title: Light-seq E14 mGFP hindgut 3

description: Columns 7, 19, 31 in processed data file

value: RCAS-mGFP electroporation into splanchnic LPM at HH17


title: D0 MG monocultured spheroid

status: Public on Jul 06 2024

type: SRA

city: Suwon-si

first: Seokgyu

last: Han

state: Gyeonggi-do

address: 2066, Seobu-ro

department: Mechanical Engineering

country: South Korea

institute: Sungkyunkwan univerisity

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Read count and normalized values were calculated by using StringTie version 2.1.3b, with parameter --rf -l -o -G -A -e
Assembly: GRCh38
Supplementary files format and content: tab-delimitedtextfilesincluderawreadcountandnormalizedvaluesforeachsample.

molecule: total RNA

organism: Homo sapiens

source_name: MG

growth_protocol: Patient-derived GBM spheroids were cultured in Dulbecco’s modified Eagle’s high glucose medium (SH30243.01, Hyclone) supplemented with 10% fetal bovine serum (FBS) (SH30919.03, Cytiva) and 1% penicillin straptomycin  (15140-122, Gibco).

extract_protocol:
Total RNA extraction was performed using the using QIAzol lysis reagent (Qiagen,79306 ) according to the manufacturer’s instructions
Libraries for bulk RNA-seq were prepared using the TruSeq Stranded mRNA Library Prep Kit.

tag: cell type

value: MG


title: shKSRP-GFP-2

city: Wuhan

first: RUI

last: Zhou

address: Donghu Road 185

country: China

institute: Wuhan University

description:
shKSRP-GFP-2 mouse primary hepatocytes
RNA-210222-RNA-210222-shksrp-GFP-2_L4

data_processing:
bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

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

tag: tissue

value: liver

value: mouse primary hepatocytes

tag: genotype/variation

value: shKSRP-GFP-


title: shKSRP-GFP+1

description:
shKSRP-GFP+1 mouse primary hepatocytes
RNA-210222-RNA-210222-shksrp-GFP+1_L4

value: shKSRP-GFP+


title: Light-seq E14 mGFP hindgut 1

city: Boston

first: Hasreet

last: Gill

state: MA

address: 77 Avenue Louis Pasteur, NRB 360

department: Genetics

country: USA

institute: Harvard Medical School

description: Columns 1, 13, 25 in processed data file

data_processing:
Light-seq barcode and UMI sequences were extracted from raw Read 1 data using the UMI-tools package
Reads were mapped to the Gallus gallus genome using STAR
QC was performed on count data using qualimap and multiqc, which showed that Hindgut replicate 1 (Sample 1 above) had an unusual featureCounts profile. This replicate was excluded from further differential expression analyses
DESeq2 was used to perform read count normalization and differential gene expression analyses
In the processed data file, each of 12 samples includes the 3 tissue types listed above, resulting in 36 columns. Only "InnerMes" was used for Figure S7 of the associated manuscript.
Assembly: GRCg6a
Supplementary files format and content: .csv Excel file includes raw counts for each sample at e14, where columns indicate tissue origin inferred from read barcodes

organism: Gallus gallus

source_name: Intestinal mesoderm

growth_protocol: Chicken embryos were incubated at 38 degrees Celsius

extract_protocol:
in situ reverse transcription was used to generate cDNA from tissue sections on slides, which was displaced from RNA via incubation for 45min in a solution containing RNaseH (NEB) and 10X Thermopol buffer
RNA-seq libraries were constructed using the Nextera XT Library Preparation Kit, following the manufacturer's protocol

treatment_protocol: in ovo electroporation of retroviral constructs--RCAS-mGFP and RCAS-Hoxd13--into midgut-level splanchnic lateral plate mesoderm at HH17

value: Intestinal mesoderm

value: subepithelial mesenchyme (InnerMes in processed data file), inner longitudinal muscle (MuscMuco in processed data file), inner superficial circumferential muscle (InnerCirc in processed data file)

tag: genotype

value: RCAS-mGFP

tag: treatment


title: old_control_2

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

data_processing:
Adaptor trimming with cutadapt
Quantification using Salmon 0.8.1v
DESeq2 normalization
Assembly: Gencode vM17 mouse assembly
Supplementary files format and content: Transcript length count and count per million (TPM)

molecule: polyA RNA

source_name: hippocampus

extract_protocol:
phenol-chloroform extraction
TruSeq RNA library v2

treatment_protocol: intraperitoneal injection of either THC:ethanol:cremophor:saline vehicle (THC dose of 0.002 mg/kg; THC donated by Prof. Mechoulam, the Hebrew University, Jerusalem) or a THC-free vehicle solution in a single administration, in a total volume of 0.1 mL/10 g bodyweight.

value: hippocampus

value: vehicle

tag: type

value: fastq


title: shKSRP-GFP-1

description:
shKSRP-GFP-1 mouse primary hepatocytes
RNA-210222-RNA-210222-shksrp-GFP-1_L4


title: D0 GBM monocultured spheroid

source_name: GBM

value: GBM


title: old_control_1


title: Normal 1

data_processing:
bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: mouse livers

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


title: Control_3

city: Shanghai

first: Hongrui

last: Chen

address: 639 Zhizaoju Road, Shanghai 200011, P.R.China.

department: Plastic and reconstruction surgery

institute: Shanghai ninth people's hospital

description: Singleron GEXSCOPE

library_source: transcriptomic single cell

data_processing:
Raw reads were processed to generate gene expression profiles using CeleScope v1.15.0 (Singleron Biotechnologies) with default parameters. Briefly, Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were aligned against the GRCh38 (hg38) transcriptome using STAR(v2.6.1b). Uniquely mapped reads were then assigned to genes with FeatureCounts(v2.0.1). Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis.
Raw sequencing data were converted to FASTQ files were aligned to human genome reference sequence (assembly: GRCH38) using the Cell Ranger 7.0.0 pipeline (10x Genomics). Human genome and gene annotations were downloaded from Ensembl genome browser 99 and processed using the Cell Ranger 7.0.0 (10x Genomics) pipeline’s mkref command. The reference was then used in the Cell Ranger “count” command to generate expression matrices.
Assembly: GRCh38
Supplementary files format and content: UMI count for each cell in mtx format and cell barcodes/genes/metadata in csv format

source_name: Adipose tissue

extract_protocol:
We used GEXSCOPETM Single Cell RNA Library Kit  to barcode single cells, capture mRNA from isolated single cells, and generate cDNA libraries for scRNA-seq. Then, individual libraries were diluted to 4 ng/μl, and pooled for sequencing on a nova6000 platform with 150 bp paired-end reads.
Different components were macrodissected and stored at 4 ℃ GEXSCOPETM Tissue Preservation Solution. Then, we washed samples for 3 times with Hanks Balanced Salt Solution (HBSS) and minced them into 1–2 mm-thick pieces, 2 ml GEXSCOPETM Tissue Dissociation Solution (Singleron Biotechnologies) was added to each sample and allowed for digestion at 37 ℃ for 15 minutes to dissociate the tissue into single cells. Then, we filtrate the samples using 40-μm sterile strainers, followed by centrifuging at 1,000 rpm for 5 minutes. After the centrifugation, the precipitation was resuspended in 1 ml phosphate-buffered saline (PBS; HyClone, Marlborough, United States). Subsequently, 2 ml GEXSCOPETM Red Blood Cell Lysis Buﬀer (Singleron Biotechnologies) was added into the cell suspension and incubated at 25°C for 10 minutes to remove red blood cells. After that, the mixture was centrifuged at 500 × g for 5 minutes, followed by re-suspending the precipitation with PBS.

value: Adipose tissue

tag: cell line

value: Control


title: PX552-GFP+2

description:
PX552-GFP+2 mouse primary hepatocytes
RNA-210222-RNA-210222-PX552-GFP+2_L4


title: oocyte, goat_24h_re4

city: Nanjing

first: Jiashuo

last: Li

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

data_processing:
adaptors and low-quality bases were removed with trim_galore
Clean reads were mapped to goat reference genome (Capra_hircus.ARS1.dna_sm.toplevel) using HISAT2
Read quantification was carried out with FeatureCounts (v2.0.6) (parameters: -t exon -g gene_id -Q 10 --primary -s 0 -p)
Differentially expressed genes (DEGs) were determined using DESeq2 (v1.40.2) (parameters: >1.5-fold change with adjusted P < 0.01)
Assembly: Capra_hircus.ARS1.dna_sm.toplevel
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Capra hircus

source_name: cumulus-oocyte complex (COC)

growth_protocol: Goat COCs were placed in TCM199 medium supplemented with 10% fetal bovine serum (FBS), 10 μg/mL follicle-stimulating hormone (FSH), 10 μg/mL luteinizing hormone (LH),1μg/mL estradiol, and 400 IU/mL of gentamicin at 38.5°C in a humidified incubator with 95% air and 5% CO2.

extract_protocol:
Samples were collected in tubes with lysis component and ribonuclease inhibitor.Then we carried out the amplification by the Smart-Seq2 method.An Oligo-dT primer was introduced to the reverse transcription reaction for first-strand cDNA synthesis,followed by PCR amplification to enrich the cDNA and magbeads purification step to clean up the production.
RNA libraries were prepared for sequencing using standard lllumina protocols.

treatment_protocol: COCs matured in vitro for 0h, 8h and 24h were respectively transferred for 5 minutes in medium preheated at 38.5°C containing 0.3% (w/v) hyaluronidase, and then denuded oocytes (DOs) were harvested and lysed in tubes with lysis buffer containing protease inhibitor and ribonuclease inhibitors.

value: cumulus-oocyte complex (COC)

value: oocyte

tag: developmental stage

value: MII

value: COCs matured in vitro

tag: time


title: young_thc_4


title: Control_2

description: Singleron GEXSCOPE


title: PX552-GFP+1

description:
PX552-GFP+1 mouse primary hepatocytes
RNA-210222-RNA-210222-PX552-GFP+1_L4

value: liver


title: young_thc_3


title: PX552-GFP-2

description:
PX552-GFP-2 mouse primary hepatocytes
RNA-210222-RNA-210222-PX552-GFP-2_L4

value: mouse primary hepatocytes


title: oocyte, goat_24h_re2


title: Control_1

description: Singleron GEXSCOPE


title: D0 NK monocultured spheroid

source_name: NK

value: NK


title: old_control_3


title: young_thc_2


title: FIL_4

description: 10x Genomics

extract_protocol:
We usedChromium Single Cell Library, Gel Bead & Multiplex Kit (10x Genomics) to barcode single cells, capture mRNA from isolated single cells, and generate cDNA libraries for scRNA-seq. Then, individual libraries were diluted to 4 ng/μl, and pooled for sequencing on a nova6000 platform with 150 bp paired-end reads.
Different components were macrodissected and stored at 4 ℃ GEXSCOPETM Tissue Preservation Solution. Then, we washed samples for 3 times with Hanks Balanced Salt Solution (HBSS) and minced them into 1–2 mm-thick pieces, 2 ml GEXSCOPETM Tissue Dissociation Solution (Singleron Biotechnologies) was added to each sample and allowed for digestion at 37 ℃ for 15 minutes to dissociate the tissue into single cells. Then, we filtrate the samples using 40-μm sterile strainers, followed by centrifuging at 1,000 rpm for 5 minutes. After the centrifugation, the precipitation was resuspended in 1 ml phosphate-buffered saline (PBS; HyClone, Marlborough, United States). Subsequently, 2 ml GEXSCOPETM Red Blood Cell Lysis Buﬀer (Singleron Biotechnologies) was added into the cell suspension and incubated at 25°C for 10 minutes to remove red blood cells. After that, the mixture was centrifuged at 500 × g for 5 minutes, followed by re-suspending the precipitation with PBS.

value: Facial infiltrating lipomatosis


title: oocyte, goat_8h_re3

value: GVBD


title: Light-seq E14 mGFP hindgut 2

description: Columns 4, 16, 28 in processed data file

value: Intestinal mesoderm

value: subepithelial mesenchyme (InnerMes in processed data file), inner longitudinal muscle (MuscMuco in processed data file), inner superficial circumferential muscle (InnerCirc in processed data file)

value: RCAS-mGFP electroporation into splanchnic LPM at HH17


title: young_thc_1

value: hippocampus


title: PX552-GFP-1

description:
PX552-GFP-1 mouse primary hepatocytes
RNA-210222-RNA-210222-PX552-GFP-1_L4


title: FIL_3

description: Singleron GEXSCOPE


title: young_control_4

value: vehicle

value: fastq


title: oocyte, goat_8h_re2


title: CQ+MT-3

city: jingzhou

first: wu

middle: zi

last: wei

state: Hubei

department: Animal Science

institute: yangtze university

description: CQ+MT-treated group of immature Sertoli cells

data_processing:
illumina bcl2fastq2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Sus scrofa11.1 whole genome using Hisat2 v2.2.1 with parameters --rna-strandness RF --dta -t -p 2.
Fragments per Kilobase per Million Mapped Fragments of(FPKM) were calculated using a protocol from Trapnell, C. et al, 2010.FPKM method can eliminate the influence of gene length and sequencing amount on the calculated gene expression.
Genome_build: Sus scrofa11.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Sus scrofa

source_name: Testis

growth_protocol: iSCs were cultured in Minimum Essential Medium (MEM) with Eagle's balanced salt solution (HyClone, USA), supplementing with 10% fetal bovine serum (Clark, Australia) and 1% penicillin-streptomycin (Gibco, USA), in a 5% CO2 incubator at 37°C.

