title: Cables2-KO E7.5 rep2

city: Tsukuba

first: Tra

middle: Thi Huong

last: Dinh

state: Ibaraki

address: 1-1-1 Tennodai

department: Faculty of Medicine

country: Japan

institute: University of Tsukuba

data_processing:
8 FASTQ files per sample were concatenated and imported to CLC Genomics Workbench (Qiagen).
Normalization is performed by quantile method for total count.
For pairwise analysis, transcription expression values were analyzed by the Empirical Analysis of DGE in CLC Genomics Workbench (Qiagen) (fold change >2, FDR < 0.05).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include expression values for each sample
Supplementary_files_format_and_content: Table with expression and normalized values for samples at same stage of development

source_name: embryo

extract_protocol:
Embryos were collected, stocked in MeOH with 2 embryos/sample. Total RNAs were extracted using Trizol reagent (Thermo Fisher Scientific) and evaluated using Agilent Bioanalyzer with RNA 6000 Pico kit (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols. Total low-input RNA was used for rRNA-depletion and library synthesis by Takara SMARTer kit (Takara). RNA-seq library was prepared with Agilent Bioanalyzer, DNA High-sensitivity kit (Agilent Technologies) and performed with Illumina NextSeq500 (Illumina) by Tsukuba i-Laboratory LLP.

tag: development stage

value: embryonic day 7.5


title: Early_mRNA_Rep1

status: Public on May 12 2021

type: SRA

city: Berkeley

first: Tina

middle: Lynn

last: Sing

state: California

address: Barker Hall, Rm 616, University of California, Berkeley

department: Molecular and Cell Biology

country: USA

institute: University of California, Berkeley

description:
mRNA isolated from synchronized meiotic time course
Sample 3

library_source: transcriptomic

data_processing:
Sequencing reads were aligned to the SK1 genome using HISAT2
Transcripts per million reads (TPM) were calculated with STRINGTIE
Genome_build: SK1 genome from Saccharomyces Genome Resequencing Project (Sanger Institute)
Supplementary_files_format_and_content: Tab-delimited text output files from STRINGTIE include TPM values for each gene

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: All cells were grown in the indicated liquid media. E. coli were grown at 37˚C and S. cerevisiae were grown at 30˚C. G418 was added to all S. cerevisiae cultures to maintain plasmid selection.

extract_protocol:
mRNA and plasmid extracts were all performed using standard techniques.
mRNA was isolated with Oligo(dT)25 Dynabeads (Ambion) and libraries were preparerd with the NEXTFLEX Rapid Directional RNA-seq Kit (PerkinElmer). cDNA sequencing libraries were prepared with the NEXTFLEX Rapid DNA-seq Kit (PerkinElmer).
mRNA-seq (Samples 1-10) and DNA-seq (Samples 11-175)

treatment_protocol: cDNA libraries were induced by growing S. cerevisiae in media containing galactose (YPGR) or uninduced by growing in media containing glucose (YPD).

tag: strain

tag: meiotic cdna library

value: Early Meiosis

tag: growth condition

value: sporulation media


title: Cables2-KO E7.5 rep1

organism: Mus musculus


title: SIO_512_1 rep1

city: Beijing

first: CH

last: Dong

address: NO.3 Park 1, Beichen West Road, Chaoyang District

department: Institute of Microbiology

country: China

institute: Chinese Academy of Sciences

description: The strain was cultured with PDA plate at 20degC, sample were collected in margin of the plated in SI stage, named as SIO.

data_processing:
Four libraries were generated using a NEB Next Ultra RNA Library Prep Kit (NEB, Ipswich, MA, USA) following the manufacturer’s recommendations.
Library quality was assessed on an Agilent Bioanalyzer 2100 system.
The cDNA library was sequenced using an Illumina HiSeqX-ten platform (Illumina Inc., USA) by Allwegene Technology Co., Ltd. (Beijing, China).
Clean data were obtained by removing reads containing adapters and poly-Ns, and low-quality reads from the raw data.
The clean reads were mapped to the M. importuna genome (Murat et al. 2018) using TopHat v2.1.0.
Genome_build: CCBAS932 v1.0 (https://mycocosm.jgi.doe.gov/Morco1/Morco1.info.html)

organism: Morchella importuna

source_name: hyphae

extract_protocol:
Two individuals were pooled as one replicate and two replicates were collected for each sample. After collection, these samples were immediately frozen in liquid nitrogen and stored at _80°C refrigerator until RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: hyphae


title: WT-CCI TJ-16

type: RNA

city: Pittsburgh

first: Travis

middle: C.

last: Jackson

state: Pennsylvania

address: 3550 Terrace Street

department: Critical Care Medicine

institute: University of Pittsburgh

description:
WT-CCI
Gene expression data from mouse cortical brain tissue

hyb_protocol: 5 micrograms of fragmented and labeled ds-cDNA was incubated overnight (16h) hybridization at 45 degrees C with rotational mixing at 60 RPM. Arrays were processed on a GeneChip® 450 Fluidics Station using manufacturer specified protocols. To remove unbound sample, arrays were first washed with non-stringent wash buffer A. The GeneChips® were then stained for ten minutes in Stain cocktail 1.  Buffer A was again used to wash-off excess stain. Signal amplification was achieved by ten minutes incubation with Stain Cocktail 2 followed by a second ten minute incubation with Stain Cocktail 1.

scan_protocol: GeneChips were scanned using theGeneArray® 3000 scanner

data_processing: The data were analyzed with Tanscriptome Analysis Console (TAC) 4.0.

label: Biotin

source_name: Cortical Brain Tissue

label_protocol: Biotinylated cDNA were prepared and applified according to the standard Affymetrix protocol from 100ng total RNA

growth_protocol: 12-15wk old mice

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Animals were given anestheisa. Control animals were allowed to recover. Injured animals were given a crainotomy folled by a CCI-TBI. 48h later animals were pufused transcardially with cold PBS, brain tissue harvested, immediately flash-frozen in liquid nitrogen, and stored at -80C.

tag: genotype

value: WT

tag: injury

value: CCI

tag: gender

value: Female


title: WT-Sham TJ-4

description:
WT-Sham
Gene expression data from mouse cortical brain tissue

value: Sham


title: SII_512_1 rep2

description: The strain was cultured with PDA plate at 20degC, sample were collected in center of the plated in SI stage, named as SII.

source_name: sclerotium

value: sclerotium


title: Starvation_mRNA_Rep2

description:
mRNA isolated from synchronized meiotic time course
Sample 2

value: Starvation


title: WT E7.5 rep3


title: SII_512_1 rep1


title: WT-Sham TJ-27


title: WT-Sham TJ-2

value: Male


title: WT-Sham TJ-1


title: WT-Sham TJ-3


title: LN4

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

data_processing:
NEBNext small RNA adapter sequence (AGATCGGAAGAGCACACGTCT) was removed and reads with 30 Phred average quality aligned to known or predicted miRNA precursors were mapped with Bowtie (v1.1.2) to the reference genome.
DESeq2 (v1.24.0) was used to normalize read count data and to test for differential expression. The sva package was applied to remove batch effects in each comparison.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw read count matrix of miRNA-derived small RNAs, tab separated values.

organism: Homo sapiens

growth_protocol: Tumor biopsies were maintained in culture medium.

extract_protocol:
RNA was extracted by Trizol (Invitrogen).
RNA-seq libraries were prepared with NEBNext Multiplex Small RNA Library Prep Kit for Illumina (New England Biolabs), and sequenced on an Illumina HiSeq 4000.

treatment_protocol: All patients were at diagnosis.

tag: tissue

value: Biopsy - Reactive lymph node

tag: disease state

value: healthy

tag: condition

tag: histology


title: huvec_normal_rep1

city: Shanghai

first: xingyu

last: yang

address: 910 Hengshan Road

institute: IPMCH

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: control_primary HUVECs_cultured for 6 days

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified byRNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany

tag: subject status

value: control patient

value: female

tag: cell type

value: primary Human Umbilical Vein Endothelial Cells (HUVECs)


title: huvec_normal_rep4


title: huvec_preeclampsia_rep4

source_name: PE_primary HUVECs_cultured for 6 days

value: preeclampsia patient


title: Sample-98 (Total Bulk RNA-seq)

city: Irvine

first: Vivek

last: Swarup

state: CALIFORNIA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

institute: University of California Irvine

data_processing:
Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
Genome_build: hg38
Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.

source_name: Control brain

extract_protocol:
Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq

tag: age

tag: Sex

value: F

tag: pmi

tag: diagnosis

value: Control

tag: brain region

value: FC

tag: isolation

value: total RNA isolation


title: Cables2-KO E7.5 rep3

tag: strain

tag: development stage

value: embryonic day 7.5


title: LN2


title: rat intestinal epithelial cells infected with Staphylococcus aureus

first: Mengrui

last: Wang

address: No. 2, Yuanmingyuan West Road

institute: China Agricultural University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ATAC-seq reads were aligned to the Rattus_norvegicus genome assembly using Bowtie2. Screen Reads with a comparison quality value of MAPQ≥30, filter out Reads that are aligned to the organelle genome, filter out Reads that are repeatedly aligned, and finally retain high-quality fully paired double-ended aligned Reads.
Use Trimmomatic (v0.36) software to filter the original sequence. (1) Cut the sequence containing connector contamination, parameter: ILLUMINACLIP:Adapter.fa:2:30:10, the maximum allowable. The mismatch is 2, the number of matching bases in palindrome mode is 30, and the number of matching bases in simple mode is 10;  (2) Use sliding window method to excise low-quality bases in Reads, parameter: SLIDINGWINDOW: 4:15, bases in the 4bp window. If the mean base mass is less than 15 then cut;  (3) Cut off the bases at both ends of the Reads, parameter: LEADING: 3 TRAILING: 3, cut off the first and end quality values of the Reads. Bases less than 3 or N;  (4) After discarding the Reads whose length is less than 36nt after Trim, the parameter: MINLEN:36.
The MACS2 software was used to detect peaks, and the basic characteristics of the peaks, such as number and average length, were counted to obtain an overview of the open regions of the whole genome of each sample.
Based on the peak detection and genome comparison information, MAnorm is used to identify the difference Peaks between the comparison groups, and finally the unique and shared Peak results between the comparison groups are obtained. Calculate the number of genes in each entry, and then apply hypergeometric test to find out GO entries that are significantly enriched in differential genes compared with the background of the entire genome.
Hypergeometric test was applied to enrichment analysis for each pathway in KEGG, and the pathways that were significantly enriched in differential genes were found.
Genome_build: Rattus_norvegicus.Rnor_6.0.89.chr
Supplementary_files_format_and_content: txt files were generated using
Supplementary_files_format_and_content: peak text files

molecule: genomic DNA

organism: Rattus norvegicus

source_name: intestinal epithelial cells

growth_protocol: S. aureus ATCC 29213 infected IEC-6 cells at MOI of 1, in DMEM medium, for 4 h

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The Nextera DNA Library Preparation Kit (Illumina) was used to perform the transposition according to the manufacturer’s manual. 50 000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 ℃. The transposed DNA fragments were purified immediately after with a MinElute PCR Purification Kit (Qiagen). After Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen) and subjected to sequencing on Illumina Novaseq 6000 using PE150.

