seq


title: 4SU RNAseq 24h Rn7sk rep 2

description: Newly synthesised RNA seq


title: Uninfected monocyte-derived macrophages, replicate 1

description:
MDM.u.1
MDM_CD4_HIV_data.txt


title: Uninfected CD4 T cells, replicate 2

description:
CD4.u.2
MDM_CD4_HIV_data.txt


title: Total RNAseq 48h calcium high control rep 2

description: Total RNA seq


title: Total RNAseq 24h control rep 3

description: Total RNA seq


title: Total RNAseq 24h Rn7sk rep 1

description: Total RNA seq


title: II.2 [NGS02042]

city: Bethesda

first: Julie

middle: E

last: Niemela

state: MD

address: 10 Center Dr

department: Dept. of Lab Medicine

institute: NIH Clinical Center

data_processing:
Read mapping and counting were performed using the Ion Torrent Suite software v4.4.2
Read counts were variance stabilized (normalized) using DeSeq2
Genome_build: Homo sapiens (human) genome assembly GRCh37 (hg19)
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with variance-stabilized (normalized) counts for every gene and every sample

source_name: Blood

extract_protocol:
Ion AmpliSeq Transcriptome Human Gene Expression Kit (Life Technologies)
Targeted Sequencing Library (>20,000 human RefSeq genes)
Ion Torrent Proton sequencing system (Life Technologies)

treatment_protocol: T cells from normal controls or patients were co-cultured with monocytes of one normal control in the presence of heat killed candida. After 3 days, T cell were enriched again to remove the monocytes and total RNA was extracted from the T cells for the RNA-sequencing (RNASeq) evaluation

value: CD3+ T cells

value: Candida-stimulated

value: CARD9 wild-type / CARD9 {delta}11

tag: disease state

value: candida esophagitis, upper respiratory infections, hypogammaglobulinemia and  low class-switched memory and plasmablast B cells

value: Blood


title: Total RNAseq 24h Rn7sk rep 4

description: Total RNA seq


title: II.3 [NGS02038]

value: asymptomatic, reduced plasmablast B-cells


title: 4SU RNAseq 24h control rep 3

description: Newly synthesised RNA seq


title: YU2 HIV infected CD4 T cells, replicate 1

description:
CD4.Y.1
MDM_CD4_HIV_data.txt


title: normal control 4 [NGS02026]

value: CARD9 wild-type / CARD9 wild-type

value: apparently healthy


title: Whole cell extract Rn7sk 18h rep 4

description: ChIPseq

data_processing:
Single-end ChIP-seq reads for PolII, H3K27ac, H3K4me1 ChIP, and WCE (whole cell extract) were quality-trimmed using Trim Galore!, and reads were mapped to the human reference genome (GRCh37/hg19) using bowtie with the parameters “-m 1 –v 2” to generate unique sequence alignments. Potential PCR duplicates were removed with MACS2 ‘filterdup’.
Genome-wide ChIP-seq read coverage was calculated using 'bedtools genomeCoverageBed', and the genome coverage files in BedGraph format were compressed to bigwig using the UCSC tool 'bedGraphToBigWig'
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Genome-wide ChIP-seq coverage in BigWig format.

extract_protocol:
18 hours after transfection cells were fixed with 1% formaldehyde for 10 minutes at room temperature. Chromatin was isolated and sonicated for 17 cycles of 30 seconds with an output of 30W, using an automated sonicator (3000; Misonix). Immunoprecipitation was carried out overnight at 4°C using 5μg of H3K4Me1 (Abcam) or 10μg of H3K27Ac (Abcam) or RNA Pol II N20 (Santa Cruz) antibodies previously bound to Dynabeads protein G (Thermo Fisher Scientific). DNA-protein complexes were eluted in 200μl of elution buffer (50mM Tris pH 8, 1mM EDTA, 1% SDS) by incubating at 65°C with brief agitation every 2-3 minutes. Cross-links were reverted both in the immunoprecipitated samples and the whole cell extract, separated from the sonicated material before immunoprecipitation, by incubating overnight at 65°C. DNA was then purified by phenol-chloroform extraction.
Libraries were prepared using NEXTflex Rapid DNA-Seq Kit (Bioo Scientific)

treatment_protocol: Cells were transfected with siRNAs, control or agains Rn7SK, using Lipofectamine RNAi and collected 18h later


title: Whole cell extract Rn7sk 18h rep 3

description: ChIPseq


title: I.1 [NGS02030]

value: asymptomatic, reduced plasmablast and  class-switched memory B-cells


title: Total RNAseq 24h Rn7sk rep 3

description: Total RNA seq


title: Whole cell extract Rn7sk 18h rep 1

description: ChIPseq


title: YU2 HIV infected CD4 T cells, replicate 2

description:
CD4.Y.2
MDM_CD4_HIV_data.txt


title: Total RNAseq 48h calcium low control rep 4

description: Total RNA seq


title: Total RNAseq 24h control rep 2

description: Total RNA seq


title: normal control 1 [NGS02015]


title: Whole cell extract control 18h rep 4

description: ChIPseq


title: Whole cell extract control 18h rep 2

description: ChIPseq


title: 4SU RNAseq 24h control rep 2

description: Newly synthesised RNA seq


title: I.2 [NGS02034]


title: 4SU RNAseq 24h Rn7sk rep 3

description: Newly synthesised RNA seq


title: normal control 1 [NGS02014]


