title: Mouse embryo fibroblast cell Ahi1-KO

first: Hongguang

data_processing:
DNBSEQ-500 software used for basecalling
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads  containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base  quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown  base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored  in FASTQ format. The clean reads were mapped to the reference genome using HISAT2  (v2.0.4). Bowtie2 (v2.2.5)  was applied to align the clean reads to the reference  coding gene set, then expression level of gene was calculated by RSEM (v1.2.12)
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: FPKM

source_name: Mouse embryo fibroblast cell

extract_protocol:
Mouse MEFs were prepared from the mouse embryos at day 13.5 and were cultured in Dulbecco’s modified Eagle′s medium (DMEM) supplemented with 10% FBS, and RNA was harvested using Trizol reagent. A-Tailing Mix was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard DNBSEQ protocols

value: embryo fibroblast cell


title: YAP-H3K4me1-r2

status: Public on Jan 01 2022

type: SRA

city: Dallas

first: Hongde

last: Li

state: Texas

address: 6001 Forest Park Road, Department of Physiology, ND13-510

country: USA

institute: UT Southwestern Medical Center

library_source: genomic

data_processing:
Data was analyzed using the encode chipseq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2)
Reads were trimmed using Trimmomatic (v0.39)
Fastq file were aligned to reference using bwa (samse) (v0.7.17-r1188)
Post-alignment filtering was done using SAMtools (v1.7), MarkDuplicates (Picard-v1.126) and bedtools (v2.26.0)
Bam were converted to tagAlign using bedtools (v2.26.0), gawk and shuf.
Cross-correlation QC scores were calculated using phantompeakqualtools (v1.2.1)
Jensen-Shannon distance were calculated using deeptools (v3.3.0) plotFingerprint
GC bias was calculated using CollectGcBiasMetrics (Picard, v1.126) and python packages: pandas, matplotlib
Peaks were called on replicates, self-pseudoreplicates, pooled data and pooled-pseudoreplicates using SPP (v1.14) in phantompeakqualtool (https://github.com/kundajelab/phantompeakqualtools)
IDR analysis was run on all pairs of replicates, self-pseudoreplicates and pooled pseudoreplicates using IDR (https://github.com/kundajelab/idr v2.0.4)
Fraction of Reads in Peaks was calculated using (bedtools v2.26.0)
Signal Tracks were created using MACSv2 (https://github.com/taoliu/MACS/)
Genome_build: mm10
Supplementary_files_format_and_content: bed file per group

molecule: genomic DNA

organism: Mus musculus

source_name: YAP transgenic mouse liver

growth_protocol: Mice were raised under normal condition.

extract_protocol:
Chromatin immunoprecipitations were performed with the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Cat# 9005, Cell Signaling Technology) according to the provided protocol. Micrococcal nuclease was used to digest DNA to 150-900 bp fragments.
Libraries were prepared using KAPA HTP Library Preparation Kit from Roche. The ChIP DNA was quantified on the Qubit® 4.0 Fluorimeter from ThermoFisher. Samples were then end repaired, 3' ends adenylated and barcoded with multiplex adapters. Samples were amplified with 15 cycles of PCR and then size selected with Ampure XP beads.

treatment_protocol: Inducible YAP expression in liver was achieved by addition of 50 mg/L doxycycline in drink water for 10 days.

tag: tissue

value: Liver

tag: strain

tag: chip antibody

value: H3K4me1 (Abcam, Cat# ab8895)


title: HCC siNC-4

city: Baton Rouge

first: Sonika

last: Patial

address: Baton Rouge, LA 70803

institute: Louisiana State University

description: individual  -4 knockdown of nontarget control,  tissue type liver

library_source: transcriptomic

data_processing:
Illumina Novaseq 6000 used for sequencing
Sequenced reads were trimmed for adaptor sequence by fastp, and masked for low-complexity or low-quality sequence, then mapped to huaman whole genome using STAR 2.6.1d
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from mapped read by featureCounts V1.5
Differeantial expression analysis with DEseq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample, and differential expressed gene for each comparasion

molecule: total RNA

organism: Homo sapiens

source_name: liver

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: cell type

value: hepatocellular carcinoma

tag: genotype/variation

value: control


title: MDA-MB-231-PRM75-DOX11-IP

city: xi'an

first: Wu

last: Ying

state: Shaan'xi

address: Changle west road

country: China

institute: Fourth Military Medical University

data_processing:
Library strategy: m6A-seq
reads aligned to human genome hg38 using the STAR (version 2.4.2a) with reference annotation GENCODE version 25
top 5,000 peakschosen for motif analysis with MEME
Peaks annotated by the function of annotatePeak of ChIPseeker
GO analysis  performed to facilitate elucidating the biological implications of unique genes in the significant or representative profiles of the gene in the experiment.
Pathway analysis used to find out the significant pathway of the genes according to KEGG database.
Genome_build: human genome hg38
Supplementary_files_format_and_content: wig files were generated

source_name: breast cancer cells

growth_protocol: The MDA-MB-231 cell line was  grown in L-15 medium supplemented with 10% fetal bovine serum (FBS), and 1% penicillin–streptomycin.

extract_protocol:
Total RNAs from breast cancer cells were extracted with TRIzol
The amount of 2 μl of 14 μl eluted RNA was reverse transcribed with High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific, USA). Once successfully immunoprecipitated methylated RNA was confirmed, further transcriptome-wide interrogation was pursued by deep sequencing using SMARTer Stranded Total RNA-Seq Kit version 2 (Pico Input Mammalian; 634413; Takara/Clontech, Japan) according to the manufacturer's protocol. A purified library was quantified using a Qubit Fluorometer (Thermo Fisher Scientific, USA), and the size distribution was checked using the Bioanalyzer 2100 system (Agilent Technologies, USA). The library preparations were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: MDA-MB-231 cells with or without PRMT5 overexpression were treated with or without 0.4 μg/ml doxorubicin for 24 hours.

tag: cell line

value: breast cancer cells

tag: treatment

value: parental cells overexpressed with PRMT5 under DOX treatment

tag: reference genome

value: human genome hg38


title: YAP-H3K4me1-r1


title: MDA-MB-231-PRM75-DOX11-input


title: Mouse embryo fibroblast cell WT

city: Suzhou

last: Zhang

address: Renai load 199

institute: Soochow University

tag: genotype

value: WT type


title: YAP-input


title: MDA-MB-231-DOX12-IP

value: parental cells treated with DOX


title: YAP-LSD1-r2

value: LSD1 (Cell signaling technology, Cat# 2184)


title: MDA-MB-231-DOX12-input


title: Control2

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

data_processing:
BGI internal software used to remove adpators and low quality reads.
Mapped to Mus Musculus (mm10) using HISAT
DEG assessed using DeSeq2 and NOIseq
Genome_build: mm10
Supplementary_files_format_and_content: excel file with count data and FPKM for each sample.

source_name: Intestinal tissue

growth_protocol: Female mice were 8 weeks of age, and were gavaged with water or PAC (200mg/kg, derived from grape extract) every 2nd day over a period of 28 days. Where mentioned mice were infected with 200 Hp larvae, 14 days after PAC treatment commenced.

extract_protocol:
Tissue was collected at euthanasia. Total RNA was extracted using miRNAeasy kits (Qiagen).
Standard BGI protocol.

value: Intestinal tissue

value: Water


title: WT-LSD1-r1

source_name: Wild type mouse liver


title: G-HD

city: Yiwu

first: jingjia

last: ye

state: zhejiang

address: chouzhoubeilu 1575

institute: zhejiang university

data_processing:
Reads were mapped to the mouse GrCm38 genome using Cell Ranger v.3.0.2.
Genome_build: mm10
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every cell

organism: Rattus norvegicus

source_name: primary cell derived from spinal cord

extract_protocol:
Animals (5 animals for each condition) were anesthetized deeply with chloral hydrate, and a 5-mm section of the spinal cord centered at the injury site was dissected. Then, the tissue was chopped and incubated for 30 min at 37°C with 2 ml of collagenase (1 mg/ml in PBS) and centrifuged at 300 g for 5 min at 4°C. Two milliliters of 0.25% trypsin-EDTA solution was added to pelleted cells after collagenase removal and incubated at 37°C for 5 min. FBS (10%) was added to stop the digestion by trypsin, and the supernatant was removed by centrifugation. Precipitate dispersed in PBS with 0.5% BSA was strained through a 30-µm cell strainer twice. Cells were collected by centrifugation, and 10 ml of erythrocyte lysate was added. After 10 min, the cell suspension was centrifuged, and the cells were resuspended in PBS for counting.
The single-cell suspension was then examined using the 10X Genomics Chromium Single Cell 3′ Reagent Kit v3 (10X Genomics) according to the manufacturer’s protocol.

value: spinal cord

tag: age

value: 6-8 weeks

value: wild type

value: GHD injection at injury site


title: WT-H3K4me2-r2

value: Liver

value: H3K4me2 (Abcam, Cat# ab7766)


title: snp_sample_12

type: genomic

city: Heidelberg

first: David

last: Reuss

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg

hyb_protocol: Illumina protocol

scan_protocol: Illumina scan protocol according to the manufacturer protocol

data_processing:
B allele Freuqencies & Log R ratios of X and Y Signals have been processed by using Illuminas Genome Studio  v2.0
processed data: B allele Frequencies (BAF) and Log R Ratios (LRR)

label: cy3, cy5

source_name: Oligosarcoma

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

tag: disease

value: Oligosarcoma


title: YAP-H3K4me2-r2


title: WT-LSD1-r2


title: snp_sample_11

source_name: Oligodendrogliom

value: Oligodendrogliom


title: MDA-MB-231-DOX11-input


title: MDA-MB-231-2-IP

value: parental cells


title: snp_sample_9


title: WT-H3K4me1-r2

value: H3K4me1 (Abcam, Cat# ab8895)


title: MDA-MB-231-2-input

value: breast cancer cells


title: snp_sample_10


title: snp_sample_8


title: MDA-MB-231-1-IP

value: human genome hg38


title: snp_sample_7


title: MidK2_D36_chrX

city: Tsukuba, Ibaraki

first: Ken

last: Nishimura

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly by RNA-seq analysis tool in CLC-Genomic Workbench
Valiantcall was performed using Basic Variant Call tool in CLC-Genomic Workbench.
Genome_build: mm10
Supplementary_files_format_and_content: variantcall file in text format

source_name: MEF+SeVdp(fKOSMaB); Day36

growth_protocol: MEF, and cells reprogrammed by SeVdp(fKOSMaB) with or without 30 nM Shield1

extract_protocol:
RNA was extracted by ISOGEN (NipponGene)
RNA-seq library was constructed with 500 ng of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra Directional RNA Library Prep Kit and (New England Biolabs).

