title: B16F10_Combi_TRX_3

description: Library name: 7797_12_TRX_2_3

value: TRX


title: Sbj1_mAb19

status: Public on Apr 09 2025

type: protein

city: Siena

first: Viola

last: Viviani

address: Via Fiorentina, 1

country: Italy

institute: GSK

description: MENB NEXT GEN-001 (V114_01) 205285/ETR

hyb_protocol: Protein arrays were first blocked 60 min in Blocking Buffer (Block it, Arrayit). The array was then incubated 1h a room temperature (RT) with mAbs diluted 0,5 ug/ml for anti-human IgG-specific analysis. After two washing with 0.1% Tween in PBS buffer (TPBS), arrays were incubated with an AlexaFluor 647-conjugated IgG anti-human (1:800 – Jackson Immunoresearch) at RT for 1 h to detect interactions. Slides were washed again as before and washed once in PBS, then rinsed in sterile water and dried.

scan_protocol: Fluorescence signals were detected by using a InnoScan 710AL (Innopsys) and the 16-bit images were generated with Mapix software at 10 µm per pixel resolution.

data_processing: Images were processed using ImaGene 9.0 software (Biodiscovery Inc, CA, USA). Elaboration and analysis of image raw fluorescence Intensity (FI) data  was performed using in-house developed R scripts. For each protein the fluorescence intensity data of the replicates was subtracted by local background values surrounding each spot and averaged, hence resulting in a single data point per sample named Mean Fluorescence Intensity (MFI).

label: AlexaFluor 647-conjugated anti-human IgG secondary antibody

molecule: protein

organism: Homo sapiens

source_name: recombinant HumAbs

label_protocol: The secondary antibody used for arrays was from Jackson Immunoresearch, (872 W Baltimore Pike, West Grove, PA 19390 USA). It was conjugated to the Alexafluor dye (Alexa 647) by the company.

extract_protocol:
Protein extracted from samples.
Briefly: bacterial pellets were either resuspended in equilibration buffer (50?mM NaH2PO4 and 300?mM NaCl, pH 8.0) before mechanical lysis by sonication or resolubilized in B-PER Bacterial Protein Extraction Reagent (B-PER, Thermo Fisher, 1?g/10?ml) or Cell-Lytic Express (Sigma-Aldrich). The unbroken cells and bacterial debris were removed by centrifugation and proteins were purified from the supernatant by IMAC (immobilized metal-ion-affinity chromatography) purification using cobalt-based chelating columns (Hitrap TALON Crude; Merck) according to the manufacturer?s instructions. Columns were washed with equilibration buffer, and proteins bound to the resin were then eluted with imidazole gradient (from 0?mM to 250?mM imidazole) in equilibration buffer. Samples were dialyzed in PBS. The recombinant PorA and PorB proteins were instead purified from inclusion bodies. PorA bacterial pellets were dissolved in Guanidine 6?M, 50?mM Tris-HCl, pH 8.5, whereas PorB bacterial pellets were lysed in 8?M Urea, 50?mM Tris-HCl, pH 8,0. The solubilized inclusion bodies were concentrated in an Amicon concentrator, 10?kDa cutoff (Millipore). Then samples were diluted into a refolding buffer (200?mM CAPS, 400?mM NaCl, 50?mM Tris-HCl, 0.3% Lauryl-N,N-dimethylamine-N-Oxide [LDAO], pH 11). The mixtures were stirred ON at 4?°C and the pH was adjusted to 8.0 with 1?N HCl. The refolded porins were loaded onto an IMAC column (HisTrap HP, GE Healthcare), washed with PBS?+?0,1% LDAO (PBSL) and eluted with PBSL containing 300?mM imidazole. The samples were concentrated with Amicon (10?kDa cutoff) and then loaded onto an S-300 Sephacryl column (GE Healthcare) and the protein was eluted in 0,1% PBSL.

treatment_protocol: Recombinant expressed monoclonal antibodies in mammalian cells

tag: subclass

tag: cell type

value: PBMC


title: B16F10_Combi_TRX_2

type: SRA

city: Amsterdam

first: Judy

last: van Beijnum

state: Noord Holland

address: CCA rm 2.52, De Boelelaan 1118

department: Medical Oncology

country: Netherlands

institute: VUMC

description: Library name: 7797_11_TRX_2_2

library_source: transcriptomic

data_processing:
bcl2fastq2 versie v2.15.0.4
Assembly: mm10
Supplementary files format and content: tab delimited text file containing raw counts for all samples

molecule: total RNA

organism: Mus musculus

source_name: sc. Flank tumor

growth_protocol: B16F10 and CT26 cells were maintained in DMEM supplemented with 10% FCS and 1% Pen/Strep and glutamine supplements. 1e5 tumor cells were injected in the flank of C57BL/6 or Balb/C mice and harvested 3 weeks p.i.

extract_protocol:
RNA was extracted using Trizol according to the manufacturers instructions
TruSeq RNA Library Prep Kit v2 (Illumina Inc., San Diego)

treatment_protocol: Mice were vaccinated with recombinant proteins

tag: tissue

value: sc. Flank tumor

tag: cell line

value: Mouse melanoma

tag: genotype

value: WT

tag: treatment

tag: batch


title: WT_2

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

country: Germany

institute: Institute for Bioinformatics and Medical Informatics

description: QELSC080A9_20231031153015__13__A_balh_WT_37h_S274

data_processing:
All reads mappings were performed against our own unpublished Amycolatopsis balhimycina genome.
The mappings of all samples were conducted with HISAT2 v2.1.0. Spliced alignment of reads was disabled (HISAT2 parameter --no-spliced-alignment). Library type was set to reverse (--rna-strandness).
resulting mapping files in SAM format were converted to BAM format using SAMtools v1.9
Gene counts for all samples were computed with featureCounts v1.6.443 based on the annotation of the respective reference genome, where the selected feature type was set to transcript records (featureCounts parameter -t transcript)
Assembly: own unpublished Amycolatopsis balhimycina genome
Supplementary files format and content: counts.txt: A tab separated matrix with samples as columns and genes as rows

organism: Amycolatopsis balhimycina

source_name: bacterial cell

growth_protocol: A. balhimycina wildtype, Δtba and Δbbr were cultivated in balhimycin production conditions for 37 h

extract_protocol:
RNA was extracted using the “Zymo Quick RNA Fungal/Bacterial Kit” (Zymo Research, CN#R2014) according to the manufacturer’s instructions. The RNA integrity was checked by agarose gel electrophoresis and residual DNA was removed by DNAseI treatment using the “DNA-free™ DNA Removal Kit” (ThermoFischer, CN#AM1906). Successful digestion was initially checked by PCR. The total RNA was quantified with a “Qubit RNA BR Assay Kit” (Thermo Fisher) and RNA integrity was checked by an Agilent 2100 BioAnalyzer with the “RNA 6000 Pico kit” (Agilent).
Library preparation and ligation were performed using “Illumina Stranded Total RNA Prep” and “Ribo-Zero Plus Microbiome”, respectively, according to the manufacturer’s instructions. In brief, 100 ng of total RNA per sample were subjected to rRNA depletion, followed by cDNA library construction, adapter ligation, and 15 cycles of barcoding PCR. The obtained libraries were quantified with the “Qubit 1x DNA HS Assay Kit” (Thermo Fisher) and the fragment distribution was checked with an Agilent 2100 BioAnalyzer using the “High Sensitivity DNA Kit” (Agilent). Libraries were subsequently pooled and sequenced on an Illumina NovaSeq 6000 device using “NovaSeq 6000 SP Reagent Kit” (v1.5) (100 cycles) with a run mode 75,10,10,0. The average number of reads obtained was 13-21x106. The sequencing was demultiplexed with the latest version of the nextflow pipeline: nf-core/demultiplex. For demultiplexing, “bcl2fastq” was used and the quality was checked with “fastp”.

value: bacterial cell

value: untreated


title: WT_1

description: QELSC079A6_20231031153015__11__A_balh_WT_37h_S273


title: H3K4Me3 CUT&RUN Repeat 3

city: Sioux Falls

first: Louis-Jan

last: Pilaz

state: SD

address: 2301 E 60th Street North

department: Pediatrics and Rare Disease

country: USA

institute: Sanford Research

description:
Library name: Sample 6
ZBTB7A CUT&RUN

library_source: genomic

data_processing:
trimming with Trim Galore
mappping with Bowtie2
read counts measured with featureCounts
merging all repeats together
1x normalization with bamCoverage
Assembly: mm10
Supplementary files format and content: Bedgraph files
Library strategy: CUT&Run

molecule: genomic DNA

source_name: E12 Embryonic Cortex

growth_protocol: Embryonic day 12 mouse cortices (n=3 each group) were dissected, and cells were dissociated with the Accumax (Sigma-Aldrich A7089) following the manufacturer’s instructions. CUT&RUN was performed according to the published protocol (Skene and Henikoff 2017, eLife) (n=3 biological replicates/antibody/genotype). 10,000 cells were used for each experiment, and 3 biological replicates were performed for each antibody and genotype.

extract_protocol:
Skene and Henikoff 2017, eLife
DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645, E7103) with index primers (NEB, E7645-S). Pippen size selection was used to remove the primer dimers.

value: E12 Embryonic Cortex

value: CD1 strain


title: BMDM_Ctr-1

city: Chicago

first: Rengul

last: Cetin-Atalay

address: 5841 S. Maryland Avenue

department: Medicine

institute: The University of Chicago

data_processing:
RNA-seq reads were pseudoaligned using kallisto 0.46.1
The Kallisto index was made with default parameters and the GENCODE (Release 39 (GRCh38.p13) and was run in quant mode with default parameters
Assembly: Mus_musculus_GRCm39
Supplementary files format and content: tsv

source_name: BMDM

growth_protocol: RPMI 1640  supplemented with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
Total
Oligo-dT mRNA directional

treatment_protocol: 1µg/ml 4-Hydroxytamoxifen

value: BMDM

value: Primary

value: Macrophage

value: Ctr


title: delta_bbr_2

description: QELSC084A7_20231031153015__32__A_balh_delta_bbr_37_h_S286

value: delta bbr

value: genetic modification (knockout)


title: B16F10_Combi_TRX_1

description: Library name: 7797_10_TRX_1_3


title: H3K4Me3 CUT&RUN Repeat 2

description:
Library name: Sample 5
ZBTB7A CUT&RUN


title: H3K4Me3 CUT&RUN Repeat 1

description:
Library name: Sample 4
ZBTB7A CUT&RUN


title: B16F10_Combi_FBN2_3

description: Library name: 7797_9_FBN2_14_3


title: RNA-seq Control ovary rep 3

city: Paris

first: Hélène

last: Lopez-Maestre

address: 25-28 rue du Dr Roux

country: France

institute: Institut Pasteur

data_processing:
adapter trimming using cutadapt (options -m 25 -O 6 --trim-n --max-n 1 -q 30), two-pass alignment using STAR (--outFilterMismatchNoverLmax 0.05 --outFilterMultimapNmax 50); counting using TEtranscripts (--mode multi)
Assembly: AaegL5 (VectorBase release 61)
Supplementary files format and content: Tab-separated counts for each gene/TE and each library

molecule: polyA RNA

organism: Aedes aegypti

source_name: Ovary

growth_protocol: 12h/12h light-dark cycle at 28℃ at 70-80% humidity

extract_protocol:
20 dissected tissues pooled and subject to TRIzol (Life Technologies) extraction; RNA for RNA-seq was treated with DNase I (Invitrogen); 200-500ng of DNase I-treated RNA used for RNA-seq library prep;
Illumina Stranded mRNA Prep kit

treatment_protocol: Ad libitum access to 10% sucrose solution

value: Ovary

value: Wild-type

value: Sugar-fed 5-8d post emergence


title: RNAseq_heart_hete-rep1

city: Guangzhou

first: HongXin

last: Zhong

address: No. 190, Open Source Avenue, Luogang District, Guangzhou, China

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

description:
8w_hete1
heart tissue from 8-week-old mice

data_processing:
Paired-end reads were handled with Trim Galore, and then mapped to mouse (mm10) genome using STAR aligner.
Transcript abundance were quantified using RSEM. Differentially expressed genes (DEGs) were determined using DESeq2.
Assembly: mm10
Supplementary files format and content: Comma-separated text file includes TPM values.