title: ASH1L_AAV9 Injected PFC_2

city: Buffalo

first: Zhen

last: Yan

address: 955 Main St

institute: SUNY Buffalo

data_processing:
The RNA sequencing libraries was constructed by TruSeq stranded total RNA plus Ribo-zero kits (Illumina) then sequencing was carried out with the HiSeq 2500 platform (Illumina)
Raw fastq paired-end sequencing reads were aligned to the mouse reference genome mm10 using RNA STAR
Gene expression of mapped reads were then measured using featureCounts, producing compatible gene expression matrices to be used for differential expression and downstream analysis.
We then used DEseq2 for differential gene expression analysis, with featureCounts data as input, under default settings.
Genome_build: mm10
Supplementary_files_format_and_content: counts (txt)

source_name: PFC

extract_protocol:
RNA extraction from PFC samples of biological duplicates in each group used the RNAeasy Mini kit (Qiagen), coupled to an RNase-free DNase step (Qiagen). The strand-specific RNA sequencing libraries were generated from 1 μg purified RNA using TruSeq stranded total RNA plus Ribo-zero kits (Illumina).
The RNA sequencing libraries was constructed by TruSeq stranded total RNA plus Ribo-zero kits (Illumina). Sequencing was carried out with the HiSeq 2500 platform (Illumina) at the Genomics and Bioinformatics Core of State University of New York at Buffalo.Reads were first trimmed using Cutadapt to remove the 3’ end adapters and trailing sequences, followed by aligning to mouse RefSeq mRNAs using TopHat2 with default parameters.

value: PFC

value: Total cell lysate (bulk)

value: shRNA_ASH1L-AAV9 Injected


title: normal control 3 [NGS02022]


title: Total RNAseq 24h control rep 4

description: Total RNA seq

value: Neonatal


title: CARD9 Null [NGS02047]

value: CARD9 null / CARD9 null

value: susceptibility to fungal infections / systemic candidiasis


title: ASH1L_AAV9 Injected PFC_1


title: Whole cell extract Rn7sk 18h rep 2

description: ChIPseq


title: RNA Pol II ChIP 18h Rn7sk rep 2

description: ChIPseq


title: RNA Pol II ChIP 18h Rn7sk rep 1

description: ChIPseq


title: GFP_AAV9 Injected PFC_2

value: GFP-AAV9 Injected


title: Total RNAseq 24h Rn7sk rep 2

description: Total RNA seq


title: normal control 2 [NGS02018]


title: Uninfected CD4 T cells, replicate 1

description:
CD4.u.1
MDM_CD4_HIV_data.txt

value: CD4 T cells

value: Uninfected


title: RNA Pol II ChIP 18h control rep 4

description: ChIPseq


title: Whole cell extract control 18h rep 3

description: ChIPseq


title: RNA Pol II ChIP 18h control rep 2

description: ChIPseq


title: Total RNAseq 24h control rep 1

description: Total RNA seq


title: GFP_AAV9 Injected PFC_1


title: GFP_PFC_3

data_processing:
The RNA sequencing libraries was constructed by TruSeq stranded total RNA plus Ribo-zero kits (Illumina) then sequencing was carried out with the HiSeq 2500 platform (Illumina)
Raw fastq paired-end sequencing reads were aligned to the mouse reference genome mm10 using RNA STAR
Gene expression of mapped reads were then measured using featureCounts, producing compatible gene expression matrices to be used for differential expression and downstream analysis.
We then used DEseq2 for differential gene expression analysis, with featureCounts data as input, under default settings.
Genome_build: mm10
Supplementary_files_format_and_content: bam file with genome alignment to mm10 genome

value: prefrontal cortex


title: GFP_PFC_2


title: Kmt5b_PFC_3

value: shRNA_Kmt5b-AAV9 Injected


title: normal control 2 [NGS02019]

value: CD3+ T cells

value: Candida-stimulated


title: H3K27Ac ChIP 18h Rn7sk rep 2

description: ChIPseq


title: H3K27Ac ChIP 18h Rn7sk rep 1

description: ChIPseq


title: H3K27Ac ChIP 18h control rep 4

description: ChIPseq


title: Whole cell extract control 18h rep 1

description: ChIPseq


title: H3K27Ac ChIP 18h control rep 3

description: ChIPseq


title: Cdc42+/-2

city: Cincinnati

first: Fukun

last: Guo

state: OH

address: 3333 Burnet Avenue

institute: Children's Hospital Medical Center

data_processing:
75bp single-end sequencing was performed on an Illumina Hi-Seq 2500.
Sequenced reads were psuedo-aligned to mm10 using the TopHat aligner.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are in text format. They contain gene ID, symbol, name, base mean, fold change, log2fold change, p value, adjusted p value, and reads for each sample

source_name: Spleen

extract_protocol:
Spleen was smashed with syringe plungers. Single cells were obtained by filtering smashed spleen with cell strainer. Red blood cells were removed by using red blood cell lysis buffer. The splenocytes were then enriched of CD4+ T cells by MACS sorting followed by FACS sorting of CD4+YFP+ Treg cells.  Total RNA was extracted using a Qiagen RNeasy Mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2101) was used with a minimum of 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Treg cells

value: Heterozygous Cdc42 knockout


title: Cdc42+/-1


title: WT2

value: Wild type (WT)


title: Kmt5b_PFC_2


title: H3K27Ac ChIP 18h Rn7sk rep 4

description: ChIPseq


title: WT1


title: RNA Pol II ChIP 18h control rep 3

description: ChIPseq


title: RNA Pol II ChIP 18h control rep 1

description: ChIPseq


title: Cdc42-/-2

value: Homozygous Cdc42 knockout


title: Kmt5b_PFC_1


title: GFP_PFC_1


title: RNA Pol II ChIP 18h Rn7sk rep 4

description: ChIPseq


title: H3K4Me1 ChIP 18h Rn7sk KD rep 4

description: ChIPseq


title: H3K4Me1 ChIP 18h Rn7sk KD rep 2

description: ChIPseq


title: H3K27Ac ChIP 18h control rep 1

description: ChIPseq