treatment_protocol: one sample treated with Staphylococcus aureus ATCC 29213 for 4 hours

tag: cell line

tag: treatment

value: intestinal


title: SIO_512_1 rep2

tag: Stage

value: hyphae


title: Cables2-KO E6.5 rep3

value: embryonic day 6.5


title: WT E7.5 rep2


title: LN5

tag: tissue


title: rat intestinal epithelial cells uninfected with Staphylococcus aureus

value: untreated


title: Starvation_mRNA_Rep1

description:
mRNA isolated from synchronized meiotic time course
Sample 1

tag: meiotic cdna library

value: Starvation

tag: growth condition

value: sporulation media


title: LN6

value: Biopsy - Reactive lymph node

tag: disease state

tag: condition

tag: histology


title: huvec_preeclampsia_rep2

tag: subject status

tag: gender

tag: cell type


title: Sample-93 (Total Bulk RNA-seq)

tag: age

tag: Sex

tag: pmi

tag: diagnosis


title: huvec_preeclampsia_rep3


title: ALCL_BIO20

value: tumor biopsy

value: ALCL patient

value: Relapsed


title: huvec_preeclampsia_rep1

value: female

value: primary Human Umbilical Vein Endothelial Cells (HUVECs)


title: huvec_normal_rep3

value: control patient


title: Sample-92 (Total Bulk RNA-seq)

value: F

value: Control

tag: brain region

tag: isolation


title: Cables2-KO E6.5 rep2

tag: strain

tag: development stage


title: Sample-99 (Total Bulk RNA-seq)

value: M

value: FC

value: total RNA isolation


title: Repeat-tagged sfgfp Nanopore Sequencing

city: Marburg

first: Lennart

last: Randau

state: Hessen

address: Karl-von-Frisch-Str. 4

department: Biology

country: Germany

institute: Phillips-Universität Marburg

description:
Extracted RNA was treated with E. coli Poly(A) Polymerase (NEB) for 30 min 37°C to add a poly(A) tail and then processed for Nanopore sequencing with the Direct RNA Sequencing Kit according to the protocol provided by Oxford Nanopore Technologies.
small RNA

data_processing:
removal of sequences of low quality (quality score limit, 0.05; maximum number of ambiguities 2)
trimming of adapter sequences
filtering by length (15-nt cutoff)
The trimmed sequences were mapped to the reference genome of Bl21 (DE3) and the sequence of the target plasmid using default settings.
Genome_build: E.coli reference genome (CP001509)  pETDuet1_sfGFP_Repeat  pBAD_sfGFP_Repeat  pBAD_lacZ_Repeat
Supplementary_files_format_and_content: The processed data files are in .wig (wiggle) format. They contain the mapping graphs of the three samples which were created from the coverage plots of the generated read track files.

organism: Escherichia coli

source_name: Repeat-tagged sfgfp

growth_protocol: Cells were grown in LB medium to logarithmic phase

extract_protocol:
The treated RNA was afterwards purified by EtOH precipitation including 1 % (v/v) glycogen.
cDNA libraries were created with the NEBNext® Multiplex Small RNA Library Pret Set for Illumunia according to the manufacturer’s instructions. 100 ng of input RNA was used and amplified cDNA libraries were separated by native PAGE for size selection of 120-250 bp. The selected sizes were extracted from the gel and EtOH precipitated Illumina HiSeq 2500 sequencing were performed at the Max-Planck Genome Centre, Cologne, according to their protocol.

treatment_protocol: RNA samples were treated with DNase I to remove potential DNA contamination. Fragmentation was achieved by addition of a ZnCl2 fragmentation buffer (final concentration: 10 mM Tris-HCl pH 6.8, 10 mM ZnCl2) and heating for 10 min at 95°C. Fragmentation was immediately stopped by putting the sample on ice and addition of 2µl 500 mM Na2-EDTA pH 8. The fragmented RNA was separated by denaturating Urea-PAGE and extracted from the gel. Fragmentation by bivalent metal ions presumably results in 2ʹ,3ʹ-cyclic phosphate and 5ʹ-OH RNA termini (Forconi & Herschlag, 2009), so fragments were first dephosphorylated (for 2ʹ,3ʹ-cyclic phosphate curation) and subsequently phosphorylated (for 5ʹ-OH curation) with T4 PNK. 15 µl of fragmented RNA was mixed with 6 µl of 5x dephosphorylation buffer (500 mM Tris-HCl pH 6.5, 500 MgAc, 25 mM β-mercaptoethanol) and 1 µl T4 PNK (Ambion) in a total volume of 30 µl and incubation for 6 h at 37 °C for dephosphorylation. For phosphorylation, 1 mM ATP and 1 µl T4 PNK were added and the mixture was further incubated for 1 h at 37 °C.

tag: promoter

value: pBAD

tag: library source

value: transcriptome


title: LN3

tag: tissue

value: healthy


title: Sample-97 (Total Bulk RNA-seq)


title: ALCL_BIO19

tag: disease state

value: Not Common


title: WT E7.5 rep1

value: embryonic day 7.5


title: Sample-9 (Total Bulk RNA-seq)

source_name: AD brain

value: AD


title: ALCL_BIO17

value: tumor biopsy

tag: condition


title: Sample-88 (Total Bulk RNA-seq)


title: Sample-96 (Total Bulk RNA-seq)


title: WT E6.5 rep2

value: embryonic day 6.5


title: Sample-86 (Total Bulk RNA-seq)


title: Sample-82 (Total Bulk RNA-seq)


title: KO5-28

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
1) RNAseq raw reads were aligned to mouse genome (mm10) using STAR v2.5.2b.
2) Gene read coverages were computed with featureCounts v1.5.2 using GENCODE annotation release M13
3) Differential expression analysis was performed using edgeR v3.22.0 with "y ~ 0 + group" design while filtering low count reads using built-in function filterByExpr
Genome_build: mm10
Supplementary_files_format_and_content: Text file in tab separated format with gene coverages in units of read counts

source_name: Brown adipose tissue (supraclavicular)

growth_protocol: Fat-specific Afadin KO and control littermates incubated at thermoneutrality for 2 weeks. Half were then transferred to cold (5 degrees celsius) for 6 hours. Mice were euthanized and BAT collected.

extract_protocol:
RNA was extracted using Trizol/chloroform extraction
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold

treatment_protocol: cold exposure for 6 hours

tag: group

tag: genotype

value: Afadin KO

tag: temperature


title: KO5-27


title: Sample-80 (Total Bulk RNA-seq)


title: Sample-95 (Total Bulk RNA-seq)


title: LN1

value: Biopsy - Reactive lymph node

tag: histology


title: Sample-94 (Total Bulk RNA-seq)

tag: age


title: Sample-77 (Total Bulk RNA-seq)

tag: Sex


title: Cables2-KO E6.5 rep1


title: Sample-75 (Total Bulk RNA-seq)

tag: pmi


title: Sample-91 (Total Bulk RNA-seq)

tag: diagnosis


title: Sample-90 (Total Bulk RNA-seq)

tag: brain region


title: ALCL_BIO18

value: ALCL patient

value: Relapsed

value: Common


title: Sample-73 (Total Bulk RNA-seq)

value: Control

tag: isolation


title: Sample-89 (Total Bulk RNA-seq)

value: M


title: Sample-87 (Total Bulk RNA-seq)

value: FC


title: WT E6.5 rep3

tag: strain


title: WT E6.5 rep1

tag: development stage


title: ALCL_BIO16


title: Sample-72 (Total Bulk RNA-seq)

value: F

value: total RNA isolation


title: ALCL_BIO15


title: Sample-81 (Total Bulk RNA-seq)


title: ALCL_BIO14

value: Complete remission


title: KO5-26


title: WT5-21

value: WT


title: Sample-8 (Total Bulk RNA-seq)


title: ALCL_BIO13


title: ALCL_BIO8


title: Sample-79 (Total Bulk RNA-seq)


title: Sample-85 (Total Bulk RNA-seq)


title: WT5-19


title: KO5-25


title: Sample-83 (Total Bulk RNA-seq)


title: ALCL_BIO12


title: Sample-78 (Total Bulk RNA-seq)


title: Sample-76 (Total Bulk RNA-seq)


title: ALCL_BIO11


title: ALCL_BIO7


title: KO5-24


title: WT5-18


title: healthy control-3

city: Jinan

first: Zhiyu

last: Li

address: Jingwu Road

department: Department of Plastic and Aesthetic Surgery

institute: Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University

description: Gene expresison without any treatment

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide.

scan_protocol: The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

source_name: Peripheral Blood, healthy control-3

label_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA from each sample was isolated using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. The purity and concentration of the total RNA samples were determined using a NanoDrop ND-1000 spectrometer (NanoDrop Technologies, Wilmington, DE, USA). RNA integrity was assessed through electrophoresis on a denaturing agarose gel.

treatment_protocol: Plasma was obtained from the blood samples via centrifugation at 2 000×g，20min and stored at -80 °C.

value: plasma

tag: gender

value: male


title: ALCL_BIO10


title: Sample-74 (Total Bulk RNA-seq)


title: KO5-23


title: Sample-69 (Total Bulk RNA-seq)


title: KO5-22


title: ALCL_BIO9


title: Sample-67 (Total Bulk RNA-seq)


title: Sample-71 (Total Bulk RNA-seq)


title: IH patient-2

description: Gene expresison without any treatment

source_name: Peripheral Blood, IH patient-2


title: Sample-70 (Total Bulk RNA-seq)


title: huvec_normal_rep2

tag: subject status

value: control patient

value: female

tag: cell type

value: primary Human Umbilical Vein Endothelial Cells (HUVECs)


title: Sample-65 (Total Bulk RNA-seq)


title: healthy control-2

description: Gene expresison without any treatment

source_name: Peripheral Blood, healthy control-2

tag: tissue


title: Sample-7 (Total Bulk RNA-seq)

value: AD


title: WT5-17


title: KO30-13

value: Afadin KO


title: ALCL_BIO1

value: tumor biopsy

tag: disease state

value: ALCL patient

tag: condition


title: Sample-64 (Total Bulk RNA-seq)


title: WT5-16

tag: group

tag: genotype


title: IH patient-3

description: Gene expresison without any treatment

source_name: Peripheral Blood, IH patient-3


title: KO30-11

tag: temperature


title: healthy control-1

description: Gene expresison without any treatment

source_name: Peripheral Blood, healthy control-1

tag: age


title: ALCL_BIO3

tag: histology


title: ALCL_BIO4

value: Not Common


title: ALCL_BIO6


title: Sample-63 (Total Bulk RNA-seq)

tag: Sex

tag: pmi

value: Control


title: KO30-14


title: Sample-66 (Total Bulk RNA-seq)

tag: diagnosis

tag: brain region


title: IH patient-1

description: Gene expresison without any treatment

source_name: Peripheral Blood, IH patient-1


title: ALCL_BIO2


title: Human keratinocytes HKC275 strain - HSD17B7 overexpression

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: 4.7ug of cRNA was hybridized for 16h at 45C. Arrays were washed and stained on GeneChip Fluidics Stations 450 (Thermo Fisher Scientific) according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned on GS300 scanner (Thermo Fisher Scientific) with AGCC Scan Control Software.

data_processing:
The analysis was performed with Transcriptome Analysis Console (TAC) Software (Thermo Fisher Scientific).
probe group file: Clariom_D_Human.r1.pgf
meta-probeset file: Clariom_D_Human.na36.hg38.transcript.csv

label: biotin

source_name: Foreskin-derived human primary keratinocytes from individuals of Caucasian ancestry - HSD17B7 overexpression

label_protocol: Samples were labelled with biotin.

growth_protocol: Human Primary Keratinocytes were cultured in serum-free keratinocyte medium (Gibco) supplemented with antibiotics, Bovine Pituitary Extract and EGF. Cells were harvested at 60-65% confluency and lysed in Tri-reagent (Sigma-Aldrich).

extract_protocol: RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo research).

treatment_protocol: Cells were infected with either a lentivirus overexpressing human HSD17B7 or control, selected with puromycin and then harvested 6d post infection.

