title: PDAC_2

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

description:
10x Genomics
scMC.merge.all.final.rds
scMC.all.3areas.final.rds
All_RCTD.final.rds

data_processing:
The sequencing outputs for all Visium datasets were preprocessed using SpaceRanger-v1.2.1 and mapped to either the latest human or mouse reference genome and the filtered matrices were converted to Seurat objects in R and used for downstream analyses.
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz : Compressed tar archives include Filtered feature-barcode matrices from Space Ranger
Supplementary files format and content: spatial.tar.gz : Compressed tar archives include processed output from Space Ranger with spatial information
Supplementary files format and content: filtered_feature_bc_matrix.h5 : Filtered feature-barcode matrices in HDF5 format
Supplementary files format and content: scMC.merge.all.final.rds : RDS file with all the samples combined
Supplementary files format and content: scMC.all.3areas.final.rds : RDS file with selected spots covering the epithelial lining of the IPMN and cancer lesions (“epilesional”); the adjacent PME (‘juxtalesional”), corresponding to two layers of spots (~200 µm) surrounding the lesion; and an additional two layers of spots located further out of the lesions (“perilesional”)
Supplementary files format and content: All_RCTD.final.rds : RDS file with RCTD weights

source_name: High grade IPMN with co-ocurring PDAC

extract_protocol:
Samples were flash frozen in liquid nitrogen, cryo-sectioned and H&E stained. After sectioning onto the Visium slides, sample processing was performed as described in the Visium 10x Genomics protocol for fresh-frozen tissue samples (15 minutes were used for permealization time)
Library preparation was performed as described in the Visium 10x genomics protocol for fresh-frozen tissue samples.  After library preparation, samples were pooled and sequenced using a NextSeq 550 (Ilumina, CA, USA).
Spatial Transcriptomics Visium 10x genomics

value: High grade IPMN with co-ocurring PDAC

tag: gender

value: M

tag: age


title: PDAC_3

status: Public on Jun 07 2023

type: SRA

country: USA

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: F


title: 1816P3M

city: Meath

first: Clare

last: Mckenna

address: Dunsaney

department: Animal Bioscience

country: Ireland

institute: Teagasc

library_source: transcriptomic

data_processing:
FASTQC software (v0.11.5) was used to check the quality of the raw sequencing reads.
Input reads were then aligned to the bovine reference genome (UMD3.1) using STAR (v2.5.1).
STAR software was used to calculate the number of sequenced fragments overlapping all protein-coding genes from the ENSEMBLv88 annotation of the bovine genome. The number of counts of reads mapping to each annotated gene from HTSeq was than collated into a single file and used for subsequent differential gene expression.
DESeq2 was applied to identify statistically significant differentially expressed genes.
A false discovery rate (FDR) of <0.1 was applied as a threshold to call genes with differential expression levels.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: zipped fastq files

organism: Bos taurus

source_name: muscle

growth_protocol: This experiment was conducted as part of larger study designed to examine the within-animal repeatability of intake, growth and feed efficiency between the growing and finishing stages of the lifespan of Charolais (CH) and Holstein Friesan (HF) beef steers fed the same diet [4]. Briefly, one hundred and sixty seven cattle comprised of 90 CH and 77 HF were used in the study. Following a dietary adaptation period, individual dry matter intake (DMI) and growth were measured over three 70 d feeding phases. Mean BW (SD) and age (SD) at the start of the feeding phase were 395 kg (37.8) and 283 d (18.3), and 294 kg (42.3) and 306 d (7.7), for CH and HF, respectively. Corresponding BW at the start of phase 3 and phase 4 were, 519 (38.3) and 441 (39.2), and 675 (49.8) and 611 (49.3), respectively. During feeding phases 1 and 3 (high concentrate 1 and 2) steers were individually offered the same concentrates (860 g/kg rolled barley, 60 g/kg soya bean meal, 60 g/kg molasses, and 20 g/kg minerals and vitamins) ad libitum plus a restricted allowance of grass silage daily. Throughout the interim period (Zero grazed grass) they were offered zero-grazed grass (DM 196 g/kg) ad libitum. The grass herbage was harvested (without chopping) twice daily from Lolium perenne dominant swards using a ‘zero-grazer’.

extract_protocol:
Total RNA was isolated from 50mg of biopsy samples using QIAzol (Qiagen, UK). Tissue samples were homogenised in 1mL of QIAzol reagent using a rotor-strator tissue lyser (Qiagen, UK) and chloroform (Sigma-Aldrich Ireland, Dublin, Ireland). RNA was subsequently precipitated and purified using the RNeasy plus Universal kit (Qiagen, UK) according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA. The quantity of the RNA isolated was determined by measuring the absorbance at 260nm using a Nanordrop spectrophotometer ND-1000 (Nanodrop Technologies, Wilmington, DE, USA). RNA quality was assessed on the Agilent Bioanalyser 2100 using the RNA 6000 Nano Lab Chip kit (Agilent Technologies Ireland Ltd., Dublin, Ireland). RNA quality was also verified by ensuring all RNA samples had an absorbance (A260/280) of between 1.8 to 2.0 and RIN (RNA integrity number) values of between 8 and 10 were deemed high quality. Any samples that had a (A260/280) absorbance of less than 1.8 were cleaned using Zymo Research RNA clean & concentrator kit (Cambridge Biosciences, UK).  High quality RNA samples were selected for cDNA synthesis.
cDNA libraries were prepared from high quality RNA following the manufacturer’s instructions using the Illumina TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA, USA). For each sample, 1 μg of RNA was used for cDNA library preparation. Briefly, mRNA was purified from total RNA and subsequently fragmented. First strand cDNA was synthesised using Superscript II Reverse Transcriptase (Applied Biosystems Ltd., Life Technologies) followed by second strand synthesis using components of the Illumina TruSeq RNA sample prep kit. Adaptors were ligated to the cDNA which was subsequently enriched by 15 cycles of PCR. Libraries were validated on the Agilent Bioanalyser 2100 using the DNA 1000 Nano Lab Chip kit. cDNA concentration was assessed using Nanordrop spectrophotometer ND-1000 (Nanodrop Technologies, Wilmington, DE, USA) and samples with >25ng/μl were deemed suitable for further analysis. Following quality control procedures, individual RNAseq libraries were pooled based on their respective sample-specific 6bp adaptors and sequenced at 50bp/sequence single-end read using and Illumina HiSeq 2500 sequencer.

treatment_protocol: Average daily live weight gain (ADG) during the RFI measurement period for each animal was computed as the coefficient of the linear regression of BW (kg) on time (d) by using the GLM procedure of SAS 9.1 (SAS Inst. INC., Cary, NC). Mid-test metabolic BW (MBW) was represented as BW0.75 35 d before the end of the test which was estimated from the intercept and slope of the regression line. Residual feed intake was calculated for each animal as the difference between actual DMI (Dry matter intake) and expected DMI. Expected DMI was computed for each animal using a multiple regression model, regressing DMI on MBW, ADG and mean lumbar BF change. Animals were ranked within breed and diet and following a power analysis (www.biomath.info/power/ttest.htm) the most extreme animals for high RFI (n=12) and low RFI (n=12) were selected for further analysis.

tag: rfi

value: Hi

tag: diet

value: ZG

tag: breed

value: CH


title: PN organoid 1 of 2

city: Houston

first: Jae-Il

last: Park

state: Texas

address: 6565 MD Anderson BLVD

department: Dept. of Experimental Radiation Oncology

institute: M.D. Anderson Cancer Center

description: Multiplexed

data_processing:
The demultiplexing, barcoded processing, and  gene counting were performed using the Cell Ranger ( v6.1.2)
Assembly: GRCm38/mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

organism: Mus musculus

source_name: esophagus

extract_protocol:
organoids from WT, PC, PN, and PCN were collected 7 days after seeding and digested with 0.05% trypsin-EDTA at 37 ℃ for 30 min.
Each group was tagged with 2 CMO tags from CellPlex kit (10x Genomics). The tagged cells of each group were pooled together with same number of cells after counting cells. cDNA library was prepared with the 10x Genomics 3’ v2 kit.

value: organoid

tag: cell type

value: epithelial cell

tag: genotype

value: Trp53;Notch1 KO

tag: treatment


title: PC organoid 2 of 2

description: Multiplexed

value: Trp53;Cdkn2a KO


title: THIOxenoHCC_roi16_seg007_otherLeukocytes

type: protein

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: protein on FFPE tissue section

hyb_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

data_processing: Raw count data of antibody-captured protein copy numbers in each segment were normalized by scaling with geometric mean of the counts of the housekeeping proteins

label: fluorescent barcode

molecule: protein

treatment_protocol: Mice were treated with vehicle control, THIO, anti-PD-L1+anti-VEGF, or anti-PD-L1+anti-VEGF+THIO and sacrificed at the end of the treatment (n=1 per group).

value: Other leukocytes (CD3-/CD45+)

value: negative

value: positive

value: THIO


title: PDAC_1


title: PC organoid 1 of 2

description: Multiplexed


title: PCN organoid 1 of 2

description: Multiplexed

value: Trp53;Cdkn2a;Notch1 KO


title: 1816P1M

value: Lo


title: 1811P4M

value: HF


title: Wild type organoid 2 of 2

description: Multiplexed

value: wild type


title: THIOxenoHCC_roi16_seg005_otherLeukocytes

description: protein on FFPE tissue section

scan_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals


title: 1811P1M


title: HG_2

source_name: High grade IPMN

value: High grade IPMN


title: PN organoid 2 of 2

description: Multiplexed


title: HG_1

value: M


title: HG_3


title: Wild type organoid 1 of 2

description: Multiplexed


title: 1797P1M


title: LG_7

source_name: Low grade IPMN

value: Low grade IPMN


title: THIOxenoHCC_roi19_seg001_otherLeukocytes

description: protein on FFPE tissue section

label_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

value: vehicle control


title: 1782P3M

value: Hi

value: ZG


title: PCN organoid 3 of 3

description:
diffgene_PCN1_WT
PCN3

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files which contain sequences of reads and corresponding base quality.
Assembly: GRCm38/mm10
Supplementary files format and content: DESEQ output files comparing 2 groups, counts, fpkms

extract_protocol: organoids from WT, PN, and PCN were collected 7 days after seeding and lysed with Rneasy Mini Kit

value: organoid

value: epithelial cell


title: LG_6

value: F


title: PCN organoid 2 of 3

description:
diffgene_PCN1_WT
PCN2


title: THIOxenoHCC_roi19_seg004_otherLeukocytes

description: protein on FFPE tissue section

value: Other leukocytes (CD3-/CD45+)


title: THIOxenoHCC_roi19_seg002_otherLeukocytes

description: protein on FFPE tissue section

value: negative


title: THIOxenoHCC_roi16_seg006_otherLeukocytes

description: protein on FFPE tissue section

value: positive


title: PCN organoid 1 of 3

description:
diffgene_PCN1_WT
PCN1


title: 1661P4M


title: 1657P4M


title: THIOxenoHCC_roi24_seg010_Tcell

description: protein on FFPE tissue section

value: T cells (CD3+)

value: anti-PD-L1 + anti-VEGF + THIO


title: THIOxenoHCC_roi19_seg003_otherLeukocytes

description: protein on FFPE tissue section


title: THIOxenoHCC_roi24_seg012_Tcell

description: protein on FFPE tissue section


title: LG_3


title: PN organoid 2 of 3

description:
diffgene_PCN1_PN1
PN2

value: Trp53;Notch1 KO


title: THIOxenoHCC_roi24_seg009_Tcell

description: protein on FFPE tissue section


title: 1656P1M

value: Lo

value: HF


title: LG_4


title: PN organoid 3 of 3

description:
diffgene_PCN1_PN1
PN3


title: PN organoid 1 of 3

description:
diffgene_PCN1_PN1
PN1


title: 1643P1M


title: LG_2


title: THIOxenoHCC_roi24_seg008_Tcell

description: protein on FFPE tissue section


title: 1668P3M


title: Wild type organoid 3 of 3

description:
diffgene_PN1_WT
WT3

value: wild type


title: LG_5


title: LG_1


title: 1639P4M


title: THIOxenoHCC_roi399_seg007_Tcell

description: protein on FFPE tissue section

value: anti-PD-L1 + anti-VEGF


title: 1639P3M


title: Wild type organoid 2 of 3

description:
diffgene_PN1_WT
WT2


title: BT20-Dox-mRNA

city: Ithaca

first: Saori

last: Uematsu

state: New York

address: 526 Campus Road, Cornell University

institute: Cornell University

data_processing:
The adaptor AAAAAAAAAAAA was trimmed by Cutadapt. The reads with length <15 nt were not included. The trimmed reads were aligned to human transcriptome, using STAR with default parameters. The uniquely mapped reads were used for analysis. TRNA-seq was analyzed following PMID: 33581077.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: BT20 cells