tag: reprogramming vector

value: SeVdp(fKOSMaB)

tag: agent

value: 30 nM shield1

tag: time point

value: Day 36


title: WT-H3K4me1-r1


title: WT-input


title: Large ex vivo 3

city: Salt Lake City

first: Jessica

middle: CS

last: Brown

state: Utah

address: 15 N Medical Drive East

department: Pathology

institute: University of Utah

description:
16298x6
JCSBrown_RNAseq_data_Repository_2020

data_processing:
Combined reads from each of the two paired-end sequencing runs
Downloaded Cryptococcus neoformans var. grubii H99 genome and gene feature files from Ensembl Fungi release 46
Created reference database using STAR version 2.7.2c with splice junctions optimized for 150 base pair reads
Removed optical duplicates using clumpify v38.34
Trimmed reads of adapters using cutadapt 1.16
Aligned trimmed reads to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates
Assigned mapped reads to annotated genes in the gene feature file using featureCounts version 1.6.3
The output files from cutadapt, FastQC, Picard CollectRnaSeqMetrics, STAR and featureCounts were summarized using MultiQC  to check for any sample outliers
Identified differentially expressed genes using a 5% false discovery rate with DESeq2 version 1.24.0
Genome_build: Cryptococcus neoformans var. grubii H99 genome from Ensembl Fungi release 46
Supplementary_files_format_and_content: Matrix table with raw gene counts

organism: Cryptococcus neoformans

source_name: large cells sorted from infected mouse lungs

growth_protocol: The ex vivo-sorted cells were extracted from mouse lung homogenate 14 days post-inoculation. Cells were sorted from a BD FACS Aria based on forward scatter-area measurements to approximate size, with "small ex vivo cells" representing the smallest 20-25% of the population, "mid ex vivo cells" the middle 20-25%, and large ex vivo cells the largest 20-25% of the population. At least 106 ex vivo cells were isolated per sort gate for each replicate. The in vitro-grown cells were cultured in either MIN (yeast nitrogen base) medium, CAP (capsule-inducing 10% Sabouraud's buffered to pH 7.4), or CAP+CM (CAP medium supplemented with conditioned medium (CM) from cells grown in MIN medium. 107 cells were harvested from the indicated medium for each replicate.

extract_protocol:
Cells were pelleted, flash frozen in liquid nitrogen, and lyophilized. Lyophilized cells were resuspended in  TRIzol (ThermoFisher Scientific catalog no. 15596026) and vortexed with a mixture of 1-mm and 0.5mm zirconium beads (BioSpec Products catalog no. 11079110z and 11079105z) in a Biospec Products mini bead beater to lyse. RNA was isolated from the lysate using phenol-chloroform extraction, followed by Qiagen RNeasy column-based cleanup.
Libraries were constructed with the NEBNext Ultra II Directional RNA Library Prep with rRNA Depletion Kit (New England BioLabs catalog no. E7760)

tag: growth condition


title: MDA-MB-231-DOX11-IP

value: parental cells treated with DOX


title: snp_sample_6


title: WT-H3K4me2-r1


title: snp_sample_5


title: MidK2_D29_chrX

source_name: MEF+SeVdp(fKOSMaB); Day29

value: Day 29


title: Large ex vivo 2

description:
16298x3
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value: large cells sorted from infected mouse lungs


title: MidK2_D22_chrX

source_name: MEF+SeVdp(fKOSMaB); Day22

value: Day 22


title: snp_sample_2


title: Mid ex vivo 2

description:
16298x2
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source_name: medium-sized cells sorted from infected mouse lungs


title: Mid ex vivo 1

description:
16093x11
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value: medium-sized cells sorted from infected mouse lungs


title: snp_sample_4


title: MidK1_D56_chrX

source_name: MEF+SeVdp(fKOSMaB); Day56

value: Day 56


title: MidK2_D18_chrX

source_name: MEF+SeVdp(fKOSMaB); Day18

value: Day 18


title: Mid ex vivo 3

description:
16298x5
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title: pt12

city: Florence

first: Paola

last: Chiarugi

state: Florence

address: Viale Morgagni 50

department: Department of Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

data_processing:
The basecalling was performed locally by Guppy (Version 5.0.16)
The reads was filtered above a quality threshold of 7
The high-quality reads were aligned to GRCh38 with minimap2  (Version 2.17-r941) with -x map-ont parameter
The SVs were called by sniffles (Version 1.0.12) and Nano-GLADIATOR (Version 1.0)
For sniffles SVs calling we used -l 50 and -s 2 parameters while for Nano-GLADIATOR the windows size was setted to 100 Kb
Genome_build: GRCh38
Supplementary_files_format_and_content: The file_processed.tsv reports the breakpoints for each sample in a .tsv file. We reported for each sample the SVs the breakpoints of the alteration. For FIP1L1-PDGFRa deletions the Chrom1 and Chrom2 are the same while for the other SVs, defined as BND, the Chrom1 and Chrom2 are not the same as the fusion gene involved were not on the same chromosome

source_name: Whole blood

extract_protocol:
The genomic DNA (gDNA) was extracted from whole blood by Maxwell RSC Buffy Coat extraction kit
1 ug of gDNA was used for library preparation step according to 1D SQK-LSK109 Nanopore kit
The gDNA was sequenced on GridION X5 platfrom for a standard 48h sequencing run

tag: sample type

value: Sample at diagnosis


title: snp_sample_3


title: MEF2_chrX

source_name: Mouse embryonic fibroblast

value: Day 0


title: snp_sample_1

value: Oligodendrogliom


title: KD3

city: Nanjing

first: Mingtian

last: Deng

state: Jiangsu

address: Weigang No.1

department: College of Animal Science and Technology

institute: Nanjing Agricultural University

data_processing:
aligment using hisat2
bam files generated using samtools
counts genererated using featureCounts
differencially expression analysis was preformed using DESeq2
Genome_build: ars1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

organism: Capra hircus

source_name: embryos

growth_protocol: in vitro culture

extract_protocol:
direct lyse
smart-seq2

treatment_protocol: microinjection

tag: developmental stage

value: 8-cell embryos

value: knockdown group


title: MidK1_D35_chrX

source_name: MEF+SeVdp(fKOSMaB); Day35

value: Day 35


title: MDA-MB-231-1-input

source_name: breast cancer cells

tag: tissue

value: breast cancer cells

value: parental cells

value: human genome hg38


title: pt11


title: LowK_D56_chrX

value: SeVdp(fKOSMaB)


title: MidK1_D52_chrX

source_name: MEF+SeVdp(fKOSMaB); Day52

value: 30 nM shield1

value: Day 52


title: Small ex vivo 3

description:
16298x4
JCSBrown_RNAseq_data_Repository_2020

source_name: small cells sorted from infected mouse lungs

tag: strain


title: KD1


title: CAP+CM rep3

description:
16093x9
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source_name: 10% Sabourauds, pH7.4, 10% conditioned medium-grown cells


title: Small ex vivo 2

description:
16298x1
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value: small cells sorted from infected mouse lungs


title: NC3

value: negative controls


title: Small ex vivo 1

description:
16093x10
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title: KD2


title: LowK_D35_chrX


title: pt10


title: CAP+CM rep2

description:
16093x6
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value: 10% Sabourauds, pH7.4, 10% conditioned medium-grown cells


title: LowK_D52_chrX


title: pt8


title: Large ex vivo 1

description:
16093x12
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value: large cells sorted from infected mouse lungs


title: pt9


title: os1537

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

description: Lymph nodes were isolated and metastatic cells (TdTom+) were FACS sorted after 1 week of treatment or control food, respetively.

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.7.1, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mus_musculus, Ensembl, GRCm38.p5, Release_91
Supplementary_files_format_and_content: tad-delimited, raw counts

source_name: metastatic melanoma cells sorted from mouse ingluinal lymph nodes

growth_protocol: Melanoma formation was induced on the back skin of Tyr::CreERT2 BRAFV600E Ptenfl/fl mice by 4OHT application on 3 consecutive days. After 1 month the animals were divded into Control and PLX4720+PD0325901 treatment groups.

extract_protocol:
Total RNA of harvested cells was extracted by RNeasy Kit (QIAGEN) according to manufacturer's instruction
RNA libraries were prepared for sequencing using standard Illumina protocols
SmartSeq2-Picelli (https://emea.illumina.com/science/sequencing-method-explorer/kits-and-arrays/smart-seq2.html)

treatment_protocol: The mice were treated for 1 week with either control food or PLX4720+PD0325901 containing food. Subsequently, the metastatic melanoma cells were isolated (TdTom+) by FACS sorting from inguinal lymph nodes

value: mouse metastatic melanoma tumor cells

tag: source

value: isolated from inguinal lymh nodes

value: Control (no inhibitor)


title: CAP+CM rep1

description:
16093x3
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title: NC1


title: NC2


title: MEF1_chrX

value: Day 0


title: CAP rep3

description:
16093x8
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source_name: 10% Sabourauds, pH7.4-grown cells

value: 10% Sabourauds, pH7.4-grown cells


title: pt7

value: Sample at diagnosis


title: pt6


title: os1545

tag: cell type


title: NC_2 [miRNA]

type: RNA

city: Kunming

first: Jing

last: Sun

state: Yunnan

address: NO. 935,JIAO LIN ROAD

institute: Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

description: MicroRNA expression data from human platelets stimuated by PBS in vitro.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 48C on GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip2 Scanner 3000 7G

data_processing: Raw data from the generated .CEL files were imported into Affymetrix Expression Console using the RMA method.

label: biotin

source_name: human plateltes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Platelets were cultured in 1640 containing 10% fetal bovine serum, 100 U/mL penicillin, and 100 U/mL streptomycin.  Platelets were cultured in 1640 containing 10% fetal bovine serum, 100 U/mL penicillin, and 100 U/mL streptomycin

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

treatment_protocol: Platelets were isolated by Ficoll-Hypaque density gradient centrifugation Kit (Solarbio,China,P6390, ). Cells were then adjusted to the concentration of 1×106/ml and incubated for 2h at at 24℃ and 5% CO2 with the 1ml/1×106 cells EBV-containing supernatant of the B95.8 marmoset cell line in vitro.