source_name: heart

growth_protocol: Mice were housed in a specific pathogen-free (SPF) facility with a 12h dark/12h light cycle and provided with food and water ad libitum.

extract_protocol:
Total RNAs from each mouse tissue were extracted, and were purified by two rounds of mRNA purification with mRNA capture beads to ensure removal of rRNA.
RNA-seq libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina, and the method was performed according to the manufacturer's instructions.

treatment_protocol: CTCF-R567W mutation were generated by CRISPR/Cas9-mediated genome editing.

value: heart

tag: age

value: 8 weeks

value: Ctcf heterozygous


title: B16F10_Combi_FBN2_2

description: Library name: 7797_8_FBN2_13_5

value: sc. Flank tumor

value: Mouse melanoma

value: WT


title: RNA-seq Control ovary rep 2


title: RNAseq_heart_hete-rep2

description:
8w_hete2
heart tissue from 8-week-old mice


title: ZBTB7A CUT&RUN Repeat 3

description:
Library name: Sample 3
ZBTB7A CUT&RUN

value: E12 Embryonic Cortex


title: B16F10_Combi_FBN2_1

description: Library name: 7797_7_FBN2_13_4


title: RNA-seq Control ovary rep 1


title: RNAseq_heart_wt-rep2

description:
8w_wt2
heart tissue from 8-week-old mice

value: wild type


title: BMDM_FG-2

value: BMDM


title: RNAseq_heart_wt-rep1

description:
8w_wt1
heart tissue from 8-week-old mice


title: CT26_LOX_3

description: Library name: 7797_6_LOX_6_2

value: Mouse colrectal cancer

value: TRXtr-LOX


title: Lmod2_enh_homo_rep2

description: heart tissue from E18.5 mouse embryo

data_processing:
Adaptors and low-quality reads were trimmed using TrimGalore. The trimmed reads were subjected to cutadapt to select the reads containing primer sequences at the 5’ end of read 1, and further remove the primer sequences with the parameters "-g primer --discard-untrimmed". These selected reads were then mapped onto the mouse mm10 genome using bowtie2 with the parameters "--very-sensitive --end-to-end --no-unal". Samtools was used to generate bam files and filter out low-quality mapped reads (MAPQ < 30) and PCR duplicates. The bam files were then processed using the r3Cseq package to generate normalized bedGraph files, which were subsequently converted into bigWig files using the bedGraphToBigWig tool for visualization.
Assembly: mm10
Supplementary files format and content: Normalized bigwig file for each sample.
Library strategy: 4C-seq

extract_protocol:
The thoroughly ground heart tissue was cross-linked with 2% formaldehyde and quenched with 0.2 M glycine. DNA was then digested with nuclease in situ. 500 ng of DNA was used as a template and linearly amplified using 5' biotin-labeled probes. The ssDNA was enriched using Dynabeads™ M-280 magnetic beads.
Illumina sequencing adaptors were introduced, followed by PCR using target-specific primers. Sequencing was performed on the Illumina NovaSeq platform.

tag: developmental stage

value: E18.5 embryo

value: Ctcf homozygous mutation


title: RNA-seq Control midgut rep 3

source_name: Midgut

value: Midgut


title: ZBTB7A CUT&RUN Repeat 1

description:
Library name: Sample 1
ZBTB7A CUT&RUN

value: CD1 strain


title: ZBTB7A CUT&RUN Repeat 2

description:
Library name: Sample 2
ZBTB7A CUT&RUN


title: CT26_LOX_1

description: Library name: 7797_4_LOX_5_2


title: lamina_propria_CD4_Tcells_rep6_mRNA

city: BETHESDA

first: Cihan

last: Oguz

state: MD

address: NIHBC 29B BG RM 1NN20, 9000 ROCKVILLE PIKE

institute: NIH

library_source: transcriptomic single cell

data_processing:
The processing of the mRNA expression data involved generating demultiplexed fastq files and count matrices (raw_feature_bc_matrix.h5 files) using Cell Ranger v6.0 (10X Genomics, Pleasanton, CA) that was run with the mm10-2020-A transcriptome reference. Specifically, "cellranger mkfastq" generated the mRNA fastq files, whereas "cellranger count" generated the mRNA count matrices (raw_feature_bc_matrix.h5 files).
VDJ (TCR) data was processed with Cell Ranger v6.0 and the vdj_GRCm38_alts_ensembl-5.0.0 reference. Specifically, "cellranger mkfastq" generated the VDJ (TCR) fastq files, whereas "cellranger vdj" generated the VDJ_filtered_contig_annotations.csv files.
HTO counts (HTO_feature_bc_matrix.tar.gz) files were generated using CITE-seq-Count v1.4.3 (https://github.com/Hoohm/CITE-seq-Count), whereas "cellranger mkfastq" generated the HTO fastq files.
feature_README.txt lists the library-specific multiplexed sample-HTO pairs.
Assembly: mm10
Supplementary files format and content: Cell Ranger scRNA-seq (mRNA) produced count matrices are in the raw_feature_bc_matrix.h5.gz files. CITE-seq-Count produced HTO count matrices are in the HTO_feature_bc_matrix.tar.gz files. The processed immune repertoire TCR (VDJ) sequencing data is provided in the filtered_contig_annotations.csv.gz files.

source_name: lamina propria

extract_protocol:
Lamina propria CD4+ T cells (cell count of 2.5 × 10^4) were isolated from each sample using a FACS AriaII (BD) cell sorter.
All samples were labeled with TotalSeqC hashtags antibodies (BioLegend), pooled, and encapsulated into droplets using a Chromium Single Cell Controller (10X Genomics), and libraries were prepared using Chromium Single Cell 5’ Reagent Kits v2 (Dual Index) with Mouse TCR Amplification Kit and 5’ Feature Barcode Kit (10X Genomics). The Controller was loaded with 2.5 × 10^4 cells per lane. mRNA, VDJ (TCR) and HTO libraries were prepared following the 10X Genomics user guide.
scRNA-seq and TCR repertoire (VDJ region) sequencing of colonic lamina propria-specific CD4+ T cells. The scRNA-seq and TCR libraries were coupled with hashtag oligo (HTO) libraries for labeling the samples in order to demultiplex the pooled libraries into wild-type and Rag1 mutant mice at 3/12 weeks of age and with/without ANMV treatment cell populations for downstream analysis. The number of libraries sequenced is six for scRNA-seq, six for TCR (VDJ) repertoire, and six for HTOs.

value: lamina propria

value: CD4+ T cells


title: lamina_propria_CD4_Tcells_rep6_HTO

library_source: other


title: Lmod2_enh_wt_rep2

description: heart tissue from E18.5 mouse embryo

value: heart


title: RNA-seq Control midgut rep 2

value: Wild-type

value: Sugar-fed 5-8d post emergence


title: CT26_PAI_3

description: Library name: 7797_3_PAI_3_4

value: sc. Flank tumor

value: TRXtr-PAI


title: lamina_propria_CD4_Tcells_rep6_VDJ


title: RNA-seq Control midgut rep 1


title: CT26_PAI_2

description: Library name: 7797_2_PAI_3_2

value: WT


title: Lmod2_enh_wt_rep1

description: heart tissue from E18.5 mouse embryo


title: lamina_propria_CD4_Tcells_rep5_VDJ


title: Lmod2_pro_homo_rep2

description: heart tissue from E18.5 mouse embryo


title: RNA-seq Control thorax rep 2

source_name: Thorax

value: Thorax


title: Lmod2_pro_homo_rep1

description: heart tissue from E18.5 mouse embryo


title: lamina_propria_CD4_Tcells_rep5_mRNA


title: RNA-seq Control thorax rep 3


title: RNA-seq Control thorax rep 1


title: CT26_PAI_1

description: Library name: 7797_1_PAI_4_3


title: lamina_propria_CD4_Tcells_rep5_HTO


title: EEDi_3

city: Hangzhou

first: Jiajia

last: Wang

address: 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: DC2.4 cell line was cultured in RPMI-1640 containing 10% fetal bovine serum, 100 mg/mL streptomycin, and 100 mg/mL penicillin.

extract_protocol:
RNA from LPS and EEDi-5285 treated DC2.4 were extracted using TRIZOL (Life Technologies) followed by purification using an RNeasy Mini Kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: DC2.4 were treated with EEDi-5285 (5 μM) for 24 h and LPS (50 ng/mL) for 6 h.

value: dendritic cell

value: wild type

value: LPS+EEDi


title: RNA-seq Dcr2R172fsX ovary rep 5

value: Ovary


title: RNA-seq Dcr2R172fsX ovary rep 4


title: EEDi_2


title: Lmod2_pro_wt_rep2

description: heart tissue from E18.5 mouse embryo

value: E18.5 embryo


title: lamina_propria_CD4_Tcells_rep4_VDJ

value: WT | Rag1_mutant


title: Lmod2_enh_homo_rep1

description: heart tissue from E18.5 mouse embryo

value: Ctcf homozygous mutation


title: CT26_LOX_2

description: Library name: 7797_5_LOX_5_3

value: Mouse colrectal cancer

value: TRXtr-LOX


title: lamina_propria_CD4_Tcells_rep4_mRNA

value: lamina propria

value: CD4+ T cells


title: EEDi_1


title: RNA-seq Dcr2R172fsX ovary rep 3


title: WT-L10-STAT5B_rep2

city: Bethesda

first: Hye Kyung

last: Lee

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and Bowtie (version 1.2.2) and Samtools (version 1.8), with the parameter ‘-m 1’ to keep only uniquely mapped reads, using the reference genome mm10. Homer30 (version 4.9.1) software was applied to generate bedGraph files, seperately. Integrative Genomics Viewer (version 2.3.98) was used for visualization with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools to remove duplicates. Homer software was applied  for the generation of bedGraph files.
Assembly: mm10
Supplementary files format and content: bedgraph of ChIP-seq

source_name: Mammary gland

growth_protocol: Mouse mammary gland tissues were harvested at day 13 and 18 of pregnant (p13, p18) of 2-month-old age for wild-type and mutant mice carrying a point mutation in Stat5b-Y665 and at day 10 of lactation (L10) after second pregnancy of Y665H mutant.