extract_protocol:
For tRNA-seq, total RNA was extacted with Trizol, deacylated in 50 mM Tris-HCl (pH 9.0) at 37 °C for 45 min and then resolved by 10% polyacrylamide TBE-urea gel (Invitrogen). tRNA (60 to 100 nt) were collected by gel excision and resolved in RNA elution buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.1 U/μL SUPERase In) overnight. After ethanol precipitation, tRNA was treated with demethylase (rtStarTM tRNA-optimized First-Strand cDNA Synthesis Kit, ArrayStar) and cleaned up. 1 μg tRNA was used for library construction. For ribo-seq, ribosome fractions separated by sucrose gradient sedimentation were pooled and digested with E. coli RNase I (Ambion, 750 U per 100 A260 units) by incubation at 4°C for 1 h. SUPERase inhibitor (50 U per 100 U RNase I) was then added into the reaction mixture to stop the digestion. Total RNA was extracted using TRIzol reagent. RNA was separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and the ribosome protected fractions were excised (25-35 nt).
RNA was dephosphorylated. Poly(A) tailing, 5’ adenylation, adaptor ligation, and library construction were carried out as described in PMID: 36824937.

tag: cell line

value: BT20 cells

value: Dox-inducible SAMD9 R1293W

value: treatment with Dox for 12 hours

tag: fraction

value: mRNA


title: Wild type organoid 1 of 3

description:
diffgene_PN1_WT
WT1

value: organoid


title: 1492P4M

value: CH


title: BT20-Dox-RPF (rep2)

data_processing:
The adaptor AAAAAAAAAAAA was trimmed by Cutadapt. The reads with length <15 nt were not included. The trimmed reads were aligned to human transcriptome, using STAR with default parameters. The uniquely mapped reads were used for analysis. TRNA-seq was analyzed following PMID: 33581077.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each sample
Library strategy: Ribo-seq

value: Ribosome protected fragment


title: BT20-Con-mRNA

value: nontreated


title: The bulb region of zigzag hair follicle at Day 12.0 [PR1507_09A2121_H1]

city: Kobe

first: Makoto

last: Takeo

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: BDR

country: Japan

institute: RIKEN

data_processing:
Genedata Profiler Genome ver. 13.0.11.
Sequence reads were trimmed for adaptor sequence.
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR ver. 2.6.0c.
Read count extraction and normalization were performed using STAR.
Assembly: mm10
Supplementary files format and content: Processed_Data.txt: Tab-delimited text file includes TPM and read values for each Sample.

source_name: hair follicle

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.0 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit and SMARter RNA Unique Dual Index Kit following manufacturer's protocols.

value: hair follicle

tag: strain

value: Induction of hair regeneration by depilation

tag: time point


title: THIOxenoHCC_roi399_seg006_Tcell

description: protein on FFPE tissue section

value: T cells (CD3+)

value: positive

value: negative


title: THIOxenoHCC_roi399_seg005_Tcell

description: protein on FFPE tissue section


title: 1492P3M

value: Lo

value: ZG


title: The bulb region of zigzag hair follicle at Day 11.5 [PR1507_08A2020_H1]


title: THIOxenoHCC_roi16_seg008_Tcell

description: protein on FFPE tissue section

value: THIO


title: 1484P4M

value: Hi


title: BT20-Con-RPF (rep2)

value: BT20 cells


title: BT20-Dox-RPF (rep1)

value: Dox-inducible SAMD9 R1293W


title: The bulb region of zigzag hair follicle at Day 12.0 [PR1507_06A1818_H1]


title: 1484P3M


title: BT20-Con-RPF (rep1)


title: The bulb region of zigzag hair follicle at Day 11.5 [PR1507_05A1717_H1]


title: 1483P3M


title: THIOxenoHCC_roi16_seg006_Tcell

description: protein on FFPE tissue section


title: HeLa-WT-VACV-tRNA (rep2)

source_name: HeLa cells

value: HeLa cells

value: WT

tag: infection

value: WT VACV

value: tRNA


title: The bulb region of zigzag hair follicle at Day 11.0 [PR1507_04A1616_H1]


title: The bulb region of zigzag hair follicle at Day 11.0 [PR1507_01A1313_H1]


title: 1320P4M

value: CH


title: HeLa-VACV-tRNA (rep2)

value: vK1-C7- VACV


title: 1320P1M


title: THIOxenoHCC_roi16_seg005_Tcell

description: protein on FFPE tissue section


title: THIOxenoHCC_roi19_seg003_Tcell

description: protein on FFPE tissue section

value: vehicle control


title: HeLa-uninfected-tRNA (rep2)

value: uninfected


title: THIOxenoHCC_roi16_seg007_Tcell

description: protein on FFPE tissue section

value: T cells (CD3+)


title: 1316P4M


title: 1101P1M


title: HeLa-VACV-tRNA (rep1)


title: V12

city: Gainesville

first: Thomas

middle: C

last: Foster

state: FL

address: 1149 S Newell Dr.

department: Neuroscience

institute: University of Florida

data_processing:
ERCC quality assurance: ERCC analysis was performed with the ERCC analysis plugin in the Torrent. Spiked samples had an R2 above 0.9.
Alignment: Ion Torrent derived reads were  aligned to the rattus norvegicus genome (rn6) using STAR 2.5.3a in the in the Partek Flow servers (Partek, Inc., St. Louis, MO).
Annotation: Gene read counts were generated from Binary Alignment Map (BAM) files and annotated to the genome using Ensembl (version 104; Partek, Inc.).
Trimming of Reads: Reads from FASTQ files produced by the Ion Torrent System were trimmed from both ends until all samplesÆ collective average Phred quality score was > 25. Reads shorter than 25 base pairs (bps) were also excluded.
Gene  with the total number of counts lower than 5 per sample was excluded from the analysis
Normalization and differential expression analysis: DESeq2 was utilized to obtain a list of DEGs. A threshold p-value lower than 0.05 was used as a cut-off to statistically filter genes
Assembly: Ensembl (version 104; Partek, Inc.).
Supplementary files format and content: Comma-separated values (.csv) files that contain the normalized counts for each sample

organism: Rattus norvegicus

source_name: DG region of the hippocampus

growth_protocol: a

extract_protocol:
Rats were briefly anesthetized with isoflurane (Patterson Veterinary, Greenly, CO) and swiftly decapitated. The brains were then rapidly removed, and the hippocampi were dissected according to previously described methods (Lein 2004; Zeier 2011). The hippocampal regions DG was separated, placed in the tubes, and flash-frozen in liquid nitrogen. All samples were stored in at -80░C until processed. RNA was isolated from subregions of a hippocampus from a single hemisphere of each animal. RNA Isolation was performed according to methods previously described (Ianov 2016; Barter 2019). Briefly, RNA was isolated using the RNeasy Lipid Tissue Mini kit (Qiagen, catalog number 74804). Total RNA was treated with DNase using the RNase-Free DNase Set (Qiagen, catalog number 79254). Concentration of total RNA was assessed using the NanoDrop 2000 spectrophotometer (Thermo Fisher catalog number ND-2000) and the RNA integrity number (RIN) was quantified using the Agilent 2200 Tapestation system with High Sensitivity RNA Screen Tape (Agilent Technologies, Santa Clara, CA). Mean RNA integrity across all samples was 9.05 (SEM ▒ 0.02) with values ranging from 8.2 to 9.3. Poly-A-selection for mRNA was performed using 250 ng of isolated total RNA in the Dynabeads mRNA DIRECT Micro kit (Thermo Fisher, catalog number 61021). External RNA Controls Consortium (ERCC) RNA Spike-In Control Mixes were included in all isolated mRNA samples (Thermo Fisher, catalog number 4456740).
Library preparation was performed using the Ion Total RNA-seq Kit v2 (Thermo Fisher, catalog number 4475936). Ion Xpress barcodes (Thermo Fisher, catalog number 4475485) were included with libraries for multiplex sequencing. In summary, isolated mRNA was fragmented with RNase III then ligated to the Ion Adapter Mix v2. RNA samples were then reverse transcribed. cDNA from each biological replicate was uniquely barcoded and amplified with 16 PCR cycles. Library concentration from each sample was quantified using the Qubit dsDNA HS Assay (Thermo Fisher, catalog number Q32851). DNA fragment size distribution was subsequently evaluated using High Sensitivity D1000 ScreenTape in the 2200 Tapestation system (Agilent Technologies, Santa Clara, CA).   Templates were prepared using the Ion Chef system (Thermo Fisher, catalog number 4484177) and sequencing was performed using the Ion Proton system (Thermo Fisher, catalog number 4476610) or Ion GeneStudio S5 system (Thermo Fisher, catalog number A38194).

treatment_protocol: a

value: Young rats (6 months)

tag: Sex

value: male

tag: machine

value: Ion Gene Studio


title: THIOxenoHCC_roi19_seg004_Tcell

description: protein on FFPE tissue section

value: positive

value: negative


title: 1100P4M

value: Hi


title: THIOxenoHCC_roi19_seg001_Tcell

description: protein on FFPE tissue section


title: Group 3 innate lymphoid cell, WT DN ILC3s rep2, H3K4me3

city: hangzhou

first: lie

last: wang

state: zhejiang

address: Zijingang Campus, Zhejiang University，Yuhangtang Road 866

department: immunology

country: China

institute: zhejiang universiry

library_source: genomic

data_processing:
All raw sequence data were quality trimmed using fastp (version0.19.7)
Aligned to the mm10 mouse genome using Bowtie2 (version 2.3.5.1) with options' –local–very-sensitive-local–no-unal–nomixed–no-discordant–phred33 -I 10 -X 700'.
PCR duplicates were removed using Picard MarkDuplicates (version 2.25.0).
Peaks were called using MACS2 (version 2.2.7.1) with options 'q 0.05'. DeepTools2 software (version 3.5.1) was used to create the peaks density plot and heatmap graph.
Visualization of peak distribution along genomic regions of interested genes was performed with IGV.
Genomic annotation was assigned using ChIPSeeker (version 1.28.3). Promoters were defined as follows: within 3000bp around the transcriptional start site (TSS).
Assembly: mm10
Supplementary files format and content: bigWig, peaks.narrowPeak(except for Input sample)
Library strategy: CUT&TAG

molecule: genomic DNA

source_name: small intestine

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Small intestinal ILC3s were sorted from siLP of aged  and young mice.  H3K4me3 Chip of three subsets of ILC3s were both performed on 100,000 cells  with modifications according to the protocol of Hyperactive In-Situ ChIP Library Prep Kit for Illumina (TD 901, Vazyme)
Briefly, sorted CCR6+ ILC3s，NKp46+ ILC3s and DN ILC3s were washed with 500 μl of wash buffer containing 1× protease inhibitor cocktail (5056489001, Sigma-Aldrich). Cell pellets were resuspended in wash buffer. After two washes with binding buffer, Concanavalin A-coated magnetic beads were added and incubated at room temperature. Bead-bound cells were resuspended in 50 μl of antibody buffer.

