title: microglia, A-/ki/ki, male, mouse 136

description: column name in the common processed data matrices: MTa001_136_M_KI_b1

value: whole brain

value: acutely isolated microglia

value: male

value: A-

value: ki/ki


title: MS_pos_2758_2

status: Public on Sep 16 2024

type: SRA

city: Toronto

first: Michael

middle: D

last: Taylor

address: 686 Bay St

country: Canada

institute: The Hospital for Sick Children

description: processed_rnaseq_count_matrix_math1cre_smom2_kcnb2_tumors.tsv

library_source: transcriptomic

data_processing:
Paired-end FASTQs were aligned to mm9 using STAR (2.5.4b). Gene-level raw counts were extracted from the ReadsPerGene outs.
Assembly: mm9
Supplementary files format and content: Gene x sample RNA count matrices.

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
RNA was extracted using the RNEasy Mini Kit (Invitrogen).
Libraries were generated using the TruSeq RNA Sample Preparation kit (Illumina).

tag: tissue

tag: genotype


title: Y_AS1697_sgNupr1.1

city: New York

first: ZHUXUAN

last: LI

state: NY

address: 417 E 68th St

department: Cancer Biology and Genetics

country: USA

institute: Memorial Sloan Kettering Cancer Center

data_processing:
FASTQ files of bulk-cell RNA-sequencing data were aligned to a custom GRCm38 / mm10 reference containing additional transgenes using STAR (version 2.7.5a). Read counts were generated using the Python package HTSeq-count (version 0.13.5). The generated sample-gene count matrices were analyzed using a combination of published packages and custom scripts. The specific analytical workflows employed are summarized below.
Assembly: mm10
Supplementary files format and content: txt file includes raw counts of each sample
Supplementary files format and content: txt file includes RPKM counts of each sample

source_name: lung adenocarcinoma

growth_protocol: Samples are all derived from primary tumors by cell sorting. No cell culture step is involved.

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen, #217004) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2 ng total RNA with RNA integrity numbers ranging from 9.0 to 9.7 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech,  #63488), with 12 cycles of amplification. Subsequently, 10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems, #KK8504) using 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 Reagent Kit (200 Cycles) (Illumina).

treatment_protocol: Tumors derived from aged (A_Mouse ID) and young (Y_Mouse ID) were subjected to CRISPR-Cas9 mediated gene knockout.

value: lung adenocarcinoma

tag: cell type

value: Primary lung tumor cells

tag: group

value: young

tag: treatment


title: MS_pos_2531


title: Y_AS1614_sgControl

value: sgControl


title: MS_pos_2284


title: MCF7-E2-1h-H3K4me1-Rep1

city: SAN DIEGO

first: Lishuan

last: Wang

state: California

address: 9500 Gilman Drive

institute: UCSD

library_source: genomic

data_processing:
cutadapt: -u 15 -U 15 -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -b -B
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) were used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
bowtie2:  -q --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
makeTagDirectory: -format sam -keepAll -tbp 1 -checkGC -sspe -fragLength given
makeUCSCfile
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: BedGraph
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: MCF7 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM, GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen). For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM.

extract_protocol:
CUT&Tag standard Protocol
PCR Ampfication

tag: antibody

value: H3K4me1(Abcam, ab8895)

tag: cell line

value: Human breast cancers


title: 8_1513_MSK


title: MS_pos_2439


title: Y_AS1709_sgNupr1.1


title: Y_AS1612_sgNupr1.1


title: 2-15-17P

description: processed_rnaseq_count_matrix_lazy_piggy_tumours.txt

value: TAM-


title: 7_1297_MSK


title: MCF7-shKAP1-TNFα-1h-CDK9-Rep1

treatment_protocol: 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM.

value: CDK9(Santa Cruz, sc-13130)


title: Y_AS1611_sgNupr1.1


title: 4_1309_MSK


title: 1_1318_MS


title: MCF7-shNTC-TNFα-1h-CDK9-Rep1


title: Y_AS1609_sgNupr1.1


title: lazy_piggy_restriction_splink_insertions_lane9

data_processing:
Paired-end FASTQ files were first demultiplexed then trimmed for transposon sequences and filtered for reads beginning with TA dinucleotides, the required insertion sequence for the Sleeping Beauty transposon. Resulting reads were mapped to mm9 using bbmap and annotated based on insertion orientation and genomic distance from the nearest gene. Lastly, total read support for each insertion were summarized to generate insertion counts.
Assembly: mm9
Supplementary files format and content: Insertion counts from IR, PB, and JX libraries for lazy piggy transposon insertions and remobilizations, annotated by sample, genomic location, insertion orientation, read support, and Left/Right library. Each row corresponds to a single insertion, and columns describe insertion annotations.
Library strategy: Restriction SPLINK gDNA-seq

extract_protocol:
Snap frozen tumour tissues were digested with proteinase K and gDNA extracted by phenol/chloroform extraction followed by ethanol precipitation.
Extracted gDNA were mechanically sheared to 300 bp fragments using a Covaris S220 sonicator. End repair was performed using an EpiCentre End-It Kit, followed by adaptor ligation. With splinkerette-adaptors ligated at both ends, BamHI was used to digest and remove gDNA fragments. Primary and secondary PCR amplifications were performed using primers specific to sites specific to either the SB transposon sequence, PB transposon sequence, or their boundary, for amplification of IR, PB, and JX libraries, respectively.


title: MCF7-shNTC-TNFα-0h-CDK9-Rep1


title: A_AH1892_sgNupr1.1

value: aged


title: A_AH1746_sgControl


title: MCF7-TNFα-1h-KAP1-Rep1

value: KAP1(Abcam, ab22553)


title: lazy_piggy_restriction_splink_insertions_lane6


title: lazy_piggy_restriction_splink_insertions_lane5


title: MCF7-TNFα-0h-KAP1-Rep1


title: MCF7-Veh-1h-H3K4me1-Rep1


title: A_AH1678_sgNupr1.2


title: MCF7-TNFα-1h-P65-Rep1

value: P65(Santa Cruz, sc-372)


title: A_AH1551_sgControl


title: lazy_piggy_restriction_splink_insertions_lane2


title: lazy_piggy_restriction_splink_insertions_lane3


title: lazy_piggy_restriction_splink_insertions_lane4


title: 6_1312_MSK


title: MCF7-TNFα-0h-P65-Rep1


title: lazy_piggy_restriction_splink_insertions_lane1


title: 3_2082_MS


title: A_AH1550_sgNupr1.2


title: LNCAPshKAP1-DHT-1h-CDK9-Rep1

source_name: LNCAP

value: LNCAP

value: Human Prostate cancers


title: No Radiation Control 96 hr Rep 3

city: Stanford

first: Katarina

last: Klett

state: CA

address: 466 Lomita Mall

institute: Stanford University

data_processing:
Sequence reads were trimmed and mapped by the Genewiz/Azenta team.
Assembly: hg38
Supplementary files format and content: tab-delimited csv file contains the raw counts for each sample

source_name: Duodenum

extract_protocol:
Whole enteroids were extracted from the hydrogels using pre-chilled 5 mM EDTA in PBS. Enteroids were then centrifuged and the remaining EDTA/PBS mixture was aspirated. The enteroid pellets were then flash-frozen using liquid nitrogen and shipped on dry ice to Azenta for library preparation and sequencing.
Library preparation was completed by Azenta/Genewiz.

value: Duodenum

value: Enteroids derived from primary duodenum cells

value: Intestinal cells

value: No radiation control


title: No Radiation Control 96 hr Rep 2


title: No Radiation Control 96 hr Rep 1


title: lazy_piggy_restriction_splink_insertions_lane7


title: No Radiation Control 1 hr Rep 3


title: LNCAP-shNTC-DHT-1h-CDK9-Rep1


title: A_AH1545_sgNupr1.2

value: lung adenocarcinoma


title: A_AH1428_sgNupr1.1

value: Primary lung tumor cells


title: LNCAP-shNTC-DHT-0h-CDK9-Rep1


title: lazy_piggy_restriction_splink_insertions_lane8


title: A_AH1548_sgNupr1.1


title: LNCAP-DHT-1h-KAP1-Rep1


title: A_AH1360_sgNupr1.1


title: 5 Gy FLASH 96 hr Rep 2

value: 5 Gy FLASH radiation


title: 5 Gy FLASH 96 hr Rep 3


title: 5 Gy FLASH 96 hr Rep 1


title: LNCAP-DHT-0h-KAP1-Rep1


title: A_AF1567_sgControl

value: sgControl


title: 5 Gy FLASH 1 hr Rep 2


title: LNCAP-DHT-1h-AR-Rep1

value: AR(Santa Cruz, sc-7305)


title: 5 Gy CONV 96 hr Rep 3

value: 5 Gy CONV radiation


title: 5 Gy FLASH 1 hr Rep 1


title: AX1388_Y_DNMTi

first: Xueqian

last: Zhuang

address: 417 E 68th Street

data_processing:
FASTQ files of bulk-cell RNA-sequencing data were aligned to a custom GRCm38 / mm10 reference containing additional transgenes using STAR (version 2.7.5a). Read counts were generated using the Python package HTSeq-count (version 0.13.5). The generated sample-gene count matrices were analyzed using a combination of published packages and custom scripts. The raw gene expression count data were filtered with filterByExpr() command and normalized with the TMM method within the edgeR pipeline (version 3.34.1) in R. Subsequently, the differentially expressed genes (DEGs) were identified with an overdispersed Poisson model adjusting for batch and sex using edgeR (version 3.34.1)
Assembly: GRCm38/mm10
Supplementary files format and content: .txt file includes raw counts for each sample

source_name: Lung

growth_protocol: Primary cells were used. No growth protocol used.

treatment_protocol: Vehicle or 10 mg/kg GSK3685032, twice daily for 8 days.

