title: ChIP-seq_WT_Naive_CD4_H3K27ac_rep2


title: 5-010 (mRNA)

status: Public on Mar 01 2023

type: SRA

city: Rochester

first: Daniel

middle: Rothschild

last: OBrien

state: MN

address: 200 First St. SW

country: USA

institute: The Mayo Clinic

library_source: transcriptomic

data_processing:
TopHat for alignment
FeatureCounts to quantify expression
Genome_build: hg38
Supplementary_files_format_and_content: tsv format containg RPKM normalized expression values

molecule: total RNA

organism: Homo sapiens

source_name: Duodenal mucosa (biopsy)

extract_protocol:
RNA was extracted from freshly frozen biopsy tissue with TRIzol (Ambion, Waltham, Massachusetts) and chloroform.  After centrifugation, the aqueous phase was purified with an RNeasy Mini Kit (Qiagen, Valencia, California). The quality of total RNA samples was assessed by using an Agilent bioanalyzer (Santa Clara, CA).
RNA libraries were prepared according to the manufacturer's instructions for the TruSeq Stranded Total RNA Library preparation kit (Illumina, San Diego, CA). Unique indices, included in the standard TruSeq kits were incorporated at the adaptor ligation step for multiplex sample loading on the flow cells. The flow cells were sequenced as 101×2 paired-end reads on an Illumina HiSeq 4000

tag: disease group

value: Functional Dyspepsia

tag: tissue

value: Duodenal mucosa (biopsy)


title: 5-009 (mRNA)


title: ChIP-seq_WT_Naive_CD4_H3K27ac_rep1

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

library_source: genomic

data_processing:
Raw reads of RNA-seq data were mapped by STAR (v2.7.3a) (Dobin et al., 2013).   Raw reads of  ChIP-seq data were mapped by Bowtie2 (Langmead and Salzberg, 2012). Mapped unique paired-end reads with MAPQ  10 were used for the following analysis. H3K4me1 ChIP-seq peaks were called by cLoops2(v0.0.3) (Cao et al., 2022)  to annotate the CNS regions for Ifng.
Assembly: mm10
Supplementary files format and content: BigWig files for RNA-seq and ChIP-seq were provided for visualization in genome browser.

molecule: genomic DNA

organism: Mus musculus

source_name: Naive CD4+ T cells

growth_protocol: Naive CD4+ T cells were tsolated by magnetic selection according to the protocol provided by the manufacturer (Stem Cell, EasySep Mouse CD4+CD62L+ T cell Isolation Kit). Isolated Naïve CD4+ T cells active with plate-bound anti-CD3(Clone: 145-2C11, 1 μg/ml, eBioscience), anti-CD28(Clone: 37.51, 3 μg/ml, eBioscience), then polarized under Th1 condition.

extract_protocol:
Detailed procedures for ChIP-Seq analysis was performed as described previously (Hu et al., 2018). For RNA-Seq, 2ng of total RNA were extracted miRNeasy Micro Kit (50) from Qiagen (Cat # 217084).
ChIP DNA were end-repaired using an End-It DNA End-Repair kit (Epicentre), universal adaptors were then ligated. The libraries were amplified using indexed primers with the PCR condition: 98°C, 10”; 67°C, 30”; 72°C, 30” for 16 cycles. The fragments between 180bp to 350bp were isolated on E-gel and subjected to sequencing on Illumina HiSeq2500.

treatment_protocol: Using DAPI to sort out live cells for Dnase-seq, ChIP-seq, and RNA-seq experiments.

tag: strain

value: mixed C57BL/6 and 129

tag: cell type

value: Naive CD4+ T cells

value: lymph node

tag: genotype


title: 5-008 (mRNA)


title: CRC0475LMO0A04012001R01000, LMO_BASALE, bio rep 1, QC ok

city: Candiolo

first: Livio

last: Trusolino

state: Turin

address: Strada Provinciale, 142 -KM 3.95

department: Oncology

country: Italy

institute: IRCCS Istituto Candiolo

data_processing:
Align with STAR on hybrid mm/hs genome
Assign counts to genes with FeatureCounts
Consider only human genes to normalize with DESeq2
QC based on evidence of lymphomatous infiltration
https://github.com/molinerisLab/StromaDistiller, https://github.com/vodkatad/RNASeq_biod_metadata
Assembly: GRCh38_GRCm38
Supplementary files format and content: merged_hs_mm.tsv.gz: raw counts for human and murine genes
Supplementary files format and content: vsd.tsv.gz: normalized expression values for human genes

molecule: polyA RNA

source_name: Colorectal Cancer

growth_protocol: Please check the linked publication

extract_protocol:
total RNA extraction
PolyA enriched
Forward Stranded

treatment_protocol: Please check the linked publication

value: Colorectal Cancer

tag: cell line

value: O

value: LM

value: WT

tag: treatment


title: RNA_398_CD8_EMRAStim

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the hg38 genome using STAR v.2.5.3 and the UCSC KnownGene reference transcriptome
Reads per kilobase per million (Rpkm) normalized gene expression counts were derived by analyzing coverage across all exons that fall within unique ENTREZ genes using the GenomicRanges package
Detected genes are defined as any gene with at least 3 rpm normalized expression counts in all replicates of any one sample group
Genome_build: hg38

source_name: CD8 EMRA T cell ex-vivo stimulated with anti-CD3/CD28 beads

extract_protocol:
One thousand cells were sorted directly into RLT buffer (79216; Qiagen) containing 1% 2-Mercaptoethanol. RNA was isolated using the Quick-RNA Microprep kit (Zymo Research; R1050).
The SMART-Seq v4 Ultra Low Input RNA Kit (634894; Takara Bio) was used for synthesis of cRNA from isolated RNA, and 400 pg of cDNA was used as input for the NexteraXT kit (Illumina).

treatment_protocol: Collected cells were separated for either immediate flow sorting (resting cells) or incubated for 42-48 hours with anti-CD3/CD28 beads for ex-vivo stimulation. 1e6 cells were added to cell suspensions in a 2:1 bead-to-cell ratio before being removed prior to flow staining

tag: donor

value: blood

tag: stimulation

value: anti-CD3/CD28 beads

tag: sorting markers


title: CRC0479LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: RNA_480_CD8_EMRAStim


title: 5-007 (mRNA)


title: RNA_253_CD8_EMRAStim


title: ChIP-seq_WT_Naive_CD4_H3K4me3_rep2


title: ChIP-seq_WT_Naive_CD4_H3K4me3_rep1


title: 5-006 (mRNA)


title: Patient#3_On-treatment week 4 sample_Responder

type: RNA

city: Milan

first: Andrea

last: Anichini

address: Via Venezian 1

department: Research

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

hyb_protocol: The Gene expression assay was performed on the NanoString nCounter platform (FLEX) using a custom codeset panel. Overnight hybridization of Reporter and Capture Probes occurred for 18 hours at 65°C, then reactions were held at 4°C until they were placed on the nCounter Prep Station. 12 samples (input of 200 ng/sample) were run per cartridge following the manufacturer’s protocol

scan_protocol: The specific amount of target molecules was quantified performing the nCounter Digital Analyzer. Each assay was scanned at 555 field of view (FOV) with a CCD camera.

data_processing: nSolver 4.0 software (NanoString Technologies) was used for quality control  (QC) with default setting. Negative control probes were used for background subtraction. For normalization geometric mean of 6 positive controls and 40 housekeeping genes were used.

source_name: metastatic melanoma

label_protocol: No label is used in Nanostring

growth_protocol: Not applicable. Samples were two 12 m thick sections from FFPE blocks of melanoma biopsies obtained pre-therapy (w0) and then at week 4 (w4) and week 12 (w12) from patients enrolled in the NIBIT-M4 guadecitabine plus Ipilimumab Trial NCT02608437.

extract_protocol: RNA was extracted from FFPE sections by TRIzol (Invitrogen). Frozen tissue was placed in 2 ml microcentrifuge tubes containing 1 ml TRIzol reagent and homogenized using the TissueLyser (Qiagen); 0.2 ml of chloroform was added to separate phases and then RNA was precipitate from the aqueous phase by mixing with 0.5 ml of  isopropyl alcohol. Quantity and quality of RNA extracted were assessed by NanoDrop ND-1000 UV-Vis Spectrophotometer (Thermo Fisher Scientific) and by Agilent 2100 Bioanalyzer (Agilent Technologies) using the RNA 6000 Nano kit (Agilent).

tag: Sex

value: M

tag: age

tag: ajcc 8th edition stage

value: STAGE IV M1a

tag: type of lesion

value: Skin

tag: response to therapy

value: CR (BOR)


title: 5-011 (mRNA)


title: 5-005 (mRNA)


title: P, Ctrl3

city: Hangzhou

first: Jianing

last: Chen

address: Qingchun Road 79#

country: China

institute: Zhejiang university

data_processing:
Library strategy: DNA-seq
Vsearch software (v2.3.4) was used for basecalling
dereplication using DADA2
Chao1, Observed species, Goods coverage, Shannon, Simpsonin our samples were calculated with QIIME2.
Blast was used for sequence alignment
feature sequences were annotated with SILVA database
Supplementary files format and content: otu_table_with_taxonomy.txt (abundance measurements), gene_counts_statistics.txt (raw counts)

organism: feces metagenome

source_name: murine feces

extract_protocol:
Total genome DNA from murine luminal samples from ileocecus was extracted for amplification
The libraries were sequenced on Illumina NovaSeq PE250 platform
DNA V4 region

value: PBS Control

value: 49 day

tag: fraction

value: rDNA


title: RNA_125_CD8_EMRAStim


title: Patient#3_Pre-therapy sample_Responder

treatment_protocol: Not applicable. Samples were two 12 m  thick sections from FFPE blocks of melanoma biopsies obtained pre-therapy (w0) and then at week 4 (w4) and week 12 (w12) from patients enrolled in the NIBIT-M4 guadecitabine plus Ipilimumab Trial NCT02608437.

value: Soft tissue


title: Patient#3_On-treatment week 12 sample_Responder


title: ChIP-seq_WT_Naive_CD4_H3K4me1_rep2

value: mixed C57BL/6 and 129

value: Naive CD4+ T cells


title: Patient#15_On-treatment week 12 sample_Non_Responder

value: STAGE IV M1c

value: PD (BOR)


title: RNA_480_CD8_EM

source_name: CD8 EM T cell


title: RNA_398_CD8_EM


title: ChIP-seq_WT_Naive_CD4_H3K4me1_rep1

value: lymph node


title: Patient#15_On-treatment week 4 sample_Non_Responder

value: Subcutaneous


title: 5-003 (mRNA)

value: Functional Dyspepsia

value: Duodenal mucosa (biopsy)


title: RNA_253_CD8_EM

value: blood


title: P16 PH 3

city: Raleigh

first: Raquel

last: Maeso-Diaz

state: United States

address: 3901 Sue Lane

institute: Duke University

data_processing:
Trim_galore trim off adapter and low quality reads
STAR aligning the reads (STAR/2.5.0c-fasrc01)
Samtools index sorted bam files
Picard remove duplicates
HTSeq quantify Gene Expression Data
Assembly: mm10_STAR_genome_idx
Supplementary files format and content: BAM counts

source_name: Hepatocytes

growth_protocol: To obtain primary hepatocytes, livers were perfused with collagenase as described.  Hepatocyte preparations were evaluated by light microscopy to assure that viability and purity were at least 95%. Freshly isolated hepatocytes were immediately processed to obtain RNA.

extract_protocol:
Global transcriptome profiling of was performed by RNA-seq using freshly isolated hepatocytes from P16-overexpressing hepatocytes or its control, GFP,  mice  before and at 48 h after PH (n=3 wild type mice/group/time point). Total RNA was extracted using RNeasy mini kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
mRNA library preparation (poly A enrichment)

treatment_protocol: C57BL/6J 3-month-old wild-type mice were obtained from Jackson Laboratories (Bar Harbor, ME).  All mice were housed in a barrier facility on 12 h:12 h light cycle with free access to water and standard chow diet (Rodent diet 20, 5033; Picolab, St. Louis, MO).  We developed an in vivo hepatocyte senescence mice model by overexpressing P16 specifically in Hepatocytes. To do that the transgene construct AAV8-TBG-eGFP-P16 (Vector Biolabs) or its control, AAV8-TBG-eGFP (Vector Biolabs), were administered in C57BL/6 wild-type mice through tail vein injection. One week after the AAV injection, 70% partial hepatectomy was performed in a subgroup of mice. Mice were sacrificed before PH (0h) and at 48 after PH to obtain primary hepatocytes (n = 3 mice/group/time point).