value: small intestine

value: Group 3 innate lymphoid cell

tag: chip antibody

value: H3K4me3 antibody (39016, Active Motif)

value: 6-8 weeks-old


title: Group 3 innate lymphoid cell, WT NKp46+ ILC3s rep2, H3K4me3


title: Group 3 innate lymphoid cell, WT CCR6+ ILC3s rep2, H3K4me3


title: V11


title: HeLa-uninfected-tRNA (rep1)

value: HeLa cells

value: WT


title: Group 3 innate lymphoid cell, KO NKp46+ ILC3s rep2, H3K4me3


title: V10


title: 1100P3M

value: Lo

value: ZG

value: CH


title: CD 6, scRNAseq, sigma

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38 p10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: sigma

extract_protocol:
Biopsies (n=4-6 per patient) were taken from involved areas of the colon of UC and CD patients with signs of endoscopic activity, placed immediately in cold Hank’s Balanced Salt Solution (HBSS) (Gibco, MA, USA) and kept at 4º until processing (<1 h). Colonic biopsies from non-IBD controls were collected from the sigmoid colon and processed in the same way. Freshly collected biopsies were washed with HBSS/DTT (Roche, Spain) 5mM for 15 min and then washed in complete medium (CM) (RPMI 1640 medium (Lonza, MD, USA) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Biosera, France), 100U/ml penicillin, 100 U/ml streptomycin and 250 ng/ml amphotericin B (Lonza), 10µg/ml gentamicin sulfate (Lonza) and 1,5mM Hepes (Lonza) for 10 minutes. Both incubations were performed at room temperature in a platform rocker. Biopsies were chopped with scalpel and placed into tubes containing 500 μl of Digestion Solution (CM + Liberase TM (0.5 Wünsch units/ml) (Roche, Spain) + DNase I (10 μg/mL) (Roche, Spain) and incubated on a shaking platform for 1h at 250 RPM at 37ºC. After incubation biopsies were filtered through a 50-μm cell strainer (CellTrics, Sysmex, USA), washed with Dulbecco’s Phosphate Buffered Saline (PBS; Gibco, USA) and resuspended in RPMI (Roswell Park Memorial Institute) medium supplemented with 0.05% of Bovine fetal serum (BSA) at a concentration of ~500.000-1·106 cells/mL (Veny et al, JCC 2020).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs 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.

value: sigma

tag: gender

value: Male

tag: disease state

value: Crohn’s disease


title: THIOxenoHCC_roi19_seg002_Tcell

description: protein on FFPE tissue section

value: T cells (CD3+)

value: vehicle control


title: CD 5, scRNAseq, sigma

description: 10x Genomics

tag: tissue


title: HeLa-WT-VACV-tRNA (rep1)

value: WT VACV

value: tRNA


title: Group 3 innate lymphoid cell, KO CCR6+ ILC3s rep2, H3K4me3

tag: age


title: 1100P1M

tag: rfi

tag: diet


title: 1078P1M

value: Hi

tag: breed


title: CD 4, scRNAseq, sigma

description: 10x Genomics


title: V6

value: Young rats (6 months)

value: male

value: Ion Gene Studio


title: CD 3, scRNAseq, descending colon

description: 10x Genomics

source_name: descending colon

value: descending colon

value: Female


title: Group 3 innate lymphoid cell, WT NKp46+ ILC3s rep1, H3K4me3

value: small intestine

tag: cell type

value: Group 3 innate lymphoid cell

value: H3K4me3 antibody (39016, Active Motif)

tag: genotype

value: 6-8 weeks-old


title: V5


title: Group 3 innate lymphoid cell, WT DN ILC3s rep1, H3K4me3


title: 47_912_Ar c/y_M

city: Los Angeles

first: Jing

last: Liu

state: California

address: 1425 San Pablo St.

department: Department of Regenerative Medicine  & Stem Cell Biology

institute: University of Southern California

data_processing:
For sample 1- 145, RNA-seq reads from fastq with length lower than 20, average quality lower than 20 were filtered through Fastp version 0.20.1. Filtered reads were then aligned to the Ensembl release 103 primary assembly by STAR version 2.7.9a. Gene counts were derived from featureCount version 2.0.1.
For sample 146 - 188, RNA-seq reads were aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.
Assembly: Mus_musculus.GRCm39.dna.primary_assembly.fa; For sample 1 - 145: Mus_musculus.GRCm39.103.gtf; For sample 146 - 188: Mus_musculus.GRCm39.101.gtf
Supplementary files format and content: 1_WashU_50SE_counts.txt; 2_BGI_PE150_counts.txt; 3_WashU_PE150_counts.txt
Supplementary files format and content: 146_155_all.gene_counts.txt, 156_188_all.gene_counts.txt

source_name: kidney

extract_protocol:
Whole kidney total RNA were extracted using Qiagen’s RNeasy Mini Kit.
Sample 1- 67 and sample 98 - 188 were submitted to the Genome Access Technology Center at the McDonnell Genome Institute at University of Washington in St. Louis. Samples 1- 67, sample 98 - 145 were prepared according to Clontech SMARTer library kit manufacturer’s protocol, sample 146 - 188 were prepared according to polyA selection library kit manufacturer’s protocol. Sample 1- 67 were indexed, pooled, and sequenced on Illumina HiSeq2500 platform for 50-bp single-end. Sample 98 - 188 were indexed, pooled, and sequenced on llumina NovaSeq S4 2X150 (4 lanes). Sample 68 to Sample 97 were indexed, pooled and sequenced at BGI genomics with DNBseq platform according to the manufacturer's protocol. For sample 146 - 188, Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.  Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.

value: kidney

value: M

value: Ar c/y

tag: treatment

tag: time

tag: fragment length

tag: library kit

value: PE100/PE150 - BGI genomics


title: CD 2, scRNAseq, sigma

description: 10x Genomics

value: sigma

value: Male

value: Crohn’s disease


title: 1840P4M

value: Hi

value: CH


title: Group 3 innate lymphoid cell, WT CCR6+ ILC3s rep1, H3K4me3


title: V3

value: Young rats (6 months)

value: male


title: CD 1, scRNAseq, ascending colon

description: 10x Genomics

source_name: ascending colon

value: ascending colon


title: Group 3 innate lymphoid cell, KO NKp46+ ILC3s rep1, H3K4me3


title: Group 3 innate lymphoid cell, KO DN ILC3s rep2, H3K4me3


title: V9

value: Ion Gene Studio


title: Group 3 innate lymphoid cell, KO DN ILC3s rep1, H3K4me3

value: small intestine


title: V2


title: 45_908_Ar c/y_M


title: 46_909_Ar c/y_M


title: Group 3 innate lymphoid cell, KO CCR6+ ILC3s rep1, H3K4me3

value: Group 3 innate lymphoid cell


title: 4572

value: Middle-aged rats (12 months)


title: UC 5, scRNAseq, rectum

description: 10x Genomics

source_name: rectum

value: rectum

value: ulcerative colitis


title: V1


title: UC 4, scRNAseq, sigma

description: 10x Genomics

value: Female


title: V4


title: 44_906_Ar c/y_M

value: kidney

value: M

value: Ar c/y


title: Group 3 innate lymphoid cell, WT NKp46+ ILC3s rep2, anti-CFP1

value: Cxxc1 antibody (provided by Prof. Hengyu Fan， Institute of Life Sciences, Zhejiang University)

value: 6-8 weeks-old


title: 4571


title: 43_898_Ar c/y_M

value: PE100/PE150 - BGI genomics


title: UC 3, scRNAseq, rectum

description: 10x Genomics


title: 4569


title: 42_897_Ar c/y_M


title: Group 3 innate lymphoid cell, WT CCR6+ ILC3s rep2, anti-CFP1


title: UC 6, scRNAseq, rectum

description: 10x Genomics


title: UC 2, scRNAseq, transverse colon

description: 10x Genomics

source_name: transverse colon

value: transverse colon

value: Male


title: 4568

value: male


title: UC 1, scRNAseq, sigma

description: 10x Genomics

value: sigma


title: 4567

value: Ion Gene Studio


title: 41_911_Six2TGC/+; Ar c/y_M

value: Six2TGC/+; Ar c/y


title: 4566


title: HC 5, scRNAseq, sigma

description: 10x Genomics

value: healthy control


title: HC 6, scRNAseq, sigma

description: 10x Genomics


title: Group 3 innate lymphoid cell, KO DN ILC3s rep2, anti-CFP1

value: small intestine

value: Group 3 innate lymphoid cell


title: Group 3 innate lymphoid cell, KO NKp46+ ILC3s rep2, anti-CFP1


title: 39_896_Six2TGC/+; Ar c/y_M


title: 38_895_Six2TGC/+; Ar c/y_M


title: Group 3 innate lymphoid cell, KO CCR6+ ILC3s rep2, anti-CFP1


title: 4110

value: Middle-aged rats (12 months)


title: HC 4, scRNAseq, sigma

description: 10x Genomics


title: 29_889_Esr1 c/c_M

value: Esr1 c/c


title: Group 3 innate lymphoid cell, WT NKp46+ ILC3s rep1, anti-CFP1


title: 4107


title: Group 3 innate lymphoid cell, WT DN ILC3s rep2, anti-CFP1


title: 28_887_Esr1 c/c_M

value: kidney


title: HC 3, scRNAseq, sigma

description: 10x Genomics

value: Female


title: HC 2, scRNAseq, sigma

description: 10x Genomics


title: Group 3 innate lymphoid cell, WT DN ILC3s rep1, anti-CFP1


title: 4105


title: 27_886_Esr1 c/c_M

value: M


title: 4106


title: Group 3 innate lymphoid cell, WT CCR6+ ILC3s rep1, anti-CFP1

value: Cxxc1 antibody (provided by Prof. Hengyu Fan， Institute of Life Sciences, Zhejiang University)


title: HC 1, scRNAseq, sigma

description: 10x Genomics


title: 40_910_Six2TGC/+; Ar c/y_M


title: Group 3 innate lymphoid cell, KO NKp46+ ILC3s rep1, anti-CFP1

value: 6-8 weeks-old


title: VCaP_DMSO_3

city: Philadelphia

first: Irfan

last: Asangani

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Illumina bcl2fastq for demultiplexing to generate fastq files
fastq files were aligned to hg19 reference genome using STAR aligner (2.7.3a) with default parameters
samtools (v1.9) was used to convert SAM to BAM and filter out duplicates and reads q<30
bamCoverage was used to convert Bam to bigwig using â€œ--normalizeUsing CPMâ€
Assembly: mm10, hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: VCaP

growth_protocol: MDVR cell lines were grown in the medium supplemented with Enzalutamide.

extract_protocol:
RNA was harvested using miRNeasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using RNA library preparation kit Illumina following manufacturer's protocols.

treatment_protocol: ARD-69 or DT-061 treatments were done at a concentration of 100 nM and 10 uM for12 hours respectivily.