tag: genotype/variation

value: HSD17B7 overexpression

tag: population

value: Caucasian ancestry

tag: line


title: Human keratinocytes HKC275 strain - Control

source_name: Foreskin-derived human primary keratinocytes from individuals of Caucasian ancestry - control


title: KO30-12

tag: strain


title: ALCL_BIO5


title: KO30-9


title: Sample-62 (Total Bulk RNA-seq)

value: M

value: FC

tag: isolation


title: Sample-60 (Total Bulk RNA-seq)

value: F

value: total RNA isolation


title: 3232: Blood T cells - CD8pos PD-1pos - Day 7 - Rep6

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

country: France

institute: INSERM U1236-MOBIDIC

data_processing:
Image analysis and base calling were performed using Illumina Real Time Analysis 2.7.7 Pipeline version with default parameters.
Raw sequencing data were checked and visualized for quality using FastQC (v0.11.5).
The RNAseq reads were aligned to the reference genome GRCh38 release 90 using STAR (v2.5).
Read summarization and gene counts were performed using the featureCounts function from the Subread package (v1.4.6).
Data normalization and differential gene expression were performed with the DESeq2 R package (v1.26.0). Data were filtered using HTSFilter R package (v1.26.0).
Significant genes were defined as p < .05 after adjustment for False Discovery Rate (FDR) correction and used for downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample reported after HTS Filtering with a threshold equal to 131.838

source_name: Blood T cells

extract_protocol:
For each T-cell sample, RNA was extracted using RNeasy Micro kit (Qiagen).
Libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit V2 - Pico Input Mammalian kit (Clontech Laboratories) following manufacturer protocols. The process was completed by Paired-End 75 bases massive parallel sequencing on Illumina HiSeq4000 and NovaSeq.

tag: cell type

value: CD3pos CD8pos PD-1pos

tag: tissue

value: blood

tag: treatment

value: Day 7 :one week of lenalidomide

tag: subject

value: subject 6


title: 3231: Blood T cells - CD8pos PD-1neg - Day 7 - Rep6

value: CD3pos CD8pos PD-1neg


title: KO30-10

tag: group

tag: genotype


title: 3230: Blood T cells - CD4pos PD-1pos - Day 7 - Rep6

value: CD3pos CD4pos PD-1pos


title: Sample-61 (Total Bulk RNA-seq)

tag: age


title: KO30-8

value: Afadin KO

tag: temperature


title: 3228: Blood T cells - CD8pos PD-1pos - Day 0 - Rep6

value: Day 0 :untreated


title: WT30-7

value: WT


title: 3229: Blood T cells - CD4pos PD-1neg - Day 7 - Rep6

value: CD3pos CD4pos PD-1neg


title: Sample-59 (Total Bulk RNA-seq)

tag: Sex

value: Control


title: 3227: Blood T cells - CD8pos PD-1neg - Day 0 - Rep6


title: WT30-5


title: WT30-4


title: Sample-6 (Total Bulk RNA-seq)

tag: pmi

value: AD


title: WT30-6


title: Sample-58 (Total Bulk RNA-seq)

tag: diagnosis


title: Human keratinocytes HKC260 strain - HSD17B7 overexpression

value: Foreskin-derived human primary keratinocytes

value: HSD17B7 overexpression

value: Caucasian ancestry


title: WT30-3


title: Human keratinocytes HKC249 strain - Control


title: Human keratinocytes HKC249 strain - HSD17B7 overexpression


title: Human keratinocytes HKC260 strain - Control


title: Human_keratinoctes_Caucasian_HKC220

source_name: Foreskin-derived human primary keratinocytes from individuals of Caucasian ancestry

value: Foreskin-derived primary keratinocytes

tag: gender

value: Male

value: Caucasian


title: 3189: Blood T cells - CD8pos PD-1pos - Day 7 - Rep5

value: CD3pos CD8pos PD-1pos

value: blood

value: subject 5


title: Sample-57 (Total Bulk RNA-seq)

value: M

tag: brain region

value: FC

value: total RNA isolation


title: 3225: Blood T cells - CD4pos PD-1neg - Day 0 - Rep6

value: Day 0 :untreated

value: subject 6


title: Human_keratinoctes_African_HKC223

source_name: Foreskin-derived human primary keratinocytes from individuals of Black African ancestry

tag: population

value: Black African


title: WT30-2

value: WT


title: WT30-1


title: Human_keratinoctes_Caucasian_HKC219


title: Sample-54 (Total Bulk RNA-seq)

value: F

value: Control


title: 3188: Blood T cells - CD8pos PD-1neg - Day 7 - Rep5

value: CD3pos CD8pos PD-1neg

value: Day 7 :one week of lenalidomide


title: 3187: Blood T cells - CD4pos PD-1pos - Day 7 - Rep5

value: CD3pos CD4pos PD-1pos


title: Sample-56 (Total Bulk RNA-seq)


title: Sample-53 (Total Bulk RNA-seq)


title: 3186: Blood T cells - CD4pos PD-1neg - Day 7 - Rep5

value: CD3pos CD4pos PD-1neg


title: Human_keratinoctes_African_HKC218

value: Foreskin-derived primary keratinocytes

value: Male


title: Human_keratinoctes_Caucasian_HKC217

value: Caucasian


title: CLL_P3_7

city: Strasbourg

first: Laurent

last: Vallat

address: 1, avenue Molière

department: Hematology

institute: Strasbourg University Hospital

data_processing:
Base-calling, quality trimming, filtering are performed by the iontorrent platform (Thermo Fisher Scientific) Torrent Suite Software v5
Reads are mapped on a two-step alignment scheme: the first mapping is done with TopHat v2.0.13 and unmapped reads are remapped using Bowtie version 2.2.2 with the –very-sensitive-local option
Abundance measurements or read counts are generated with htseq-count of the python HTSeq 0.6
Genome_build: hg19
Supplementary_files_format_and_content: Read counts in csv format

source_name: Peripheral blood

growth_protocol: CLL cell isolation: CLL B-cells were negatively selected from fresh blood samples using the RosetteSep B cell enrichment cocktail (StemCell Technologies) and density gradient centrifugation (Ficoll Paque Plus, GE Healthcare Life sciences). Cell purity was then controlled by flow cytometry after CD19+/CD5+ staining and ranged from 96% to 99% (median 97%).

extract_protocol:
RNA was harvested using Trizol reagent and extract using Rneasy Minikit (Qiagen cat#74104). Ribosomal RNA was depleted with the Low Input RiboMinu Eukaryote System v2 kit (Thermo Fisher Scientific).
Ion Total RNA-seq kit v2 (Thermo Fisher Scientific) according to the manufacturer's instructions. The libraries were loaded two by two at a concentration of 20 pM on an Ion PI™ Chip using the Ion Chef Instrument (Thermo Fisher Scientific)

treatment_protocol: Cell activation and culture conditions: CLL cells were stimulated with 10 µg/ml of soluble F(ab’)2 anti-human IgM (Jackson ImmunoResearch), 100 ng/ml of CD40L (Enzo Life Science), 10 ng/ml of IL-4 (R&D Systems-Bio-Techne) and 25 ng/ml of IL-21 (Invitrogen) as described previously (Schleiss, Sci Rep, 2019). Anti-IgM, IL-4 and CD40L were added at T0 and IL-21 was added at 24h. Cells were then cultured in RPMI 1640 Medium (Gibco) supplemented with 10% fetal calf serum (Dutscher) and 1% penicillin/streptomycin (Gibco) at 37°C, in an atmosphere enriched with 5% CO2.

value: female

tag: tumor

value: chronic lymphocytic leukemia

tag: clinical stage

value: Binet A/RAI 0 (untreated patient)

value: primary CLL cells

tag: biological features

value: IGHV Unmutated; ZAP70pos

tag: experimental conditions

value: stimulated

tag: time point

tag: time after stimulation


title: Sample-51 (Total Bulk RNA-seq)

source_name: Control brain

value: FC

tag: isolation

value: total RNA isolation


title: 3226: Blood T cells - CD4pos PD-1pos - Day 0 - Rep6

tag: cell type

tag: tissue

value: blood

tag: treatment

value: Day 0 :untreated

tag: subject

value: subject 6


title: CLL_P3_8

tag: Sex


title: Sample-50 (Total Bulk RNA-seq)

tag: age

value: F

tag: pmi

value: AD


title: Sample-52 (Total Bulk RNA-seq)

value: M

tag: diagnosis

value: Control


title: 3184: Blood T cells - CD8pos PD-1neg - Day 0 - Rep5

value: CD3pos CD8pos PD-1neg

value: subject 5


title: CLL_P3_6

value: female


title: Sample-5 (Total Bulk RNA-seq)

tag: brain region


title: CLL_P3_4

value: chronic lymphocytic leukemia


title: Human_keratinoctes_Caucasian_HKC215

value: Foreskin-derived primary keratinocytes

tag: gender

value: Male

tag: population

value: Caucasian


title: Human_keratinoctes_Caucasian_HKC214


title: Human_keratinoctes_Caucasian_HKC216


title: 3182: Blood T cells - CD4pos PD-1neg - Day 0 - Rep5

value: CD3pos CD4pos PD-1neg


title: Human_keratinoctes_African_HKC212

value: Black African


title: Human_keratinoctes_Caucasian_HKC213


title: 3173: Blood T cells - CD8pos PD-1pos - Day 7 - Rep4

value: CD3pos CD8pos PD-1pos

value: Day 7 :one week of lenalidomide

value: subject 4


title: Sample-46 (Total Bulk RNA-seq)

value: FC

value: total RNA isolation


title: CLL_P3_3

tag: tumor

tag: clinical stage

value: Binet A/RAI 0 (untreated patient)

value: primary CLL cells

value: IGHV Unmutated; ZAP70pos

value: stimulated


title: Human_keratinoctes_African_HKC211


title: 3183: Blood T cells - CD4pos PD-1pos - Day 0 - Rep5

value: CD3pos CD4pos PD-1pos

value: blood

value: Day 0 :untreated

value: subject 5


title: CLL_P3_5

value: female

value: chronic lymphocytic leukemia

tag: biological features

tag: experimental conditions


title: Human_keratinoctes_African_HKC210

value: Foreskin-derived primary keratinocytes

value: Male


title: CLL_P2_8

value: male

tag: time point

tag: time after stimulation


title: Sample-48 (Total Bulk RNA-seq)

value: F

value: AD

tag: isolation


title: CLL_P3_2

tag: cell type


title: Sample-44 (Total Bulk RNA-seq)

value: FC


title: 3172: Blood T cells - CD8pos PD-1neg - Day 7 - Rep4

value: CD3pos CD8pos PD-1neg

tag: tissue

tag: treatment

value: Day 7 :one week of lenalidomide

value: subject 4


title: CLL_P3_1

tag: Sex

value: Binet A/RAI 0 (untreated patient)

value: primary CLL cells

value: IGHV Unmutated; ZAP70pos


title: CLL_P3_0

value: unstimulated (T0)


title: CLL_P2_7

value: stimulated


title: 3171: Blood T cells - CD4pos PD-1pos - Day 7 - Rep4

value: CD3pos CD4pos PD-1pos

value: blood

tag: subject


title: Sample-49 (Total Bulk RNA-seq)

tag: age

tag: pmi

value: total RNA isolation


title: 3185: Blood T cells - CD8pos PD-1pos - Day 0 - Rep5

value: CD3pos CD8pos PD-1pos

value: Day 0 :untreated

value: subject 5


title: Sample-47 (Total Bulk RNA-seq)

value: M

tag: diagnosis

tag: brain region


title: CLL_P2_6

value: male

value: chronic lymphocytic leukemia


title: Human_keratinoctes_African_HKC208

value: Foreskin-derived primary keratinocytes

tag: gender

value: Male

tag: population

value: Black African


title: 3170: Blood T cells - CD4pos PD-1neg - Day 7 - Rep4

value: CD3pos CD4pos PD-1neg

value: Day 7 :one week of lenalidomide

value: subject 4


title: 3168: Blood T cells - CD8pos PD-1neg - Day 0 - Rep4

value: CD3pos CD8pos PD-1neg


title: Sample-45 (Total Bulk RNA-seq)