value: Hepatocytes

value: 3 months-old

tag: aav8-tbg-gfp or aav8-tbg-gfp-p16

tag: quiescent or regenerating

value: Regenerating


title: 5-002 (mRNA)

tag: disease group

tag: tissue


title: P16 PH 2

tag: cell type

tag: strain


title: 5-001 (mRNA)


title: Patient#13_On-treatment week 12 sample_Non_Responder

value: F

value: STAGE IV M1a


title: P16 PH 1


title: RNA_480_CD8_EMStim

source_name: CD8 EM T cell ex-vivo stimulated with anti-CD3/CD28 beads

value: anti-CD3/CD28 beads


title: GFP PH 3


title: Patient#13_On-treatment week 4 sample_Non_Responder


title: CDS20_RV_PAB

city: Minneapolis

first: Lauren

last: Mills

address: 420 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

data_processing:
FASTQ files were trimmed to remove adapter sequences and low quality sequence with trimmomatic
high quality sequencing data was aligned to Sscrofal1.1 using HISAT2
gene level read counts were caculated by featurecounts using Sus_scrofa.Sscrofal1.1.106.gtf
differentially gene expression analysis was performed using DESeq2
Assembly: Sscrofal1.1
Supplementary files format and content: subread_counts.txt (raw read counts in tab delimited text file )
Supplementary files format and content: DEgenes_RV_control-band.txt  (DESeq2 differential gene expression analysis results )

organism: Sus scrofa

source_name: Right Ventricle

growth_protocol: Four (n=4) Yorkshire Cross castrated male piglets aged 4.5±0.6 weeks and weighing 6.4±1.3 kg on the day of surgery were used in this study. Four (n=4) pigs of similar age and weight were housed at the University of Minnesota Research Animal Resources facility for 8 weeks and these animals served as controls. Animals were anesthetized and underwent pulmonary artery banding. The main pulmonary artery was accessed via a left thoracotomy and an umbilical tape looped around the vessel and cinched until the peak systolic pressure in the right ventricle increased to two-thirds of peak systemic pressure, or approximately 30-40 mmHg. After the ligature was secured, the chest was closed using standard techniques and the animals weaned from anesthesia, recovered and transferred to postoperative housing. In the postoperative period, animals were closely monitored by veterinary staff for clinical signs of right ventricular failure including dyspnea, inappetence, lethargy and ascites on palpation.

extract_protocol: RNA was isolated with a PureLink RNA Mini kit (Thermo Fisher) with DNase (Zymo Research, Irvine, CA) according to manufacturer’s instructions. Frozen RV tissue from PAB and control piglets was pulverized and incubated in TRIzolTM Reagent (Thermo Fisher) for 5 min. Chloroform was added, and the samples incubated for 3 min. Samples were centrifuged for 15 min at 12,000g. The aqueous phase was transferred to a new tube, and an equal volume of 70% ethanol was added. Then samples were centrifuged through the spin cartridge at 12,000g for 15 sec. Samples were washed with one half volume of wash buffer I, then 10 µL of DNase I in reaction buffer was added to the column. After 15 min, the column was washed with one half volume of wash buffer I, and twice with wash buffer II. The samples were centrifuged at 12,000g for 2 min to dry the membrane. Then 20 l RNase-free water was added to the center of the spin cartridge, and the cartridge was incubated at 65℃ for 1 minute. Samples were centrifuged at 12,000g for 2 min. RNA concentration was determined by spectrophotometry with a NanoDrop 2000(Thermo Fisher), and samples used for bulk RNA-sequencing.

value: Right Ventricle

tag: breed

value: Yorkshire Cross

value: Pulmonary Artery Banded


title: RNA_398_CD8_EMStim


title: 5-004 (mRNA)


title: RNA_253_CD8_EMStim


title: GFP PH 1


title: CDS18_RV_PAB

tag: treatment


title: CDS19_RV_PAB


title: GFP PH 2


title: Patient#10_On-treatment week 4 sample_Non_Responder

value: M

value: Skin


title: Patient#10_On-treatment week 12 sample_Non_Responder

value: PD (BOR)


title: RNA_125_CD8_EMStim

tag: donor


title: CDS15_RV_PAB


title: RNA_125_CD8_EM

tag: stimulation


title: RNA_480_CD8_CM

source_name: CD8 CM T cell

tag: sorting markers


title: Patient#15_Pre-therapy sample_Non_Responder

tag: Sex

value: STAGE IV M1c


title: CDS33_RV_Ctl


title: Patient#10_Pre-therapy sample_Non_Responder

tag: age


title: P16 2

value: Quiescent


title: RNA_398_CD8_CM


title: Patient#8_On-treatment week 12 sample_Non_Responder

tag: ajcc 8th edition stage


title: CDS32_RV_Ctl


title: P16 3


title: RNA_253_CD8_CM


title: Patient#8_On-treatment week 4 sample_Non_Responder

tag: type of lesion

value: Subcutaneous


title: CDS31_RV_Ctl


title: RNA_125_CD8_CM


title: Patient#13_Pre-therapy sample_Non_Responder

tag: response to therapy


title: GFP 3


title: CDS30_RV_Ctl


title: Patient#8_Pre-therapy sample_Non_Responder


title: P16 1


title: Patient#7_On-treatment week 12 sample_Non_Responder

value: IIIC

value: Lymph node


title: RNA_480_CD8_CMStim

source_name: CD8 CM T cell ex-vivo stimulated with anti-CD3/CD28 beads

value: blood


title: CaptureC_pDC_2

city: Aachen

first: Zhijian

last: Li

state: North Rhine-Westphal

address: Pauwelsstr. 19

country: Germany

institute: RWTH Aachen University

data_processing:
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2 -v 3) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads and mapping to restriction enzyme fragments (custom scripts)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Assembly: mm9
Supplementary files format and content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

source_name: Plasmacytoid dendritic cells

extract_protocol: NuTi Capture-C combines 3C library preparation with oligonucleotide capture for IRF8 promoter viewpoint restriction fragments, as described in Downes et al., Nat. Commun. 12, 1-15, 2021 and Downes et al., Nat. Protoc. 17, 445-475, 2022.

value: Plasmacytoid dendritic cells


title: GFP 2

value: Hepatocytes

value: 3 months-old


title: RNA_398_CD8_CMStim


title: GFP 1


title: CaptureC_pDC_1


title: Patient#7_On-treatment week 4 sample_Non_Responder


title: WT_CD3neg_KO_CD3pos_HTO

city: Hamburg

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

institute: University Medical Center Hamburg-Eppendorf

library_source: transcriptomic single cell

data_processing:
10x Genomics raw sequencing data were processed using CellRanger software (version 5.0.0, 10x Genomics, Pleasanton, CA) and the human genome GRCh38-2020-A release as the reference (function cellranger count). The matrices of cells and the unique molecular identifier (UMI) count were obtained and further processed by the R package Seurat (version 4.0.1)
To remove potential doublets, cutoff values for number of expressed genes (nGene) were determined for samples following visual inspection of the distribution of nGene and nUMI for each cell. The cells with higher nGene values were excluded. We further removed low-quality cells with high mitochondrial genes of all detected genes
Assembly: GRCh38-2020-A and mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (linked to the corresponding *_GEX sample records)

source_name: kidney

growth_protocol: For single cell suspension kidneys were dissected and incubated for 40 min at 37°C in RPMI medium (including 0.01 M HEPES; 0.5 mL filtered FBS and 0.4µg/ mL DNase and 8 µg/ mL collagenase D). The samples were homogenized using a gentleMACS (Miltenyi Biotec).

extract_protocol:
Cells were loaded on a 10x Chromium single cell instrument.
All steps were performed according to standard protocol of the Chromium single cell 5’ v2 kit to generate high-quality cDNA libraries.

tag: tissue/cell type

value: kidney cells

tag: disease

value: NTN induction

tag: genotype

value: Wildtype CD3 negative and Csf2 KO CD3 positive


title: RNA_253_CD8_CMStim

value: anti-CD3/CD28 beads


title: Patient#7_Pre-therapy sample_Non_Responder


title: CaptureC_cDC2_2

source_name: Classical dendritic cell

value: Classical dendritic cell


title: WT_CD3neg_KO_CD3pos_GEX


title: RNA_125_CD8_CMStim


title: CaptureC_cDC2_1


title: RNA_480_CD4_N

source_name: CD4 naive T cell


title: Patient#6_On-treatment week 4 sample_Non_Responder

value: M

value: STAGE IV M1a


title: CaptureC_cDC1_2


title: RNA_398_CD4_N


title: Patient#2_On-treatment week 12 sample_Non_Responder

value: Skin

value: PD (BOR)


title: WT_CD3pos_KO_CD3neg_GEX

value: Wildtype CD3 positive and Csf2 KO CD3 negative


title: NTC 3

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

data_processing:
Fastq files were aligned to mm10 mouse reference genome (GRCm38.39) and per-gene counts quantified by RSEM (1.3.1)
based on the gene annotation Mus_musculus.GRCm38.89.chr.gtf.
Assembly: mm10
Supplementary files format and content: gene expression TPM in txt file

source_name: CD8 T cells

growth_protocol: Not applicable

extract_protocol:
Magnetically enriched CD8 T cells after 72hrs of CD3/CD28 stimulation
Bulk RNA-seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Not applicable

value: male

tag: genotype/variation

value: control

value: CD8 T cells


title: Patient#2_On-treatment week 4 sample_Non_Responder


title: NTC 2


title: CaptureC_cDC1_1


title: RNA_125_CD4_N

tag: tissue

value: blood


title: CaptureC_CDP_2

source_name: Dendritic cell progenitor

tag: cell type

value: Dendritic cell progenitor


title: Patient#2_Pre-therapy sample_Non_Responder


title: NTC 1

tag: strain


title: CaptureC_CDP_1


title: CaptureC_MPP_2

source_name: Multi-potent progenitor cell

value: Multi-potent progenitor cell


title: ARKO 3

value: AR-deficient


title: RNA_398_CD4_NStim

source_name: CD4 naive T cell ex-vivo stimulated with anti-CD3/CD28 beads


title: WT_CD3pos_KO_CD3neg_HTO

value: kidney cells


title: Patient#1_On-treatment week 4 sample_Non_Responder

value: F

value: STAGE IV M1c

value: Subcutaneous


title: ARKO 2


title: Patient#6_Pre-therapy sample_Non_Responder


title: ARKO 1


title: Patient#14_On-treatment week 12 sample_Responder

value: PR (BOR)


title: Patient#14_On-treatment week 4 sample_Responder

value: M


title: RNA_253_CD4_N


title: RNA_480_CD4_EM

source_name: CD4 EM T cell


title: 38:8 ROK

city: Stockholm

first: Emmanuelle

last: Charrin

address: Alfred Nobels Alle 8

country: Sweden

institute: Karolinska Institute

description: Raw counts ROK.txt

data_processing:
bcl2fastq v2.20.0.422 program was used to convert and demultiplex Bcl files
STAR 2.7.5b was used to index the mouse reference genome mm10/GRCm38 and align fastq files
mapped reads were counted in annotated exons using featureCounts v1.5.1. (annotations and ref genome from Ensembl)
The count table from featureCOunts was imported into R/Bioconductor and DGE performed using EdgeR
Genes that had 1 count per million in 3 samples were used and normalized using TMM normalization. The gene counts were transformed to log2-counts per million using voom with samples weights and subsequent differential gene expression analysis was performed in limma.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Tubular fraction

extract_protocol:
Kidneys were perfused with dynabeads upon sacrifice. Using enzymatic digestion and a magnetic stand glomerular fraction was separated from the rest of the kidney (ROK). Trizol reagent was added to each fraction to harvest RNA. TruSeq RNA SamplePrep kit (illumina) was used to construct libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Kidney