value: Lung

value: Primary mouse lung epithelial cells

value: wildtype


title: LNCAP-DHT-0h-AR-Rep1


title: 5 Gy CONV 96 hr Rep 2


title: No Radiation Control 1 hr Rep 2


title: 5 Gy CONV 96 hr Rep 1


title: 5 Gy CONV 1 hr Rep 3


title: No Radiation Control 1 hr Rep 1


title: 5 Gy CONV 1 hr Rep 1


title: WT-Veh-1h-HAKAP1S824D-Rep1

value: HA(Abcam, ab9110)

value: Human breast cancers


title: AX1385_A_Veh


title: WT-E2-1h-HAKAP1S824D-Rep1


title: AX1386_A_DNMTi


title: 5 Gy CONV 1 hr Rep 2


title: WT-Veh-1h-HAKAP1S824A-Rep1


title: AX1384_A_DNMTi


title: WT-E2-1h-HAKAP1S824A-Rep1


title: AX1383_Y_DNMTi


title: WT-Veh-1h-HAKAP1-Rep1


title: AX1381_Y_Veh


title: AX1382_A_Veh


title: 5 Gy FLASH 1 hr Rep 3


title: KO-KAP1-E2-1h-PolIIS5P-Rep1

value: S5P(Active motif, 61085)


title: WT-E2-1h-HAKAP1-Rep1


title: AX1387_Y_Veh


title: AX1379_A_DNMTi


title: WT-Veh-1h-PolIIS5P-Rep1


title: KO-KAP1-E2-1h-MED26-Rep1

value: MED26(Cell Signaling, 13641S)


title: AX1378_Y_Veh


title: AX1377_A_Veh


title: WT-E2-1h-PolIIS5P-Rep1


title: CT_scTCR

city: Chengdu

first: Zedong

last: Jiang

state: Sichuan

address: Guoxue road

country: China

institute: Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.2.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/piplines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-seq

molecule: total RNA

source_name: Tumor

extract_protocol:
An appropriate amount of human cardiac septal tissue was taken and placed into the serum-free medium with sterile forceps, and the tissue was minced with sterile scissors and filtered through a 40 μm filter to obtain the cell suspension. Subsequently, an appropriate amount of type II collagenase was added, and digestion was carried out in a 37 ℃ water bath for 20 min to terminate the enzyme digestion, and the residual collagenase was washed away by centrifugation-discarding the supernatant and resuspending with culture medium. 300g-500g for 5 min-8 min to remove the cellular debris. Finally, erythrocyte lysis was performed using erythrocyte lysis solution.
The single cell suspension was loaded onto a 10X Chromium A Chip and the scRNA-Seq libraries were constructed following the protocol of the 10X genomics Chromium Single Cell Immune Profiling Solution. After the RT reaction, droplets were broken and barcoded-cDNA was purified with DynaBeads, followed by PCR-amplification. Sequencing libraries of single-cell transcriptomes suitable for Illumina sequencing platform were constructed after partial cDNA fragments and splicing. The remaining cDNA was enriched for the immune receptor (TCR), and the enriched products were amplified by PCR to construct a sequencing library suitable for the Illumina sequencing platform.

value: Tumor


title: SG_scTCR

description: 10x Genomics


title: WT-Veh-1h-MED26-Rep1


title: WT-E2-1h-MED26-Rep1


title: KO-KAP1-E2-1h-ELL2-Rep1

value: ELL2(Santa Cruz, sc-376611)


title: KO-KAP1-Veh-1h-MED26-Rep1


title: SG_scRNA

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.2.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/piplines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
An appropriate amount of human cardiac septal tissue was taken and placed into the serum-free medium with sterile forceps, and the tissue was minced with sterile scissors and filtered through a 40 μm filter to obtain the cell suspension. Subsequently, an appropriate amount of type II collagenase was added, and digestion was carried out in a 37 ℃ water bath for 20 min to terminate the enzyme digestion, and the residual collagenase was washed away by centrifugation-discarding the supernatant and resuspending with culture medium. 300g-500g for 5 min-8 min to remove the cellular debris. Finally, erythrocyte lysis was performed using erythrocyte lysis solution.
Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, CM cells were resuspended in the master mix and loaded together with partioning oil and gel beads into the chip to generate the gel bead-n-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single was retrotranscripted cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UM) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropriated sized fragments were selected with SPRIseclect reagent for subsequent library construction. During the library construction Illumina R2 primer R2 sequence, paried-end constructs with P5 and P7 sequences and a sample index were added.


title: CT_scRNA

description: 10x Genomics


title: WT-E2-1h-ELL2-Rep1


title: KO-KAP1-Veh-1h-ELL2-Rep1


title: siMdm2-LPS+IFNg-5

city: Hung Hom

first: Kelvin

middle: Ka-lok

last: Wu

state: Kowloon

address: Y938, Lee Shau Kee Building, The Hong Kong Polytechnic University

country: Hong Kong

institute: The Hong Kong Polytechnic University

data_processing:
RNA-seq reads were preceded by removing adapters using cutadapt (v4.5) followed by quality assessment with FastQC (v0.12.1). Raw reads were mapped against the GRCm39 mouse genome assembly using STAR aligner (v2.7.10b) with the default options. The number of reads mapped to each of genes was counted by using featureCounts of subread package (v 2.0.3), with the option: -s 0 -p --countReadPairs -t exon -g gene_id. To visualize expression levels by principal component analysis (PCA), count data were first normalized using VST method from DESeq2 R package (v1.36.0).
Assembly: GRCm39 mouse genome assembly
Supplementary files format and content: csv file with raw counts for each sample
Supplementary files format and content: csv file with normalized count for each sample

source_name: macrophage

growth_protocol: Bone marrow-derived macrophages were maintained in DMEM supplemented with 10% Fetal bovine serum and 1% penicillin (100 U/ml) and streptomycin (100 μg/ml)

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Catalog# 74104, Qiagen) following manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Bone marrow-derived macrophages were transfected with siRNA targeting Mdm2 or a scramble control, followed by stimulation with100 ng/ml LPS from Escherichia coli O111:B4 and 100 ng/ml recombinant mouse IFNγ (Catalog# 485-MI, R&D Systems) for 20 hours.

value: macrophage

value: siMdm2, LPS+IFNg


title: siMdm2-LPS+IFNg-2


title: AX1380_Y_DNMTi


title: siMdm2-LPS+IFNg-3


title: WT-Veh-1h-ELL2-Rep1


title: siMdm2-LPS+IFNg-1


title: KO-KAP1-E2-1h-PAF1-Rep1

value: PAF1(Abcam, ab137519)


title: siMdm2-LPS+IFNg-4


title: KO-KAP1-Veh-1h-PolIIS5P-Rep1


title: siScramble-LPS+IFNg-4

value: siScramble, LPS+IFNg


title: WT-E2-1h-PAF1-Rep1


title: siScramble-LPS+IFNg-5


title: WT-Veh-1h-PAF1-Rep1


title: KO-KAP1-Veh-1h-PAF1-Rep1


title: KO-KAP1-E2-1h-BRD4-Rep1

value: BRD4(Santa Cruz, sc-518021)


title: siScramble-LPS+IFNg-1


title: KO-KAP1-Veh-1h-BRD4-Rep1


title: WT-E2-1h-BRD4-Rep1


title: siScramble-LPS+IFNg-2


title: M25+ Pseudobulk

city: Augusta

first: Klaus

last: Ley

state: GA

address: 1410 Laney Walker Blvd

institute: Immunology Center of Georgia

description: 10X Genomics

data_processing:
Libraries were mapped with Cell Ranger’s count pipeline.
Subsequently, multiple libraries were aggregated with the aggr pipeline. Aggregated data was then imported into the R environment. Seurat (4.4.0) was used to filter and identify clusters.
Cells with less than 200 genes and more than 2,500 genes were excluded from further analysis. Furthermore, cells with more than 5% UMIs coming from mitochondrial genes were filtered out. Genes expressed in less than 3 cells were ignored.
The gene expression matrices were then normalized and scaled. Principal Component Analysis was performed on the scaled data.
A pseudo-bulk analysis was performed on the single cell transcriptome by summarizing the raw counts across all the identified cells.
Assembly: GRCm38
Supplementary files format and content: Csv files including raw gene counts after pseudobulk analysis

source_name: spleen

extract_protocol:
Tetramer+ cells were sorted into 1.5 mL collection tubes containing 500 μl of PBS:FBS (1:1) supplemented with RNase inhibitor (Takara, Mountain View, Ca, USA; 1:100). After sorting, ice-cold PBS was added to reach a final volume of 1400 μl. The cells were centrifuged (400 x g, 5 minutes, 4°C), cell suspension were incubated with the 10x Genomics Master Mix, loaded onto a Chromium Next GEM Chip (10x Genomics, Pleasanton, CA, USA)
Library construction was performed according to the Chromium Next GEM Single Cell 5’ Protocol.
Samples were processed using 10X v2 chemistry as per the manufacturer’s recommendations; 11 and 12 cycles were used for cDNA amplification and library preparation, respectively.

value: spleen

value: CD4 T cells

value: M25+ cells

tag: strain


title: WT-Veh-1h-BRD4-Rep1


title: C251_KO

city: Wonju

first: Seung-Phil

last: Hong

address: 20 Ilsan-ro

department: Department of Dermatology

country: South Korea

institute: Yonsei University Wonju College of Medicine

data_processing:
NovaSeq S4PE100 reads were trimmed and filtered using Partek Flow. High quality reads were aligned using TopHat v2.1.0 for alignment into BAM files.
BAM files were imported into the RNA-seq pipeline of Partek FLow, version 9.0.20.0202 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq Transcripts 93 2020-02-03). Exclusions include a mininum reads of 30 in one out of 6 samples. RPKM values were log2-transformed with an offset value of 0.000001.
Assembly: mm39
Supplementary files format and content: txt, gene counts

source_name: epidermis

growth_protocol: Hnrnpu KO mice vs control mice

extract_protocol:
Epidermis was separated from dermis, and RNA was extract by using PureLinkTMRNA mini kit.
RNA-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: Hnrnpu was knocked out using a loxP-cre system

value: epidermis

value: Hnrnpu knockout

tag: age

value: postnatal day 0


title: KO-KAP1-Veh-1h-CDK9-Rep1

value: CDK9(Santa Cruz, sc-13130)


title: C242_KO


title: KO-KAP1-E2-1h-CDK9-Rep1

value: Human breast cancers


title: C250_control

value: Heterogenous


title: WT-E2-1h-CDK9-Rep1


title: C217_KO


title: C216_control

value: Wild type


title: WT-Veh-1h-CDK9-Rep1


title: C241_contol


title: TNC-/-_04

city: Saltlake city

last: Jurynec

state: UT

institute: University of Utah

data_processing:
Raw data were analyzed for per base sequence quality (>30), per sequence GC content, adapter (universal Illumina adapter) removal using FASTQC v0.11.9.
The sequencing reads were mapped to the mouse reference genome (GRCm39 release 110 ) using HISAT2 v2.2.1 .
Aligned reads were counted using HTSeq v2.0.2, and the counts were then analyzed for differential gene expression using median-ratio-normalization with Deseq2 v1.38.3.
Assembly: mm39
Supplementary files format and content: tab-deliminated text file_including raw counts for each samples

source_name: Shoulder joints

extract_protocol:
Whole shoulder joints were dissected and total RNA 151 was isolated
Sequencing libraries were generated using NEBNext® UltraTM RNALibrary Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations. mRNA is captured with the PolyA enrichment method.

treatment_protocol: Shoulder rotator cuff repair model

value: Shoulder joints

value: Tnc-/-

value: repair of the supraspinatus tendon of the left shoulder


title: TNC-/-_03


title: WT-E2-1h-H3K4me1-Rep1

value: H3K4me1(Abcam, ab8895)


title: WT-Veh-1h-H3K4me1-Rep1


title: TNC-/-_01


title: KO-KAP1-E2-1h-H3K4me1-Rep1


title: siScramble-LPS+IFNg-3

value: macrophage


title: WT_RCR_L3B


title: TNC-/-_02


title: KO-KAP1-Veh-1h-H3K27Ac-Rep1

value: H3K27Ac(Active motif, 39085)


title: WT-E2-1h-H3K27Ac-Rep1


title: WT_RCR_L2B


title: WT-Veh-1h-H3K27Ac-Rep1


title: KO-KAP1-E2-1h-H3K27Ac-Rep1


title: WT_RCR_L1B


title: Aldh1a1_WT_control

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
RNA samples were extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer's instruction.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: Lung

value: Wildtype

value: no treatment


title: KO-KAP1-Veh-1h-PolIIS2P-Rep1

value: S2P(Active motif, 91116)


title: Aldh1a1_KO_control

value: Aldh1a1 -/-


title: m25+ cells treated with PD1i/CD73i_Sorted Sample2

data_processing:
FASTQ files were generated with bcl2fastq (Illumina). Quality control checks were performed using FastQC v0.12.1 and MultiQC version v1.12. RNA-seq reads were trimmed using Trimmomatic v0.39. The STAR (v2.7.10a with default parameters) aligner was used to map the transcriptomes of the mouse bulk RNA-seq data to GENCODE GRCm39 (Release M33). Raw read gene counts were obtained using HTSeq-count v2.02, which were used for the differential gene expression analysis (DEA).
Assembly: GRCm39
Supplementary files format and content: Comma-separated values (CSV) file

source_name: draining LN

extract_protocol:
Library preparation was performed using a modified version of the Smart-Seq2 method as described by Rosales et al.
Barcoded libraries were pooled in equimolar amounts and sequenced using an S1 flow cell on a NovaSeq 6000 System (Illumina, San Diego, CA, USA) with 50 bp paired-end reads.