extract_protocol:
Trizol reagent (Sigma) was used to isolate the total RNA of samples collected from three controls (DMSO-1, DMSO-2 and DMSO-3) 、three CQ-treated (CQ-1, CQ-2 and CQ-3)and three CQ+MT-treated (CQ-MT-1, CQ-MT-2 and CQ-MT-3) iSC cells.
The libraries were constructed and sequenced on an inllumina novaseq6000 (Illumina, San Diego, CA, USA) in a single lane.

treatment_protocol: The cells were seeded at a density of approximately 1×105 cells/mL, and cultured for 6h, before treated with   Chloroquine (CQ, HY-17589, MedChem Express, New Jersey, USA)) at 20μM and 20μM CQ + 10nM MT(Melatonin, M5250, Sigma-Aldrich).

value: immature sertoli cells

tag: age

value: 80 to 90 days gestation

tag: agent

value: Chloroquine + Melatonin


title: oocyte, goat_8h_re1

value: cumulus-oocyte complex (COC)

value: oocyte


title: FIL_1

description: Singleron GEXSCOPE

value: Adipose tissue


title: CQ+MT-1


title: FIL_2

description: Singleron GEXSCOPE


title: young_control_3


title: oocyte, goat_24h_re3

value: MII

value: COCs matured in vitro


title: oocyte, goat_0h_rep3

value: GV


title: CQ-3

description: CQ-treated group of immature Sertoli cells

value: Chloroquine


title: oocyte, goat_0h_rep2


title: CQ+MT-2


title: oocyte, goat_0h_rep1


title: HeLa-141 cells, HT-Luc-141, rep2

city: Daejeon

first: Yoosik

last: Kim

address: Daehak-ro

institute: KAIST

description:
141_results.csv
gene_count_matrix_141.csv
1412

data_processing:
Reads are aligned with STAR aligner. (ver 2.7.9a)
Gene expression is quantified with "--quantmode" option in STAR.
Differential gene expression analysis is performed with DESeq2 Biocondor/R package
Assembly: hg38
Supplementary files format and content: csv file for DESeq2 analysis results, showing baseMean, log2FoldChange, lfcSE, stat, pvalue, and adjusted pvalue; csv file for inputs to DESeq2 analysis.

source_name: Cervix

extract_protocol:
RNA was extracted using Trizol following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using Truseq Stranded mRNA Prep kit Library Prep Kit following manufacturer's protocols.

value: Cervix

value: epithelial cell

value: Ectopic overexpression of miR-141

value: HT-Luc-141 transfection


title: young_control_1

value: hippocampus


title: HeLa-141 cells, HT-PKR-141, rep1

description:
141_results.csv
gene_count_matrix_141.csv
141_pkr1

value: HT-PKR-141 transfection


title: si3

city: Zhengzhou

first: Gu

last: Zhuoyu

address: Jianshe East No.1

institute: Zhengzhou Univeristy

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: human_sapiens.GRCh38
Supplementary files format and content: All_reads_counts.xls

source_name: lung adenocarcinoma

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

value: lung adenocarcinoma

value: cancer cell

value: HNRNPD si


title: si2


title: E15 chick embryonic midgut with inducible HOXD13 expression vector

city: BOSTON

first: CHANGHEE

last: LEE

address: 77 AVENUE LOUIS PASTEUR

description:
chick embryonic gut cells
HGL8

data_processing:
All libraries were mapped using cellranger (7.1.0) and the associated custom reference (see processed files) that includes either EGFP (HGL5M, HGL5H) or codon-optimized hoxd13 transgene, mScarlet, mNeonGreen.P2A.TetOn sequences (HGL6/HGL7/HGL8)
HGL5 library was MULTI-seq multiplexed library and based on the demultiplexed barcode filtered to contain only relevant cellular barcodes that have correct MULTI-seq barcodes called. All libraries were processed with cellsnp-lite and vireo (Huang et al. 2019) to computationally infer the sample genotype, and the doublets were removed.
Assembly: Custom Galgal6a genome build (NCBI)
Supplementary files format and content: Seurat objects in .RDS format. All processed file names match to the library names.
Supplementary files format and content: The .fa.gz and .gtf.gz files constitute the minimal reference information to generate the reference for cellranger count (to generate the count matrix from the single cell fastq files)

source_name: gut

extract_protocol:
Single cell suspensions were generated by first dissecting guts in ice-cold 1X PBS. Whole guts were placed in DMEM + 10% chick embryo extract at 37°C until all samples were dissected and ready for dissociation. For pPIDNB experiment samples, dissected guts were observed under epifluorescence to isolate regions with mScarlet+ transgenic cells. 2-3mm gut segments, 1 from each replicate, were then incubated at 37°C in 1mL dispase for 10min as for bulk RNA sequencing sample preparation, followed by 1 PBS wash. Gut pieces (pooled by condition) were placed in the open caps of Eppendorf tubes containing 500µL 0.25% Trypsin-EDTA (Sigma) and mechanically disrupted using forceps. Tubes were then closed and inverted before placing samples at 37°C for 12-15min. Samples were mechanically disrupted with P1000 and P200 pipettes every 2min during the first half of the incubation, and with a 1mL syringe/25G needle during the second half.  When pPIDNB midgut, pPIDNB-HOXD13 midgut, and electroporated control hindgut suspensions were homogenous with no visible tissue clumps, 400µL of ice cold DMEM + 4% FBS was added to each sample, which was then strained using a 5mL polystyrene round-bottom tube with a 35µm nylon mesh cell strainer cap. After one spin at 800xg for 5min at 4°C, samples were resuspended in DMEM + 4% FBS, labeled for 5min with DAPI, and placed on ice. To enrich for mScarlet+ cells, midgut samples were iteratively sorted 3 times for approximately 30min each using an On-chip Sort microfluidic chip sorter. The mScarlet+mNeon+DAPI- population was gated to select for living cells with induced transgene expression. Trypan blue staining before and after all samples were sorted confirmed minimal cell death due to time spent on ice. After straining again through a 70µm mesh strainer and cell counting using a hemocytometer, sorted suspensions in 1X PBS were used for GEM generation according to the 10X Chromium Next GEM Single Cell v3.1 (Dual Index) protocol
10X scRNA-seq v3.1 chemistry (Dual-index)

value: gut

value: embryonic gut cells

value: Sparsely electroporated with pPIDNB-HOXD13 expression vector, treated at E8 with doxycycline for induction (mScarlet and doxycycline expressed)


title: CQ-1

value: immature sertoli cells

value: 80 to 90 days gestation


title: DMSO-3

description: control group of immature Sertoli cells

value: DMSO


title: HeLa-141 cells, HT-Luc-141, rep1

description:
141_results.csv
gene_count_matrix_141.csv
1411


title: HeLa cells, HT-PKR-141, rep2

description:
HeLa_results.csv
gene_count_matrix_HeLa.csv
hela_pkr2

value: HeLa

value: WT


title: si1


title: E15 chick embryonic hindgut

description:
chick embryonic gut cells
HGL7


title: NC3

value: HNRNPD NC


title: HeLa cells, HT-PKR-141, rep1

description:
HeLa_results.csv
gene_count_matrix_HeLa.csv
hela_pkr1

value: Cervix

value: epithelial cell


title: HeLa-141 cells, HT-PKR-141, rep2

description:
141_results.csv
gene_count_matrix_141.csv
141_pkr2

value: Ectopic overexpression of miR-141


title: DMSO-2

description: control group of immature Sertoli cells

value: 80 to 90 days gestation


title: E15 chick embryonic midgut with empty vector control

description:
chick embryonic gut cells
HGL6

value: Sparsely electroporated with pPIDNB backbone vector, treated at E8 with doxycycline for induction (for mScarlet expression alone)


title: DMSO-1

description: control group of immature Sertoli cells


title: young_control_2

value: hippocampus

value: vehicle

value: fastq


title: E14 chick embryonic hindgut

description:
chick embryonic gut cells
HGL5H

value: gut


title: CQ-2

value: Chloroquine


title: NC2

value: lung adenocarcinoma

value: cancer cell


title: HeLa cells, HT-Luc-141, rep2

description:
HeLa_results.csv
gene_count_matrix_HeLa.csv
hela_luc2

value: HT-Luc-141 transfection


title: E14 chick embryonic midgut

description:
chick embryonic gut cells
HGL5M

value: embryonic gut cells


title: NC1


title: mmu_ptch_EZH2i_2

status: Public on Jul 05 2024

city: Philadelphia

first: Duancheng

last: Guo

state: PA

address: 333 Cottman AVE

institute: Fox Chase Cancer Center

description: bulk transcriptome

data_processing:
Paired-end RNA sequencing fastq files were processed for adapter and low quality base call removal. Each paired-end file was split into equal read numbers across all conditions to account for library depths. Files were then mapped to either the mm39 or hg38 gencode genome index with the light-weight transcript abundance quantifier, Salmon. Variance-mean dispersions of raw counts were estimated using the negative binomial generalized linear modeling Wald test.
Assembly: mouse:mm39, human:hg38
Supplementary files format and content: Comma-separated values text file of raw counts for each sample.

source_name: MB tumor cells treated with GSK126

growth_protocol: Medulloblastoma cells were suspended in NB-B22 culture medium (Neurobasal, 1mmol/L sodium pyruvate, 2mml/L L-glutamine, B22 supplement, and 1% penicillin/streptomycin).

extract_protocol:
Primary cells were freshly isolated from tumor-bearing mice at 6 to 8 weeks of age. Briefly, tumor tissues were isolated from mouse brains and digested in a papain solution to obtain a single cell suspension and then centrifuged through a 35% and 65% Percoll gradient. Cells from the 35% to 65% interface were suspended in Dulbecco's PBS (DPBS) plus 0.5% BSA. Cells were then suspended in NB-B22 (Neurobasal medium with B22 supplement. Cell suspension was plated on poly-D-lysine (PDL)-coated coverslips (BD Biosciences).
Total RNA was extracted from tumor cells treated with T3 or PBS. Strand-specific mRNA-seq libraries for the Illumina platform were generated and sequenced following the manufacturer’s protocol. High-quality total RNA was used as input for the so-called dUTP library preparation method. Briefly, the mRNA fraction was purified from total RNA by polyA capture, fragmented and subjected to first-strand cDNA synthesis with random hexamers in the presence of Actinomycin D. The second-strand synthesis was performed incorporating dUTP instead of dTTP. Barcoded DNA adapters were ligated to both ends of the double-stranded cDNA and subjected to PCR amplification. The resultant library was checked on a Bioanalyzer (Agilent) and quantified. The libraries were multiplexed, clustered, and sequenced on an Illumina NovaSeq X Plus. The sequencing run was analyzed with the Illumina BCL-Convert, with demultiplexing based on sample- specific barcodes.

treatment_protocol: For in vitro experiments, 200nM of T3 was added to the culture medium for 48 hours. For EZH2i conditions, 1mM of GSK126 was added to culture. Controls were treated with PBS only.

value: MB tumor cells treated with GSK126

value: primary murine medulloblastoma cells

value: ptch-/-


title: mmu_ptch_EZH2i_3

description: bulk transcriptome


title: mmu_ptch_EZH2i_1

description: bulk transcriptome


title: mmu_ptch_PBS_3

description: bulk transcriptome

source_name: MB tumor cells treated with PBS

value: MB tumor cells treated with PBS

value: PBS


title: mmu_ptch_T3_3

description: bulk transcriptome

source_name: MB tumor cells treated with T3

value: MB tumor cells treated with T3


title: mmu_ptch_PBS_1

description: bulk transcriptome


title: mmu_ptch_PBS_2

description: bulk transcriptome


title: mmu_ptch_T3_2

description: bulk transcriptome


title: mmu_ptch_T3_1

description: bulk transcriptome


title: HeLa cells, HT-Luc-141, rep1

description:
HeLa_results.csv
gene_count_matrix_HeLa.csv
hela_luc1

value: Cervix

value: HeLa

value: epithelial cell

value: WT


title: VWM233_19999 PBMCs, 4h, Control

city: Durham

first: C. Ryan

last: Campbell

state: NC

address: 130 Science Dr

department: Evolutionary Anthropology

institute: Duke University

data_processing:
TM-3’-seq data were first filtered with trimmomatic (version 0.38, Bolger, Lohse, & Usadel, 2014) to remove adapter sequence and stretches of low-quality bases, as well as reads <20 bp following trimming.
Remaining trimmed reads were mapped to the meerkat genome (GCF_006229205.1, https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_006229205.1/) using the STAR two-pass method (version 2.7.10ac, Dobin, Davis et al., 2013)
Mapped reads were aggregated to the gene level using HTseq (version 2.0, Putri, Anders et al., 2022) based on overlap with annotated gene exons. As expected based on the library preparation method we used, mapped reads were highly biased towards the 3’ end of genes
Assembly: meerkat - GCF_006229205.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Suricata suricatta

source_name: peripheral blood mononuclear cells

extract_protocol:
We prepared RNA-sequencing libraries for each sample (control, Dex-challenged, Gard-challenged, LPS-challenged) by purifying mRNA using the miRNeasy Mini Kit (Qiagen).
Libraries were generated following the Transposase Mediated 3′ RNAseq (TM3’seq) protocol (Pallares, Picard, & Ayroles, 2020) with an input of 50 ng total RNA.

treatment_protocol: Purified PBMCs from each sample were cultured for 4 hours in (i) media only (control condition), (ii) media with 10 ng/mL lipopolysaccharide (LPS from the E. coli O111:B4 strain), to mimic bacterial exposure; (iii) media plus 1.0 μg/mL Gardiquimod (Gard), which activates Toll-like receptor 7 signaling; or (iv) media plus 1.0 μM Dexamethasone (Dex), a synthetic glucocorticoid. The cells were then incubated in parallel for 4 hours (37 C and 5% CO2), washed with 1× PBS, lysed, and stored immediately at -80° C until library preparation.