tag: fraction

value: Tubular

value: 9 weeks old

value: WT

value: nephrotoxic serum-induced injury (NTS)


title: 49:3 ROK

description: Raw counts ROK.txt

value: 10 weeks old

value: Alb-hKL

tag: treatment


title: Patient#14_Pre-therapy sample_Responder

source_name: metastatic melanoma


title: RNA_125_CD4_NStim

tag: donor

value: blood

value: anti-CD3/CD28 beads


title: RNA_253_CD4_NStim

tag: stimulation


title: Patient#1_Pre-therapy sample_Non_Responder

value: PD (BOR)


title: RNA_480_CD4_NStim

tag: sorting markers


title: 49:2 ROK

description: Raw counts ROK.txt


title: RNA_398_CD4_EM


title: AP-32

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

institute: ICGEB

description:
30 million of RAW 264.7 underwent anti-HuR antibody+LPS+DMSO treatment
AP-32

data_processing:
Raw sequences files’ quality was checked via FastQC (v 0.11.9, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
We have performed reads alignment to the mouse reference genome using STAR aligner (Spliced Transcripts Alignment to a Reference, v 2.7.7a)
Counts derive from HT-seq counts integrated in star aligner
Differentially expressed genes (DEGs) were generated using the package DESeq2.
Assembly: Mus musculus GRCm39.103 (GTF file), Mus musculus GRCm39 DNA primary assembly fasta
Supplementary files format and content: Counts from HT-seq counts integrated in star aligner

source_name: RAW 264.7 cells

growth_protocol: Murine macrophages RAW264.7 (ICLC, Genova) cell lines were maintained in high glucose Dulbecco’s modified Eagle’s medium (DMEM) by adding 10% fetal bovine serum (FBS, Lonza), 2 mM L-glutamine, 100 U/ml penicillin-streptomycin (Lonza) in standard growth conditions.

extract_protocol:
For RIP-seq,TRIzol reagent was added directly to the beads for HuR-bound RNA isolation and processed for library preparation. For RNA-seq TRIzol reagent was added directly to the cells pellets
RNAs from INPUT and RIP were tested for quality using Bioanalyzer and 7ng of the extracted RNA, having RIN higher than 9, were used for fragmentation at 94 °C for 4 min. RNA libraries were generated using the SMART-Seq Stranded Kit (Takara).

treatment_protocol: Cells have been harvested after treatments for 6 hours with LPS (1 ug/ml) TMs (10 uM) or DMSO and lysed with 20 mM Tris–HCl at pH 7.5, 100 mM KCl, 5 mM MgCl2, and 0.5% NP-40 supplemented with 1% protease inhibitor cocktail (Sigma Aldrich) and 100 units of RiboLOCK RNase inhibitor (Thermo Fisher Scientific) for 10 min on ice and centrifuged at 15 000 × g for 10 min at 4°C.

tag: replica

value: anti-HuR antibody+LPS+DMSO treatment


title: 49:7 Glom

description: Raw counts GLOM.txt

source_name: Glomerular fraction

value: Glomerular

tag: age


title: Patient#12_On-treatment week 4 sample_Responder

tag: Sex

value: F

tag: ajcc 8th edition stage

value: STAGE IV M1a

value: Skin

value: SD (BOR)


title: AP-33

description:
30 million of RAW 264.7 underwent anti-HuR antibody+LPS+TM7nox treatment
AP-33

value: anti-HuR antibody+LPS+TM7nox treatment


title: RNA_253_CD4_EM


title: Patient#12_On-treatment week 12 sample_Responder

tag: type of lesion

tag: response to therapy


title: AP-31

description:
30 million of RAW 264.7 underwent anti-HuR antibody+DMSO treatment
AP-31

value: anti-HuR antibody+DMSO treatment


title: RNA_125_CD4_EM


title: AP-30

description:
30 million of RAW 264.7 underwent LPS+TM7nox treatment
AP-30

value: LPS+TM7nox treatment


title: 49:1 ROK

description: Raw counts ROK.txt

value: Kidney

value: Tubular


title: CaptureC_MPP_1

value: Multi-potent progenitor cell


title: Patient#11_On-treatment week 12 sample_Responder

value: M

value: Soft tissue


title: RNA_480_CD4_EMStim

source_name: CD4 EM T cell ex-vivo stimulated with anti-CD3/CD28 beads

value: blood


title: 49:1 Glom

description: Raw counts GLOM.txt

value: 10 weeks old

value: WT

value: nephrotoxic serum-induced injury (NTS)


title: RNA_398_CD4_EMStim

value: anti-CD3/CD28 beads


title: AP-28

description:
30 million of RAW 264.7 underwent DMSO treatment
AP-28

value: DMSO treatment


title: 38:7 ROK

description: Raw counts ROK.txt

value: 9 weeks old

value: Alb-hKL


title: AP-27

description:
30 million of RAW 264.7 underwent IgG+LPS+TM7nox treatment
AP-27

value: IgG+LPS+TM7nox treatment


title: Patient#11_On-treatment week 4 sample_Responder

value: STAGE IV M1a

value: SD (BOR)


title: RNA_253_CD4_EMStim


title: AP-26

description:
30 million of RAW 264.7 underwent IgG+LPS+DMSO treatment
AP-26

value: IgG+LPS+DMSO treatment


title: 38:7 Glom

description: Raw counts GLOM.txt

value: Kidney

value: Glomerular


title: Patient#5_On-treatment week 12 sample_Responder

value: IIIC

value: Skin

value: CR (BOR)


title: RNA_125_CD4_EMStim

value: blood


title: AP-25

description:
30 million of RAW 264.7 underwent IgG+DMSO treatment
AP-25

value: IgG+DMSO treatment


title: 49:2 Glom

description: Raw counts GLOM.txt

value: 10 weeks old

value: WT


title: RNA_480_CD4_CM

source_name: CD4 CM T cell


title: Patient#12_Pre-therapy sample_Responder

value: F


title: 38:4 ROK

description: Raw counts ROK.txt

value: Tubular

value: nephrotoxic serum-induced injury (NTS)


title: Patient#5_Pre-therapy sample_Responder

value: M


title: RNA_253_CD4_CM


title: 38:5 ROK

description: Raw counts ROK.txt

value: 9 weeks old

value: Alb-hKL


title: AP-29

description:
30 million of RAW 264.7 underwent LPS+DMSO treatment
AP-29

value: LPS+DMSO treatment


title: Patient#4_On-treatment week 12 sample_Responder

value: STAGE IV M1a

value: PR (BOR)


title: 38:4 Glom

description: Raw counts GLOM.txt

value: Kidney

value: Glomerular


title: AP-23

description:
30 million of RAW 264.7 underwent anti-HuR antibody+LPS+DMSO treatment
AP-23

value: anti-HuR antibody+LPS+DMSO treatment


title: Patient#4_On-treatment week 4 sample_Responder

value: Skin


title: RNA_125_CD4_CM

value: blood


title: AP-22

description:
30 million of RAW 264.7 underwent anti-HuR antibody+DMSO treatment
AP-22

value: anti-HuR antibody+DMSO treatment


title: Patient#5_On-treatment week 4 sample_Responder

value: IIIC

value: CR (BOR)


title: AP-21

description:
30 million of RAW 264.7 underwent LPS+TM7nox treatment
AP-21

value: LPS+TM7nox treatment


title: YoungMale-Brain-NoStim-6_S5

city: Bar Harbor

first: Gareth

last: Howell

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
NGSQCToolkit v2.3 for the removal of adapters and trimming low quality bases (Phred < 30)
Bowtie2 v2.2.0 to align reads
RSEM v1.2.12 to quantify gene expression as counts per million (cpm), TPM or FPKM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include expected raw counts, TPM and FPKM values for each sample, but only raw counts were used for downstream analysis

source_name: Brain

extract_protocol:
Cells were collected into 350ul of RLT lysis buffer with B-mercaptoethanol and stored in -80C until RNA isolation.  Cells were homogenized by syringe in RLT buffer from a RNeasy Micro Kit (Qiagen).  For each sample, total RNA was isolated according to the manufacturer’s protocol (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD3e+CD8+CD44hiCD62Llo T cells were sorted and were incubated with PMA/ionomycin (500X) for 2hrs at 37C water bath

value: CD8 T cells

value: NoStim

value: Male

value: Young


title: Patient#11_Pre-therapy sample_Responder

value: M

value: Soft tissue

value: SD (BOR)


title: Patient#4_Pre-therapy sample_Responder

value: STAGE IV M1a

value: PR (BOR)


title: YoungMale-Brain-NoStim-5_S4


title: AP-20

description:
30 million of RAW 264.7 underwent LPS+DMSO treatment
AP-20

value: LPS+DMSO treatment


title: 38:5 Glom

description: Raw counts GLOM.txt

value: Kidney

value: Glomerular

value: 9 weeks old

value: Alb-hKL

value: nephrotoxic serum-induced injury (NTS)


title: RNA_398_CD4_CMStim

source_name: CD4 CM T cell ex-vivo stimulated with anti-CD3/CD28 beads

value: blood

value: anti-CD3/CD28 beads


title: YoungMale-Brain-NoStim-4_S3

value: CD8 T cells


title: AP-19

description:
30 million of RAW 264.7 underwent DMSO treatment
AP-19

value: DMSO treatment


title: RNA_253_CD4_CMStim


title: YoungMale-Brain-NoStim-3_S2

value: NoStim

value: Male


title: RNA_125_CD4_CMStim

source_name: CD4 CM T cell ex-vivo stimulated with anti-anti-CD3/CD28 beads


title: AP-15

description:
30 million of RAW 264.7 underwent anti-HuR antibody+LPS+TM7nox treatment
AP-15

value: anti-HuR antibody+LPS+TM7nox treatment


title: YoungMale-Brain-NoStim-2_S1

value: Young


title: Ischemic gastrocnemius with proanthocyanidins treatment_adult mice_rep3

city: Luzhou city

first: Du

last: Chao

address: 25 Taiping Street, Jiangyang district

institute: The Affiliated Hospital of Southwest Medical University

description: sample name: 177

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

source_name: Ischemic gastrocnemius

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol:
Experimental animals were male and commercially-available C57BL/6 mice (Tengxin biotechnology co. LTD, Chongqing,China).
All mice were raised in Pathogen-free room and the room was maintained at a constant temperature of 23±1℃ with a 12 h light/dark cycle. Food and water were available ad libitum in the home cages.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: Six mice were anesthetized with 1% pentobarbital sodium solution (30 mg kg-1), and unilateral hindlimb ischemia was induced by femoral artery ligation. Then, those mice were divided into two groups randomly, they were treated via intraperitoneal injection daily from days 0 to 7 with with sterile water or proanthocyanidins. Mice were deeply anesthetized with pentobarbital sodium and then ischemic gastrocnemius were collected at days 7.