value: draining LN

value: PD1 inhibitor/CD73 inhibitor


title: WT-E2-1h-PolIIS2P-Rep1


title: WT-Veh-1h-PolIIS2P-Rep1


title: m25+ cells treated with PD1i/CD73i_Sorted Sample1


title: KO-KAP1-Veh-1h-H3K4me1-Rep1


title: m25+ cells treated with isotype/vehicle_Sorted Sample2

value: isotype/vehicle


title: WT-E2-1h-PolII-Rep1

value: PolII(Abcam, ab26721)

value: Human breast cancers


title: KO-KAP1-E2-1h-PolII-Rep1


title: m25+ cells treated with isotype/vehicle_Sorted Sample1


title: KO-KAP1-Veh-1h-PolII-Rep1


title: p6+ cells treated with PD1i/CD73i_Sorted Sample2


title: WT-Veh-1h-PolII-Rep1


title: KO-KAP1-E2-1h-TOP1cc-Rep1

value: TOP1cc(Milloipore, MABE1084)


title: p6+ cells treated with isotype/vehicle_SortedSample1


title: p6+ cells treated with isotype/vehicle_Sorted Sample2


title: WT-E2-1h-TOP1cc-Rep1


title: WT-Veh-1h-TOP1cc-Rep1


title: KO-KAP1-Veh-1h-GATA3-Rep1

value: GATA3(Santa Cruz, sc-268)


title: KO-KAP1-E2-1h-PolIIS2P-Rep1


title: KO-KAP1-Veh-1h-TOP1cc-Rep1


title: EpiLC_RNASEQ_TASOR_KO+ADDBACK_rep2

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

data_processing:
The RNA-seq reads were aligned to the mm10 mouse reference genome using the STAR aligner (Dobin, 2013) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 10-bp windows across the genome using deepTools for presentation as genome browser tracks (Ramirez et al, 2014).
The seqeunce length was 148 for R1 and 148 for R2 for paired-end data.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Epiblast like stem cells

growth_protocol: ESCs were cultured under naive conditions (DMEM/F12+Neurobasal, N2 supplement, B27 supplement, 2 mM Glutamax, NEAA, 0.1 mM 2-mercaptoethanol, 1% fatty acid free BSA, 1 uM PD0325901, 3 uM CHIR99021, and leukemia inhibitory factor (LIF)).

extract_protocol:
RNA was extracted using a Qiagen RNeasy kit.
Libraries were constructed according to the Illumina Tru-seq protocol.

treatment_protocol: Epiblast like stem cells were transitioned from naïve conditions to FA media for 48 hrs (DMEM/F12+Neurobasal, N2 supplement, B27 supplement, 2 mM Glutamax, NEAA, 0.1 mM 2-mercaptoethanol, 1% fatty acid free BSA, 12 ng/mL FGF2, 20 ng/mL Activin A).

value: Epiblast like stem cells

value: TASOR KO

value: TASOR cDNA


title: KO-KAP1-E2-1h-GATA3-Rep1


title: EpiLC_RNASEQ_TASOR_KO+ADDBACK_rep1


title: EpiLC_RNASEQ_WT+ADDBACK_rep1

value: WT


title: WT-Veh-1h-GATA3-Rep1


title: WT-E2-1h-GATA3-Rep1


title: EpiLC_RNASEQ_TASOR_KO_rep2


title: EpiLC_RNASEQ_TASOR_KO_rep1


title: KO-KAP1-E2-1h-ERα-Rep1

value: ERα(Santa Cruz; sc-8002)


title: p6+ cells treated with PD1i/CD73i_Sorted Sample1


title: WT-E2-1h-ERα-Rep1


title: EpiLC_RNASEQ_WT_rep2


title: EpiLC_RNASEQ_WT_rep1


title: MCF7-shGATA3-E2-1h-KAP1-Rep1

value: KAP1(Abcam, ab22553)


title: ESC_RNASEQ_TASOR_KO+ADDBACK_rep1

source_name: Embryonic stem cells

value: Embryonic stem cells


title: MCF7-shGATA3-Veh-1h-KAP1-Rep1


title: EpiLC_RNASEQ_WT+ADDBACK_rep2


title: MCF7-shERα-Veh-1h-KAP1-Rep1


title: MCF7-shERα-E2-1h-KAP1-Rep1


title: ESC_RNASEQ_TASOR_KO_rep1


title: MCF7-shNTC-E2-1h-KAP1-Rep1


title: ESC_RNASEQ_WT+ADDBACK_rep2


title: ESC_RNASEQ_WT_rep1


title: ESC_RNASEQ_WT_rep2


title: MCF7-shNTC-Veh-1h-KAP1-Rep1


title: EpiLC_CUTTAG-H3K9me3_TASOR_KO_MET_rep1

data_processing:
The CUT&Tag reads were aligned to the mm10 mouse reference genome using the Bowtie2 aligner (Langmead, 2012) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 10-bp windows across the genome using deepTools for presentation as genome browser tracks (Ramirez et al, 2014).
The seqeunce length was 150 for R1 and 150 for R2 for paired-end data.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Samples were prepared according to the Epicypher CUT&Tag protocol.
Libraries were constructed according to the Illumina Nextera protocol.

treatment_protocol: Epiblast like stem cells were transitioned from naïve conditions to FA media for 48 hrs (DMEM/F12+Neurobasal, N2 supplement, B27 supplement, 2 mM Glutamax, NEAA, 0.1 mM 2-mercaptoethanol, 1% fatty acid free BSA, 12 ng/mL FGF2, 20 ng/mL Activin A). MET inficates treatment with 1 uM MCC950 (NLRP3 inhibitor) and 5 uM Emricasan Caspase inhibitor during the transition from ESC to EpiLC.

value: 1 uM MCC950 and 5 uM Emricasan


title: KO-KAP1-Veh-1h-ERα-Rep1


title: MCF7-Veh-NU7441-1h-pS824-Rep1


title: MCF7-E2-NU7441-1h-pS824-Rep1


title: MCF7-Veh-DMSO-1h-pS824-Rep1


title: EpiLC_CUTTAG-H3K9me3_WT_rep1


title: MCF7-E2-NU7441-1h-ERα-Rep1


title: MCF7-E2-DMSO-1h-pS824-Rep1


title: WT-Veh-1h-ERα-Rep1


title: ESC_RNASEQ_TASOR_KO+ADDBACK_rep2


title: MCF7-Veh-NU7441-1h-ERα-Rep1


title: MCF7-E2-DMSO-1h-ERα-Rep1


title: ESC_CUTTAG-FLAG-TASOR_TASOR_KO+ADDBACK_rep3


title: ESC_CUTTAG-FLAG-TASOR_TASOR_KO+ADDBACK_rep4


title: ESC_RNASEQ_WT+ADDBACK_rep1


title: ESC_CUTTAG-FLAG-TASOR_TASOR_KO+ADDBACK_rep2


title: ESC_RNASEQ_TASOR_KO_rep2


title: ESC_CUTTAG-FLAG-TASOR_TASOR_KO+ADDBACK_rep1


title: MCF7-Veh-DMSO-1h-ERα-Rep1


title: MCF7-E2-1h-KAP1-pS824-Rep1


title: MCF7-Veh-1h-KAP1-pS824-Rep1


title: ESC_CUTTAG-H3K9me3_TASOR_KO+ADDBACK_rep1


title: ESC_CUTTAG-H3K9me3_TASOR_KO_rep1


title: MCF7-E2-1h-KAP1-pS473-Rep1


title: ESC_CUTTAG-H3K9me3_WT_rep1


title: EpiLC_CUTTAG-H3K9me3_TASOR_KO+ADDBACK_rep1


title: MCF7-E2-1h-KAP1-Ab2-Rep1

value: KAP1(Gene Tex, GTX102226)


title: EpiLC_ATAC_TASOR_KO_MET_rep2

data_processing:
The ATAC-seq reads were aligned to the mm10 mouse reference genome using the Bowtie2 aligner (Langmead, 2012) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 10-bp windows across the genome using deepTools for presentation as genome browser tracks (Ramirez et al, 2014).
The seqeunce length was 150 for R1 and 150 for R2 for paired-end data.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Samples were prepared according to the Illumina Nextera protocol.
Libraries were constructed according to the Illumina Nextera protocol.


title: MCF7-Veh-1h-KAP1-pS473-Rep1


title: EpiLC_ATAC_TASOR_KO+ADDBACK_rep2


title: EpiLC_CUTTAG-H3K9me3_TASOR_KO_rep1


title: MCF7-Veh-1h-KAP1-Ab2-Rep1


title: MCF7-E2-1h-KAP1-Ab1-Rep1


title: EpiLC_ATAC_TASOR_KO_rep2


title: MCF7-Veh-1h-KAP1-Ab1-Rep1


title: EpiLC_ATAC_TASOR_KO+ADDBACK_rep1


title: MCF7-E2-1h-H3K27Ac-Rep1

value: H3K27Ac(Active motif, 39085)


title: EpiLC_ATAC_TASOR_KO_rep1


title: MCF7-E2-1h-P300-Rep1


title: MCF7-Veh-1h-H3K27Ac-Rep1


title: EpiLC_ATAC_WT_rep2


title: ESC_ATAC_TASOR_KO+ADDBACK_rep2


title: MCF7-Veh-1h-P300-Rep1


title: MCF7-E2-1h-ERα-Rep1

value: ERα(Santa Cruz, sc-8002)


title: ESC_ATAC_TASOR_KO+ADDBACK_rep1


title: HDA9-SD,H3K9ac,CUT&Tag-seq

city: Wuhan

first: Xiangsong

last: Chen

state: Hubei

address: Bayi Road

institute: Wuhan university

data_processing:
reads from each sample were mapped to the TAIR10 genome using bowtie2
samtools were used to extract mapped Q30 reads
Assembly: TAIR10
Supplementary files format and content: bigWig file
Library strategy: CUT&Tag

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: A. thaliana plants were growth on 1/2X MS agar (0.6%) + 1% sucrose  at 22 degree under a 16-h-light/8-h-dark photoperiod.