value: peripheral blood mononuclear cells

value: Control


title: VWM233_19999 PBMCs, 4h, Gard

value: Gard


title: VECM009_20009 PBMCs, 4h, LPS

value: LPS


title: VWM233_19999 PBMCs, 4h, LPS


title: VECM009_20009 PBMCs, 4h, Gard


title: VECM009_20009 PBMCs, 4h, Control


title: VWM233_19999 PBMCs, 4h, Dex

value: Dex


title: VECM009_20009 PBMCs, 4h, Dex


title: Olfactory_bulb_OVA_rep1

type: RNA

city: Fukuoka

first: Eizo

last: Tanaka

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Neurology

country: Japan

institute: Kyushu University Graduate School of Medical Sciences

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay Mouse array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

label: biotin

source_name: Olfactory bulb, P28 mice inhaled with OVA

label_protocol: The cRNA was amplified, labeled using GeneChip WT PLUS Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: strain

tag: gender

value: female

value: Brain


title: VWM232_19995 PBMCs, 4h, LPS


title: wnt activation-5

city: Guangzhou

first: Hongyan

last: Huang

state: --- Select One ---

address: 253 Industrial Avenue middle, Haizhu District, Guangzhou

institute: Southern Medical University, Zhujiang hospital

description: lncRNAs expression in TNBC tissues

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 085539_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: triple-negative breast cancer patient tissue sample

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

extract_protocol: RNA of breast cancer tissues was extracted from the MDA-NB-231 using phenol-alcohol, sheared to approximately 300-500 bp using a Covaris S220 instrument.

