title: SM-KIPIB

value: PostCA


title: Hem_WT_2

status: Public on Jun 01 2023

type: SRA

city: paris

first: Frederic

last: Causeret

address: 24 bd de montparnasse

department: Imagine Institute

country: France

institute: Inserm

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed to counts matrix with Cell Ranger version 3.1.0 using default parameters and the mm10 mouse genome reference to which the sequenced of YFP and tdTomato were added.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Mus musculus

source_name: embryonic brain

extract_protocol:
For each dataset, a region spanning the dorsal pallial midline was dissected on both hemispheres and dissociated using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec) on the gentleMACS Octo Dissociator following the manufacturer’s instructions. Remaining clumps of cells and debris were removed via two rounds of centrifugation for 3 min at 200 g followed by filtration through 30 µm cell strainers (Miltenyi Biotec). To ensure all remaining cells aggregates were dissociated, we finally pipetted the suspension through Gel Saver tips (QSP) and proceeded to a last filtration through a 10 µm cell strainer (pluriSelect). Cell viability and concentration were assessed using a MACSQuant flow cytometer (Miltenyi Biotec). Approximatively 20000 cells were used as input on the 10X Genomics Chromium Controller for a targeted cell recovery of 10000 cells per library. The entire procedure, from the sacrifice of the pregnant female until loading the controller, was achieved in 2h.
Single Cell 3′ Library and Gel Bead Kit v3

tag: tissue

value: embryonic brain

tag: strain

tag: developmental stage

tag: genotype

value: wild-type


title: SM-KIPI2

city: Birmingham

first: Changde

last: Cheng

state: AL

address: 1824 6th Ave S, Wallace Tumor Institute 520A

department: Medicine

country: USA

institute: University of Alabama at Birmingham

library_source: transcriptomic

data_processing:
Bulk RNA data were processed using St. Jude Cloud workflow for the analysis of RNA-Seq differential expression (WARDEN) (McLeod et al., 2021).
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Lysate from 1000 cells was processed by the Immunological Genome Project protocol (www.immgen.org): final sort of 1,000 cells directly into 5ɥl lysis buffer (TCL Buffer (Qiagen) with 1% 2-Mercaptoethanol). After sort vortex, keep on ice for 5 minutes, give a quick spin. Freeze on dry ice.
Follow Genome Project protocol (www.immgen.org): 5 ul of the lysates are used for each sample for Smart-seq2 library construction, prepared as previously described (Picelli et al., 2013; Picelli et al., 2014) with slight modifications. Briefly, total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and converted to cDNA via reverse transcription. First strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 12 cycles using barcoded primers such that each sample carries a specific combination of eight base Illumina P5 and P7 barcodes and pooled together prior to sequencing. Smart-seq paired-end sequencing is performed on an Illumina NextSeq500 (two full NextSeq runs per batch of 96 samples, for 10M raw reads/sample on average) using 2 x 38bp reads with no further trimming.

value: Blood

tag: cell type

tag: group


title: NACE2i treatment, lung bronchiole_H023 4

city: Brisbane

first: Quan

last: Nguyen

state: Queensland

address: 22 Burns Street, Indooroopilly

country: Australia

institute: Institute for Molecular Bioscience

data_processing:
save-interim-files=false
quality-trim-score=20
2color-trimming=True
adapter1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length=10
adapter-trim-max-mismatch=3
barcode-max-mismatch=1
stitching-max-mismatch=2
dedup-hd=1
threads=4
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_COVID19_v1.0.pkc)
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Values represented in the collapsed target counts tab are the geometric mean of the probes for a given target--in the case that multiple probes were used-- and excludes any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments and features.
Library strategy: GeoMx Seq

organism: Mesocricetus auratus

source_name: lung

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

value: lung

tag: tissue region

value: bronchiole

value: multiple cell types

tag: disease

value: SARS-CoV-2 infection

tag: treatment

tag: slide id

tag: roi number

tag: area


title: norm3_NORM

type: RNA

city: Sao Paulo

first: Gabriela

middle: Sarti

last: Kinker

state: SP

address: 440 Tagua street

department: International Research Center

country: Brazil

institute: A. C. Camargo Cancer Center

hyb_protocol: Gene expression was evaluated using the Nanostring nCounter hybridization platform with the nCounter PanCancer Immune Profiling Panel (730 immune-related genes plus 40 internal reference genes) and the nCounter Low RNA Input Kit, according to the manufacturer’s instructions

scan_protocol: Samples were scanned at maximum resolution on a nCounter Digital Analyzer, using 555 FOVs (fields of view).

data_processing: Gene counts from each sample were first background-corrected by subtracting the geometric mean of counts from negative control probes, and any counts below zero were reset to zero. To control for platform-associated sources of variation, background-corrected gene counts were multiplied by a sample-specific normalization factor calculated based on the average upper quartile of counts from positive control probes: Nposi = uq(CountPosi)/avg[uq(CountPosi…21)], for sample i, with 21 being the total number of samples analyzed. Similarly, counts were next normalized based on the average upper quartile of counts from 13 housekeeping genes that were detected in at least 30% of samples. Two samples with large housekeeping gene scaling factors (abs(log2(Nhk)) > 2.5) were excluded, for a final n of 5 normal pancreatic tissues, 4 CD23neg TLSs, 4 CD23low TLSs and 6 CD23high TLSs. Finally, expression levels were quantified as Enano = ln(NormCounts + 1) and 30 undetected genes (Enano = 0)  were excluded from subsequent analysis.

source_name: treatment-naive primary PDAC

extract_protocol: PDAC-associated TLSs were classified using immunohistochemistry into three maturation stages based on the presence of CD23+ mature follicular dendritic cells (mFDCs): i) initial stage with no CD23 staining; ii) intermediate stage with scattered CD23+ cells displaying a dendritic morphology; iii) final stage with a meshwork of CD23+ mFDCs. Digitalized slides were reviewed blindly by two senior pathologists. Tumors from eight patients harboring TLSs with varying maturation stages were selected for the laser capture microdissection procedure. Ten serial 7 μm sections of FFPE tissue from each selected tumor were mounted on nuclease-free, UV-irradiated PEN Membrane Slides (Zeiss), deparaffinized and stained with Cresyl Violet prior to laser capture microdissection using the Zeiss PALM system with a 10x objective. Dissected tissues were collected in Adhesive Caps tubes (Zeiss). To maximize the RNA yield for gene expression analysis, we combined 4 TLSs with matching classifications per tube. Normal, non-inflamed adjacent tissue was used as control. RNA extraction was performed following the PALM protocol (Zeiss) with components of the QIAGEN RNeasy FFPE Kit. RNA quality was assessed using the high sensitivity RNA ScreenTape system (Agilent) in a 4200 TapeStation.

value: Adjacent normal tissue

tag: class

value: CTR


title: TLS8_CD23high

value: PDAC-associated TLS


title: norm1_NORM


title: TLS7_CD23high


title: Hem_WT_1

description: 10x Genomics


title: SM-KIPI1


title: NACE2i treatment, lung bronchiole_H023 3


title: Ovary,cKO,rep3

city: Beijing

first: xiaohong

last: Yao

address: No. 2 Yuanmingyuan West Road, Haidian District, Beijing

country: China

institute: China Agricultural University

description:
The function of granulosa cells
cKO3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.0.5
fpkm values generated with DESeq2.
Assembly: Mus musculus GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: ovary

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.  Agilent 2100 bioanalyzer
The library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanaly.

value: ovary

value: granulosa cells

value: cKO


title: NACE2i treatment, lung bronchiole_H023 2


title: SM-KIPHZ


title: TLS3_CD23low


title: SM-KIPIA


title: Ovary,cKO,rep2

description:
The function of granulosa cells
cKO2


title: Ovary,cKO,rep1

description:
The function of granulosa cells
cKO1


title: T15_CD23low


title: NACE2i treatment, lung bronchiole_H023 1


title: TLS14_CD23low


title: NACE2i treatment, lung bronchiole_H023 5


title: SM-KIPI9


title: Ovary,WT,rep3

description:
The function of granulosa cells
ctl3

value: WT


title: Control, lung alveoli_H05 5

value: alveoli

value: Control


title: TLS13_CD23low


title: Control, lung alveoli_H05 4


title: Control, lung alveoli_H05 3


title: SM-KIPHU

value: PostCA


title: norm6_NORM


title: 7-93WT

city: irvine

first: Siwei

last: Chen

state: CA

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

data_processing:
Alignment to reference assembly mm10 using Tuxedo bowtie
Mapping results filtering performed using Tuxedo cuffquant
Read counting for each gene and normalization to FPKM values performed using Tuxedo cuffnorm
Assembly: mm10
Supplementary files format and content: csv of FPKM of the raw sequencing data

source_name: Cerebral cortex

extract_protocol:
Qiagen Rneasy Midi kit
Universal Plus mRNA-Seq kit (Tecan Genomics)
RNAseq, paired-end 150 bp mode on NovaSeq 6000 (Illumina)

value: Cerebral cortex

value: C57BL/6J background

tag: age

tag: time of harvest

value: Slc6a8 WT


title: SM-KIPI8

value: Blood


title: Control, lung alveoli_H05 6

value: lung


title: SM-KIPHT


title: SM-KIPHS


title: Ovary,WT,rep2

description:
The function of granulosa cells
ctl2


title: TLS9_CD23high


title: norm2_NORM


title: TLS6_CD23high


title: SM-KIPHY


title: 5-46WT


title: 6-50WT


title: SM-KIPHR


title: 4-33KO

value: Slc6a8 KO


title: SM-KIPHQ


title: Ovary,WT,rep1

description:
The function of granulosa cells
ctl1


title: 3-3KO


title: Control, lung bronchiole_H05 6

value: bronchiole

value: multiple cell types

value: SARS-CoV-2 infection


title: Control, lung bronchiole_H05 5


title: TLS4_CD23high

value: PDAC-associated TLS


title: Control, lung alveoli_H05 1


title: Control, lung bronchiole_H05 4


title: Control, lung alveoli_H05 2


title: Control, lung bronchiole_H05 3


title: SM-KIPHP


title: 1-92KO


title: Control, lung bronchiole_H05 2


title: SM-KIPHN


title: TLS1_CD23neg


title: TLS12_CD23high


title: AAV-RNF146 expressed, replicate 4

city: Seongbuk-gu, Seoul

first: Seoyeon

last: Kim

address: 145, Anam-ro

country: South Korea

institute: Korea University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt with parameters -j 6 -u 15 -U 15 -a AGATCGGAAGAGCACACGTCT -A AGATCGGAAGAGCGTCGTGTA -m 100:100 -q 30 -Q 30.
Quantification of transcript expression was performed using Salmon version 1.9.0 in quasi-mapping-based mode onto the mouse reference transcriptome (GRCm39).
Assembly: Quantified estimates were converted into normalized gene-level counts using R package tximport, and differential gene expression analysis was performed with R package DESeq2.
Supplementary files format and content: GRCm39
Supplementary files format and content: tab-delimited text files include normalized count matrix table from DESeq

source_name: PFC

extract_protocol:
4 weeks after the viral injection, mice were given a short anesthesia using 2.5% isoflurane-mixed gas to extract mice brain. Total RNA was extracted from dissected prefrontal cortices.
Library was constructed using TruSeq stranded mRNA kit.