tag: tissue/cell type

value: platelets


title: CAP rep2

description:
16093x5
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title: pt4


title: pt5


title: NC_3 [miRNA]


title: os1562


title: os1540


title: pt2


title: os1488


title: pt1


title: CAP rep1

description:
16093x2
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title: MIN rep3

description:
16093x7
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source_name: Yeast nitrogen base-grown cells

value: Yeast nitrogen base-grown cells


title: Cocultured stem cells at day 6

status: Public on Dec 31 2021

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

description: Single cell RNA-seq of cocultured stem cells day 6.

data_processing:
Fastq files were generated using bcl2fastq (version 2.20.0.422).
Demultiplexing and counting sequences were performed using Cellranger (version 6.0.1) with mouse reference dataset (refdata-gex-mm10-2020-A) provided by 10x Genomics.
Cells were decomposed and clustered using Seurat (version 4.0).
Genome_build: mm10
Supplementary_files_format_and_content: loupe and plain text

source_name: PrES, ES and TS cells

growth_protocol: ESCs and PrESCs were dissociated to single cells by incubation with 1x TrypLE™ Select at 37℃ for 5 min. Cells were washed with NDiff227 medium twice, counted using haemocytometer, and suspended to the EP formation medium: NDiff227 with103U/ml ESGRO LIF, 3μM CHIR99021, 25ng/ml PDGF-AA, 1×penicillin-streptomycin. 2.1×104 ESCs and 3.5×104 PrESCs in 3ml of EP formation medium were added to a well of AggreWell plate (7000 microwells/well, 3 ESCs/microwell and 5 PrESCs/microwell). The AggreWell plate was kept allowing cells to precipitate by gravity and was placed at 37℃ and 5% CO2 for 24 hours to form EP structures. After 24 hours, TSCs maintained in the serum TS medium were dissociated to single cell by incubation with 1x 0.05% trypsin-EDTA at 37℃ for 5 min. Cells were washed with 20% FBS/RPMI1640 medium twice, counted using haemocytometer, and suspended to the ETP formation medium: NDiff227/MEF-conditioned 20% FBS/RPMI1640(1:1) with 103U/ml ESGRO LIF, 3μM CHIR99021, 25ng/ml human PDGF-AA, 12.5ng/ml human FGF4, 1ng/ml heparin (Sigma), and 25ng/ml human PDGF-AA (R&D), 1×penicillin-streptomycin, 0.1mM β-ME. The EP formation medium was largely removed by gently aspiration and 1.4×105 TSCs in ETP formation medium were added to a well of the plate (20 TSCs/microwell). The AggreWell plate was kept allowing cells to precipitate by gravity and was placed at 37℃ and 5% CO2 for 2 days to form EP structures. After 2 days, The ETP formation medium were largely removed by gently aspiration and 3ml of ETP differentiation medium: RPMI1640/DMEMF12/Neurobasal(2:1:1) with 10% FBS, 0.5×N2, 0.5×B27, 12.5ng/ml FGF4, 1ng/ml heparin, 1×sodium pyruvate, and L-glutamine. The AggreWell plate was placed at 37℃ and 5% CO2 for 3 days to differentiate ETP structures.

extract_protocol:
For scRNA-seq analysis with the 10X genomics chromium, single cell libraries were prepared an the 10x Choromium with a target of 9000 cells. Chromium Next GEM Single Cell 3’GEM, Library & Gel Bead Kit v3.1 (10x Genomics) was used.
All single-cell RNA-sequencing was performed with a NextSeq 2000 (Illumina).

value: PrES+ES+TS

tag: day

value: PrES:CD1, ES:B6N129X1F1, TS:CD1


title: pt3


title: MIN rep2

description:
16093x4
JCSBrown_RNAseq_data_Repository_2020


title: NC_1 [miRNA]


title: EBV_2 [miRNA]

description: MicroRNA expression data from human platelets infected by EBV in vitro.

source_name: human plateltes infected by EBV

tag: treatment

value: infected by EBV


title: EBV_3 [miRNA]


title: os1487


title: Cocultured stem cells at day 3

description: Single cell RNA-seq of cocultured stem cells day 3.


title: Cocultured stem cells at day 0

description: Single cell RNA-seq of cocultured stem cells.


title: grains, WT30, 3

city: Zhengzhou

first: Dongyun

last: Ma

address: No.15 Longzihu College Park,Zhengzhou New District,Zhengzhou

institute: Henan Agricultural University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > 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. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Genome_build: IWGSC 45
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Triticum aestivum

source_name: grains

extract_protocol:
Grains were crashed quickly on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Wild type-Zhoumai22

value: immature grain

value: 30 days after anthesis

tag: phenotype

value: wild type


title: grains, HP30, 2

value: High antioxidant activity


title: grains, WT30, 2


title: grains, WT30, 1


title: grains, WT20, 3

value: 20 days after anthesis


title: grains, WT20, 2


title: grains, WT20, 1


title: MIN rep1

description:
16093x1
JCSBrown_RNAseq_data_Repository_2020


title: grains, HP30, 1


title: D12 forebrain organoids mixed / B6.129 background

city: New York

first: Daniel

last: Medina Cano

email: medinacd@mskcc.org, dmcdmc156@gmail.com

state: New York

address: 411E 67th St

department: Developmental Biology

institute: MSKCC

data_processing:
Fastq files were converted into matrix of counts per cell with CellRanger (10xGenomics cloud)
Matrix of cells was QCd using CellBender (doi: https://doi.org/10.1101/791699)
Resulting matrix ("cleared" folder) was used as starting point for Seurat analyses (Rstudio, v4 Seurat - doi: 10.1016/j.cell.2021.04.048), where cells with more than 10% mitochondrial reads were excluded
Genome_build: mm10
Supplementary_files_format_and_content: Seurat object (Seurat.rds) and cleared_feature_bc_matrix folder with matrix
Seurat file used for all analyses, already clustered and Qced
Cells included in the analyses after CellBender

source_name: Organoid

growth_protocol: For forebrain organoid generation, EpiSC colonies were detached using Collagenase IV (0.1 u/μL), washed once with PBS-/-, and then dissociated into a single cell suspension using Accutase. EpiSCs were then seeded at 1,000 cells/microwell in an Aggrewell plate in EB formation media containing 50 nM chroman-1, 5 μM emricasan, 100 nM LDN, 10 μM SB431542, 100 nM PD173074 and 100 nM LGK974 in N2B27 (B27 without vitamin A) media. After 24h, the EBs were recovered and transferred to the same media but without chroman-1 and emricasan and embedded in Matrigel as previously described (Qian et al., 2018). Briefly, 66.7 μL of EBs + media were mixed with 100uL of Matrigel using wide-bore tips. The mix was added to a non-adherent 6-well plate without touching the edges of the well and incubated at 37C for 30min. After 30 min, 3mL of warm media were added on top. At day 2, the media was changed to plain N2B27 (B27 without vitamin A) with 100 ng/mL Fgf8b and kept for 48 h more. Day 4 EBs were recovered from Matrigel using cell recovery solution (Corning) and incubating for 30 min at 4C. After day the EBs were transferred to a Petri dish and kept in N2B27 (B27 Supplement with vitamin A) with BDNF and GDNF while shaking at 65 rpm (Infors HT, Celltron benchtop shaker).

extract_protocol:
Accutase dissociation, followed by scRNA-seq (10x Genomics, Single Cell 3' Kit v3.1, dual index), following the manufacter's guidelines - 9,000 cells were aimed in a single run
scRNA-seq (10x Genomics, Single Cell 3' Kit v3.1, dual index), following manufacter's guidelines

value: EpiSC-derived forebrain organoids


title: grains, HP20, 2


title: EBV_1 [miRNA]


title: grains, HP30, 3


title: grains, HP20, 3


title: grains, HP20, 1


title: Igf2bp2_IP_rep3

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Sequencing reads were aligned to the mouse genome (mm9; NCBI Build 37) using  bowtie2 (Langmead and Salzberg, 2012) with default parameters. Transcript abundance based on NCBIM37.67 annotations was determined using HTSeq (Anders et al. 2015) in “union” mode.  Differential enrichment and count normalization were performed using DESeq (Anders and Huber, 2010). Only differentially enriched (p<0.05) transcripts with an absolute read pileup >10 in the Igf2bp2 IP and with at least 2-fold enrichment over controls were retained as enriched.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files containing HTseq output for each sample

growth_protocol: 1x10^7 day 6 differentiated scWAT adipocytes were harvested.

extract_protocol:
Cell lysate was incubated with Igf2bp2, IgG, or no antibody, and interactors were captured using protein A/G beads (Santa Cruz). Captured RNAs were isolated using Trizol.
Sequencing libraries were prepared using a SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio), pooled, and sequenced on an Illumina HiSeq platform.

treatment_protocol: RNA coimmunprecipitation was done as described (Rinn et al., 2007). Cells were lysed and mechanically sheared using a dounce homogenizer.

value: subcutaneous (inguinal) white adipose tissue

value: day 6 differentiated

tag: antibody

value: anti-IGF2BP2 (Abcam, Ab151463)


title: Igf2bp2_IP_rep2


title: Igf2bp2_IP_rep1


title: MSC5 Cont

city: Tokyo

first: Sanshiro

last: Kanazawa

address: 7-3-1, Hongo, Bunkyo-ku

department: Oral and Maxillofacial Surgery

institute: The University of Tokyo Hospital

description: Gene expression data from bone marrow derived MSCs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 High-Resolution

data_processing: Affymetrix GeneChip Command Console Software (AGCC)

source_name: Mus musculus MSCs after cocultured without HSC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip 3’IVT Express Kit User Manual, 2002, Affymetrix).

growth_protocol: C57BL/6JJcl mice (6 weeks old) were purchased from CLEA Japan, Inc. (Tokyo, Japan).The mice were kept under specific pathogen–free conditions in our animal facility at the University of Tokyo.

extract_protocol: When the MSCs were cocultured with HSCs for 6 days, total RNA was extracted with TRI reagent following the manufacturer's instructions (Sigma-Aldrich Co. LLC, MA, US).