value: breast tumor tissue

value: Female

tag: sample group

value: activation group

tag: molecule subtype

value: lncRNAs


title: VWM232_19995 PBMCs, 4h, Dex


title: wnt inactivation-3

description: lncRNAs expression in TNBC tissues

value: inactivation group


title: VWM232_19995 PBMCs, 4h, Control


title: wnt inactivation-4

description: lncRNAs expression in TNBC tissues


title: VWF231_20001 PBMCs, 4h, Control


title: VWF231_20001 PBMCs, 4h, Dex


title: VWM225_19997 PBMCs, 4h, Dex


title: VWM225_19997 PBMCs, 4h, LPS


title: VMPM024_19993 PBMCs, 4h, Dex


title: wnt activation-1

description: lncRNAs expression in TNBC tissues


title: wnt inactivation-2

description: lncRNAs expression in TNBC tissues


title: VMPF025_19991 PBMCs, 4h, LPS


title: VMPM024_19993 PBMCs, 4h, Gard


title: VMPM024_19993 PBMCs, 4h, LPS


title: VMPF025_19991 PBMCs, 4h, Control


title: wnt inactivation-1

description: lncRNAs expression in TNBC tissues


title: wnt activation-2

description: lncRNAs expression in TNBC tissues


title: VMPF029_19982 PBMCs, 4h, LPS


title: wnt activation-4

description: lncRNAs expression in TNBC tissues


title: VMPF029_19982 PBMCs, 4h, Dex


title: VWM225_19997 PBMCs, 4h, Gard


title: wnt activation-3

description: lncRNAs expression in TNBC tissues


title: VMPM024_19993 PBMCs, 4h, Control


title: VWM225_19997 PBMCs, 4h, Control


title: VMPM027_19984 PBMCs, 4h, Dex


title: Olfactory_bulb_PBS_rep1

source_name: Olfactory bulb, P28 mice inhaled with PBS


title: VMPF026_19980 PBMCs, 4h, Dex


title: wnt inactivation-5

description: lncRNAs expression in TNBC tissues


title: VMPF026_19980 PBMCs, 4h, Gard


title: VMPF029_19982 PBMCs, 4h, Control


title: VMPF026_19980 PBMCs, 4h, Control


title: VMPF026_19980 PBMCs, 4h, LPS


title: VCRF009_19952 PBMCs, 4h, Dex


title: VCRF009_19952 PBMCs, 4h, Gard


title: VCRF009_19952 PBMCs, 4h, LPS


title: VHMM036_19795 PBMCs, 4h, Dex


title: VHMM036_19795 PBMCs, 4h, Gard


title: VHMM034_19797 PBMCs, 4h, Dex


title: VHMM036_19795 PBMCs, 4h, LPS


title: VHMM036_19795 PBMCs, 4h, Control


title: VCRF009_19952 PBMCs, 4h, Control


title: VHMM034_19797 PBMCs, 4h, Gard


title: VHMM034_19797 PBMCs, 4h, LPS


title: VNQM010_19755 PBMCs, 4h, Gard


title: VMPM027_19984 PBMCs, 4h, Gard


title: VNQM010_19755 PBMCs, 4h, Control


title: VMPM027_19984 PBMCs, 4h, LPS


title: VHMM034_19797 PBMCs, 4h, Control


title: VNQM010_19755 PBMCs, 4h, LPS


title: VNQM008_19757 PBMCs, 4h, Dex


title: VNQM008_19757 PBMCs, 4h, Gard


title: VNQM010_19755 PBMCs, 4h, Dex


title: VNQM007_19751 PBMCs, 4h, Dex


title: VNQM008_19757 PBMCs, 4h, Control


title: VNQM008_19757 PBMCs, 4h, LPS


title: VNQM007_19751 PBMCs, 4h, Gard


title: VNQM007_19751 PBMCs, 4h, LPS


title: VNQM007_19751 PBMCs, 4h, Control


title: VNQM006_19753 PBMCs, 4h, LPS


title: VNQM006_19753 PBMCs, 4h, Dex


title: VNQM006_19753 PBMCs, 4h, Gard


title: VNQF009_19749 PBMCs, 4h, Control


title: VNQF009_19749 PBMCs, 4h, Dex


title: VMPF022_19634 PBMCs, 4h, Dex


title: VNQF009_19749 PBMCs, 4h, LPS


title: VMPF022_19634 PBMCs, 4h, Gard


title: VJXF127_19613 PBMCs, 4h, Dex


title: VJXF127_19613 PBMCs, 4h, LPS


title: VJXM131_19586 PBMCs, 4h, Gard


title: VJXM131_19586 PBMCs, 4h, Dex


title: VMPF022_19634 PBMCs, 4h, Control


title: VJXF129_19583 PBMCs, 4h, Control


title: VJXM131_19586 PBMCs, 4h, LPS


title: VJXF129_19583 PBMCs, 4h, Dex


title: VJXF128_19580 PBMCs, 4h, Gard


title: VJXF129_19583 PBMCs, 4h, Gard


title: VNQM006_19753 PBMCs, 4h, Control


title: VJXM131_19586 PBMCs, 4h, Control


title: VTSF005_19570 PBMCs, 4h, Control


title: VJXF129_19583 PBMCs, 4h, LPS


title: VJXF127_19613 PBMCs, 4h, Gard


title: VNQF009_19749 PBMCs, 4h, Gard


title: VTSF005_19570 PBMCs, 4h, LPS


title: VJXF128_19580 PBMCs, 4h, Control


title: VJXF127_19613 PBMCs, 4h, Control


title: VMPF022_19634 PBMCs, 4h, LPS


title: VWM213_19476 PBMCs, 4h, Gard


title: VJXF128_19580 PBMCs, 4h, Dex


title: VTSF005_19570 PBMCs, 4h, Gard


title: VWM213_19476 PBMCs, 4h, Dex


title: VWM213_19476 PBMCs, 4h, Control


title: VWM213_19476 PBMCs, 4h, LPS


title: VZUF048_19562 PBMCs, 4h, LPS


title: VJXF128_19580 PBMCs, 4h, LPS


title: VWM216_19474 PBMCs, 4h, Gard


title: VWM216_19474 PBMCs, 4h, Dex


title: VWM216_19474 PBMCs, 4h, LPS


title: VWM216_19474 PBMCs, 4h, Control


title: VWM210_19472 PBMCs, 4h, Dex


title: VWM210_19472 PBMCs, 4h, Gard


title: VWM210_19472 PBMCs, 4h, LPS


title: VWF215_19463 PBMCs, 4h, Dex


title: VWM210_19472 PBMCs, 4h, Control


title: VWF215_19463 PBMCs, 4h, Gard


title: VWF212_19460 PBMCs, 4h, Gard


title: VLM247_19437 PBMCs, 4h, Dex


title: VWF215_19463 PBMCs, 4h, LPS


title: VWF215_19463 PBMCs, 4h, Control


title: VWF212_19460 PBMCs, 4h, Dex


title: VLM247_19437 PBMCs, 4h, Gard


title: VWF212_19460 PBMCs, 4h, Control


title: VLM247_19437 PBMCs, 4h, Control


title: VLM247_19437 PBMCs, 4h, LPS


title: VLM245_19435 PBMCs, 4h, Control


title: VLM245_19435 PBMCs, 4h, LPS


title: VLM245_19435 PBMCs, 4h, Dex


title: VLM245_19435 PBMCs, 4h, Gard


title: VLM234_19433 PBMCs, 4h, LPS


title: VLM234_19433 PBMCs, 4h, Control


title: VLM234_19433 PBMCs, 4h, Dex


title: VHMF030_19427 PBMCs, 4h, Dex


title: VHMF030_19427 PBMCs, 4h, Gard


title: VHMF019_19430 PBMCs, 4h, Gard


title: VHMF030_19427 PBMCs, 4h, LPS


title: VHMF019_19430 PBMCs, 4h, Control


title: VHMF001_19424 PBMCs, 4h, Dex


title: VHMF001_19424 PBMCs, 4h, LPS


title: VHMF001_19424 PBMCs, 4h, Control


title: VWF212_19189 PBMCs, 4h, Dex


title: VWF212_19189 PBMCs, 4h, Gard


title: VWF215_19038 PBMCs, 4h, Dex


title: VWF215_19038 PBMCs, 4h, Gard


title: VWF212_19189 PBMCs, 4h, Control


title: VLM234_19433 PBMCs, 4h, Gard


title: VWF215_19038 PBMCs, 4h, LPS


title: VWF212_19189 PBMCs, 4h, LPS


title: VWF212_19036 PBMCs, 4h, Dex


title: VMPF029_19982 PBMCs, 4h, Gard


title: VHMF001_19027 PBMCs, 4h, Dex


title: VWF212_19036 PBMCs, 4h, Control


title: VWF215_19038 PBMCs, 4h, Control


title: VHMF001_19027 PBMCs, 4h, Control


title: VHMF001_19027 PBMCs, 4h, Gard


title: VHMF030_19427 PBMCs, 4h, Control


title: VHMF001_19027 PBMCs, 4h, LPS


title: VHMF019_19430 PBMCs, 4h, LPS


title: VHMF001_19424 PBMCs, 4h, Gard


title: VHMF019_19024 PBMCs, 4h, Dex


title: VHMF019_19024 PBMCs, 4h, LPS


title: VHMF019_19024 PBMCs, 4h, Control


title: VHMF019_19024 PBMCs, 4h, Gard


title: VMPF020_18992 PBMCs, 4h, Gard


title: VMPF020_18992 PBMCs, 4h, Dex


title: VMPF020_18992 PBMCs, 4h, LPS


title: VWF212_19036 PBMCs, 4h, Gard


title: VUBM016_18753 PBMCs, 4h, Dex


title: VVHM117_18869 PBMCs, 4h, LPS


title: VUBM016_18753 PBMCs, 4h, Control


title: VWF212_19036 PBMCs, 4h, LPS


title: VUBM016_18753 PBMCs, 4h, Gard


title: VVHM117_18869 PBMCs, 4h, Control


title: VUBM016_18753 PBMCs, 4h, LPS


title: VUBF013_18752 PBMCs, 4h, Dex


title: VUBF013_18752 PBMCs, 4h, Control


title: VUBF013_18752 PBMCs, 4h, Gard


title: VLF241_18732 PBMCs, 4h, Dex


title: VLM211_18744 PBMCs, 4h, LPS


title: VLM211_18744 PBMCs, 4h, Gard


title: VLM211_18744 PBMCs, 4h, Dex


title: VLF241_18732 PBMCs, 4h, LPS


title: VUBF013_18752 PBMCs, 4h, LPS


title: VLF241_18732 PBMCs, 4h, Control


title: VLF241_18732 PBMCs, 4h, Gard


title: VLF235_18736 PBMCs, 4h, Control


title: VLF235_18736 PBMCs, 4h, Dex


title: VLF235_18736 PBMCs, 4h, LPS


title: VLM211_18744 PBMCs, 4h, Control


title: VLF230_18734 PBMCs, 4h, Dex


title: VLF230_18734 PBMCs, 4h, Gard


title: VLF235_18736 PBMCs, 4h, Gard


title: VVHM117_18869 PBMCs, 4h, Gard


title: VMPF020_18992 PBMCs, 4h, Control


title: VHMM021_18713 PBMCs, 4h, LPS


title: VLF230_18734 PBMCs, 4h, Control


title: VHMM021_18713 PBMCs, 4h, Dex


title: VHMM021_18713 PBMCs, 4h, Gard


title: VHMM021_18713 PBMCs, 4h, Control


title: VHMM023_18711 PBMCs, 4h, Dex


title: VHMM023_18711 PBMCs, 4h, Gard


title: VHMM023_18711 PBMCs, 4h, LPS


title: VZUF032_18671 PBMCs, 4h, Dex


title: VZUF029_18669 PBMCs, 4h, Dex


title: VHMM023_18711 PBMCs, 4h, Control


title: VZUF029_18669 PBMCs, 4h, Gard


title: VMPM027_19984 PBMCs, 4h, Control


title: VZUF029_18669 PBMCs, 4h, Control


title: VZUF028_18673 PBMCs, 4h, Gard


title: VZUF032_18671 PBMCs, 4h, LPS


title: VZUF028_18673 PBMCs, 4h, Dex


title: VZUF032_18671 PBMCs, 4h, Gard


title: VZUF029_18669 PBMCs, 4h, LPS


title: VLF230_18734 PBMCs, 4h, LPS


title: VZUF028_18673 PBMCs, 4h, Control


title: VZUF032_18671 PBMCs, 4h, Control


title: VZUF028_18673 PBMCs, 4h, LPS


title: VHMF010_18566 PBMCs, 4h, Dex


title: VHMF010_18566 PBMCs, 4h, Control


title: VHMF015_18558 PBMCs, 4h, Gard


title: VHMF015_18558 PBMCs, 4h, Dex


title: VHMF015_18558 PBMCs, 4h, LPS


title: VHMF022_18709 PBMCs, 4h, Dex


title: VHMF001_18550 PBMCs, 4h, Control


title: VHMF015_18558 PBMCs, 4h, Control


title: VHMF001_18550 PBMCs, 4h, LPS


title: VMPM015_18532 PBMCs, 4h, Dex


title: VHMF001_18550 PBMCs, 4h, Gard


title: VMPM015_18532 PBMCs, 4h, LPS


title: VMPM015_18532 PBMCs, 4h, Control


title: VMPF019_18536 PBMCs, 4h, Dex


title: VMPF019_18536 PBMCs, 4h, Gard


title: VHMF010_18566 PBMCs, 4h, Gard


title: VMPF020_18528 PBMCs, 4h, LPS


title: VMPM017_18534 PBMCs, 4h, LPS


title: VMPF019_18536 PBMCs, 4h, Control


title: VMPF019_18536 PBMCs, 4h, LPS


title: VMPF020_18528 PBMCs, 4h, Dex


title: VMPM017_18534 PBMCs, 4h, Control


title: VMPF020_18528 PBMCs, 4h, Gard


title: VMPM017_18534 PBMCs, 4h, Gard


title: VVHM117_18530 PBMCs, 4h, Gard


title: VMPF020_18528 PBMCs, 4h, Control


title: VMPM017_18534 PBMCs, 4h, Dex


title: VHMF001_18550 PBMCs, 4h, Dex


title: VVHM117_18530 PBMCs, 4h, Dex


title: VLM239_18526 PBMCs, 4h, Gard


title: VLM239_18526 PBMCs, 4h, Dex


title: VLM239_18526 PBMCs, 4h, LPS


title: VLM242_18523 PBMCs, 4h, Gard


title: VLM239_18526 PBMCs, 4h, Control


title: VLM242_18523 PBMCs, 4h, Dex


title: VLM242_18523 PBMCs, 4h, LPS


title: VLM242_18523 PBMCs, 4h, Control


title: VMPM015_18532 PBMCs, 4h, Gard


title: VJXM095_18524 PBMCs, 4h, Gard


title: VJXM095_18524 PBMCs, 4h, LPS


title: VVHM117_18530 PBMCs, 4h, LPS


title: VVHF129_18514 PBMCs, 4h, Gard


title: VVHF127_18510 PBMCs, 4h, Gard


title: VVHM117_18530 PBMCs, 4h, Control


title: VVHF129_18514 PBMCs, 4h, Control


title: VVHF129_18514 PBMCs, 4h, Dex


title: VJXM095_18524 PBMCs, 4h, Control


title: VVHF129_18514 PBMCs, 4h, LPS


title: VWM209_18508 PBMCs, 4h, LPS


title: VVHF127_18510 PBMCs, 4h, Dex


title: VWM208_18512 PBMCs, 4h, Gard


title: VVHF127_18510 PBMCs, 4h, LPS


title: VLM221_18506 PBMCs, 4h, Dex


title: VWM208_18512 PBMCs, 4h, LPS


title: VWM209_18508 PBMCs, 4h, Dex


title: VWM208_18512 PBMCs, 4h, Dex


title: VLM221_18506 PBMCs, 4h, Gard


title: VWM208_18512 PBMCs, 4h, Control


title: VJXM095_18524 PBMCs, 4h, Dex


title: VMPM017_18430 PBMCs, 4h, Dex


title: VMPM017_18430 PBMCs, 4h, Gard


title: VMPM017_18430 PBMCs, 4h, Control


title: VLM221_18506 PBMCs, 4h, Control


title: VMPM017_18430 PBMCs, 4h, LPS


title: VMPM015_18428 PBMCs, 4h, Gard


title: VMPM015_18428 PBMCs, 4h, LPS


title: VVHF127_18510 PBMCs, 4h, Control


title: VWM209_18508 PBMCs, 4h, Gard


title: VWM209_18508 PBMCs, 4h, Control


title: VMPM015_18428 PBMCs, 4h, Control


title: VVHM111_18424 PBMCs, 4h, Control


title: VVHM111_18424 PBMCs, 4h, Gard


title: VVHM111_18424 PBMCs, 4h, LPS


title: VVHM117_18426 PBMCs, 4h, Gard


title: VVHM111_18424 PBMCs, 4h, Dex


title: VVHM117_18426 PBMCs, 4h, Dex


title: VVHM117_18426 PBMCs, 4h, Control


title: VJXM095_18396 PBMCs, 4h, LPS


title: VJXM095_18396 PBMCs, 4h, Control


title: VVHF127_18394 PBMCs, 4h, Gard


title: VVHF127_18394 PBMCs, 4h, Dex


title: VVHF129_18392 PBMCs, 4h, LPS


title: VJXM095_18396 PBMCs, 4h, Gard


title: VVHF127_18394 PBMCs, 4h, LPS


title: VLM221_18506 PBMCs, 4h, LPS


title: VVHF127_18394 PBMCs, 4h, Control


title: VBBF117_18368 PBMCs, 4h, Dex


title: VBBF117_18368 PBMCs, 4h, Gard


title: VBBF117_18368 PBMCs, 4h, LPS


title: VLF241_18326 PBMCs, 4h, Gard


title: VBBF117_18368 PBMCs, 4h, Control


title: VLF241_18326 PBMCs, 4h, Dex


title: VLF241_18326 PBMCs, 4h, Control


title: VLF241_18326 PBMCs, 4h, LPS


title: VLF235_18324 PBMCs, 4h, Dex


title: VJXM095_18396 PBMCs, 4h, Dex


title: VLF235_18324 PBMCs, 4h, LPS


title: VVHM117_18426 PBMCs, 4h, LPS


title: VLF235_18324 PBMCs, 4h, Gard


title: VLF230_18322 PBMCs, 4h, Gard


title: VVHF129_18392 PBMCs, 4h, Gard


title: VLF235_18324 PBMCs, 4h, Control


title: VWF176_18296 PBMCs, 4h, Gard


title: VLF230_18322 PBMCs, 4h, Control


title: VWF176_18296 PBMCs, 4h, Dex


title: VLF230_18322 PBMCs, 4h, Dex


title: VHMM017_18284 PBMCs, 4h, LPS


title: VWF176_18296 PBMCs, 4h, LPS


title: VHMM017_18284 PBMCs, 4h, Gard


title: VHMM007_18282 PBMCs, 4h, LPS


title: VLF230_18322 PBMCs, 4h, LPS


title: VWF176_18296 PBMCs, 4h, Control


title: VHMM007_18282 PBMCs, 4h, Control


title: VHMM017_18284 PBMCs, 4h, Control


title: VHMM007_18282 PBMCs, 4h, Dex


title: VHMM007_18282 PBMCs, 4h, Gard


title: VZUF032_18280 PBMCs, 4h, LPS


title: VZUF032_18280 PBMCs, 4h, Gard


title: VZUF032_18280 PBMCs, 4h, Dex


title: VZUF029_18279 PBMCs, 4h, Dex


title: VZUF032_18280 PBMCs, 4h, Control


title: VZUF028_18276 PBMCs, 4h, Control


title: VZUF028_18276 PBMCs, 4h, Dex


title: VZUF029_18279 PBMCs, 4h, LPS


title: VVHF129_18266 PBMCs, 4h, Gard


title: VZUF028_18276 PBMCs, 4h, Gard


title: VVHF129_18266 PBMCs, 4h, Dex


title: VZUF028_18276 PBMCs, 4h, LPS


title: VVHF129_18266 PBMCs, 4h, Control


title: VLF241_18256 PBMCs, 4h, Dex


title: VVHF127_18264 PBMCs, 4h, LPS


title: VVHF127_18264 PBMCs, 4h, Control


title: VVHF129_18266 PBMCs, 4h, LPS