extract_protocol:
CUT&Tag Assay Kit (pAG-Tn5) for Illumina（Abclonal, RK20265）
DNA Index Kit：Dual DNA Adapter 96 Kit for One-step DNA Lib Prep (ABclonal, Cat: RK20290)

treatment_protocol: 10 day seedlings

tag: line

value: seedling


title: ESC_ATAC_TASOR_KO_rep2


title: Col-0,H3K9ac,CUT&Tag-seq


title: hda9,H3K9ac,CUT&Tag-seq


title: WT-E2-1h

data_processing:
cutadapt: -u 15 -U 15 -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -b -B
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) were used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
bowtie2:  -q --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
makeTagDirectory: -format sam -keepAll -tbp 1 -checkGC -sspe -fragLength given
samtools; bamCoverage
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: BedGraph

extract_protocol:
ATAC-seq standard Protocol
PCR Ampfication


title: HDA9-SA,H3K9ac,CUT&Tag-seq


title: KO-KAP1-E2-1h


title: MCF7-Veh-1h-ERα-Rep1

data_processing:
cutadapt: -u 15 -U 15 -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -b -B
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) were used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
bowtie2:  -q --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
makeTagDirectory: -format sam -keepAll -tbp 1 -checkGC -sspe -fragLength given
makeUCSCfile
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: BedGraph
Library strategy: CUT&Tag


title: ESC_ATAC_TASOR_KO_rep1


title: KO-KAP1-Veh-1h


title: EpiLC_ATAC_TASOR_KO_MET_rep1


title: CR4, biol rep 3

city: Nanjing

first: Tingting

address: NO.1 Weigang

institute: NANJING AGRICULTURAL UNIVERSITY

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome GCF_001433935.1_IRGSP-1.0 using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GCF_001433935.1_IRGSP-1.0
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

organism: Oryza sativa

source_name: Japanese rice

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Leaf

value: OsMP1 knockdown

value: untreated


title: CR4, biol rep 2


title: Bone marrow (Young Y9)

city: Buffalo

first: Jonathan

middle: E

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

institute: University at Buffalo

data_processing:
illumina bcl2fastq2 demultiplexing
Assembly: mm10
Supplementary files format and content: featureCounts gene quantifications in tsv format

source_name: Tibia

extract_protocol:
Total RNA was obtained from Sorted Cd11b+Ly6GLy6C+ M-MDSC from young and old mice using RNeasy Mini (Qiagen)
illumina TruSeq RNA Stranded library preparation
Paired-end sequencing on the illumina NovaSeq6000

value: Tibia

value: Bone Marrow

tag: time

value: 6 months


title: ESC_ATAC_WT_rep1


title: ESC_ATAC_WT_rep2


title: WT-Veh-1h

value: Human breast cancers


title: EpiLC_ATAC_WT_rep1

value: Epiblast like stem cells

value: TASOR KO


title: 395_IIR-KO

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

country: Germany

institute: Helmholtz Zentrum München German Research Center for Environmental Health

description:
MUC18397
10x Genomics

data_processing:
The alignment, barcoded processing and gene counting were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/3.1/what-is-cell-ranger)
For QC, filtering, doublet detection, normalization, batch correction and differential gene expression the scanpy python packages v.1.9.1, anndata v0.8, scrublet v0.2.3, doubletdetection v4.2, scvi-tools v0.17.1, harmonypy v0.0.6 and the R packages Seurat v4.1.1, sctransform v0.3.3 and edgeR 3.36.0 were used. Scripts for preprocessing will be available here: https://github.com/michiste/2023_Siehler_IIR-KO_SC-islets
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pluripotent stem cell-derived islets

extract_protocol:
Stage 6 SC-islets were washed with PBS and dissociated with TrypLE Express for 15 min at 37°C. Cells were dissociated by pipetting up and down. Cell were then washed with warm DMEM media, resuspended in FACS-buffer (2% FCS, 2mM EDTA in PBS) and incubated with SYTOX-Blue for 5 min at room temperature. Live cells were then isolated by FACS and collected in 2% FCS in PBS. Subsequently, sorted cells were washed once with 2% FCS in PBS and cell numbers were determined using a hemocytometer. Approximately 16500 cells were loaded on one chip lane.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, SC-islet cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: pluripotent stem cell-derived islets (stage 6)

value: pluripotent stem cell-derived islets

value: stage 6


title: CR4, biol rep 1


title: 394_WT

description:
MUC18396
10x Genomics


title: Bone marrow (Young Y6)


title: Bone marrow (Young Y5)


title: Hei, biol rep 2

value: WT


title: Bone marrow (Young Y2)


title: Hei, biol rep 3


title: Bone marrow (Young Y1)


title: s14

city: Shanghai

first: Xiaoshen

last: Zhang

state: Shanghai

address: 1239 siping road

institute: Tongji University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone metastasis

extract_protocol:
Nuclei was isolated and counted with a cell counter (Thermo Fisher, Countess II).
Using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 (10X Genomics), nuclei were immediately loaded onto a Chromium Single Cell Processor (10X Genomics) for barcoding of RNA from single nuclei. Sequencing libraries were constructed according to the manufacturer’s instructions (10× Genomics)

value: bone metastasis

tag: disease state

tag: Stage

value: IV

tag: Sex

value: m

tag: driver gene_mutations


title: sz

description: 10x Genomics

value: f


title: s13

description: 10x Genomics


title: Hei, biol rep 1

value: Leaf


title: Bone marrow (Young Y10)


title: AMS002 + pVector + AHLS R3

city: Columbus

first: Brian

last: Ahmer

state: OH

address: 776 Biomedical Research Tower, 460 W 12th Ave

department: Microbial Infection and Immunity

institute: The Ohio State University

description:
total RNA from sdiA mutant Typhi grown in LB with AHL with vector control
pAMS130_transcript_count_matrix.csv

data_processing:
Quality (FastQC)
Trimming (Trimmomatic)
Mapping (Bowtie2)
Assembly (Stringtie)
Quantification and assignation (Stringtie)
Assembly: CP001363
Supplementary files format and content: txt file
Supplementary files format and content: raw transcript counts of each treatment group

organism: Salmonella enterica subsp. enterica serovar Typhi

source_name: late exponential phase

growth_protocol: Each strain was grown over-night in LB at 37C. Washed cells were diluted 1:100 in LB broth + AHLs. Plasmid containing strains were treated with arabinose. Cells were re-grown until late exponential phase at 37C, shaking.

extract_protocol:
Cell pellets were frozen at -80. Total RNA was extracted from cells using the Purelink RNA mini kit (Invitrogen). Residual DNA was removed by Dnase digestion
Construction was performed by OSU Shared genomics resources

tag: culture medium

value: LB Broth

value: late exponential phase

value: sdiA::kan + pBAD

value: AHL + arabinose


title: HCC_FoxM1

city: Xi'an Shaanxi

first: Xiang

address: Changle West Road 169

institute: The Fourth Military Medical University

data_processing:
ChIP DNA was end-blunted and added with an "A" base so the adaptors from Illumina with a “T” can ligate on the ends.
Then we used magnetic beads to recover the target size fragments and performed PCR amplification to obtain the library to be sequenced.
The constructed library was checked for quality by agarose electrophoresis. Libraries were quantified using Qubit 2.0 to determine if the library concentration was suitable for use on the machine.
After the library quality inspection was qualified, different libraries were sequenced on the Illumina sequencer according to the requirements of effective concentration and target data volume.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using a HiSeq Rapid Duo cBot Sample Loading Kit (Illumina) according to the manufacturer's instructions.
MACS2 (v2.1.1) was used to call peak, giving a robust and high resolution ChIP-Seq peak predictions. Peaks were annotated related genes using Homer (v4.10). ChIPseeker (v1.5.1) was used to depict the reads distribution on chromosomes. Homer (v4.10) was used to search motif and analyze transcription factors.
Assembly: hg38
Supplementary files format and content: *.txt: Tab-delimited text files

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Genomic DNA degradation and contamination were monitored on 1% agarose gels. DNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). The DNA concentration was measured using a Qubit® DNA Assay Kit in a Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). A total amount of 50 ng DNA per sample was used as input material for the ChIP sample preparations.
The Chip-Seq library construction mainly includes the steps of cell cross-linking, cell lysis, protein co-immunoprecipitation, extraction of co-precipitated complex DNA, and construction of DNA next-generation sequencing library. Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: Human hepatocellular carcinoma

tag: chip antibody

value: anti-FoxM1 (Santa Cruz Biotechnology sc-376471)


title: Bone marrow (Old O7)

tag: tissue

value: Tibia

value: Bone Marrow

value: 24 months


title: Bone marrow (Old O6)


title: HCC_Input [FoxM1]

value: IgG


title: AMS002 + pVector + AHLs R1

tag: genotype


title: HCC_ASPM

tag: cell type

value: anti-ASPM (proteintech; 26223-1-AP)


title: Bone marrow (Old O5)


title: AMS002 + pSdiA + AHLs R3

description:
total RNA from sdiA mutant Typhi grown in LB with AHL expressing sdiA on plasmid
pAMS130_transcript_count_matrix.csv

value: sdiA::kan + pBAD-SdiA


title: Bone marrow (Old O4)


title: Bone marrow (Old O2)


title: AMS002 + pSdiA + AHLs R2


title: AMS002 + pSdiA + AHLs R1


title: L_BCR

city: Guangzhou

first: Zhenhua

last: Luo

state: Guangzhou

address: Number 58, zhongshan er road, Yuexiu,

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
The raw data of 5’ single cell RNA sequencing were aligned to human transcriptome (GRCh38) using CellRanger (v3.1.0) count function.
The raw data of TCR and BCR V(D)J sequencing were aligned to human transcriptome (GRCh38) using CellRanger (v3.1.0) vdj function.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.tar: Tar archives include matrix.mtx, barcodes.tsv, and features.tsv files. Matrix table with raw gene counts for every gene and every single cells.
Supplementary_files_format_and_content: *_annotations.csv: High-level annotations of each high-confidence, cellular contig information of B cell receptor and T cell receptor for each patient.

source_name: liver

extract_protocol:
0.5 cm3 liver tissue was cut into very small fragments. The tissue was digested in dissociation buffer (0.8 mg/ml of Collagenase II, 1.5 mg/ml of Collagenase IV, Dispase,12 U/ml of DNase I, 3 mmol/L of CaCl2 in DMEM media with 10% FBS) for 30 minutes at 37℃. The cell suspensions were filtered through 40 µm cell strainers. Then, red cells were removed by ACK lysing buffer with incubation at ice for 10 minutes. Cell pellets were washed twice with 1xDPBS buffer and resuspended in 200 µl 1xDPBS buffer.
Single cell suspensions were subjected to single cell 5’ RNA sequencing library construction according to the instructions of the Chromium Next GEM Single Cell 5' Kit v2. (10X Genomics). Briefly, single cell suspensions mixed with RT-PCR master mix was loaded with partitioning oil and nanoliter-scale gel beads into the single-cell 5’ chip. Then, RNA transcripts were barcoded within single cells and reverse transcribed into cDNA, which were purified, amplified, end-repaired, and ligated with adapters to generate a single multiplexed library. The TCR- and BCR V(D)J libraries were generated with aliquots of cDNA using the Chromium Single Cell V(D)J Enrichment Kit v1.1.