treatment_protocol: Sca-1+, Pdgfr-α+ cells (MSC) and Lin-, Sca-1+ and c-Kit+ cells (HSC) derived from mice bone marrow were used. For co-culture,  3.0 × 103 of MSCs and 7.0 × 103 of HSCs were cultured in 12-well dishes with IMDM containing 20% FBS. In the case of direct co-culture, MSCs are seeded and cultured on the plate at 37°C for 24 hours, and then HSC or KG-1 is seeded. In the case of indirect co-culture, MSCs are seeded on the bottom of transwells, and cultured at 37°C for 24 hours, and then HSCs are seeded on the inserts. The co-culture was  6 days, and both cells were harvested at the point. The harvested cells were subjected to cell counting by fluorescence microscopy (leica microsystems).

value: C57BL6/J, 6 weeks old, male, bone marrow


title: IgG_ctrl_IP_rep1


title: IgG_ctrl_IP_rep3


title: IgG_ctrl_IP_rep2


title: MSC4 Cont


title: MSC2 Cont


title: MSC5 Assay

source_name: Mus musculus MSCs after cocultured with HSC


title: MSC3 Assay


title: MSC6 Assay


title: Peritoneal Cell, LPS 40h, rep 1

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

country: France

institute: TAGC INSERM U1090

description: Gene expression from peritoneal cell after 40h LPS

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl/Sample containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl/Sample of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The slides were scanned with The Agilent Microarray Scanner®. Visualization and results were retrieved using Feature Extraction® software

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

source_name: Peritoneal Cell, LPS 40h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Peritoneal cell are extract after PBS injection, Total RNA was extracted using the RNeasy extraction mini kit

treatment_protocol: Mouse are injected in peritoneum or not with 200 μL (35 mg/kg) of lipopolysaccharide from Pseudomonas aeruginosa

tag: gender

value: Female

tag: age

value: 9-10 weeks

value: LPS 40h

value: Peritoneal Cell


title: Peritoneal Cell, LPS 40h, rep 4


title: Peritoneal Cell, LPS 40h, rep 2


title: MSC3 Cont


title: Peritoneal Cell, LPS 1h, rep 2

description: Gene expression from peritoneal cell after 1h LPS

source_name: Peritoneal Cell, LPS 1h

value: LPS 1h


title: Peritoneal Cell, LPS 1h, rep 1


title: Peritoneal Cell, control, rep 3

description: Gene expression from peritoneal cell

source_name: Peritoneal Cell, control

value: control


title: Peritoneal Cell, LPS 1h, rep 3


title: MSC6 Cont


title: Peritoneal Cell, control, rep 2

description: Gene expression from peritoneal cell


title: MSC4 Assay


title: Peritoneal Cell, LPS 1h, rep 4


title: Peritoneal Cell, LPS 40h, rep 3


title: Peritoneal Cell, control, rep 4

description: Gene expression from peritoneal cell


title: No_Ab_ctrl_IP_rep2


title: No_Ab_ctrl_IP_rep3


title: Peritoneal Cell, control, rep 1

description: Gene expression from peritoneal cell


title: No_Ab_ctrl_IP_rep1


title: lncRAP2_odd_probes_rep3

data_processing:
Sequencing reads were aligned to the mouse genome (mm9; NCBI Build 37) using  bowtie2 (Langmead and Salzberg, 2012) with default parameters. Mapped reads across biological replicates were merged using samtools (Li et al 2009). Peak calling was performed on uniquely-mapped reads relative to input control using MACS (Zhang et al. 2008) with default parameters and “--bw=300 --mfold 10 30”.  Peak coverage was quantified using BEDTools (Quinlan and Hall 2010), and only peaks with an average per-base coverage greater than 10 reads were retained. Then only peaks with a read density enrichment at least 2-fold greater than the background model and with an absolute read pileup >10 were considered enriched. Finally, peaks in the experimental sample overlapping with peaks in the input control were excluded from further analysis. Peaks satisfying these criteria were considered high-confidence peaks.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files containing MACS output (filtered peaks) in BED format

growth_protocol: 1x107 day 6 differentiated scWAT adipocytes were harvested

extract_protocol:
Total RNA was isolated using Trizol, with 10% taken as input RNA control. Biotinylated lncRAP2-targeting probes were hybridized and retrieved using Dynabeads MyOne Streptavidin C1 magnetic beads (Life Technologies). Captured RNAs were isolated using Trizol.
Sequencing libraries were prepared using a SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio), pooled, and sequenced on an Illumina HiSeq platform.

treatment_protocol: RIA-seq was conducted as described (Chu et al., 2011; Kretz et al., 2013). Cells were crosslinked with 1% Glutaraldehyde and lysates were sonicated in a Bioruptor (Diagenode).


title: lncRAP2_even_probes_rep3


title: lncRAP2_odd_probes_rep2


title: lncRAP2_even_probes_rep1


title: Input_RNA_rep1


title: Input_RNA_rep3


title: lncRAP2_odd_probes_rep1


title: Input_RNA_rep2


title: MSC2 Assay


title: MSC1 Assay


title: MSC1 Cont


title: KO-Gly-2 [RNA-seq]

city: Wuhan

first: Haoran

last: Liu

state: Hubei

address: Jiefang avenue 1095

department: Urology

institute: Tongji Hospital

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

source_name: kidney

growth_protocol: All animals were raised in the Animal Facilities of Tongji Hospital under pathogen-free conditions according to the "NIH Guide for the Care and Use of Laboratory Animals".

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

treatment_protocol: Each mouse was intraperitoneally injected with saline or glyoxylate acid (Gly) (75 mg/kg/d, 200 μl) from day 1 to day 7. Animals were euthanized after 7 days, and kidney samples were collected at the time of euthanasia.

value: kidney

value: intraperitoneally injected with glyoxylate acid

tag: genotype


title: KO-Ctrl-5 [RNA-seq]

value: intraperitoneally injected with saline


title: KO-Gly-6 [RNA-seq]


title: KO-Gly-4 [RNA-seq]


title: KO-Gly-5 [RNA-seq]


title: KO-Gly-1 [RNA-seq]


title: KO-Ctrl-6 [RNA-seq]


title: KO-Gly-3 [RNA-seq]


title: KO-Ctrl-4 [RNA-seq]


title: KO-Ctrl-3 [RNA-seq]


title: Mice inoculated with gut microbiota from healthy controls, rep 3

city: Chongqing

first: Anna

address: 1 Youyi Road, Yuzhong Dist.

institute: Chongqing Medical University

description: miRNA expression after inoculating with gut microbiota from healthy controls

hyb_protocol: miRNAs were hybridized on the miRCURY™ LNA Array (v.18.0) and incubate at 95°C for 2 min. After hybridization, disassembled the hybridization assembly, and wash the slides at 56℃ for 2min. using Wash buffer

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. We use Median Normalization Method to obtain “Normalized Data”, Normalized Data= (Foreground-Background)¬/¬median, the median is 50 percent quantile of microRNA intensity which is larger than 30 in all samples after background correction. After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test.

source_name: Hippocampus of mice inoculated with gut microbiota from healthy controls

label_protocol: miRNAs were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit  and incubate 30 min.at 37℃

extract_protocol: Total RNA was harvested using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions. After having passed RNA quantity measurement using the NanoDrop 1000

value: Hippocampus

value: male


title: KO-Ctrl-2 [RNA-seq]


title: lncRAP2_even_probes_rep2

tag: time point


title: Mice inoculated with gut microbiota from major depressive disorder patients, rep 3

description: miRNA expression after inoculating with gut microbiota from major depressive disorder patients

source_name: Hippocampus of mice inoculated with gut microbiota from major depressive disorder patients


title: KO-Ctrl-1 [RNA-seq]


title: Mice inoculated with gut microbiota from major depressive disorder patients, rep 1

value: inoculating with gut microbiota from major depressive disorder patients


title: Mice inoculated with gut microbiota from healthy controls, rep 1

value: inoculating with gut microbiota from healthy controls


title: Mice inoculated with gut microbiota from healthy controls, rep 2


title: WT-Gly-5 [RNA-seq]

value: wild type


title: WT-Gly-6 [RNA-seq]


title: WT-Gly-4 [RNA-seq]


title: WT-Gly-2 [RNA-seq]


title: WT-Ctrl-4 [RNA-seq]


title: WT-Ctrl-5 [RNA-seq]


title: WT-Ctrl-6 [RNA-seq]


title: WT-Gly-3 [RNA-seq]


title: Mice inoculated with gut microbiota from major depressive disorder patients, rep 2


title: WT-Ctrl-3 [RNA-seq]


title: WT-Ctrl-2 [RNA-seq]


title: WT-Ctrl-1 [RNA-seq]


title: Not stimulated - CBLB KO - Replicate 1

city: Toronto

first: Pamela

last: Ohashi

state: Ontario

address: 610 University Ave

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
FASTQ files were mapped using STAR v2.5.2 aligner with transcript coordinates from GENCODE release M19 using mouse genome GRCm38 (mm10)
Reads were summarized per transcript using RSEM v1.3.0 (35) using the Gencode transcript coordinates.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files containing per-gene raw counts for each sample, and for all samples combined, with one Ensembl gene id per row.

source_name: CD8+ T-cells

extract_protocol:
RNA was extracted from stimulated T cell (>99% CD8+ purity) using RNeasy Mini Kit (CAT# 74104, Qiagen) according to established instructions.
After quantity and quality assessment using Agilent Bioanalyzer RNA Nano 6000 Kit (CAT# 5067-1511, Agilent) and Qubit BRRNA kit (CAT# Q10210, Thermo Fisher Scientific), RNA libraries were prepared by removing ribosomal RNA using the TruSeq Stranded Total RNA kit (CAT# 20020596, Illumina).
After cDNA preparation, the paired-end libraries were sequenced on NextSeq 500 (Illumina) using 100 bp protocol.

value: CBLB Knockout


title: Not stimulated - CBLB WT - Replicate 1

value: CBLB WT


title: Not stimulated - CBLB WT - Replicate 3


title: 12 hours stimulation - CBLB WT + anti-CD3 anti-CD28 stimulation - Replicate 3

tag: stimulation

value: anti-CD3 + anti-CD28


title: Not stimulated - CBLB KO - Replicate 2


title: Not stimulated - CBLB KO - Replicate 3


title: 12 hours stimulation - CBLB WT + anti-CD3 stimulation - Replicate 3


title: 12 hours stimulation - CBLB WT + anti-CD3 stimulation - Replicate 1


title: WT-Gly-1 [RNA-seq]


title: 12 hours stimulation - CBLB WT + anti-CD3 stimulation - Replicate 2


title: 12 hours stimulation - CBLB KO + anti-CD3 anti-CD28 stimulation - Replicate 3


title: 12 hours stimulation - CBLB KO + anti-CD3 anti-CD28 stimulation - Replicate 1


title: 12 hours stimulation - CBLB KO + anti-CD3 anti-CD28 stimulation - Replicate 2


title: 12 hours stimulation - CBLB KO + anti-CD3 stimulation - Replicate 1


title: 12 hours stimulation - CBLB KO + anti-CD3 stimulation - Replicate 2


title: 12 hours stimulation - CBLB KO + anti-CD3 stimulation - Replicate 3


title: Not stimulated - CBLB WT - Replicate 2


title: MDA-MB-231 D_1

city: Freiburg

first: Maria

middle: Elena

last: Hess

address: Breisacherstr. 153

department: Institute for Medical Bioinformatics and Systemsmedicine

institute: Universitaetsklinikum Freiburg

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 hg19 or mm10 whole genome using Kallisto with the parameter --plaintext.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample.