title: VLF241_18256 PBMCs, 4h, Control


title: VLF240_18262 PBMCs, 4h, Gard


title: VVHF127_18264 PBMCs, 4h, Gard


title: VLF241_18256 PBMCs, 4h, LPS


title: VLF235_18260 PBMCs, 4h, Dex


title: VLF241_18256 PBMCs, 4h, Gard


title: VVHF127_18264 PBMCs, 4h, Dex


title: VZUF029_18279 PBMCs, 4h, Gard


title: VZUF029_18279 PBMCs, 4h, Control


title: VLF240_18262 PBMCs, 4h, Dex


title: VLF230_18258 PBMCs, 4h, Dex


title: VLF240_18262 PBMCs, 4h, LPS


title: VLF230_18258 PBMCs, 4h, Gard


title: VLF230_18258 PBMCs, 4h, LPS


title: VLF230_18258 PBMCs, 4h, Control


title: VUBF020_18244 PBMCs, 4h, Gard


title: VLF235_18260 PBMCs, 4h, LPS


title: VUBF020_18244 PBMCs, 4h, LPS


title: VLF235_18260 PBMCs, 4h, Control


title: VUBF020_18244 PBMCs, 4h, Dex


title: VWM216_18254 PBMCs, 4h, Dex


title: VUBF020_18244 PBMCs, 4h, Control


title: VLF240_18262 PBMCs, 4h, Control


title: VWM216_18254 PBMCs, 4h, Control


title: VWM216_18254 PBMCs, 4h, Gard


title: VWM216_18254 PBMCs, 4h, LPS


title: VLF235_18260 PBMCs, 4h, Gard


title: VWF215_18250 PBMCs, 4h, Control


title: VWF215_18250 PBMCs, 4h, Dex


title: VWF215_18250 PBMCs, 4h, Gard


title: VWM214_18248 PBMCs, 4h, Gard


title: VWM214_18248 PBMCs, 4h, Dex


title: VWM213_18252 PBMCs, 4h, Dex


title: VWF215_18250 PBMCs, 4h, LPS


title: VWM213_18252 PBMCs, 4h, LPS


title: VWM213_18252 PBMCs, 4h, Control


title: VWM213_18252 PBMCs, 4h, Gard


title: VUBF019_18246 PBMCs, 4h, Dex


title: VWM214_18248 PBMCs, 4h, Control


title: VUBF019_18246 PBMCs, 4h, Control


title: VJXM114_18238 PBMCs, 4h, Dex


title: VUBF019_18246 PBMCs, 4h, Gard


title: VJXM114_18238 PBMCs, 4h, Gard


title: VJXM114_18238 PBMCs, 4h, LPS


title: VUBF019_18246 PBMCs, 4h, LPS


title: VJXM114_18238 PBMCs, 4h, Control


title: VJXM113_18240 PBMCs, 4h, Control


title: VJXM113_18240 PBMCs, 4h, Dex


title: VJXF112_18242 PBMCs, 4h, Gard


title: VJXF112_18242 PBMCs, 4h, LPS


title: VJXM113_18240 PBMCs, 4h, Gard


title: VZUF029_18235 PBMCs, 4h, Dex


title: VZUF029_18235 PBMCs, 4h, Gard


title: VZUF029_18235 PBMCs, 4h, Control


title: VJXF112_18242 PBMCs, 4h, Control


title: VCVM001_18224 PBMCs, 4h, Dex


title: VZUF029_18235 PBMCs, 4h, LPS


title: VCVM001_18224 PBMCs, 4h, Gard


title: VCVM001_18224 PBMCs, 4h, Control


title: VJXF080_18222 PBMCs, 4h, Dex


title: VJXF080_18222 PBMCs, 4h, LPS


title: VVHM123_18214 PBMCs, 4h, LPS


title: VJXF080_18222 PBMCs, 4h, Gard


title: VVHM123_18214 PBMCs, 4h, Gard


title: VVHM123_18214 PBMCs, 4h, Control


title: VZUF032_18202 PBMCs, 4h, Dex


title: VZUF032_18202 PBMCs, 4h, LPS


title: VZUF032_18202 PBMCs, 4h, Gard


title: VZUF028_18204 PBMCs, 4h, Dex


title: VJXM113_18240 PBMCs, 4h, LPS


title: VZUF028_18204 PBMCs, 4h, Gard


title: VZUF028_18204 PBMCs, 4h, LPS


title: VZUF028_18204 PBMCs, 4h, Control


title: VHMF015_18200 PBMCs, 4h, Dex


title: VHMF015_18200 PBMCs, 4h, LPS


title: VHMF010_18198 PBMCs, 4h, LPS


title: VHMF015_18200 PBMCs, 4h, Control


title: VCVM001_18224 PBMCs, 4h, LPS


title: VHMF010_18198 PBMCs, 4h, Dex


title: VHMF010_18198 PBMCs, 4h, Control


title: VHMF001_18196 PBMCs, 4h, Gard


title: VHMF010_18198 PBMCs, 4h, Gard


title: VHMF001_18196 PBMCs, 4h, Dex


title: VLF223_18164 PBMCs, 4h, Dex


title: VHMF001_18196 PBMCs, 4h, Control


title: VVHF129_18161 PBMCs, 4h, LPS


title: VLF223_18164 PBMCs, 4h, LPS


title: VVHM123_18214 PBMCs, 4h, Dex


title: VLF223_18164 PBMCs, 4h, Control


title: VHMF015_18200 PBMCs, 4h, Gard


title: VVHF129_18161 PBMCs, 4h, Dex


title: VLF223_18164 PBMCs, 4h, Gard


title: VVHF127_18159 PBMCs, 4h, Dex


title: VVHF129_18161 PBMCs, 4h, Control


title: VVHF127_18159 PBMCs, 4h, LPS


title: VVHF129_18161 PBMCs, 4h, Gard


title: VZUF032_18202 PBMCs, 4h, Control


title: VVHF127_18159 PBMCs, 4h, Gard


title: VVHF110_18157 PBMCs, 4h, Dex


title: VVHF110_18157 PBMCs, 4h, Gard


title: VHMF010_18154 PBMCs, 4h, Dex


title: VVHF110_18157 PBMCs, 4h, Control


title: VHMF010_18154 PBMCs, 4h, LPS


title: VHMF010_18154 PBMCs, 4h, Control


title: VHMF001_18152 PBMCs, 4h, Dex


title: VHMF001_18152 PBMCs, 4h, LPS


title: VVHF110_18157 PBMCs, 4h, LPS


title: VHMF001_18152 PBMCs, 4h, Control


title: VVHF129_18148 PBMCs, 4h, LPS


title: VVHF129_18148 PBMCs, 4h, Dex


title: VVHF129_18148 PBMCs, 4h, Control


title: VVHF127_18150 PBMCs, 4h, Dex


title: VVHF127_18150 PBMCs, 4h, Gard


title: VHMF001_18152 PBMCs, 4h, Gard


title: VVHF110_18146 PBMCs, 4h, Gard


title: VVHF127_18150 PBMCs, 4h, LPS


title: VVHF127_18159 PBMCs, 4h, Control


title: VVHM128_18124 PBMCs, 4h, Dex


title: VVHM128_18124 PBMCs, 4h, LPS


title: VVHF110_18146 PBMCs, 4h, Dex


title: VVHF127_18150 PBMCs, 4h, Control


title: VVHF109_18116 PBMCs, 4h, Dex


title: VVHF110_18146 PBMCs, 4h, Control


title: VVHF109_18116 PBMCs, 4h, LPS


title: VVHF109_18116 PBMCs, 4h, Gard


title: VHMF010_18154 PBMCs, 4h, Gard


title: VVHF109_18116 PBMCs, 4h, Control


title: VZUF028_18072 PBMCs, 4h, Dex


title: VVHF110_18146 PBMCs, 4h, LPS


title: VZUF028_18072 PBMCs, 4h, Gard


title: VZUF028_18072 PBMCs, 4h, LPS


title: VVHM128_18124 PBMCs, 4h, Control


title: VVHF129_18148 PBMCs, 4h, Gard


title: VLM228_18068 PBMCs, 4h, Dex


title: VZUF028_18072 PBMCs, 4h, Control


title: VLM228_18068 PBMCs, 4h, Gard


title: VLM228_18068 PBMCs, 4h, Control


title: VWM205_18070 PBMCs, 4h, Dex


title: VWM205_18070 PBMCs, 4h, LPS


title: VWM205_18070 PBMCs, 4h, Control


title: VVHM128_18124 PBMCs, 4h, Gard


title: VJXM095_18054 PBMCs, 4h, Control


title: VJXM095_18054 PBMCs, 4h, Dex


title: VJXM095_18054 PBMCs, 4h, Gard


title: VWM209_18022 PBMCs, 4h, Dex


title: VWM209_18022 PBMCs, 4h, LPS


title: VWM205_18070 PBMCs, 4h, Gard


title: VWM208_18016 PBMCs, 4h, Dex


title: VWM208_18016 PBMCs, 4h, Gard


title: VWM209_18022 PBMCs, 4h, Gard


title: VWM208_18016 PBMCs, 4h, Control


title: VVHF110_17979 PBMCs, 4h, Gard


title: VLM228_18068 PBMCs, 4h, LPS


title: VVHF110_17979 PBMCs, 4h, Control


title: VVHF109_17973 PBMCs, 4h, Dex


title: VVHF110_17979 PBMCs, 4h, LPS


title: VVHF109_17973 PBMCs, 4h, Control


title: VVHF109_17973 PBMCs, 4h, LPS


title: VVHF109_17973 PBMCs, 4h, Gard


title: VWM209_17961 PBMCs, 4h, Dex


title: VWM209_17961 PBMCs, 4h, LPS


title: VWM209_17961 PBMCs, 4h, Gard


title: VWM209_17961 PBMCs, 4h, Control


title: VJXM095_18054 PBMCs, 4h, LPS


title: VWM208_17955 PBMCs, 4h, LPS


title: VVHF110_17979 PBMCs, 4h, Dex


title: VWM208_17955 PBMCs, 4h, Control


title: VWM208_17955 PBMCs, 4h, Gard


title: VWM205_17967 PBMCs, 4h, Dex


title: VWM208_18016 PBMCs, 4h, LPS


title: VWM205_17967 PBMCs, 4h, Gard


title: VWM205_17967 PBMCs, 4h, Control


title: VVHM111_17950 PBMCs, 4h, Gard


title: VWM205_17967 PBMCs, 4h, LPS


title: VWM209_18022 PBMCs, 4h, Control


title: VVHM111_17950 PBMCs, 4h, LPS


title: VVHM103_17944 PBMCs, 4h, Dex


title: VVHM103_17944 PBMCs, 4h, LPS


title: VVHM103_17944 PBMCs, 4h, Gard


title: VVHM103_17944 PBMCs, 4h, Control


title: VLM228_17926 PBMCs, 4h, LPS


title: VLM228_17926 PBMCs, 4h, Gard


title: VWM208_17955 PBMCs, 4h, Dex


title: VLM228_17832 PBMCs, 4h, LPS


title: VLM228_17832 PBMCs, 4h, Dex


title: VLM228_17832 PBMCs, 4h, Gard


title: VLM221_17826 PBMCs, 4h, Dex


title: VLM221_17826 PBMCs, 4h, LPS


title: VLM221_17826 PBMCs, 4h, Gard


title: VLM221_17826 PBMCs, 4h, Control


title: VLF227_17820 PBMCs, 4h, Dex


title: VLF227_17820 PBMCs, 4h, LPS


title: VLF206_17794 PBMCs, 4h, Dex


title: VLF206_17794 PBMCs, 4h, Gard


title: VLM228_17792 PBMCs, 4h, Dex


title: VLM228_17792 PBMCs, 4h, Gard


title: VLM228_17792 PBMCs, 4h, LPS


title: VVHM111_17950 PBMCs, 4h, Control


title: VVHF109_17790 PBMCs, 4h, Dex


title: VLF227_17820 PBMCs, 4h, Gard


title: VLM228_17926 PBMCs, 4h, Dex


title: VLM228_17792 PBMCs, 4h, Control


title: VVHF109_17790 PBMCs, 4h, Gard


title: VVHF109_17790 PBMCs, 4h, LPS


title: VVHF109_17790 PBMCs, 4h, Control


title: VLF227_17820 PBMCs, 4h, Control


title: VVHM112_17743 PBMCs, 4h, Dex


title: VVHM112_17743 PBMCs, 4h, LPS


title: VVHM112_17743 PBMCs, 4h, Gard


title: VVHM112_17743 PBMCs, 4h, Control


title: VVHM111_17736 PBMCs, 4h, LPS


title: VVHM103_17730 PBMCs, 4h, Dex


title: VVHM111_17736 PBMCs, 4h, Gard


title: VVHM103_17730 PBMCs, 4h, Control


title: VVHM103_17730 PBMCs, 4h, LPS


title: VVHM103_17730 PBMCs, 4h, Gard


title: VLF206_17794 PBMCs, 4h, Control


title: VLF223_17728 PBMCs, 4h, LPS


title: VLF223_17728 PBMCs, 4h, Gard


title: VLF223_17728 PBMCs, 4h, Control


title: VLM211_17714 PBMCs, 4h, Dex


title: VLM211_17714 PBMCs, 4h, LPS


title: VLM211_17714 PBMCs, 4h, Gard


title: VLM211_17714 PBMCs, 4h, Control


title: VVHF115_17712 PBMCs, 4h, LPS


title: VVHF115_17712 PBMCs, 4h, Control


title: VVHF113_17708 PBMCs, 4h, Dex


title: VVHF113_17708 PBMCs, 4h, Gard


title: VVHM111_17736 PBMCs, 4h, Dex


title: VVHF113_17708 PBMCs, 4h, LPS


title: VVHF113_17708 PBMCs, 4h, Control


title: VVHF115_17712 PBMCs, 4h, Gard


title: VVHF109_17710 PBMCs, 4h, Gard


title: VVHF109_17710 PBMCs, 4h, Control


title: VHMM002_17644 PBMCs, 4h, Dex


title: VLF223_17728 PBMCs, 4h, Dex


title: VHMM002_17644 PBMCs, 4h, LPS


title: VHMM002_17644 PBMCs, 4h, Gard


title: VHMM002_17644 PBMCs, 4h, Control


title: VVHM112_17592 PBMCs, 4h, LPS


title: VVHF109_17710 PBMCs, 4h, LPS


title: VVHM117_17594 PBMCs, 4h, Gard


title: VVHM111_17590 PBMCs, 4h, Dex


title: VVHM112_17592 PBMCs, 4h, Control


title: VVHF115_17712 PBMCs, 4h, Dex


title: VVHM111_17590 PBMCs, 4h, LPS


title: VVHM111_17590 PBMCs, 4h, Control


title: VVHM103_17588 PBMCs, 4h, Dex


title: VVHF109_17710 PBMCs, 4h, Dex


title: VVHM103_17588 PBMCs, 4h, Gard


title: VVHM103_17588 PBMCs, 4h, LPS


title: VVHM103_17588 PBMCs, 4h, Control


title: VLM238_17505 PBMCs, 4h, LPS


title: VLM238_17505 PBMCs, 4h, Control


title: VLM237_17507 PBMCs, 4h, LPS


title: VLM237_17507 PBMCs, 4h, Gard


title: VLM237_17507 PBMCs, 4h, Dex


title: VVHM117_17594 PBMCs, 4h, Dex


title: VLM236_17503 PBMCs, 4h, LPS


title: VLM236_17503 PBMCs, 4h, Dex


title: VLM236_17503 PBMCs, 4h, Gard


title: VLF235_17509 PBMCs, 4h, Gard


title: VLM234_17511 PBMCs, 4h, LPS


title: VLF235_17509 PBMCs, 4h, Dex


title: VLF235_17509 PBMCs, 4h, LPS


title: VLM236_17503 PBMCs, 4h, Control


title: VLF235_17509 PBMCs, 4h, Control


title: VLM234_17511 PBMCs, 4h, Dex


title: VLM234_17511 PBMCs, 4h, Gard


title: VVHF118_17499 PBMCs, 4h, Gard


title: VVHF118_17499 PBMCs, 4h, LPS


title: VZUF029_17491 PBMCs, 4h, LPS


title: VZUF029_17491 PBMCs, 4h, Dex


title: VLM234_17511 PBMCs, 4h, Control


title: VLM238_17505 PBMCs, 4h, Dex


title: VLM238_17505 PBMCs, 4h, Gard


title: VVHF118_17499 PBMCs, 4h, Dex


title: VZUF029_17491 PBMCs, 4h, Control


title: VZUF028_17493 PBMCs, 4h, Control


title: VZUF028_17493 PBMCs, 4h, Dex


title: VVHM112_17481 PBMCs, 4h, Gard


title: VVHM112_17481 PBMCs, 4h, Dex


title: VVHM112_17481 PBMCs, 4h, Control


title: VZUF028_17493 PBMCs, 4h, Gard


title: VLM237_17507 PBMCs, 4h, Control


title: VVHM111_17489 PBMCs, 4h, LPS


title: VVHM111_17489 PBMCs, 4h, Gard


title: VVHM111_17489 PBMCs, 4h, Dex


title: VVHM111_17489 PBMCs, 4h, Control


title: VVHF100_17475 PBMCs, 4h, LPS


title: VVHM103_17477 PBMCs, 4h, Gard


title: VVHF100_17475 PBMCs, 4h, Gard


title: VVHM114_17479 PBMCs, 4h, Gard


title: VVHF100_17475 PBMCs, 4h, Dex


title: VVHM114_17479 PBMCs, 4h, Control


title: VVHM114_17479 PBMCs, 4h, Dex


title: VZUF029_17491 PBMCs, 4h, Gard


title: VVHF042_17473 PBMCs, 4h, Gard


title: VLM228_17832 PBMCs, 4h, Control


title: VWM210_17469 PBMCs, 4h, LPS


title: VVHF042_17473 PBMCs, 4h, Dex


title: VWM210_17469 PBMCs, 4h, Control


title: VVHF042_17473 PBMCs, 4h, Control


title: VVHF042_17473 PBMCs, 4h, LPS


title: VWM210_17469 PBMCs, 4h, Gard


title: VWM209_17467 PBMCs, 4h, Gard


title: VWF212_17471 PBMCs, 4h, LPS


title: VWF212_17471 PBMCs, 4h, Dex


title: VWF212_17471 PBMCs, 4h, Gard


title: VWM209_17467 PBMCs, 4h, Control


title: 02002-B2

first: Qinglei

last: Gao

address: Jiefang Avenue

department: Department of Gynecological Oncology

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

library_source: genomic

data_processing:
Sequences were processed and analyzed using MiXCR (Bolotin et al., 2015).
Assembly: hg38
Supplementary files format and content: Tab-separated values files
Library strategy: Bulk TCR-seq

molecule: genomic DNA

source_name: Peripheral blood mononuclear cells

extract_protocol:
Peripheral blood mononuclear cells were collected from donators using Streck Cyto-Chex BCT (Streck, La Vista, NE, USA). PBMCs were isolated from the peripheral blood mononuclear cells with FICOLL (TBD sciences, LTS1077) and were re-suspended with 1 x PBS for TCR-seq. Fresh tumor samples were shipped in Mylteni Biotec® Tissue Storage Solution and maintained at 4 ºC until processing.
DNA from patient-matched PBMC and tumor samples of ovarian cancer patients was extracted using the QIAamp DNA Mini Kit (QIAGEN, Germany, 51304) following the manufacturer’s instructions.
The TCRβ CDR3 DNA amplification was performed using multiplex PCR primers from Zhang et al. (Genetics. 2015;201(2):459-72) to amplify the rearranged CDR3 regions of TCRβ, including 30 forward V primers and 13 reverse J primers. After multiplexed PCR, single-stranded PCR products were produced via denaturation and then underwent the circularization program. The replication of single-stranded circle DNA molecules was achieved through rolling cycle amplification, resulting in the generation of a DNA nanoball (DNB) containing multiple copies of DNA. High-quality DNBs were then loaded into patterned nanoarrays using MGISEQ 2000.