tag: diagnosis

value: Biliary Atresia

value: liver


title: HCC_Input [ASPM]


title: Bone Marrow (Old O1)


title: L_TCR


title: K_BCR


title: AMS001 + AHLs R2

description:
total RNA from sdiA mutant Typhi grown in LB with AHL
Ty2_transcript_count_matrix.csv

tag: treatment

value: AHL


title: Ty2 + AHLs R3

description:
total RNA from wild-type Typhi grown in LB with AHL
Ty2_transcript_count_matrix.csv

value: wild-type


title: K_TCR


title: K_CELL


title: AMS001 + AHLs R1


title: Ty2 + AHLs R2


title: J_TCR


title: AMS002 + pVector + AHLs R2


title: Ty2 + AHLs R1


title: I_TCR


title: G_TCR

value: Choledochal Cyst


title: H_TCR


title: p-circGLIS3_RNA transfected fibroblasts, 2

type: RNA

city: Stockholm

first: Yongjian

address: Solnavägen 1

country: Sweden

institute: Karolinska Institutet

description:
Fibroblasts transfected with plasmid-circGLIS3_RNA
ProcessedData.xlsx

hyb_protocol: Standardized array processing procedures recommended by Affymetrix, including hybridization, fluidics processing, and scanning, were used

data_processing:
Expression data were analyzed by using Transcriptome Analysis Console 4.0. The follwoing criteria were used for data analysis: Array Type: Clariom_S_Human Analysis Type: Expression (Gene) Analysis Version: version 2 Summarization Method: Gene Level - SST-RMA Pos vs Neg AUC Threshold: 0,7 Genome Version: hg38 (Homo sapiens) Annotation: Clariom_S_Human.r1.na36.hg38.a1.transcript.csv Condition (Comparison): circRNA kd; ctr
Expression Analysis Settings: • Gene-Level Fold Change < -2 or > 2 • Gene-Level P-Value < 0,05 • Anova Method: ebayes • A Probeset (Gene/Exon) is considered expressed if ≥ 50% samples have DABG values below DABG Threshold. • DABG < 0,05

label: biotin

label_protocol: One hundred fifty nanograms of total RNA was used to prepare cDNA following the GeneChip WT PLUS Reagent Kit labeling protocol

growth_protocol: Human dermal fibroblasts (hDFs) isolated from plastic surgery skin were cultured in DMEM medium (Gibco™) supplemented with 10% fetal bovine serum (FBS, Gibco™) and 1% penicillin/streptomycin (Gibco™) at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted from the cells using TRIzol reagent (ThermoFisher Scientific).

treatment_protocol: Third passage hDFs were seeded in 24-well plates. At 60-70% confluence, cells were transfected with siRNA control, si-circGLIS3, p-Ctrl, p-circGLIS3 or p-circGLIS3_RNA using Lipofectamine 3000 (ThermoFisher Scientific). After 24 hours, cells were harvested for RNA extraction.

value: Skin

value: Fibroblasts


title: p-circGLIS3_RNA transfected fibroblasts, 1

scan_protocol: Standardized array processing procedures recommended by Affymetrix, including hybridization, fluidics processing, and scanning, were used

source_name: Fibroblasts transfected with plasmid-circGLIS3_RNA


title: p-circGLIS3 transfected fibroblasts, 2

description:
Fibroblasts transfected with plasmid-circGLIS3
ProcessedData.xlsx


title: AMS001 + AHLs R3

value: LB Broth

value: late exponential phase


title: J_BCR


title: F_TCR


title: PolllS2P-KCL-1h-REP1

city: SAN DIEGO

first: Lishuan

address: 9500 Gilman Drive

institute: UCSD

source_name: primary mouse neuronal cells

extract_protocol:
CUT&Tag standard Protocol
PCR Ampfication

tag: antibody

value: PolII(Abcam, ab26721)

value: primary mouse neuronal cells

value: mouse neuronal


title: PolllS2P-KCL-0h-REP1

tag: cell line


title: CDK9-KCL-1h-REP1

value: CDK9(Santa Cruz, sc-13130)


title: CDK9-KCL-0h-REP1


title: I_BCR


title: H_BCR


title: G_BCR


title: L_CELL


title: H3K27Ac-KCL-0h-REP1

value: H3K27Ac(Active motif, 39085)


title: F_BCR


title: KAP1-KCL-1h-REP1

value: KAP1(Abcam, ab22553)


title: H3K27Ac-KCL-1h-REP1


title: I_CELL


title: p-circGLIS3 transfected fibroblasts, 1

source_name: Fibroblasts transfected with plasmid-circGLIS3


title: p-Ctrl transfected fibroblasts, 2

description:
Fibroblasts transfected with plasmid control
ProcessedData.xlsx

value: plasmid control


title: KAP1-KCL-30min-REP1


title: H_CELL


title: p-Ctrl transfected fibroblasts, 1

source_name: Fibroblasts transfected with plasmid control


title: J_CELL


title: Asymptomatic [S22]

city: Karachi

first: Asghar

last: Nasir

state: Sindh

address: Stadium Road

department: Pathology and Laboratory Medicine

country: Pakistan

institute: Aga Khan University

description: gene expression data

hyb_protocol: Clariom S Array Type gene expression, Affymetrix

scan_protocol: GeneChipTM Scanner 3000 7G

data_processing: CEL files were analysed using the TCAS Transcriptome Analysis Software Suite (version 2) using the Summarization Method: Gene Level - SST-RMA Pos vs Neg AUC Threshold: 0.7 against Genome Version: hg38 (Homosapiens)

source_name: blood

growth_protocol: RNA was extracted from whole blood collected in Plasma/EDTA tube.

extract_protocol: Qiagen RNA Blood Mini Kit (Qiagen, GmbH, Germany)

treatment_protocol: no treatment

value: SARS-CoV-2 positive-Human blood

tag: group

value: Asymptomatic


title: Asymptomatic [S20]

description: gene expression data

label_protocol: Clariom S Array Type gene expression, Affymetrix


title: Asymptomatic [S18]

description: gene expression data


title: Asymptomatic [S19]

description: gene expression data


title: Asymptomatic [S21]

description: gene expression data


title: E_TCR

value: Biliary Atresia

value: liver


title: CREB1-KCL-1h-REP1

last: Wang

value: CREB1(Milloipore, 17-600)


title: G_CELL

value: Choledochal Cyst


title: F_CELL


title: KAP1-KCL-0h-REP1


title: IPt_Monocytes_gex_rep1

city: South San Francisco

first: Sandra

last: Melo

address: 1 DNA Way

institute: Genentech, Inc.

data_processing:
cellranger-7.1.0, Cumulus version 2.4.1
Assembly: GRCm38
Supplementary files format and content: h5ad file
Library strategy: CITE-seq

source_name: lung

extract_protocol:
Cells were processed according to 10x Genomics Chromium Single-cell 5′ Gene Expression workflow (V2 version) and, in parallel, Chromium Single-cell V(D)J Enrichment protocol
Cells were processed according to 10x Genomics Chromium Single-cell 5′ Gene Expression workflow (V2 version) and, in parallel, Chromium Single-cell V(D)J Enrichment protocol

treatment_protocol: CD45.1 Csf2raKO mice were transplanted with CD45.2 WT alveolar macrophages. aNotch2 or control antibody was applied IT to the mice. Lung intersitital macrophages, monocytes, and alveolar machrophages were isolated, labeled with CD45.1 and CD45.2 CITE-Seq antibodies and analyzed using the 10x system (5').

value: lung

value: Monocytes

value: Csf2raKO CD45.1 monocytes/macrophages; CD45.2 WT AMs

value: aNotch2 or ctrl antibody

tag: library type

value: mRNA


title: C_TCR


title: D_TCR


title: A_TCR


title: B_TCR


title: E_BCR


title: IPt_InterstitialMacrophages_gex_rep2

value: Interstitial Macrophages


title: IPt_AlveolarMacrophages_gex_rep1

value: Alveolar Macrophages


title: IPt_Monocytes_adt_rep1

data_processing:
cellranger-7.1.0, Cumulus version 2.4.1
Assembly: GRCm38
Supplementary files format and content: h5ad file

value: ADT/HTO

tag: adt

value: CD45.1, CD45.2, mouse IgG2a

tag: hto

value: totalseq-c-anti-mouse-hashtags 1-11


title: Asymptomatic [S16]

description: gene expression data


title: CREB1-KCL-30min-REP1

value: primary mouse neuronal cells

value: mouse neuronal


title: CREB1-KCL-0h-REP1


title: Asymptomatic [S17]

description: gene expression data

value: SARS-CoV-2 positive-Human blood

value: Asymptomatic


title: Asymptomatic [S15]

description: gene expression data


title: D_BCR

value: Biliary Atresia

value: liver


title: Asymptomatic [S11]

description: gene expression data


title: Asymptomatic [S12]

description: gene expression data


title: IPt_AlveolarMacrophages_adt_rep1

value: totalseq-c-anti-mouse-hashtags 1-8


title: IPt_InterstitialMacrophages_adt_rep1

value: lung

value: totalseq-c-anti-mouse-hashtags 1-9


title: Asymptomatic [S14]

description: gene expression data


title: C_BCR


title: E_CELL


title: KO12. Ctla-4 knockout

city: Hangzhou

first: Qin

middle: Lu

last: lu

address: Gudun Road, Xihu District

institute: zhejiang university

data_processing:
The differentially expressed genes (DEGs) were identified with absolute Log2 fold change > 1 and adjusted p-value < 0.05 by R package DESeq2. Gene Ontology (GO) enrichment and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were performed by the OmicStudio (http://www.omicstudio.cn/tool) tools. Gene-set enrichment analysis was performed using software GSEA (v4.1.0, https://www.gsea-msigdb.org/gsea/index.jsp), and the heatmap was generated using the R package ggplot2. For the protein-protein interaction (PPI) networks, the DEGs were retrieved in STRING (version 11.5, https://string-db.org/) database (combined score > 0.4), and the PPI network was visualized by Cytoscape software (version 3.9.1)6. The betweenness centrality (BC) was calculated using the CytoNCA plugin in Cytoscape software.
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: intestine

extract_protocol:
Total RNAs were isolated from wild-type or ctla-4-/- intestines (three biological replicates) using TRIzol reagent following the manufacturer's instructions (Takara).
cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit (NEB), and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio (Hangzhou, China).

value: intestine

value: leukocyte

value: Ctla-4 KO


title: KO11, Ctla-4 knockout


title: D_CELL


title: ATAC-seq_aNS_rep2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 3.0.0a7 with FDR < 0.0001 (Zhang et al., Model-based Analysis of ChIP-Seq). Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded. Remaining peaks were unified to represent a common set of regions for all samples. Counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2). Peaks were annotated with the promoter (TSS +- 5000 nt) of the nearest gene based on Ensembl release 109. Contrasts were created with DESeq2 based on the normalized count peak matrix with all size factors set to one. Peaks were classified as significantly differential at average count > 10 and -1 < log2FC > 1.
Assembly: mm10
Supplementary files format and content: atac_peaks.bed: bed file containing peak positions for TOBIS analysis
Supplementary files format and content: counts.matrix.norm_anno.txt: text file contianing library-size normlaized count on unified peaks

source_name: V-SVZ derived

growth_protocol: Adult neural stem-/progenitor cells were isolated from the lateral walls of the lateral ventricle and propagated in culture medium at 37°C, 5% CO2 in the presence of EGF and FGF2 to allow for the formation of free-floating neurospheres (Schramm and Schulte, 2014, Grebbin et al., 2016).