tag: cell line

value: VCaP

value: prostate cancer

tag: source

value: Derived from VCAP

value: WT

value: dmso


title: 26_890_Six2TGC/+; Esr1 c/c_M

tag: Sex

value: Six2TGC/+; Esr1 c/c

value: PE100/PE150 - BGI genomics


title: 4077

value: male

tag: machine

value: Ion Gene Studio


title: VCaP_DMSO_2


title: 4074


title: Group 3 innate lymphoid cell, KO DN ILC3s rep1, anti-CFP1

value: small intestine

value: Group 3 innate lymphoid cell

tag: chip antibody


title: 4070

value: Middle-aged rats (12 months)


title: 24_885_Six2TGC/+; Esr1 c/c_M

value: kidney


title: VCaP_DMSO_1


title: 25_888_Six2TGC/+; Esr1 c/c_M


title: Group 3 innate lymphoid cell, young gut NKp46+ ILC3s rep3, H3K4me3

data_processing:
All raw sequence data were quality trimmed using fastp (version0.19.7)
Aligned to the mm10 mouse genome using Bowtie2 (version 2.3.5.1) with options' –local–very-sensitive-local–no-unal–nomixed–no-discordant–phred33 -I 10 -X 700'.
PCR duplicates were removed using Picard MarkDuplicates (version 2.25.0).
Peaks were called using MACS2 (version 2.2.7.1) with options 'q 0.05'. DeepTools2 software (version 3.5.1) was used to create the peaks density plot and heatmap graph.
Visualization of peak distribution along genomic regions of interested genes was performed with IGV.
Genomic annotation was assigned using ChIPSeeker (version 1.28.3). Promoters were defined as follows: within 3000bp around the transcriptional start site (TSS).
Assembly: mm10
Supplementary files format and content: bigWig (except for Input sample)

value: H3K4me3 antibody (39016, Active Motif)

tag: strain


title: VCaP-EnzaR_3

source_name: VCaP-EnzaR

value: VCaP-EnzaR


title: 4069


title: VCaP-EnzaR_2


title: 22_884_Six2TGC/+; Esr1 c/c_F

tag: tissue

value: F


title: Group 3 innate lymphoid cell, young gut DN ILC3s rep3, H3K4me3

tag: age

value: 6-8 weeks-old


title: Group 3 innate lymphoid cell, young gut CCR6+ ILC3s rep3, H3K4me3


title: 21_883_Six2TGC/+; Esr1 c/c_F


title: 4036


title: 4035


title: Group 3 innate lymphoid cell, aged gut NKp46+ ILC3s rep3, H3K4me3


title: 20_769_Six2TGC/+; Esr1 c/c_F


title: 4032


title: VCaP-EnzaR_1


title: Group 3 innate lymphoid cell, aged gut DN ILC3s rep3, H3K4me3


title: 19_768_Six2TGC/+; Esr1 c/c_F


title: 23_892_Six2TGC/+; Esr1 c/c_F


title: Group 3 innate lymphoid cell, KO CCR6+ ILC3s rep1, anti-CFP1

value: Cxxc1 antibody (provided by Prof. Hengyu Fan， Institute of Life Sciences, Zhejiang University)


title: 18_766_Six2TGC/+; Esr1 c/c_F


title: 4031


title: 4011


title: VCaP-EnzaR-DT061_1

value: prostate cancer


title: Group 3 innate lymphoid cell, aged gut CCR6+ ILC3s rep3, H3K4me3


title: 14_894_Esr1 c/c_F

value: Esr1 c/c


title: VCaP-EnzaR-ARD69_3

value: Derived from VCAP

value: WT


title: 13_893_Esr1 c/c_F


title: Group 3 innate lymphoid cell, young gut DN ILC3s rep2, H3K4me3


title: Group 3 innate lymphoid cell, young gut NKp46+ ILC3s rep2, H3K4me3


title: 4010


title: 4009


title: 12_891_Esr1 c/c_F


title: Group 3 innate lymphoid cell, young gut CCR6+ ILC3s rep2, H3K4me3


title: 4007


title: VCaP-EnzaR-ARD69_2


title: Group 3 innate lymphoid cell, aged gut NKp46+ ILC3s rep2, H3K4me3


title: VCaP-EnzaR-ARD69_1


title: VCaP-EnzaR-DT061_3


title: in vivo, HT_graft CD8

city: NEW BRUNSWICK

first: Xiaosheng

last: Tan

state: NJ

address: 89 French St

institute: RUTGERS

description:
IN VIVO All_samples_rpkm.txt
WTHT_H_CD8

data_processing:
Illumina NovaSeq 6000 or DNBSEQ-T7 were used for basecalling. Samples are sequenced on the platform to get image files, which are transformed by the software  of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated.
Sequencing data contains a number of connectors, low-quality Reads, fastp (v0.21.0) software was used to filter the sequencing data to get high quality sequence for further analysis .
Trimmed sequence reads were mapped to GRCh38 and GRCm38 using HISAT2 v2.1.0. (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
StringTie(v2.1.5) statistics were used to compare the Read Count values on each gene as the original expression of the gene, and FPKM were used to standardize the expression.
Assembly: GRCh38 and GRCm38
Supplementary files format and content: RPKMs

source_name: Graft

extract_protocol:
RNA was harvested using TRIzol. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC Stranded mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: sample type

value: in vivo

value: Graft

value: primary

value: CD8+ T

value: heart transplantation


title: VCaP-EnzaR-DT061_2


title: 4006

value: male

value: Ion Gene Studio


title: Plx403-LCMT1_2

source_name: LNCAP parental over-expressing LCMT1

value: LNCAP parental over-expressing LCMT1

value: Derived from LNCAP


title: Group 3 innate lymphoid cell, aged gut CCR6+ ILC3s rep2, H3K4me3

value: small intestine

value: Group 3 innate lymphoid cell

value: H3K4me3 antibody (39016, Active Motif)


title: Plx403-LCMT1_1


title: Group 3 innate lymphoid cell, aged gut DN ILC3s rep2, H3K4me3


title: in vivo, HT_splenic CD4

description:
IN VIVO All_samples_rpkm.txt
WTHT_S_CD4

source_name: spleen

value: spleen

value: CD4+ T


title: in vivo, HT_splenic CD8

description:
IN VIVO All_samples_rpkm.txt
WTHT_S_CD8


title: Plx403-LacZ_2

source_name: LNCAP parental over-expressing LACZ

value: LNCAP parental over-expressing LACZ

value: prostate cancer


title: Group 3 innate lymphoid cell, young gut NKp46+ ILC3s rep1, H3K4me3

value: 6-8 weeks-old


title: 4005

value: Middle-aged rats (12 months)


title: in vivo, HT_graft CD4

description:
IN VIVO All_samples_rpkm.txt
WTHT_H_CD4

value: in vivo

value: Graft

value: WT


title: Plx403-LacZ_1


title: 4004


title: Group 3 innate lymphoid cell, young gut DN ILC3s rep1, H3K4me3


title: in vivo, splenic CD8

description:
IN VIVO All_samples_rpkm.txt
WT_S_CD8

value: primary

value: CD8+ T

value: no treatment


title: 3996

value: male

value: Ion Gene Studio


title: LNCap-EnzaR-DT061_3

source_name: LNCaP-EnzaR

value: LNCaP-EnzaR

value: Derived from LNCAP


title: 3999


title: in vivo, splenic CD4

description:
IN VIVO All_samples_rpkm.txt
WT_S_CD4


title: 3994


title: Group 3 innate lymphoid cell, young gut CCR6+ ILC3s rep1, H3K4me3

value: small intestine

value: Group 3 innate lymphoid cell

value: H3K4me3 antibody (39016, Active Motif)


title: in vitro, lycorine treated splenic CD4+ T, 2

description:
IN VITRO All_samples_rpkm.txt
2R-2

value: in vitro

value: spleen

value: CD4+ T


title: LNCap-EnzaR-DT061_1

value: prostate cancer


title: LNCap-EnzaR-DT061_2


title: Group 3 innate lymphoid cell, aged gut NKp46+ ILC3s rep1, H3K4me3


title: Group 3 innate lymphoid cell, aged gut DN ILC3s rep1, H3K4me3


title: in vitro, lycorine treated splenic CD4+ T, 1

description:
IN VITRO All_samples_rpkm.txt
2R-1


title: 3989

value: Middle-aged rats (12 months)


title: 3988


title: LNCap-EnzaR-ARD69_3


title: in vitro, control splenic CD4+ T, 2

description:
IN VITRO All_samples_rpkm.txt
0R-2


title: Group 3 innate lymphoid cell, aged gut CCR6+ ILC3s rep1, H3K4me3


title: 3985


title: 3984


title: 2-day miR-205 inducible Rep2

city: Chicago

first: Rui

last: Yi

state: Illinois

address: 765 N FAIRBANKS CT

department: Pathology, Feinberg School of Medicine

institute: Northwestern University

data_processing:
RNA-seq reads (150nt, paired-end) were aligned to the mouse genome (NCBI37/mm10) using Hisat2 (version 2.1.0).
The resulting sam files were converted to bam files using SAMtools (version 1.3.1).
Expression measurement of each gene was calculated from the resulting alignment bam file by HT-seq.
Differentially expressed genes were determined using DEseq2 using default settings.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include baseMean, log2FoldChange, pValue..

source_name: P44 hair follicle stem cells

extract_protocol:
Gender matched mice (Ctrl and miR-205Ind) harboring a K14-H2BGFPallele were fed doxycycline for 2 or 4 days and euthanized to collect back skin samples. Hair coats were shaved and removed. Subcutaneous fat was removed, and back skin samples were minced into small pieces and incubated with 0.25% collagenase (Worthington, LS004188) in 10 mL 1x HBSS buffer at 37°C for 2 hours with rotation. After collagenase treatment, 10 mL cold PBS was added, and sample suspension was centrifugated at 400 g for 10 minutes at 4°C to get the pellet. The pellet was resuspended with 5 ml pre-warmed 0.25% trypsin/EDTA (Gibco) for 7 minutes at 37°C and the digestion was blocked by adding 10 mL cold 1x PBS with 3% chelated FBS. The suspension was extensively triturated with a 25 ml pipette and filtered through a 40 m cell strainer, followed by centrifugation at 400 g for 5 minutes at 4°C. The pelleted cells were resuspended in cold 1x PBS with 3% chelated FBS. Suspended cells were incubated with appropriated antibodies for 1 hour on ice. After washing away unbounded antibodies, DAPI was used to exclude dead cells. Live hair follicle stem cells  from both control and miR-205 inducible animals  were collected from FACS sorting machine with cell surface proteins and H2BGFP signals.
Total RNAs from FACS-purified cells were isolated using TRIZOL (Invitrogen). RNA quality was assessed by Agilent 2100 bioanalyzer. RNA Samples with RNA integrity numbers (RIN) > 8 were used to make libraries and perform RNA-seq assay. Libraries were prepared by following manufacturer’s protocol (NEBNext Ultra Directional RNA Library Prep Kit). The cDNA libraries were quality-checked with bioanalyzer and sequenced at Genomics and Microarray Core Facility at University of Colorado Denver on Illumina NovaSeq 6000.

treatment_protocol: miR-205 inducible mouse was feed Doxcyclin chow for 2 days from P42-P44 or for 4 days from P49-P53.

tag: cells

value: hair follicle stem cells

value: treated with doxcyclin for 2 days


title: 2-day miR-205 inducible Rep1


title: Control_Spleen

city: Beijing

first: Wei-Na

last: Jin

state: Beijing

address: NO.119, Southwest of the Fourth Ring Road, Fengtai District

department: China National Clinical Research Center for Neurological Diseases

institute: Beijing Tiantan Hospital, Capital Medical University

description: 10x Genomics

data_processing:
Raw files (FASTQ format) were processed with Cell Ranger software (v5.0.1), which performed mapping to the mm10 transcriptome, filtering, barcode counting and UMI counting and finally generated feature-by-barcode UMI matrix. Scrublet software was employed to remove potential doublets for individual samples. Seurat (v3.1.5) was used for downstream analysis. Low-quality cells, <500 genes expressed or with <2500 UMIs, were excluded at the initial quality-control step. Cells >15% mitochondrial UMIs were removed. Library-size normalization was performed on the UMI-collapsed gene expression values for each cell barcode, by scaling the total number of transcripts and multiplying by 10,000. Data were then log-transformed for further downstream analysis.
Assembly: mm10
Supplementary files format and content: tab-separated values files