source_name: human triple-negative breast cancer cells (source: ATCC®; HTB-26™)

growth_protocol: Cells were cultured in DMEM high glucose, pyruvate supplemented with 10% fetal bovine serum, 1% Penicillin/Streptomycin and 1% L-Glutamine at 37 °C with 5% CO2 and 21% O2. Cells were seeded 16 h beforethe first RNA isolation (T0). Remaining plates were treated with BKM at EC50 or DMSO as solvent control for 3 h following second extraction.

extract_protocol:
RNA was isolated using the Universal RNA Purification Kit (E3598; Roboklon) incorporating a DNA digestion step using the RNase-Free DNase Set (79254; Qiagen). RNA quantity, integrity, and quality was measured using a Bioanalyser. RNA was diluted in RNAse-free H20 to obtain 40 µl of 40 ng/ml RNA and was prepared according to the DKFZ manual.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were untreated before the first extraction (T0). Plates were treated with BKM at EC50 or DMSO as solvent control for 3 h before the second extraction.

value: DMSO 1:38461.5 diluted Replicate 1

tag: medium

tag: cell line


title: MDA-MB-231 BKM_3

value: 1300 nM BKM (EC50) Replicate 3

value: DMEM high glucose, pyruvate supplemented with 10% fetal bovine serum, 1% Penicillin/Streptomycin and 1% L-Glutamine


title: MDA-MB-231 M_1

value: only Medium (T0) Replicate 1


title: MDA-MB-231 D_3

value: DMSO 1:38461.5 diluted Replicate 3


title: MDA-MB-231 BKM_2

value: 1300 nM BKM (EC50) Replicate 2


title: MDA-MB-231 M_3

value: only Medium (T0) Replicate 3


title: MCF7 D_3

source_name: human luminal A breast cancer cells (source: ATCC®; HTB-22™)

value: DMSO 1:250000 diluted Replicate 3


title: MDA-MB-231 D_2

value: DMSO 1:38461.5 diluted Replicate 2


title: 12 hours stimulation - CBLB WT + anti-CD3 anti-CD28 stimulation - Replicate 2


title: MCF7 BKM_2

value: 200 nM BKM (EC50) Replicate 2


title: MCF7 M_3


title: MCF7 BKM_1

value: 200 nM BKM (EC50) Replicate 1


title: MCF7 D_2

value: DMSO 1:250000 diluted Replicate 2


title: MCF7 D_1

value: DMSO 1:250000 diluted Replicate 1


title: MCF7 M_2

value: only Medium (T0) Replicate 2


title: gi-60s-2

city: wuhan

first: wu

middle: xiao

last: man

address: Donghu South Road

institute: Institute of Hydrobiology, Chinese Academy of Sciences

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GCGD:Grass Carp Genome Database http://bioinfo.ihb.ac.cn/gcgd/php/index.php?page=download
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Ctenopharyngodon idella

source_name: grass carp

extract_protocol:
Gills were removed, flash-frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X).First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: tissue

value: gill

value: three months

value: grass carp were cultured at saline-  alkali water with the concentration   of 6%

tag: health condition

value: the body of grass carp was injured


title: gi-60s-1

value: grass carp were cultured at saline-alkali water with the concentration of 6%


title: gi-30s-1

value: grass carp were cultured at saline-alkali water with the concentration of 3%


title: gi-60-1

value: healthy


title: gi-60-3


title: gi-30s-3


title: gi-30s-2


title: MDA-MB-231 M_2

value: DMEM high glucose, pyruvate supplemented with 10% fetal bovine serum, 1% Penicillin/Streptomycin and 1% L-Glutamine


title: gi-30-3


title: gi-60-2


title: MDA-MB-231 BKM_1

value: 1300 nM BKM (EC50) Replicate 1


title: gi-30-2


title: gi-30-1


title: MCF7 BKM_3

value: 200 nM BKM (EC50) Replicate 3


title: gi-con-1

value: untreated


title: gi-con-3


title: TMP_T_2

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

data_processing:
After merging mutiple files,  alignment (with HISAT2 2.2.0) and quantification (default parameters) of RNAseq reads were performed using the nf-core/rnaseq version 3.3 pipeline available at https://github.com/nf-core/rnaseq (Ewels et al, 2020).
Genes with multiple loci were excluded from the analysis and only protein-coding genes were further analyzed.
The reads were summarized use featureCounts function in Rsubread version 2.0.1.
For downstream data transformation, filtering and normalization, the default methods of the anota2seq R package were used (Oertlin et al, 2019).
Analysis of changes in mRNA abundance and  translational efficiencies leading to altered protein levels or buffering was carried out with anota2seq using default parameters (biological replicate was used as a batch effect in anota2seq) of the anota2seqRun function (Oertlin et al, 2019). This was implemented for the following contrasts: no PABP vs PABP.
Genome_build: GRCh38
Supplementary_files_format_and_content: The processed data files include gene symbols, RNA sequencing counts and anota2seq normalized expression levels.

source_name: PABPC1DHFR HeLa cells

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 50 U/mL penicillin, and 50 µg/mL streptomycin.

extract_protocol:
Gradient fractions corresponding to >3 associated ribosomes were collected and RNA was extracted using TRIzol reagent
Biological triplicate libraries were prepared from total cytoplasmic or heavy polysome RNA fractions

treatment_protocol: Cells were seeded in a 15-cm dish and cultured in the presence or absence of TMP for 12 hours, at which point they reached 80% confluency.Three biological replicates were generated and polysome-profiling was performed as previously described (Gandin et al. 2014).

value: PABPC1DHFR HeLa cells

tag: rna

value: Cytosolic

tag: replicate

tag: pabp expression

value: PABP


title: non-enhnaced epiF3 [Epi15_P1]

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

data_processing:
Raw sequencing reads were quality-controlled and trimmed with TrimGalore (version 0.4.1)
Alignments were performed using STAR (version 2.7.3a) with –twopassMode = Basic and –outFilterMultimapNmax = 1  parameters  (Grant et al., 2011)
The read count data were generated from the BAM files by using QoRTs software package (Hartley and Mullikin, 2015) --minMAPQ 25
edgeR (version 3.26.8) was used to calculate the differential expression.
Genome_build: Sorghum bicolor reference genome build NCBIv3
Supplementary_files_format_and_content: Text file with GENEID and COUNTS formatted for DESeq

organism: Sorghum bicolor

source_name: Tx430 genetic background

growth_protocol: Sorghum seeds were grown under greenhouse condition at 28℃ (day) / 22℃ (night), and 14-hour day  length.

extract_protocol:
Total RNA from each sample was extracted by NucleoSpin RNA Plant kit (Macherey-Nagel, Germany) following manufacturer’s protocol, including genomic DNA removal.
RNA libraries were constructed as described in the TruSeq RNA Sample Preparation v2 Guide.

treatment_protocol: 3 biological replicated of epiF3 non-enhanced (Epi15) and 2 biological replicates of EpiF3 enhanced (Epi68) lines were sequenced. Young leaves of 4-weeks old plants were flash freezed in liquid nitrogen. Tissues were ground by motor and pestle in liquid nitrogen.

tag: replicate type

value: biological rep 1

value: Young leaf tissue

tag: developmental stage

value: 4-week-old plants

tag: genotype/variation

value: non-enhnaced epiF3


title: non-enhnaced epiF3 [Epi15_P3]

value: biological rep 3


title: enhanced epiF3 [Epi68_P1]

value: enhanced epiF3


title: gi-con-2

value: gill

value: three months

tag: treatment


title: enhanced epiF3 [Epi68_P3]

value: biological rep 2


title: TMP_P_3

tag: cell type

value: Polysome associated


title: gi-60s-3

value: grass carp were cultured at saline-  alkali water with the concentration   of 6%

value: the body of grass carp was injured


title: MCF7 M_1

value: only Medium (T0) Replicate 1

value: DMEM high glucose, pyruvate supplemented with 10% fetal bovine serum, 1% Penicillin/Streptomycin and 1% L-Glutamine


title: non-enhnaced epiF3 [Epi15_P2]


title: TMP_T_3

value: PABPC1DHFR HeLa cells


title: TMP_P_2


title: TMP_P_1


title: TMP_T_1

value: Cytosolic


title: noTMP_T_2

value: No PABP


title: noTMP_P_1


title: PyB6-313 D_3

source_name: murine epithelial breast cancer cells from the MMTV-PyMT mouse model (source: Reinheckel lab)

value: DMSO 1:33333.33 diluted Replicate 3


title: PyB6-313 D_1

value: DMSO 1:33333.33 diluted Replicate 1


title: noTMP_T_3


title: noTMP_T_1


title: noTMP_P_2


title: noTMP_P_3


title: PyB6-313 D_2

value: DMSO 1:33333.33 diluted Replicate 2


title: PyB6-313 M_3

value: only Medium (T0) Replicate 3


title: PyB6-313 BKM_3

value: 1500 nM BKM (EC50) Replicate 3


title: PyB6-313 BKM_2

value: 1500 nM BKM (EC50) Replicate 2


title: PyB6-313 BKM_1

value: 1500 nM BKM (EC50) Replicate 1


title: PyB6-313 M_1


title: PyB6-313 M_2

value: only Medium (T0) Replicate 2


title: IV2_ASD

city: Pittsburgh

first: Polakit

last: Teekakirikul

address: 530 45th street 8120 Rangos Research Center

institute: university of pittsburgh

description: Genomic DNA extracted from samples was genotyped using Illumina Human Infinium Omni2.5-8 v1.11 BeadChip (Illumina).