value: F

value: AD

value: FC


title: 3167: Blood T cells - CD4pos PD-1pos - Day 0 - Rep4

value: CD3pos CD4pos PD-1pos

value: blood


title: 3169: Blood T cells - CD8pos PD-1pos - Day 0 - Rep4

value: CD3pos CD8pos PD-1pos

value: Day 0 :untreated


title: Sample-42 (Total Bulk RNA-seq)

value: total RNA isolation


title: Sample-43 (Total Bulk RNA-seq)


title: CLL_P2_5

value: male

tag: tumor

tag: clinical stage

value: Binet A/RAI 0 (untreated patient)

value: primary CLL cells

value: IGHV Unmutated; ZAP70pos

value: stimulated


title: Sample-41 (Total Bulk RNA-seq)

value: M


title: Sample-4 (Total Bulk RNA-seq)


title: 3532: Blood T cells - CD4pos PD-1pos - Day 7 - Rep3

value: Day 7 :one week of lenalidomide

value: subject 3


title: CLL_P2_3

value: chronic lymphocytic leukemia

tag: biological features

tag: experimental conditions


title: 3166: Blood T cells - CD4pos PD-1neg - Day 0 - Rep4

value: CD3pos CD4pos PD-1neg

value: subject 4


title: Sample-40 (Total Bulk RNA-seq)

value: AD

value: FC


title: CLL_P2_2

tag: time point

tag: time after stimulation


title: Human_keratinoctes_African_HKC207

tag: cell type

value: Foreskin-derived primary keratinocytes

value: Male

value: Black African


title: Human_keratinoctes_Caucasian_HKC202

value: Caucasian


title: Human_keratinoctes_African_HKC204


title: Sample-38 (Total Bulk RNA-seq)

value: F

tag: isolation

value: total RNA isolation


title: 3531: Blood T cells - CD4pos PD-1neg - Day 7 - Rep3

tag: tissue

value: blood

tag: treatment


title: 3530: Blood T cells - CD4pos PD-1pos - Day 0 - Rep3

value: CD3pos CD4pos PD-1pos

value: Day 0 :untreated

tag: subject


title: Human_keratinoctes_Caucasian_HKC200


title: Human_keratinoctes_African_HKC201


title: 3529: Blood T cells - CD4pos PD-1neg - Day 0 - Rep3


title: CLL_P2_1

tag: Sex

value: male

value: Binet A/RAI 0 (untreated patient)

value: primary CLL cells

value: IGHV Unmutated; ZAP70pos

value: stimulated


title: 3252: Blood T cells - CD8pos PD-1pos - Day 7 - Rep2

value: CD3pos CD8pos PD-1pos

value: Day 7 :one week of lenalidomide

value: subject 2


title: Sample-37 (Total Bulk RNA-seq)

tag: age

tag: pmi

value: AD

value: FC


title: Sample-36 (Total Bulk RNA-seq)

value: M

tag: diagnosis

tag: brain region


title: CLL_P1_8

value: female

value: chronic lymphocytic leukemia


title: Human_keratinoctes_African_HKC205

value: Foreskin-derived primary keratinocytes

tag: gender

value: Male

tag: population

value: Black African


title: Human_keratinoctes_African_HKC206


title: Human_keratinoctes_African_HKC197


title: Human_keratinoctes_Caucasian_HKC196

value: Caucasian


title: Human_keratinoctes_Caucasian_HKC193


title: 3251: Blood T cells - CD8pos PD-1neg - Day 7 - Rep2

value: CD3pos CD8pos PD-1neg

value: blood


title: CLL_P2_0

value: male

tag: tumor

tag: clinical stage

value: Binet A/RAI 0 (untreated patient)

value: primary CLL cells

value: unstimulated (T0)


title: Human_keratinoctes_Caucasian_HKC192


title: Sample-35 (Total Bulk RNA-seq)

value: total RNA isolation


title: CLL_P1_7

tag: biological features

value: IGHV Unmutated; ZAP70pos

tag: experimental conditions

value: stimulated


title: Human_keratinoctes_Caucasian_HKC194


title: 3250: Blood T cells - CD4pos PD-1pos - Day 7 - Rep2

value: CD3pos CD4pos PD-1pos

value: Day 7 :one week of lenalidomide

value: subject 2


title: Sample-34 (Total Bulk RNA-seq)

value: M

value: AD

value: FC


title: 3248: Blood T cells - CD8pos PD-1pos - Day 0 - Rep2

value: CD3pos CD8pos PD-1pos

value: Day 0 :untreated


title: Sample-33 (Total Bulk RNA-seq)


title: CLL_P1_5

value: female

value: chronic lymphocytic leukemia

tag: time point

tag: time after stimulation


title: Human_keratinoctes_African_HKC191

tag: cell type

value: Foreskin-derived primary keratinocytes

value: Male

value: Black African


title: 3247: Blood T cells - CD8pos PD-1neg - Day 0 - Rep2

value: CD3pos CD8pos PD-1neg

tag: tissue

value: blood


title: CLL_P1_6

value: Binet A/RAI 0 (untreated patient)

value: primary CLL cells

value: IGHV Unmutated; ZAP70pos


title: Sample-32 (Total Bulk RNA-seq)

value: F

tag: isolation

value: total RNA isolation


title: CLL_P1_3

value: stimulated


title: Sample-31 (Total Bulk RNA-seq)

value: M

value: AD


title: 3246: Blood T cells - CD4pos PD-1pos - Day 0 - Rep2

value: CD3pos CD4pos PD-1pos

tag: treatment

tag: subject

value: subject 2


title: 3249: Blood T cells - CD4pos PD-1neg - Day 7 - Rep2

value: CD3pos CD4pos PD-1neg

value: Day 7 :one week of lenalidomide


title: CLL_P1_2

tag: Sex

value: female

value: chronic lymphocytic leukemia


title: Sample-3 (Total Bulk RNA-seq)

tag: age

tag: pmi

value: FC


title: 3245: Blood T cells - CD4pos PD-1neg - Day 0 - Rep2

value: Day 0 :untreated


title: Sample-28 (Total Bulk RNA-seq)

tag: diagnosis

tag: brain region


title: CLL_P1_4


title: 3224: Blood T cells - CD8pos PD-1pos - Day 7 - Rep1

value: CD3pos CD8pos PD-1pos

value: blood

value: subject 1


title: CLL_P1_0

value: Binet A/RAI 0 (untreated patient)

value: primary CLL cells

value: IGHV Unmutated; ZAP70pos

value: unstimulated (T0)


title: 3223: Blood T cells - CD8pos PD-1neg - Day 7 - Rep1

value: CD3pos CD8pos PD-1neg


title: Sample-27 (Total Bulk RNA-seq)

value: M

value: AD

value: total RNA isolation


title: Sample-26 (Total Bulk RNA-seq)

value: F


title: 3222: Blood T cells - CD4pos PD-1pos - Day 7 - Rep1

value: CD3pos CD4pos PD-1pos

value: Day 7 :one week of lenalidomide


title: CLL_NP3_7

value: female

value: chronic lymphocytic leukemia

value: stimulated


title: Sample-30 (Total Bulk RNA-seq)

value: FC


title: 3221: Blood T cells - CD4pos PD-1neg - Day 7 - Rep1

value: CD3pos CD4pos PD-1neg

value: blood


title: Human_keratinoctes_African_HKC189

value: Foreskin-derived primary keratinocytes

tag: gender

value: Male

tag: population

value: Black African


title: CLL_P2_4

value: male

tag: tumor

tag: clinical stage

value: Binet A/RAI 0 (untreated patient)

value: primary CLL cells

value: IGHV Unmutated; ZAP70pos


title: Human_keratinoctes_African_HKC190


title: Human_keratinoctes_African_HKC188


title: Sample-25 (Total Bulk RNA-seq)

value: M

value: AD

value: total RNA isolation


title: CLL_NP3_6

tag: biological features

tag: experimental conditions


title: Sample-24 (Total Bulk RNA-seq)


title: Human_keratinoctes_Caucasian_HKC187

value: Caucasian


title: CLL_P1_1

value: female

tag: time point

tag: time after stimulation


title: Human_keratinoctes_Caucasian_HKC247

tag: cell type


title: Human_keratinoctes_African_HKC246


title: 3220: Blood T cells - CD8pos PD-1pos - Day 0 - Rep1

value: CD3pos CD8pos PD-1pos

tag: tissue

value: Day 0 :untreated

value: subject 1


title: Human_keratinoctes_Caucasian_HKC244


title: Human_keratinoctes_African_HKC245


title: Human_keratinoctes_African_HKC242


title: Human_keratinoctes_Caucasian_HKC243


title: CLL_NP3_5

value: chronic lymphocytic leukemia

value: stimulated


title: 3218: Blood T cells - CD4pos PD-1pos - Day 0 - Rep1

value: CD3pos CD4pos PD-1pos

value: blood

tag: treatment


title: Sample-23 (Total Bulk RNA-seq)

value: F

value: FC

tag: isolation


title: CLL_NP3_8

tag: Sex

value: Binet A/RAI 0 (untreated patient)


title: Human_keratinoctes_Caucasian_HKC241

value: Foreskin-derived primary keratinocytes

value: Male


title: 3219: Blood T cells - CD8pos PD-1neg - Day 0 - Rep1

value: CD3pos CD8pos PD-1neg

tag: subject


title: Sample-202 (Total Bulk RNA-seq)

tag: age

tag: pmi

value: Control

value: CB


title: CLL_NP3_4

value: primary CLL cells

value: IGHV Unmutated; ZAP70pos


title: Sample-22 (Total Bulk RNA-seq)

value: M

tag: diagnosis

value: AD

tag: brain region

value: total RNA isolation


title: CLL_NP3_3

value: female

value: chronic lymphocytic leukemia


title: CLL_NP3_1

value: stimulated


title: 3217: Blood T cells - CD4pos PD-1neg - Day 0 - Rep1

value: CD3pos CD4pos PD-1neg

value: blood

value: Day 0 :untreated

value: subject 1


title: CLL_NP3_2

value: Binet A/RAI 0 (untreated patient)


title: Wheezer sample 16

city: London

first: Clare

middle: Margaret

last: Lloyd

address: Inflammation, Repair and Development, National Heart and Lung Institute, Sir Alexander Fleming Building

department: National Heart and Lung Institute

country: United Kingdom

institute: Imperial College London

data_processing:
Adapter sequences were removed and reads aligned to the Hg38 genome using the COBWeb aligner. A minimum 90 % sequence identity and match length of 25 base pairs, with a maximum 5 % sequence identity gap and maximum 1 novel splice event, were required for reads to align to a transcript.
Transcripts were quantified from aligned reads using the DESeq method
Low abundance transcripts for which 5 or more raw reads were not detected in at least 2 of 8 samples were removed prior to analysis
Genome_build: Hg38, 2016.12.01
Supplementary_files_format_and_content: .csv file containing DESeq-normalised expression values for each sample and for each transcript detected above the lower threshold. Both Ensembl IDs and gene IDs are shown

source_name: Sorted airway macrophages

extract_protocol:
AMs were bead sorted and immediately lysed in TRIZol reagent. Lysates were mixed 5:1 with chloroform and centrifuged at 10 000 g for 10 minutes at 4oC to obtain RNA in top aqueous layers. Aqueous layers were then mixed with an equal volume of 70 % ethanol and RNA extracted using the RNeasy Mini Kit from QIAGEN with on-column DNase digestion, as per manufacturer's instructions.
200 ng RNA per sample was polyA-purified and converted to cDNA sequencing libraries using the Illumina TruSeq Stranded mRNA v2 kit, with unique indexes per sample to allow multiplexing.