treatment_protocol: AAV2/1-hsyn-RNF146-eGFP or AAV2/1-hsyn-eGFP virus was injected in mice prefrontal cortex bilaterally.

value: PFC

value: AAV-RNF146 expressed


title: TLS11_CD23neg


title: TLS2_CD23neg


title: Control, lung bronchiole_H05 1


title: SM-KIPHX


title: AAV-RNF146 expressed, replicate 3


title: NACE2i treatment, lung alveoli_H017 6


title: SM-KIPHW


title: SM-KIPHO


title: 2-1KO


title: SM-KIPHV


title: AAV-RNF146 expressed, replicate 2


title: AAV-eGFP expressed, replicate 4

value: AAV-eGFP expressed


title: SM-KIPHI


title: TLS10_CD23neg


title: NACE2i treatment, lung alveoli_H017 5


title: NACE2i treatment, lung alveoli_H017 4


title: AAV-eGFP expressed, replicate 2

value: WT


title: AAV-RNF146 expressed, replicate 1


title: SM-KIPHM


title: SM-KIPHG


title: NACE2i treatment, lung alveoli_H017 3

value: alveoli


title: SM-KIPHH


title: norm4_NORM

value: Adjacent normal tissue

value: CTR


title: NACE2i treatment, lung alveoli_H017 1


title: AAV-eGFP expressed, replicate 3


title: NACE2i treatment, lung alveoli_H017 2


title: NACE2i treatment, lung bronchiole_H017 6


title: Brain, Sham4

city: Hangzhou

first: Wangxiao

last: Bao

address: Qingchun Road 79#

institute: Zhejiang University School of Medicine

data_processing:
cutadapt-1.9
After removed the low quality bases and undetermined bases ,we used HISAT2 software  to map reads to the genome
The mapped reads of each sample were assembled using StringTie with default parameters
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software
After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM
Assembly: mm10
Supplementary files format and content: Excel file include FPKM and count values for each Sample

source_name: cerebral cortex

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
We performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: cerebral cortex

value: Sham


title: SM-KIPHD

value: PostCA


title: SM-KIPHF

value: Blood


title: Liver, tube-nosed bat, rep 1

city: Boston

first: Alexander

last: Tyshkovskiy

state: Massachusetts

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital, Harvard Medical School

data_processing:
To generate reference sequences and identify species-specific ortholog gene sets, pipeline from (Ma et al., 2016) was utilized. Published annotated genomes in Ensembl or NCBI were used if available. Otherwise, de novo transcriptomes were assembled with Trinity.
Reads were mapped to the species-specific ortholog sets using STAR (Dobin et al., 2013).Read counting was performed by featureCounts (Liao et al., 2014).
Supplementary files format and content: comma-separated values file includes gene counts for each sample

organism: Murina leucogaster

source_name: Liver

extract_protocol:
After sacrifice, organs were removed and frozen on dry ice. RNA was extracted from tissues with PureLink RNA Mini Kit and passed to sequencing.
Sequencing libraries were prepared as described in (Fushan et al., 2015)

treatment_protocol: The 39 organ samples for young adults of baboon (Papio anubis), beaver (Castor canadensis), and long-tailed macaque (Macaca fascicularis) were collected from the Southwest National Primate Research Center (SNPRC). The 9 organ samples for young adults of chipmunk (Tamias sibiricus), American black bear (Ursus americanus), sugar glider (Petaurus breviceps), tube-nosed bat (Murina leucogaster), and white-footed mouse (Peromyscus leucopus) were collected as previously described (Fushan et al., 2015).

value: Liver

tag: Sex

value: male

value: adult

value: wild type


title: SM-KIPHC


title: Brain, Sham5


title: Brain, Sham3


title: AAV-eGFP expressed, replicate 1


title: NACE2i treatment, lung bronchiole_H017 5

value: lung

value: bronchiole

value: multiple cell types

value: SARS-CoV-2 infection


title: SM-KIPHB


title: Liver, chipmunk, rep 2

organism: Tamias sibiricus


title: NACE2i treatment, lung bronchiole_H017 4


title: NACE2i treatment, lung bronchiole_H017 3


title: NACE2i treatment, lung bronchiole_H017 2


title: SM-KIPHL


title: Brain, TBI5

value: TBI


title: Brain, TBI4


title: Brain, Sham1


title: Control, lung alveoli_H06 6

value: Control


title: SM-KIPHE


title: Liver, chipmunk, rep 1


title: SM-KIPHJ


title: Mr_pFC094_CATIE_R4_Malform

city: Verona

first: Andrea

last: Minio

address: Via dell'Artigliere 8

department: Applied Biotechnologies

country: Italy

institute: Università di Verona

data_processing:
clipping of adapters and quality trimming with Trimmomatic, ver. 0.36, parameters: “ILLUMINACLIP:2:30:10 LEADING:7 TRAILING:7 SLIDINGWINDOW:10:20 MINLEN:36”
mapped using Bowtie2, ver. 2.3.4.1, parameters: “–non-deterministic -k 1 –very-sensitive -t”
Read counts with GenomicAlignments, ver 1.18.1
Assembly: Mror_plus_Cacao.CDS.reference.fasta
Supplementary files format and content: tabular text file, tab delimited
Supplementary files format and content: Fasta sequences

organism: Moniliophthora roreri

extract_protocol:
2–3 agar plugs were transferred from cultures grown on V8 agar plate to 250 ml conical flask containing 50 ml potato dextrose broth and grown at room temperature (22–25°C) while shaking at 100 rpm. Cultures were allowed to grow for 10–15 days. Mycelia were washed with sterile water and collected by centrifuging at 20,000 g for 10 min followed by flash freezing in liquid nitrogen and freeze drying. Freeze-dried mycelia were ground in a mortar and pestle in liquid nitrogen and transferred to a 50 mL centrifuge tube containing 15 mL of 65°C extraction buffer (Bailey et al., 2005)
Illumina TruSeq RNA sample preparation kit v.2, Illumina TruSeq RNA sample preparation kit v.1

tag: cell line

value: Malform

tag: replicate


title: NACE2i treatment, lung bronchiole_H017 1

tag: tissue


title: SM-KIPHK


title: Mr_pFC068_CATIE_R4_Necrotic

value: Necrotic


title: Control, lung alveoli_H06 5

value: alveoli


title: Brain, TBI2

value: cerebral cortex


title: Mr_pFC108_CATIE_R4_Necrotic


title: Brain, TBI3


title: Mr_pFC073_CATIE_R7_Chlorotic

value: Chlorotic


title: Control, lung alveoli_H06 4


title: Brain, Sham2

value: Sham


title: SM-KIPH6

value: Blood

value: PostCA


title: E13.5 Foxd1Cre;Ptch1 (flox/-) sample 3

city: Toronto

first: Norman

middle: D

last: Rosenblum

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore.
Trimmed sequence reads were alligned to the reference genome using the STAR aligner, v.2.6.0c.
STAR alignments were processed to extract raw counts for genes using htseq-count v.0.6.1p2.
Two-condition differential gene expression was performed with DESeq2 v.1.26.0s.
Assembly: mm10/m38.p5, Gencode M16 gene models
Supplementary files format and content: tsv file contains GeneID, GeneName, baseMean (mean of normalized counts for all samples), log2 FoldChange (used for selections of DEGs), lfcSE, Wald statistic, Wald test p-value, BH adjusted p-value (used for selection of DEGs), and each sample name.

source_name: whole kidney

extract_protocol:
RNA was harvested using Rneasy micro extraction kit (Qiagen).
RNA libraries for RNA-seq were prepared using mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: whole kidney

value: Foxd1Cre;Ptch1 (flox/-)


title: SM-KIPHA


title: Control, lung alveoli_H06 3


title: SM-KIPH4


title: Mr_pFC058_CATIE_R7_Necrotic


title: E13.5 Foxd1Cre;Ptch1 (flox/-) sample 2


title: Control, lung alveoli_H06 1


title: Brain, TBI1


title: Control, lung alveoli_H06 2


title: Mr_pFC064_CATIE_R7_Necrotic


title: SM-KIPH3


title: Mr_pFC041_CATIE1000_Malform


title: SM-KIPH5


title: E13.5 Foxd1Cre;Ptch1 (flox/-) sample 1


title: Mr_pFC042_CATIE1000_Malform


title: Control, lung bronchiole_H06 4


title: Mr_pFC044_CATIE1000_Malform


title: SM-KIPH2


title: E13.5 Ptch1 (flox/+) sample 3

value: Ptch1 (flox/+)


title: SM-KIPH1


title: Mr_pFC091_Pound7_Malform


title: Control, lung bronchiole_H06 5

value: lung


title: E13.5 Ptch1 (flox/+) sample 2


title: Control, lung bronchiole_H06 6

value: bronchiole


title: Control, lung bronchiole_H06 3

value: multiple cell types


title: SM-KIPGZ


title: E13.5 Ptch1 (flox/+) sample 1


title: Control, lung bronchiole_H06 2

value: SARS-CoV-2 infection


title: MB3_2

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

data_processing:
For each sample, RNA-seq clean reads were obtained that mapped to mm10  using HISAT2 (hierarchical indexing for spliced alignment of transcripts) v2.0.477.
Sequencing read counts were calculated using Stringtie (v.1.3.0).
Then expression levels from different samples were normalized by the Trimmed Mean of M values (TMM) method.
The normalized expression levels of different samples were converted to FPKM (Fragments Per Kilobase of transcript per Million mapped fragments). The edgeR package of R was used to analyze the difference between intergroup gene expression, the P-values were calculated, and the multiple hypothesis test was performed. The P-value threshold was determined by controlling the FDR (False Discovery Rate) with the Benjamini algorithm. The corrected P-value is called the q-value.
Differentially expressed genes (DEGs) were defined as transcripts with a fold change in expression level (according to the FPKM value) greater than 2.0 and a q-value less than 0.05.
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: an excel file include count and FPKM values for total 4 Sample

source_name: peritoneal cavity

growth_protocol: Wildtype C56BL/6 mice were intraperitoneally injected with 2ml of sterile 3% thioglycolate medium per mice, after 3 days, peritoneal cells were harvested by lavaging the peritoneal cavity . Adherent peritoneal macrophages were cultured in DMEM media containing 10% FBS and at 37°C.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina, USA) following the manufacturer’s instructions.mRNA was enriched with oligo(dT) beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers.This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).

treatment_protocol: Peritoneal macrophages were pre-treated with MB-3(50μM) or DMSO and then stimulated with LPS (100ng/ml) for 4 hours.

value: peritoneal cavity

value: primary cell

value: peritoneal macrophages

value: wildtype C57BL/6

value: pre-treated with MB-3 and stimulated with LPS for 4h


title: SM-KIPGY


title: SM-KIPH8


title: DMSO_2

value: pre-treated with DMSO and stimulated with LPS for 4h


title: SM-KIPH9


title: Mr_pFC013_Pound7_Malform

value: Malform


title: Control, lung bronchiole_H06 1

value: Control


title: P1296R [205061410106_R08C01]

type: genomic

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

hyb_protocol: DNA extraction and Infinium MethylationEPIC BeadChip (850K) array were carried out following Infinium HD Methylation Assay Protocol by the Molecular Genomics Core of Norris Cancer Center at University of Southern California.