extract_protocol:
Chromatin was fixed with formaldehyde (1% final concentration) for 10min at room temperature, and then quenched with glycine (0.125 M final concentration). Samples were processed as previously described. The following antibodies were used for ChIP-seq: STAT5A (Santa Cruz Biotechnology, sc-271542), STAT5B (ThermoFisher scientific, 13-5300), NFIB (Sigma-Aldrich, HPA003956), H3K27ac (Abcam, ab4729) and RNA polymerase II (Abcam, ab5408). Libraries for next-generation sequencing were prepared and sequenced with a HiSeq 3000 or Novaseq 6000 instrument (Illumina). Libraries for sequencing were prepared using standard Illumina protocols.
Libraries for sequencing were prepared using standard Illumina protocols.

value: Mammary gland

tag: strain

tag: Stage

value: day 10 of lactation (L10)

tag: chip-seq antibody


title: lamina_propria_CD4_Tcells_rep4_HTO


title: lamina_propria_CD4_Tcells_rep3_VDJ


title: WT-L10-STAT5B_rep1

value: STAT5B (ThermoFisher scientific, 13-5300)


title: LPS_2

value: LPS


title: RNA-seq Dcr2R172fsX midgut rep 2

value: Midgut

value: Sugar-fed 5-8d post emergence


title: lamina_propria_CD4_Tcells_rep3_mRNA


title: LPS_1

value: dendritic cell


title: RNA-seq Dcr2R172fsX midgut rep 1


title: STAT5B-Y665H-L10-PolII_rep1

value: day 10 of lactation (L10) after second pregnancy

value: RNA polymerase II (Abcam, ab5408)


title: lamina_propria_CD4_Tcells_rep3_HTO


title: STAT5B-Y665H-L10-PolII_rep2


title: Adult_Mouse2

data_processing:
bcl2fastq2 versie v2.15.0.4
Assembly: mm10
Supplementary files format and content: tab delimited text file containing raw counts for all samples
Supplementary files format and content: csv files per sample containing raw counts

source_name: Whole organism

growth_protocol: Where applicable, B16F10 cells were maintained in DMEM supplemented with 10% FCS and 1% Pen/Strep and glutamine supplements. 1e5 tumor cells were injected in the flank of C57BL/6 mice and harvested when 1000mm3 in size

extract_protocol:
From whole tissues or sorted cells, RNA was extracted using Trizol according to the manufacturers instructions
TruSeq RNA Library Prep Kit v2 (Illumina Inc., San Diego)

treatment_protocol: No treatment was applied

value: Whole organism

value: Adult mouse


title: STAT5B-Y665H-L10-H3K27ac_rep2

value: H3K27ac (Abcam, ab4729)


title: lamina_propria_CD4_Tcells_rep2_VDJ

value: WT | Rag1_mutant


title: RNA-seq Dcr2R172fsX thorax rep 3

value: Thorax


title: Lmod2_pro_wt_rep1

description: heart tissue from E18.5 mouse embryo

value: heart

value: E18.5 embryo

value: wild type


title: Adult_Mouse1


title: RNA-seq Dcr2R172fsX thorax rep 2


title: RNA-seq Dcr2R172fsX thorax rep 1


title: lamina_propria_CD4_Tcells_rep2_mRNA

value: lamina propria

value: CD4+ T cells


title: STAT5B-Y665H-L10-STAT5B_rep2

value: Mammary gland

value: STAT5B (ThermoFisher scientific, 13-5300)


title: LPS_3

value: LPS


title: lamina_propria_CD4_Tcells_rep2_HTO


title: STAT5B-Y665H-L10-H3K27ac_rep1


title: EmbryoE18_2_1

value: Embryo gestation day 18


title: EmbryoE18_2_2


title: lamina_propria_CD4_Tcells_rep1_VDJ


title: STAT5B-Y665H-L10-STAT5B_rep1


title: EmbryoE18_1_2


title: lamina_propria_CD4_Tcells_rep1_mRNA


title: RNA-seq Dcr2R172fsX midgut rep 3

value: Midgut

value: Sugar-fed 5-8d post emergence


title: STAT5B-Y665H-L10-STAT5A_rep2

value: day 10 of lactation (L10) after second pregnancy

value: STAT5A (Santa Cruz Biotechnology, sc-271542)


title: EmbryoE18_1_1

value: Whole organism


title: Intestinal enteroids, D3, Layer, replicate 1

city: Edinburgh

first: Jianxuan

last: Sun

state: Midlothian

address: The University of Edinburgh, Easter Bush Campus

country: United Kingdom

institute: Roslin Institute

description:
Library name: Sample 7
10X Chromium, 3’ v3.1 chemistry

data_processing:
Mapping of reads to the genome, assignment of reads to cellular barcodes, and collapsing of unique molecular identifiers (UMIs) was performed with StarSolo v2.7.10a. The same tool was used to attribute reads to cellular barcodes and de-duplicate unique molecular identifiers (UMIs). The analysis was restricted to protein coding genes by specifying annotations with a gene_biotype of “protein coding”. The genome index was generated with standard settings and “sjdbOverhang” set to 99 to account for the 100bp read length. Reads were mapped with the “STAR” command with the following settings: soloCBstart = 1, soloCBlen = 16, soloUMIstart = 17, soloUMIlen = 12, soloBarcodeReadLength = 0, outFilterScoreMinOverLread = 0.66, outFilterMatchNminOverLread = 0.66 soloUMIfiltering = MultiGeneUMI_CR, soloCellFilter = EmptyDrops_CR, limitOutSJcollapsed = 2500000, soloCellReadStats = Standard
Assembly: Gallus gallus GCA 016700215.2 Ensembl 110 genome
Supplementary files format and content: Tab separated value (tsv) and matrix (mtx) format. Contains gene names (features.tsv), cell barcodes (barcodes.tsv) and UMI count (matrix.mtx)

molecule: nuclear RNA

organism: Gallus gallus

source_name: Intestinal enteroids

extract_protocol:
The villi were dissociated into single cells for fluorescence-activated cell sorting (FACS). Dissociation was performed using 0.25% Trypsin-EDTA solution (1X) (Gibco, UK) for 15 min at 37°C, with gentle pipetting up and down every 5 minutes. The reaction was stopped with DMEM containing 10% FBS (Gibco, UK). Single cells from the dissociated villi were washed twice in PBS supplemented with 1% BSA (Sigma-Aldrich, UK) at 400 x g for 5 min (at 4°C) and resuspended in PBS with 1% BSA and 0.4 U/μL of Protector RNase inhibitor (3335399001, Roche; collection buffer). At day 3 the organoids were dissociated using the same procedure as used for the villi. Cell viability and counts were assessed using a hemacytometer. The cells were maintained on ice before FACS was performed using a Bigfoot Cell Sorter (Thermo Fisher Scientific, UK) to obtain a population of live, single cells. Cells were collected in low retention 1.5 ml Eppendorf tubes containing 100 μL of collection buffer.
scRNA-seq libraries were prepared by the Roslin Institute Genomics Platform Facility, using the 10X Genomics Chromium Next GEM Single Cell 3’ Kit (v3.1) following the manufacturer’s protocol. FACS sorted cells for eight samples (n=2 per broiler and layer at Day 0 and Day 3) were re-counted using a hemacytometer and diluted to 700-1,200 cells per µL. Each sample was loaded onto a Chromium Chip G lane targeting 5,000 cells per sample. After encapsulation by gel beads in emulsion (GEMs), the mRNA was captured, barcoded and reverse transcribed, before the emulsion was broken and the cDNA pooled, purified and amplified using 12 PCR cycles. The cDNA was fragmented, end-repaired and size-selected to optimise amplicon size, followed by adaptor ligation and sample indexing (11 PCR cycles). The resulting libraries were pooled in equimolar concentrations and sequenced on an Illumina NextSeq 2000 using NextSeq 1000/2000 P3 Reagents (100 cycles) v3 Kit, over two P3 flow cells. PhiX Control v3 library was spiked at a concentration of ~1%.

treatment_protocol: Duodenum, jejunum, and ileum were extracted from chicken embryos (ED19) and immediately placed in phosphate-buffered saline (PBS, Mg2+ and Ca2+ free) until further processing. For each independent culture, intestines from four embryos were pooled. The enteroids were generated according to Nash et al. with minor modifications10. Briefly, intestinal tissues were longitudinally opened and cut into 3 mm pieces. The tissues underwent enzymatic digestion and villi were collected using a 70 µm cell strainer (Corning, UK) and by rinsing the inverted strainer with subsequent centrifugation at 107 x g for 4 min. Half of the collected villi were seeded in Petri dishes with 12 ml of Floating Organoid Media (FOM), consisting of Advanced DMEM/F12 supplemented with 1X B27 Plus, 10 mM HEPES, 2 mM L-Glutamine, and 50 U/mL Penicillin/Streptomycin (Thermo Fisher Scientific, Paisley, UK), whereas the other half were processed for scRNA-Seq. The enteroids were cultured at 37°C with 5% CO2 in petri dishes to remove fibroblasts. The following day, enteroids were collected, washed in Advanced DMEM/F12, re-plated in fresh Petri dishes and cultured for an additional two days. The enteroids on day 3 of culture were dissociated and sorted using the same procedures as the fresh villi, described below.

value: Intestinal enteroids

tag: breed

value: Layer

tag: time point


title: Intestinal enteroids, D3, Layer, replicate 2

description:
Library name: Sample 8
10X Chromium, 3’ v3.1 chemistry


title: STAT5B-Y665H-L10-STAT5A_rep1


title: Intestinal enteroids, D3, Broiler, replicate 2

description:
Library name: Sample 6
10X Chromium, 3’ v3.1 chemistry

value: Broiler


title: STAT5B-Y665H-p18-STAT5A_rep1

value: day 18 of pregnant (p18)


title: EmbryoE11_2_2

value: Embryo gestation day 11


title: Intestinal enteroids, D3, Broiler, replicate 1

description:
Library name: Sample 5
10X Chromium, 3’ v3.1 chemistry


title: STAT5B-Y665F-p18-STAT5A_rep3


title: EmbryoE11_2_1


title: Intestinal enteroids, D0, Layer, replicate 2

description:
Library name: Sample 4
10X Chromium, 3’ v3.1 chemistry


title: Dorsal spinal cord, monkey SNL model, No.5, Ipsi

city: Izunokuni, Shizuoka

first: Hiroshi

last: Yamane

address: 632-1 Mifuku

department: Pharmaceuticals Research Center

country: Japan

institute: Asahi Kasei Pharma Corporation

data_processing:
The raw sequence data were quality-checked with fastp (version 0.22.0)
The raw sequence data were aligned to the Macaca fascicularis 6.0 monkey genome with STAR (version 2.7.9a)
The raw sequence data were quantified for gene-level counts and transcripts per million (TPM) data using RSEM (version 1.3.1)
Assembly: GCA_011100615.1
Supplementary files format and content: Excel file includes expected counts and TPM values for each sample

organism: Macaca fascicularis

source_name: Spinal cord (Ipsi)

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen).
Sequence libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA) following manufacturer's instruction.