value: Peripheral blood mononuclear cells

value: CD3+ T cells

tag: treatment phase

value: Post


title: VWF212_17471 PBMCs, 4h, Control


title: 02002-B1

value: Pre


title: VHMF010_17459 PBMCs, 4h, LPS


title: VHMF010_17459 PBMCs, 4h, Dex


title: 02002-T2

source_name: Tumor

value: Tumor


title: 02002-T1


title: 02001-B1


title: VHMF010_17459 PBMCs, 4h, Gard

value: peripheral blood mononuclear cells


title: 02001-B2


title: VWM209_17467 PBMCs, 4h, Dex


title: 02001-T1


title: VBBF109_17457 PBMCs, 4h, Gard


title: VBBF109_17457 PBMCs, 4h, Dex


title: 01075-B2


title: 01075-B1


title: VBBF109_17457 PBMCs, 4h, Control

value: Control


title: VBBM111_17455 PBMCs, 4h, Control


title: VBBM111_17455 PBMCs, 4h, Gard

value: Gard


title: VBBM111_17455 PBMCs, 4h, Dex


title: 01075-T1


title: 01072-B1


title: VLF227_17453 PBMCs, 4h, Controlb


title: 01072-T2


title: VLF227_17453 PBMCs, 4h, Controla


title: 01072-B2


title: VLF227_17453 PBMCs, 4h, Gard


title: VHMF010_17459 PBMCs, 4h, Control


title: VLF227_17453 PBMCs, 4h, Dex


title: 01072-T1


title: VLF230_17427 PBMCs, 4h, LPS

value: LPS


title: VLF230_17427 PBMCs, 4h, Dex

value: Dex


title: 01069-B2


title: VLF230_17427 PBMCs, 4h, Gard


title: 02001-T2


title: 01069-B1


title: 01069-T2


title: VHMM008_17380 PBMCs, 4h, LPS


title: VBBM111_17455 PBMCs, 4h, LPS


title: 01069-T1


title: 01068-B2


title: VHMM008_17380 PBMCs, 4h, Dex


title: 01075-T2


title: 01068-B1


title: VHMM008_17380 PBMCs, 4h, Gard


title: VHMM008_17380 PBMCs, 4h, Control


title: 01068-T2


title: 01068-T1


title: VQLF018_17378 PBMCs, 4h, Dex


title: VQLF018_17378 PBMCs, 4h, Control


title: VQLF018_17378 PBMCs, 4h, Gard


title: 01062-B1


title: 01062-T2


title: 01030-B2


title: VWM208_17376 PBMCs, 4h, Gard


title: 01030-B1


title: VWM208_17376 PBMCs, 4h, LPS


title: VWM208_17376 PBMCs, 4h, Dex


title: VLM228_17926 PBMCs, 4h, Control


title: 01030-T2


title: VWM208_17376 PBMCs, 4h, Control


title: 01030-T1


title: VWM207_17374 PBMCs, 4h, LPS


title: VWM207_17374 PBMCs, 4h, Dex


title: 01025-B1


title: 01025-B2


title: 01024-B2


title: 01025-T2


title: 01024-B1


title: VWM205_17370 PBMCs, 4h, LPS


title: VWM205_17370 PBMCs, 4h, Dex


title: 01024-T2


title: 01024-T1


title: VWM205_17370 PBMCs, 4h, Control


title: VLM157_17372 PBMCs, 4h, LPS


title: 01025-T1


title: 01062-B2


title: VWM205_17370 PBMCs, 4h, Gard


title: VWM207_17374 PBMCs, 4h, Control


title: 01016-B2


title: VLM157_17372 PBMCs, 4h, Dex


title: 01016-B1


title: VLM157_17372 PBMCs, 4h, Control


title: 01016-T2


title: VZUM006_17356 PBMCs, 4h, Dex


title: 01013-B2


title: VVHM119_17353 PBMCs, 4h, LPS


title: 01016-T1


title: VWM207_17374 PBMCs, 4h, Gard


title: 01013-B1


title: VZUM006_17356 PBMCs, 4h, Control


title: 01013-T2


title: VVHM119_17353 PBMCs, 4h, Dex


title: 01006-B2


title: VVHM119_17353 PBMCs, 4h, Gard


title: 01006-T2


title: VVHF110_17348 PBMCs, 4h, LPS


title: 01006-T1


title: VVHF110_17348 PBMCs, 4h, Dex


title: VVHM119_17353 PBMCs, 4h, Control


title: VVHF110_17348 PBMCs, 4h, Gard


title: VVHF115_17350 PBMCs, 4h, Dex


title: VVHF110_17348 PBMCs, 4h, Control


title: VLM157_17372 PBMCs, 4h, Gard


title: VVHF115_17350 PBMCs, 4h, Control


title: RPE_inf_1

city: Bethesda

first: Hong

last: Liu

state: MD

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

data_processing:
Libraries were multiplex sequenced. Some samples were sequenced on Illumina HiSeq2500 and 3000 Sequencers (NIDDK Genomics Facility), and some with an Illumina NovaSeq6000  (NHLBI Genomics Facility).
Single-end, 50 base reads were collected and converted by bcl2fastq (version 2) into fastq files and aligned on (GRCm38/mm10) using STAR (version 2.7.10b)
Reads were counted by FeatureCounts (subread v2.0.6) and normalized as counts per million mapped reads (cpm). To compare transcript abundance, data were quantified using Kallisto (v0.46.0) as transcripts per million reads (TPM).
Assembly: GRCm38/mm10
Supplementary files format and content: comma-separated text file includes transcripts per kilobase million for RPE and counts-per-million for retina and single-cone sample

source_name: RPE

extract_protocol:
For single cell analyses, cones labeled with a Thrb2Cre driver were dissociated from superior and inferior pieces of retina of Mct8-KO and control male mice at 2 months of age. Cones were isolated individually by micromanipulator to minimize contamination by rods, then examined visually for cone morphology and integrity before library construction. For dissected retina and isolated RPE cells, all samples were taken from superior and inferior areas around the vertical mid-line of the eye, then incubated in RNAprotect Cell reagent before RNA extraction with Qiagen RNeasy kit.
Single cell RNA-seq library library construction with SMART-Seq v4 Ultra Low Input RNA kit and ThruPLEX DNA-Seq Kit, purified RNA from different retina and RPE samples were constructed into RNA-seq libraries with SMARTer stranded total RNA sample prep kit and ThruPLEX DNA-Seq Kit.

value: RPE

value: inferior-RPE

value: wt

value: 3 month


title: VVHF115_17350 PBMCs, 4h, Gard


title: WT_retina_sup_4

source_name: retina

value: retina

value: Superior-retina


title: WT_retina_sup_3


title: RPE_sup_1

value: Superior-RPE

value: 5 month


title: VVHM107_17352 PBMCs, 4h, LPS


title: WT_retina_sup_2


title: VVHM107_17352 PBMCs, 4h, Dex


title: VVHM107_17352 PBMCs, 4h, Control


title: WT_retina_inf_4

value: inferior-retina


title: VVHM107_17352 PBMCs, 4h, Gard


title: WT_retina_inf_2


title: WT_retina_sup_1


title: WT_retina_inf_3


title: 01006-B1

value: Peripheral blood mononuclear cells

value: CD3+ T cells


title: 01013-T1

value: Tumor

value: Pre


title: WT_retina_inf_1


title: VJXM100_17332 PBMCs, 4h, LPS

value: peripheral blood mononuclear cells


title: VLM224_17328 PBMCs, 4h, Control

value: Control


title: VLM224_17328 PBMCs, 4h, Gard

value: Gard


title: VJXM100_17332 PBMCs, 4h, Dex

value: Dex


title: Tshr_ko_retina_sup_2

value: Tshr-/-


title: Tshr_ko_retina_sup_3


title: Tshr_ko_retina_inf_2


title: Tshr_ko_retina_inf_3


title: Tshr_ko_retina_sup_1


title: Tshr_ko_retina_inf_1


title: VJXM100_17332 PBMCs, 4h, Control


title: VJXM098_17336 PBMCs, 4h, LPS

value: LPS


title: Mct8_ko_retina_sup_4


title: VJXM098_17336 PBMCs, 4h, Gard


title: VJXM098_17336 PBMCs, 4h, Dex


title: VLM224_17328 PBMCs, 4h, LPS


title: VLM224_17328 PBMCs, 4h, Dex


title: Mct8_ko_retina_sup_2


title: Mct8_ko_retina_sup_1


title: VLF227_17320 PBMCs, 4h, Gard


title: Mct8_ko_retina_inf_4


title: VLF227_17320 PBMCs, 4h, Control


title: VLF227_17320 PBMCs, 4h, LPS


title: VHMM002_17273 PBMCs, 4h, Control


title: VLF227_17320 PBMCs, 4h, Dex


title: Mct8_ko_retina_inf_1


title: Mct8_ko_retina_inf_2


title: VJXM100_17332 PBMCs, 4h, Gard


title: VHMM002_17273 PBMCs, 4h, Dex


title: VHMM002_17273 PBMCs, 4h, LPS


title: VHMM002_17273 PBMCs, 4h, Gard


title: VHMM003_17215 PBMCs, 4h, Control


title: VHMM003_17215 PBMCs, 4h, Gard


title: Mct8_ko_retina_sup_3


title: Sevo1

first: Lei

last: Lei

state: Henan

address: No.1 Jianshe east road

department: Department of Anesthesiology, Pain and Perioperative Medicine

institute: The First Affiliated Hospital of Zhengzhou University

description: small RNA

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8 (O -Line Base Caller software, v1.8).
Sequencing quality are examined by FastQC and trimmed reads (pass Illumina quality  lter, trimmed 5 , 3 -adaptor bases by cutadapt) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2.
The expression pro ling of tRFs & tiRNAs and miRNA can be calculated based on counts of reads mapped.
The difierentially expressed tRFs & tiRNAs and miRNAs are screened based on the count value with R package edgeR.
Assembly: mm10
Supplementary files format and content: Excel file include expression profiles of tRFs & tiRNAs for each Sample

organism: Rattus norvegicus

source_name: Sperm

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
Agarose electrophoresis was used to check the integrality of total RNA samples, and then the samples were quanti ed on the NanoDrop ND-1000 instrument. Total RNA samples were  rst pretreated as following to remove some RNA modi cations that interfere with small RNA-seq library construction: 3  -aminoacyl (charged) deacylation to 3 -OH for 3 adaptor ligation, 3 -cP (2 ,3 -cyclic phosphate) removal to 3 -OH for 3 adaptor ligation, 5 -OH (hydroxyl group) phosphorylation to 5 -P for 5  -adaptor ligation, m1A and m3C demethylation for e cient reverse transcription. Pretreated total RNA of each sample was taken for tRF & tiRNA-seq library preparation. Library preparation procedures included: 1) 3 -adapter ligation; 2) 5 -adapter ligation; 3) cDNA synthesis; 4) PCR ampli cation; 5) size selection of ∼134-160bp PCR ampli ed fragments (corresponding to ∼14-40nt small RNAs). The completed libraries were quanti ed by Agilent 2100 Bioanalyzer. Libraries were mixed in equal amounts according to the quanti cation results, and used for sequencing on the instrument.
small RNA sequencing

value: Sperm


title: Con1

description: small RNA


title: Sevo2

description: small RNA


title: Input

city: Amsterdam

first: Katarina

last: Ochodnicka

address: Meibergdreef 9

country: Netherlands

institute: AmsterdamUMC

data_processing:
Color signal/SOLiD signal was base-called into reads with manufacturer's software (Lifescope).
Sequencing reads were quality trimmed by clipping at 3 consecutive nucleotides with quality score less than 10. Reads shorter than 18 nucleotides were discarded.
The read were cleaned of PCR duplicates.
The reads were mapped onto mouse genome (MM9 assembly) using Bowtie.
The peaks were called using MACS (v1.4.2), MFOLD=4
Peaks called in Input were subtracted from peaks called in AH2 and R2K.Artm cell lines. Then the peaks called in R2K.Artm were subtracted from peaks called in AH cell line. In rhis way the RAG-dependent NBS1 peaks were obtained
Assembly: mm9
Supplementary files format and content: bed