source_name: Spleen

extract_protocol:
Single-cell suspensions were prepared from pooled mouse spleen and brain tissues at 72 h after ICH induced by autologous blood injection or sham operations.CD45+ cells were isolated at 4°C using flow-cytometry.As there are few T cells in sham brain, we optimized the  FACS-sorting and also isolated the the CD45hi cells in the sham brain. This allows us to obtain enough CD4+ T cells in sham brains for sub-clustering and data processing.
Library was performed according to the manufacter’s instructions (single-cell 3' v.2 kit, 10× Genomics). Cell viability was ≥90% for all samples. Cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel beads-in- emulsion (GEM), which were used to reverse-transcribe mRNA and amplify the derived cDNA. Specifically, gel beads work as delivery system of millions of oligo primers each containing (a) a partial Read 1 primer sequence used for sequencing on the flow cell, (b) a 16-bp cell barcode called 10× barcode that serves as the unique molecular address for that particular bead, (c) the unique molecular identifier (UMI) which is a 10-bp randomer different for each oligo of a bead used for digital mRNA counting, and (d) a 30-bp poly dT tail which allows the primers to hybridize to mature mRNAs for first-strand cDNA synthesis. Once partitioned with the cells and reverse transcription (RT) reagents, the gel bead dissolves and its oligo primers are released into the aqueous environment of the GEM. The cell captured in the GEM is also lysed and the content of the GEM (oligos, lysed cell components, and master mix) is incubated in an RT reaction to generate full-length, barcoded cDNA from the poly A-tailed mRNA transcripts. The RT reaction is primed by the barcoded gel bead oligo and the reverse transcriptase incorporates a template switch oligo via a template switching reaction at the 50 end of the transcript. The GEMs are then broken and single-stranded barcoded cDNAs from thousands of cells are pooled. A bulk cDNA PCR amplification follows to generate enough material for library generation. During library preparation after an enzymatic fragmentation, Read 2 is added by adapter ligation, and finally paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Spleen

value: CD45+ cells

value: Sham induction


title: 2-day Ctrl Rep2

value: untreated


title: 3983

source_name: DG region of the hippocampus

value: male

value: Ion Gene Studio


title: 3890


title: ICH_Spleen

description: 10x Genomics

value: Intracerebral hemorrhage model  induction


title: LNCap-EnzaR_2

value: LNCaP-EnzaR

value: Derived from LNCAP

value: WT

value: dmso


title: 2-day Ctrl Rep1


title: ICH_Brain

description: 10x Genomics

source_name: Brain

value: Brain


title: OE_2

status: Public on Jun 06 2023

city: Wuhan

first: Feng

state: Hubei

address: Air Road 13

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

data_processing:
Illumina Casava1.7 software used for basecalling.
Low-complexity or low-quality sequence of the original data were filtered to obtain high-quality clean data, which were then compared to the reference genome of human species to obtain comprehensive transcript information using bowtie v0.12.2.
We took RPKM (Reads per Kilobase per Million Reads) as A measure of gene expression (Mortazavi a. et al. 2008).
The differentially expressed genes were screened from the difference multiples and the significant levels. Here, we use the absolute value of FC >1.5 and p-value<0.05 as the standard to indicate that the gene is a differentially expressed gene.
Genome_build: human NCBI genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: circHIPK3-overexpressed HPC cell

growth_protocol: All the cells were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was isolated from HPC cell lines with RNeasy Mini kit (QIAGEN, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HPC cells were stably transfected with circHIPK3-overexpression lentivirus and an empty lentivirus, respectively.

value: HPC

value: Conditionally immortalized human podocyte cell line


title: LNCap-EnzaR-ARD69_2

value: prostate cancer


title: NC_1

source_name: HPC cell in control group

value: control


title: NC_2


title: LNCap-EnzaR-ARD69_1


title: D20-156075

city: Cambridge

first: Dunaduan

last: Ma

state: Ma

address: 77 Massachusetts Ave

department: Koch Institute

institute: MIT

data_processing:
Quality control:QC was carried out by MIT BMC/BCC in house pipeline including sequencing error rate estimation, sequencing reads complexity estimation, fastqc report, sample contamination estimation, intergenic reads percentile calculation, intronic reads percentile calculation, UTR reads percentile calculation, gene coding reads percentile calculation, and rRNA contamination estimation. Besides, sense to antisense reads ratio was calculated to indicate strand specificity. Hierarchical clustering and heatmap creation were carried out by TIBCO Spotfire 7.11.1.0.12 basing on log2(fpkm+1) values of the expressed coding genes to observe sample relationship and to detect outliers.
RNA-Seq mapping: against GRCm38/mm10 reference for mouse sequences using STAR/2.5.3a
Gene expression was quantitated using RSEM v. 1.3.0
Gene set enrichment analyses was performed by GSEA 2-2.0.13 basing on normalized expression values
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: txt file. Each gene per row and each sample per column(raw counts from RSEM)

source_name: Tumor

extract_protocol: Total RNA was isolated from primary cells or tumors, using the RNeasy Plus Mini Kit (Qiagen) and sequenced on an Illumina HiSeq2000. At least 5000 cells were sorted  directly  in lysis buffer for specifc T cell progenitor populations in the thymus while at least 5 million cells have used for RNA isolation form thymic lymphomas. Unless otherwise indicated samples from tumors were isolated without sorting specific polulations.

value: Thymic Lymphoma

value: LCK-Cdc20(D/AAA); MYCChr6


title: D20-156076


title: in vitro, control splenic CD4+ T, 1

description:
IN VITRO All_samples_rpkm.txt
0R-1

value: in vitro

value: spleen

value: primary

value: CD4+ T


title: LNCap-EnzaR_1


title: D20-156073


title: D20-156074


title: D20-156070


title: D20-156072


title: D20-156069


title: D20-156071


title: D20-156068


title: D20-156067


title: OE_1


title: Control-DMSO-40h-Rep1

type: RNA

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

country: United Kingdom

institute: UCL

hyb_protocol: Hybridisation to Affymetrix Mouse Gene 2.0 ST arrays was performed for 16 hours at 45C with constant rotation. Samples were hybridised according to the Affymetrix specifications: hybridisation cocktails were heated at 99C for 5 minutes and then at 45C for another 5 minutes. Samples were centrifuged at max speed for 1 minute and 200ul was transferred to each array. Hybridisation was carried out for 16 hours at 45C and 60 rpm. Fluidics washing was FS450_0001.

scan_protocol: Arrays were scanned with an Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data was normalised using rma function from the oligo package in R

label: biotin

label_protocol: Up to 5.5g of total RNA was fragmented and labelled using the Affymetrix GeneChip Whole Transcript Sense Target Labelling Assay as outlined in the manufacturer's instructions.

extract_protocol: RNA was extracted using the PicoPure RNA Isolation Kit (ThermoFisher, Cat. KIT0202) performed according to the manufacturer's instructions.

treatment_protocol: Fetal Thymi were dissected from E17.5 Rag1-/- embryos. Thy1.2+ cells were magnetically purified from fresh E17.5 thymi (Control-0h) and 40h stimulated with anti-CD3 + DMSO (Control-DMSO-40h) or anti-CD3 + 50uM 79-6 (79-6-40h).  RNA was extracted from these cells.

value: DMSO

value: E17.5 Fetal Thymus

value: Thy1.2+ cells


title: 79-6-40h-Rep2

value: 50uM 79-6 for 40hrs


title: 79-6-40h-Rep1


title: D20-156065


title: Control-DMSO-40h-Rep2


title: Control-0h-Rep2

source_name: Control-0h_E17.5 Rag1-/- Thymocytes


title: Control-0h-Rep1


title: D20-156061

value: CD4-Cdc20(D/AAA); MYCChr6


title: D20-156060


title: D20-156059


title: D20-156057


title: D20-156056


title: D20-156058


title: N0-3

city: Shanghai

first: Liufu

last: Wang

address: No. 999, Huchenghuan Rd

institute: Shanghai Ocean University

data_processing:
Quality control  (Trimmomatic version 0.40)
De novo assembly (Trinity vesion 2.4)
Functional annotation (Blastx)
Unigene quantification (bowtie2 Version 2.4.5 and eXpress), analysis of differentially expressed unigenes (DEGs) (DESeq package), cluster  analysis, GO and KEGG enrichment (R based on the hypergeometric distribution)
CDS&SSR analysis (ESTScan)
Assembly: none
Supplementary files format and content: The excel files include FPKM values for each Sample

organism: Auxenochlorella pyrenoidosa

extract_protocol:
Algal cells in every group were harvested to separate total RNA by TRIzol liquids (Invitrogen, USA). Then, they were removed genomic DNA using RNase-free DNase I (Fermentas, Canada). The standards used to select total RNA for subsequent analyses were OD260/280 ≥ 1.8, 28S/18S rRNA ratio ≥ 1.0, RIN value ≥ 7.0, as well as the amount and concentration of total RNA ≥ 3 μg and 50 ng/μL, respectively.
Oligo (dT) magnetic beads (Yeasen, China) were added to purify mRNA from total RNA. The fragmenting of mRNA and the synthesis of double stranded cDNA were completed by NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA).

tag: group


title: N0-1


title: D20-156055


title: N0-2


title: N0.5-3


title: N0.5-1


title: D20-156054


title: D20-156063


title: N1-3


title: D20-156053


title: D20-156064


title: D20-156066


title: D20-156052


title: D20-156062


title: N1-2


title: D20-156048


title: N1.5-2


title: D20-156047

value: RERT2-Cdc20(D/AAA); MYCChr6


title: N1-1


title: N1.5-3


title: D20-156051


title: D20-156046


title: D20-156045


title: N0.5-2


title: D20-156044

value: LCK-Cdc20(+/D); MYCChr6


title: D20-156042


title: D20-156049


title: D20-156041


title: OLD3

city: Chongqing

first: xiaoqin

last: luo

address: Medical College Road, Yuzhong District

institute: chongqing medical university

data_processing:
1.The sequencing data was filtered with SOAPnuke by Removing reads containing sequencing adapter
2.Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%
3.Removing reads whose unknown base ('N' base) ratio is more than 5%
4.Afterwards, clean reads were obtained and stored in FASTQ format
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: read count
Supplementary files format and content: FPKM

source_name: cochlea

growth_protocol: cochlear of c57bl/6j mice

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer
DNase I was used to digest double-stranded and single-stranded DNAin total RNA, then, magnetic beads were purified to recover the reaction products, RNase H or Ribo-Zero method (human, mouse, plants) (Illumina, USA) was used to remove the rRNA. Purified mRNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand Reaction System by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to carry out end repair. The cDNA fragments with adapters were amplyfied by PCR, and the products were purified byAmpure XP Beads. Library was validating on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products above were heated denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library

treatment_protocol: basal parts of cochlear

value: cochlea

value: old


title: D20-156043


title: OLD2


title: YOUNG2

value: young


title: D20-156050


title: D20-156039


title: D20-156038


title: OLD1


title: YOUNG1


title: YOUNG3


title: D20-156037


title: D20-156040


title: N1.5-1


title: Ribominus-97H,generation8

city: Guangzhou

first: Hong

last: Lu

address: No. 601, West Huangpu Avenue, Tianhe District, Guangzhou

institute: jinan university

description: total RNA of MHCC97H

data_processing:
Then reads were mapped to transcripts using the hyperaccurate mapping algorithm FANSe3 in the next-generation sequencing analysis platform “Chi Cloud” (http://www.chi-biotech.com).
Sequence reads were trimmed for adaptor sequence/low-quality sequence using  algorithm FANSe3 in the next-generation sequencing analysis platform “Chi Cloud” (http://www.chi-biotech.com).
Trimmed sequence reads were mapped to algorithm FANSe3 in the next-generation sequencing analysis platform “Chi Cloud” (http://www.chi-biotech.com).
Read count extraction and normalization were performed using  algorithm FANSe3 in the next-generation sequencing analysis platform “Chi Cloud” (http://www.chi-biotech.com).
Assembly: hg18
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: These cells were cultured in DMEM medium with 10% FBS and 1% penicillin/streptomycin. All cell lines culture environment was 37 °C, 5% CO2.

extract_protocol:
RNA was harvested using TRIzol RNA extraction reagent (Ambion, Austin,TX). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol:
For mRNA-seq, our study used two methods to construct the sequencing library, including Oligo (dT) method and the rRNA depletion method.
For RNA-degraded samples treated with RNase A, the library construction method of  rRNA depletion method was used.