tag: gender

value: male

value: 10-12 weeks old

value: Ischemic gastrocnemius

value: proanthocyanidins


title: Ischemic gastrocnemius with proanthocyanidins treatment_adult mice_rep2

description: sample name: 176


title: AP-14

description:
30 million of RAW 264.7 underwent anti-HuR antibody+LPS+DMSO treatment
AP-14

value: anti-HuR antibody+LPS+DMSO treatment


title: ATAC_480_CD8_N

data_processing:
Raw sequencing reads were mapped to the hg38 version of the mouse genome using Bowtie-1.1.1
For each sample peaks of accessibility were identified and annotated using MACS2 with the default settings.  A consensus set of peaks were compiled using the mergePeaks HOMER function.  Read depth for each peak was computed in R/Bioconductor with the GenomicRanges package and normalized to reads per peak per million (rppm).
Genome_build: hg38

source_name: CD8 naive T cell

extract_protocol:
10,000 cells were centrifuged for 10 minutes at 500xg, and tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1X TD buffer (10 mM TAPS-NaOH pH 8.1, 5 mM MgCl2, 10% DMF), 2.5 μl Tn5 transposase, 0.1% Tween 20 and 0.02% Digitonin) and then incubated for 1 h at 37°C
DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc)

tag: patient id


title: RNA_480_CD4_CMStim


title: AP-13

description:
30 million of RAW 264.7 underwent anti-HuR antibody+DMSO treatment
AP-13

value: anti-HuR antibody+DMSO treatment


title: ATAC_398_CD8_N


title: AgedMaleSpleenPlusStim40_S11

source_name: Spleen

value: PlusStim

value: Aged


title: ATAC_253_CD8_N


title: AP-12

description:
30 million of RAW 264.7 underwent LPS+TM7nox treatment
AP-12

value: LPS+TM7nox treatment


title: AgedMaleSpleenPlusStim39_S9


title: Ischemic gastrocnemius with proanthocyanidins treatment_adult mice_rep1

description: sample name: 171


title: AgedMaleSpleenPlusStim38_S5


title: fkbp39del_fkbp41del_totalRNA_2

city: Memphis

first: Mario

last: Halic

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

data_processing:
base calling with RTA1.18.64
Sequenced reads were trimmed for the adaptor sequence, then mapped to the S.pombe genome with Novoalign (http://www.novocraft.com) randomly assigned.
Reads mapping with two or fewer mismatches were retained.
Enrichment was calculated with our house Perl scripts
Normalization to reads per million
Genome_build: Genome_build: Schizosaccharomyces_pombe.ASM294v1.18
Supplementary_files_format_and_content: Supplementary_files_format_and_content: can be viewed with IGV browser: http://www.broad.mit.edu/igv

organism: Schizosaccharomyces pombe

growth_protocol: cells were grown in liquid, rich YES medium

extract_protocol:
ChIP libraries: IP of crosslinked (1% formaldehyde, 15 min) sonycated lysate, followed by decrosslinking and protein and RNA degradation. DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). Nascent RNA: RNA was labeled with 4 Thiouracil (Sigma), extracted, after removal of DNA was treated EZ-Link HPDP-Biotin (Thermo Scientific). Labeled RNA was recovered using streptavidin beads (Roche). RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB). Total RNA was  isolated applying the hot phenol method. RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB).
Libraries were prepared using NEBnext Ultra Directional RNA or DNA Ultra II Library Prep Kit for Illumina (NEB), following the manufacturer instruction.

tag: strain number

tag: target molecule

value: total RNA

tag: genotype/variation


title: AP-11

description:
30 million of RAW 264.7 underwent LPS+DMSO treatment
AP-11

value: LPS+DMSO treatment


title: fkbp41del_totalRNA_2


title: AP-10

description:
30 million of RAW 264.7 underwent DMSO treatment
AP-10


title: AgedMaleSpleenPlusStim37_S6

tag: strain

tag: cell type

value: CD8 T cells


title: ATAC_125_CD8_N

tag: tissue

value: blood


title: Ischemic gastrocnemius withsterile water treatment_adult mice_rep2

description: sample name: 169

tag: treatment

value: control


title: fkbp39del_totalRNA_2


title: Ischemic gastrocnemius withsterile water treatment_adult mice_rep3

description: sample name: 173


title: Ischemic gastrocnemius withsterile water treatment_adult mice_rep1

description: sample name: 167


title: AgedMaleSpleenPlusStim36_S2

value: Male


title: ATAC_480_CD8_NStim

source_name: CD8 naive T cell ex-vivo stimulated with anti-CD3/CD28 beads

tag: stimulation

value: anti-CD3/CD28 beads


title: ATAC_398_CD8_NStim

tag: sorting markers


title: AP-06

description:
30 million of RAW 264.7 underwent anti-HuR antibody+LPS+TM7nox treatment
AP-06

tag: replica

value: anti-HuR antibody+LPS+TM7nox treatment


title: AP-05

description:
30 million of RAW 264.7 underwent anti-HuR antibody+LPS+DMSO treatment
AP-05


title: wildtype_totalRNA_2

source_name: wild type

value: wild type


title: AgedMaleSpleenNoStim34_S4

value: NoStim

tag: age


title: AP-24

description:
30 million of RAW 264.7 underwent anti-HuR antibody+LPS+TM7nox treatment
AP-24


title: fkbp39del_fkbp41del_totalRNA_1


title: AgedMaleSpleenNoStim33_S3

tag: Sex


title: ATAC_253_CD8_NStim


title: AP-04

description:
30 million of RAW 264.7 underwent anti-HuR antibody+DMSO treatment
AP-04


title: ATAC_125_CD8_NStim


title: ATAC_480_CD8_EMRA

source_name: CD8 EMRA T cell


title: AP-03

description:
30 million of RAW 264.7 underwent LPS+TM7nox treatment
AP-03


title: fkbp39del_totalRNA_1


title: AgedMaleSpleenNoStim31_S7


title: RNA_398_CD4_CM

tag: donor


title: fkbp41del_totalRNA_1


title: AP-02

description:
30 million of RAW 264.7 underwent LPS+DMSO treatment
AP-02


title: AP-01

description:
30 million of RAW 264.7 underwent DMSO treatment
AP-01

value: DMSO treatment


title: AgedMaleSpleenNoStim30_S10


title: wildtype_totalRNA_1


title: ATAC_253_CD8_EMRA


title: fkbp41del_Ytm1_ChIP9

source_name: FLAG-Ytm1, fkbp41Δ

tag: antibody used for ip

value: FLAG magnetic resin, Sigma-Aldrich Anti-FLAG® M2 Magnetic Beads, M8823, lot number SLBD2467V/SLBQ3807V

value: Ytm1 bound DNA

value: FLAG-Ytm1, fkbp41delta


title: AgedMale-Brain-PlusStim-22_S2

value: PlusStim


title: RE-4

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

description: HL_1_3_W62_4_20191128N_GCCGCAAC_TCATGTCT_S459_L004

data_processing:
Sequenced reads were trimmed for removing out adaptor, and low-quality sequences using trim_galore(v0.6.6) with parameters: "--illumina --paired"
Trimmed reads were mapped to mouse reference genome (mm10) using tophat (v2.1.1) with default parameters.
Mapped reads were then used to estmate the abundance of gene expression using cufflinks(v2.2.1) with default parameters.
FPKM values in the genes.fpkm_tracking file were converted into Transcripts Per Million (TPM) values.
Genome_build: mm10
Supplementary_files_format_and_content: TPM

growth_protocol: HL-1 cells were cultured in Dulbecco's Modified Eagle's Medium with 10% foetal bovine serum (FBS) and 1% Pen‐Strep antibiotics at 37°C and 5% CO2.

extract_protocol:
The total RNA was extracted from 1x10^6 cells using the TRIzol reagent and converted to cDNA using the PrimeScript RT Reagent Kit (Takara Bio)
Libraries were prepared using standard illunima protocol

treatment_protocol: HL-1 cells were innfected by virus packaging pCDH and lentiCRISPRv2 (CON), and cells were cultured with 10%FBS; HL-1 cells were innfected by virus sgRNA Wdr62 gene (KD), and cells were cultured with 10%FBS; KD cells was innfected by virus packaging pCDH-WDR62-WT-flag (RE), and cells were cultured with 10%FBS.

tag: cell line

value: Cardiac Muscle Cell Line

tag: genotype

value: Overexpressing WDR65 in KD


title: ATAC_125_CD8_EMRA

tag: patient id


title: RE-3

description: HL_1_3_W62_3_20191128N_TTATATCT_GTCTGCAC_S458_L004

value: Overexpressing WDR64 in KD


title: AgedMale-Brain-PlusStim-21_S7

value: Aged


title: ATAC_480_CD8_EMRAStim

source_name: CD8 EMRA T cell ex-vivo stimulated with anti-CD3/CD28 beads


title: AgedMale-Brain-PlusStim-20_S3

value: CD8 T cells


title: background_Ytm1_ChIP9

tag: strain number


title: ATAC_398_CD8_EMRAStim

value: blood


title: Ytm1_ChIP9

tag: target molecule


title: AgedMaleSpleenNoStim32_S12


title: RE-2

description: HL_1_3_W62_2_20191128N_TGTAATCA_AATCTCCA_S457_L004

value: Overexpressing WDR63 in KD


title: AgedMale-Brain-PlusStim-19_S4

value: Male


title: RE-1

description: HL_1_3_W62_1_20191128N_CTGTGGCG_CACTAGCC_S456_L004

value: Overexpressing WDR62 in KD


title: ATAC_253_CD8_EMRAStim

value: anti-CD3/CD28 beads


title: fkbp41del_Ytm1_ChIP8

tag: genotype/variation


title: ATAC_398_CD8_EMRA


title: AgedMale-Brain-NoStim-9_S8

tag: strain


title: ATAC_125_CD8_EMRAStim


title: AgedMale-Brain-NoStim-8_S7

tag: cell type


title: KD-3

description: HL_1_3_3_20191128N_CTACCAGG_CAACTGAT_S454_L004

value: knockdown Wdr62 by Crispr/Cas11


title: background_Ytm1_ChIP8

value: wild type


title: Ytm1_ChIP8


title: AgedMale-Brain-NoStim-7_S6

value: NoStim


title: fkbp39del_fkbp41del_Ytm1_ChIP7

source_name: FLAG-Ytm1, fkbp39Δfkbp41Δ

value: FLAG magnetic resin, Sigma-Aldrich Anti-FLAG® M2 Magnetic Beads, M8823, lot number SLBD2467V/SLBQ3807V

value: FLAG-Ytm1, fkbp39deltafkbp41delta


title: ATAC_480_CD8_EM

source_name: CD8 EM T cell

tag: tissue


title: ATAC_398_CD8_EM


title: KD-2

description: HL_1_3_2_20191128N_AAGACACT_TGACAGCA_S453_L004

tag: treatment

value: knockdown Wdr62 by Crispr/Cas10


title: fkbp41del_Ytm1_ChIP7

value: Ytm1 bound DNA

value: FLAG-Ytm1, fkbp41delta


title: AgedMale-Brain-NoStim-12_S11


title: ATAC_253_CD8_EM

tag: stimulation


title: KD-1

description: HL_1_3_1_20191128N_TCTCGGTC_CTGACATC_S452_L004

value: Cardiac Muscle Cell Line

value: knockdown Wdr62 by Crispr/Cas9


title: AgedMale-Brain-NoStim-11_S10

value: Aged


title: CON-3

description: HL_1_PCDH_3_20191128N_TACTTAGC_AGGTACCA_S450_L004

value: WT

value: stable express vector


title: ATAC_125_CD8_EM

value: blood

tag: sorting markers


title: ATAC_480_CD8_EMStim

source_name: CD8 EM T cell ex-vivo stimulated with anti-CD3/CD28 beads


title: AgedMale-Brain-NoStim-10_S9

value: CD8 T cells

value: Male


title: AgedFemaleBrainPlusStim27_S8

value: PlusStim

value: Female


title: CON-2

description: HL_1_PCDH_2_20191128N_CCAGAGCT_CGAACTTC_S449_L004


title: Fkbp41_ChIP3

value: HA antibody, Santa Cruz Biotechnology, (F-7):sc-7392, lot number #E1517

value: Fkbp41 bound DNA


title: fkbp41del_Ytm1_ChIP6

value: FLAG magnetic resin, Sigma-Aldrich Anti-FLAG® M2 Magnetic Beads, M8823, lot number SLBD2467V/SLBQ3807V


title: CON-1

description: HL_1_PCDH_1_20191128N_TCGCCTTG_GCTGATTC_S448_L004


title: ATAC_398_CD8_EMStim

value: anti-CD3/CD28 beads


title: AgedFemale-Brain-PlusStim-25_S5


title: AgedFemaleBrainPlusStim26_S1


title: KO-PEN-BCG-2

city: Sapporo

first: Tatsuaki

last: Mizutani

address: N15W7, Kita-ku

country: Japan

institute: Hokkaido University

data_processing:
We removed adapters and trimmed low quality bases at the ends of reads with Cutadapt (ver. 1.18) and TrimGalore (ver. 0.5.0).
GRCm38.86 gtf file was downloaded from ENSEMBL (ftp://ftp.ensembl.org) and applied as gene annotation file.
Reads were mapped to GRCm38 mouse genome using Hisat2 (ver. 2.1.0) with default settings.
Normalized read counts and fold change values were calculated using FeatureCounts (ver. 1.4.5) and DESeq2 (ver. 1.26.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized_gene_counts_*.txt: Matrix tables with normalized read counts for every gene and every sample.