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina protocol

data_processing:
High density genotyping was performed using the Illumina Omni2.5-8 v1.3 BeadChip SNP Array.  The genotype data generated comprising ~2.3 million SNP markers underwent quality control,  filtering criteria and genotype error checking. We removed SNPs with MAF <0.01, call genotyping  rate <99%, Hardy-Weinberg equilibrium p value <0.00001, duplicated locus, and being on nonautosome and chromosome 6:28477796-33448353. In addition, SNPs with missing locus  frequency in public database, existence of multiple alleles (>2) and high linkage disequilibrium  (LD) were eliminated. Using MERLIN (21), parametric linkage analysis under autosomal  dominant model with a penetrance of 1 and mutant allele frequency of 0.0001, and nonparametric  linkage analysis were both implemented on a set of SNP genotypes. Focusing on candidat.gze linkage  regions, haplotypes were constructed using MERLIN.
Processed data includes: Genotype and GC score

label: Atrial septal defect

source_name: Atrial septal defect

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from blood samples was genotyped using Infinum Omni 2.5-8 v1.3 Genotyping BeadChips (Illumina).

tag: gender

value: Female

value: Blood

tag: disease state

value: Atrial septal defect


title: V2_ASD

description: Genomic DNA extracted from samples was genotyped using Illumina Human Infinium Omni2.5-8 v1.13 BeadChip (Illumina).


title: IV5_ASD

description: Genomic DNA extracted from samples was genotyped using Illumina Human Infinium Omni2.5-8 v1.12 BeadChip (Illumina).

value: Male


title: V3_Healthy

description: Genomic DNA extracted from samples was genotyped using Illumina Human Infinium Omni2.5-8 v1.6 BeadChip (Illumina).

label: Healthy

source_name: Healthy

value: Healthy


title: III2_Healthy

description: Genomic DNA extracted from samples was genotyped using Illumina Human Infinium Omni2.5-8 v1.10 BeadChip (Illumina).


title: IV1_Healthy

description: Genomic DNA extracted from samples was genotyped using Illumina Human Infinium Omni2.5-8 v1.8 BeadChip (Illumina).


title: V4_ASD

description: Genomic DNA extracted from samples was genotyped using Illumina Human Infinium Omni2.5-8 v1.4 BeadChip (Illumina).


title: VI2_ASD

description: Genomic DNA extracted from samples was genotyped using Illumina Human Infinium Omni2.5-8 v1.5 BeadChip (Illumina).


title: VI1_ASD

description: Genomic DNA extracted from samples was genotyped using Illumina Human Infinium Omni2.5-8 v1.3 BeadChip (Illumina).


title: III3_ASD

description: Genomic DNA extracted from samples was genotyped using Illumina Human Infinium Omni2.5-8 v1.9 BeadChip (Illumina).


title: ampWMCs

city: College station

first: Ling

last: Yu

state: TX

address: 588 Raymond Stotzer Pkwy

institute: TAMU

data_processing:
Mapping of reads to transcripts and cells
Quality control
Genome_build: mm10
Supplementary_files_format_and_content: Barcodes, Genes and Matrix files are the output of the 10X pipeline.

source_name: Outbred CD1 digit amputation wound 4 days post-amputation, 18 digits

growth_protocol: ampWMCs are passage 1 primary cultures of cells isolated from neonatal non-regenerative digit amputation wounds. Cells were cultured on fibronectin coated dishes in DMEM supplemented with 2mM glutamine, 0.05 mg/ml gentamycin 10 ng/ml EGF, 10 ng/ml PDGF, 0.5 ng/ml LIF and 2% fetal bovine serum in 10 cm culture dishes. Cells were incubated at 37°C under 5% carbon dioxide and collected at 80% confluency.

extract_protocol:
Single-cell sample preparation was conducted according to Sample Preparation Demonstrated Protocol provided by 10X Genomics as follows: 1 mL of cell suspension was pelleted in Eppendorf tubes by centrifugation (400g, 5min). The supernatant was discarded, and the cell pellet was then resuspended in 1X PBS with 0.04% BSA, followed by two washing procedures by centrifugation (150g, 3min). After the second wash, cells were resuspended in ~500 uL 1X PBS with 0.04% BSA followed by gently pipetting mix 10-15 times.
Libraries were prepared using the Chromium Controller (10X Genomics, CA) in conjunction with the single-cell 3’ v3 kit. Briefly, the cell suspension was diluted in nuclease-free water according to manufacturer instructions to achieve a targeted cell count of 10,000. The cDNA synthesis, barcoding and library preparation were then carried out according to the manufacturer's instructions. the library was sequenced in the Molecular Genomic Workspace of the Texas A&M Institute for Genome Sciences on a Novaseq 6000 sequencer (Illumina, San Diego).

value: Digit Wound Mesenchymal cells

tag: culture type

value: Neonate Primary culture

tag: passage

value: Passage 1, 80% confluent


title: IV4_ASD

description: Genomic DNA extracted from samples was genotyped using Illumina Human Infinium Omni2.5-8 v1.7 BeadChip (Illumina).


title: ESC-NPC_H9

status: Public on Dec 29 2021

city: Seoul

first: WEIWEI

last: GAO

address: Anam-ro

country: South Korea

institute: Korea University

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(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

value: nephron progenitor cell derived from ESC-H9


title: ESC-NPC_BG01

value: nephron progenitor cell derived from ESC-BG01


title: UC-F

source_name: urine cell

value: urine cell

value: female


title: UC-M

value: male


title: iNPC-F

source_name: induced nephron progenitor

value: urine cell induced nephron progenitor cell


title: Homozygous dpolh mutant_part1

status: Public on Dec 28 2021

city: Montpellier

first: Domenico

last: Maiorano

address: 141, rue de la cardonille

institute: CNRS

data_processing:
Alignment performed with BWA version 0.7.12-r1039. Command was: "bwa mem -M R1.fastq R2.fastq"
Variant Calling performed with Freebayes version 0.9.20. Command was "freebayes -f dm6.fa -0 --genotype-qualities --region chr2L:0-3000000 -b bamFile"
Variant annotation performed with VEP version 82. Command was: "variant_effect_predictor.pl -i vcf_file.vcf.gz -o  vcf_file_annotated.json --species drosophila_melanogaster --cache --offline --plugin Blosum62 --json --fork 6 --symbol"
Genome_build: DM6
Supplementary_files_format_and_content: VCF and annotated variant calls JSON

organism: Drosophila melanogaster

source_name: whole single fly

growth_protocol: Drosophila melanogaster stocks were maintained in K-Resin vials (25 X 95 mm) and polypropylene bottles (57 L X 57 W X 103 mm) inside a thermostatic room at 25 °C with alternating light and dark for an equal amount of hours per day.

extract_protocol:
Each fly was crushed with a pestle in a 1,5 mL-1 tube containing 170 µL of extraction buffer (Tris-HCl pH 8.0; 50mM; EDTA 50mM; SDS 1 %). Proteinase K (555 µg µL-1) was added once the tissues had been completely grinded. After incubating 15 min at room temperature, cellular debris was removed twice by potassium acetate addition (0,83 M) and centrifugation with a bench-top centrifuge (max speed) at 4 °C for 10 min. DNA was isolated by double phenol/chloroform/isoamyl alcohol (25:24:1) extraction and ethanol precipitation overnight at -20 °C with glycogen (20 µg) followed by centrifugation at 4 °C. Precipitated DNA was washed with cold ethanol 70 %, dried at room temperature for 30 min and dissolved in water. The quality of extracted DNA (about 150 ng) was verified by agarose gel electrophoresis.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

tag: strain

value: dpol EXC215/TM3 Sb w1118; PolHExc2.15 /Oregon R

value: adult

tag: genotype

value: Homozygous dpolh mutant


title: iNPC-M


description: Gene expression after inoculating with gut microbiota from major depressive disorder patients

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 1.5 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized on Mouse LncRNA Array v2.0 (8 x 60K, Arraystar) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Scanner G2505C using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Agilent Feature Extraction software (version 11.0.1.1) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Specific activity and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted using TRIzol® Reagent (Invitrogen life technologies) following the manufacturer's recommendations. Total RNA from each sample was quantified using the NanoDrop ND-1000 and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis. RNA was purified from total RNA after removal of rRNA using mRNA-ONLY™ Eukaryotic mRNA Isolation Kit (Epicentre)

value: Hippocampus

tag: age


description: Gene expression after inoculating with gut microbiota from healthy controls

tag: tissue


value: inoculating with gut microbiota from healthy controls


title: Heterozygous mutant_part1

value: Heterozygous dpolh mutant


title: Homozygous dpolh mutant_part2


title: Mice inoculated with gut microbiota from healthy controls, rep 3


title: LEC1

city: Trondheim

first: Stefan

last: Blankvoort

address: Olav Kyrresgt 9

department: Kavli Institute for systems Neuroscience

country: Norway

institute: NTNU

description: scATAC reads

data_processing:
Snap File was made from Demultiplexed Fastq files.
Most steps in the SNAPatac pipeline were followed to cluster, reduce dimensionality, identify cell types and find differentially accessible regions.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.snap: Snap Files that can be used as starting point for the SNAPatac pipeline.
Supplementary_files_format_and_content: ALL_MEC_LEC_umap.rds: R object that is the result of the SNAPatac pipeline.
Supplementary_files_format_and_content: *.singlecell.csv: Comma-separated text files; starting point for Snap pipeline.

source_name: Neural tissue

extract_protocol: Protocol provided by 10X. For details, see methods section of corresponding paper.

treatment_protocol: Microdissected and flash frozen.

value: WT

value: lateral entorhinal cortex


title: MEC1

description: scATAC reads

value: medial entorhinal cortex


title: MEC2

description: scATAC reads


value: inoculating with gut microbiota from major depressive disorder patients


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL2077A3395M5-T)

status: Public on Dec 10 2021

city: Houston

first: Yuya

last: Sasaki

address: 1515 Holcombe Blvd

institute: M.D. Anderson Cancer Center

data_processing:
Basecalls performed using CASAVA version 1.8.2
Raw-sequencing data from the Illumina platform were converted to a fastq format and aligned to the reference genome (hg19) using the Burroughs–Wheeler Aligner using MEM mode with following parameters: -k 31 -T 100 -t 8 -M.
The aligned BAM files were subjected to mark duplication, realignment, and recalibration, using Picard and GATK with default parameters.
Preprocessed BAM files were then analyzed to detect SNV and small insertions and deletions (indels), using MuTect and Pindel, respectively, against pooled unmatched normal sequences developed in house.
Genome_build: hg19
Supplementary_files_format_and_content: Mutect/Pindel calling tab-separated values matrix

source_name: Bone marrow cells

growth_protocol: Not applicable.