value: CD206+ airway macrophages

tag: patient diagnosis

value: preschool wheeze


title: Wheezer sample 15


title: Sample-201 (Total Bulk RNA-seq)

value: Control


title: Wheezer sample 14


title: CLL_NP3_0

tag: tumor

value: unstimulated (T0)


title: Sample-21 (Total Bulk RNA-seq)

value: F

value: FC


title: Sample-20 (Total Bulk RNA-seq)

value: M


title: Sample-200 (Total Bulk RNA-seq)

value: CB


title: CLL_NP2_8

value: male

tag: clinical stage

value: primary CLL cells

value: IGHV Unmutated; ZAP70pos


title: Non-wheezer sample 23

value: chronic cough without wheeze


title: Sample-2 (Total Bulk RNA-seq)

value: AD

value: total RNA isolation


title: Non-wheezer sample 21


title: Human_keratinoctes_Caucasian_HKC240

value: Foreskin-derived primary keratinocytes

tag: gender

value: Male

tag: population

value: Caucasian


title: Human_keratinoctes_African_HKC239

value: Black African


title: Human_keratinoctes_African_HKC236


title: Sample-199 (Total Bulk RNA-seq)


title: Non-wheezer sample 22

value: CD206+ airway macrophages


title: Human_keratinoctes_African_HKC235


title: Human_keratinoctes_African_HKC234


title: Non-wheezer sample 20


title: Human_keratinoctes_Caucasian_HKC233


title: CLL_NP2_5

value: chronic lymphocytic leukemia

value: Binet A/RAI 0 (untreated patient)

tag: biological features

tag: experimental conditions

value: stimulated

tag: time point


title: Human_keratinoctes_African_HKC237

tag: cell type


title: Non-wheezer sample 18

tag: tissue


title: Sample-198 (Total Bulk RNA-seq)

value: Control

tag: isolation


title: Human_keratinoctes_Caucasian_HKC238


title: Sample-197 (Total Bulk RNA-seq)

tag: Sex

value: M


title: CLL_NP2_4

tag: time after stimulation


title: CLL_NP2_7


title: CLL_NP2_2


title: Sample-196 (Total Bulk RNA-seq)

tag: age

value: CB


title: CLL_NP2_3

value: male


title: CLL_NP2_6

value: primary CLL cells


title: Human_keratinoctes_Caucasian_HKC232


title: SI-2

first: Ji

address: Yiheyuan 5#

institute: Peking University

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
We used Cellranger v3.1.0 (10X Genomics) to deal with the raw reads and quantify the expression level.
Next, the UMI count matrix were analyzed using Seurat pipeline.
Genome_build: hg38
Supplementary_files_format_and_content: files which include the barcodes, features and expression values of RefSeq genes.

source_name: human adult small intestine

extract_protocol:
All patients had signed written informed consent. Ileal crypt samples were collected from 2 right-sided colon cancer patients immediately after surgical resection.
We dissociate the samples into single cells and constructed the libraries using 10x Genomics (3' Library, Kit v3). Libraries were sequenced using Illumina HiSeq 4000 platform with 150-bp paired-end reads.

tag: region

value: ileal crypt


title: Sample-195 (Total Bulk RNA-seq)

tag: pmi

tag: diagnosis


title: Human_keratinoctes_Caucasian_HKC231


title: SI-1

description: polyA RNA


title: CLL_NP2_0

value: IGHV Unmutated; ZAP70pos

value: unstimulated (T0)


title: Sample-194 (Total Bulk RNA-seq)

value: F

tag: brain region

value: total RNA isolation


title: CLL_NP2_1

tag: tumor


title: Human_keratinoctes_African_HKC230

value: Foreskin-derived primary keratinocytes

value: Male


title: RKIP_5

city: Chicago

middle: Ekrem

last: Yesilkanal

state: IL

address: 929 E 57th St

department: Ben May Department for Cancer Research

institute: The University of Chicago

data_processing:
Adaptor sequences were removed using Trim Galore!
Sequences were mapped using RNA STAR.
Read counts were calculated using featureCounts.
Read counts normalization and differential expression analysis between CONTROL vs. RKIP samples were performed using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized read counts from DESeq2 for all the features

source_name: BM1 xenograft tumors

growth_protocol: 1 million BM1 or BM1-RKIP cells were injected orthotopically into athymic nude mice and tumors were isolated when the tumor size reached roughly 200mm3.

extract_protocol:
Tumor samples were snap-frozen in liquid nitrogen, pulvarized, and total RNA was collected immediately using TRI reagent.
RNA quality assessment, library preparation, and sequencing of the tumor RNA samples were all performed by the Genomics Facility staff at the University of Chicago following the facility's standardized protocols. Quality of the samples were assessed using a Bioanalyzer, and the samples were determined to be of high quality with an average RNA integrity number (RIN) of 8.6.

tag: treatment

value: RKIP overexpression


title: RKIP_4


title: Human_keratinoctes_Caucasian_HKC229

tag: gender

value: Caucasian


title: Human_keratinoctes_Caucasian_HKC228

tag: population


title: RKIP_3


title: Sample-193 (Total Bulk RNA-seq)


title: Sample-192 (Total Bulk RNA-seq)


title: CLL_NP1_7

value: female

value: chronic lymphocytic leukemia

tag: clinical stage

tag: biological features


title: CLL_NP1_8

value: Binet A/RAI 0 (untreated patient)

tag: experimental conditions

value: stimulated

tag: time point


title: Sample-191 (Total Bulk RNA-seq)

value: Control


title: SY5Y_48h rep2

city: Shenzhen

first: SHAO

middle: MIN

last: YANG

state: guangdong

address: Nanshan

department: Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center

institute: Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine

data_processing:
CASAVA version 1.4 software used for basecalling.
The "dirty" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads were  removed, then mapped to Rattus_norvegicus whole genome using bowtie2 with parameters for PE reads: -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 16 -k 200
Reads Per Kilobase of exon per Megabase of library size (RPKM) method was used in calculated expression level.
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each Sample ...

source_name: SH-SY5Y cells

extract_protocol:
SH-SY5Y cells with Varicella-Zoster Virus-Infected were flash frozen on dry ice, and RNA was harvested using Trizol reagent. BGIseq500 RNA library 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

tag: cell type

value: SH-SY5Y cells

value: infected with rOka for 48h


title: RKIP_2


title: RKIP_1


title: Sample-190 (Total Bulk RNA-seq)

value: M

value: CB

tag: isolation


title: CLL_NP1_6

tag: Sex

value: primary CLL cells

value: IGHV Unmutated; ZAP70pos


title: SY5Y_48h rep1


title: SY5Y_48h rep3


title: CONTROL_7

value: control


title: CLL_NP1_4

tag: time after stimulation


title: CONTROL_6


title: Sample-189 (Total Bulk RNA-seq)

tag: age

value: F

value: total RNA isolation


title: CLL_NP1_5


title: Human_keratinoctes_African_HKC227

value: Foreskin-derived primary keratinocytes

value: Male

value: Black African


title: SY5Y_24h rep2

value: infected with rOka for 24h


title: Human_keratinoctes_African_HKC225


title: Human_keratinoctes_Caucasian_HKC224

value: Caucasian


title: Human_keratinoctes_African_HKC226


title: Sample-188 (Total Bulk RNA-seq)


title: CLL_NP1_2

value: female

value: chronic lymphocytic leukemia

value: Binet A/RAI 0 (untreated patient)


title: CONTROL_5


title: SY5Y_24h rep1

value: SH-SY5Y cells


title: Sample-19 (Total Bulk RNA-seq)

source_name: AD brain

value: AD

value: FC


title: SY5Y  rep2

value: mock


title: Sample-186 (Total Bulk RNA-seq)

value: M

value: Control

value: CB


title: CONTROL_4

value: control


title: CONTROL_3


title: Sample-187 (Total Bulk RNA-seq)

value: F

value: total RNA isolation


title: CLL_NP1_1

value: primary CLL cells

value: IGHV Unmutated; ZAP70pos

value: stimulated


title: CONTROL_2


title: CLL_NP1_3


title: SY5Y  rep1


title: SY5Y  rep3


title: SY5Y_24h rep3

value: infected with rOka for 24h


title: Sample-181 (Total Bulk RNA-seq)


title: Sample-185 (Total Bulk RNA-seq)


title: Tr4_2

city: Wuhan

first: Jie

last: Wu

state: Hubei

address: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1277

department: Department of Cardiovascular Surgery

data_processing:
Raw reads were filtered first to remove low-quality or adaptor sequences by SOAPnuke (v1.5.6).
Cleaned reads were mapped to the mm10 genome using Bowtie2 (v2.2.5), where only uniquely mapped reads were retained.
We used MACS2 (v2.1.2) to call peaks (open chromatin regions) using the parameter '--bw 200 -s 50 -p 1e-5 -m 10 30 --broad -B --trackline'. With which the IDR (v2.0.4) was applied to measure the reproducibility of findings identified from replicate sample.
The different enrichment peaks from different sample was plotted by MAnorm (v1.1), the significant regions were picked up if |M|≥ 1 and p-value ≤10-5.
The gene element annotation of peak or different enrichment peak from different samples was carry out by Bedtools (v2.16.2) intersect mode with overlap 50% as well.
To identify the position of nucleosomes, broad peaks called by MACS2 were analyzed using NucleoATAC (v0.3.4).
Genome_build: mm10
Supplementary_files_format_and_content: Comma-Separated peak called  bed file by MACS2  for each sample

source_name: CD4+ T cells

extract_protocol:
The cell preparation was begin with harvesting and counting intact and homogenous cell, which followed by centrifuging those 50,000 cells for about 5min at 500g, 4°C. Washing those cells once with 50μl of cold PBS buffer and centrifuging them again under the same condition after removing and discarding supernatant. Removing and discarding supernatant again， and pipetted up and down to resuspend the cell pellet in 50μl of cold lysis buffer gently, which also obey centrifuge but for 10 min this time.
After discarding the supernatant, the resuspension of the nuclei pellet we obtained should be carried out immediately in the prepared transposition reaction mix which contained Nextera Tn5 Transposase from Nextera kit. Incubated the transposition reaction at 37°C for 30 min. A Qiagen MinElute PCR Purification Kit is used to transposition, purify instantly, following by which the 10μl elution buffer (Buffer EB from the MinElute kit consisting of 10 mM Tris-HCl [pH 8.0]) was applied to elute transposed DNA. Finally the PCR amplification was performed to amplify transposed DNA fragments, combine the following in a 0.2 ml PCR tube with enough thermal cycle. As is known to us, prior to amplification, adapters have to be completed with a 72°C extension step, as well as the qPCR and library quality control using gel electrophoresis is provided. Libraries were pooled at equimolar ratios with barcodes and sequenced on the BGISEQ-500 platform (BGI-Shenzhen, China)

treatment_protocol: Naive CD4+ T cells (CD62LhighCD44lowCD25-) were sorted from spleen of 7 weeks old male WT C57BL/6 by FACSAria II (BD) and stimulated with plate-bound anti-CD3 (5 µg/ml, 145-2C11; BioLegend) plus soluble anti-CD28 (1 µg/ml, 37.51; BioLegend) in the presence of human TGF-b1 (5 ng/mL; PeproTech) and mouse IL-2 (10 ng/mL; PeproTech) with or without mouse IL-4 (15 ng/mL; PeproTech) for 48 hr in 96-well tissue-culture plates (BIOFIL) at 5 × 10e4 cells per well. Follow by proceeding to extraction of nuclei, transposition and library preparation for sequencing (ATAC-seq)