source_name: BCGPEN

growth_protocol: After 6 hours of BCG or casein injections, WT and S100A9 KO peritoneal neutrophils collected using the mouse neutrophils isolation MACS kit (Miltenyi Biotec).

extract_protocol:
Total RNA was extracted with RNeasy mini kit (QIAGEN).
TruSeq stranded mRNA Library Prep. Kit (Illumina) was used for library construction.

treatment_protocol: BCG (strain Tokyo 172) was cultured in Middlebrook 7H9 medium enriched with oleic acid-albumin-dextrose-catalase supplement (BD Biosciences, Heidelberg, Germany) until mid-log phase and then frozen in 1 mL aliquots at -80°C until use. For quantification of the CFU, mycobacteria were serially diluted in Middlebrook 7H9 medium and plated on Middlebrook 7H10 agar plates (BD Biosciences). After 4 weeks of incubation at 37°C, the CFU were quantified. Casein solution (7.5%) was purchased from Cayman Chemical.

value: Peritoneal neutrophils

value: S100a9 KO

value: 6 hours after intraperitoneal injection with BCG


title: Fkbp41_ChIP2


title: ATAC_125_CD8_EMStim


title: KO-PEN-BCG-1


title: background_Fkbp41_ChIP2

value: wild type


title: KD-4

description: HL_1_3_4_20191128N_ACTGTATC_TGCTATTA_S455_L004

value: Cardiac Muscle Cell Line

value: knockdown Wdr62 by Crispr/Cas12


title: fkbp41del_Fkbp39_ChIP4

source_name: Fkbp39-HA, fkbp41Δ

value: Fkbp39 bound DNA

value: Fkbp39-HA, fkbp41delta


title: ATAC_480_CD8_CM

source_name: CD8 CM T cell

value: blood


title: AgedFemale-Brain-PlusStim-24_S9

source_name: Brain

value: CD8 T cells

value: Aged


title: AgedFemale-Brain-PlusStim-23_S11

value: PlusStim


title: fkbp39del_fkbp41del_Ytm1_ChIP6

value: Ytm1 bound DNA

value: FLAG-Ytm1, fkbp39deltafkbp41delta


title: WT-PEN-BCG-3

value: WT


title: CON-4

description: HL_1_PCDH_4_20191128N_GTCTGATG_ATATCCGA_S451_L004

value: stable express vector


title: ATAC_398_CD8_CM


title: Fkbp39_ChIP4

value: HA antibody, Santa Cruz Biotechnology, (F-7):sc-7392, lot number #E1517


title: background_Fkbp41_ChIP3

value: Fkbp41 bound DNA


title: AgedFemale-Brain-NoStim-17_S8

value: NoStim

value: Female


title: WT-PEN-BCG-2

value: Peritoneal neutrophils

value: 6 hours after intraperitoneal injection with BCG


title: WT-PEN-BCG-1


title: background_Fkbp39_ChIP4

value: wild type


title: AgedFemale-Brain-NoStim-16_S12


title: ATAC_125_CD8_CM


title: ATAC_253_CD8_EMStim

value: anti-CD3/CD28 beads


title: fkbp41del_Fkbp39_ChIP3

value: Fkbp39 bound DNA

value: Fkbp39-HA, fkbp41delta


title: AgedFemale-Brain-NoStim-15_S6

value: CD8 T cells


title: ATAC_480_CD8_CMStim

source_name: CD8 CM T cell ex-vivo stimulated with anti-CD3/CD28 beads

value: blood


title: AgedFemale-Brain-NoStim-14_S1

value: Aged


title: KO-PEN-Cas-2

source_name: CasPEN

value: S100a9 KO

value: 6 hours after intraperitoneal injection with casein


title: AgedFemale-Brain-NoStim-13_S10


title: ATAC_398_CD8_CMStim


title: KO-PEN-Cas-1


title: ATAC_253_CD8_CMStim


title: WT-PEN-Cas-2

value: WT


title: ATAC_125_CD8_CMStim


title: seed of QSZ, 10℃14d, rep2

first: wenjia

last: wang

address: No. 198, Shiqiao Road, Hangzhou, Zhejiang Province

institute: Zhejiang Academy of Agricultural Sciences

data_processing:
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).
We aligned reads of all samples to the Solanum lycopersicum（https://solgenomics.net/ftp/genomes/Solanum_lycopersicum/assembly/build_3.00/S_lycopersicum_chromosomes.3.00.fa） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: MSU_V7.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Oryza sativa

source_name: seed

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

value: seed

value: 14 day under 10 C


title: seed of QSZ, 10℃14d, rep3


title: ATAC_480_CD4_N

source_name: CD4 naive T cell


title: WT-PEN-Cas-1


title: ATAC_253_CD8_CM


title: fkbp39Δ_nascentRNA_10min_3

value: nascent RNA


title: wildtype_nascentRNA_10min_3


title: fkbp39Δ_nascentRNA_2min_3


title: ATAC_398_CD4_N


title: KO-PEN-Cas-3


title: ATAC_253_CD4_N


title: N5

city: Wanju

first: Kyung-Tai

last: Lee

state: JeonBuk

address: 1500 Kongjwipatjwi

department: Animal Genomics and Bioinformatics Division

country: South Korea

institute: National Institute of Animal Science

data_processing:
For base calling of Illumina sequencer produced raw pictures, real-time analysis (RTA) software was used and using the BCL to fastq Illumina software, the produced BCL image files were converted to FASTQ raw readings
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CanFam3.1 reference genome using Hisat2 v2.2.1 and FeatureCounts from the Subread package v2.0.1, the mapped reads were utilized to construct a count matrix
Differential expression (DE) analysis of lymphoma and non–lymphoma groups was performed using the DESeq2 package in R
Genome_build: CanFam3.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Canis lupus familiaris

source_name: Non-lymphoma

extract_protocol:
Blood sample using the Trizol/chloroform/isopropanol method according to the manufacturer's instructions (InvitrogenTM, Carlsbad, CA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: Control

value: Blood


title: N6


title: fkbp39Δ_nascentRNA_10min_2


title: wildtype_nascentRNA_2min_3


title: seed of QSZ, 10℃14d, rep1


title: Fkbp39_ChIP3

value: HA antibody, Santa Cruz Biotechnology, (F-7):sc-7392, lot number #E1517


title: seed of QSZ, 10℃12d, rep3

value: 12 day under 10 C


title: ATAC_125_CD4_N

first: Chris

last: Scharer

address: 1510 Clifton Rd, Suite 3086A

institute: Emory University


title: background_Fkbp39_ChIP3

value: Fkbp bound DNA

value: wild type


title: fkbp39Δ_nascentRNA_2min_2


title: seed of QSZ, 10℃12d, rep1


title: N4


title: wildtype_nascentRNA_10min_2


title: ATAC_480_CD4_NStim

source_name: CD4 naive T cell ex-vivo stimulated with anti-CD3/CD28 beads

value: anti-CD3/CD28 beads


title: N3


title: seed of QSZ, 10℃10d, rep3

value: 10 day under 10 C


title: ATAC_398_CD4_NStim


title: wildtype_nascentRNA_2min_2

source_name: wild type


title: ATAC_253_CD4_NStim


title: N2


title: seed of WR04-6, 10℃14d, rep3


title: fkbp39Δ_nascentRNA_10min_1


title: seed of QSZ, 10℃12d, rep2


title: N7


title: ATAC_125_CD4_NStim


title: fkbp39Δ_nascentRNA_2min_1


title: L7

description: marie

source_name: Lymphoma

value: Disease


title: wildtype_nascentRNA_10min_1


title: ATAC_398_CD4_EM

source_name: CD4 EM T cell

value: blood


title: ATAC_480_CD4_EM


title: seed of WR04-6, 10℃14d, rep1


title: wildtype_nascentRNA_2min_1


title: L5


title: seed of WR04-6, 10℃14d, rep2


title: seed of WR04-6, 10℃12d, rep3


title: fkbp39Δ_Ytm1_ChIP7

source_name: FLAG-Ytm1, fkbp39Δ

value: FLAG-Ytm1, fkbp39{delta}

tag: chip antibody

value: FLAG magnetic resin, Sigma-Aldrich Anti-FLAG® M2 Magnetic Beads, M8823, lot number SLBD2467V/SLBQ3807V

value: Ytm1 bound DNA


title: ATAC_253_CD4_EM


title: L6


title: seed of WR04-6, 10℃12d, rep2


title: ATAC_125_CD4_EM


title: L4


title: seed of QSZ, 10℃10d, rep2


title: wildtype_Ytm1_ChIP7


title: L3


title: ATAC_480_CD4_EMStim

source_name: CD4 EM T cell ex-vivo stimulated with anti-CD3/CD28 beads


title: L2


title: background_Ytm1_ChIP7


title: N1


title: ATAC_398_CD4_EMStim


title: fkbp39Δ_Ytm1_ChIP6


title: seed of WR04-6, 10℃10d, rep3


title: seed of WR04-6, 10℃10d, rep2


title: L1


title: ATAC_253_CD4_EMStim


title: ATAC_125_CD4_EMStim


title: seed of WR04-6, 10℃10d, rep1


title: wildtype_Ytm1_ChIP6


title: Release_Day21_Rep4

city: Los Alamos

first: Eric

middle: M

last: Small

state: New Mexico

address: Bikini Atoll Rd.

department: Earth and Environmental Sciences Division

institute: Los Alamos National Laboratory

data_processing:
Samples were de-multiplexed using the standard Ion Torrent S5 protocol, and sequencing reads were matched to H3/H4 library mutant barcodes provided by Dharmacon corresponding to the H3/H4 mutant library generated by Dai et al 2006. Fuzzy read matching was used to match reads and barcodes to account for sequencer error and varied read length following de-multiplexing and adapter clipping. Reads and barcodes were identified as a match when they occurred within a Levenshtein distance of 1. Custom gpuized software was developed to match reads to barcodes by application of the Levenshtein edit distance formula along a sliding window (barcode length (available at https://github.com/ericmsmall/Levenshtein). Reads were CPM normalized and used for downstream comparisons.
Supplementary files format and content: Comma-separated-matrix includes rows corresponding to strain names from Dai et al 2006 and provided by Dharmacon in the documentation of the H3/H4 non-essential histone mutant library. Column names correspond to .fastq files analyzed. Each cell contains the number of mutant barcode counts matched to a read in a prepared library after demultiplexing, by application of custom software, which are then CPM normalized.
Library strategy: Bar-Seq

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: For each of the 4 biological replicates the five 96-well pates containing the H3/H4 mutant library (Dharmacon # YSC5106) were thawed at room temperature. The libraries were replica pinned (V&P Scientific Library Copier, VP 381) to YPD OmniTray plates (Thermo, 242811). Colonies were allowed to develop for one day at 30°C before replica pinning to SC-URA + 100 µg/ml nourseothricin (Gold Bio, N-500) OmniTray plates for selection. After two days at 30°C, the colonies were replica pinned back to YPD OmniTray plates and grown for an additional two days at 30°C. The replica pinner was then pressed firmly into the colonies that arose from all 5 plates and used to inoculate 25mL of YPD in an OmniTray by gently swirling the cell-covered pinner in the medium. The resulting pooled cells were inoculated into 200mL of YPD+AMP+Adenine medium to a final OD600 of 0.0025, and was the starting culture for the proliferating, quiescent, stationary phase, and released cell samples.