growth_protocol: The cells were cultured in RPMI1640 (Life Technologies, Bleiswijk, the Netherlands) supplemented with 2 mM of L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, and 10% FCS

extract_protocol:
The cells were washed in RPMI1640 containing cocktail of protease and phosphatase inhibitors: 100 uM PMSF, 1 mM sodium ortho-vanadate, 2mM sodium fluoride and 1.25mM beta-glycero-phosphate. Crosslinking of the chromatin was achieved by resuspending the cells in RPMI1640 at 2.106/mL density and adding 37% formaldehyde (1% final formaldehyde concentration) and incubated in 37°C water bath for 5min. The crosslinking reaction was terminated by adding glycine to a final concentration of 125mM using 2.5M stock solution. The cells were washed in PBS and stored at -80°C for at least overnight. The cells were re-suspended at a concentration of 40.106 cell/mL in sonication buffer (2% SDS, 10 mM EDTA, 50mM Tris-Cl at pH=8, and containing the cocktail of protease and phosphatase inhibitors as mentioned above) and subjected to ultrasound sonication to obtain DNA fragments of average length of 250bp. Following the sonication, the cells were diluted in a dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-Cl pH=8, 167 mM NaCl) and incubated with 5ug of an antibody per sample for 2.5h at 4°C, after with Protein A on beads was added to each sample and the incubation continued for another 2.5h at 4°C. The beads were washed with series of buffers, the low salt buffer (0.1% SDS, 1%, 2 mM EDTA, 20 mM Tris-Cl, pH=8, 150 mM NaCl), high-salt buffer (0.1% SDS, 1%, 2 mM EDTA, 20 mM Tris-Cl, pH=8, 500 mM NaCl), LiCl buffer (250 mM LiCl, 1% deoxycholate, 1% NP-40, 1mM EDTA, 10 mM Tris-Cl pH=8), TE buffer (10 mM Tris-Cl pH=8, 1mM EDTA)  and finally the elution buffer (0.5% SDS, 5 mM EDTA, 10 mM Tris-Cl, pH=8, 300 mM NaCl) to elute the protein-chromatin complexes off the beads. The samples were heated overnight at 65°C to reverse the crosslinking, followed by addition of Protease K and RNase A and subsequent overnight incubation at 55°C to destroy remaining protein and RNA.
The massive parallel sequencing was performed on ABI SOLiD 5500 platform. First the sonicated ChIP DNA samples were quantified by Quant-iTTM dsDNA High-Sensitivity Assay Kit (Thermo Fisher) according to the manufacturer’s protocol. Next the libraries for high throughput sequencing were prepared using Fragment Library Preparation kit for 5500 Series SOLiD Systems (Applied Biosystems) according to the manufacturer’s protocol, briefly, the DNA fragments were first blunt-ended and phosphorylated at the 5’end. Next the DNA fragment size-selection was performed on Agencourt AMPure® XP beads and separated on 2% agarose gel. The fragments of 250bp bp size were selected by gel excision. Then, the dA-tail was ligated onto the size-selected DNA using A-tailing enzyme and using T4 DNA ligase the P1-T and Barcode-T adaptors and barcodes were ligated onto the DNA fragments. These adaptors/barcodes are designed to be compatible with the reverse-read sequencing on 5500 Series SOLiD™ sequencers. Prior to ligation-mediated PCR the sample was incubated at 72°C for 20 minutes in PCR mix to let the DNA diffuse out of the gel and to perform nick translation on non-ligated 3′-ends of DNA fragments. Finally, the libraries were amplified using Platinum® PCR amplification kit and the final size-distribution was checked using Agilent Technologies 2100 Bioanalyzer™.  To sequence the libraries an amplification on P1 beads was performed in an emulsion PCR (ePCR), followed by enrichment of the templated beads. Templated bead preparation was performed using the SOLiD® EZ Bead™ System (Applied Biosystems) according to the manufacturers’ protocol. Emulsion was dispensed into 96-well plate and cycled for 60 cycles. After amplification emulsion was broken with butanol, beads were enriched for template positive beads, 3′-end extended and covalently attached onto sequencing slides. Physically separated samples were deposited on one sequencing slide and sequenced using standard settings on the 5500 Series SOLiDTM sequencer

value: mouse v-Abl-transformed pre-B cells

tag: chip antibody


title: VHMM002_17213 PBMCs, 4h, Gard

tag: cell type


title: Mct8_ko_retina_inf_3

tag: tissue

value: retina

value: 3 month


title: VHMM002_17213 PBMCs, 4h, Dex


title: R2K.A_NBS1

value: monoclonal rabbit anti-NBS1 antibody, (#32074), Abcam


title: Ath RPFs, rRNA depletion version 2

city: Potsdam

first: Reimo

last: Zoschke

address: Am Mühlenberg 1

country: Germany

institute: Max Planck Institute of Molecular Plant Physiology

description:
Ath_depletion_v2
counts_over_CDS-Arabidopsis.xlsx
library_stats.xlsx

library_source: other

data_processing:
library strategy: Ribosome Profiling (Ribo-seq)
Arabidopsis:The Arabidopsis GTF gene annotations (v45) and TAIR10 genome were downloaded from ensembl (https://plants.ensembl.org/index.html). Cutadapt (Martin, 2011) was used to remove adapters and UMIs. Ribo-seq contaminants are generally defined as rRNA, tRNA and snoRNA. These sequences were extracted from the gene annotation file, and converted to fasta format using bedtools (Quinlan and Hall, 2010). Importantly, the nuclear 25S and 5S are missing from the Arabidopsis gene annotations. Thus, these sequences were obtained from the following sources: 25S rRNA (https://www.ncbi.nlm.nih.gov/nuccore/X52320.1) and the 5S rRNA database (http://combio.pl/rrna/). Contaminants were filtered out using STAR aligner (Dobin et al., 2013) with the following parameters: --outFilterMismatchNoverLmax 0.1 --outReadsUnmapped Fastx –outSAMmultNmax 1. After contaminant filtering, the remaining reads were mapped to the genome using STAR aligner using the following parameters: --outFilterMismatchNoverLmax 0.1 --alignIntronMax 8000 --outSAMmultNmax 1. Mapped reads were counted over annotated CDS using FeatureCounts (Liao et al., 2014) using the parameters: -M -s 1 -t CDS -g gene_id.
Tobacco: There are two available genomes for tobacco, which are both available from solgenomics (https://solgenomics.net/). The most recent version was used for alignment (Edwards et al., 2017) since it is conveniently assembled into chromosomes. Nuclear rRNA sequences used to filter the Ribo-seq libraries were obtained from NCBI; 26S (AF479172.1), 18S (AJ236016.1), 5.8S (AJ300215.1) and 5S (AJ222659.1). The tobacco chloroplast (NC_001879.2) and mitochondrial (NC_006581.1) genomes were also obtained from NCBI. Chloroplast and mitochondrial rRNA sequences were extracted from the respective genome annotations. The remainder of the analysis pipeline follows the same structure as what was performed for Arabidopsis.
Assembly: Arabidopsis: TAIR10 genome  (https://plants.ensembl.org/index.html) using the Arabidopsis GTF gene annotations (v45)
Assembly: Tobacco: The Edwards genome assembly was used (solgenomics (https://solgenomics.net/). The chloroplast genome (NC_001879.2) and mitochondria genome (NC_006581.1) were obtained from NCBI.
Supplementary files format and content: "library_stats.xlsx" contains information on the proportion of reads mapping to rRNA, nuclear genome, plastid genome, and mitochondria genome.
Supplementary files format and content: "counts_over_CDS-Arabidopsis.xlsx" contains the number of reads mapping to annotated Arabidopsis coding sequences (CDS)
Supplementary files format and content: "counts_over_CDS-Tobacco.xlsx" contains the number of reads mapping to annotated Tobacco coding sequences (CDS)

molecule: other

organism: Arabidopsis thaliana

source_name: 14-day old seedlings

growth_protocol: The tissue used for the comparison of RNase I and MNase digestion, was derived from 8-day old Arabidopsis seedlings (Col-0) grown on ½ Murashige and Skoog medium (Murashige and Skoog, 1962) with 6.8% agar and 1% sucrose, grown at 100 µmol m-2s-1 for 16h/8h light/dark cycles at 20 °C. The tissue used for refining RNase I treatment and rRNA depletion were derived from 14-day old Arabidopsis seedlings (Col-0), grown on ½ Murashige and Skoog media with 1% agar, grown at 100 µmol m-2s-1 for 12h/12h light/dark cycles at 20 °C. Nicotiana tabacum tissue was derived from leaves harvested from 28-day old plants grown on soil at 350 µmol m-2s-1 in 16h/8h light/dark cycles at 12 °C.

extract_protocol:
RPF isolation: RPFs were isolated as previously described (Trösch et al., 2018) with the following modifications. The units (U) of ribonuclease used in this study are normalized to one mL of plant lysate, derived from 100 mg of plant fresh weight. 300 mg frozen plant tissue was homogenized in liquid nitrogen with a mortar and pestle followed by the addition of 3 mL ribosome extraction buffer (0.2 M sucrose, 0.2 M KCl, 40 mM Tris-OAc pH 8.0, 10 mM MgCl2, 10 mM 2-Mercaptoethanol, 2% (v/v) polyoxyethylene (10) tridecyl ether, 1% (v/v) Triton X-100, 100 μg/mL chloramphenicol, 100 μg/mL cycloheximide). After brief mixing, a 0.5 mL aliquot of the lysate was flash frozen and stored at -80 °C for later total RNA extraction using TRIzol reagent (ThermoFisher cat# 15596026). This total RNA can be used for standard RNA-seq experiments. This step is especially important if the calculation of translation efficiencies is desired (i.e., the normalization of Ribo-seq data to RNA-seq data). The remaining lysate was filtered through glass wool, followed by centrifugation for 10 min at 15,000 x g at 4 °C to remove cell debris. 2.5 mL of the clarified lysate were incubated at specified concentrations of RNase1 or MNase for 1 h at room temperature with gentle rotation to degrade mRNA regions that are not covered and protected by translating ribosomes. Since Ca2+ is a known cofactor of MNase, samples digested with MNase include 5 mM CaCl2. The ribonuclease-treated lysate contains mainly monosomes which were loaded onto a 2 mL sucrose cushion (30% (w/v) sucrose, 40 mM Tris-Acetate pH 8.0, 100 mM KCl, 15 mM MgCl2, 0.1 mg/mL chloramphenicol, 0.1 mg/mL cycloheximide, 0.2% β-MeEtOH) and centrifuged (OptimaTM L-80 XP Ultracentrifuge - Beckman Coulter) for 1.5 h at 303,800 x g at 4 °C. The supernatant was then carefully aspirated and the pelleted monosomes resuspended in 0.5 mL footprint isolation buffer (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0, 100 mM NaCl, 1% (w/v) SDS, 0.1 M EGTA pH 8.0). The RNA was immediately extracted from this pellet using 0.5 mL TRIzol reagent. Next RPFs were size-selected through electrophoresis on a 12% denaturing polyacrylamide gel (19:1, acrylamide:bisacrylamide) prepared in 1x TBE buffer (89 mM Tris, 89 mM Boric Acid, 2mM EDTA pH 8.0) containing 8 M urea. To this end, 25 μg RNA were resuspended in 40 μL of ribosome footprint loading buffer (90% (v/v) deionized formamide, 20 mM Tris-HCl pH 7.5, 20 mM EDTA pH 8.0, 0.04% (w/v) bromophenol blue, and 0.04% (w/v) xylene cyanol) and denatured for 10 min at 70 °C. The gel was run in 1x TBE buffer with a constant power of 30 W at constant temperature of 12 °C (achieved by a cooling unit). Co-migrating pre-stained RNA ladder (Biodynamics Laboratory cat# DM253) was used to visualize the regions of the gel to excise RPFs. All RPFs that were not rRNA-depleted were size-selected between 20-50 nt. All rRNA-depleted RPFs were size-selected between 20-35 nt. RNA was eluted from the excised gel piece in 4 mL TESS (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0, 0.1 M NaCl, 0.2% (w/v) SDS) by overnight incubation at 4 °C with gentle rotation. Eluted RNA was isolated with 4 mL of phenol:chloroform:isoamyl alcohol (25:24:1), followed by overnight ethanol precipitation at -20 °C. To increase purity and further narrow the volume, the RNA pellet was resuspended in 0.1 M NaCl (500 μL) and subjected to a second round of phenol:chloroform:isoamyl alcohol (25:24:1) extraction, followed by two washes with chloroform:isoamylalcohol (24:1) and overnight ethanol precipitation at -20 °C. The received RPF pellet was washed twice with 75% ethanol and resuspended in 20 μL RNase-free water.
Library preparation: T4 polynucleotide kinase (PNK; ThermoFisher, cat#EK0031) reactions were carried out in 18 µL volume with 100 ng of RPFs without ATP for 10 min at 37 °C to promote the 3’-dephosphorylation reaction. Next, 2 µL ATP (10 mM) was added, followed by another incubation for 30 min at 37 °C. PNK was inactivated by heating to 65 °C for 20 min. 20 ng RPFs were directly used as input for the NEXTflex small RNA-seq kit v3 (Perkin Elmer, cat# NOVA-5132-06) according to manufacturer’s instructions. The final libraries were PCR amplified using 15-17 PCR cycles.