tag: strain

tag: tissue

value: spleen

value: CD4+ T cells

value: polarization with mouse IL-4  for 48 h


title: Sample-182 (Total Bulk RNA-seq)

tag: pmi

tag: diagnosis


title: CLL_NP1_0

value: female

tag: tumor

value: chronic lymphocytic leukemia

value: Binet A/RAI 0 (untreated patient)

value: unstimulated (T0)


title: Sample-180 (Total Bulk RNA-seq)

value: M

tag: brain region


title: Sample-18 (Total Bulk RNA-seq)

value: AD

value: FC


title: Sample-179 (Total Bulk RNA-seq)

value: Control

value: CB


title: CONTROL_1

tag: treatment

value: control


title: Sample-178 (Total Bulk RNA-seq)

value: total RNA isolation


title: MeiosisII_Comp_Screen_YPD_Day5_Rep3

first: Tina

last: Sing

address: Barker Hall, Rm 616, University of California, Berkeley

institute: University of California, Berkeley

description:
Inducible cDNA library transformed into yeast
Sample 145

data_processing:
Library strategy: DNA-Seq
Sequencing reads were aligned to the SK1 genome using HISAT2
Transcripts per million reads (TPM) were calculated with STRINGTIE
Genome_build: SK1 genome from Saccharomyces Genome Resequencing Project (Sanger Institute)
Supplementary_files_format_and_content: Tab-delimited text output files from STRINGTIE include TPM values for each gene

extract_protocol:
mRNA and plasmid extracts were all performed using standard techniques.
mRNA was isolated with Oligo(dT)25 Dynabeads (Ambion) and libraries were preparerd with the NEXTFLEX Rapid Directional RNA-seq Kit (PerkinElmer). cDNA sequencing libraries were prepared with the NEXTFLEX Rapid DNA-seq Kit (PerkinElmer).
mRNA-seq (Samples 1-10) and DNA-seq (Samples 11-175)

value: UB20279 + pUB914-<Meiosis II cDNA library>

tag: meiotic cdna library

value: Meiosis II

tag: growth condition

value: YPD + G418


title: MeiosisII_Comp_Screen_YPD_Day4_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 144


title: Tr_1

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

value: spleen

value: polarization without mouse IL-4  for 48 h


title: Tr_2

value: CD4+ T cells


title: Sample-176 (Total Bulk RNA-seq)

value: F


title: Sample-177 (Total Bulk RNA-seq)


title: No-tumor-1-Tim4-minus-low

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: Partek_Bulk_No_tumor_Tim-4low_vs_Tim-4high_DESeq2(R)/Partek_Bulk_No_tumor_Tim-4low_vs_Tim-4high_DESeq2(R).txt

data_processing:
Alignment to STAR - 2.6.1d
DESEQ2® - 3.5
Genome_build: mm10
Supplementary_files_format_and_content: Raw gene count matrix
Supplementary_files_format_and_content: Raw transcript count matrix

source_name: Sorted peritoneal macrophages

growth_protocol: Sorted Tim-4low vs Tim-4high macrophages from in vivo.

extract_protocol:
Sorted cells were frozen in trizol reagent and RNA extraction was performed by Genewiz.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In the mice bearing MC38-LG tumor intraperitoneally, they received anti-Tim-4 7 days after tumor challenge and were harvested 10 days after tumor challenge. A subset of mice were not tumor challenged and were harvested on the same day.

tag: tumor or no tumor

value: No Tumor

value: No treatment

tag: sorted macrophage population


title: No-tumor-3-Tim4-plus-hi


title: No-tumor-2-Tim4-minus-low


title: No-tumor-2-Tim4-plus-hi


title: No-tumor-1-Tim4-plus-hi


title: MeiosisII_Comp_Screen_YPD_Day3_Rep3

city: Berkeley

description:
Inducible cDNA library transformed into yeast
Sample 143


title: Iso-3-Tim4-minus-low

description: Partek_Bulk_Tumor_Tim-4high_Iso_vs_aTim-4_DESeq2(R)/Partek_Bulk_Tumor_Tim-4high_Iso_vs_aTim-4_DESeq2(R).txt

value: Tumor

value: Isotype


title: Iso-2-Tim4-plus-hi


title: MeiosisII_Comp_Screen_YPD_Day2_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 142


title: Sample-174 (Total Bulk RNA-seq)

value: M


title: No-tumor-3-Tim4-minus-low


title: Iso-3-Tim4-plus-hi


title: Iso-2-Tim4-minus-low


title: Iso-1-Tim4-plus-hi


title: Tr4_1

value: polarization with mouse IL-4  for 48 h


title: Sample-175 (Total Bulk RNA-seq)

value: Control


title: Iso-1-Tim4-minus-low


title: MeiosisII_Comp_Screen_YPGR_Day4_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 139

value: YPGR + G418


title: Sample-173 (Total Bulk RNA-seq)

value: CB


title: Sample-172 (Total Bulk RNA-seq)

value: total RNA isolation


title: aTim4-3-Tim4-plus-hi


title: MeiosisII_Comp_Screen_YPGR_Day3_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 138

value: UB20279 + pUB914-<Meiosis II cDNA library>


title: MeiosisII_Comp_Screen_YPGR_Day2_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 137

value: Meiosis II


title: Sample-170 (Total Bulk RNA-seq)


title: Sample-171 (Total Bulk RNA-seq)


title: aTim4-2-Tim4-plus-hi


title: aTim4-3-Tim4-minus-low


title: MeiosisII_Comp_Screen_YPD_Day1_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 141

value: YPD + G418


title: MeiosisII_Comp_Screen_YPGR_Day1_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 136


title: aTim4-2-Tim4-minus-low


title: aTim4-1-Tim4-plus-hi


title: Sample-17 (Total Bulk RNA-seq)

value: AD

value: FC


title: MeiosisII_Comp_Screen_YPD_Day3_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 133


title: Sample-169 (Total Bulk RNA-seq)


title: MeiosisII_Comp_Screen_YPD_Day2_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 132


title: MeiosisII_Comp_Screen_YPD_Day4_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 134


title: Sample-168 (Total Bulk RNA-seq)


title: MeiosisII_Comp_Screen_YPD_Day1_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 131


title: aTim4-1-Tim4-minus-low


title: Sample-167 (Total Bulk RNA-seq)


title: Sample-166 (Total Bulk RNA-seq)


title: VM294

first: Stuart

middle: Aidan

last: Quinn

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
Demultiplexing of BCL files was performed  with 10x Cell Ranger’s mkfastq command.
Initial analysis and alignment was done with Cell Ranger’s count command with Cell Ranger’s reference mm10 version 1.2.0 using Cell Ranger 2.0.0.
We transform cell data into count matrices (pandas v0.23.0) and removed ribosomal and mitochondrial genes.
Genome_build: mm10

molecule: polyA RNA

source_name: Whole spleen

extract_protocol:
We loaded splenocytes suspensions (around 5000 cells per sample) isolated from whole spleen.
10× Chromium instrument (10× Genomics) was used for the library preparation ( Chromium Single Cell 3′ v2 Reagent Kit)

value: TMX

tag: status

value: lymphoma

tag: genotype

value: CD4-CreERT2 Tet2f/f Vav1-myo1f


title: MeiosisII_Comp_Screen_YPGR_Day5_Rep3

description:
Inducible cDNA library transformed into yeast
Sample 140


title: VM236


title: VM231


title: 4OH-Tam injected C57BL6/J

city: Farmington

first: William

middle: F

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
FASTQ files were generated and demultiplexed using Illumina bcl2fastq 2.18.0.12.
R1 (26p) corresponds to a 16bp cell barcode + 10bp UMI barcode and R2 (98bp) contains the biological read. I1 corresponds to the 8bp Illumina I7 index of each read.
A filtered digital gene expression matrix was generated for each gene expression library against the 10X Genomics mm10 reference build (version 2.1.0, GRCm38.84) using 10X Genomics Cellranger count version 2.2.0
Supplementary_files_format_and_content: Counts matrices are in Matrix Market CSR format and gzipped.  Rows correspond to genes in the associated genes.tsv.gz and columns correspond to cell-barcodes in associated barcodes.tsv.gz

source_name: Ventral parafacial region

extract_protocol:
Brainstem slices were prepared using a vibratome in ice cold, high sucrose slicing solution. Slicing solution was equilibrated with a 5% CO2-95% O2 gas mixture before use. Transverse brainstem slices (300 μm thick) were prepared and then immediately enzymatically treated at 34°C with protease XVIII (6 mg/mL) for 6 minutes. After enzyme incubation, slices were washed three times in cold dissociation solution and then transferred to an enzyme inhibitor mix containing trypsin inhibitor (10 mg/mL) and bovine serum albumin (BSA, 10 mg/mL) in cold sucrose dissociation solution. Shortly thereafter, slices were transferred to a glass Petri dish on ice. Using a plastic transfer pipette and scalpel, each region of interest was micro-dissected out of the slices and manually separated into sterile microcentrifuge tubes. Tissue chunks were then warmed to 34°C for 10 minutes before trituration.
A single cell suspension was achieved by trituration using a 25 and 30 gauge needles sequentially, attached to a 2 mL syringe. Samples were triturated for an average of 5 minutes. Immediately after, the samples were placed back on ice and filtered through a 30-micron filter into sterile microcentrifuge tubes for cell viability assessment. Cell viability for each sample was assessed on a Countess II automated cell counter (ThermoFisher), and 12,000 cells were loaded for capture onto an individual lane of a Chromium Controller (10X Genomics). Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform according to the manufacturer’s protocol (#CG00052) using version 2 (V2) chemistry. cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR. All libraries were sequenced on individual lanes of an Illumina HiSeq4000 targeting 6,000 barcoded cells with an average sequencing depth of 50,000 reads per cell.
10X scRNA-seq

tag: batch

tag: condition

value: 4OH- Tam injection

tag: 10x chemistry version


title: Sample-165 (Total Bulk RNA-seq)

address: 3400 Bio Sci 3

institute: University of California Irvine

data_processing:
Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
Genome_build: hg38
Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.

extract_protocol:
Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq

tag: age

tag: Sex

tag: isolation


title: MeiosisII_Comp_Screen_YPGR_Day5_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 130

tag: strain


title: Sample-164 (Total Bulk RNA-seq)

value: F

tag: pmi

tag: diagnosis


title: MeiosisII_Comp_Screen_YPGR_Day4_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 129


title: C57BL6/J

value: WT


title: MeiosisII_Comp_Screen_YPD_Day5_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 135


title: VM58

value: CD4-Cre Vav1-myo1f


title: MeiosisII_Comp_Screen_YPGR_Day3_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 128


title: Sample-163 (Total Bulk RNA-seq)

value: M

tag: brain region


title: TJ4

tag: treatment


title: TJ13

value: pre-lymphoma

value: CD4-CreERT2 Vav1-myo1f


title: S. aureus RPF replicate 1

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

description: ribosome-protected mRNA fragments

data_processing:
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10
Genome read mapping using bowtie (1.2.2), parameters: -l 16 -n 1 -e 50 -m 1 --strata –best y
Read counting using bedtools, version 2.26.0, parameter: -s
Genome_build: NC_009641.1, NCBI
Supplementary_files_format_and_content: Unique read counts per gene and million mapped reads RPM

organism: Staphylococcus aureus

source_name: Staphylococcus aureus

growth_protocol: Cells were cultured in complex medium (TSB) and collected at OD550 of 1.0.