tag: animal id

value: Spinal cord (Ipsi)

value: SNL surgery


title: EmbryoE11_1_2


title: Dorsal spinal cord, monkey SNL model, No.4, Cont

source_name: Spinal cord (Cont)

value: Spinal cord (Cont)


title: STAT5B-Y665F-p18-STAT5A_rep1

value: Mammary gland


title: STAT5B-Y665F-p18-STAT5A_rep2


title: TEC_2

source_name: EC isolated from melanoma tumor in mouse

value: CD31 and/or CD34 sorted endothelial cells


title: Intestinal enteroids, D0, Broiler, replicate 2

description:
Library name: Sample 2
10X Chromium, 3’ v3.1 chemistry


title: Dorsal spinal cord, monkey SNL model, No.4, Ipsi


title: STAT5B-Y665F-p13-STAT5A_rep2

value: day 13 of pregnant (p13)


title: Intestinal enteroids, D0, Broiler, replicate 1

description:
Library name: Sample 1
10X Chromium, 3’ v3.1 chemistry


title: EmbryoE11_1_1


title: Dorsal spinal cord, monkey SNL model, No.3, Cont


title: CAR_Rapa_3

city: Los Angeles

first: Jeffrey

last: Harding

state: CA

address: 405 Hilgard Avenue

institute: University of California Los Angeles

description: Library name: C64-16

data_processing:
FastQC,UMI-tools,Trim Galore!,BBSplit,SortMeRNA,STAR,Salmon,SAMtools,Picard MarkDuplicates
Assembly: Star Using GRCh38
Supplementary files format and content: Salmon TPM file

source_name: spleen

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using illumina mRNA-Seq Library Kit following manufacturer's protocols.

value: spleen

value: CAR-T

value: CAR-T-Rapamycin


title: STAT5B-Y665F-p13-STAT5A_rep1


title: Dorsal spinal cord, monkey SNL model, No.3, Ipsi


title: NEC

source_name: EC isolated from murine heart lung liver kidney; pooled for N=2 mice


title: lamina_propria_CD4_Tcells_rep1_HTO

value: lamina propria

value: CD4+ T cells

value: WT | Rag1_mutant


title: CAR_Rapa_2

description: Library name: C64-11


title: Dorsal spinal cord, monkey SNL model, No.2, Cont


title: TEC_1

value: EC isolated from melanoma tumor in mouse


title: Dorsal spinal cord, monkey SNL model, No.5, Cont


title: siamang-iPS-0927F-C1

city: Inuyama

first: Yusuke

last: Hamazaki

state: Aichi

institute: Center for the Evolutionary Origins of Human Behavior, Kyoto University

description: Library name: iPSC_0297F-C1

data_processing:
Trim Galore was used for adapter and quality trimming with the -fastqc option (https://zenodo.org/records/7598955). Sequencing reads from small ape cells were mapped to nomLeu3 using STAR (PMID: 23104886), and uniquely mapped reads were retained for further analyses. BAM files were converted to BED format, and PCR duplicates were removed. The intersectBed tool in Bedtools was used to sum reads of overlapping exons of genes homologous to those of hg38 (PMID: 20110278). Only the first read of paired-end reads was included in the count. Transcripts per kilobase million (TPM) values were calculated for normalization using Pandas.
Assembly: nomLeu3
Supplementary files format and content: txt file including TPM value of gene expressions

organism: Symphalangus syndactylus

source_name: iPSC

growth_protocol: Skin specimens were obtained from two lar gibbons (Hylobates lar) (GAIN-ID: 0023 [Jessica, a 24-year-old female] and GAIN-ID: 0247 [Kyutaro, a 21-year-old male]), one Abbott’s gray gibbon (Hylobates abbotti) (GAIN-ID: 0159 [Anna, an estimated 46-year-old female]), and two siamangs (Symphalangus syndactylus) (GAIN-ID: 0105 [Matsu, a 32-year-old female] and GAIN-ID: 0297 [Peach, an 11-year-old female]). These samples were provided by the Japan Monkey Centre, the Toyohashi Zoo and Botanical Park, and the Great Ape Information Network (GAIN) for primary cultures. Each skin specimen was minced into small pieces and transferred onto tissue culture dishes (353002; Corning, Glendale, AZ, USA) with 15% fetal bovine serum (FBS)/Dulbecco’s modified Eagle’s medium (DMEM) medium, which consists of DMEM with high glucose (044-29765; Wako, Osaka, Japan) supplemented with 15% FBS, 1× non-essential amino acids (139-15651; Wako), 1× GlutaMAX Supplement (35050061; Gibco, Waltham, MA, USA), 1 mM sodium pyruvate (190-14881; Wako), 0.11 mM 2-mercaptoethanol (21985-023; Gibco), and 100 units/ml penicillin and 100 µg/ml streptomycin (168-23191; Wako). Fibroblast outgrowth from the skin pieces was observed after approximately one week of culture. The fibroblasts were subsequently passaged though single-cell dissociation with 0.25% trypsin/ethylenediaminetetraacetic acid (EDTA) and expanded in 15% FBS/DMEM medium on 0.1% gelatin-coated culture dishes at 37°C with 5% CO2. Small ape skin fibroblasts were seeded at 1.0 × 105 cells/well on 0.1% gelatin-coated culture plates. The following day, the cells were transduced with six human reprogramming factors (OCT3/4, KLF4, SOX2, c-MYC, LIN28, and NANOG) using SRV iPSC-3 Vector (S1011626A; Tokiwa Bio, Ibaraki, Japan) at a multiplicity of infection (MOI) of 3 for GAIN-ID: 0247, 0159, 0105, 0297. For GAIN-ID: 0023, transduction was performed with four human reprogramming factors (OCT3/4, KLF4, SOX2, and c-MYC) using the SRV iPSC-1 Vector (S1011624A; Tokiwa Bio) at an MOI of 3. The transduction procedure involved incubating the cells with the respective SRV vectors at room temperature for 2 hours, followed by overnight incubation at 37°C with 5% CO2. 24 hours post-transduction, the cells were dissociated with 0.25% trypsin/EDTA and reseeded onto iMatrix-511-coated 24-well culture plates at 1.0 × 104 cells/well. The medium was changed every other day under two different conditions. For condition A, cells were cultured in 15% FBS/DMEM medium from day 1 to day 7, followed by StemFit AK02N medium (AK02N; Ajinomoto, Tokyo, Japan) without supplements from day 7 to approximately day 21. Thereafter, the cells were maintained in StemFit AK02N medium. For condition B, StemFit AK02N medium without supplements was used from day 1 to day 7 or 14, followed by continued culture in StemFit AK02N medium. Emerging EGFP+ reprogrammed colonies were manually picked and cultured in StemFit AK02N medium on iMatrix-511-coated culture plates.　To remove SRV vectors from expanded EGFP+ reprogrammed cells, small interfering RNA (siRNA) transfection was performed according to the manufacturer’s instructions (S1011626A; Tokiwa Bio). Briefly, EGFP+ reprogrammed cells, after several serial passages, were dissociated with TrypLE Express (12604021; Gibco) and seeded at 0.75 × 104 cells/well in StemFit AK02N medium supplemented with 10 μM Y-27632 (036-24023; Wako) on iMatrix-511-coated 24-well culture plates. On the next day, the medium was replaced with fresh StemFit AK02N medium. The cells were transfected with siRNA (sense: CAAUAGUUCACGCUGAAAGUG; anti-sense: CUUUCAGCGUGAACUAUUGCU) using Lipofectamine RNAiMAX (13778100; Thermo Fisher Scientific, Waltham, MA, USA) on day 1 and 4 after plating. The siRNA-transfected cells were passaged upon reaching sub-confluency and maintained in StemFit AK02N medium on iMatrix-511-coated culture plates. For subcloning SRV-free iPSCs, the siRNA-transfected cells were seeded at 0.5 × 103 cells/cm2, and EGFP- colonies were manually picked up and expanded as iPSCs in StemFit AK02N medium on iMatrix-511-coated culture dishes.

extract_protocol:
Total RNA was extracted using ISOGEN (317-02503; Nippon Gene, Tokyo, Japan) and Direct-Zol RNA Miniprep (R2050; Zymo Research, Irvine, USA).
cDNA library preparation and sequencing were performed by Azenta Japan (Tokyo, Japan). Briefly, cDNA libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420; New England Biolabs) and sequenced on an Illumina NovaSeq with a 2 x 150 bp paired-end configuration. Each sample yielded approximately 20 million sequencing reads.

value: iPSC


title: STAT5B-Y665H-L10_rep4

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome mm10 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). Rsubread (Liao et al., Nucleic Acids Research, 2013) was was applied to calculate raw read counts.
Assembly: mm10
Supplementary files format and content: raw read counts from RNA-seq samples

growth_protocol: Total RNA-seq was done for the mammary tissues at at day 13 and 18 of pregnant (p13, p18) of 2-month-old age of wild-type and mutant mice carrying a point mutation in Stat5b-Y665 and at day 10 of lactation (L10) after second pregnancy of Y665H mutant .

extract_protocol:
Total RNA was extracted from frozen mammary tissue from mice and purified with RNeasy Plus Mini Kit (Invitrogen, 12183018A). Ribosomal RNA was removed from 1ug of total RNAs and cDNA was synthesized using SuperScript III (Invitrogen). Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301) and paired-end sequencing was done with a HiSeq 3000 or Novaseq 6000 instrument (Illumina).
Libraries for sequencing were prepared using standard Illumina protocols.


title: CAR_Rapa_1

description: Library name: C64-10


title: STAT5B-Y665H-L10_rep3

value: day 10 of lactation (L10) after second pregnancy


title: siamang-iPS-0297F-A5

description: Library name: iPSC_0297F-A5


title: Intestinal enteroids, D0, Layer, replicate 1

description:
Library name: Sample 3
10X Chromium, 3’ v3.1 chemistry

value: Intestinal enteroids

value: Layer


title: siamang-iPS-0105F-B2

description: Library name: iPSC_0105F-B2


title: Dorsal spinal cord, monkey SNL model, No.1, Cont


title: Dorsal spinal cord, monkey SNL model, No.1, Ipsi

value: Spinal cord (Ipsi)


title: STAT5B-Y665H-L10_rep1


title: siamang-iPS-0105F-B1

description: Library name: iPSC_0105F-B1


title: CAR_1

description: Library name: C64-17


title: small RNA-seq Dcr2R172fsX ovary rep 5

description:
Small RNA
21nt_counts_GEO.tsv
HVC2BGXM-Dcr-ovary-pool-3_S3

data_processing:
adapters and polyA/T/C/G trimmed with cutadapt (options: ‘-e 0.15 -O 6 --trimmed-only -m 18 --match-read-wildcards -q 20)
reads aligned using bowtie (options: -v 1 -a -M 1); filtered for reads mapping to annotated tRNA, snRNA, snoRNA, miRNA and piRNA-clusters;  subset to 21nt only; counted using TEtranscripts (--mode multi)
Assembly: AaegL5 (VectorBase release 61)
Supplementary files format and content: Tab-separated values for filtered 21nt-long reads (Gene/TE - Counts - RPM -  Library)

extract_protocol:
20 dissected tissues pooled and subject to TRIzol (Life Technologies) extraction; 5 µg of total RNA used for small RNA-seq library prep
NEB Next Multiplex Small RNA Library Prep kit

value: Ovary

value: Sugar-fed 5-8d post emergence


title: TAM-AdV-mSS-4

city: Nanjing

first: yenan

last: Zhang

state: Jiangsu

address: Hankou Road

institute: Medical School of Nanjing University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Mus_musculus (GRCm39)
Supplementary files format and content: tab-delimited text files include tpm values for each samples

source_name: sorted TAMs

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Subcutaneous 14-day H22-CAR -bearing BALB/c mice were intratumorally injected with PBS, 5 × 10^8 IFU AdV-Ctrl, or 5 × 10^8 IFU AdV-mSS twice. Forty-eight hours post-treatment, we harvested tumor tissue and sorted these TAMs by anti-mouse F4/80 MicroBeads (Miltenyi biotec). Samples were stored at −80 °C.