data_processing:
Right and left colon locations were analyzed individually. For all analyses, probes were removed in minfi if: they had a detection P-value<0.01; were cross-reactive; contained a SNP at the single base extension or CpG interrogation site at any MAF; were not present in a CpG context; were present on either sex chromosome. Given the cancer-related nature of some of the datasets analyzed, we also assessed probes in SeSAMe. Probes that failed under default parameters were also removed prior to analysis. For all analyses, DMRs were generated using DMRcate on beta values. A comparison of DMRs across conditions was then carried out by setting lambda=1000 and minimum CpGs=7.
matrix processed value definition: Normalized Betas

label: Cy3, Cy5

molecule: genomic DNA

source_name: Colon Organoid

label_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

growth_protocol: Normal 3D colon organoids included in the study were developed from biopsies of proximal or distal colon using a modification of the method described by Sato et al. After isolation, colon crypts were embedded in Matrigel, and cell lines were established in growth media that included: advanced DMEM/F-12, 100U/ml penicillin, 100μg/ml streptomycin, 10mM Hepes, 1x N2, 1x B27, 2mM GlutaMAX, 1mM N-acetyl-cysteine, 10mM gastrin, 50% L-WRN conditioned media, 500nM A83-01, 10uM SB202190, 10mM nicotinamide, 50ng/ml EGF, 10μM Y27632. Colon organoids were grown and passaged as needed in 48-well culture plates.

extract_protocol: Genomic DNA was extracted using the Qiagen UCP DNA kit (Catalog No: 56204; Qiagen; Hilden, Germany) with few exceptions. For elution, a 5 minute final incubation of Buffer AUE was preferred to increase yield. Further, the elution step was carried out twice using two volumes of 25μl. DNA quality was assessed using gel electrophoresis to ensure that DNA was not heavily fragmented.

value: F

tag: smoking

value: Current/Former

tag: phenotype

value: CTL

tag: run

value: B

tag: colon location

value: Right


title: MrC26_My_C

tag: genotype

value: mycelia

value: C


title: MB3_1

tag: cell type


title: P1296L [205061410106_R07C01]

scan_protocol: DNA extraction and Infinium MethylationEPIC BeadChip (850K) array were carried out following Infinium HD Methylation Assay Protocol by the Molecular Genomics Core of Norris Cancer Center at University of Southern California.

value: Left


title: BCS24DR3

city: hangzhou

first: xiong

last: jiangyan

address: sandun street

institute: zhejiang University

data_processing:
A cDNA library constructed by technology from the pooled RNA from samples of Hordeum vulgare was sequenced run with Illumina Novaseq TM 6000 sequence platform. Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.
We aligned reads of all samples to the Hordeum vulgare reference genome using HISA
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples)
Assembly: Hordeum_vulgare.IBSC_v2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Hordeum vulgare

source_name: leaf

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedur
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol

tag: strain

value: leaf

tag: treatment

value: drought


title: SM-KIPH7

value: Blood

tag: group

value: PostCA


title: BCS24DR2


title: DMSO_1

value: peritoneal cavity

value: primary cell

value: peritoneal macrophages

value: wildtype C57BL/6


title: P1293R [205061410106_R06C01]

value: M

value: LS


title: P1293L [205061410106_R05C01]

value: Current/Former


title: SM-KIPGX


title: P1083R [205061410106_R04C01]

value: Never

value: CTL


title: Zfp352OE 12h rep2

city: HangZhou

first: Zhengyi

last: Li

state: ZheJiang

address: 866 Yuhangtang Rd, Hangzhou

department: Institute of Genetics

data_processing:
Quality control for raw reads was performed by FastQC v0.11.8
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt v2.9
Trimmed sequence reads were mapped to GRCm38/mm10 using STAR,Reads with maximal 1000 multiple mapped sites and no more than 3 mismatches were retained, and only the best hit was kept (parameters- --outFilterMultimapNmax 1000, --outFilterMismatchNmax 3, --outSAMmultNmax 1).
Quantification was calculated by FeatureCounts v2.0.0(parameters- -p -B -P -C)
Differentially expressed genes (DEGs) and transposable elements (DE-TEs) were generated by R package EdgeR v3.30.3
Assembly: GRCm38(mm10)
Supplementary files format and content: bigwig

source_name: E14 WT

growth_protocol: E14 cells were cultured in DMEM high glucose with 15% FBS,100X NEAA,100X L-Glutamine,1000X β–Mercaptoethanol,homemade LIF on gelatin pre-coated plate.

extract_protocol:
RNA was harvested using trizol. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Next R UltraTM RNA Library Prep Kit (strand-unspecific, ployA-specific) following manufacturer's protocols.

treatment_protocol: Dox(1mg/ml) was added to the medium at 1ug/ml ratio

value: E14 WT

value: embryonic stem cell

value: dox treatment


title: Zfp352OE 12h rep1


title: SM-KIPDA

value: Healthy


title: SM-KIPDB


title: BCS24CK3

value: leaf

value: ck


title: BCS24DR1

value: drought


title: Zfp352OE 0h rep2

value: no treatment


title: BCS24CK2


title: SM-KIPD9

value: Blood


title: P1083L [205061410106_R03C01]

value: B

value: Left


title: Zfp352OE 0h rep1


title: SM-KIPD8


title: P1086L [205061410106_R01C01]

value: F


title: DuxOE 72h rep2

value: Tet-dox-induced-Dux


title: P1273L [205061410097_R06C01]

value: M


title: P1262R [205061410097_R03C01]

value: Right


title: P1273R [205061410097_R05C01]

value: Current/Former


title: BCS8DR1


title: SM-KIPD7


title: SM-KIPD6


title: SM-KIPD2


title: BCS8DR2


title: BCS8CK3


title: P1230R [205061410097_R02C01]

value: Never

value: LS


title: SM-KIPD1


title: Mr_pFC019_Pound7_Malform

value: Malform


title: DuxOE 48h rep1

value: E14 WT

value: embryonic stem cell

value: dox treatment


title: DuxOE 36h rep2


title: BCS8CK1

value: leaf

value: ck


title: SM-KIPCZ

value: Healthy


title: P1179R [205061410082_R08C01]

value: CTL


title: P1230L [205061410097_R01C01]

value: B


title: BCS8DR3

value: drought


title: DuxOE 48h rep2


title: DuxOE 72h rep1


title: BCS24CK1


title: P1166R [205061410082_R07C01]

value: F


title: DuxOE 36h rep1

value: Tet-dox-induced-Dux


title: DuxOE 12h rep1


title: SM-KIPCW

value: Blood


title: SM-KIPCX


title: P1166L [205061410082_R06C01]

value: Left


title: DuxOE 24h rep1


title: SM-KIPCY


title: DuxOE 24h rep2


title: DuxOE 12h rep2


title: SM-KIPCV


title: BCS8CK2


title: SM-KIPCU


title: SM-KIPD4


title: P1103R [205061410082_R04C01]

value: M

value: Right


title: SM-KIPD5


title: P1103L [205061410082_R03C01]

value: Never


title: P1247R [205061410080_R08C01]

value: Current/Former


title: DuxOE 0h rep2

value: E14 WT

value: no treatment


title: SM-KIPD3


title: P1062R [205061410082_R02C01]

value: LS


title: P1208L [205061410082_R05C01]


title: shSusd2_Rep1_set3

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: wild type mESC infected with Susd2 shRNA

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC mm9 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: mm9
Supplementary files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

source_name: mouse embryonic stem cells

growth_protocol: Cells were maintained serum free neurobasal+DMEM/F12 media supplemented with 2i+LIF

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Cells were treated with DMSO, LTX, HPX or LTX+HPX for 48 hours; for shRNA knockdown, cells were infected with lentiviruses expressing the shRNA and selected with puromycin.

value: mouse embryonic stem cells

tag: passages

value: Low passages (6-10)

value: wild type


title: P1247L [205061410080_R07C01]

value: CTL


title: shSusd2_Rep2_set3


title: DuxOE 0h rep1

value: embryonic stem cell


title: SM-KIPCO

value: Healthy


title: SM-KIPCN


title: shCd109_Rep2_set3

description: wild type mESC infected with Cd109 shRNA


title: shCth_Rep2_set3

description: wild type mESC infected with Cth shRNA

value: shCth


title: P1212R [205061410080_R04C01]

value: B


title: P1214L [205061410080_R02C01]

value: F


title: SM-KIPCL

value: Blood

value: PostCA


title: SM-KIPCP


title: P1129L [205061410080_R05C01]

value: Left


title: SM-KIPCM


title: IPEC-J2_ZnO-high conc._ETEC_6 hours_replica 2

city: Lelystad

first: Marcel

last: Hulst

state: Flevoland

address: Edelhertweg 15

department: Livestock research

country: Netherlands

institute: Animal Sciences Group

description:
IPEC-J2_ZnO-0.01% (w/v) conc._ETEC_6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
Zn-E6Hd

hyb_protocol: Hybridization was performed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labeling protocol from Agilent in the hybridization oven (G2545A hybridization Oven Agilent Technologies) The hybridization temperature was 65°C with rotation speed 10 rpm for 17 hours. After 17 hours the arrays were washed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent.

scan_protocol: Agilent microarray slides (G2519F Sus scrofa Agilent-035953, costumized in situ oligonucleotide array printed in 8 patches of 60K) harbouring 43,803 probes, were used and scanned using the DNA microarray scanner with Surescan high resolution Technology (Agilent Technologies). Agilent Scan Control with resolution of 5µ, 16 bits and PMT of 100%.

data_processing: Feature extraction was performed using protocol 10.7.3.1 (v10.7) for 1 color gene expression. Background subtracted signal intensity (gBGSubSignal).

organism: Sus scrofa

source_name: IPEC-J2_ZnO-0.01% (w/v) conc._ETEC_6h

label_protocol: Labelling was done as recommended by Agilent Technologies using the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labeling. 500 ng RNA of each sample was amplified and labelled with the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling kit and 600 ng of Cy3 labelled cRNA was used for hybridisation on each patch.

extract_protocol: Total RNA was isolated from IPEC-J2 monolayers with TRIzol® reagent (Invitrogen) and treated with DNase. The RNA was further purified using QIAamp MinElute Virus Spin Kit columns (Qiagen, Venlo, the Netherlands) according to the manufacturers’ instructions.