extract_protocol:
Cells from 30 ml culture grown in TSB medium to OD550=1 were harvested by rapid centrifugation and resuspended in 390 µl ice cold lysis buffer (composition is given in del Campo et al. 2015, doi: 10.1371/journal.pgen.1005613). Cells were disrupted by cell homogenisation (FastPrep-24 ™, MP Biomedicals) with 0.5 ml glass beads (diameter 0.1 mm) for 30 s at 6.5 m/s followed by incubation on ice for 5 min. These steps were repeated twice. To remove cell debris, cell lysates were centrifuged and processed for generation of ribosome-protected fragments. 100 A260 units of ribosome-bound mRNA complex was digested with micrococal nuclease (10 units/µl, Fermentas) for 10 min, RT in 10 mM Tris pH 9.2 containing 50 mM NH4Cl, 10 mM MgCl2, 0.2% triton X-100 and 20 mM CaCl2 to obtain monosomes.
RNA-size selection and generation of the cDNA libraries was performed as described (Ingolia et al, 2009; doi: 10.1126/science.1168978 and del Campo et al. (2015), doi: 10.1371/journal.pgen.1005613). Fragments with a size of 20-35-nt RNA were size selected on a denaturing 15% polyacrylamide gel.

value: Newman


title: MeiosisII_Comp_Screen_YPGR_Day1_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 126

tag: meiotic cdna library

value: YPGR + G418


title: Sample-161 (Total Bulk RNA-seq)

first: Vivek

last: Swarup

value: Control

value: CB

value: total RNA isolation


title: Sample-160 (Total Bulk RNA-seq)


title: MeiosisII_Comp_Screen_YPGR_Day2_Rep2

description:
Inducible cDNA library transformed into yeast
Sample 127

value: UB20279 + pUB914-<Meiosis II cDNA library>

value: Meiosis II

tag: growth condition


title: TJ11

value: TMX


title: 48h after treatment rep 2

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

description: mRNA

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to human genome using bowtie.
Reads counts for all genes.
Genome_build: Human genome hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is gene IDs and the second column is reads counts.

source_name: U87MG cell line

growth_protocol: U87MG cells are grown in DMEM medium supplemented with 10% FBS and 1% P/S. The cells are split every 3-4 days and change the medium every 2 days.

extract_protocol:
Cells were harvested after differentiation and total RNA was isolated with RNeasy isolation kit (Qiagen) according to manufacturer’s instructions. On-column DNase treatment was performed to remove genomic DNA contamination (Qiagen).
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit.

treatment_protocol: Cells were treated with enzalutamide for different time points before isolating the total RNA from the cells.

tag: cell line

value: enzalutamide 48hr


title: MeiosisII_Comp_Screen_YPD_Day5_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 125

value: YPD + G418


title: 24h after treatment rep 2

description: mRNA

value: enzalutamide for 24hr


title: Sample-16 (Total Bulk RNA-seq)

value: AD

value: FC


title: Sample-159 (Total Bulk RNA-seq)


title: MeiosisII_Comp_Screen_YPD_Day4_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 124


title: 24h after treatment rep 1

description: mRNA


title: 4h after treatment rep 2

description: mRNA

value: enzalutamide for 4hr


title: S. aureus RPF replicate 2

description: ribosome-protected mRNA fragments


title: Sample-158 (Total Bulk RNA-seq)

value: M


title: TJ9

value: vehicle

value: normal


title: Sample-162 (Total Bulk RNA-seq)


title: TJ7

value: CD4-CreERT2 Vav1-myo1f


title: MeiosisII_Comp_Screen_YPD_Day3_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 123


title: TJ5

value: lymphoma

value: CD4-Cre Vav1-myo1f


title: MeiosisII_Comp_Screen_YPD_Day2_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 122


title: Sample-156 (Total Bulk RNA-seq)

value: F

value: Control

value: CB


title: TJ3


title: 4h after treatment rep 1

description: mRNA


title: MeiosisII_Comp_Screen_YPD_Day1_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 121

value: UB20279 + pUB914-<Meiosis II cDNA library>

value: Meiosis II


title: Sample-155 (Total Bulk RNA-seq)

value: total RNA isolation


title: VM98-tumor-Total

data_processing:
Reads were mapped to mm10 mouse reference genome using HISAT2 (v 2.1.0) with default parameters.
Count matrix were generated with Htseq (v 0.5.4) with genecode moose transcript reference annotation vM24.
Genome_build: mm10

extract_protocol:
RNA was extracted with RNeasy Micro Kit (Qiagen) following manufacturer's guidelines.
We performed RNA library preparations and next generation sequencing using the SMART-Seq v4 Ultra Low Input Kit for Sequencing for full-length cDNA synthesis and amplification at Genewiz
Illumina Nextera XT Library Preparation Kit was used for library preparation. Sequencing was performed on an Illumina HiSeq platform (Illumina).

tag: tissue

value: Whole spleen

value: tumor

value: CD4-CreVav1Myo1f fl/wt


title: MeiosisII_Comp_Screen_YPGR_Day5_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 120

value: YPGR + G418


title: Sample-154 (Total Bulk RNA-seq)


title: MeiosisII_Comp_Screen_YPGR_Day4_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 119


title: VM98-tumor-CD4

source_name: CD4+ T Cells

value: CD4+ T Cells

tag: status


title: 48h after treatment rep 1

description: mRNA

value: enzalutamide 48hr


title: VM645-WT-total

tag: genotype


title: MeiosisII_Comp_Screen_YPGR_Day3_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 118


title: Scramble-2

city: Augusta

first: Biaoru

state: GA

department: Pediatrics

institute: MCG

description: control region

data_processing:
GALAXY used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human genome 38 whole genome using tophat alighment
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol.transcript and by the size of the library.
exons from all isoforms of a gene were merged to create one meta-transcript.
meta-transcript were counted and normalized by the size
Genome_build: human genome 38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human CD34 cells

growth_protocol: Human adult CD34+ stem cells isolated from peripheral blood of healthy adults were grown in one-phase liquid culture system.

extract_protocol:
RNA was harvested using Trizol 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: At day-15 in the 28-day culture period, silenced KLF1 erytrhoid cells are used for RNA-seq

tag: sample type

value: control region

tag: genotype/variation

tag: cell type

value: CD34 cells


title: TJ1

value: TMX

value: pre-lymphoma

value: CD4-CreERT2 Vav1-myo1f


title: Scramble-3

description: control region


title: Sample-153 (Total Bulk RNA-seq)

city: Irvine

tag: age

value: M


title: MeiosisII_Comp_Screen_YPGR_Day2_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 117


title: Sample-152 (Total Bulk RNA-seq)

tag: Sex

value: F

value: Control


title: VM645-WT-CD4

value: normal


title: Sample-151 (Total Bulk RNA-seq)

value: AD

value: CB

tag: isolation


title: Sample-150 (Total Bulk RNA-seq)

value: total RNA isolation


title: Scramble-1

description: control region


title: VM645-tumor-CD4

tag: strain

value: tumor


title: MeiosisII_Comp_Screen_YPGR_Day1_Rep1

description:
Inducible cDNA library transformed into yeast
Sample 116

value: UB20279 + pUB914-<Meiosis II cDNA library>

value: Meiosis II


title: Sample-149 (Total Bulk RNA-seq)

tag: pmi


title: shKLF1-3-3

description: knockdown KLF1-3

value: 5’-terminal without function region


title: VM58-tumor-Total

value: Whole spleen

value: CD4-CreVav1Myo1f fl/wt


title: VM58-tumor-CD4

value: CD4+ T Cells


title: Control rep 1

description: mRNA


title: Late_Destination_Vector

description:
cDNA inserted into pUB914 via Gateway cloning
Sample 20

value: DHalpha + pUB914-<Late cDNA library>

value: Late Meiosis

value: LB + Ampicillin


title: Sample-148 (Total Bulk RNA-seq)

value: M

tag: diagnosis


title: shKLF1-3-1

description: knockdown KLF1-3

value: CD34 cells


title: MeiosisII_Destination_Vector

description:
cDNA inserted into pUB914 via Gateway cloning
Sample 19

value: DHalpha + pUB914-<Meiosis II cDNA library>


title: VM388-tumor-Total


title: MeiosisI_Destination_Vector

description:
cDNA inserted into pUB914 via Gateway cloning
Sample 18

value: DHalpha + pUB914-<Meiosis I cDNA library>

value: Meiosis I


title: shKLF1-2-3

description: knockdown KLF1-2

value: Transcription Factor II H


title: Sample-147 (Total Bulk RNA-seq)

value: AD

tag: brain region

value: CB

value: total RNA isolation


title: VM388-tumor-CD4

value: tumor


title: shKLF1-2-2

description: knockdown KLF1-2


title: Sample-146 (Total Bulk RNA-seq)

value: F


title: shKLF1-2-1

description: knockdown KLF1-2


title: Starvation_Destination_Vector

description:
cDNA inserted into pUB914 via Gateway cloning
Sample 16

value: DHalpha + pUB914-<Starvation cDNA library>

value: Starvation


title: VM216-total

value: Whole spleen

value: normal


title: Exp3_HSPB3_OE_Rep3

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
RNA-seq data was analyzed using the RNA-seq module from the snakePipes package (Bhardwaj et al 2019). Human annotation (genome build hg38) from the Gencode release 27 was used as reference for mapping and read counting. Differential gene expression analysis was done using DESeq2 (Love et al 2014). Outlier replicates, identified based on PCA plots, were removed. Heatmaps were visualized using pheatmap package (Raivo Kolde (2019)).
Genome_build: hg38
Supplementary_files_format_and_content: Raw read counts in txt

extract_protocol:
For gene expression analysis on LHCN-M2 cells, total RNA was isolated using Trizol (R2050; Zymo Research, USA), as per manufacturer’s instructions. Followed by purification using RNA Clean & Concentrator (R1017; Zymo Research, USA) and DNase I Set (E1010; Zymo Research, USA), as per manufacturer’s instructions.
Library Preparation was done using TruSeq Stranded mRNA, according to manufactures protocol.

tag: condition

value: HSPB2 overexpression


title: Sample-145 (Total Bulk RNA-seq)


title: shKLF1-1-3

description: knockdown KLF1-1

value: zinc finger at 3'-terminal


title: Sample-144 (Total Bulk RNA-seq)


title: Control rep 2

description: mRNA

tag: treatment


title: shKLF1-3-2

description: knockdown KLF1-3

value: 5’-terminal without function region


title: VM211-total


title: shKLF1-1-2

description: knockdown KLF1-1

value: CD34 cells


title: Exp3_HSPB3_OE_Rep1


title: VM216-CD4

value: CD4+ T Cells


title: TA025

value: pre-lymphoma


title: Sample-142 (Total Bulk RNA-seq)

value: M


title: Sample-143 (Total Bulk RNA-seq)


title: shKLF1-1-1

description: knockdown KLF1-1


title: Exp3_GFP_OE_Rep3

value: GFP overexpression


title: Exp3_GFP_OE_Rep2


title: TA024


title: Exp3_HSPB3_OE_Rep2


title: Early_Destination_Vector

description:
cDNA inserted into pUB914 via Gateway cloning
Sample 17

value: DHalpha + pUB914-<Early cDNA library>

tag: meiotic cdna library

value: Early Meiosis

tag: growth condition

value: LB + Ampicillin


title: 243_R5020 [7200514]

city: Lausanne

first: Fabio

last: De Martino

address: EPFL SV ISREC UPBRI Station 19

country: Switzerland

institute: EPFL

data_processing:
Raw reads were aligned to the mouse genome (hg19) using TopHat (v2.0.11).
Gene counts were generated using FeatureCounts (v1.5.1). Data preprocessing was done using the DESEQ2 package from Bioconductor (v3.11).
Genome_build: hg19
Supplementary_files_format_and_content: Raw read counts from FeatureCounts (v1.5.1).