tag: cell type

value: hepatocellular cells

value: WT

value: Use library construction of  rRNA depletion method to construct a library for RNA


title: Ribominus-97H,generation9

description: total RNA of MHCC97H

tag: genotype


title: Ribominus-97H,generation5

description: total RNA of MHCC97H

tag: treatment


title: Ribominus-97H,generation7

description: total RNA of MHCC97H


title: Ribominus-97H,generation6

description: total RNA of MHCC97H


title: Ribominus-97H,generation4

description: total RNA of MHCC97H


title: D20-156036

value: Thymic Lymphoma


title: Ribominus-97H,generation3

description: total RNA of MHCC97H


title: D20-156034


title: Ribominus-97H,generation2

description: total RNA of MHCC97H


title: D20-156033


title: D20-156032


title: D20-156035


title: D20-156031


title: D20-156030


title: repeat-97H,generation9

description: total RNA of MHCC97H

value: The RNA of MHCC105H was collected in batches at different times


title: repeat-97H,generation8

description: total RNA of MHCC97H

value: The RNA of MHCC104H was collected in batches at different times


title: repeat-97H,generation7

description: total RNA of MHCC97H

value: The RNA of MHCC103H was collected in batches at different times


title: repeat-97H,generation6

description: total RNA of MHCC97H

value: The RNA of MHCC102H was collected in batches at different times


title: D20-156029


title: D20-156026


title: repeat-97H,generation5

description: total RNA of MHCC97H

value: The RNA of MHCC101H was collected in batches at different times


title: D20-156027


title: repeat-97H,generation4

description: total RNA of MHCC97H

value: The RNA of MHCC100H was collected in batches at different times


title: D20-156025


title: repeat-97H,generation3

description: total RNA of MHCC97H

value: The RNA of MHCC99H was collected in batches at different times


title: D20-156024


title: D20-156021


title: repeat-97H,generation1

description: total RNA of MHCC97H

value: The RNA of MHCC97H was collected in batches at different times


title: 97H-5min-RNaseA

description: total RNA of MHCC97H

value: For RNA-degraded samples treated with RNase A, the library construction method of  rRNA depletion method was used.


title: repeat-97H,generation2

description: total RNA of MHCC97H

value: The RNA of MHCC98H was collected in batches at different times


title: D20-156022


title: 97H-1h-RNaseA

description: total RNA of MHCC97H


title: D20-156023


title: D20-156018

source_name: Non-tumoral thymus

value: Normal Thymus

value: RERT2-Cdc20(D/AAA); MYCChr6


title: 97H-2min-RNaseA

description: total RNA of MHCC97H


title: D20-156019


title: Ribominus-97H,generation1

description: total RNA of MHCC97H


title: 97H-30s-RNaseA

description: total RNA of MHCC97H


title: 97H-1min-RNaseA

description: total RNA of MHCC97H


title: D20-156028


title: D20-156016

value: RERT2-Cdc20(+/D); MYCChr6


title: D20-156017


title: 97H-generation8-Ribominus

description: total RNA of MHCC97H

value: hepatocellular cells

value: Use library construction of  rRNA depletion method to construct a library for degraded RNA


title: 97H-generation9-Ribominus

description: total RNA of MHCC97H

value: WT


title: 97H-NC

description: total RNA of MHCC97H


title: D20-156015


title: D20-156020


title: D20-156011


title: D20-156012


title: D20-156014


title: D20-156010


title: D20-156008


title: 97H-generation7-polyA+mRNA

description: total RNA of MHCC97H

value: Use library construction of Oligo (dT) method to construct a library for degraded RNA


title: 97H-generation2-Ribominus

description: total RNA of MHCC97H


title: 97H-generation8-polyA+mRNA

description: total RNA of MHCC97H


title: D20-156007


title: 97H-generation6-Ribominus

description: total RNA of MHCC97H


title: D20-156013


title: 97H-generation7-Ribominus

description: total RNA of MHCC97H


title: D20-156009


title: 97H-generation6-polyA+mRNA

description: total RNA of MHCC97H


title: D20-156006


title: 97H-generation9-polyA+mRNA

description: total RNA of MHCC97H


title: D20-156005


title: 97H-generation2-polyA+mRNA

description: total RNA of MHCC97H


title: 97H-generation4-polyA+mRNA

description: total RNA of MHCC97H


title: D20-156004


title: D20-156003


title: 97H-generation4-Ribominus

description: total RNA of MHCC97H


title: 97H 10mRNA-seq experimenter2

description: total RNA of MHCC97H

value: RNA libraries for RNA-seq were prepared by experimenter11


title: D20-156002


title: 97H 8mRNA-seq experimenter2

description: total RNA of MHCC97H

value: RNA libraries for RNA-seq were prepared by experimenter9


title: ChIP-seq of Plasmodium blood stages: SZ no antibody control

city: San Antonio

first: Evelien

middle: M

last: Bunnik

address: 7703 Floyd Curl Dr.

department: Microbiology, Immunology, and Molecular Genetics

institute: University of Texas Health Science Center at San Antonio

description: 3D7 No Ab SZ

data_processing:
Paired-end data generated for histone PTM ChIP-seq was treated as single-end data so that all ChIP-seq data could be processed in the same way, and only read one was processed for analysis. Following quality assessment of the reads using FastQC (v0.11.8) (reads with a quality score ³ 30 were retained), adaptor sequences were trimmed using Trim-galore (v0.5.0). ChIP-seq data were mapped to the P. falciparum 3D7 genome v3.0, release 44 or the P. berghei ANKA genome v3.0, release 49 with Bowtie2 (v2.3.5). Reads were filtered with SAMtools (v1.9) to remove sequences that aligned to the genome more than once (option -q 10) and duplicates were removed using markduplicates from Picard (v2.18.29-SNAPSHOT). Using bamCompare from the deeptools suite (v3.2.0), log2(ChIP/input) bigwig files with reads extended to 150 bp were generated from bam files. Input and no antibody bigwig files were generated with bamCoverage from deeptools (v3.2.0).
Assembly: P. falciparum 3D7 genome v3.0, release 44 or P. berghei ANKA genome v3.0, release 49
Supplementary files format and content: bigwig files showing log2(ChIP/input), except for input and no antibody samples which not normalized

organism: Plasmodium falciparum

extract_protocol:
Parasites were crosslinked with 1% paraformaldehyde. Crosslinked parasites were washed with 1 ml cold PBS containing protease inhibitors (cOmplete protease inhibitor cocktail) then incubated on ice with 1 ml nuclear extraction buffer [f.c.: 10 mM HEPES, 10 mM KCl, 0.1 mM EDTA, 0.1 mM EGTA, 1 mM DTT, 200 mM AEBSF, cOmplete protease inhibitor cocktail, Phos Stop phosphatase inhibitor in nuclease-free water]. After 35 min., NP-40/IGEPAL was added to a final concentration of 0.25% and the solution was homogenized by passing the mixture seven times through a 26 G needle. Extracted nuclei were pelleted by centrifugation at 2,100 × g for 20 min. at 4°C. Supernatant was removed and the pelleted nuclei were resuspended in 130 µl of cold shearing buffer [f.c.: 0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 7.5, cOmplete protease inhibitor cocktail, Phos Stop phosphatase inhibitor in nuclease-free water] and transferred to a microTUBE. Chromatin was fragmented with an M220 sonicator (Covaris) with the following settings: 5% duty cycle, 75 W peak incident power, 200 cycles per burst at 6°C for 300 sec. Fragmented chromatin was transferred to a pre-lubricated, low binding 1.5 ml tube. The microTUBE was washed with 70 µl of shearing buffer after which the solution was combined with the fragmented chromatin for a total volume of 200 µl. For each developmental stage (schizont, merozoite, ring, and hepatic merozoite) 30 µl of sheared chromatin was collected at this point for use as an input sample and stored at -70°C until decrosslinking. Chromatin was diluted 1:1 in ChIP dilution buffer [f.c.: 30 mM Tris-HCl pH 8.0, 3 mM EDTA, 0.1% SDS, 300 mM NaCl, Triton X-100, supplemented with cOmplete protease inhibitor cocktail and Phos Stop phosphatase inhibitor in nuclease-free water] then precleared by incubation with protein A agarose/salmon sperm DNA beads (50 µl beads per 1 ml sheared chromatin) for 1 hour at 4°C with agitation to reduce non-specific background. Following the incubation, the beads were pelleted by centrifugation at 100 × g for 1 min. at RT. The supernatant containing the chromatin was moved to a new low-binding tube and incubated overnight at 4°C with agitation with 2 µg of antibody against the histone PTM of interest. Protein A agarose/salmon sperm DNA beads (25 µl beads per 500 µl sonicated chromatin) were washed with 500 µl ChIP dilution buffer and blocked with 1 mg/ml BSA for 1 hour at 4°C with agitation to reduce non-specific binding. Agarose beads were washed 3 times with 500 µl ChIP dilution buffer, then added to the chromatin suspension and incubated for 1 hour at 4°C with agitation. Agarose beads were pelleted by centrifugation at 100 × g for 1 min. at RT, and the supernatant was discarded. Beads were washed twice at 4°C for 15 min. with agitation 1 ml high salt wash buffer [f.c.: 1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 nM NaCl in nuclease-free water], 1 ml low salt wash buffer [f.c.: 1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl, in nuclease-free water], and 1 ml lithium chloride wash buffer [f.c.: 0.25 M LiCl, 1% NP-40/IGEPAL, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0 in nuclease-free water]. Beads were then washed twice for 15 min. with TE buffer [f.c.: 10 mM Tris-HCl pH 8.0, 1 mM EDTA in nuclease-free water] at RT with agitation. Chromatin bound to agarose beads was eluted by incubating with 125 µl elution buffer [f.c.: 1% SDS, 0.1 M NaHCO3 in nuclease-free water] for 15 min. at RT with agitation. The elution was repeated, and fractions combined for a total of 250 µl. Samples were reverse crosslinked by adding NaCl to a final concentration of 0.5 M and incubating overnight at 45°C. RNase A was then added to a final concentration of 0.6 μg/ml and incubated at 37°C for 30 min. Samples were then incubated with EDTA (f.c.: 1 mM), Tris-HCl pH 7.5 (f.c.:4 mM), and proteinase K (0.8 U) for 2 hours at 45°C. DNA was isolated using 2 volumes sparQ beads according to manufacturer’s instructions. ChIP DNA was stored at -20°C until library preparation. Input samples were incubated with 0.6 μg RNase A per µl for 30 min. at 37°C, then incubated with 0.8 U proteinase K overnight at 45°C. DNA was isolated using 2 volumes sparQ beads according to manufacturer’s instructions and stored at -20°C until library preparation.
Libraries from ChIP samples were prepared using the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB #E6040) or the NEBNext Ultra II DNA library prep kit for Illumina (NEB #E7645) according to manufacturer’s instructions with the following modification. Libraries were amplified using i7 index primers and i5 universal primer (NEBNext multiplex oligos for Illumina index primers set 1 and 2, NEB #E7335 and #E7500) with KAPA HiFi hot start ready mix with the following program: initial denaturation at 98°C for 45 sec.; 15 cycles of (98°C for 15 sec., 55°C for 30 sec., 62°C for 30 sec.); and final extension at 62°C for 5 min. Libraries were purified using 0.9 volumes sparQ beads according to manufacturer’s instructions. Libraires were sequenced with the Illumina HiSeq 2500 or Illumina NextSeq500 to generate 50 bp single-end reads or 75 bp paired-end reads, respectively.

tag: Stage

value: Schizont (40 hpi)

tag: isolation

value: Schizonts (40 hpi) were magnetically seperated from uninfected and ring infected erythrocytes, then released from erythrocytes by saponin treatment.


title: ChIP-seq of Plasmodium blood stages: SZ input

description: 3D7 input SZ


title: ChIP-seq of Plasmodium blood stages: MZ no antibody control

description: 3D7 No Ab MZ

value: Merozoite

value: Magentically isolated schizonts (40 hpi) were incubated with E64 for 8 hours and then merozoites were mechanically released by filteration.