value: IPEC-J2 cultured cells

value: ZnO-0.01% (w/v) conc_ETEC

tag: time


title: SM-KIPCT


title: IPEC-J2_ZnO-high conc._ETEC_2 hours_replica 1

description:
IPEC-J2_ZnO-0.01% (w/v) conc._ETEC_2h_replica 1
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
Zn-E2H

source_name: IPEC-J2_ZnO-0.01% (w/v) conc._ETEC_2h


title: P1129R [205061410080_R06C01]

tag: age

value: Never

value: Right


title: P1074L [205061410080_R01C01]

value: M

value: Current/Former


title: shCd109_Rep1_set3

value: mouse embryonic stem cells

value: Low passages (6-10)


title: shParvb_Rep2_set3

description: wild type mESC infected with Parvb shRNA

value: shParvb

value: wild type


title: IPEC-J2_ZnO-high conc._6 hours_replica 2

description:
IPEC-J2_ZnO-0.01% (w/v) conc._6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
Zn-6Hd

source_name: IPEC-J2_ZnO-0.01% (w/v) conc._6h

value: ZnO-0.01% (w/v) conc


title: shCth_Rep1_set3

description: wild type mESC infected with Cth shRNA

value: shCth


title: IPEC-J2_ZnO-high conc._ETEC_2 hours_replica 2

description:
IPEC-J2_ZnO-0.01% (w/v) conc._ETEC_2h_replica 2
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
Zn-E2Hd


title: IPEC-J2_ZnO-high conc._ETEC_6 hours_replica 1

description:
IPEC-J2_ZnO-0.01% (w/v) conc._ETEC_6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
Zn-E6H


title: shParvb_Rep1_set3


title: shMcf2_Rep2_set3

description: wild type mESC infected with Mcf2 shRNA


title: SM-KIPCK

source_name: Blood


title: SM-KIPCJ


title: IPEC-J2_ZnO-low conc._ETEC_6 hours_replica 2

description:
IPEC-J2_ZnO-0.0001% (w/v) conc._ETEC_6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
Zn-E6Ld

source_name: IPEC-J2_ZnO-0.0001% (w/v) conc._ETEC_6h

value: ZnO-0.0001% (w/v) conc_ETEC


title: P1119R [205061410059_R06C01]

value: CTL

value: B


title: P1125R [205061410059_R08C01]

value: F

value: LS


title: shMcf2_Rep1_set3

description: wild type mESC infected with Mcf2 shRNA


title: shGlipr2_Rep2_set3

description: wild type mESC infected with Glipr2 shRNA


title: IPEC-J2_ZnO-low conc._6 hours_replica 1

description:
IPEC-J2_ZnO-0.0001% (w/v) conc._6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
Zn-6L

value: IPEC-J2 cultured cells


title: IPEC-J2_ZnO-high conc._6 hours_replica 1

description:
IPEC-J2_ZnO-0.01% (w/v) conc._6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
Zn-6H


title: SM-KIPCS

value: Blood

value: Healthy


title: P1269R [205061410059_R04C01]

value: Never

value: Right


title: IPEC-J2_ZnO-low conc._ETEC_6 hours_replica 1

description:
IPEC-J2_ZnO-0.0001% (w/v) conc._ETEC_6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
Zn-E6L


title: P1125L [205061410059_R07C01]

value: Current/Former

value: Left


title: P1269L [205061410059_R03C01]


title: IPEC-J2_ZnO-low conc._6 hours_replica 2

description:
IPEC-J2_ZnO-0.0001% (w/v) conc._6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
Zn-6Ld


title: SM-KIPCR


title: P1236L [205061410059_R02C01]

value: M


title: IPEC-J2_PSY2-high conc._ETEC_6 hours_replica 2

description:
IPEC-J2_PSY2-0.01% (w/v) conc._ETEC_6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSY2-E6Hd

source_name: IPEC-J2_PSY2-0.01% (w/v) conc._ETEC_6h

value: PSY2-0.01% (w/v) conc_ETEC


title: shGlipr2_Rep1_set3

value: mouse embryonic stem cells

value: Low passages (6-10)

value: wild type


title: SM-KIPCQ


title: IPEC-J2_PSY2-high conc._ETEC_6 hours_replica 1

description:
IPEC-J2_PSY2-0.01% (w/v) conc._ETEC_6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSY2-E6H


title: IPEC-J2_ZnO-high conc._2 hours_replica 2

description:
IPEC-J2_ZnO-0.01% (w/v) conc._2h_replica 2
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
Zn-2Hd

source_name: IPEC-J2_ZnO-0.01% (w/v) conc._2h

value: ZnO-0.01% (w/v) conc


title: IPEC-J2_ZnO-high conc._2 hours_replica 1

description:
IPEC-J2_ZnO-0.01% (w/v) conc._2h_replica 1
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
Zn-2H


title: shPLKO_Rep1_set3

description: wild type mESC infected with control shRNA

value: shPLKO


title: P1186L [205061410059_R01C01]

value: B


title: SM-KIPCI

value: PostCA


title: SM-KIPCH


title: shSdc4_Rep2_set2

description: wild type mESC infected with Sdc4 shRNA


title: P1151L [205061410046_R07C01]

value: CTL


title: IPEC-J2_PSY2-medium conc._ETEC_6 hours_replica 2

description:
IPEC-J2_PSY2-0.001% (w/v) conc._ETEC_6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSY2-E6Md

source_name: IPEC-J2_PSY2-0.001% (w/v) conc._ETEC_6h

value: IPEC-J2 cultured cells

value: PSY2-0.001% (w/v) conc_ETEC


title: SM-KIPCD

value: Blood


title: IPEC-J2_PSY2-medium conc._ETEC_6 hours_replica 1

description:
IPEC-J2_PSY2-0.001% (w/v) conc._ETEC_6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSY2-E6M


title: shSdc4_Rep1_set2

description: wild type mESC infected with Sdc4 shRNA


title: P1089R [205061410046_R06C01]

value: F

value: Never

value: LS


title: IPEC-J2_PSY2-high conc._ETEC_2 hours_replica 2

description:
IPEC-J2_PSY2-0.01% (w/v) conc._ETEC_2h_replica 2
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSY2-E2Hd

source_name: IPEC-J2_PSY2-0.01% (w/v) conc._ETEC_2h


title: shPLKO_Rep2_set3


title: SM-KIPCC


title: SM-KIPCB


title: shNcoa6_Rep2_set2

description: wild type mESC infected with Ncoa6 shRNA


title: SM-KIPCA


title: shNcoa6_Rep1_set2


title: IPEC-J2_PSY2-high conc._ETEC_2 hours_replica 1

description:
IPEC-J2_PSY2-0.01% (w/v) conc._ETEC_2h_replica 1
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSY2-E2H


title: shKhdc3_Rep2_set2

description: wild type mESC infected with Khdc3 shRNA


title: IPEC-J2_PSY2-high conc._6 hours_replica 2

description:
IPEC-J2_PSY2-0.01% (w/v) conc._6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSY2-6Hd


title: SM-KIPC9


title: P1210L [205061400186_R07C01]

value: Left


title: P1263R [205061410046_R02C01]

value: Right


title: P1089L [205061410046_R05C01]


title: P1096L [205061410046_R03C01]

value: M


title: SM-KIPC8


title: shKhdc3_Rep1_set2

value: mouse embryonic stem cells


title: shHormad1_Rep2_set2

description: wild type mESC infected with Hormad1 shRNA

value: Low passages (6-10)


title: P1290L [205061400186_R06C01]

value: Current/Former


title: SM-KIPC7


title: shHormad1_Rep1_set2

value: wild type


title: SM-KIPC6


title: P1290R [205061400186_R05C01]


title: IPEC-J2_PSY2-high conc._6 hours_replica 1

description:
IPEC-J2_PSY2-0.01% (w/v) conc._6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSY2-6H


title: shDdc_Rep2_set2

description: wild type mESC infected with Ddc shRNA

value: shDdc


title: shDdc_Rep1_set2

description: wild type mESC infected with Ddc shRNA


title: P1105R [205061400186_R04C01]

value: B


title: SM-KIPCF

value: PostCA


title: P1105L [205061400186_R03C01]


title: shBhmt_Rep2_set2

description: wild type mESC infected with Bhmt shRNA

value: shBhmt


title: P1173R [205061400186_R02C01]

value: CTL


title: P1229R [202878220075_R08C01]

value: A


title: shBhmt_Rep1_set2

description: wild type mESC infected with Bhmt shRNA


title: SM-KIPCE

value: Blood


title: IPEC-J2_PSY1-high conc._ETEC_2 hours_replica 2

description:
IPEC-J2_PSY1-0.01% (w/v) conc._ETEC_2h_replica 2
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSY1-E2Hd

source_name: IPEC-J2_PSY1-0.01% (w/v) conc._ETEC_2h

value: IPEC-J2 cultured cells

value: PSY1-0.01% (w/v) conc_ETEC


title: IPEC-J2_PSY2-high conc._2 hours_replica 2

description:
IPEC-J2_PSY2-0.01% (w/v) conc._2h_replica 2
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSY2-2Hd


title: IPEC-J2_PSY2-medium conc._6 hours_replica 2

description:
IPEC-J2_PSY2-0.001% (w/v) conc._6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSY2-6Md


title: IPEC-J2_PSY2-high conc._2 hours_replica 1

description:
IPEC-J2_PSY2-0.01% (w/v) conc._2h_replica 1
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSY2-2H


title: SM-KIPC5


title: IPEC-J2_PSY2-medium conc._6 hours_replica 1

description:
IPEC-J2_PSY2-0.001% (w/v) conc._6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSY2-6M


title: shPLKO_Rep2_set2

value: shPLKO


title: P1215R [202878220075_R07C01]

value: F

value: LS


title: SM-KIPCG


title: P1210R [202878220075_R06C01]

value: Never

value: Right


title: shPLKO_Rep1_set2

value: mouse embryonic stem cells

value: Low passages (6-10)


title: IPEC-J2_PSY1-high conc._6 hours_replica 2

description:
IPEC-J2_PSY1-0.01% (w/v) conc._6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSY1-6Hd


title: SM-KIPBZ


title: SM-KIPC1


title: IPEC-J2_PSY1-high conc._ETEC_6 hours_replica 1

description:
IPEC-J2_PSY1-0.01% (w/v) conc._ETEC_6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSY1-E6H

source_name: IPEC-J2_PSY1-0.01% (w/v) conc._ETEC_6h


title: IPEC-J2_PSY1-high conc._ETEC_6 hours_replica 2

description:
IPEC-J2_PSY1-0.01% (w/v) conc._ETEC_6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSY1-E6Hd


title: IPEC-J2_PSY1-high conc._ETEC_2 hours_replica 1

description:
IPEC-J2_PSY1-0.01% (w/v) conc._ETEC_2h_replica 1
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSY1-E2H


title: SM-KIPBY


title: shUtf1_Rep1_set1

description: wild type mESC infected with Utf1 shRNA

value: wild type


title: shUtf1_Rep2_set1

description: wild type mESC infected with Utf1 shRNA


title: shSparc_Rep2_set1

description: wild type mESC infected with Sparc shRNA

value: shSparc


title: P1183R [202878220075_R04C01]

value: Current/Former


title: P1143R [202878220075_R03C01]


title: SM-KIPBW

value: PostCA


title: IPEC-J2_PSA3-high conc._ETEC_6 hours_replica 2

description:
IPEC-J2_PSA3-0.052% (w/v) conc._ETEC_6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA3-E6Hd

source_name: IPEC-J2_PSA3-0.052% (w/v) conc._ETEC_6h

value: PSA3-0.052% (w/v) conc_ETEC


title: P1135R [202878220075_R02C01]


title: P1202R [202878220075_R05C01]