extract_protocol:
gDNA was isolated by a modified smash and grab protocol (Long et al. 2020 and Hoffman & Winston 1987). Briefly, frozen cell pellets were thawed on ice, resuspended in 300µL smash and grab buffer (2% Triton X-100, 1% SDS, 0.1M NaCl, 0.01M Tris, pH 8.0, 1mM EDTA) and transferred to an Eppendorf tube. Three hundred µL of unbuffered phenol-chloroform-isoamyl alcohol (25:24:1 v/v) and 0.3 g of glass beads (Sigma, G8772) were added, and the cells were vortexed at highest speed for 6 minutes, on a disruptor genie (Scientific Industries SI-D248). The lysate was transferred to a new tube, the beads were washed with 200 µL TE, and the wash was combined with the lysate.  DNA was precipitated by overnight incubation at -80°C after addition of 70% ethanol and 0.3M sodium acetate.  Precipitated DNA was resuspended in 400µL TE plus 1.2µL RNAse A (25mg/mL, Sigma, R4642) and incubated at 37°C for 80 minutes. An additional phenol-chloroform extraction was performed, followed by two ethanol precipitations. Isolated gDNA was diluted 1:20, and the concentration was determined by NanoDrop. One hundred ng of gDNA was used as input for library preparation.
A two-step PCR protocol modified from Robinson et al. 2014 was utilized to generate multiplexed Ion Torrent Bar-seq libraries. In step 1, UPTAGs from a single sample were amplified using High Fidelity Platinum Taq (Thermo,11304), 1.5mM MgSO4, and primers U1H-ATGTCCACGAGGTCTCT and D1H-CGGTGTCGGTCTCGTAG by low-cycle PCR (94˚C 2' (94˚C 1', 53˚C 1', 72˚C 45s)x20; 72˚C 10', 4 ˚C ∞). Clean-up of PCR products and removal of gDNA was performed using Omega Biotek NGS beads using a double-ended 1.8x/1.0x size selection. One ng of the cleaned-up and amplified UPTAG library was used for subsequent library preparation. In step 2, samples were barcoded for multiplexing, and sequencing adapters were added using the Ion Torrent fusion method (publication #4468326). A1 adapter primers are listed in Supplemental Table 2, with all A1 primers sharing the following features (A1NNNNNNNNNNNNATGTCCACGAGGTCTCT). Additionally, to circumvent off-target amplification, the P1 bead adapter primer was designed with homology to the D2H region of the mutant barcode cassette:  P1- trP1GATGATGAATTCGAGCTGGG. Barcoded sequencing adapters corresponding to individual samples were fused to UPTAG libraries by low-cycle PCR (94˚C 2' (94˚C 1', 68˚C 1', 72˚C 45s) x10, 72˚C 10', 4 ˚C ∞). Clean-up of PCR products was performed with Omega Biotek NGS beads using a double-ended 1.8x/1.2x size selection. Libraries were quantified by qPCR (Thermo, 4468802) and sequenced on an Ion Torrent S5.

tag: developmental stage

value: 21 Day Release Cell

value: yeast cell


title: ATAC_480_CD4_CM

city: Atlanta

source_name: CD4 CM T cell


title: fkbp39Δ_Ytm1_ChIP5


title: Pig 66 - Normal, energy treatment

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

data_processing:
Adaptor sequences and low quality reads removed
Mapped to Sus Scrofa genome (11.1)
DEG assessed using DeSeq2
Assembly: Sscrofa11.1
Supplementary files format and content: excel file with count data and Ensembl gene ID for each sample

source_name: Liver

growth_protocol: piglets were reared indoors for 72 hours after birth

extract_protocol:
Total RNA was extracted using mRNAeasy kits (Qiagen)
Standard BGI

treatment_protocol: energy supplement consisted of a commercial available treatment (Piggy Boost, Hatting Agro, Horsens, Denmark)

value: Liver

value: Normal

value: energy treatment


title: Release_Day21_Rep3


title: wildtype_Ytm1_ChIP5


title: ATAC_398_CD4_CM


title: seed of WR04-6, 10℃12d, rep1

city: Hangzhou

value: seed


title: Pig 68 - Normal, energy treatment


title: Release_Day21_Rep2


title: Pig 64 - Normal, energy treatment


title: Pig 65 - IUGR, energy treatment

value: IUGR


title: ATAC_253_CD4_CM


title: Pig 61 - Normal, no treatment

value: no treatment


title: Release_Day21_Rep1


title: ATAC_125_CD4_CM


title: background_Ytm1_ChIP5


title: Stationary_Phase_Day21_Rep4

value: Stationary Phase Cell


title: fkbp39Δ_Ytm1_ChIP4


title: Pig 59 - IUGR, energy treatment


title: ATAC_480_CD4_CMStim

source_name: CD4 CM T cell ex-vivo stimulated with anti-CD3/CD28 beads


title: Pig 58 - IUGR, energy treatment


title: wildtype_Ytm1_ChIP4


title: Stationary_Phase_Day21_Rep3


title: ATAC_398_CD4_CMStim


title: background_Ytm1_ChIP6

value: wild type


title: ATAC_253_CD4_CMStim

value: anti-CD3/CD28 beads


title: Stationary_Phase_Day21_Rep2


title: fkbp39Δ_Ytm1_ChIP3


title: background_Ytm1_ChIP4


title: Pig 52 - Normal, no treatment


title: Release_Day14_Rep4

value: 14 Day Release Cell


title: ATAC_125_CD4_CMStim

source_name: CD4 CM T cell ex-vivo stimulated with anti-anti-CD3/CD28 beads


title: Pig 53 - IUGR, energy treatment


title: Stationary_Phase_Day21_Rep1


title: wildtype_Ytm1_ChIP3


title: Ezra_seq_HEK293_Starvation_rep1

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

data_processing:
Library strategy: Ezra-seq
The adaptor AAAAAAAAAAAA was trimmed by Cutadapt. The reads with length <15 nt were not included.
The trimmed reads were aligned to human or mouse transcriptome, using STAR with default parameters. The uniquely mapped reads were used for analysis.
Genome_build: GRCm38/GRCh38
Supplementary_files_format_and_content: The processed files are read count  on mRNAs. The first column is the ENSEMBL transcript ID. The second column is the read count on mRNA.

source_name: HEK293, stably expressing H-2Kb

growth_protocol: HEK293-Kb or MEF cells are maintained in Dulbecco’s Modification of Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
A total of 4 plates (10-cm) HEK293-Kb cells grown to 80% confluency were changed with fresh medium to remove the dead cells 2 h before harvesting.Cells were washed by cold PBS and lysed in the polysome lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 100 μg/mL cycloheximide with 2 % Triton X-100). The lysates were cleared by centrifugation at 14,000 rpm for 10 min at 4 °C. 15-45 % (wt/vol) sucrose density gradients were freshly prepared in a SW41 ultracentrifuge tube using a Gradient Master. 500 μL of cytosolic extracts were loaded onto sucrose gradients followed by ultracentrifugation for 2 h 30 min at 32,000 rpm 4 °C in a SW41 rotor. Polysome profiles were recorded at A254 using the Brandel Gradient Fractionation System and an ISCO UA-6 UV/Vis detector. An aliquot of ribosome fractions representing monosome or polysome were collected followed by digestion with E. coli RNase I (750 U per 100 A260 units) by incubation at 4 °C for 1 h. Total RNA was extracted using Trizol LS reagent. Purified RNAs were used for cDNA library construction.
The ribosome-protected mRNA fragments were separated on a 15% polyacrylamide TBE-urea gel and visualized using SYBR Gold. Selected regions in the gel corresponding to 25–35 nt were excised. RNA fragments were dissolved by soaking overnight in 400 μL RNA elution buffer (300mM NaOAc, pH 5.2, 1mM EDTA, 0.1 U mL−1 SUPERase_In). The gel debris was removed using a Spin-X column, followed by ethanol precipitation. Purified RNA fragments were resuspended in nuclease-free water and quantified using Qubit 2.0 Fluorometer. A fraction of RNAs (10~200 ng) were used for cDNA library construction. In brief, 10 μL RNAs were mixed thoroughly with 1 μL T4 PNK (10 U), 1 μL purified TS2126 and 1 μL PAP1 enzyme in 7 μL Ezra buffer). The mixture was incubated at 37°C for 30 min followed by 65°C for 20 min. After ethanol precipitation at -20°C for 30 min, the dissolved RNA pellet was mixed with 0.5 μM 5’ end adaptor followed by ligation for 90 min at 22 °C in a 10 μL reaction mixture (1 × T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated KQ). The ligated RNA sample was mixed with 1 μl 0.5 mM dNTP and 1 μl 0.5 μM RT primer and incubated at 65 °C for 3 min, followed by incubation on ice for 1 min. The reaction mix was then added with 9 μl cDNA synthesis mix (5 × first strand buffer, 0.1 M DTT and 750 μg/μl m-MLV-mut5) followed by incubation at 50°C for 30 min. The synthesized cDNAs were mixed with 10 μL rRNA depletion oligo mix tagged with biotin (1 μL 25 μM oligo mix and 3 μL 20 × SSC buffer) and heated at 94°C for 30 s followed by slowly cooling down (3 °C/min) to 37 °C. 30 μL pre-washed streptavidin magnetic beads was added to each sample and stay at room temperature for 10 min. After placing on magnet stand for 1 min, the supernatant was transferred to a new tube and precipitated by ethanol. rRNA depleted cDNAs were amplified by PCR using barcoded sequencing primers. The PCR contains 1 × HF buffer, 0.2 mM dNTP, 0.5 μM oligonucleotide primers, and 0.5 U Phusion polymerase. PCR was carried out under the following conditions: 98 °C, 30 s; (98 °C, 5 s; 68 °C, 15 s; 72 °C, 10 s) for 12 cycles; 72 °C, 3 min. PCR products were separated on a 8% polyacrylamide TBE gel. Expected DNA at 180 bp was excised and recovered from DNA gel elution. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled into sequencing lanes, which were sequenced using NextSeq 500.

value: HEK293, stably expressing H-2Kb

value: Starvation


title: Release_Day14_Rep2


title: Ezra_seq_HEK293_Starvation_rep2


title: fkbp39Δ_Ytm1_ChIP1

value: FLAG-Ytm1, fkbp39{delta}


title: fkbp39Δ_Ytm1_ChIP2

value: FLAG magnetic resin, Sigma-Aldrich Anti-FLAG® M2 Magnetic Beads, M8823, lot number SLBD2467V/SLBQ3807V


title: Release_Day14_Rep1


title: wildtype_Ytm1_ChIP1

value: Ytm1 bound DNA


title: Pig 49 - IUGR, energy treatment


title: Stationary_Phase_Day14_Rep4


title: Pig 47 - IUGR, energy treatment


title: background_Ytm1_ChIP1


title: Ezra_seq_HEK293_shScram_rep2

extract_protocol:
A total of 4 plates (10-cm) HEK293-Kb cells grown to 80% confluency were changed with fresh medium to remove the dead cells 2 h before harvesting.Cells were washed by cold PBS and lysed in the polysome lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 100 μg/mL cycloheximide with 2 % Triton X-100). The lysates were cleared by centrifugation at 14,000 rpm for 10 min at 4 °C. 15-45 % (wt/vol) sucrose density gradients were freshly prepared in a SW41 ultracentrifuge tube using a Gradient Master. 500 μL of cytosolic extracts were loaded onto sucrose gradients followed by ultracentrifugation for 2 h 30 min at 32,000 rpm 4 °C in a SW41 rotor. Polysome profiles were recorded at A254 using the Brandel Gradient Fractionation System and an ISCO UA-6 UV/Vis detector. An aliquot of ribosome fractions representing monosome or polysome were collected followed by digestion with E. coli RNase I (750 U per 100 A260 units) by incubation at 4 °C for 1 h. Total RNA was extracted using Trizol LS reagent. Purified RNAs were used for cDNA library construction.
The ribosome-protected mRNA fragments were separated on a 15% polyacrylamide TBE-urea gel and visualized using SYBR Gold. Selected regions in the gel corresponding to 25–35 nt were excised. RNA fragments were dissolved by soaking overnight in 400 μL RNA elution buffer (300mM NaOAc, pH 5.2, 1mM EDTA, 0.1 U mL−1 SUPERase_In). The gel debris was removed using a Spin-X column, followed by ethanol precipitation. Purified RNA fragments were resuspended in nuclease-free water and quantified using Qubit 2.0 Fluorometer. A fraction of RNAs (10~200 ng) were used for cDNA library construction. In brief, 10 μL RNAs were mixed thoroughly with 1 μL T4 PNK (10 U), 1 μL purified TS2126 and 1 μL PAP1 enzyme in 7 μL Ezra buffer). The mixture was incubated at 37°C for 30 min followed by 65°C for 20 min. After ethanol precipitation at - 20°C for 30 min, the dissolved RNA pellet was mixed with 0.5 μM 5’ end adaptor followed by ligation for 90 min at 22 °C in a 10 μL reaction mixture (1 × T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated KQ). The ligated RNA sample was mixed with 1 μl 0.5 mM dNTP and 1 μl 0.5 μM RT primer and incubated at 65 °C for 3 min, followed by incubation on ice for 1 min. The reaction mix was then added with 9 μl cDNA synthesis mix (5 × first strand buffer, 0.1 M DTT and 750 μg/μl m-MLV-mut5) followed by incubation at 50°C for 30 min. The synthesized cDNAs were mixed with 10 μL rRNA depletion oligo mix tagged with biotin (1 μL 25 μM oligo mix and 3 μL 20 × SSC buffer) and heated at 94°C for 30 s followed by slowly cooling down (3 °C/min) to 37 °C. 30 μL pre-washed streptavidin magnetic beads was added to each sample and stay at room temperature for 10 min. After placing on magnet stand for 1 min, the supernatant was transferred to a new tube and precipitated by ethanol. rRNA depleted cDNAs were amplified by PCR using barcoded sequencing primers. The PCR contains 1 × HF buffer, 0.2 mM dNTP, 0.5 μM oligonucleotide primers, and 0.5 U Phusion polymerase. PCR was carried out under the following conditions: 98 °C, 30 s; (98 °C, 5 s; 68 °C, 15 s; 72 °C, 10 s) for 12 cycles; 72 °C, 3 min. PCR products were separated on a 8% polyacrylamide TBE gel. Expected DNA at 180 bp was excised and recovered from DNA gel elution. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts  of barcoded samples were pooled into sequencing lanes, which were sequenced using NextSeq 500.