title: ChIP-seq of Plasmodium blood stages: MZ input

description: 3D7 input MZ


title: D20-156001


title: 97H 7mRNA-seq experimenter2

description: total RNA of MHCC97H

value: RNA libraries for RNA-seq were prepared by experimenter8


title: D18-182181

source_name: Early Tumor

value: Thymic Lymphoma_DP


title: ChIP-seq of Plasmodium blood stages: MZ H3K27me

description: 3D7 H3K27me MZ


title: 97H 6mRNA-seq experimenter2

description: total RNA of MHCC97H

value: RNA libraries for RNA-seq were prepared by experimenter7


title: 97H 5mRNA-seq experimenter2

description: total RNA of MHCC97H

value: RNA libraries for RNA-seq were prepared by experimenter6


title: ChIP-seq of Plasmodium blood stages: SZ H3K27me

description: 3D7 H3K27me SZ


title: D18-182180

value: Thymic Lymphoma


title: ChIP-seq of Plasmodium blood stages: MZ H3K4me

description: 3D7 H3K4me MZ


title: D18-182179


title: ChIP-seq of Plasmodium blood stages: SZ H3K4me

description: 3D7 H3K4me SZ


title: ChIP-seq of Plasmodium blood stages: MZ H3K4me3 rep1

description: 3D7 H3K4me3 MZ Rep 1


title: 97H 4mRNA-seq experimenter2

description: total RNA of MHCC97H

value: RNA libraries for RNA-seq were prepared by experimenter5


title: ChIP-seq of Plasmodium blood stages: SZ H3K4me2

description: 3D7 H3K4me2 SZ


title: D18-182177


title: D18-182178


title: 97H 9mRNA-seq experimenter2

description: total RNA of MHCC97H

value: RNA libraries for RNA-seq were prepared by experimenter10


title: 97H 3mRNA-seq experimenter2

description: total RNA of MHCC97H

value: hepatocellular cells

value: RNA libraries for RNA-seq were prepared by experimenter4


title: D18-182176


title: ChIP-seq of Plasmodium blood stages: MZ H3K9ac

description: 3D7 H3K9ac MZ


title: ChIP-seq of Plasmodium blood stages: MZ H3K27ac

description: 3D7 H3K27ac MZ


title: ChIP-seq of Plasmodium blood stages: SZ H3K27ac

description: 3D7 H3K27ac SZ


title: 97H 1mRNA-seq experimenter2

description: total RNA of MHCC97H

value: WT

value: RNA libraries for RNA-seq were prepared by experimenter2


title: 97H 2mRNA-seq experimenter2

description: total RNA of MHCC97H

value: RNA libraries for RNA-seq were prepared by experimenter3


title: AU-565 (TEQUILA-seq, blocking oligos(+), multiplex(+))

first: Yi

last: Xing

address: 9054 Colket Translational Research Bldg. 3501 Civic Center Blvd.

department: Executive Director, Department of Biomedical and Health Informatics

institute: The Children’s Hospital of Philadelphia

description:
Target_gene_panel.txt
BRCA_TEQUILA-seq_refinement_N2_R0_abundance.esp
BRCA_TEQUILA-seq_refinement_N2_R0_updated.gtf

data_processing:
(LONG-READ SEQUENCING) Basecalling was performed in fast mode with Guppy (version 4.0.15) for all Nanopore sequencing data in this study (https://community.nanoporetech.com/downloads). Basecalling of direct RNA and cDNA libraries were done using config files rna_r9.4.1_70bps_fast.cfg and dna_r9.4.1_450bps_fast.cfg respectively.
(LONG-READ SEQUENCING) Reads were then mapped to either the SIRVome or hg19 reference genome using minimap2 (v2.17) with parameters “-a -x splice -ub -k 14 -w 4 --secondary=no” and either SIRV transcript annotations or GENCODE v34 annotations (https://www.gencodegenes.org/human/release_34lift37.html).
(LONG-READ SEQUENCING) Alignment files (SAM format) were next processed by ESPRESSO (https://github.com/Xinglab/espresso) using default settings and either SIRV transcript annotations or GENCODE v34 annotations. Reads that either map to the mitochondrial genome or contain large continuous insertions (≥20 nt) in the raw alignment were filtered out by ESPRESSO.
Assembly: (LONG-READ SEQUENCING) hg19, SIRVome
Supplementary files format and content: (LONG-READ SEQUENCING) .esp files are tab-delimited matrices generated by ESPRESSO that contain read count estimates for all identified isoforms (rows) across all samples (columns); .gtf files generated by ESPRESSO are in GTF format and provide genomic coordinates for all identified transcript isoforms and their corresponding exons
(SHORT-READ SEQUENCING) Paired-end Illumina sequencing data with 150-bp read length for SH-SY5Y cells were generated from libraries prepared following the TruSeq Stranded mRNA protocol (Illumina, Cat. #20020595)
(SHORT-READ SEQUENCING) Reads from the 3 samples were pooled and aligned to the GRCh37/hg19 reference genome using STAR on two-pass mode with default settings and transcript annotations from GENCODE v34.
(SHORT-READ SEQUENCING) Exon skipping events were detected and quantified from short-read alignment files using rMATS (v4.1.1) with default settings.
Assembly: (SHORT-READ SEQUENCING) hg19
Supplementary files format and content: (SHORT-READ SEQUENCING) SH-SY5Y_SE.MATS.JC.txt is a tab-delimited file that contains coordinates and junction read counts associated with all identified exon skipping events

molecule: polyA RNA

growth_protocol: Cell line was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA 30-4500 K™). Cell lines were cultured according to ATCC recommendations and were authenticated by the supplier.

extract_protocol:
Total RNA of breast cancer cell lines was extracted using TRIzol reagent (Invitrogen, #15596018).
A 200 ng aliquot of total RNA was used as templates for cDNA synthesis following the SMART-seq2 protocol. 500 ng of amplified cDNA were used for hybridization and capture following TEQUILA-seq protocol with blocking oligos included. The final nanopore 1D library waw constructed using 200 to 500 ng of post-capture amplified cDNA according to the SQK-NBD114.24 protocol. Briefly, cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 min and 65°C for 20 min. The cDNA was then purified with 1× volume of AMPure XP beads and eluted in 10 μl of nuclease-free water. Native barcode ligation was performed using 7.5 μl of end-prepped DNA, 2.5 μl of native barcodes and 10 μl of Blunt/TA Ligase Master Mix (NEB, #M0367) by incubating at room temperature for 20 min. To inactivate the ligase, 2 μl of EDTA was added to each ligation reaction. Barcoded cDNA samples were then pooled and purified using 0.4× volume of AMPure XP beads and eluted in 35 μl of nuclease-free water. Next, adapter ligation was performed using 30 μl of pooled barcoded samples, 5 μl of native adapter, 10 μl of 5× NEBNext Quick ligation reaction buffer and 5 μl of NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 20 min. After ligation, libraries were purified using 0.45× volume of AMPure XP beads and short fragment buffer.

tag: lineage

value: Human breast cancer HER2 enriched

tag: nanopore library type


title: HCC1806 (TEQUILA-seq, blocking oligos(+), multiplex(+))

tag: cell line

value: Human breast cancer basal A


title: MCF7 (TEQUILA-seq, blocking oligos(+), multiplex(+))

value: Human breast cancer luminal


title: ChIP-seq of Plasmodium blood stages: MZ H3K4me2

description: 3D7 H3K4me2 MZ

value: Merozoite


title: D18-182175


title: MCF7 (TEQUILA-seq, blocking oligos(+), multiplex(-))

extract_protocol:
Total RNA of breast cancer cell lines was extracted using TRIzol reagent (Invitrogen, #15596018).
A 200 ng aliquot of total RNA was used as templates for cDNA synthesis following the SMART-seq2 protocol. 500 ng of amplified cDNA were used for hybridization and capture following TEQUILA-seq protocol with blocking oligos included. The final nanopore 1D library waw constructed using 200 to 500 ng of post-capture amplified cDNA according to the SQK-LSK109 protocol. Briefly, cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 min and 65°C for 20 min. The cDNA was then purified with 1× volume of AMPure XP beads and eluted in 60 μl of nuclease-free water. Adapter ligation was performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, libraries were purified using 0.45× volumes of AMPure XP beads and short fragment buffer.


title: ChIP-seq of Plasmodium blood stages: MZ H3K4me3 rep2

description: 3D7 H3K4me3 MZ Rep 2

value: Magentically isolated schizonts (40 hpi) were incubated with E64 for 8 hours and then merozoites were mechanically released by filteration.


title: ChIP-seq of Plasmodium blood stages: SZ H3K9ac

description: 3D7 H3K9ac SZ

value: Schizont (40 hpi)

value: Schizonts (40 hpi) were magnetically seperated from uninfected and ring infected erythrocytes, then released from erythrocytes by saponin treatment.


title: AU-565 (TEQUILA-seq, blocking oligos(+), multiplex(-))


title: D18-182173

value: Normal Thymus_DN2


title: MCF7 (TEQUILA-seq)

extract_protocol:
Total RNA of breast cancer cell lines was extracted using TRIzol reagent (Invitrogen, #15596018).
A 200 ng aliquot of total RNA was used as templates for cDNA synthesis following the SMART-seq2 protocol. 500 ng of amplified cDNA were used for hybridization and capture following TEQUILA-seq protocol. The final nanopore 1D library waw constructed using 200 to 500 ng of post-capture amplified cDNA according to the SQK-LSK109 protocol. Briefly, cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 min and 65°C for 20 min. The cDNA was then purified with 1× volume of AMPure XP beads and eluted in 60 μl of nuclease-free water. Adapter ligation was performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, libraries were purified using 0.45× volumes of AMPure XP beads and short fragment buffer.

value: TEQUILA-seq, blocking oligos(-), multiplex(-)


title: 97H 4 wuhan mRNA-seq

description: total RNA of MHCC97H

value: RNA libraries for RNA-seq were prepared by Chi Biotech Co. Ltd.


title: MDA-MB-157 (TEQUILA-seq, blocking oligos(+), multiplex(+))

value: Human breast cancer basal B


title: MDA-MB-157 (TEQUILA-seq, blocking oligos(+), multiplex(-))


title: D18-182172

value: Thymic Lymphoma_DP


title: ChIP-seq of Plasmodium blood stages: SZ H3K4me3

description: 3D7 H3K4me3 SZ


title: 97H 3 wuhan mRNA-seq

description: total RNA of MHCC97H

value: hepatocellular cells


title: 97H 9 wuhan mRNA-seq

description: total RNA of MHCC97H


title: 97H 1 wuhan mRNA-seq

description: total RNA of MHCC97H


title: AU-565 (TEQUILA-seq)


title: HCC1806 (TEQUILA-seq)


title: D18-182171

value: Thymic Lymphoma


title: MHCC97H cells, generation9 Ribo

description: Ribosome-Nascentchain Complex of MHCC97H

value: WT


title: D18-182174


title: MDA-MB-157 (TEQUILA-seq)


title: MHCC97H cells, generation8 Ribo

value: Ribosome-Nascentchain Complex of MHCC97H


title: MCF7 (1D cDNA)

description:
BRCA_1D_cDNA_N2_R0_abundance.esp
BRCA_1D_cDNA_N2_R0_updated.gtf

data_processing:
Basecalling was performed in fast mode with Guppy (version 4.0.15) for all Nanopore sequencing data in this study (https://community.nanoporetech.com/downloads). Basecalling of direct RNA and cDNA libraries were done using config files rna_r9.4.1_70bps_fast.cfg and dna_r9.4.1_450bps_fast.cfg respectively.
Reads were then mapped to either the SIRVome or hg19 reference genome using minimap2 (v2.17) with parameters “-a -x splice -ub -k 14 -w 4 --secondary=no” and either SIRV transcript annotations or GENCODE v34 annotations (https://www.gencodegenes.org/human/release_34lift37.html).
Alignment files (SAM format) were next processed by ESPRESSO (https://github.com/Xinglab/espresso) using default settings and either SIRV transcript annotations or GENCODE v34 annotations. Reads that either map to the mitochondrial genome or contain large continuous insertions (≥20 nt) in the raw alignment were filtered out by ESPRESSO.
Assembly: hg19, SIRVome
Supplementary files format and content: .esp files are tab-delimited matrices generated by ESPRESSO that contain read count estimates for all identified isoforms (rows) across all samples (columns); .gtf files generated by ESPRESSO are in GTF format and provide genomic coordinates for all identified transcript isoforms and their corresponding exons
Paired-end Illumina sequencing data with 150-bp read length for SH-SY5Y cells were generated from libraries prepared following the TruSeq Stranded mRNA protocol (Illumina, Cat. #20020595)
Reads from the 3 samples were pooled and aligned to the GRCh37/hg19 reference genome using STAR on two-pass mode with default settings and transcript annotations from GENCODE v34.
Exon skipping events were detected and quantified from short-read alignment files using rMATS (v4.1.1) with default settings.
Assembly: hg19
Supplementary files format and content: SH-SY5Y_SE.MATS.JC.txt is a tab-delimited file that contains coordinates and junction read counts associated with all identified exon skipping events