extract_protocol:
For each of two replicates, cells (10.000/12.000, respectively) were subjected to cell lysis (Tris-HCl 10 mM, NaCl 2 mM, MgCl2 3 mM, Igepal 0.1%) and transposase reaction mix (Nextera) treatment with occasional snap mixing. Following purification of the DNA fragments was done by MinElute PCR Purification Kit (Qiagen).
Amplification of Library together with Indexing Primers was performed as described elsewhere (Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (2013) Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang & William J Greenleaf. Nature Methods. doi:10.1038/nmeth.2688).

treatment_protocol: Adult V-SVZ stem-/ and progenitor cells cultured for 48 h as free-floating aNS were purified by 3% BSA-gradient, and treated with accutase for singularization.

value: V-SVZ derived

value: primary cells

value: aNS cells

value: C57Bl/6J WT


title: C_CELL


title: KO9, Ctla-4 knockout


title: ATAC-seq_aNS_rep1


title: IPt_InterstitialMacrophages_adt_rep2

value: Interstitial Macrophages

value: Csf2raKO CD45.1 monocytes/macrophages; CD45.2 WT AMs

value: aNotch2 or ctrl antibody

value: ADT/HTO

value: CD45.1, CD45.2, mouse IgG2a

value: totalseq-c-anti-mouse-hashtags 1-10


title: Symptomatic [S8]

description: gene expression data

value: SARS-CoV-2 positive-Human blood

value: Symptomatic


title: B_BCR

value: Biliary Atresia

value: liver


title: WT8, control

value: intestine

value: Wildtype


title: Symptomatic [S7]

description: gene expression data


title: Symptomatic [S6]

description: gene expression data


title: Asymptomatic [S9]

description: gene expression data

value: Asymptomatic


title: A_BCR


title: KO, scRNAseq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Leukocytes were collected from the intestine samples through Ficoll-Hypaque (1.080 g/mL) density-gradient centrifugation. Briefly,the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh (Greiner Bio-OneGmbH, Germany). The cell suspension was suspended in Leibovitz's L-15 Medium (L-15, Gibco) supplemented with penicillin (100 U/ml, Sigma-Aldrich), streptomycin (100 μg/ml, Sigma-Aldrich) and heparin sodium (10 U/ml, Sigma-Aldrich). The cell suspension was slowly added into a Ficoll-Hypaque (1.080 g/mL) density-gradient centrifugation, centrifuged at 1,200 g for 25 min, and the cell layer of the interface was carefully aspirated and then washed with ice-cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue (Sigma, St. Louis, MO, USA), which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 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. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: leukocyte

value: Ctla-4 KO


title: Symptomatic [S5]

description: gene expression data


title: WT7, control


title: Symptomatic [S4]

description: gene expression data


title: A_CELL


title: WT1, control


title: B_CELL


title: WT, scRNAseq


title: Symptomatic [S2]

description: gene expression data


title: Asymptomatic [S10]

description: gene expression data


title: Ovary, Chek2KO, IR, rep4

status: Public on Sep 15 2024

city: Bar Harbor

first: Ewelina

last: Bolcun-Filas

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
nf-core/rnaseq (version1.4.3dev)
FastQC (version 0.11.9) was used to determine the quality of the FASTQ files. Adapter trimming  was  conducted with Trim Galore (version 0.6.5). Salmon (version 1.3.0) was  used transcript-level quantitation. RNA-seq data quality control was performed with RSeQC (version 3.0.1) An aggregation of the quality control for the RNA-seq analysis was performed with MultiQC (version 1.9).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes row counts for each sample

source_name: ovary

extract_protocol:
RNA was extracted using miRNeasy micro extraction kit (Qiagen)
Libraries were constructed using the KAPA mRNA HyperPrep Kit (KAPA Biosystems)

value: ovary

value: irradiated 0.5Gy


title: Ovary, Chek2KO, IR, rep5


title: Ovary, Chek2KO, IR, rep3


title: Ovary, Chek2KO, IR, rep2


title: Stereo-seq coronal section

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

description: Fresh frozen Stereo-seq spatial transcriptome sequencing

data_processing:
BGI's SAW pipeline (v7.0.0) was used to process fastq files into resulting gene expression matrices.
Assembly: galGal6
Supplementary files format and content: ipr and tar.gz: BGI formatted image files
Supplementary files format and content: barcodeToPos.h5: Stereo-seq mask file
Supplementary files format and content: counts_bin1.gem: GEM formatted binned counts file including X/Y coordinates
Library strategy: Spatial Transcriptomics (Stereo-seq)

organism: Gallus gallus

source_name: Telencephalon

extract_protocol:
Telencephalons from 15 days old domestic chickens were dissected and immediately snap-frozen in isopentane for 10 min. Afterwards, the telencephalon was embedded in Tissue-Tek OCT cryo embedding compound, 10μm sections were cut using a cryostat and placed on the Stereo-seq chip
Tissue optimization was performed using the Stereo-seq Permeabilization kit according to the manufacturer’s protocol. Following this, the spatial transcriptomics analysis was performed using the Stereo-seq Transcriptomics kit according to the manufacturer’s protocol.

value: Telencephalon

tag: tissue region

value: coronal section

tag: breed

value: broiler


title: Ovary, Chek2KO, IR, rep1


title: Ovary, Chek2KO, nonIR, rep6

value: non-irradiated


title: Ovary, Chek2KO, nonIR, rep5


title: Ovary, Chek2KO, nonIR, rep3


title: Ovary, Chek2KO, nonIR, rep4


title: Ovary, WT, IR, rep6

value: wildtype


title: Ovary, Chek2KO, nonIR, rep1


title: Ovary, WT, IR, rep5


title: Symptomatic [S3]

description: gene expression data


title: Asymptomatic [S13]

description: gene expression data


title: Ovary, WT, IR, rep4


title: Ovary, WT, IR, rep1


title: Ovary, WT, IR, rep3


title: Ovary, WT, nonIR, rep6


title: Ovary, WT, nonIR, rep5


title: Ovary, WT, nonIR, rep3


title: Ovary, WT, nonIR, rep2


title: Ovary, WT, nonIR, rep1


title: Ovary, Chek2KO, nonIR, rep2


title: Ovary, WT, IR, rep2


title: BM_KO2_PMN

city: Munich

first: Johan

last: Duchene

state: - Please Select -

address: Pettenkoferstrasse, 9

department: IPEK

institute: LMU

description: Gene expression data from murine bone marrow nucleated erythroid cells (NEC), monocytes (Mono), and polymorphonuclear neutrophils (PMN)

hyb_protocol: cRNA (> 20 µg) was subjected to hybridization at 45 °C for 16 hours on separate Affymetrix Clariom D Arrays for Mouse, previously known as Affymetrix Mouse Transcriptome Array 1.0 (ThermoFisher, Germany). Microarrays underwent two binding cycles involving anti-Biotin antibodies and a Streptavidin-phycoerythrin conjugate.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® 3000 Scanner (ThermoFisher, Germany).

data_processing: Probe intensities were analyzed with Transcriptome Analysis Console (TAC) software v4.0.2 (ThermoFisher, Germany) following an assessment of quality control metrics. Affymetrix probes were annotated to the mouse genome GRCm38/mm10. Analysis was conducted with TAC default settings and quantile normalization method.

label: Biotin

source_name: bone marrow

label_protocol: The preparation of fragmented Biotin-labeled sense-strand cDNA was carried out using the Affymetrix GeneChip® WT PICO Reagent kit (ThermoFisher, Germany) following the manufacturer's instructions. 2 ng total RNA per sample was spiked with polyadenylated transcripts, subjected to reverse transcription into cDNA, and subsequently converted into cRNA through in vitro transcription.

growth_protocol: ACKR1-deficient mice generated with 129P2/OlaHsd ES cells were backcrossed for more than 10 generations onto a C57BL/6J background and maintained as a heterozygous breed. All experimental procedures were performed with 8- to 12-week-old male mice.

extract_protocol: RNA extraction was carried out using the RNeasy Mini Kit (Qiagen, Germany) following the manufacturer's instructions.

treatment_protocol: Femurs were flushed with PBS, bone marrow cells were stained with lineage markers for NECs, PMNs, and Monos for 30 minutes at 4 °C. On average, 2 x 106 NECs, 1 x 106 PMNs, and 0.5 x 106 Monos were sorted using a FACSAria II instrument (BD Biosciences, Germany). Sorted populations were snap-frozen on dry ice and stored at -80°C.

tag: strain

value: ACKR1 KO

value: PMN

tag: mouse id


title: PmMYB_SELEX_2

city: Fuzhou

first: mao

last: fei

state: Fujian

address: Shangxiadianlu NO.15

department: National Engineering Research Center of JUNCAO

institute: Fujian Agriculture and Forestry University

library_source: other

data_processing:
*library strategy: Systematic evolution of ligands by exponential enrichment (SELEX)
The raw data after removing adaptors and low-quality reads (Q < 20) through Trim Galore were aligned to the Tifleaf3 reference genome (v4) using HISAT2, and gene expression levels were calculated by stringtie using the default parameters.
Adapter and low-quality sequences were filtered out using Trim Galore and the paired-end sequences were merged, followed by importing the sequencing results into Rstudio to remove PCR repeats to obtain clean reads. Enrichments of all 10-mers were computed and de novo motifs were discovered using Autoseed with reported parameters.
Assembly: Tifleaf3 reference genome
Supplementary files format and content: txt(TPM)
Supplementary files format and content: bw

molecule: other

organism: Cenchrus americanus

source_name: MYB

growth_protocol: Pearl millet (accessions: Tifleaf3) were planted in a greenhouse at a density of one plant per pot (filled charcoal soil mixed with vermiculite in a 3:1 ratio), and grown at a temperature of 28 °C during the light period (16 h) and 22°C during the dark period (8 h).

extract_protocol:
To measure gene expressions, 0.2 g of each tissue was collected for RNA-seq.
RNA-seq: Total RNA was extracted from each sample using the RNeasy Plus Mini Kit (Vazyme Biotech, Beijing, China), and cDNA libraries were generated using the NEBNext Ultra RNA Library Prep Kit (NEB).
SELEX-seq: Using 2 µL of fusion protein mixed with 6 µL of SELEX initial library (101 bp, 30 ng/µL) and 30 µL of TCAPT buffer (140 mM KCl, 5 mM NaCl, 1 mM MgCl2, 3 µM ZnSO4, 100 µM EGTA, 10 mM Tris, pH 8, 0.1% Tween), incubation was performed at 25 °C for 1 h. The DNA-protein complex was then enriched using Halo-tagged magnetic beads (Promega, G7282) and washed with a HydroSpeed plate washer (Tecan, 30190101) to remove DNA fragments that non-specifically bind to the protein. The specifically bound DNA fragments on the beads were then amplified using PCR, and then used as the input library for the next round of SELEX.