value: 14-day old seedlings

tag: nuclease treatment

value: 600 Units RNaseI

tag: rrna depletion

value: yes

value: Wild type

value: RPFs treated with rRNA depletion version 2

tag: molecule type

value: ribosome protected fragment


title: VHMM002_17213 PBMCs, 4h, Control

value: peripheral blood mononuclear cells

tag: treatment


title: Ath RPFs, rRNA depletion version 1

description:
Ath_depletion_v1
counts_over_CDS-Arabidopsis.xlsx
library_stats.xlsx

tag: genotype

value: RPFs treated with rRNA depletion version 1


title: Ath RPFs, 550 U RNaseI

description:
Ath_RNaseI_550U
counts_over_CDS-Arabidopsis.xlsx
library_stats.xlsx

value: 550 Units RNaseI

value: no

value: RPFs generated using 550 U RNaseI


title: VHMM007_17196 PBMCs, 4h, Control

value: Control


title: VHMM007_17196 PBMCs, 4h, LPS

value: LPS


title: VCVM001_17194 PBMCs, 4h, Gard

value: Gard


title: Ath RPFs, 700 U RNaseI

description:
Ath_RNaseI_700U
counts_over_CDS-Arabidopsis.xlsx
library_stats.xlsx

value: 700 Units RNaseI

value: RPFs generated using 700 U RNaseI


title: Ath RPFs, 700 U RNaseI, replicate2

description:
Ath_RNaseI_700U_B
counts_over_CDS-Arabidopsis.xlsx
library_stats.xlsx


title: Con2

description: small RNA

value: Sperm


title: VMPM005_17192 PBMCs, 4h, Control


title: Ath RPFs, 400 U RNaseI

description:
Ath_RNaseI_400U
counts_over_CDS-Arabidopsis.xlsx
library_stats.xlsx

value: 14-day old seedlings

value: 400 Units RNaseI

value: RPFs generated using 400 U RNaseI


title: Ath RPFs, 250 U RNaseI

description:
Ath_RNaseI_250U
counts_over_CDS-Arabidopsis.xlsx
library_stats.xlsx

source_name: 8-day old seedlings

value: 8-day old seedlings

value: 250 Units RNaseI

value: Wild type

value: RPFs generated using 250 U RNaseI


title: VBBM128_NA PBMCs, 4h, Gard

value: peripheral blood mononuclear cells


title: Ath RPFs, 125 U RNaseI

description:
Ath_RNaseI_125U
counts_over_CDS-Arabidopsis.xlsx
library_stats.xlsx

value: 125 Units RNaseI

value: RPFs generated using 125 U RNaseI

value: ribosome protected fragment


title: VBBM128_NA PBMCs, 4h, LPS


title: Ath RPFs, 63 U RNaseI

description:
Ath_RNaseI_63U
counts_over_CDS-Arabidopsis.xlsx
library_stats.xlsx

value: 63 Units RNaseI

value: no

value: RPFs generated using 62.5 U RNaseI


title: VHMM002_17213 PBMCs, 4h, LPS

value: LPS


title: Ath RPFs, 300 U MNase

description:
Ath_MNase_300U
counts_over_CDS-Arabidopsis.xlsx
library_stats.xlsx

value: 300 Units MNase

value: RPFs generated using 300 U MNase


title: Nta RPFs, no rRNA depletion

description:
NTa_depleted
counts_over_CDS-Tobacco.xlsx
library_stats.xlsx

organism: Nicotiana tabacum

source_name: leaves harvested from 28-day old plants

value: leaves harvested from 28-day old plants

value: RPFs without rRNA depletion


title: Ath RPFs, 150 U MNase

description:
Ath_MNase_150U
counts_over_CDS-Arabidopsis.xlsx
library_stats.xlsx

value: 150 Units MNase

value: RPFs generated using 150 U MNase


title: AH2_NBS1

tag: cell line

value: mouse v-Abl-transformed pre-B cells

value: monoclonal rabbit anti-NBS1 antibody, (#32074), Abcam


title: mitfa_low, zf, scRNAseq

city: Delhi

first: Vivek

middle: T

last: Natarajan

state: Delhi

address: Mathura Road

country: India

institute: CSIR-IGIB

description:
10x Genomics
Sample 1

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were done using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: mitfa:GFP+ cells

extract_protocol:
Tg(mitfa:GFP) zebrafish embryos at 24hpf were dechorinated using 5 mg/ml pronase for 10-15 min, deyolked in Ringer's solution (ice cold) using a micropipette tip and spun at 100 g for 2 min at 4°C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30 min at room temperature, after discarding the supernatent. Clumps were removed by passing the cells through a 70 μm cell strainer and washing twice with ice cold phosphate-buffered saline. The cells expressing low and high levels of mitfa:GFP were then sorted using a flow cytometer and taken for library preparation.
Libraries was prepared according to the manufacter’s instructions (single cell 3’ v3.1 (single index) protocol, 10x Genomics). Briefly, 24hpf mitfa:GFP low and high zebrafish cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and sample index were added.

value: mitfa:GFP+ cells

tag: population

value: mitfa:GFP low

value: 24 hours post fertilization


title: 01056

city: Wuhan

data_processing:
Sequences were processed and analyzed using MiXCR (Bolotin et al., 2015).
Assembly: hg38
Supplementary files format and content: Tab-separated values files
Library strategy: TCR-seq

extract_protocol:
Peripheral blood was collected from donators using Streck Cyto-Chex BCT (Streck, La Vista, NE, USA). PBMCs were isolated from the peripheral blood with FICOLL (TBD sciences, LTS1077) and were re-suspended with 1 x PBS for further immunostaining and T-cell sorting.
For sorting of CD4+ T cells, the PBMCs (derived from P35-P44) were preincubated with Fixable Viability Dye as well and then stained with antibodies including CD4-PerCP/Cyanine5.5 (Biolegend, 300529) and CD8-FITC (Biolegend, 300905). After immunostaining, the cell pellets were re-suspended with 200μl 1 x PBS supplemented with 0.5% BSA and EDTA. Sorting for bulk TCR-seq was performed using a FACSAria (BD Biosciences).
DNA from CD4+ T cells was extracted using a commercially available kit (QIAamp DNA Mini Kit, QIAGEN; catalog: 51306). We performed multiplex PCR amplification of the CDR3 region of the TCR-β chain. The primer sequences used were filed as part of a Chinese patent (CN105087789A). To amplify all possible V(D)J combinations, a set of 32 forward V and 13 reverse J primers was used in multiplex PCR1 assays. In the second round, PCR2 was performed using universal primers. Paired-end sequencing of the libraries was completed with a read length of 100 bp using the DNBSEQ-T7RS sequencer (MGI, China) platform.

value: Peripheral blood mononuclear cells

value: CD4+ T cells


title: 02008


title: 01060


title: Ath RPFs, 75 U MNase

description:
Ath_MNase_75U
counts_over_CDS-Arabidopsis.xlsx
library_stats.xlsx

value: 8-day old seedlings

value: 75 Units MNase

value: Wild type

value: RPFs generated using 75 U MNase

value: ribosome protected fragment


title: VCVM001_17194 PBMCs, 4h, LPS

value: peripheral blood mononuclear cells

value: LPS


title: 01055


title: Patient_PB_PBMC_IGHCA

city: Leiden

first: Mirjam

last: van der Burg

address: Albinusdreef 2

department: Pediatrics

institute: Leiden University Medical Center

data_processing:
Sequences were demultiplexed based on their multiplex identifier sequence and 40 nucleotides trimmed from both sides to remove the primer sequence using the ARGalaxy demultiplex tool. Illumina FASTQ files were paired (PEAR), demultiplexed, trimmed with cutadapt.
Sequence allocation was performed using IMGT/High-V-Quest (Alamyar E, Duroux P, Lefranc MP, Giudicelli V. IMGT((R)) tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS. Methods Mol Biol. 2012;882:569-604)
Assembly: GRCh38
Supplementary files format and content: IMGT-HighVQuest output (cutadapt*tar.gz file)

source_name: Blood

extract_protocol:
RNA was isolated using the GenElute™ Total RNA Purification Kit (Sigma-Aldrich) and transcribed into cDNA using random hexamer primers and Superscript III® (both Invitrogen).
Amplicon-seq: IGH transcripts of the samples were amplified using the forward VH1-6 FR1 (BIOMED-2) primers and custom IGHG, IGHA and IGHM reverse primers (sequence available upon request). PCR products were purified and sequenced using 2x300 Illumina sequencing (Illumina).

treatment_protocol: Secondary lymphoid organ samples of the patient were flow sorted into 5 B-cell subsets: naïve, centroblasts (CB), centrocytes (CC), memory B-cells (memB) and plasmablasts (PB)

value: Blood

value: memory B cells


title: Patient_PB_PBMC_CmCH1

value: naive and memory B cells


title: Patient_PB_PBMC_IGHCG


title: 01054


title: Patient_LN_plasmablast_IGHCM

source_name: Secondary lymphoid organ

value: Secondary lymphoid organ

value: plasmablasts


title: Patient_LN_naive_IGHCM

value: naive B cells


title: Patient_LN_naive_IGHCG


title: 01053


title: 01050


title: 01051


title: Patient_LN_plasmablast_IGHCG


title: Patient_LN_naive_IGHCA


title: Patient_LN_memB_IGHCM


title: Patient_LN_memB_IGHCG


title: mitfa_high, zf, scRNAseq

description:
10x Genomics
Sample 2

value: mitfa:GFP+ cells

value: mitfa:GFP high

tag: age


title: T75A_24h_Caf, rep3

city: Jena

first: Konstantin

last: Riege

address: Beutenbergstraße 11

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

description:
R44_T75A_24_Caf.N3
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq v2.20.0.422
Raw data was quality trimmed and clipped for Illumina universal adapter. Potential sequencing errors were detected and corrected using Rcorrector and rRNA fragments have been depleted using SortMeRNA.
Reads were mapped on GRCm38 (mm10) genome reference using segemehl, if applicable deduplicated for over-amplified PCR fragments via Unique Molecular Identifiers using UMI-tools and quantified on Ensembl v102 derived gene annotation utilizing featureCounts. Variance stabilized counts were inferred by DESeq2.
Assembly: mm10 (Ensembl v102)
Supplementary files format and content: Tab delimited text files include raw, variance stabilized and TPM normalized read counts for each sample.

source_name: Brain

growth_protocol: Mice were at least 8 weeks old and were housed in a 12L:12D light cycle.

extract_protocol:
RNA extraction involved resuspension in Trizol and chloroform precipitation, followed by washing with isopropanol and 75% ethanol. Subsequently, cDNA conversion was performed using the GoScript™ Reverse Transcriptase kit (#A5001, Promega).
1) Library was prepared using Novogene NGS RNA Library Prep Set (PT042) according to manufacturer instructions. 2) Libraries were prepared from 500 ng of input material (total RNA) using NEBNext Ultra II Directional RNA Library Preparation Kit in combination with NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors RNA) following the manufacturer's instructions (NewEngland Biolabs).

treatment_protocol: 1) At four time points (4h, 10h, 16h, 22h), mice were intraperitoneally (i.p.) injected with 7.5 mg/kg caffeine (#, C0750, Sigma) or saline at an injection volume of 10ml/kg body weight and tested 2h later. NPB ((#CSB-MP015971HU-100, Cusabio) was injected at doses of 1, 3, and 10 nM into the NAc. NPB was diluted in ddH2O up to 100 nM and then diluted with artificial cerebrospinal fluid, which also served as a control. CYM50769 (#1067-25mg, Sigma Aldrich) was injected into the NAc at doses of 0.1 – 10 μM. CYM50769 was diluted in DMSO up to 100 μM and then diluted in artificial cerebrospinal fluid, which also served as a control solution containing the proper concentration of DMSO (#3525, Tocris). 2) Bilateral stereotaxic surgery into the NAc was essentially performed as described (doi: 10.1038/nm.4386). Viruses were utilized at concentrations from 2 x 10^10 (OE) to 6 x 10^11 (GFP ctrl) particles * 0.1ml: pAAV.1-CAG-GFP (#37825, Addgene), OE-Npbwr1-GFP: pAAV-CAG-GFP-P2A-Npbwr1-WPRE1. Npbwr1-regulating AAVs were custom-made by Charitè viral vector core, Berlin, Germany. All AAVs were serotype 1.

value: Brain

tag: region

value: Nucleus accumbens

value: 12h dark, Caffeine

tag: Sex

value: male


title: T75A_24h_Caf, rep4

description:
R60_T75A_24_Caf.N4
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

tag: strain


title: Patient_LN_centrocyte_IGHCM

value: centrocytes


title: T75A_24h_Caf, rep2

description:
R28_T75A_24_Caf.N2
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: 01049

value: Peripheral blood mononuclear cells

value: CD4+ T cells


title: 01052


title: T75A_24h_Sal, rep3

description:
R43_T75A_24_Sal.N3
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: 12h dark, Saline


title: Patient_LN_centrocyte_IGHCA


title: T75A_24h_Caf, rep1

description:
R12_T75A_24_Caf.N1
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Patient_LN_memB_IGHCA


title: Patient_LN_centroblast_IGHCM

value: centroblasts


title: Patient_LN_centrocyte_IGHCG


title: T75A_24h_Sal, rep4

description:
R59_T75A_24_Sal.N4
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Patient_LN_plasmablast_IGHCA


title: T75A_24h_Sal, rep2

description:
R27_T75A_24_Sal.N2
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Patient_LN_centroblast_IGHCG


title: T75A_24h_Sal, rep1

description:
R11_T75A_24_Sal.N1
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Patient_LN_centroblast_IGHCA