title: Ezra_seq_HEK293_sheIF5B_rep1


title: Pig 55 - Normal, no treatment


title: Pig 46 - IUGR, energy treatment


title: Stationary_Phase_Day14_Rep3


title: Pig 50 - Normal, energy treatment


title: background_Ytm1_ChIP3


title: Fkbp39_ChIP2

value: HA antibody, Santa Cruz (F-7), sc-7392, lot number #E1517

value: Fkbp39 bound DNA


title: Ezra_seq_HEK293_shScram_rep1


title: Pig 45 - Normal, energy treatment

value: Liver


title: Stationary_Phase_Day14_Rep2

value: yeast cell


title: Ezra_seq_HEK293_sheIF5B_rep2


title: Ezra_seq_HEK293_try4


title: Ezra_seq_HEK293_CHX_treatment


title: Release_Day7_Rep4

value: 7 Day Release Cell


title: background_Fkbp_ChIP2


title: Fkbp41_ChIP1

value: Fkbp41 bound DNA


title: Release_Day14_Rep3


title: Pig 42 - Normal, no treatment

value: Normal


title: Pig 48 - Normal, no treatment

value: no treatment


title: Ezra_seq_HEK293_try3


title: Fkbp39_ChIP1


title: Pig 43 - IUGR, no treatment

value: IUGR


title: Stationary_Phase_Day14_Rep1

value: Stationary Phase Cell


title: Ezra_seq_HEK293_try1


title: Release_Day7_Rep1


title: background_Fkbp_ChIP1

value: wild type

value: Fkbp bound DNA


title: Pig 39 - IUGR, energy treatment

value: energy treatment


title: WT_D2_4

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

hyb_protocol: Hybridizations overnight to Mouse Clariom D microarrays (ThermoFisher) and post-hybridization washing, and staining were done with GeneChip™ Hybridization, Wash, and Stain Kit, Fluidics Station 450.

scan_protocol: Scans were done on 7G scanner according to manufacturer protocols

data_processing: Microarray data were analyzed with custom codes in R.

label: biotin

organism: Rattus norvegicus

source_name: Nucleus accumbens

label_protocol: biotin-labeled cDNA using 90 ng of total RNA and the GeneChip™ WT PLUS Reagent Kit

extract_protocol: RNA from the Ribo-TRAP assay were submitted to the Medical University of South Carolina Proteogenomics Facility for DNA microarray analysis

treatment_protocol: Rats were injected in the NAc with either AAV-DIO-L10aGFP or a 50-50 mixture of AAV-HDAC5-3SA and AAV-L10aGFP. After about 4 weeks of expression, NAc tissue was harvested using native GFP fluorescence as a guide

tag: batch

tag: Sex

value: f


title: Ezra_seq_BT20_cells_rep2


title: Stationary_Phase_Day7_Rep4


title: Pig 44 - Normal, energy treatment


title: Ezra_seq_BT20_cells_Rep1


title: WT_D2_2


title: Stationary_Phase_Day7_Rep3


title: WT_D2_3


title: Release_Day7_Rep2


title: WT_D2_1

value: m


title: Release_Day7_Rep3


title: Stationary_Phase_Day7_Rep2


title: Pig 33 - IUGR, energy treatment


title: P48d14_Naive_4

description: geneRpkm.detected.csv

data_processing:
Raw sequencing reads were mapped to the hg38 using STAR and the UCSC KnownGene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor and normalized to fragments per kilobase per million (FPKM).  Genes were filtered for detection based on being expressed at greater than or equal to 10 reads per million in all samples for at least one group.
Genome_build: hg38
Supplementary_files_format_and_content: Annotation file containing RPKM normalized read counts for all detected genes.

source_name: Naïve

extract_protocol:
Cells were FACS sorted from PBMCs according to the indicated sort markers into RLT+1%Bme using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
All purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara). Final libraries were constructed using 400 pg of cDNA as input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

tag: donor id

value: F

value: IgD+ CD19+ CD27 neg CD3 neg CD4 neg

tag: h1 tetramer

value: PBMC

tag: days post influenza pr8 infection


title: Pig 34 - Normal, no treatment


title: Ezra_seq_HEK293_try2

value: HEK293, stably expressing H-2Kb


title: P48d14_FcrL5pos_TETpos_IgDneg_MBC_2

description: geneRpkm.detected.csv

source_name: FCRL5 positive HA+IgD neg B cell

value: IgDneg  CD38 lo/med CD19+ CD3 neg CD4 neg

value: positive


title: P48d14_ASC_3

description: geneRpkm.detected.csv

source_name: ASC

value: IgDneg  CD27+ CD38 hi CD19+ CD3 neg CD4 neg


title: Qfraction_Day7_Rep4

value: Q cell

value: yeast cell


title: Pig 38 - IUGR, no treatment

value: Liver

value: no treatment


title: Pig 32 - Normal, energy treatment

value: Normal


title: Pig 31 - Normal, energy treatment


title: WT_D1_6

tag: genotype


title: P48d14_FcrL5neg_TETpos_IgDneg_MBC_1

description: geneRpkm.detected.csv

source_name: FCRL5 negative HA+IgD neg B cell


title: Qfraction_Day7_Rep3


title: P46d14_Naive_4

description: geneRpkm.detected.csv


title: WT_D1_3


title: Pig 29 - IUGR, energy treatment

value: IUGR


title: Pig 30 - Normal, no treatment


title: Qfraction_Day7_Rep2


title: P46d14_ASC_3

description: geneRpkm.detected.csv


title: WT_D1_2


title: Qfraction_Day7_Rep1


title: Pig 27 - IUGR, no treatment


title: P46d14_FcrL5pos_TETpos_IgDneg_MBC_2

description: geneRpkm.detected.csv


title: DiaxieReleased_Rep4

value: Diauxie Release Cell


title: P46d14_FcrL5neg_TETpos_IgDneg_MBC_1

description: geneRpkm.detected.csv


title: HDAC5_D2_4


title: Pig 26 - IUGR, no treatment


title: Stationary_Phase_Day7_Rep1

value: Stationary Phase Cell


title: Pig 25 - IUGR, energy treatment

value: energy treatment


title: DiaxieReleased_Rep3


title: DiaxieReleased_Rep2


title: Pig 22 - Normal, energy treatment


title: HDAC5_D2_3

value: f


title: P52d7_ASC_3

description: geneRpkm.detected.csv

value: F


title: Pig 21 - IUGR, no treatment


title: WT_D1_5

value: m


title: WT_D1_4


title: HDAC5_D2_1


title: DiaxieReleased_Rep1


title: HDAC5_D1_6


title: Pig 20 - Normal, no treatment


title: P52d7_FcrL5pos_TETpos_IgDneg_MBC_2

description: geneRpkm.detected.csv

value: PBMC


title: P52d7_FcrL5neg_TETpos_IgDneg_MBC_1

description: geneRpkm.detected.csv


title: WT_D1_1


title: Diauxie_Rep4

value: Diauxic Cell


title: P48d7_Naive_4

description: geneRpkm.detected.csv

value: IgD+ CD19+ CD27 neg CD3 neg CD4 neg


title: HDAC5_D1_5


title: Pig 18 - IUGR, energy treatment


title: Diauxie_Rep3


title: Diauxie_Rep2


title: P52d7_Naive_4

description: geneRpkm.detected.csv


title: Pig 36 - IUGR, no treatment


title: Pig 17 - IUGR, no treatment


title: P48d7_ASC_3

description: geneRpkm.detected.csv


title: HDAC5_D1_4


title: Pig 14 - Normal, no treatment


title: HDAC5_D1_3


title: Log_Rep4

value: Log Cell


title: HDAC5_D1_2


title: P48d7_FcrL5pos_TETpos_IgDneg_MBC_2

description: geneRpkm.detected.csv

value: IgDneg  CD38 lo/med CD19+ CD3 neg CD4 neg

value: positive


title: Log_Rep3

value: yeast cell


title: Pig 11 - IUGR, energy treatment

value: Liver


title: P46d7_Naive_4

description: geneRpkm.detected.csv


title: Pig 12 - IUGR, no treatment

value: no treatment


title: HDAC5_D1_1


title: Log_Rep2


title: Pig 10 - IUGR, no treatment


title: Log_Rep1


title: Diauxie_Rep1


title: Pig 9 - Normal, no treatment

value: Normal


title: Pig 7 - Normal, energy treatment


title: P48d7_FcrL5neg_TETpos_IgDneg_MBC_1

description: geneRpkm.detected.csv


title: D6

city: Huhhot

first: Yue

last: Song

address: No. 306, Zhaowuda Road

department: College of Veterinary

institute: Inner Mongolia Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads 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.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: quadriceps muscle

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: quadriceps muscle

value: catgut embedding acupoint 2


title: P46d7_FcrL5neg_TETpos_IgDneg_MBC_1

description: geneRpkm.detected.csv

value: Female


title: P54d14_Naive_4

description: geneRpkm.detected.csv

value: Male


title: P46d7_ASC_3

description: geneRpkm.detected.csv

value: IgDneg  CD27+ CD38 hi CD19+ CD3 neg CD4 neg


title: Pig 5 - IUGR, no treatment

value: IUGR


title: Pig 4 - Normal, energy treatment

value: energy treatment


title: P54d14_ASC_3

description: geneRpkm.detected.csv

value: PBMC


title: D3


title: D2


title: P54d14_FcrL5pos_TETpos_IgDneg_MBC_2

description: geneRpkm.detected.csv


title: Pig 1 - Normal, energy treatment


title: P54d14_FcrL5neg_TETpos_IgDneg_MBC_1

description: geneRpkm.detected.csv


title: Plasma_MCI_007

city: shanghai

first: wei

last: zhang

address: 600 South Wan Ping Road

department: Geriatric Psychiatry

institute: Shanghai Mental Health Center

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

data_processing: After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

source_name: plasma

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: Blood samples of all participants were collected after fasting for 12 hours. Then plasma was separated by centrifugation at 3,000 rpm for 20 minutes at 4C.

tag: age

tag: gender


title: P51d14_Naive_4

description: geneRpkm.detected.csv


title: Naïve 4

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

data_processing: Gene expression profiling was then performed using the nCounter® Myeloid Innate Immunity Panel (NanoString Technologies, Seattle, WA). The normalized data were log2 transformed.