value: MYB


title: PmMYB_SELEX_1


title: BM_KO2_NEC

value: NEC


title: LS9_2

data_processing:
The raw data after removing adaptors and low-quality reads (Q < 20) through Trim Galore were aligned to the Tifleaf3 reference genome (v4) using HISAT2, and gene expression levels were calculated by stringtie using the default parameters.
Adapter and low-quality sequences were filtered out using Trim Galore and the paired-end sequences were merged, followed by importing the sequencing results into Rstudio to remove PCR repeats to obtain clean reads. Enrichments of all 10-mers were computed and de novo motifs were discovered using Autoseed with reported parameters.
Assembly: Tifleaf3 reference genome
Supplementary files format and content: txt(TPM)
Supplementary files format and content: bw

source_name: stalk

value: stalk


title: Ovary, WT, nonIR, rep4


title: BM_KO1_NEC


title: BM_KO5_Mono

value: Mono


title: LS9_1


title: BM_WT3_PMN


title: BM_WT3_NEC


title: LS8_2


title: Control_RNAseq_replicate2

city: Armilla

first: Elena

last: Gómez-Díaz

state: Granada

address: Avda. del Conocimiento, 17

department: Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN)

country: Spain

institute: Spanish National Research Council (CSIC)

data_processing:
Quality control of RNA-seq data was performed with FastQC v0.11.9. A replicability test based on correlation analysis and principal component analysis (PCA), support the use of the different samples as replicates.
We used SortMeRNA v4.2.0 to determine and eliminate possible ribosomal RNA contamination.
Filtered reads were mapped to the reference genome (Anopheles gambiae PEST genome, version P4.12) available in VectorBase (release 53), using Salmon v.0.11.2.
This software is specifically used for the alignment and quantification of isoforms and was run using the standard parameters -l A --validateMappings --go 4 --mismatchSeedSkip 5.
For this analysis we applied a conservative filter, only isoforms with a count value greater than 10 were considered as being expressed
Assembly: AgamP4.12 (VectorBase)

organism: Anopheles gambiae

source_name: salivary glands

growth_protocol: Three- to five-day-old female A.gambiae mosquitoes were sourced from an outbred colony established in 2008 and repeatedly replenished with F1 from wild-caught mosquito females collected in Kou Valley (11°23'14"N, 4°24'42"W), 30 km from Bobo-Dioulasso, south-western Burkina Faso (West Africa). Mosquitoes were maintained under standard insectary conditions (27 ± 2°C, 70 ± 5% relative humidity, 12:12 LD)

extract_protocol:
Dissection of mosquito midguts and salivary glands was performed in situ on adult females at 7 days post-blood meal. To determine infection levels, mosquito guts were dissected 7 days after blood feeding and were stained with 2% Mercurochrome before microscopic examination. Tissues were maintained in ice-cold Schneider’s insect culture medium (Sigma-Aldrich) and fresh tissues were immediately processed for chromatin and RNA analyses
Total RNA was extracted from fresh mosquito tissues (~25 midguts and ~ 50 salivary glands) using the mirVana™ RNA Isolation Kit (Ambion®) according to the manufacturer protocol and used for mRNA library preparation. RNA concentration was quantified using a Qubit® 2.0 Fluorometer, and RNA integrity was determined with an Agilent 2100 Bioanalyzer. Illumina libraries were prepared and sequenced at the HudsonAlpha Institute for Biotechnology, using an Illumina HiSeq2000 sequencer, standard directional RNA-seq library construction, 50 bp paired end reads with ribosomal reduction (RiboMinus™ Eukaryote Kit, Ambion®)

treatment_protocol: Females were fed through membranes on gametocyte-infected blood from malaria patients. To eliminate transmission-blocking factors, venous blood was collected and the serum was replaced by a non-immune AB serum to avoid transmission of human blocking factors

value: salivary glands

tag: time

value: 14 days

tag: infection status

value: Non-infected

tag: replicate


title: BM_KO5_NEC


title: BM_KO3_Mono


title: Control_RNAseq_replicate1

tag: tissue


title: BM_WT3_Mono

tag: cell type


title: BM_WT2_NEC


title: BM_KO1_Mono


title: BM_KO5_PMN


title: LS8_1

tag: genotype


title: BM_WT2_Mono


title: BM_KO4_PMN


title: BM_WT4_NEC


title: BM_WT1_PMN


title: BM_WT1_Mono


title: Infection_RNAseq_replicate1

value: Infected


title: LS7_2

tag: treatment


title: LS7_1


title: PWH-4-t3-HIV1

city: Baltimore

first: Annukka

last: Antar

state: MD

address: 733 North Broadway Room 869

department: Medicine - Infectious Diseases

institute: Johns Hopkins School of Medicine

data_processing:
Proprietary to Adaptive Biotech. See these papers, PMID: 24157944 and PMID: 19706884
Supplementary files format and content: tab-deliminated text file includes productive and unproductive CDR3 TCRβ sequences (unproductive sequences not used in manuscript)

source_name: CD4 T Cell

extract_protocol:
Genomic DNA was isolated (QIAamp DNA Mini or Micro kit, Qiagen, or Quick-DNA Miniprep, Zymo Research) from sorted cells, quantified (Qubit 3.0 or 4 fluorometer, dsDNA quantitation, high sensitivity or broad range assays, ThermoFisher Scientific, or by NanoDrop 2000 spectrophotometer, ThermoFisher Scientific) and diluted in Tris-acetate-EDTA to a concentration of 10-50 ng/μL (for a total of up to 1-3 μg per sample).
Proprietary to Adaptive Biotech. See these papers, PMID: 24157944 and PMID: 19706884

value: CD4 T Cell

tag: hiv serostatus

value: Positive

tag: cmv serostatus

tag: Sex

value: female


title: BM_WT2_PMN


title: LS6_1


title: LS6_2


title: LS5_2


title: PWH-4-t3-HIV3


title: PWH-4-t3-CMV2


title: PWH-4-t3-HIV2


title: LS4_2


title: LS5_1


title: Infection_RNAseq_replicate2


title: PWH-4-t3-CMV3


title: LS4_1


title: LS3_2


title: PWH-4-t3-CD3CD28-2


title: PWH-4-t3-CD3CD28-3


title: IPt_InterstitialMacrophages_gex_rep1

value: lung

value: Interstitial Macrophages

value: Csf2raKO CD45.1 monocytes/macrophages; CD45.2 WT AMs

value: aNotch2 or ctrl antibody

tag: library type

value: mRNA


title: PWH-4-t3-DMSO2


title: PWH-4-t3-CD3CD28-1


title: PWH-4-t3-no stim


title: LS3_1


title: LS2_1


title: LS1_2


title: PWH-1-t3-DMSO1

value: male


title: PWH-4-t3-DMSO3


title: PWH-1-t3-HIV1


title: TS5_2


title: TS6_1


title: TS6_2


title: LS1_1


title: PWH-4-t3-CMV1


title: PWH-1-t3-DMSO3


title: TS4_2


title: PWH-1-t3-CMV1


title: PWH-1-t3-HIV2


title: TS4_1


title: PWH-1-t3-DMSO2


title: Ovary, Chek2KO, IR, rep6

value: ovary

value: irradiated 0.5Gy


title: PWH-1-t3-CMV2


title: TS3_2

value: stalk


title: TS2_2


title: PWH-1-t3-CMV3


title: TS3_1


title: TS2_1


title: PWH-1-t3-CD3CD28-2


title: PWH-4-t3-DMSO1


title: PWH-1-t3-no stim


title: TS1_2


title: TS1_1


title: PWH-1-t3-HIV3


title: PWH-1-t3-CD3CD28-1


title: PWH-1-t3-CD3CD28-3


title: PWH-1-t2-rmCD4


title: PWH-1-t1-rmCD4


title: SS2_2


title: SS3_1


title: TS5_1


title: PWH-1-t0-rmCD4


title: SS1_2


title: SS2_1


title: SS1_1


title: PWH-3-t1-rmCD4


title: PWH-3-t0-rmCD4


title: PWH-2-t1-rmCD4


title: PWH-2-t2-rmCD4


title: PWH-2-t0-rmCD4


title: FS1_2


title: PWH-4-t1-rmCD4


title: PWH-4-t0-rmCD4


title: FS1_1


title: DEL-19-rmCD4


title: DEL-12-rmCD4


title: LS2_2


title: Aeromonas veronii, ArgR, ChIP

city: Haikou City, Hainan Province

first: Chaolun

last: Liu

address: 58 Minlan Road, Haikou City, Hainan Province, China

institute: Hainan University

data_processing:
Basecalls were perforemed using bcl2fastq v2.17 for novaseq output.
Raw data were trimmed using Trimmomatic v0.39 to proceed  the removal of adapter contamination, reads filtering(remove reads with N≥10%) and quality filtering (remove reads with Q-score>20) .
The clean data were aligned to the genome of Aeromonas veronii strain C4 using Bowtie2 v2.4.4.
Peaks were called using MACS2 (v2.1.2).
Assembly: the genome of Aeromonas veronii strain C4
Supplementary files format and content: Excels file that inclue ArgR_peaks information

organism: Aeromonas veronii

source_name: strain C4

growth_protocol: Cells were cultured in LB at 30 ℃

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After  cell lysis, chromatin was sonicated using micrococcal nuclease and ultrasonic treatment.
The construction of a ChIP-Seq library primarily involved the following steps: Cell crosslinking by methyl alcohol, cell lysis and fragmentizing the DNA into 200-1000 bp, protein immunoprecipitation, co-immunoprecipitation complex DNA extraction, and the construction of a DNA sequencing library were performed using Illumina Hiseq.

tag: cell line

value: strain C4

value: prokaryotic cell

tag: chip antibodiy


title: PWH-4-t2-rmCD4


title: DEL-17-rmCD4


title: DEL-15-rmCD4


title: SS3_2


title: PWH-3-t2-rmCD4


title: Neurospora crassa Crf4-3 mutant, KTC, rep 2

city: Beijing

first: pengju

last: YU

address: No.1 Beichen West Road

institute: Institute of Microbiology, Chinese Academy of Sciences

data_processing:
Basecalling was performed using a software developed for DNBSEQ-T7.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2, then mapped to Neurospora crassa whole genome (GCA_000182925.2) using HISAT v2.0.4 with parameters -p 8 --phred64 --sensitive -I 1 -X 10000
After analyzing the efficiency of aligned clean reads to reference genome by Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200, gene expression were calculated as Fragments Per Kilobase of exon per Megabase of library size (FPKM) using RSME v1.2.12 with default parameters.
Differential expressed genes were caracterized using a protocol from Audic S. et al., Genome Research, 1997.
Assembly: GCA_000182925.2
Supplementary files format and content: excel file include FPKM values for all Samples and data for differential expressed genes between each two Samples, as well as the annotation of each genes.

organism: Neurospora crassa

source_name: mycelia

growth_protocol: Briefly, 14 small pieces of mycelial mats (1-2 mm2) were grown in liquid Vogel’s medium for 12 h and then treated with or without sterol biosynthesis inhibitors for 12 h.

extract_protocol:
Harvested samples were immediately frozen, and then ground into fine powder in liquid nitrogen. Total RNA extraction was performed according to the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Ketoconazole (Sigma) was added, with final concentration of 1.5 μg/mL.