growth_protocol:
Cell line was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA 30-4500 K™). Cell lines were cultured according to ATCC recommendations and were authenticated by the supplier.
See above

extract_protocol:
Total RNA of breast cancer cell lines was extracted using TRIzol reagent (Invitrogen, #15596018).
A 200 ng aliquot of total RNA was used as templates for cDNA synthesis following the SMART-seq2 protocol. Nanopore 1D libraries were constructed using 1 μg of amplified cDNA according to the standard SQK-LSK109 protocol. Briefly, cDNA products were end-repaired and dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (NEB, # E7546) by incubating at 20°C for 20 min and 65°C for 20 min. The cDNA was then purified with 1× volume of AMPure XP beads and eluted in 60 μl of nuclease-free water. Adapter ligation was performed using NEBNext Quick T4 DNA ligase (NEB, #E6056) at room temperature for 10 min. After ligation, libraries were purified using 0.45× volumes of AMPure XP beads and short fragment buffer.
See above
See above

value: 1D cDNA


title: D18-182170


title: HCC1806 (TEQUILA-seq, blocking oligos(+), multiplex(-))


title: AU-565 (1D cDNA)

value: Human breast cancer HER2 enriched


title: D18-182169


title: HCC1806 (1D cDNA)

value: Human breast cancer basal A


title: MHCC97H cells, generation6 Ribo


title: MDA-MB-157 (1D cDNA)


title: MHCC97H cells, generation7 Ribo


title: D18-182167

value: Normal Thymus_DN4


title: MHCC97H cells, generation5 Ribo


title: BRCA_39-1 (TEQUILA-seq)

description:
ENSG00000097007,ENSG00000163322,ENSG00000115170,ENSG00000123908,ENSG00000142208,ENSG00000105221,ENSG00000117020,ENSG00000171094,ENSG00000179477,ENSG00000184675,ENSG00000167522,ENSG00000134982,ENSG00000169083,ENSG00000078061,ENSG00000117713,ENSG00000049618,ENSG00000189079,ENSG00000150347,ENSG00000171456,ENSG00000143970,ENSG00000149311,ENSG00000175054,ENSG00000085224,ENSG00000087586,ENSG00000178999,ENSG00000103126,ENSG00000168646,ENSG00000167601,ENSG00000166710,ENSG00000105393,ENSG00000163930,ENSG00000138376,ENSG00000105327,ENSG00000142867,ENSG00000171791,ENSG00000171552,ENSG00000153094,ENSG00000113916,ENSG00000183337,ENSG00000023445,ENSG00000197299,ENSG00000107779,ENSG00000157764,ENSG00000012048,ENSG00000139618,ENSG00000141867,ENSG00000136492,ENSG00000010671,ENSG00000179218,ENSG00000198286,ENSG00000142453,ENSG00000064012,ENSG00000067955,ENSG00000110395,ENSG00000110092,ENSG00000118971,ENSG00000112576,ENSG00000105173,ENSG00000262919,ENSG00000120217,ENSG00000103855,ENSG00000105369,ENSG00000007312,ENSG00000070831,ENSG00000134371,ENSG00000039068,ENSG00000167258,ENSG00000135446,ENSG00000105810,ENSG00000132964,ENSG00000124762,ENSG00000111276,ENSG00000147889,ENSG00000147883,ENSG00000123080,ENSG00000245848,ENSG00000115163,ENSG00000149554,ENSG00000183765,ENSG00000079432,ENSG00000143207,ENSG00000005339,ENSG00000099942,ENSG00000205755,ENSG00000009307,ENSG00000182578,ENSG00000119535,ENSG00000102974,ENSG00000163599,ENSG00000168036,ENSG00000036257,ENSG00000121966,ENSG00000083799,ENSG00000152207,ENSG00000204209,ENSG00000043093,ENSG00000162733,ENSG00000100697,ENSG00000083520,ENSG00000132002,ENSG00000130816,ENSG00000119772,ENSG00000088305,ENSG00000104885,ENSG00000113360,ENSG00000120875,ENSG00000112242,ENSG00000074266,ENSG00000172889,ENSG00000146648,ENSG00000173674,ENSG00000156976,ENSG00000151247,ENSG00000163435,ENSG00000154582,ENSG00000100393,ENSG00000116016,ENSG00000119888,ENSG00000044524,ENSG00000145242,ENSG00000135333,ENSG00000154928,ENSG00000141736,ENSG00000065361,ENSG00000178568,ENSG00000104884,ENSG00000163161,ENSG00000175595,ENSG00000134899,ENSG00000105722,ENSG00000157554,ENSG00000116285,ENSG00000091831,ENSG00000006468,ENSG00000139083,ENSG00000108799,ENSG00000106462,ENSG00000187741,ENSG00000158169,ENSG00000083857,ENSG00000109670,ENSG00000162344,ENSG00000186895,ENSG00000075388,ENSG00000077782,ENSG00000066468,ENSG00000068078,ENSG00000160867,ENSG00000091483,ENSG00000154803,ENSG00000102755,ENSG00000122025,ENSG00000037280,ENSG00000129514,ENSG00000183770,ENSG00000150907,ENSG00000114861,ENSG00000162613,ENSG00000010810,ENSG00000102145,ENSG00000179348,ENSG00000107485,ENSG00000111087,ENSG00000088256,ENSG00000156052,ENSG00000087460,ENSG00000132522,ENSG00000166923,ENSG00000183454,ENSG00000082701,ENSG00000187837,ENSG00000158373,ENSG00000163041,ENSG00000132475,ENSG00000168148,ENSG00000188375,ENSG00000275714,ENSG00000278828,ENSG00000275379,ENSG00000197153,ENSG00000183598,ENSG00000203811,ENSG00000286522,ENSG00000287080,ENSG00000197409,ENSG00000274750,ENSG00000277775,ENSG00000273983,ENSG00000019991,ENSG00000206503,ENSG00000234745,ENSG00000135100,ENSG00000159184,ENSG00000174775,ENSG00000160223,ENSG00000117318,ENSG00000138413,ENSG00000182054,ENSG00000027697,ENSG00000017427,ENSG00000140443,ENSG00000167244,ENSG00000263528,ENSG00000185811,ENSG00000136634,ENSG00000168685,ENSG00000123999,ENSG00000122641,ENSG00000040933,ENSG00000109452,ENSG00000165458,ENSG00000171105,ENSG00000137265,ENSG00000169047,ENSG00000185950,ENSG00000162434,ENSG00000096968,ENSG00000105639,ENSG00000177606,ENSG00000073614,ENSG00000126012,ENSG00000147050,ENSG00000128052,ENSG00000079999,ENSG00000157404,ENSG00000136826,ENSG00000118058,ENSG00000272333,ENSG00000055609,ENSG00000167548,ENSG00000183955,ENSG00000128944,ENSG00000133703,ENSG00000131023,ENSG00000150457,ENSG00000166407,ENSG00000254087,ENSG00000172175,ENSG00000169032,ENSG00000126934,ENSG00000065559,ENSG00000095015,ENSG00000073803,ENSG00000006062,ENSG00000100030,ENSG00000102882,ENSG00000119487,ENSG00000125952,ENSG00000143384,ENSG00000137337,ENSG00000135679,ENSG00000198625,ENSG00000184634,ENSG00000213999,ENSG00000133895,ENSG00000105976,ENSG00000174197,ENSG00000187098,ENSG00000076242,ENSG00000117400,ENSG00000020922,ENSG00000095002,ENSG00000113318,ENSG00000116062,ENSG00000135097,ENSG00000153944,ENSG00000173531,ENSG00000164078,ENSG00000198793,ENSG00000132781,ENSG00000136997,ENSG00000116990,ENSG00000134323,ENSG00000172936,ENSG00000129152,ENSG00000104320,ENSG00000124151,ENSG00000141027,ENSG00000172260,ENSG00000196712,ENSG00000186575,ENSG00000116044,ENSG00000100906,ENSG00000136352,ENSG00000167034,ENSG00000148400,ENSG00000134250,ENSG00000074181,ENSG00000204301,ENSG00000181163,ENSG00000213281,ENSG00000165671,ENSG00000109685,ENSG00000147548,ENSG00000065057,ENSG00000198400,ENSG00000148053,ENSG00000140538,ENSG00000143228,ENSG00000102900,ENSG00000149269,ENSG00000101349,ENSG00000083093,ENSG00000143799,ENSG00000196092,ENSG00000163939,ENSG00000188389,ENSG00000197646,ENSG00000134853,ENSG00000113721,ENSG00000140992,ENSG00000082175,ENSG0000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BRCA_TEQUILA-seq_N2_R0_abundance.esp
BRCA_TEQUILA-seq_N2_R0_updated.gtf

value: Human breast cancer luminal

value: TEQUILA-seq


title: BRCA_40-2 (TEQUILA-seq)


title: D18-182166

value: Normal Thymus_DN3


title: BRCA_40-1 (TEQUILA-seq)


title: MHCC97H cells, generation4 Ribo


title: BRCA_39-2 (TEQUILA-seq)


title: BRCA_38-2 (TEQUILA-seq)


title: D18-182165

value: Normal Thymus_DN1


title: BRCA_38-1 (TEQUILA-seq)


title: BRCA_37-2 (TEQUILA-seq)


title: MHCC97H cells, generation3 Ribo


title: BRCA_37-1 (TEQUILA-seq)


title: D18-182164

value: Normal Thymus_DP


title: MHCC97H cells, generation2 Ribo


title: D18-182163


title: D18-182168


title: BRCA_36-2 (TEQUILA-seq)


title: BRCA_36-1 (TEQUILA-seq)


title: Hela cells,generation12

description: total RNA of Hela

source_name: Hela

value: Hela

value: cervical cancer cells

value: Normal subculture without special treatment


title: BRCA_34-1 (TEQUILA-seq)


title: D18-182162


title: BRCA_35-1 (TEQUILA-seq)


title: Hela cells,generation11

description: total RNA of Hela


title: D18-182161


title: BRCA_33-2 (TEQUILA-seq)


title: BRCA_35-2 (TEQUILA-seq)


title: D18-182160


title: Hela cells,generation10

description: total RNA of Hela


title: D18-182159


title: BRCA_33-1 (TEQUILA-seq)


title: Hela cells,generation9

description: total RNA of Hela


title: D18-182158


title: BRCA_32-1 (TEQUILA-seq)


title: Hela cells,generation8

description: total RNA of Hela


title: BRCA_31-2 (TEQUILA-seq)


title: Hela cells,generation7

description: total RNA of Hela


title: D18-182157


title: BRCA_34-2 (TEQUILA-seq)


title: BRCA_31-1 (TEQUILA-seq)


title: BRCA_30-2 (TEQUILA-seq)


title: BRCA_29-1 (TEQUILA-seq)


title: Hela cells,generation6

description: total RNA of Hela


title: BRCA_32-2 (TEQUILA-seq)


title: BRCA_28-2 (TEQUILA-seq)


title: Hela cells,generation5

description: total RNA of Hela


title: D18-182156


title: BRCA_30-1 (TEQUILA-seq)


title: BRCA_27-2 (TEQUILA-seq)


title: BRCA_27-1 (TEQUILA-seq)


title: Hela cells,generation4

description: total RNA of Hela


title: BRCA_26-2 (TEQUILA-seq)


title: D18-182154


title: BRCA_25-2 (TEQUILA-seq)


title: D18-182153