source_name: splenic CD11b+ myeloid cells

growth_protocol: Groups of wild type C57BL/6 mice were either untreated (naive, group D) or were injected i.p. with 20e6 allogeneic T cell depleted BALB/c splenocytes alone (group FN) with CTLA4-Ig (150µg i.p. once on day 2, Abatacept, Bristol-Myers Squibb, New York, NY, group DC), or CTLA4Ig plus recombinant EPO (5000 units/kg i.p. daily, epoetin alfa, Amgen, Thousand Oaks, CA, group DCE). On day 7, splenic CD11b+ myeloid cells were isolated by positive selection (kit #18970, STEMCELL, Vancouver, BC, Canada).

extract_protocol: RNA was isolated using TRIzol (Thermo Fisher Scientific, Waltham, MA) and cleaned using RNeasy Mini Kit (Qiagen, Hilden, Germany).

value: Naïve

value: splenic CD11b+ myeloid cells


title: Plasma_MCI_005

value: male


title: D1


title: P46d7_FcrL5pos_TETpos_IgDneg_MBC_2

description: geneRpkm.detected.csv

value: F

value: IgDneg  CD38 lo/med CD19+ CD3 neg CD4 neg


title: Plasma_MCI_003


title: Plasma_NC_9012


title: D4


title: C5

value: catgut embedding acupoint 1


title: D5


title: P51d14_FcrL5pos_TETpos_IgDneg_MBC_2

description: geneRpkm.detected.csv

value: positive


title: Naïve 2


title: HDAC5_D2_2

value: f


title: Pig 3 - Normal, no treatment

value: Liver

value: Normal

value: no treatment


title: C6

value: quadriceps muscle


title: P51d14_FcrL5neg_TETpos_IgDneg_MBC_1

description: geneRpkm.detected.csv

value: Male


title: Plasma_NC_4066


title: C4


title: P51d14_ASC_3

description: geneRpkm.detected.csv

value: IgDneg  CD27+ CD38 hi CD19+ CD3 neg CD4 neg


title: Plasma_NC_3436


title: Naïve 1


title: P54d7_Naive_4

description: geneRpkm.detected.csv

value: IgD+ CD19+ CD27 neg CD3 neg CD4 neg


title: C2


title: Naïve 3


title: C3


title: C1


title: Allo spleen cells 3

value: Allo spleen cells


title: Plasma_NC_3437


title: P54d7_FcrL5neg_TETpos_IgDneg_MBC_1

description: geneRpkm.detected.csv

value: PBMC


title: Plasma_MCI_002

value: Female


title: Plasma_NC_5952


title: Allo spleen cells 4

value: splenic CD11b+ myeloid cells


title: Allo spleen cells 1


title: B5

value: treadmill


title: Allo spleen cells 2


title: P51d7_Naive_4

description: geneRpkm.detected.csv


title: primary plasma cells from extramedullary myeloma patients 4

city: Wuhan

first: Chunyan

last: Sun

state: HUBEI

address: 1277 Jiefang Dadao, Wuhan 430022, China

department: Hematology

institute: Wuhan Union Hospital

hyb_protocol: 1ug of each labeled cRNA was fragmented by adding 5ul 10×Blockong Agent and 1ul of 25× Fragmentation Buffer, then heated the mixture at 60℃ for 30min,finally 25ul 2×GE Hybridzation buffer was added to dilute the labeled cRNA. 50ul of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide.

scan_protocol: scanned with Agilent DNA Microarray Scanner(Agilent p/n G2565BA)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v 12.1 software package (Agilent Technologies).

source_name: primary plasma cells

label_protocol: Sample labeling with Arraystar RNA Flash Labeling Kit. Briefly, mRNA was purified from total RNA after removal of rRNA. Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method.

growth_protocol: primary plasma cells of bone marrow from MM patients and primary plasma cells of soft-tissue from extramedullary myeloma patients were collected with non-anticoagulant tubes, palced at -80℃within 1 hour.

extract_protocol: Total RNA extracted using TRIzol® Reagent following manufacturer's instructions

tag: sample type

value: primary plasma cells from hematogenous spread to the brain


title: Allo spleen cells CTLA4-Ig 4

value: Allo spleen cells CTLA4-Ig

tag: cell type


title: B4

tag: tissue


title: P51d7_ASC_3

description: geneRpkm.detected.csv


title: P51d7_FcrL5pos_TETpos_IgDneg_MBC_2

description: geneRpkm.detected.csv

value: IgDneg  CD38 lo/med CD19+ CD3 neg CD4 neg


title: Allo spleen cells CTLA4-Ig 3

tag: treatment


title: Allo spleen cells CTLA4-Ig 2


title: primary plasma cells from extramedullary myeloma patients 2

value: primary plasma cells from hematogenous spread to the soft chest tissue


title: B2


title: P54d7_ASC_3

description: geneRpkm.detected.csv


title: Allo spleen cells CTLA4-Ig 1


title: P55d7_Naive_4

description: geneRpkm.detected.csv


title: A6

value: blank


title: B1


title: primary plasma cells from extramedullary myeloma patients 1

value: primary plasma cells from hematogenous spread to the skin


title: P55d7_ASC_3

description: geneRpkm.detected.csv


title: B3


title: primary plasma cells from extramedullary myeloma patients 3

value: primary plasma cells from hematogenous spread to the oral mucosa


title: Allo spleen cells CTLA4-Ig EPO 3

value: Allo spleen cells CTLA4-Ig EPO


title: primary plasma cells from multiple myeloma

value: CD138+ cells derived from bone marrow


title: P55d7_FcrL5pos_TETpos_IgDneg_MBC_2

description: geneRpkm.detected.csv

value: Male

value: positive


title: A4

value: quadriceps muscle


title: P51d7_FcrL5neg_TETpos_IgDneg_MBC_1

description: geneRpkm.detected.csv


title: Allo spleen cells CTLA4-Ig EPO 2


title: Allo spleen cells CTLA4-Ig EPO 4


title: P55d7_FcrL5neg_TETpos_IgDneg_MBC_1

description: geneRpkm.detected.csv


title: A3


title: Kasumi-1_SMARCA5FKBP12_24hdTAG47_1 [PRO-seq]

city: Nashville

first: Scott

middle: W

last: Hiebert

state: TN

address: 512 B Preston Research Building

department: Biochemistry

institute: Vanderbilt University

description:
24hr_500nM_dTAG47
biotinylated RNA

data_processing:
Library strategy: PRO-seq
Adaptors were trimmed and short/low quality sequence filtered by Trimmomatic-0.32: ILLUMINACLIP:adaptor.txt:2:30:7 TRAILING:15 MINLEN:15
Reverse complement sequence was generated using fastx_reverse_complement from the FASTX toolkit (v 0.0.13).
Reverse complement sequences were aligned to the human genome (hg19)+ S2 genome using bowtie2 (v2.2.2).
samtools -view generated .bam file with hg19 chromosomes.
Differential transcript analysis was carried out using the Nascent RNA Sequencing Analysis (NRSA) pipeline - pause_PROseq.pl with DESeq normalization.
Differential eRNA analysis was carried out using the Nascent RNA Sequencing Analysis (NRSA) pipeline - eRNA.pl
Bedgraph files were generated by Homer makeUCSCfile.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Homer-generated bedgraph files. neg.bedGraph: negative strand, plus.bedGraph: positive strand.
Supplementary_files_format_and_content: Differential gene transcription analysis generated by NRSA; tab-delimited text files. gb_change.txt: gene body changes, Enhancer_change: eRNA changes.

source_name: Kasumi-1 cells

growth_protocol: Kasumi-1 cells were grown in RPMI +20% FBS +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine.

extract_protocol:
Following nuclear run-on, total RNA was isolated by Trizol extraction and biotinylated RNA isolated by streptavidin bead binding.
Following hydrolysis of RNA, 3' adaptors were ligated to biotinylated RNA fragments. After 5'Cap removal and end repair, 5' adaptors were also ligated. Adaptor-ligated RNA fragments were reverse transcribed and cDNA libraries amplified using indexed primers.

treatment_protocol: Cells were treated with 500 nM dTAG-47 for the indicated timepoints.

tag: cell line

tag: genotype/variation

tag: time point


title: A5


title: B2_PpyrLBI_high

first: Tianmin

last: Wang

address: Huaxia Middle Road, 393

department: School of Life Science and Technology

institute: ShanghaiTech University

data_processing:
quality trimming step using cutadapt (v2.10) command with a quality threshold of 20
the pooled sample was demultiplexed according to the anchored barcode of the first seven nucleotides at the 5’-end from the first read
internal adaptor sequence embedding in some second reads with too short insert was also trimmed
a minimum length threshold of 20 bp for both the first and second reads was used to filter out those pair-end reads with too short insert
bowtie2 (v2.4.1) to align the second read to a reference genome (NC000913.3) (default setting)
Feature counting was carried out using R method summarizeOverlaps from GenomicAlignments package (v1.26.0) in a strand-specific manner, giving rise to a read count table for each gene.
Assembly: NC000913.3
Supplementary files format and content: gene raw count data, comma-delimited matrix table

organism: Escherichia coli K-12

source_name: RNA-seq data, using miniBac-seq method to generate RNA-seq data from PpyrLBI_high biofilm periphery cells, replicate 2

growth_protocol: A single colony was picked from the LB agar plate and inoculated to 3 ml of LB broth in a 15 ml centrifuge tube, and incubated at 37 ℃ in a shaker of 220 rpm. After overnight incubation (~ 12 h), we sub-cultured 100 L seed into 5 mL fresh LB broth (2% volume) in 50 mL centrifuge tube and grown for two hours at 37 ℃ with shaking at 220 rpm to reach exponential stage (OD600 ~ 0.6). The culture was centrifuged by 7,000 g for 3 min, and then the pellet was washed once with 1 mL PBS buffer, centrifuged again and resuspended with 0.4 mL PBS buffer. Then the cells would be loaded into microfluidic sytem cultured at 37 ℃ with M63B1. After around 36 hours cultivation, the biofilm reached 1000 um radius. Finally, cells in biofilm were extracted from microfluidic system for FACS sorting and further library consrtruction.

extract_protocol:
Bacterial RNA was obtained utilizing the RNAClean XP beads (Beckman, A63987). Lysate was prepared using lysozyme and proteinase K
miniBac-seq, a customized bacterial RNA-seq library construction method, see description of our paper for details

tag: strain

value: bacterial cells


title: A1


title: Kasumi-1_SMARCA5FKBP12_24hdTAG47_2 [PRO-seq]

description:
24hr_500nM_dTAG47
biotinylated RNA


title: B6


title: A2


title: B1_PpyrLBI_high

source_name: RNA-seq data, using miniBac-seq method to generate RNA-seq data from PpyrLBI_high biofilm periphery cells, replicate 1


title: Kasumi-1_SMARCA5FKBP12_6hdTAG47_1 [PRO-seq]

description:
6hr_500nM_dTAG47
biotinylated RNA


title: Allo spleen cells CTLA4-Ig EPO 1


title: Kasumi-1_SMARCA5FKBP12_6hdTAG47_2 [PRO-seq]

description:
6hr_500nM_dTAG47
biotinylated RNA


title: B1_PpyrLBI_low

source_name: RNA-seq data, using miniBac-seq method to generate RNA-seq data from PpyrLBI_low biofilm periphery cells, replicate 1


title: B2_PpyrLBI_low

source_name: RNA-seq data, using miniBac-seq method to generate RNA-seq data from PpyrLBI_low biofilm periphery cells, replicate 2


title: Kasumi-1_SMARCA5FKBP12_2hdTAG47_2 [PRO-seq]

description:
2hr_500nM_dTAG47
biotinylated RNA


title: dsapD_periphery_B2

source_name: RNA-seq data, using miniBac-seq method to generate RNA-seq data from ΔsapD biofilm periphery cells, replicate 2

value: delta sapD


title: dsapD_periphery_B1

source_name: RNA-seq data, using miniBac-seq method to generate RNA-seq data from ΔsapD biofilm periphery cells, replicate 1


title: Kasumi-1_SMARCA5FKBP12_2hdTAG47_1 [PRO-seq]

description:
2hr_500nM_dTAG47
biotinylated RNA


title: Kasumi-1_SMARCA5FKBP12_0hdTAG47_2 [PRO-seq]

description: biotinylated RNA

value: Untreated