source_name: EPCAM+ Human Microstructures_R5020

growth_protocol: We transcriptionally profiled 3 samples of human microstructures derived from 3 different patients stimulated with either ETOH, natural progesterone (P4) or promegestone (R5020) using RNA-seq

extract_protocol:
RNA was extracted from EPCAM+ cells using miRNeasy Mini Kit (Qiagen).
Libraries were preparred using Truseq Stranded RNA producing single-end reads of 100 bp and sequenced on Illumina Hiseq 2500 instrument.

tag: subject id

tag: tissue

value: EPCAM+ Human Microstructures


title: 229_R5020 [7190514]


title: TA023

tag: status

tag: genotype


title: Sample-141 (Total Bulk RNA-seq)

value: AD

value: CB

value: total RNA isolation


title: Sample-139 (Total Bulk RNA-seq)

value: F


title: TA022


title: 220_R5020 [7150514]


title: 243_CTRL [3200514]

source_name: EPCAM+ Human Microstructures_ETOH

value: ETOH


title: Sample-138 (Total Bulk RNA-seq)


title: Exp2_shHSPB3_Rep3

value: HSPB3 knock-down


title: TA021


title: 229_CTRL [3190514]


title: Sample-137 (Total Bulk RNA-seq)


title: Exp2_shHSPB3_Rep1


title: VM211-CD4

value: normal


title: TA020


title: Sample-136 (Total Bulk RNA-seq)


title: Exp2_shCTRL_Rep3

value: Control


title: 243_P4 [11200514]

source_name: EPCAM+ Human Microstructures_P4


title: 220_CTRL [3150514]


title: TA019


title: Sample-135 (Total Bulk RNA-seq)


title: Sample-14 (Total Bulk RNA-seq)

value: FC


title: Exp2_shCTRL_Rep2


title: Sample-134 (Total Bulk RNA-seq)


title: TA018

value: CD4+ T Cells


title: 3R5020 [M3_R5020]

data_processing:
Raw reads were aligned to the mouse genome (mm9) using TopHat (v2.0.11).
Gene counts were generated using FeatureCounts (v1.5.1). Data preprocessing was done using the DESEQ2 package from Bioconductor (v3.11).
Genome_build: mm9
Supplementary_files_format_and_content: Raw read counts from FeatureCounts (v1.5.1).

source_name: mouse organoids stimulated with R5020

growth_protocol: We transcriptionally profiled 3 biological replicates of mouse organoids treated with either ETOH or R5020 using RNA-seq

extract_protocol:
RNA was extracted from epithelial-enriched material using miRNeasy Mini Kit (Qiagen).
Libraries were preparred using Truseq Stranded RNA producing single-end reads of 100 bp and sequenced on Illumina Hiseq 2500 instrument.

tag: tissue/cell type

value: Mouse Mammary Organoids Enriched in Epithelial Cells

value: promegestone (R5020)


title: Exp2_shCTRL_Rep1


title: 220_P4 [11150514]


title: Exp1_R116P_HSPB3_OE_Rep3

value: R116P-HSPB3 overexpression


title: Fb259_fibroblast

type: genomic

first: Paola

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Hybridization is done at 48°C for 16 hours in hybridisation chamber.

scan_protocol: Chips are scanned in the iScan from illumina (setting Infinium LCG).

data_processing:
All genomic DNAs were assayed on Illumina HumanOmni2.5-8M bead chip arrays to feature 2372784 single nucleotide polymorphism (SNP) markers for each DNA sample. Samples with low genotyping rate (<95%) were removed. SNPs that have a call rate lower than 0.95 were removed.  PLINK 1.07 and GCTA analysis tools were used for data QC and processing. Genetic relationship matrix (GRM) between pairs of individuals were estimated in our samples. “snpStats” (Bioconductor) was used as statistical tool for SNP association studies.
SNP Name, Sample ID, Allele 1 Forward, Allele 2 Forward, Allele 1 Top, Allele 2 Top, Allele 1 AB, Allele2 AB, GC Score, X, Y.

label: C-Bio and A-DNP

source_name: foreskin-derived dermal fibroblasts

label_protocol: ddCTP and GTP are labelled with biotin and ddATP and TTP with DNP (Dinitrophenol). The nucleotides are then stained with Fluorescent streptavidin and anti-DNP Ab.

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

tag: ancestry

value: Caucasian

tag: gender

value: male

value: foreskin-derived dermal fibroblasts


title: Sample-132 (Total Bulk RNA-seq)

tag: age

tag: Sex

value: M


title: Exp2_shHSPB3_Rep2


title: Sample-133 (Total Bulk RNA-seq)

value: AD

tag: isolation


title: Fb258_fibroblast


title: 3ETOH [M3_CTRL]

source_name: mouse organoids stimulated with ETOH


title: 2ETOH [M2_CTRL]


title: Exp1_HSPB3_OE_Rep4

value: HSPB3 overexpression


title: Fb249_fibroblast


title: Sample-130 (Total Bulk RNA-seq)

tag: pmi

value: CB

value: total RNA isolation


title: Sample-131 (Total Bulk RNA-seq)

tag: diagnosis


title: Exp1_R116P_HSPB3_OE_Rep2


title: Exp1_HSPB3_OE_Rep3


title: 1R5020 [M1_R5020]


title: 229_P4 [11190514]

value: EPCAM+ Human Microstructures


title: Fb248_fibroblast


title: Fb247_fibroblast


title: Sample-129 (Total Bulk RNA-seq)

value: F

tag: brain region


title: 1ETOH [M1_CTRL]

value: ETOH


title: Fb244_fibroblast


title: Sample-128 (Total Bulk RNA-seq)


title: Exp1_GFP_OE_Rep4

tag: condition

value: GFP overexpression


title: BMDCs_MnCl2

city: Beijing

first: Zhengfan

last: Jiang

address: No.5 Yiheyuan Road Haidian District

data_processing:
Illumina Casava1.8 software used for basecalling.
The adaptor of sequenced reads were deleted. Then sequenced reads were masked for low-complexity or low-quality sequence, then mapped to mm9 cDNA reference using bwa0.7.16.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9 cDNA reference
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: BMDCs

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: treatment

value: MnCl2 (200 μM)

tag: time

tag: cell type

value: BMDCs


title: 2R5020 [M2_R5020]

value: Mouse Mammary Organoids Enriched in Epithelial Cells


title: Fb243_fibroblast

city: Biella

last: Ostano

tag: tissue


title: Exp3_GFP_OE_Rep1


title: Sample-126 (Total Bulk RNA-seq)


title: Exp1_GFP_OE_Rep3


title: Sample-125 (Total Bulk RNA-seq)


title: Sample-13 (Total Bulk RNA-seq)

value: FC


title: Sample-124 (Total Bulk RNA-seq)


title: les17-mutant-3

city: zheng zhou

first: xiaohuan

last: mu

address: zhengzhou long zi hu

institute: Henan Agricultural University

data_processing:
Clean reads were derived after removal of low quality regions and adapter sequences from raw reads. Then clean reads were aligned to the maize reference genome (B73 RefGen_v4, available online: https://www.maizegdb.org/assembly/) using HISAT2
Aligned reads from HISAT2 mapping were subjected to String Tie for DeNovo Transcript assembly
The expression of each gene was normalized to fragments per kilobase of transcript per million reads (FPKM) to compare among different samples. The R package “DESeq2” were used to identify differentially expressed genes with fold changes (FC) above 2 and False Discovery Rate (FDR) lower than 0.05
Genome_build: B73 RefGen_v4
Supplementary_files_format_and_content: FPKMs

organism: Zea mays

extract_protocol:
Total RNA was extracted from sample using the Trizol reagent
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s manual and index codes were added to attribute sequences to each sample

value: leaf


title: les17-mutant-2


title: Exp1_HSPB3_OE_Rep2


title: Exp1_GFP_OE_Rep1


title: BMDCs_LPS

value: LPS (100 ng/ml)


title: Sample-122 (Total Bulk RNA-seq)


title: Exp1_GFP_OE_Rep2


title: Exp1_HSPB3_OE_Rep1


title: les17-mutant-1


title: Sample-123 (Total Bulk RNA-seq)


title: CPPED1 + ethanol, sample 3

city: Oulu

first: Antti

last: Haapalainen

address: Aapistie 5A

department: CRC

country: Finland

institute: University of Oulu

data_processing:
The base calling was done using bcl2fastq (v. 2.17)
Read alignment was done using star (2.5.2b) to hg38 human genome reference
Genewise read counts were calculated using subread (v1.5.1)
Genome_build: Human GRCh38
Supplementary_files_format_and_content: files are tab delimited text files containing the genewise read counts for each sample

source_name: placenta

growth_protocol: he HTR-8/Svneo cells were cultured in RPMI 1640 medium supplemented with 10 % fetal bovine serum, 100 U/ml penicillin, 100 mg/ml streptomycin, 2 mM glutamine and 1 mM sodium pyruvate.

extract_protocol:
RNA was isolated by using Trizol reagent and RNeasy Micro Kit
Library preparation was done according to Illumina TruSeq® Stranded mRNA kit protocol.

treatment_protocol: The transfection with siRNA was done either with 30 nM siRNA pair or 30 nM siRNA universal negative control and using approximately 100 000 cells and duoble transfection. The first transfection was done in suspension and the second transfection in adherent cells. After 24 hours of second transfection, negP4 and CPPED1P4 cells were treated with 100 ng of P4 that had been dissolved in 0.1 % EtOH. negEtOH and CPPED1EtOH cells were treated only with 0.1% EtOH.

tag: cell line

value: placenta

tag: rna interference

value: CPPED1 siRNA

value: ethanol


title: CPPED1 + ethanol, sample 2


title: Fb240_fibroblast

value: Caucasian

value: male

value: foreskin-derived dermal fibroblasts


title: Fb238_fibroblast


title: Fb233_fibroblast


title: Fb232_fibroblast


title: Sample-121 (Total Bulk RNA-seq)

source_name: AD brain

value: M

value: AD

value: CB

value: total RNA isolation


title: les17-wt-3

tag: genotype


title: les17-wt-2


title: Fb231_fibroblast

tag: ancestry


title: BMDCs_control

institute: Peking University

value: control


title: CPPED1 + ethanol, sample 1


title: Sample-120 (Total Bulk RNA-seq)

value: F


title: Fb241_fibroblast

tag: gender


title: les17-wt-1


title: Fb229_fibroblast


title: Sample-12 (Total Bulk RNA-seq)

tag: age


title: les10-mutant-3


title: Fb228_fibroblast


title: les10-mutant-2


title: negative + ethanol, sample2

value: non-targeting siRNA


title: Sample-119 (Total Bulk RNA-seq)

tag: Sex


title: Fb224_fibroblast


title: Fb253_fibroblast

value: African


title: CPPED1 + progesterone, sample3

value: progesterone + ethanol


title: Sample-118 (Total Bulk RNA-seq)

tag: isolation


title: les10-mutant-1

value: leaf


title: les10-wt-3


title: Sample-116 (Total Bulk RNA-seq)

tag: pmi


title: CPPED1 + progesterone, sample2


title: CPPED1 + progesterone, sample1


title: Fb252_fibroblast


title: Fb251_fibroblast


title: Sample-117 (Total Bulk RNA-seq)

tag: diagnosis


title: Sample-115 (Total Bulk RNA-seq)

tag: brain region


title: negative + ethanol, sample3


title: negative + progesterone, sample2


title: les4-mutant-3


title: les10-wt-2


title: Fb246_fibroblast


title: Fb250_fibroblast


title: les10-wt-1


title: negative + progesterone, sample3


title: Sample-113 (Total Bulk RNA-seq)


title: Sample-112 (Total Bulk RNA-seq)


title: negative + progesterone, sample1


title: Fb245_fibroblast