value: sorted TAMs

value: TAMs sorted from subcutaneous H28-CAR tumors injected with AdV-mSS


title: TAM-AdV-mSS-3


title: siamang-SRV3-0297F-C-3

description: Library name: SRV_0297F-C-3

source_name: SRV+ cells

value: SRV+ cells


title: siamang-SRV3-0105F-B2

description: Library name: SRV_0105F-B2


title: small RNA-seq Dcr2R172fsX ovary rep 4

description:
Small RNA
21nt_counts_GEO.tsv
HVC2BGXM-Dcr-ovary-pool-2_S2


title: small RNA-seq Dcr2R172fsX ovary rep 3

description:
Small RNA
21nt_counts_GEO.tsv
HVC2BGXM-Dcr-ovary-pool-1_S1


title: Dorsal spinal cord, monkey SNL model, No.2, Ipsi

value: SNL surgery


title: small RNA-seq Dcr2R172fsX midgut rep 3

description:
Small RNA
21nt_counts_GEO.tsv
HVC2BGXM-Dcr-midgut-pool-3_S6

value: Midgut


title: TAM-AdV-Ctrl-4

value: TAMs sorted from subcutaneous H28-CAR tumors injected with AdV-Ctrl


title: Fibroblast-0297F

description: Library name: Fibroblast_0297F

source_name: fibroblasts

value: fibroblasts


title: CAR_3

description: Library name: C64-34

value: spleen

value: CAR-T


title: siamang-SRV3-0105F-B1

description: Library name: SRV_0105F-B1


title: small RNA-seq Dcr2R172fsX midgut rep 2

description:
Small RNA
21nt_counts_GEO.tsv
HVC2BGXM-Dcr-midgut-pool-2_S5


title: Fibroblast-0105F

description: Library name: Fibroblast_0105F


title: small RNA-seq Dcr2R172fsX midgut rep 1

description:
Small RNA
21nt_counts_GEO.tsv
HVC2BGXM-Dcr-midgut-pool-1_S4


title: STAT5B-Y665H-L10_rep2

value: Mammary gland


title: CAR_2

description: Library name: C64-24


title: TAM-AdV-Ctrl-3

value: TAMs sorted from subcutaneous H27-CAR tumors injected with AdV-Ctrl


title: Mock_replicate1

type: RNA

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

institute: European Brain Research Institute

description: primary cultures of rat cerebellar Granule Cells (GCs)

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to 4x44K Agilent whole rat genome oligonucleotide microarray (grid ID 014879), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. The hybridized microarrays were disassembled at room temperature in Agilent Gene Expression Wash Buffer 1. After the disassembly, the microarrays were washed in Gene Expression Buffer 1 for one minute at room temperature, followed by washing with Gene Expression Wash Buffer 2 for one minute at 37°C. The microarrays were then treated with acetonitrile for one minute at room temperature.

scan_protocol: Post-hybridization image acquisition was accomplished using the Agilent Scanner G2564C. Data extraction from the 20 bits TIFF images was accomplished by Agilent Feature Extraction ver 10.7.3.1 software using the standard Agilent one-color gene expression extraction protocol (GE1_1100_Jul11).

data_processing: The “gProcessedSignal” data column of the Feature Extraction *.txt output file was used, containing the median signals corrected by spatial and multiplicative detrend. Data quality filtering was performed using Microsoft Excel, discarding features with the Feature Extraction flag gIsWellAboveBG=0 in any sample, wich is a statistical method approximately equivalent to discarding features with a Signal/Noise ratio smaller than 2.0-3.0, where Signal = (median of the spot - median spot background level) and Noise is the Standard Deviation of the median spot background. Data were normalized to the 75th percentile in Log2 scale. Then differential gene lists were obtained from filtered data using Microsoft Excel. Differentially expressed genes were identified by a combination the and foldchange ratio between the means of the two groups.

organism: Rattus norvegicus

source_name: rat cerebellar Granule Cells (GCs), mock control

label_protocol: 200ng of Poly A+RNA were labelled, using Cyanine 3-CTP (Agilent) in separate labelling reactions, with the Agilent Low Imput Linear Amplification Kit and purified with Qiagen’s RNeasy mini spin columns.

growth_protocol: Primary cultures enriched in granule neurons (GCs) were obtained from dissociated cerebella of 8-day-old Wistar rats. Cells were seeded (3 x 10E6 cells/dish) on poly-L-lysine-coated 35-mm plastic dishes in Gibco Basal  Medium Eagle (BME, ThermoFisher Scientific) supplemented with 10% heat-inactivated fetal calf serum (Gibco), 2 mM glutamine (Gibco), and 25 mM KCl and 100 µg/ml gentamycin (Gibco). Ara-C (10 mM)  was added to the culture medium 24h after plating to prevent proliferation of non-neuronal cells.

extract_protocol: Total RNA was isolated by using the Total RNA purification kit (NorgenBiotek). RNA quantity was determined by A260 nm using a NanoDrop UV-VIS spectrophotometer. RNA quality was checked by BioAnalyzer 2100 instrument (Agilent Technologies).

treatment_protocol: Granule cells were seeded into 35-mm plastic dishes previously coated with poly-L-lysine at a concentration 3.5 x 10E5 cells/dish. After four hours, cells were infected for 18 hours with the virus-containing supernatant from pLenti6/V5-GW/EmGFP-miR-LMNA (Lmna-KD) or pLenti6/V5-GW/EmGFP-miRNeg (mock control), and then fresh medium was added.

value: cerebellum

value: 8-day-old rat

value: Wistar

value: mock control


title: Infected Salivary Gland, time 72, LD, Sample 2

city: Berkeley

first: Filipa

last: Rijo-Ferreira

address: Koshland Hall

institute: UC Berkeley

description: Library name: Sample 62

data_processing:
FASTQC
STAR
Cutadapt
Assembly: PlasmoDB-26_PbergheiANKA from plasmoDB.org and Anopheles-stephensi-SDA-500_AsteS1.6 from vectorbase.org
Supplementary files format and content: RPKMs for each organism and timepoint

organism:
Plasmodium berghei
Anopheles stephensi

source_name: Salivary glands

extract_protocol:
RNA was extracted using Trizol LS reagent according to manufactor's instructions.
mRNA-seq libraries were prepared using the TruSeq RNA Library Preparation Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol:
[infection protocol]  Anopheles stephensi mosquitos were reared at 28°C and 80% humidity under a 12-h/ 12-h light/dark cycle and fed on 10% glucose (Sigma) and 0.2% 4-aminobenzoic acid (Millipore Sigma) in MilliQ water changed daily. Female Anopheles stephensi mosquitos 4-5 days old were allowed to bite two mice (BALB/c, male, 7-8 weeks of age) infected with Plasmodium berghei ANKA (GFPcon, 259cl2 for one hour). After the infectious bloodmeal, mosquitos were kept in 12h light/12h dark, at constant temperature of 20ºC. Mosquitos were fed by cotton pads soaked with 10% glucose (Sigma) and 0.2% 4-aminobenzoic acid (Millipore Sigma) in MilliQ water changed daily.
[collection protocol] Two independent experiments were done. On day 16 post-bloodmeal, mosquitos were divided into smaller cages holding ~30-40 mosquitos. On day 19, mosquitos were either maintained in the 12h light/dark schedule (LD) or kept in constant darkness (DD) for salivary gland collection that started on day 20 every 4h for 2 days (experiment 1) or on day 21 for 3 days (experiment 2). When combining both experiments, for each dataset (LD or DD) the first 48h (13 timepoints) have two independent experiments, each timepoint with a pool of salivary glands from ~20 mosquitos. The additional 24h (6 timepoints) have one replicate of pooled salivary glands (~20 mosquitos). Each dissected mosquito showed ~30-50,000 sporozoites/mosquito. Mosquito euthanasia was achieved by CO2 to avoid a putative cold shock response of gene expression. Dissections of salivary glands were performed in PBS with RNAse inhibitor (Invitrogen) (0.1U/μl) to avoid a nutrient rich environment that could reset the circadian rhythm of cells and each dissected tissue was snap frozen with a minimum volume of PBS. RNA was extracted from whole salivary glands using TRIzol LS according to manufacturer’s instructions (Life Technologies). Measurements were taken from the samples discussed in this paragraph.

value: Salivary glands

value: WT

value: light/dark


title: small RNA-seq Dcr2R172fsX thorax rep 3

description:
Small RNA
21nt_counts_GEO.tsv
HVC2BGXM-Dcr-carcass-pool-3_S9

value: Thorax

value: Sugar-fed 5-8d post emergence


title: Mock_replicate2


title: Lmna_KD_replicate1

source_name: rat cerebellar Granule Cells (GCs), knock-down for Lmna

value: knock-down for Lamin A for 18h


title: Infected Salivary Gland, time 72, DD, Sample 2

description: Library name: Sample 61

value: dark


title: TAM-AdV-mSS-2

value: sorted TAMs

value: TAMs sorted from subcutaneous H28-CAR tumors injected with AdV-mSS


title: small RNA-seq Dcr2R172fsX thorax rep 2

description:
Small RNA
21nt_counts_GEO.tsv
HVC2BGXM-Dcr-carcass-pool-2_S8


title: TAM-AdV-Ctrl-1

value: TAMs sorted from subcutaneous H25-CAR tumors injected with AdV-Ctrl


title: Infected Salivary Gland, time 68, LD, Sample 2

description: Library name: Sample 60


title: TAM-PBS-3

value: TAMs sorted from subcutaneous H24-CAR tumors injected with PBS


title: TAM-AdV-mSS-1


title: γδ T cells from neutropenic mouse Rep4

city: Borstel

first: Sebastian

last: Marwitz

address: Parkallee 3a

department: Histology

institute: Research Center Borstel - Leibniz Lung Center

hyb_protocol: Agilent Low Input Quick Amp Labelling Kit One Color according to manufacturers instructions

scan_protocol: Agilent SureScan microarray Scanner (G2600D SG11474142) at 5 µm per pixel.

data_processing: Data has been log-transformed and normalized (percentile shift) within the Agilent GeneSpring V13 software. Compromised probes were removed prior to analysis.