title: SM-KIPBV


title: P1117R [202878220074_R08C01]


title: IPEC-J2_PSA3-medium conc._ETEC_6 hours_replica 2

description:
IPEC-J2_PSA3-0.0052% (w/v) conc._ETEC_6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA3-E6Md

value: PSA3-0.0052% (w/v) conc_ETEC


title: IPEC-J2_PSY1-high conc._2 hours_replica 1

description:
IPEC-J2_PSY1-0.01% (w/v) conc._2h_replica 1
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSY1-2H


title: IPEC-J2_PSY1-high conc._6 hours_replica 1

description:
IPEC-J2_PSY1-0.01% (w/v) conc._6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSY1-6H


title: SM-KIPBU


title: IPEC-J2_PSY1-high conc._2 hours_replica 2

description:
IPEC-J2_PSY1-0.01% (w/v) conc._2h_replica 2
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSY1-2Hd


title: IPEC-J2_PSA3-high conc._ETEC_6 hours_replica 1

description:
IPEC-J2_PSA3-0.052% (w/v) conc._ETEC_6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA3-E6H


title: P1112R [202878220074_R07C01]

value: CTL

value: A


title: SM-KIPBX

value: Blood


title: shAlpl_Rep1_set1

description: wild type mESC infected with Alpl shRNA

value: shAlpl


title: IPEC-J2_PSA3-medium conc._ETEC_6 hours_replica 1

description:
IPEC-J2_PSA3-0.0052% (w/v) conc._ETEC_6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA3-E6M

value: IPEC-J2 cultured cells


title: IPEC-J2_PSA3-high conc._ETEC_2 hours_replica 1

description:
IPEC-J2_PSA3-0.052% (w/v) conc._ETEC_2h_replica 1
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSA3-E2H

source_name: IPEC-J2_PSA3-0.052% (w/v) conc._ETEC_2h


title: shAlpl_Rep2_set1

description: wild type mESC infected with Alpl shRNA


title: SM-KIPBT


title: shDazl_Rep2_set1

description: wild type mESC infected with Dazl shRNA

value: shDazl


title: P1111R [202878220074_R06C01]

source_name: Colon Organoid

value: F

value: LS


title: P1109R [202878220074_R05C01]

value: Never

value: Right


title: SM-KIPC4


title: shDazl_Rep1_set1

description: wild type mESC infected with Dazl shRNA

value: mouse embryonic stem cells

value: Low passages (6-10)


title: SM-KIPC3


title: P1102R [202878220074_R04C01]


title: shFabp3_Rep2_set1

description: wild type mESC infected with Fabp3 shRNA

value: wild type


title: shMap6_Rep2_set1

description: wild type mESC infected with Map6 shRNA


title: P1086R [202878220074_R03C01]


title: IPEC-J2_PSA3-high conc._6 hours_replica 2

description:
IPEC-J2_PSA3-0.052% (w/v) conc._6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA3-6Hd


title: SM-KIPBS


title: SM-KIPBO


title: shMap6_Rep1_set1

description: wild type mESC infected with Map6 shRNA


title: shPLKO_Rep2_set1

description: wild type mESC infected with control shRNA

value: shPLKO


title: SM-KIPBN

value: PostCA


title: IPEC-J2_PSA3-high conc._6 hours_replica 1

description:
IPEC-J2_PSA3-0.052% (w/v) conc._6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA3-6H


title: P1082R [202878220074_R02C01]

value: Current/Former


title: shPLKO_Rep1_set1


title: SM-KIPC2


title: SM-KIPBL


title: shFabp3_Rep1_set1


title: SM-KIPBM


title: IPEC-J2_PSA3-medium conc._6 hours_replica 1

description:
IPEC-J2_PSA3-0.0052% (w/v) conc._6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA3-6M


title: mESC_KO_LTX_Rep2

description: MLL3/4KO mESC treatd with lometrexol

value: LTX


title: mESC_KO_LTX_Rep1

description: MLL3/4KO mESC treatd with lometrexol


title: IPEC-J2_PSA2-high conc._ETEC_6 hours_replica 2

description:
IPEC-J2_PSA2-0.01% (w/v) conc._ETEC_6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA2-E6Hd

source_name: IPEC-J2_PSA2-0.01% (w/v) conc._ETEC_6h

value: PSA2-0.01% (w/v) conc_ETEC


title: SM-KIPBJ


title: SM-KIPBK


title: IPEC-J2_PSA3-medium conc._6 hours_replica 2

description:
IPEC-J2_PSA3-0.0052% (w/v) conc._6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA3-6Md


title: mESC_KO_LTX_HPX_Rep2

description: MLL3/4KO mESC treatd with lometrexol and hypoxanthine


title: IPEC-J2_PSA3-high conc._ETEC_2 hours_replica 2

description:
IPEC-J2_PSA3-0.052% (w/v) conc._ETEC_2h_replica 2
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSA3-E2Hd

value: PSA3-0.052% (w/v) conc_ETEC


title: IPEC-J2_PSA3-high conc._2 hours_replica 1

description:
IPEC-J2_PSA3-0.052% (w/v) conc._2h_replica 1
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSA3-2H


title: IPEC-J2_PSA2-medium conc._ETEC_6 hours_replica 2

description:
IPEC-J2_PSA2-0.001% (w/v) conc._ETEC_6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA2-E6Md

source_name: IPEC-J2_PSA2-0.001% (w/v) conc._ETEC_6h

value: PSA2-0.001% (w/v) conc_ETEC


title: SM-KIPBI

value: Blood


title: SM-KIPBH


title: IPEC-J2_PSA2-high conc._ETEC_6 hours_replica 1

description:
IPEC-J2_PSA2-0.01% (w/v) conc._ETEC_6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA2-E6H

value: IPEC-J2 cultured cells


title: mESC_KO_HPX_Rep2

description: MLL3/4KO mESC treatd with hypoxanthine

source_name: mouse embryonic stem cells

value: HPX


title: mESC_KO_LTX_HPX_Rep1


title: IPEC-J2_PSA2-medium conc._ETEC_6 hours_replica 1

description:
IPEC-J2_PSA2-0.001% (w/v) conc._ETEC_6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA2-E6M


title: IPEC-J2_PSA3-high conc._2 hours_replica 2

description:
IPEC-J2_PSA3-0.052% (w/v) conc._2h_replica 2
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSA3-2Hd


title: SM-KIPBR


title: IPEC-J2_PSA2-high conc._6 hours_replica 2

description:
IPEC-J2_PSA2-0.01% (w/v) conc._6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA2-6Hd


title: IPEC-J2_PSA2-high conc._ETEC_2 hours_replica 2

description:
IPEC-J2_PSA2-0.01% (w/v) conc._ETEC_2h_replica 2
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSA2-E2Hd

source_name: IPEC-J2_PSA2-0.01% (w/v) conc._ETEC_2h


title: mESC_KO_HPX_Rep1

description: MLL3/4KO mESC treatd with hypoxanthine


title: mESC_KO_DMSO_Rep2

description: MLL3/4KO mESC treatd with DMSO

value: DMSO


title: SM-KIPBQ


title: SM-KIPBP


title: mESC_KO_DMSO_Rep1

description: MLL3/4KO mESC treatd with DMSO


title: IPEC-J2_PSA2-high conc._6 hours_replica 1

description:
IPEC-J2_PSA2-0.01% (w/v) conc._6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA2-6H


title: IPEC-J2_PSA2-high conc._ETEC_2 hours_replica 1

description:
IPEC-J2_PSA2-0.01% (w/v) conc._ETEC_2h_replica 1
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSA2-E2H


title: mESC_WT_LTX_Rep1

description: wild type mESC treatd with lometrexol


title: IPEC-J2_PSA2-medium conc._6 hours_replica 1

description:
IPEC-J2_PSA2-0.001% (w/v) conc._6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA2-6M


title: SM-KIPBG


title: IPEC-J2_PSA2-medium conc._6 hours_replica 2

description:
IPEC-J2_PSA2-0.001% (w/v) conc._6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA2-6Md


title: M_3

city: Jerusalem

first: Marjorie

last: Pick

address: Kiryat Hadassah p.o.b 12000

department: Hematology

country: Israel

institute: Hadassah Medical Organization

data_processing:
Fastq files were created with bcl2fastq, v2.17.1.14, raw reads were quality-trimmed at both ends, using in-house Perl scripts, with a quality threshold of 32, then adapter sequences were removed with cutadapt, version 1.9.1, filtering out reads that became shorter than 15 nt (-m parameter).
Processed reads were filtered using the fastq_quality_filter program of the FASTX package, version 0.0.14, with parameters -q 20 and -p 90, then aligned to the human genome with TopHat, v2.0.14. The genome version was GRCh38, with annotations from Ensembl release 84. Alignment was done with parameters -G genes.gtf, -N 5, --read-gap-length 5, --read-edit-dist 10, --segment-length 20 and --read-realign-edit-dist 3.
Quantification was done with the Cufflinks package, v2.2.1, using the cuffquant program with the genome bias correction (-b parameter), multi-mapped reads assignment algorithm (-u parameter) and masking for short genes (-M parameter). Raw counts were obtained by running cuffnorm on the cuffquant output.
Normalization and differential expression were done with the DESeq2 package, version 1.12.4. Only genes with at least 2 counts over all samples were used for analysis with default parameters. The significance threshold was taken as padj<0.1 (default).
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file with the relevant data for each gene (rows). Columns A-I have general gene details; columns J-O have the raw counts per sample; columns P-U have the normalized counts per sample; column V has the average signal (baseMean); columns W-AA have the results of the statistical testing. The exact meaning of each column is given in the header rows (1-2).

source_name: multiple myeloma JJN3 cell line

growth_protocol: cell lines were grown and maintained in RPMI media both supplemented with 10% Fetal Calf Serum L-Glutamine, penicillin, streptomycin and incubated at 37°C, 5% CO2. All cell lines are passaged bi-weekly and tested for mycoplasm.

extract_protocol:
To extract RNA we used Qiagen RNEasy mini kit and the quality of RNA tested with the RNA 6000 Nano Bio analyzer (Agilent Technologies, CA. USA).
Transcriptome libraries were prepared using the Illumina TruSeq RNA library preparation kit (Illumina #RS-122-2001), according to the manufactures’ recommendedprotocol, starting with approximately 1.2ug of total RNA. The amplified indexed libraries were quantified using Invitrogen Qubit fluorometer and equally pooled according to pool design

treatment_protocol: The 600 base pair LC gene was cloned and inserted into the multiple cloning site of the minusDsRed-GFP expressing lentivirus generating lentivirus plasmids cloned with the amyloidogenic Lambda LC cDNA sequences from patients with AL in the cardiac (H) and another LC cDNA sequence from a second patient with AL in the kidney - nephrotic (K) and a third patients LC sequence whom suffered from non-amyloidogenic MM (M) as a control sequence expressing GFP.