extract_protocol:
Genomic DNA was extracted from bone marrow or peripheral blood samples using a QIAamp DNA Mini kit (QIAGEN, Hilden, Germany).
After sample quality control, targeted capture DNA sequencing using custom designed SureSelect panel of 295 genes (Agilent Technologies, Santa Clara, CA, USA) was performed
Targeted capture DNA sequencing

treatment_protocol: Samples were either bone marrow samples obtained from previously untreated patients.

value: Ph-positive ALL

value: bone marrow

value: leukemic cell

tag: Sex

value: Female

tag: outcome

value: Complete Response


title: Heterozygous mutant_part2


value: male


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL3174A7373M6-T)

value: Male


title: Adult IVD 3

status: Public on Dec 07 2021

city: Los Angeles

first: Wensen

last: Jiang

state: CA

address: 127 S San Vicente Blvd

department: Board of Governors Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

data_processing:
Seurat package (v4.0.1) in R (v4.0.3) has been used to process the data of four samples.
CreateSeuratObject function to transform the loaded data into a Seurat object for each sample.
FindIntegrationAnchors and IntegrateData were used to integrate the four samples’ data together.
RunPCA function.
DimPlot function was then used with “UMAP” reduction to obtain the 2D Uniform Manifold Approximation and Projection (UMAP) plot.
FindNeighbors and FindClusters functions further classified all cells.
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx files.

source_name: Cells harvested from the whole IVD

growth_protocol: Not grown.

extract_protocol:
The IVDs were dissected, nucleus pulposus identified and washed with Phosphate Buffered Saline (PBS). The tissue was manually minced and enzymatically digested. Tissue was digested with Pronase Protease (Millipore, Temecula, CA) in growth media, followed by ~18 hour digestion of Collagenase Type 1S in growth media. The resulting sample was pushed through a 70μm cell strainer and cells were isolated via centrifugation. The pellet was resuspended in phosphate buffered saline at a concentration of 1,500 cells/μL and 100uL of sample was processed for single-cell RNA sequencing.
Chromium Single-cell 3' v2 libraries were prepared on a Chromium Controller with chips and reagents from Single-cell Gene Expression v2 kits following the manufacturer’s protocols (10x Genomics). The libraries were then sequenced using paired-end sequencing on an Illumina NovaSeq. Samples were sequenced with raw sequencing data analyzed and visualized with pre-release versions of Cell Ranger 3.0.0 and Loupe Cell Browser 3.0.0. Raw sequencing data was demultiplexed and converted to fastq format by using bcl2fastq v2.20 (Illumina, San Diego, CA). Fragment analysis of indexed libraries was performed on the Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA).

value: Intervertebral disc

value: Adult


title: Adult IVD 2


title: WT/WT rep 1

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

description: replicate 1

hyb_protocol: Purified and labeled cRNA was then hybridized for 18 hrs onto MouseRef-8 v2 expression BeadChips (Illumina, USA) following the manufacturer’s instructions

scan_protocol: After the recommended washing, the chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina) and the accompanying software.

data_processing:
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina),
background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model,
variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
Data post-processing and graphics were performed with in-house developed functions in MATLAB.
Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the
Unweighted Pair-Group Method using Average (UPGMA) linkage method

source_name: WT/WT rep 1

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 18h)

tag: rescued or normal

value: normal


title: L80A-res rep 1

description: replicate 1

source_name: L80A-res rep 1

value: rescued


title: LEC2

description: scATAC reads

tag: replicate


title: DM rep 4

status: Public on Dec 21 2021

description: replicate 4

hyb_protocol: Samples were hybridized to Affymetrix Mouse Genome 430 2.0 chip, following the manufacturer’s instructions

scan_protocol: Data generation was controlled by the Affymetrix GeneChip Command Console AGCC Version 2.0.0.1029 software of AGCC Portal and the Expression Console Version 1.1 was used for data quality control and analysis application (Affymetrix).

data_processing:
Normalyzation was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model,
Data post-processing and graphics were performed with in-house developed functions in MATLAB.
Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the
Unweighted Pair-Group Method using Average (UPGMA) linkage method

source_name: DM rep 4

label_protocol: Biotinylated cRNA were prepared for Affymetrix arrays following the manufacturer's instructions.

extract_protocol: Total RNA was isolated using RNeasy mini kit (Qiagen) following the manufacturer's instructions.

tag: patient condition

value: DM


title: DM rep 1

description: replicate 1

source_name: DM rep 1


title: Ctr rep 4

description: replicate 4

source_name: Ctr rep 4

value: Ctrl


title: ZHBTc4 rep 1

description: replicate 1

source_name: ZHBTc4 rep 1


title: WT/WT rep 2

description: replicate 2

source_name: WT/WT rep 2


title: L80A/L80A rep 2

description: replicate 2

source_name: L80A/L80A rep 2


title: ZHBTc4 rep 2

description: replicate 2

source_name: ZHBTc4 rep 2


title: L80A-res rep 2

description: replicate 2

source_name: L80A-res rep 2


title: DM rep 3

description: replicate 3

source_name: DM rep 3


title: Ctr rep 3

description: replicate 3

source_name: Ctr rep 3


title: WT-res rep 2

description: replicate 2

source_name: WT-res rep 2


title: L80A/L80A rep 1

description: replicate 1

source_name: L80A/L80A rep 1


title: Neonatal IVD 1

value: Neonatal


title: Ctr rep 2

description: replicate 2

source_name: Ctr rep 2


title: DM rep 6

description: replicate 6

source_name: DM rep 6


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL1995A7395M0-T)

source_name: Bone marrow cells


title: DM rep 2

description: replicate 2

source_name: DM rep 2


title: DM rep 5

description: replicate 5

source_name: DM rep 5


title: Adult IVD 1

source_name: Cells harvested from the whole IVD


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL1689A7467M2-T)


title: Neonatal IVD 3


title: Neonatal IVD 2


title: Ctr rep 1

description: replicate 1

source_name: Ctr rep 1


title: MB-5-L-Rep2

status: Public on Dec 06 2021

city: Chicago

first: Matthew

last: Piron

state: IL

address: 900 E 57th St. KCBD 8230A

institute: University of Chicago

data_processing:
Alignments made using Illuminca web App: RNA-Seq Alignment using the STAR protocol
Diff. Expression data was generated using Illiumina webbased App: RNA-Seq Differential Expresion using DESq2
Genome_build: hg19
Supplementary_files_format_and_content: text file (tab-delimited)

source_name: Adipose tissue biopsy

extract_protocol:
RNA-solv via Omega Bio-tek RNA Kit II
Contact Uchicago genomics core http://fgf.uchicago.edu/index.php
mRNA directional

value: 40 yr

value: subcutaneous adipose tissue

tag: protocol

value: late eating


title: MB-9-E-Rep2

value: 35 yr

value: early eating


title: WT-res rep 1

description: replicate 1

source_name: WT-res rep 1


title: EpiLC_pK27R_1_Pol2

city: Copenhagen

first: Aditya

last: Sankar

email: cnj376@ku.dk, aditya.sankar@embl.de

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

institute: University of Copenhagen

description: Chromatin

data_processing:
Concatenated fastq files were processed in a Galaxy environment with standard parameters for adaptor trimming using the Trimmomatic (v0.38) including initial Illumina CLIP step for TruSeq3 (Single-ended, for MiSeq and HiSeq) and sliding window trimming.
Trimmed fastq files were mapped using bowtie2 (v2.3.4.1) using standard settings to both mm10 (patch4) and dm6 genomes. The reads mapping exactly one time (unique) were noted for each genome to generate scaling factor for downstream normalization purposes.
The mm10 mapped bam files were filtered for unique reads using Rmdup (v1.3.1) using standard settings. This downstream bam file containing unique reads were converted to 6-column BED files using bedtools (v2.29.2).
BED files were then uploaded onto EaSeq (v1.111) software using standard import settings for ChIPSeq (see https://easeq.net) and each file was newly describe to include the spike-in normalization factor in addition to standard FPKM normalization (automatic in EaSeq). No peak-calling was performed for these datasets.
Further details are found in the associated methods section of the manuscript.
Genome_build: mm10 (patch4), dm6 (spike-in)
Supplementary_files_format_and_content: [EpiLC_ChIP_quantification.xlsx]  Quantified ChIP signal intensities for genes and enhancers for all samples in separate tab; genome build mm10
Supplementary_files_format_and_content: [Unique_reads_mm10_dm6_Dec2021.xlsx]  Read information from ChIP files used to calculate scaling factor for spike-in normalization; genome build mm10/dm6
Supplementary_files_format_and_content: [Enhancers_EpiLC_Buecker_2014_mm10.txt]  The mm10 liftover genomic co-ordinates for reanalyzed enhancers originally defined in mouse EpiLCs from Buecker et al., Cell Stem Cell 2014 (PMID: 24905168). Triple positivity for p300, H3K4me1 and H3K27ac were defined as enhancers; genome build mm10

source_name: EpiLC

growth_protocol: mESCs were grown in feeder-free standard naïve pluripotent growth conditions including LIF and 2i (GSK3 and MEK1 inhibitors) and 2 million mESCs were plated in each human plasma fibronectin coated 10cm tissue culture dish and subjected to a 48 hour EpiLC differentiation protocol with media change after 24 hours prior to harvesting chromatin at 48 hours.

extract_protocol:
Chromatin was extracted from crosslinked cells using "SDS lysis" buffer containing (100mM NaCl, 50mM Tris-Cl pH8, 5mM EDTA pH8, 0.2% sodium azide and 0.5% SDS). Chromatin was then pelleted and resuspended on ice in sonication/IP buffer that is a 2:1 mix of "SDS lysis" buffer and cold "Triton dilution" buffer (100mM Tris-Cl pH8.6, 100mM NaCl, 5mM EDTA pH8, 0.2% sodium azide, and 5% Triton X-100), prior to sonication using a Diagenode Bioruptor Pico.
ChIP libraries were prepared using the NEBNext Ultra II DNA library preparation kit (Catalog E7645S/L) according to manufacturers guidelines including the recommended size selection step.

treatment_protocol: For all ChIPs, cells were crosslinked in 1% formaldehyde for 10 minutes and quenched with 0.125M glycine before cell lysis for chromatin preparation.