source_name: γδ T cells, FACS sorted from lymph node and spleen

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from total RNA using the One-Color Low Loq-Input Quick-Amp Labelling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from 0.5 to 1 million purified living γδ T cells with the QIAmp Mini Kit (Qiagen) according to the manufacturer's instructions

tag: Sex

value: male

value: Mcl-1f/f plus LysMCre

value: lymph node and spleen


title: Infected Salivary Gland, time 68, DD, Sample 2

description: Library name: Sample 59


title: small RNA-seq Dcr2R172fsX thorax rep 1

description:
Small RNA
21nt_counts_GEO.tsv
HVC2BGXM-Dcr-carcass-pool-1_S7

source_name: Thorax


title: TAM-PBS-2

value: TAMs sorted from subcutaneous H23-CAR tumors injected with PBS


title: small RNA-seq Control ovary rep 3

description:
Small RNA
21nt_counts_GEO.tsv
HGKKYBGXM-Sis-ovary-pool-3_S3

source_name: Ovary

value: Ovary

value: Wild-type


title: Infected Salivary Gland, time 64, LD, Sample 2

description: Library name: Sample 58

value: Salivary glands


title: γδ T cells from neutropenic mouse Rep3


title: TAM-PBS-1

value: TAMs sorted from subcutaneous H22-CAR tumors injected with PBS


title: γδ T cells from neutropenic mouse Rep2


title: TAM-AdV-Ctrl-2

value: TAMs sorted from subcutaneous H26-CAR tumors injected with AdV-Ctrl


title: Infected Salivary Gland, time 64, DD, Sample 2

description: Library name: Sample 57

value: WT


title: γδ T cells from neutropenic mouse Rep1


title: Infected Salivary Gland, time 60, LD, Sample 2

description: Library name: Sample 56

value: light/dark


title: small RNA-seq Control ovary rep 1

description:
Small RNA
21nt_counts_GEO.tsv
HGKKYBGXM-Sis-ovary-pool-1_S1

value: Sugar-fed 5-8d post emergence


title: γδ T cells from littermate ctrl mouse Rep4

value: Mcl-1f/wt plus LysMCre


title: Lmna_KD_replicate2

value: cerebellum

value: 8-day-old rat

value: Wistar

value: knock-down for Lamin A for 18h


title: hGULL_rescue_3

first: Haiming

last: Cao

address: 9000 Rockville Pike

department: NHLBI

data_processing:
The FASTQ read files were first trimmed and cleaned using fastp/0.23.2 and assessed for quality using FastQC/0.11.8.
The reads were then aligned using HISAT2/2.2.1.0 with an index created using the GRCm38.p6 genome.
The trimmed reads were aligned with default settings of HISAT2/2.2.1.0 and quantified using featureCounts (subread/2.0) with mouse GENCODE vm24.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include TPM (Transcripts Per Million) for each sample

source_name: Liver

extract_protocol:
The RNAs that have been extracted by Trizol were purified using the MagMAX RNA extraction kit (Thermo Fisher Scientific, Cat.AM1830).
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific

value: Liver


title: small RNA-seq Control midgut rep 3

description:
Small RNA
21nt_counts_GEO.tsv
HGKKYBGXM-Sis-midgut-pool-3_S6

source_name: Midgut

value: Midgut


title: Infected Salivary Gland, time 60, DD, Sample 2

description: Library name: Sample 55

value: dark


title: hGULL_rescue_2


title: Infected Salivary Gland, time 56, LD, Sample 2

description: Library name: Sample 54


title: MDA-MB-231, Rib_CA_2

city: Lianyungang

first: Song

middle: meng

last: wei

address: China

institute: Jiangsu Ocean University

description: Library name: Rib_CA_2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text file includes the raw counts for each sample

growth_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: MDA-MB-231 cells were treated with or without Rib_CA for 24 hr, respectively, and incubated in 5% CO2 at 37oC.

value: Human Breast Cancer Cell


title: small RNA-seq Control midgut rep 2

description:
Small RNA
21nt_counts_GEO.tsv
HGKKYBGXM-Sis-midgut-pool-2_S5


title: γδ T cells from littermate ctrl mouse Rep3

value: male

value: lymph node and spleen


title: MDA-MB-231, Rib_CA_1

description: Library name: Rib_CA_1


title: γδ T cells from littermate ctrl mouse Rep2


title: hGULL_rescue_1


title: small RNA-seq Control midgut rep 1

description:
Small RNA
21nt_counts_GEO.tsv
HGKKYBGXM-Sis-midgut-pool-1_S4

value: Wild-type


title: Infected Salivary Gland, time 56, DD, Sample 2

description: Library name: Sample 53

value: Salivary glands


title: mGULL_knockdown_4


title: MDA-MB-231, DMSO_2

description: Library name: DMSO_2

value: DMSO


title: small RNA-seq Control thorax rep 3

description:
Small RNA
21nt_counts_GEO.tsv
HGKKYBGXM-Sis-carcass-pool-3_S9

value: Thorax


title: Infected Salivary Gland, time 52, LD, Sample 2

description: Library name: Sample 52

value: WT

value: light/dark


title: γδ T cells from littermate ctrl mouse Rep1

value: Mcl-1f/wt plus LysMCre


title: MDA-MB-231, DMSO_1

description: Library name: DMSO_1


title: Infected Salivary Gland, time 52, DD, Sample 2

description: Library name: Sample 51


title: mGULL_knockdown_2


title: hGULL_rescue_4


title: XR7

city: hefei

first: Xiaoke

last: Yang

address: Sanlian street

department: Department of Rheumatology and Immunology

institute: First Affiliated Hospital of Anhui Medical University

description:
Library name: sample3
FPKM.XR7

data_processing:
Raw data;Clean Data (fastq format) Remove low quality reads and adapter [software:Cutadapt,FASTQC];Map the reads of each sample to the reference gename [software: tophat] Transcripts Assembly [gtf format) Assemble each sample independently [software: StringTiel]  Merged all assemblies to create a single merged gtf [software: StringTle]  Merged all assemblies to create a single merged gtf [software: gffcompara]  Transcripts exprossion profilos (mRNAs, IncRNAs,.l [software: StringTie]
Candidate IncRNAs ;Remove unqualified transcripts Length s 200 and covernees3; Ditferent expression known mRNAs, known IncRNAs and novel nshoas [Taofkware: Ballgown]
Assembly: GRCh38.p12
Supplementary files format and content: FPKM values for each Sample

source_name: blood

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen,CA,USA) following the manufacturer's procedure. The total RNA quantity and punity were analysis of Bioanalyzer 2100(Agilent, CA,USA) with RIN number >7.0. Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(illumina. San Diego, USA). And then we performed the single end sequencing (36bp or 50bp ) on an Illumina Hiseq2500 at the LC-B10 /Hangzhou, China) following the vendar's recommended protocol
Whole transcriptome sequencing requires the construction of two sequencing libraries, a small RNA library and a strand-specific library with ribosomal RNA depletion, and then sequencing on the machine. The length of the small RNA is short, generally less than 50 nt, and the sequencing strategy is 50 SE. The other three types of RNA sequences are generally larger than 200, usually more than 1000, and up to tens of thousands, and 150PE sequencing libraries are constructed by fragmentation. Finally, miRNA sequence information can be obtained from small RNA libraries, and mRNA, lncRNA, and circRNA sequence information can be obtained from strand-specific libraries of deribosomes.

value: blood

value: PBMC

tag: sample group

value: rheumatoid arthritis (RA)


title: Infected Salivary Gland, time 48, LD, Sample 2

description: Library name: Sample 50


title: GC patients

first: Fangfang

last: Jin

address: 138 Xianlin Avenue, Qixia District

department: Department of Clinical Laboratory, Nanjing Drum Tower Hospital, Drum Tower Hospital Clinical College

institute: Nanjing University of Chinese Medicine

description: Library name: Sample2

data_processing:
Small RNA sequences were annotated using the software SPORTS1.1 (updated from SPORTS1.0) with one mismatch tolerance (SPORTS1.1 parameter setting: -M 1). Reads were mapped to the following individual non-coding RNA databases sequentially: (1) the miRNA database miRBase 21; (2) the genomic tRNA database GtRNAdb; (3) the mitochondrial tRNA database mitotRNAdb; (4) the rRNA and YRNA databases assembled from the National Center for Biotechnology Information nucleotide and gene database; (5) the piRNA databases, including piRBase and piRNABank; and (6) the non-coding RNAs defined by Ensembl and Rfam 12.3. The tsRNAs were annotated based on both pre-tRNA and mature tRNA sequences.
Mature tRNA sequences were derived from the GtRNAdb and mitotRNAdb sequences using the following procedures: (1) predicted introns were removed; (2) a CCA sequence was added to the 3′ ends of all tRNAs; and (3) a G nucleotide was added to the 5′ end of histidine tRNAs. The tsRNAs were categorized into four types based on the origin of the tRNA loci: 5′ tsRNA (derived from the 5′ end of pre-/mature tRNA); 3′ tsRNA (derived from the 3′ end of pre-tRNA); 3′ tsRNA-CCA end (derived from the 3′ end of mature tRNA); and internal tsRNAs (not derived from 3′ or 5′ loci of tRNA). For the rsRNA annotation, we mapped the small RNAs to the parent rRNAs in an ascending order of rRNA sequence length to ensure a unique annotation of each rsRNA (for example, the rsRNAs mapped to 5.8S rRNA would not be further mapped to the genomic region overlapped by 5.8S and 45S rRNAs). Differentially expressed sncRNA analysis was performed using the R package DESeq2.
Assembly: GRCh38
Supplementary files format and content: processed data file presents the expression levels of sncRNAs in healthy and gastric cancer (GC) groups, filtered based on two criteria: (1) read counts greater than 10, and (2) fold change (FC) greater than 10 between GC and healthy groups.

source_name: plasma extracellular vesicle

extract_protocol:
Total RNA was extracted using TRIzol Reagent (1 ml; Invitrogen; 15596018). Small RNAs of 15–50 nucleotides was selected.
The RNA segment was separated by PAGE, then a 15- to 45-nucleotide stripe was selected and recycled. The adapters were obtained from the QIAseq® miRNA Library Kit (QIAGEN: 331505) and ligated sequentially. The amplified flow cell was sequenced on the Illumina system by epibiotek (Guangzhou Epibiotek Co., Ltd., Guangzhou, China).

value: plasma extracellular vesicle

tag: disease state

value: gastric cancer


title: M_R_R3

city: Shenzhen

first: jianhui

last: liang

state: Guangdong

address: 1068 Xueyuan Avenue, Nanshan District

institute: Shenzhen Institute of Science and Technology

data_processing:
Data filtering : The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification : Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis: Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation: To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Supplementary files format and content: text

source_name: osteoclast

growth_protocol: Bone marrow mononuclear cells (BMMCs) were isolated from 6- to 8-week-old C57BL/6J mice by dissecting intact tibia and femur post-euthanasia. The bone marrow cavity was washed with DMEM complete medium, and cells were filtered and separated using an animal bone marrow mononuclear cell isolation kit. After overnight culture in αMEM complete medium , non-adherent cells were supplemented with 50 ng/mL of M-CSF for adhesion and differentiation into bone marrow-derived macrophages. The BMMCs were differentiated into bone marrow-derived macrophages using 50 ng/mL of M-CSF for two days. This was followed by the addition of 50 ng/mL of M-CSF and 100 ng/mL of sRANKL for an additional 4 days to promote their differentiation into osteoclast.

extract_protocol:
The cell samples were homogenized in Trizol (Invitrogen) and processed for RNA extraction according to the manufacturer’s instructions.
200ng RNA, Hieff NGS C102P1 Ultima Dual-mode mRNA

treatment_protocol: M1-M3:  M-CSF(50ng/mL)for 2 days; M_R1-M_R3: MCSF (50ng/mL) and RANKL (100ng/mL) for 2 days; M_R_B1-M_R_B3: MCSF (50ng/mL), RANK (100ng/mL), and 1 μM BMS309403 for 2 days,  M_R_R1-M_R_R3:  MCSF (50ng/mL), RANK (100ng/mL), and 1 μM RHC80267 for 2 day.