tag: disease state

value: Plasma cell dyscrasia

tag: expression

value: non-amyloidogenic LCs


title: mESC_WT_LTX_Rep2

description: wild type mESC treatd with lometrexol


title: IPEC-J2_PSA2-high conc._2 hours_replica 2

description:
IPEC-J2_PSA2-0.01% (w/v) conc._2h_replica 2
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSA2-2Hd

tag: cell line


title: K_2

value: Amyloid light-chain (AL) amyloidosis LCs


title: shSparc_Rep1_set1

description: wild type mESC infected with Sparc shRNA

value: mouse embryonic stem cells

value: shSparc


title: IPEC-J2_PSA2-high conc._2 hours_replica 1

description:
IPEC-J2_PSA2-0.01% (w/v) conc._2h_replica 1
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSA2-2H


title: K_1


title: mESC_WT_HPX_Rep2

description: wild type mESC treatd with hypoxanthine

value: Low passages (6-10)

value: wild type


title: IPEC-J2_PSA1-medium conc._ETEC_6 hours_replica 1

description:
IPEC-J2_PSA1-0.0052% (w/v) conc._ETEC_6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA1-E6M

value: PSA1-0.0052% (w/v) conc_ETEC


title: H_2


title: IPEC-J2_PSA1-high conc._ETEC_6 hours_replica 2

description:
IPEC-J2_PSA1-0.052% (w/v) conc._ETEC_6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA1-E6Hd

source_name: IPEC-J2_PSA1-0.052% (w/v) conc._ETEC_6h

value: PSA1-0.052% (w/v) conc_ETEC


title: mESC_WT_LTX_HPX_Rep1

description: wild type mESC treatd with lometrexol and hypoxanthine


title: IPEC-J2_PSA1-medium conc._ETEC_6 hours_replica 2

description:
IPEC-J2_PSA1-0.0052% (w/v) conc._ETEC_6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA1-E6Md


title: IPEC-J2_PSA1-high conc._ETEC_6 hours_replica 1

description:
IPEC-J2_PSA1-0.052% (w/v) conc._ETEC_6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA1-E6H


title: mESC_WT_HPX_Rep1

description: wild type mESC treatd with hypoxanthine


title: mESC_WT_LTX_HPX_Rep2


title: mESC_WT_DMSO_Rep2

description: wild type mESC treatd with DMSO


title: M_1


title: IPEC-J2_PSA1-high conc._ETEC_2 hours_replica 2

description:
IPEC-J2_PSA1-0.052% (w/v) conc._ETEC_2h_replica 2
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSA1-E2Hd

source_name: IPEC-J2_PSA1-0.052% (w/v) conc._ETEC_2h


title: IPEC-J2_PSA1-high conc._6 hours_replica 1

description:
IPEC-J2_PSA1-0.052% (w/v) conc._6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA1-6H


title: IPEC-J2_PSA1-high conc._6 hours_replica 2

description:
IPEC-J2_PSA1-0.052% (w/v) conc._6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA1-6Hd


title: H_1


title: gRNA-MED25-plusDOX-rep3

first: Graham

last: MacLeod

state: ON

address: 144 College Street

department: Pharmaceutical Sciences

institute: University of Toronto

data_processing:
Illumina NextSeq-500 Instrument
fastq mapped to hg19 and quantified using Kallisto
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and every sample

growth_protocol: Cells were grown in serum-free, growth factor supplemented media on laminin coated plates

extract_protocol:
RNA extracted with Trizol reagent
TruSeq V2mRNA-enriched library kit

treatment_protocol: DOX treatment for 7 days

value: Glioblastoma stem cell

tag: grna

value: DOX


title: mESC_KO_Rep3

description: MLL3/4KO cells


title: psoriasis vulgaris peripheral blood sample (SAMPLE 63)

city: Changsha

first: Min

last: Deng

state: Hunan

address: Renmin Middle Road 139

department: Dermatology

institute: the Second Xiangya Hospital of Central South University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 850k Beadchip using standard Illumina protocol

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

data_processing: Data was extracted with the champ R package, the results were not normalized.

label: Cy5 and Cy3

source_name: peripheral blood 63

label_protocol: Standard Illumina Protocol

growth_protocol: no

extract_protocol: genomic DNA was extracted and purified from whole blood samples usingQiagen DNeasy Kit according to standard instructions

treatment_protocol: no

tag: gender

value: male

tag: tissue

value: peripheral blood

value: psoriasis vulgaris


title: gRNA-MED25-minusDOX-rep4

value: untreated


title: gRNA-MED25-plusDOX-rep2


title: IPEC-J2_PSA1-medium conc._6 hours_replica 2

description:
IPEC-J2_PSA1-0.0052% (w/v) conc._6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA1-6Md

value: IPEC-J2 cultured cells


title: mESC_KO_Rep2

description: MLL3/4KO cells


title: psoriasis vulgaris peripheral blood sample (SAMPLE 60)

source_name: peripheral blood 60

value: female


title: mESC_KO_Rep1

description: MLL3/4KO cells


title: IPEC-J2_PSA1-medium conc._6 hours_replica 1

description:
IPEC-J2_PSA1-0.0052% (w/v) conc._6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
PSA1-6M


title: gRNA-MED25-minusDOX-rep3


title: IPEC-J2_PSA1-high conc._2 hours_replica 2

description:
IPEC-J2_PSA1-0.052% (w/v) conc._2h_replica 2
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSA1-2Hd


title: mESC_WT_Rep3

description: normal cells


title: gRNA-MED25-minusDOX-rep2


title: mESC_WT_Rep2

description: normal cells


title: normal peripheral blood sample (SAMPLE 55)

description: normal peripheral blood sample

source_name: peripheral blood 55

value: normal


title: gRNA-MED25-minusDOX-rep1


title: IPEC-J2_PSA1-high conc._ETEC_2 hours_replica 1

description:
IPEC-J2_PSA1-0.052% (w/v) conc._ETEC_2h_replica 1
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSA1-E2H


title: psoriasis vulgaris peripheral blood sample (SAMPLE 62)

source_name: peripheral blood 62


title: psoriatic arthritis peripheral blood sample (SAMPLE 59)

source_name: peripheral blood 59

value: psoriatic arthritis


title: psoriatic arthritis peripheral blood sample (SAMPLE 64)

source_name: peripheral blood 64


title: psoriatic arthritis peripheral blood sample (SAMPLE 57)

source_name: peripheral blood 57


title: psoriasis vulgaris peripheral blood sample (SAMPLE 61)

source_name: peripheral blood 61


title: mESC_WT_DMSO_Rep1

description: wild type mESC treatd with DMSO

value: DMSO


title: IPEC-J2_9631-high conc._ETEC_6 hours_replica 2

description:
IPEC-J2_9631-0.01% (w/v) conc._ETEC_6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
9631-E6Hd


title: gRNA-MED25-plusDOX-rep1


title: gRNA-AAVS1-plusDOX-rep4


title: psoriasis vulgaris peripheral blood sample (SAMPLE 51)

source_name: peripheral blood 51


title: normal peripheral blood sample (SAMPLE 54)

description: normal peripheral blood sample

source_name: peripheral blood 54


title: mESC_WT_Rep1

description: normal cells

value: mouse embryonic stem cells


title: psoriasis vulgaris peripheral blood sample (SAMPLE 56)

source_name: peripheral blood 56


title: gRNA-AAVS1-plusDOX-rep3


title: sh-nc3

first: Yun

middle: Jin

last: Zhu

state: zhejiang

address: Jiefang road 88

institute: Department of Cardiology, Second Affiliated Hospital, College of Medicine, Zhejiang University.

data_processing:
Illumina Casava 1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database  of splice junctions based on the gene model annotation file and thus a better mapping  result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCm38(mm10)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: cardiomyocytes

growth_protocol: Neonatal mouse ventricular CMs (CMs) were isolated from 1-day-old C57BL/6J mice

extract_protocol:
Total RNA was extracted from CMs using TRIzol® after CMs were transfected with shRNA-GDF11 and sh-Vector for 48h.
Preparation of library and sequencing of transcriptome were carried out using Illu-mina HiSeq X Ten (Novogene Bioinformatics Technology Co., Ltd., Beijing, China).

treatment_protocol: Small hairpin RNA (shRNA) against GDF11 was constructed and packaged by Vigene Biosciences (Jinan, China). For knockdown of GDF11, CMs were transfected with shRNA-GDF11/sh-Vector (MOI=200) according to the manufacturer’s instructions.

value: primary cardiomyocytes

value: transfected with sh-nc-3


title: sh-nc2

value: transfected with sh-nc-2


title: psoriasis vulgaris peripheral blood sample (SAMPLE 52)

source_name: peripheral blood 52


title: psoriasis vulgaris peripheral blood sample (SAMPLE 53)

source_name: peripheral blood 53


title: IPEC-J2_9631-high conc._ETEC_2 hours_replica 2

description:
IPEC-J2_9631-0.01% (w/v) conc._ETEC_2h_replica 2
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
9631-E2Hd


title: IPEC-J2_PSA1-high conc._2 hours_replica 1

description:
IPEC-J2_PSA1-0.052% (w/v) conc._2h_replica 1
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
PSA1-2H


title: gRNA-AAVS1-plusDOX-rep2


title: sh-nc1

value: transfected with sh-nc-1


title: IPEC-J2_9631-high conc._ETEC_2 hours_replica 1

description:
IPEC-J2_9631-0.01% (w/v) conc._ETEC_2h_replica 1
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
9631-E2H


title: gRNA-AAVS1-plusDOX-rep1


title: gRNA-AAVS1-minusDOX-rep4


title: sh200-2

value: transfected with sh-GDF11-2


title: gRNA-AAVS1-minusDOX-rep3

value: Glioblastoma stem cell


title: psoriatic arthritis peripheral blood sample (SAMPLE 58)

source_name: peripheral blood 58


title: psoriatic arthritis peripheral blood sample (SAMPLE 47)

source_name: peripheral blood 47


title: gRNA-AAVS1-minusDOX-rep2


title: sh200-1

value: transfected with sh-GDF11-1


title: WT_5

city: Buenos Aires

first: Lucia

middle: F

last: Franchini

address: Vuelta de Obligado 2490

country: Argentina

institute: INGEBI-CONICET

data_processing:
Reads were aligned to the mouse genome (mm10) using HISAT2
Gene expression levels were calculated using featureCounts
Differential expression analysis was done using limma with the voom method. Library sizes were normalized with the TMM methods. Weights were applied to samples. eBayes was used with robust settings (robust=TRUE).
Lowly expressed genes were filtered on minimum CPM = 0.5 and at least 3 samples,
The minimum fold change was set at 1.5 and p-value threshold at 0.01. P-values were corrected by the (Benjamini and Hochberg 1995) method.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: cochlea

extract_protocol:
Cochleas were removed, frozen on RNA-later, and RNA was harvested using the CRC protocol (Vikhe et al. 2015).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cochlea

value: post natal day 8


title: normal peripheral blood sample (SAMPLE 50)

description: normal peripheral blood sample

source_name: peripheral blood 50

value: peripheral blood


title: IPEC-J2_9631-high conc._2 hours_replica 2

description:
IPEC-J2_9631-0.01% (w/v) conc._2h_replica 2
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
9631-2Hd


title: IPEC-J2_9631-high conc._6 hours_replica 1

description:
IPEC-J2_9631-0.01% (w/v) conc._6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
9631-6H