value: EpiLC

tag: chip antibody

value: Pol2 (Cell Signaling (Catalog 14958, clone D8L4Y))

tag: strain background


title: EpiLC_ABE_7_10_Pol2

description: Chromatin

tag: cell type

value: ABE


title: EpiLC_pK27R_2_H3K27ac_Rb

description: Chromatin

value: H3K27ac_Rb (Cell Signaling (Catalog 8173, clone D5E4))


title: MB-9-L-Rep1

tag: gender

value: Male


title: EpiLC_SUZ12KO_H3K27ac_Rb

description: Chromatin


title: MB-9-E-Rep1


title: EpiLC_ABE_7_10_H3K27ac_Rb

description: Chromatin


title: SUZ12KO_H3K27ac_Rb

description: Chromatin

source_name: mESCs

value: mESCs


title: MB-6-L-Rep2

value: Female

value: 58 yr


title: MB-6-E-Rep1


title: MB-5-E-Rep2


title: MB-5-L-Rep1


title: ABE_7_10_H3K27me3_rep2

description: Chromatin

value: H3K27me3 (Cell Signaling (Catalog 9733, clone C36B11))


title: MB-5-E-Rep1


title: EpiLC_pK27R_2_Pol2

description: Chromatin


title: EpiLC_SUZ12KO_Pol2

description: Chromatin


title: EpiLC_pK27R_1_H3K27ac_Rb

description: Chromatin


title: pK27R_2_Pol2

data_processing:
Concatenated fastq files were processed in a Galaxy environment with standard parameters for adaptor trimming using the Trimmomatic (v0.38) including initial Illumina CLIP step for TruSeq3 (Single-ended, for MiSeq and HiSeq) and sliding window trimming
Trimmed fastq files were mapped using bowtie2 (v2.3.4.1) using standard settings to both mm10(patch4) and dm6 genomes. The reads mapping exactly one time (unique) were noted for each genome to generate scaling factor for downstream normalization purposes
the mm10 mapped bam files were filtered for unique reads using Rmdup (v1.3.1) using standard settings. This downstream bam file containing unique reads were converted to 6-column BED files using bedtools (v2.29.2).
BED files were then uploaded onto EaSeq (v1.111) software usign standard import settings for ChIPSeq (see https://easeq.net) and each file was newly describe to include the spike-in normalization factor in addition to standard FPKM normalization (automatic in EaSeq). No peak-calling was performed for these datasets
Further details are found in the associated methods section of the manuscript
Genome_build: mm10 (patch4), dm6 (spike-in)
Supplementary_files_format_and_content: [ChIP_signals_features_mESCS_mm10.xlsx]  Quantified ChIP signal intensities for genes and enhancers for all samples in separate tab; genome build mm10
[Non redundant gene bodies_mm10.txt]  The non-redundant regionset is used from Sankar et al., Nature Cell Biology 2020 (PMID: 32231309); genome build mm10
[Unique_reads_mm10_dm6_Dec2021.xlsx]  Read information from ChIP files used to calculate scaling factor for spike-in normalization; genome build mm10/dm6
[Enhancers_mESCs_Whyte_2013_mm10.txt]  The mm10 liftover genomic co-ordinates for enhancers defined in mESCs from Whyte et al., Cell 2013 (PMID: 23582322); genome build mm10

growth_protocol: mESCs were grown in feeder-free standard naïve pluripotent growth conditions including LIF and 2i (GSK3 and MEK1 inhibitors)

extract_protocol:
Chromatin was extracted from crosslinked cells using "SDS lysis" buffer containing (100mM NaCl, 50mM Tris-Cl pH8, 5mM EDTA pH8, 0.2% sodium azide and 0.5% SDS). Chromatin was then pelleted and resuspended on ice in sonication/IP buffer that is a 2:1 mix of "SDS lysis" buffer and cold "Triton dilution" buffer (100mM Tris-Cl pH8.6, 100mM NaCl, 5mM EDTA pH8, 0.2% sodium azide, and 5% Triton X-100), prior to sonication using a Diagenode Bioruptor Pico.
ChIP libraries were prepared using the NEBNext Ultra II DNA library preparation kit (Catalog E7645S/L) according to manufacturers guidelines including the recommended size selection step

treatment_protocol: For most ChIPs, cells were crosslinked in 1% formaldehyde for 10 minutes and quenched with 0.125M glycine before cell lysis for chromatin preparation: Only for Med1 ChIP, cells were pre-treated with 2 mM disuccinimidyl glutarate (DSG) for 30 minutes at room temperature prior to formaldehyde cross-linking as described before.


title: cK27R_1_Med1

value: Med1 (Bethyl Laboratories (Catalog A300-793A))


title: MB-6-L-Rep1


title: SUZ12KO_H3K27me3

description: Chromatin


title: MB-9-L-Rep2


title: ABE_7_10_H3K27ac_Rb_rep2

description: Chromatin


title: ABE_7_10_Med1_input


title: cK27R_1_H3K27ac_Ms

value: H3K27ac_Ms (Thermofisher (Catalog MA5-23516))


title: EpiLC_input

description: Chromatin


title: ABE_7_10_Pol2_input


title: cK27R_2_H3K27ac_Rb


title: ABE_7_10_Histone_input


title: pK27R_2_Med1


title: cK27R_2_Med1


title: pK27R_1_Med1


title: pK27R_1_Pol2


title: cK27R_1_Pol2


title: cK27R_2_Pol2


title: cK27R_1_H3K27ac_Rb


title: pK27R_2_H3K27ac_Ms


title: pK27R_1_H3K27me2

value: H3K27me2 (Cell Signaling (Catalog 9728, clone D18C8))


title: ABE_7_10_Pol2


title: ABE_7_10_H3K27me2


title: pK27R_1_H3K27ac_Ms


title: cK27R_2_H3K27ac_Ms


title: ABE_7_10_H3K27ac_Ms


title: pK27R_2_H3K27ac_Rb


title: pK27R_1_H3K27ac_Rb


title: ABE_7_10_Med1


title: cK27R_2_H3K27me3


title: cK27R_1_H3K27me3


title: pK27R_1_H3K27me3


title: ABE_7_10_H3K27ac_Rb


title: ABE_7_10_H3K27me3


title: pK27R_2_H3K27me3


title: pK27R_2_H3K27me2


title: cK27R_1_H3K27me2


title: cK27R_2_H3K27me2


title: 4-Adipo-Late-rep1

description:
Subject4
SAMPLE 9

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomeStudio software

label_protocol: Biotinylated cRNA were prepared with Illumina prep kits

extract_protocol: Total RNA obtained from SubQ adipose biopsy under early or late eating protocols.

value: 53 yr


title: 4-Adipo-Late-rep2

description:
Subject4
SAMPLE 10

tag: mean age

value: subcutaneous adipose tissue


title: 4-Adipo-Early-rep1

description:
Subject4
SAMPLE 11


title: PfBDP7Ty_GlmS_anti-Ty_mature S

status: Public on Nov 09 2021

city: Erlangen

first: Michaela

last: Petter

address: Wassertrumstr. 3-5

department: Mirkobiologisches Institut

institute: Univeritätsklinikum Erlangen

description: Accel2S Ultra DNA library kit

data_processing:
Quality control of samples using FastQC version 0.11.8
Trimming using TrimGalore version 0.6.5 and Cutadapt version 2.8
Mapping with Bowtie2 version 2.3.5.1 against Plasmdium genome version 28
BAM files with Samtools version 1.2
Bigwig files of log2 ratios with Deeptools version 3.3.1
Genome_build: PlasmoDB-28_Pfalciparum3D7_Genome.fasta / PlasmoDB-28_Pfalciparum3D7.gff (available on PlasmoDB)
Supplementary_files_format_and_content: Bigwig files with Log2 ratio ChIP/Input

organism: Plasmodium falciparum

source_name: P. falciparum in vitro culture

growth_protocol: Plasmodium falciparum parasites were cultured in RPMI-HEPES medium containing 5% O+ red blood cells, 0.2% sodium bicarbonate and 0.25% Albumax (Gibco) and 5% human serum (AB+). Parasitaemia was maintained at 0.5%-10%. Parasites cultures were incubated at 37ºC in 1% O2, 5% CO2 and 94% N2.

extract_protocol:
Cultures were fixed with 1% PFA and nuclei were isolated. Chromatin was fragmented by sonication before immunoprecipitation of Protein/DNA complexes.
Libraries were generated using the Accel2S PLUS DNA Library kit (Swift Biosciences). Library amplification was performed using the KAPA Hifi PCR kit (KK2101) according to published procedures (PMID: 26067602).

tag: parasite line

tag: Stage

value: mature schizont


title: 3-Adipo-Early-rep1

description:
Subject3
SAMPLE 7

value: 27 yr


title: 3-Adipo-Early-rep2

description:
Subject3
SAMPLE 8

value: early eating


title: PfBDP7Ty_GlmS_anti-Ty_early S

description: Accel2S Ultra DNA library kit

value: early schizont


title: Ctrl_1

status: Public on Nov 16 2021

first: dong

last: chen

address: GaoXin 2nd Road

institute: ablife

data_processing:
FastQC (Version 0.9.5) was employed to detect the quality of filtered fragments in fastq format.
Adaptors and low quality bases were trimmed from raw   sequencing reads using FASTX-Toolkit (Version 0.0.13), reads < 16 nt were   discarded
the remaining reads were aligned to the GRCh38 genome by TopHat2   (52) with 4 mismatches
Uniquely mapped reads were used to calculate read number   and FPKM (paired-end fragments per kilobase of exon per million fragments mapped)   value for each gene.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include reads count and FPKM values for each Sample.

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231-NTC cells and  MDA-MB-231-shCALR cells were cultured in Dulbecco's modified Eagle's medium (DMEM) with 10% FBS (HyClone).

extract_protocol:
Total RNA was isolated using the miRNeasy Mini kit (Qiagen), including the optional on-column DNA digestion with the RNase-Free DNase Set (Qiagen).
After isolation, total RNA was used to generate polyA-enriched strand-specific cDNA libraries (TruSeq stranded mRNA library preparation kit, Illumina). Libraries were sequenced on a Illumina NextSeq 500 sequencer with HighOutput

treatment_protocol: mRNA was prepared from cells at circa 70% confluency.

tag: cell line

value: Control


title: Ctrl_3

tag: genotype


title: Ctrl_2


title: CALR_KD3

value: CALR Knockdown


title: CALR_KD2


title: CALR_KD1