value: osteoclast

tag: cell type

value: macrophage

value: MCSF, RANKL, RHC80267


title: Infected Salivary Gland, time 48, DD, Sample 2

description: Library name: Sample 49

tag: tissue

value: dark


title: mGULL_knockdown_1

value: Liver


title: M_R_R2

tag: cell line


title: small RNA-seq Control ovary rep 2

first: Hélène

last: Lopez-Maestre

address: 25-28 rue du Dr Roux

institute: Institut Pasteur

description:
Small RNA
21nt_counts_GEO.tsv
HGKKYBGXM-Sis-ovary-pool-2_S2

value: Ovary

tag: genotype

value: Wild-type

value: Sugar-fed 5-8d post emergence


title: 100nM E2 washout, 40m + 320m replicate 2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated actuely for 40mins with 100 nM E2 then washed out for the indicated time.
MCF-7_E2washout_40m_320.sorted_strandSp.Reverse.bw.gz

data_processing:
The RNA-seq reads were aligned to the hg38 human reference genome using star aligner.
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig - Browser Tracks showing normalized count for visualization on IGV or UCSC geneome browser

source_name: ER+ breast adenocarcinoma

growth_protocol: MCF-7 human epithelia cells from breast adenocarsinoma cells from American Type Cell Culture (ATCC) were maintained in MEM supplemented with 5% calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin. MCF-7 cells were maintained in phenol red-free MEM supplimented with 5% charcoal-dextrantreated calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin for at least 3 days prior to experimentation.

extract_protocol:
MCF-7 cells were seeded at at density of 0.5x10^6 cells per well in a 6-well plate and treated as described above. Total RNA was isolated using the Qiagen RNeasy Plus Mini kit (Qiagen, 74136) according to the manufacturer's protocol.
RNA-seq libraries were generated as previously described with the following modifications [24]. Total RNA from MCF-7 cells treated as indicated was isolated using the Qiagen RNeasy Plus Mini kit (Qiagen, 74136) according to the manufacturer's protocol. Total RNA was then enriched for mRNA using Dynabeads Oligo(dT)25 (Invitrogen, 61002). Further fragmentation, first-strand cDNA synthesis, and subsequent procedures have been done as described [25].The libraries were subjected to quality control analyses, such as optimizing the number of PCR cycles required to amplify each set of libraries, quantifying the final library yield by Qubit fluorometer (Invitrogen, Q32851), and checking the size distribution of the final library by DNA ScreenTape system (Agilent Technologies, G2964AA, 5067–5584, and 5067–5603). The libraries were barcoded with indices as described for the Illumina TruSeq RNA Prep kit, multiplexed, and sequenced using Illumina NextSeq (2000) by 100 bp single-end sequencing.

treatment_protocol: MCF-7 cells  maintained in phenol red-free MEM supplimented with 5% charcoal-dextran treated calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin were seeded at a density of 0.5 x 10^6 cells per well in a 6-well dish one day prior to experimentation. At least biological replicates were used for each experimental condition. For E2 continuous treatment, 100 nM E2 was applied to the cells for the indicated times prior to collection. For E2 washout treatments, cells were treated with 100 nM of E2 for 40 mins., washed onced in stripped medium, then inclubated in stripped medium for the remainder of the experiment.

value: ER+ breast adenocarcinoma

value: epithelial cells

tag: treatment

value: 100nM E2 washout


title: Infected Salivary Gland, time 44, LD, Sample 2

description: Library name: Sample 48

value: Salivary glands

value: WT

value: light/dark


title: GULL_control_3

institute: NIH


title: GULL_control_4


title: M_R_R1


title: Infected Salivary Gland, time 44, LD, Sample 1

description: Library name: Sample 47


title: GULL_control_2


title: Infected Salivary Gland, time 44, DD, Sample 2

description: Library name: Sample 46


title: 100nM E2 washout, 40m + 140m replicate 2

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated actuely for 40mins with 100 nM E2 then washed out for the indicated time.
MCF-7_E2washout_40m_140.sorted_strandSp.Reverse.bw.gz


title: M_R_B3

value: MCSF, RANKL, BMS309403


title: GULL_control_1


title: mGULL_knockdown_3


title: M_R_B2


title: 100nM E2 washout, 40m + 320m replicate 1

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated actuely for 40mins with 100 nM E2 then washed out for the indicated time.
MCF-7_E2washout_40m_320.sorted_strandSp.Forward.bw.gz


title: small RNA-seq Control thorax rep 2

city: Paris

description:
Small RNA
21nt_counts_GEO.tsv
HGKKYBGXM-Sis-carcass-pool-2_S8

value: Thorax


title: small RNA-seq Control thorax rep 1

description:
Small RNA
21nt_counts_GEO.tsv
HGKKYBGXM-Sis-carcass-pool-1_S7


title: 100nM E2 washout, 40m + 80m replicate 2

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated actuely for 40mins with 100 nM E2 then washed out for the indicated time.
MCF-7_E2washout_40m_80.sorted_strandSp.Reverse.bw.gz


title: STAT5B-Y665H-p18_rep2

source_name: Mammary gland

growth_protocol: RNA-seq was done for the mammary tissues at day 13 and 18 of pregnant (p13, p18) at 2-month-old age for wild-type and mutant mice carrying a point mutation in Stat5b-Y665.

value: Mammary gland

value: day 18 of pregnancy (p18)


title: STAT5B-Y665H-p18_rep3


title: Infected Salivary Gland, time 44, DD, Sample 1

description: Library name: Sample 45


title: STAT5B-Y665H-p18_rep1


title: Infected Salivary Gland, time 40, LD, Sample 1

description: Library name: Sample 43


title: M_R3

value: osteoclast

value: macrophage

value: MCSF and RANKL


title: 100nM E2 washout, 40m + 80m replicate 1

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated actuely for 40mins with 100 nM E2 then washed out for the indicated time.
MCF-7_E2washout_40m_80.sorted_strandSp.Forward.bw.gz


title: Infected Salivary Gland, time 40, LD, Sample 2

description: Library name: Sample 44


title: 100nM E2 washout, 40m + 140m replicate 1

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated actuely for 40mins with 100 nM E2 then washed out for the indicated time.
MCF-7_E2washout_40m_140.sorted_strandSp.Forward.bw.gz


title: Healthy controls

description: Library name: Sample1

value: plasma extracellular vesicle

value: healthy


title: Infected Salivary Gland, time 40, DD, Sample 1

description: Library name: Sample 41

value: dark


title: M_R1


title: M_R_B1


title: STAT5B-Y665F-p18_rep3


title: 100nM E2 washout, 40m + 20m replicate 1

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated actuely for 40mins with 100 nM E2 then washed out for the indicated time.
MCF-7_E2washout_40m_20.sorted_strandSp.Forward.bw.gz


title: Infected Salivary Gland, time 40, DD, Sample 2

description: Library name: Sample 42


title: M_R2


title: 100nM E2 washout, 40m + 20m replicate 2

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated actuely for 40mins with 100 nM E2 then washed out for the indicated time.
MCF-7_E2washout_40m_20.sorted_strandSp.Reverse.bw.gz


title: M3

source_name: bone marrow-derived macrophages

value: bone marrow-derived macrophages

value: MCSF


title: STAT5B-Y665F-p18_rep4


title: M2


title: Infected Salivary Gland, time 36, LD, Sample 1

description: Library name: Sample 39


title: STAT5B-Y665F-p18_rep2


title: Infected Salivary Gland, time 36, LD, Sample 2

description: Library name: Sample 40


title: STAT5B-Y665F-p18_rep1


title: 100nM E2 washout, 40m + 0m replicate 2

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated actuely for 40mins with 100 nM E2 then washed out for the indicated time.
MCF-7_E2washout_40m_0.sorted_strandSp.Reverse.bw.gz

value: ER+ breast adenocarcinoma

value: epithelial cells


title: M1


title: DMSO, vehicle control - washout replicate 2

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated actuely for 40mins with DMSO then washed out for the indicated time.
MCF-7_E2washout_veh.sorted_strandSp.Reverse.bw.gz

value: DMSO

value: vehicle control - washout


title: JL_7765_2354069__mousemethylation

type: genomic

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description:
genetically modified GNPs implantation into the mouse cerebellum
205730000024_R02C01

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Data processing involved reading IDAT files using the minfi (v1.44) and sesame (v1.61) packages, with normalization steps including quality masking, inferring Infinium I channel, dye bias correction, and PooBah adjustment to generate beta values for methylation levels (betas_table.txt)

label: Cy5 and Cy3

source_name: tumor,mouse

label_protocol: Standard Illumina Protocol

growth_protocol: For Elp1HET or WT ;Ptch1gRNA MB models, GNPs were isolated from cerebella of P7 Elp1+/-;Cas9-eGFP mice (Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J, JAX#024858) and cultured on Poly-D-Lysine coated dishes in Granule Cell Medium (GCM) (50 ml Neurobasal Medium containing 1x Penicillin/Streptomycin, 2 mM Glutamine, 4.5% D-(+)-Glucose, 1x SPITE Medium Supplement, 1x Oleic Acid Albumin/Linoleic Acid, 1x B27, 1x N-Acetyl Cysteine), and 1 μg/ml recombinant mouse Shh (PeproTech, Inc. Cat#100-45). Next day, the transduction was performed with lentivirus mix carrying guide RNA targeting Ptch1 (gRNA-31 GAGATCTCAGAGCGTGGCT and gRNA-41 GCATAGTGATATGGGTTTCG). After 24 h, the GNPs were harvested from the dishes and suspended in ice cold PBS.For Elp1WT or gRNA;Ptch1gRNA;p53NULL MB models, GNPs were isolated from cerebella of P7 p53NULL mice (B6.129S2-Trp53tm1Tyj/J, JAX#002101) and subjected to the same procedures as described above, except that the virus carrying guide RNA targeting Elp1 was also added for transduction to knockout both the alleles of Elp1 (gRNA-17 TATGACGTCCCCAGAGG).

extract_protocol: Genomic DNA was isolated from tissue samples using the AllPrep DNA/RNA Mini Kit (QIAGEN)

treatment_protocol: NSG mice were injected orthotopically with 1 million cells and monitored for signs of tumor growth with biweekly MRI imaging. Mice were observed daily and euthanized at the onset of signs of sickness including lethargy and neurological abnormalities.

value: tumors


title: Infected Salivary Gland, time 36, DD, Sample 1

description: Library name: Sample 37

value: Salivary glands

value: WT


title: DMSO, vehicle control - washout replicate 1

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated actuely for 40mins with DMSO then washed out for the indicated time.
MCF-7_E2washout_veh.sorted_strandSp.Forward.bw.gz


title: Infected Salivary Gland, time 32, LD, Sample 2

description: Library name: Sample 36

value: light/dark


title: STAT5B-Y665F-p13_rep2

first: Hye Kyung

last: Lee

institute: National Institutes of Health (NIH)

value: Mammary gland

value: day 13 of pregnancy (p13)


title: Infected Salivary Gland, time 36, DD, Sample 2

description: Library name: Sample 38


title: 100nM E2 induction, 6h replciate 2

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.
MCF-7_E2induction_6h.sorted_strandSp.Reverse.bw.gz

value: 100nM E2 induction


title: Infected Salivary Gland, time 32, LD, Sample 1

description: Library name: Sample 35


title: JL_4787_2354061__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
205333480118_R06C01


title: JL_7763_2354068__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
205730000024_R01C01


title: Infected Salivary Gland, time 32, DD, Sample 2

description: Library name: Sample 34


title: JL_7248_2354067__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
205333480118_R06C02


title: STAT5B-Y665F-p13_rep3


title: Infected Salivary Gland, time 32, DD, Sample 1

description: Library name: Sample 33


title: 100nM E2 induction, 3h replicate 2

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.
MCF-7_E2induction_3h.sorted_strandSp.Reverse.bw.gz


title: STAT5B-Y665H-p18-H3K27ac_rep2

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and Bowtie (version 1.2.2) and Samtools (version 1.8), with the parameter ‘-m 1’ to keep only uniquely mapped reads, using the reference genome mm10. Homer30 (version 4.9.1) software was applied to generate bedGraph files, seperately. Integrative Genomics Viewer (version 2.3.98) was used for visualization with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools to remove duplicates. Homer software was applied  for the generation of bedGraph files.
Assembly: mm10
Supplementary files format and content: bedgraph of ChIP-seq

growth_protocol: Mouse mammary gland tissues were harvested at day 13 and 18 of pregnant (p13, p18) of 2-month-old age for wild-type and mutant mice carrying a point mutation in Stat5b-Y665.