title: IPEC-J2_9631-high conc._ETEC_6 hours_replica 1

description:
IPEC-J2_9631-0.01% (w/v) conc._ETEC_6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
9631-E6H


title: normal peripheral blood sample (SAMPLE 49)

description: normal peripheral blood sample

source_name: peripheral blood 49


title: IPEC-J2_9631-high conc._6 hours_replica 2

description:
IPEC-J2_9631-0.01% (w/v) conc._6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
9631-6Hd


title: IPEC-J2_9631-high conc._2 hours_replica 1

description:
IPEC-J2_9631-0.01% (w/v) conc._2h_replica 1
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
9631-2H


title: IPEC-J2_ETEC_6 hours_replica 3

description:
IPEC-J2_ETEC (no extract)_6h_replica 3
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
E6H

source_name: IPEC-J2_ETEC (no extract)_6h

value: ETEC (no extract)


title: 5-day p21 induction rep2

city: Stanford

first: Leighton

middle: Harrison

last: Daigh

address: 318 Campus Dr, Clark W200

department: Chemical and Systems Biology

institute: Stanford University

data_processing:
Read quality was checked using FastQC 0.11.3
RNA sequencing read alignment was performed using hisat2 and tabulated with featureCounts (subread package) against GENCODE v29 gene models
DESeq2 was used for differential analysis using 3 biological replicates
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: Normalized abundance measurements were determined for each annotated gene using DESeq2
Supplementary_files_format_and_content: Raw counts

source_name: Breast epithelial cell line

growth_protocol: MCF10-A cells expressing either mVenus-p16, mVenus-p21, or mVenus alone under a doxycycline-inducible promoter (see Constructs section for additional details) were seeded at 150,000 cells/well in a 6-well plate and cultured in cultured in phenol red-free DMEM/F12  supplemented with 5% horse serum, 20 ng/mL EGF, 10 μg/mL insulin, 500 μg/mL hydrocortisone, and 100 ng/mL cholera toxin at 37˚C and 5% CO2

extract_protocol:
RNA was extracted using Qiagen RNeasy mini kit according to manufacturer’s instructions
Library construction was performed using KAPA Stranded mRNA-Seq kit (Roche). mRNA was purified using oligo-dT beads. A-tailing was then performed, followed by dual-index 8mer adapter ligation and library amplification

treatment_protocol: Doxycycline (50 ng/ml) was added 20 hours after seeding to induce transgene expression. After 24 hours, fresh media containing doxycycline and DMSO or Torin2 (100 nM, only for mVenus-p16 cells) was added. Media was refreshed every 48 hours and cells were harvested after 5 days

tag: dox-inducible protein


title: WT_3


title: psoriatic arthritis peripheral blood sample (SAMPLE 48)

source_name: peripheral blood 48

value: male


title: gRNA-AAVS1-minusDOX-rep1

value: untreated


title: psoriasis vulgaris peripheral blood sample (SAMPLE 42)

source_name: peripheral blood 42

value: female

value: psoriasis vulgaris


title: IPEC-J2_ETEC_6 hours_replica 4

description:
IPEC-J2_ETEC (no extract)_6h_replica 4
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
E6Hd

value: IPEC-J2 cultured cells


title: IPEC-J2_ETEC_6 hours_replica 2

description:
IPEC-J2_ETEC (no extract)_6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
E6Md


title: 5-day p21 induction rep1


title: psoriatic arthritis peripheral blood sample (SAMPLE 46)

source_name: peripheral blood 46

value: psoriatic arthritis


title: WT_2


title: sh200-3

value: primary cardiomyocytes

value: transfected with sh-GDF11-3


title: WT_1


title: IPEC-J2_ETEC_6 hours_replica 1

description:
IPEC-J2_ETEC (no extract)_6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
E6M


title: 5-day p16 induction Torin2 treated rep3


title: KO_5


title: 5-day p16 induction Torin2 treated rep2


title: KO_4


title: IPEC-J2_ETEC_2 hours_replica 2

description:
IPEC-J2_ETEC (no extract)_2h_replica 2
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
E2Hd

source_name: IPEC-J2_ETEC (no extract)_2h


title: 5-day p16 induction Torin2 treated rep1


title: 5-day p16 induction rep3


title: KO_3


title: 5-day p21 induction rep3


title: KO_2


title: normal peripheral blood sample (SAMPLE 43)

description: normal peripheral blood sample

source_name: peripheral blood 43

value: normal


title: IPEC-J2_control_6 hours_replica 4

description:
IPEC-J2_culture medium (no extract or ETEC)_6h_replica 4
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
6Md

value: culture medium (no extract or ETEC)


title: IPEC-J2_ETEC_2 hours_replica 1

description:
IPEC-J2_ETEC (no extract)_2h_replica 1
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
E2H


title: 5-day p16 induction rep2


title: KO_1


title: IPEC-J2_control_6 hours_replica 3

description:
IPEC-J2_culture medium (no extract or ETEC)_6h_replica 3
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
6M


title: IPEC-J2_control_6 hours_replica 2

description:
IPEC-J2_culture medium (no extract or ETEC)_6h_replica 2
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
6Hd


title: psoriasis vulgaris peripheral blood sample (SAMPLE 45)

source_name: peripheral blood 45


title: 5-day p16 induction rep1


title: Ch12 treated with TGFb for 24 hours

city: Bethesda

first: Yongbing

last: Zhao

state: Maryland

address: 10 Center Drive RooM 13C101A

department: NIAMS

institute: National Institutes of Health

description: library: RNAch1224hTGFb

data_processing:
Base calling: Illumina CASAVA 1.8.2
mRNA-Seq: Align raw reads to the reference genome with STAR.
mRNA-Seq: Quantify transcript and gene abundances with RSEM.
mRNA-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
Genome_build: mm10

source_name: Ch12 cell line

growth_protocol: CH12 B lymphoma cells were cultured in RPMI-1640 media supplemented with 10% FBS (Gemini), 1% Penicillin-Streptomycin and 50 µM of b-mercaptoethanol (Thermo Fisher Scientific).

extract_protocol:
mRNA-seq: Total RNA was extracted from 0.5 million cultured cells using RNAqueous™ Total RNA Isolation Kit (AM1912). mRNA was then isolated using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB E7490).
mRNA-seq: Standard RNA-Seq library preparation was performed following Illumina's RNA-Seq protocol v2. 50 cycles of sequencing data.

treatment_protocol: Cultured CH12 B cells were treated with TGFb (5 ng/ml; 240-B R&D systems) for a period of 6 h or 24 h before harvesting.

value: Ch12 cell line

value: treated with TGFb for 24 hours

tag: experimental type

value: mRNA-Seq


title: 5-day mVenus induction rep3

value: mVenus


title: IPEC-J2_control_6 hours_replica 1

description:
IPEC-J2_culture medium (no extract or ETEC)_6h_replica 1
Gene expression analysis after 6 hours of incubation in IPEC-J2 cells
6H


title: WT_4

value: cochlea

value: post natal day 8


title: IPEC-J2_control_2 hours_replica 2

description:
IPEC-J2_culture medium (no extract or ETEC)_2h_replica 2
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
2Hd


title: 5-day mVenus induction rep2


title: Ch12 control

description: library: RNAch12WT

value: control


title: IPEC-J2_control_2 hours_replica 1

description:
IPEC-J2_culture medium (no extract or ETEC)_2h_replica 1
Gene expression analysis after 2 hours of incubation in IPEC-J2 cells
2H


title: C-POPs-Mix 0.5_5

city: Ottawa

first: Hyojin

last: Lee

address: 75 Laurier Ave E

department: Biology

institute: University of Ottawa

library_source: genomic

data_processing:
Microbiome profiling was performed using EZbiocloud Apps (ChunLab inc., Korea).
Taxonomic assignment was performed using ChunLab’s 16S rRNA database (DB ver. PKSSU4.0)
OUT-picking was conducted using UCLUST algorithm
PICRUSt analysis was conducted with Comparative MTP Analyzer platform
Assembly: GRCz11 (GCA_000002035.4) v99

organism: Danio rerio

source_name: Intestine

growth_protocol: Zebrafish (Danio rerio, wild-type AB strain) aged 10–12 months were maintained in a flow-through system (Tecniplast, Buguggiate, Italy) with a 14-h light/10-h dark photoperiod at a temperature of 28.5°C ± 0.5°C and pH of 7.0–7.5. The zebrafish were fed thrice daily with Gemma micro 300 (Skretting, West-brook, Maine, USA).

extract_protocol:
Total genomic DNA was extracted individually using the isopropanol method.
Amplification of genomic DNA targeting the V3–V4 region of the 16S rRNA gene was conducted using the paired primers 341F (5′-CCTACGGGNGGCWGCAG-3′) and 805R (5′-GACTACHVGGGTATCTAATCC-3′).
PCR products were sequenced using the Illumina Miseq sequencing system (Illumina Inc., USA) according to the manufacturer’s instructions.

treatment_protocol: A total of 360 zebrafish (including 180 females and 180 males) were randomly assigned to three tanks. Each tank per concentration was comprised of 15 females and 15 males. Adult zebrafish were exposed to 0.02, 0.1, 0.5 μg/L C-POPs-Mix for 12 weeks in an automatic flow-through exposure system (TOX-MIXII, Hanalab, Daejeon, South Korea).

value: Intestine

tag: Sex

value: Female

value: WT

value: 84 days


title: Thrombus scRNA-seq

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

description: GEO users can load the raw fastq-files into the BD Rhapsody WTA pipeline (access provided by BD upon request) in order to receive Mols_per_cell.csv for this single cell sample.

data_processing:
Processing of raw reads was done using the BD Rhapsody WTA Analysis Pipeline v1.0 which  takes the FASTQ files, a reference genome file (GRCm38) and a transcriptome annotation (genecodevM19) file for alignment. Molecular counts per cell generated by the pipeline were used for data analysis in Partek Flow.
Raw paired sequencing data consist of R1 and R2 file. Sample demultiplexing is done based on information from R1 that contain cell label and R2 reads that contain mRNA sequences and tag sequences. Each of R1 reads sequenced contain the cell label although not every corresponding R2 read contain tag sequence. To demultiplex samples, firstly the cell labels are annotated in order to determine putative cells. After determination of putative cells, each of cells have assigned cluster of reads R1 and associated R2 reads. Based on tag sequence in group of R2 reads assigned to cell, each cell is assigned to sample tag.    Detailed description on annotation of cell labels (step 2) and determination of putative cells (step 6) followed by determination of sample of origin (step 7) can be found in BD Single Cell Genomics Bioinformatics Handbook (GMX_BD-Rhapsody-genomics-informatics_UG_EN.pdf) Available tag sequences used for sample multiplexing can be found in Attachement_B2_SampleTagSequences_MusMusculus_ver1.fasta for Mouse.
Tregs from Thrombus were sample tagged by Sample tag 08 (BD): Sample Tag 8-- 5'-TCGCTGCCGTGCTTCATTGTCGCCGTTCTAACCTCCGATGTCTCG-3'
Genome_build: reference genome GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.