value: mycelia

value: Crf4-3 knockout

value: Ketoconazole


title: Neurospora crassa Crf4-3 mutant, KTC, rep 3


title: Symptomatic [S1]

description: gene expression data

value: SARS-CoV-2 positive-Human blood

tag: group

value: Symptomatic


title: DEL-18-rmCD4

value: CD4 T Cell

value: Positive


title: Ctl-4-t2-rmCD4

value: Negative

value: female


title: Neurospora crassa Crf4-3 mutant, Control, rep 3

value: No treatment


title: Neurospora crassa Crf4-3 mutant, Control, rep 2


title: DEL-13-rmCD4


title: Ctl-4-t1-rmCD4


title: Neurospora crassa Crf4-3 mutant, Control, rep 1


title: Aeromonas veronii, Input, ChIP

value: Flag


title: Ctl-4-t0-rmCD4


title: Neurospora crassa, KTC, rep 3

value: WT


title: Ctl-4-t1-rCD4


title: Neurospora crassa, KTC, rep 2


title: Neurospora crassa, KTC, rep 1


title: Neurospora crassa, Control, rep 3


title: Ctl-3-t2-rCD4

value: male


title: Neurospora crassa, Control, rep 2


title: DEL-16-rmCD4


title: Ctl-3-t1-rCD4


title: Dox22W_G1825_ST

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

data_processing:
The sequencing outputs for all Visium datasets were preprocessed using SpaceRanger-v2.1.0 and mapped to mouse reference genome (mm10). Filtered matrices were used for downstream analyses.
Assembly: mm10
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
Library strategy: Spatial Transcriptomics Visium 10x genomics

source_name: Pancreas

growth_protocol: Pancreas-specific p48Cre; KrasLSL-G12D; Rosa26LSL-rtTA; Tg (TetO-GnasR201C) mice were fed with 60 PPM of Dox diet starting from 8 weeks of age and maintained till 22 weeks of age and samples were collected, corresponding control mice were fed normal diel

extract_protocol:
Samples were fixed with PFA and H&E stained. After sectioning onto the Visium slides, sample processing was performed as described in the Visium 10x Genomics protocol for FFPE samples.
Library preparation was performed as described in Visium Spatial for FFPE Gene Expression kit mouse transcriptome (10X Genomics).  After library preparation, samples were pooled and sequenced using NovaseqX plus (Ilumina, CA, USA).

value: Pancreas

value: doxycycline feed

tag: gender

value: Female

tag: age

value: 5 Months 4 days


title: P9

city: Worcester

first: Michael

last: Frisoli

state: Massachusetts

address: 364 Plantation St.

department: Dermatology

institute: University of Massachusetts Chan Medical School

description: Illumina NextSeq550, NextSeq2000, NovaSeq6000. (See meta.data.tsv for cell source)

data_processing:
https://github.com/garber-lab/inDrop_Processing
Assembly: hg38_v34
Supplementary files format and content: 10x format with additional `meta.data.tsv` containing single cell metadata available on series record.
Supplementary files format and content: 10x file format for each individual, available on sample record.

extract_protocol: inDrop protocol as described by Zilionis et al. and Gellatly et al. (https://pubmed.ncbi.nlm.nih.gov/27929523/, https://pubmed.ncbi.nlm.nih.gov/34516831/).

value: suction skin blister fluid


title: Neurospora crassa Crf4-3 mutant, KTC, rep 1

value: mycelia

value: Crf4-3 knockout


title: Neurospora crassa, Control, rep 1


title: Dox22W_G1817_ST

value: Male


title: P8


title: Ctl-3-t2-rmCD4


title: NoDox22W_G1796_ST

value: normal feed

value: 5 Months 7 days


title: P5


title: Ctl-3-t1-rmCD4

value: CD4 T Cell

value: Positive


title: P6


title: P4


title: P7


title: NoDox22W_G1743_ST


title: P3


title: Ctl-3-t0-rmCD4

value: Negative


title: MD24, scRNAseq

city: St Leonards

first: Jose Antonio

last: Lopez-Escamez

state: NSW

address: 10 Westbourne St

department: Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute

country: Australia

institute: The University of Sydney

description: 10 X Genomics

data_processing:
The cellranger-arc mkfastq.gz function from Cell Ranger ARC V.2.0.0 was used to demultiplex Illumina’s base calling files (BCL) into a fastq.gz format for downstream analysis. FASTAQ files were analyzed using Cell Ranger ARC v.2.0.2 and aligned with GRCh38 for the human genome reference, as per 10x Genomics guidelines to generate a filtered matrix file for downstream analysis.
Assembly: GRch38
Supplementary files format and content: H5 files

source_name: Blood

extract_protocol:
PBMCs were thawed and diluted in RPMI + 10% FBS, and cells were counted. To eliminate granulocytes with extracellular DNA, we sorted cells stained in CD66. We continued to isolate the nuclei from a million cells per sample. Briefly, we centrifuged cells (300rcf 5min 4C). The supernatant was removed, replaced with 1 mL refrigerated lysis buffer, and incubated for 3 min before resuspension. The nuclei were centrifuged again (500 rcf, 4°C, 5 min). The pellet was resuspended in 1 mL Diluted Nuclei Buffer and passed through a 40 μm cell strainer. All steps were performed on ice. Nuclei were stained and counted. Nuclei were collected into 10% BSA. 1 U/mL RNase inhibitor (Sigma–Aldrich, 03335402001) was added to all final solutions
RNA libraries were generated from amplified cDNA. Pair-end sequencing for the 24 samples was performed by using a Hiseq X Illumina sequencing platform.

value: Blood

tag: disease

value: Meniere Disease

value: PBMC


title: Ctl-2-t2-rCD4

value: male


title: P1


title: P2


title: Ctl-4-t2-rCD4

value: female


title: MI23, scRNAseq

description: 10 X Genomics

value: Migraine


title: Ctl-2-t1-rCD4


title: CB48


title: CB46


title: HC22, scRNAseq

description: 10 X Genomics

value: healthy


title: Ctl-2-t1-rmCD4


title: CB44


title: CB43


title: Ctl-2-t0-rmCD4


title: CB27


title: HC21, scRNAseq

description: 10 X Genomics


title: CB23


title: HC20, scRNAseq

description: 10 X Genomics


title: Ctl-2-t2-rmCD4


title: CB22


title: HC19, scRNAseq

description: 10 X Genomics


title: CB21


title: Ctl-1-t2-rCD4


title: CB19


title: CB20


title: MD18, scRNAseq

description: 10 X Genomics


title: MD17, scRNAseq

description: 10 X Genomics


title: CB17


title: Hela-WT-Input2

city: wuhan

first: linjian

last: xia

address: wuhan

institute: wuhan University

data_processing:
Quality control of Ψ-RIP Seq data was performed using FastQC. Low quality bases and adaptor contamination were deleted by Trimmomatic (v. 0.33.0) . Raw Sequencing reads were aligned using Hisat2 (v. 2.1.0) to the hg38, mm10, dm6 or spike-in reference genome. The mapped reads were filtered with Picard (http://broadinstitute.github.io/picard, v. 2.16.0) to remove PCR duplicates and SAMtools (v. 1.7)  to remove the reads with mapping quality below 30. METPEAK was used to identify peaks .
For RIP-seq, reads mapping and processing were performed as described for Ψ-RIP Seq data above. MACS2  was used to identify peaks.
For RNA-seq,  reads mapping and processing were performed as described for Ψ-RIP Seq data above. FeatureCounts (v. 1.6.3) was used to calculate the number of reads mapped to each gene. Dapars were used to calculate APA events.
Genome_build: hg38/mm10/dm6

source_name: Hela

growth_protocol: HEK293T and HeLa cells were grown in DMEM medium (C11995500BT, Gibco) containing 10% FBS (Biological Industries) and 1% Penicillin-Streptomycin (15140-122, Gibco) at 37°C with 5% CO2. Mouse embryonic stem cells (mESCs) E14TG2a were cultured with N2 (17502048, Gibco), B27 (17504044, Gibco) base medium supplemented with 1× GlutaMAX (35050061, Gibco), 1× MEM Non-Essential Amino Acids (11140050, Gibco), 0.15 mM L-thioglycerol (M6145, Sigma), 1% Penicillin-Streptomycin (15140-122, Gibco), 25 μg/ml BSA (A1933, Sigma), 1μM MEK inhibitor PD0325901 (S1036, Selleck Chemicals), 3μM GSK3β inhibitor CHIR99021 (S1263, Selleck Chemicals), 2% KOSR (A3181502, Gibco) and 1000 U/ml ESGRO leukemia inhibitory factor LIF (ESG1107, Millipore) on plates coated with 0.2% gelatin (V900863, Sigma) at 37°C with 5% CO2.

extract_protocol:
For RNA-seq, total RNA was extracted with TRNzol reagent (DP424, Tiangen). For Ψ-RIP seq, total RNA was extracted with TRNzol reagent (DP424, Tiangen). mRNA was isolated from the total RNA using the Dynabeads mRNA Purification Kit (61006, Invitrogen) for two round of poly(A)+ RNA selection and then using the RiboMinus Transcriptome Isolation Kit (K155002, Invitrogen) for rRNA depletion. RNA was fragmented into 150-300 nt fragments and incubated with anti-Pseudouridine mAb (D347-3, MBL). Then the mixture was subjected to Dynabeads protein G binding. After washing, the bound RNA was eluted by competition with Pseudouridine (HY-113061, MCE). RNA was recovered with Hieff NGS RNA Cleaner (12602ES03, Yeasen). For CFIm25-RIP seq, flag-3C-HA-CFIm25 stable overexpression HEK293T cells were crosslinked in 0.5% formaldehyde containing PBS. After DNase I treated, sonicated, incubated with MonoRab Anti-DYKDDDDK Affinity Resin (L00766, GenScript) and extensive washed, RNA was eluted by Recombinant HRV 3C Protease (S3CP01, SinoBiological ) cleavage.
RNA-seq libraries were generated using  NEBNext Ultra II RNA Library Prep Kit (E7770, NEB ). RIP-seq libraries were generated using SMARTer Stranded Total RNA-Seq Kit v2 -Pico Input Mammalian (Takara) following the manual.

treatment_protocol: NC/CFIm25 shRNA knockdown cells were generated by lentiviral infection and puromycin selection.

value: Hela

value: untreated

tag: protocol

value: RIP

tag: rip reagent


title: Ctl-1-t1-rmCD4


title: Hela-WT-IP2

value: anti-Pseudouridine mAb (D347-8, MBL)

tag: replicate


title: MI16, scRNAseq

description: 10 X Genomics

tag: tissue


title: Hela-WT-IP1

value: anti-Pseudouridine mAb (D347-7, MBL)


title: MD15, scRNAseq

description: 10 X Genomics

tag: cell type


title: Hela-WT-Input1


title: 293T-WT-Input2


title: Ctl-1-t2-rmCD4


title: MI14, scRNAseq

description: 10 X Genomics


title: 293T-WT-Input1


title: CB31

value: suction skin blister fluid


title: 293T-WT-IP2

value: anti-Pseudouridine mAb (D347-4, MBL)


title: 293T-WT-IP1

value: anti-Pseudouridine mAb (D347-3, MBL)