extract_protocol:
Chromatin was fixed with formaldehyde (1% final concentration) for 10min at room temperature, and then quenched with glycine (0.125 M final concentration). Samples were processed as previously described. The following antibodies were used for ChIP-seq: STAT5A (Santa Cruz Biotechnology, sc-271542), STAT5B (ThermoFisher scientific, 13-5300), NFIB (Sigma-Aldrich, HPA003956), H3K27ac (Abcam, ab4729) and RNA polymerase II (Abcam, ab5408). Libraries for next-generation sequencing were prepared and sequenced with a HiSeq 3000 or Novaseq 6000 instrument (Illumina). Libraries for sequencing were prepared using standard Illumina protocols.
Libraries for sequencing were prepared using standard Illumina protocols.

value: day 18 of pregnancy (p18)

value: H3K27ac (Abcam, ab4729)


title: JL_4786_2354060__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
205333480118_R05C01


title: 100nM E2 washout, 40m + 0m replicate 1

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated actuely for 40mins with 100 nM E2 then washed out for the indicated time.
MCF-7_E2washout_40m_0.sorted_strandSp.Forward.bw.gz

value: 100nM E2 washout


title: 100nM E2 induction, 3h replicate 1

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.
MCF-7_E2induction_3h.sorted_strandSp.Forward.bw.gz


title: Infected Salivary Gland, time 28, LD, Sample 2

description: Library name: Sample 32


title: STAT5B-Y665H-p18-PolII_rep2

value: RNA polymerase II (Abcam, ab5408)


title: STAT5B-Y665H-p18-H3K27ac_rep1


title: JL_7247_2354065__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
205333480118_R04C02


title: STAT5B-Y665F-p13_rep4


title: Infected Salivary Gland, time 28, LD, Sample 1

description: Library name: Sample 31


title: 100nM E2 induction, 6h replciate 1

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.
MCF-7_E2induction_6h.sorted_strandSp.Forward.bw.gz


title: 100nM E2 induction, 2h replicate 1

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.
MCF-7_E2induction_2h.sorted_strandSp.Forward.bw.gz


title: JL_4781_2354064__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
205333480118_R03C02


title: STAT5B-Y665F-p13_rep1


title: JL_4937_2354066__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
205333480118_R05C02


title: STAT5B-Y665H-p18-PolII_rep1


title: 100nM E2 induction, 1h replicate 1

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.
MCF-7_E2induction_1h.sorted_strandSp.Forward.bw.gz


title: JL_4789_2354063__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
205333480118_R02C02


title: STAT5B-Y665H-p18-STAT5B_rep2

value: STAT5B (ThermoFisher scientific, 13-5300)


title: Infected Salivary Gland, time 28, DD, Sample 1

description: Library name: Sample 29

value: dark


title: Infected Salivary Gland, time 28, DD, Sample 2

description: Library name: Sample 30


title: 100nM E2 induction, 40m replicate 2

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.
MCF-7_E2induction_40m.sorted_strandSp.Reverse.bw.gz

value: ER+ breast adenocarcinoma


title: 100nM E2 induction, 2h replicate 2

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.
MCF-7_E2induction_2h.sorted_strandSp.Reverse.bw.gz

value: epithelial cells


title: STAT5B-Y665H-p18-NFIB_rep1

value: NFIB (Sigma-Aldrich, HPA003956)


title: MB-Ptch1-Elp1-7757_2193127__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
205333480081_R06C01


title: Infected Salivary Gland, time 24, LD, Sample 2

description: Library name: Sample 28


title: STAT5B-Y665H-p18-STAT5B_rep1


title: DMSO, vehicle control - induction replicate 2

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with DMSO
MCF-7_E2induction_veh.sorted_strandSp.Reverse.bw.gz

value: DMSO, vehicle control - induction


title: MB-Ptch1-Elp1-4938_2193126__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
205333480081_R05C01

value: tumors


title: STAT5B-Y665H-p18-NFIB_rep2


title: 100nM E2 induction, 40m replicate 1

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.
MCF-7_E2induction_40m.sorted_strandSp.Forward.bw.gz


title: MB-Ptch1-Elp1-4783_2193125__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
205333480081_R04C01


title: Infected Salivary Gland, time 24, DD, Sample 2

description: Library name: Sample 26

value: Salivary glands


title: STAT5B-Y665F-p18-STAT5B_rep2


title: Infected Salivary Gland, time 24, DD, Sample 1

description: Library name: Sample 25

value: WT


title: Infected Salivary Gland, time 24, LD, Sample 1

description: Library name: Sample 27

value: light/dark


title: DMSO, vehicle control - induction replicate 1

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with DMSO
MCF-7_E2induction_veh.sorted_strandSp.Forward.bw.gz


title: 100nM E2 induction, 1h replicate 2

description:
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.
MCF-7_E2induction_1h.sorted_strandSp.Reverse.bw.gz


title: STAT5B-Y665F-p18-STAT5B_rep1

value: Mammary gland


title: JL_7760_2354062__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
205333480118_R01C02


title: MB-Ptch1-7758_2193124__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
205333480081_R03C01


title: MT2

city: Xianyang

first: Young

last: Tang

state: Shaanxi

address: #22 Xinong Road, Yangling District

department: College of Veterinary Medicine

institute: Northwest A&F University

description: Library name: Sample12

data_processing:
1.Clean reads were obtained by removing adapter-containing, poly-N, and low-quality reads from raw data. The reference genome index was built using Hisat2 v2.0.5, and paired-end clean reads were aligned to the reference genome.
2.The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
3.FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
4.Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
5.Used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: ncbi_bos_taurus_gcf_002263795_3_ars_ucd2_0 and ensembl_107_mus_musculus_c57bl6nj_c57bl_6nj_v1_toplevel
Supplementary files format and content: Normalized Counts.csv

source_name: Blastocyst

extract_protocol:
Total RNA was extracted from bESCs and mESCs using the RNeasy Mini Kit (Qiagen, #74104) following the manufacturer’s protocol.
Total RNA was purified to obtain mRNA using poly-T beads. mRNA was fragmented and reverse transcribed into first-strand cDNA with random hexamers and M-MuLV Reverse Transcriptase. Second-strand synthesis was done with DNA Polymerase I and RNase H. DNA ends were blunted and adenylated, followed by ligation of hairpin loop adaptors. cDNA fragments (370–420 bp) were selected using AMPure XP system. PCR amplification was performed with Phusion polymerase, universal primers, and index primers. Final PCR products were purified and library quality assessed on Agilent Bioanalyzer 2100.

value: Blastocyst

value: embryonic stem cells

tag: batch


title: Infected Salivary Gland, time 20, LD, Sample 2

description: Library name: Sample 24


title: MB-Ptch1-4789_2193123__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
205333480081_R02C01


title: STAT5B-Y665F-p18-NFIB_rep2

address: 8 CENTER DR RM 107

value: day 18 of pregnancy (p18)


title: Infected Salivary Gland, time 20, LD, Sample 1

description: Library name: Sample 23


title: STAT5B-Y665F-p18-NFIB_rep1


title: MB-Ptch1-4786_2193122__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
205333480081_R01C01


title: MC2

description: Library name: Sample10


title: JH35_MUT_2351_2629203__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
207363410070_R06C01


title: STAT5B-Y665F-p18-PolII_rep3


title: JH35_MUT_2458_2629208__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
207363410070_R05C02


title: STAT5B-Y665F-p18-PolII_rep2


title: Infected Salivary Gland, time 20, DD, Sample 2

description: Library name: Sample 22


title: MC1

description: Library name: Sample9


title: Infected Salivary Gland, time 20, DD, Sample 1

description: Library name: Sample 21


title: STAT5B-Y665F-p18-PolII_rep1


title: Infected Salivary Gland, time 16, LD, Sample 1

description: Library name: Sample 19


title: Infected Salivary Gland, time 16, LD, Sample 2

description: Library name: Sample 20


title: LPS+LDO_2

city: xi'an

first: Wei

last: Gaofei

address: beilin

institute: Northwestern Polytechnical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: BMDM

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: BMDM

value: Bone marrow-derived macrophages

value: LPS+LDO


title: JH35_MUT_2456_2629207__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
207363410070_R04C02


title: JH35_MUT_2217_2629202__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
207363410070_R05C01


title: LPS+LDO_3


title: Infected Salivary Gland, time 16, DD, Sample 2

description: Library name: Sample 18


title: STAT5B-Y665F-p18-H3K27ac_rep2

city: Bethesda

value: H3K27ac (Abcam, ab4729)


title: LPS+LDO_1


title: JH35_MUT_2209_2629201__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
207363410070_R04C01


title: LPS_3

value: LPS


title: JH35_MUT_2453_2629206__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
207363410070_R03C02


title: MT1

description: Library name: Sample11


title: Infected Salivary Gland, time 16, DD, Sample 1

description: Library name: Sample 17

value: dark


title: LPS_2


title: STAT5B-Y665F-p18-H3K27ac_rep1


title: WT-p18-STAT5B_rep3

value: STAT5B (ThermoFisher scientific, 13-5300)


title: Infected Salivary Gland, time 12, LD, Sample 2

description: Library name: Sample 16


title: WT-p18-STAT5B_rep2


title: JH35_MUT_2365_2629205__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
207363410070_R02C02


title: Infected Salivary Gland, time 12, DD, Sample 2

description: Library name: Sample 14


title: JH35_WT_2470_2629200__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
207363410070_R03C01


title: WT-p18-STAT5B_rep1


title: ATO-2

city: Shanghai

first: Jia

middle: bing

last: Li

address: 197, Ruijin Er Street

institute: Shanghaijiaotong university

description: CDX model in C57 mice treated with ATO

data_processing:
The raw reads were initially processed using FastQC (v0.10.1) for quality control;
adapter sequences and poor-quality reads were removed using Cutadapt (v1.9.1)
Quality-filtered reads were then aligned to the Mus musculus genome (GRCm38) using HISAT2 (v2.0.1)
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: tumor

extract_protocol:
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS
Total RNA was isolated using TRIzol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: condition

value: C57 mice ATO group

value: tumor

value: ATO


title: WT-p18-NFIB_rep2

value: NFIB (Sigma-Aldrich, HPA003956)


title: WT-p18-NFIB_rep1

value: WT


title: Infected Salivary Gland, time 12, DD, Sample 1

description: Library name: Sample 13

source_name: Salivary glands

value: Salivary glands


title: ATO-1

description: CDX model in C57 mice treated with ATO