source_name: CD25+ cells enriched by positive selection (EasySep™ Mouse CD25 Regulatory T Cell Positive Selection Kit, # 18782) from day 12 thrombi (n=10)

extract_protocol:
Thrombus and vein wall tissue were mechanically disrupted and pushed through a 40µm cell strainer. Apoptotic cells were cleared from the cell suspension via the manufacturer´s instructions (EasySep™ Dead Cell Removal -Annexin V- Kit, #17899) and CD25+ cells enriched via positive selection (EasySep™ Mouse CD25 Regulatory T Cell Positive Selection Kit, # 18782).
Libraries were generated following the BD Rhapsody System mRNA WTA and Sample Tag Library Preparation protocol (BD Biosciences).

treatment_protocol: Thrombosis was induced in 8-12-week-old mice with a minimum body weight of 25 grams by ligation of the Vena Cava Inferior and all visible tributaries.

value: day 12 thrombi and vein wall tissue (multiplexed)

value: CD25+ cells


title: psoriasis vulgaris peripheral blood sample (SAMPLE 38)

source_name: peripheral blood 38

value: male

value: peripheral blood

value: psoriasis vulgaris


title: 5-day mVenus induction rep1


title: psoriatic arthritis peripheral blood sample (SAMPLE 40)

source_name: peripheral blood 40

value: psoriatic arthritis


title: C-POPs-Mix 0.5_4

tag: genotype


title: normal peripheral blood sample (SAMPLE 35)

description: normal peripheral blood sample

source_name: peripheral blood 35

value: normal


title: psoriatic arthritis peripheral blood sample (SAMPLE 37)

source_name: peripheral blood 37

value: female


title: OCILy10_MZ1_Rep3

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR
For each gene, the counts per millions have been normalized (TMM normalization, edgeR) and logged (base 2)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with log2 counts per million (CPM) for every gene and every sample

growth_protocol: All cell lines were cultured according to the recommended conditions. All media were supplemented with foetal bovine serum, penicillin-streptomycin-neomycin (5,000 units penicillin, 5 mg streptomycin and 10 mg neomycin/mL, Sigma) and L-glutamine (1%). Cell line identity was authenticated by short tandem repeat (STR) DNA profiling.

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

treatment_protocol: cells treated for 6 hours and 14 days with MZ1

tag: time point

value: 6 hrs


title: psoriatic arthritis peripheral blood sample (SAMPLE 39)

source_name: peripheral blood 39


title: C-POPs-Mix 0.5_3


title: rpf_zuo1KO_heat_shock(+)_rep2

city: Ann Arbor

first: mehmet

last: tardu

state: MI

address: 930 N University Ave

department: Chemistry

institute: University of Michigan

data_processing:
Sequencing data analysis is quite similar both for mRNA-seq and Ribo-seq data until P-site offset calculation step. Briefly, adapter contaminations and low-quality reads (quality score < Q30) were filtered out from the raw reads of mRNA-seq and Ribo-seq data using cutadapt tool.
Then, rRNA and tRNA contaminations were removed by aligning reads to the non-coding RNA (ncRNA) sequences using Bowtie2. Next, the remaining sequences, that do not align to ncRNAs, were then aligned against the transcriptome (coding RNA) of S. cerevisiae using Hisat2.
After that, perfect match alignments were extracted from alignment output. Finally, samtools was used to count the number of mapped reads for each gene from mRNA-seq data.
For further downstream analysis of Ribo-seq data, 3’- and 5’-end P-site offset values were determined using riboWaltz. These P-site offset values are required to find where ribosomes are located on each RPFs.
After P-site offset calculation, actively translating ribosomes that represent trinucleotide periodicity were identified. Then, number of mapped RPFs were counted for each codon position within a gene using samtools.
Genome_build: R64-1-1
Supplementary_files_format_and_content: raw read counts

organism: Saccharomyces cerevisiae

source_name: zuo1Δ_heat-shock stress

growth_protocol: Wild type and mutant S. cerevisiae  single colonies were selected and inoculated into the 10 mL of growth media (defined synthetic complete medium (SC) with 2% glucose) in the presence/absence of selective markers to grow overnight at 30 °C.

extract_protocol:
Total RNA from 10 mL cells at 0.6 OD600 were isolated using hot acid phenol method and treated with RNase-free DNase I to get rid of residual genomic DNA contamination. Then, quantity and quality of the RNA was assessed using Qubit Fluorometer 2.0 and Bioanalyzer RNA 6000 Pico Kit, respectively. Only the RNA samples with 28S:18S ≥ 1 and the RNA integration number (RIN) ≥ 8 were used for mRNA-seq library construction.
After quality checking, mRNA-seq libraries were prepared using TruSeq mRNA Sample Preparation Kit according to manufacturer’s instructions. First, messenger RNAs (mRNAs) were purified from 1 μg of total RNA using oligo (dT) magnetic beads followed by fragmentation of purified mRNAs using fragmentation buffer. Second, fragmented mRNAs were subjected to first strand complementary DNA (cDNA) synthesis using random hexamer-primers, and then second strand of cDNA was synthesized using DNA polymerase I and RNase H. Third, the double-stranded cDNAs were purified using AMPure XP beads, eluted with resuspension buffer, and then subjected to 3′ end adenine nucleotide addition. Finally, sequencing adaptors were ligated to the adenylated fragments and amplified with 14 rounds of PCR. Enriched cDNA libraries were used for cluster generation and sequencing. Paired-end sequencing (75 bp x 2) were carried out for two cDNA libraries (two biological replicates of each sample) using the Illumina HiSeq 4000 sequencing platform.  To prepare Ribo-seq libraries, 200 mL yeast cells were harvested and filtered using a 0.45 μM Whatman membrane using a vacuum filter apparatus. After filtration, cells were immediately scraped from the filter with a straight-edge metal spatula and plunged into 50 mL liquid nitrogen. Next, samples were grinded using Spex 6775 freezing grinding mill in the presence of 10 mL lysis buffer (20 mM Tris (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide, 1% Triton X-100, 25 U/mL DNase I). Then, RNA concentration of the cell lysates was determined using Qubit RNA HS Assay Kit with the Qubit Fluorometer 2.0. Next, 30 µg total RNA was diluted to 200 µL with polysome buffer (20 mM Tris (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide) and digested using 15 U RNase I for 45 min at room temperature. After that, 10 µL SUPERase*In RNase inhibitor was added to the samples to stop the digestion reaction. To pellet the ribosomes, samples were transferred to a 13 mm × 51 mm polycarbonate ultracentrifuge tube that contains 0.9 ml sucrose cushion (1 M sucrose in polysome buffer) and centrifuged at 70,000 rpm for 2 hours. Translucent ribosome pellets were resuspended in 300 µL polysome buffer followed by RNA purification using TRIzol reagent according to manufacturer’s instructions. Then, samples were run on 15% polyacrylamide TBE-Urea gel for 60 min at 200 V followed by gel-purification of ~20-40 nt ribosome protected footprint (RPF) fragments using 17-34 nt length oligos as markers. Next, RPFs were treated with T4 PNK in order to heal the 2′–3′ cyclic phosphate that results from RNase I cleavage. After end-healing reaction, preadenylated adapter oligos (35 nt length) were ligated to RPFs using T4 Rnl2(tr) K227Q ligase. Then, excess adapter oligos in the reaction were depleted by adding Yeast 5′-deadenylase and RecJ exonuclease enzymes directly to the ligase reaction and incubated at 30 0C for 45 min. After that, samples were purified using Oligo Clean & Concentrator kit followed by ribosomal RNA (rRNA) depletion using yeast Ribo-Zero Gold rRNA removal kit according to manufacturer’s instructions. Next, samples were reverse transcribed using Protoscript II. Then, reverse transcription products were separated from the unextended primer products by polyacrylamide TBE-Urea gel electrophoresis followed by gel-purification of the full-length reverse transcription products (80-120 nt length). Next, purified full length cDNAs were circularized using CircLigase II. Afther that, 10-15 rounds of PCR enrichment of the libraries were performed with the proper forward and reverse primers. Enriched libraries were used for cluster generation and sequencing. Single-end (50 bp) sequencing was carried out for two cDNA libraries (two biological replicates of each sample) using the Illumina HiSeq 4000 sequencing platform.

treatment_protocol: Then, cells were diluted to 0.05 OD600 with the appropriate growth media and grown until 0.6 OD600. Oxidative and heat-shock stress experiments were performed using this culture. Before stress experiments, 200 mL of cell culture was harvested and used as a control (un-stressed) to compare with stress-induced samples. To induce the oxidative stress, cells at 0.6 OD600 were treated with 0.25 mM H2O2 for 30 min at 30 °C. For heat-shock experiments cells at 30 °C were heat-shocked by adding an equal volume of fresh medium at 44 °C, to immediately reach a final temperature of 37 °C followed by incubation at 37 °C for 45 min.

tag: strain background

value: heat-shock stress

tag: molecule type

value: Ribosome protected footprints (RPFs)


title: Ch12 treated with TGFb for 6 hours

description: library: RNAch126hTGFb

tag: cell type

value: Ch12 cell line

tag: treatment

value: treated with TGFb for 6 hours

value: mRNA-Seq


title: OCILy10_MZ1_Rep2


title: C-POPs-Mix 0.5_2

value: Intestine

value: Female

tag: time


title: rpf_zuo1KO_heat_shock(+)_rep1


title: psoriatic arthritis peripheral blood sample (SAMPLE 41)

source_name: peripheral blood 41

tag: age


title: OCILy10_MZ1_Rep1


title: normal peripheral blood sample (SAMPLE 36)

description: normal peripheral blood sample

source_name: peripheral blood 36

tag: disease state


title: C-POPs-Mix 0.1_9

value: WT

value: 84 days


title: human brain EC Nox4 10MOI

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: Ad-LacZ 10MOI

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Human brain endothelial cells, initiated from normal brain cortical tissues, were purchased from Cell Systems Corporation. The cells were cultured using a CS-C complete medium kit (Cell Systems) at 37°C in 5% CO2 in a humidified incubator.

extract_protocol: Total RNAs from cells were collected by RNeasy mini kit with the RNase-free DNase set (QIAGEN).

treatment_protocol: Adenovirus harboring Nox4 (Ad-Nox4) or LacZ (Ad-LacZ, as a control) was generated using the AdMax system. Cells were transduced with Ad-LacZ or Ad-Nox4 at an MOI of 5–10 for 48 h.

value: human brain endothelial cells

tag: treatement

value: Ad-LacZ 10MOI

source_name: Ad-NOX4 10MOI

value: Ad-NOX4 10MOI


title: psoriasis vulgaris peripheral blood sample (SAMPLE 44)

source_name: peripheral blood 44

value: male

value: peripheral blood

value: psoriasis vulgaris


title: rpf_zuo1KO_control_rep2

source_name: zuo1Δ_unstressed (control)

value: unstressed (control)


title: C-POPs-Mix 0.1_8


title: C-POPs-Mix 0.5_1


title: psoriasis vulgaris peripheral blood sample (SAMPLE 31)

source_name: peripheral blood 31


title: psoriasis vulgaris peripheral blood sample (SAMPLE 34)

source_name: peripheral blood 34


title: rpf_zuo1KO_control_rep1


title: C-POPs-Mix 0.1_7