title: H9_EGFP_OE48h_smartseq_rep1

data_processing:
Illumina Casava1.8 software used for basecalling.
All RNA-seq data were trimmed by Trim Galore (v0.6.4) then mapped to transcriptome of mm9/hg19 by STAR (v2.5.3a). The gene expression level was calculated by Cufflinks (v2.2.1) based on the annotation of hg19 refFlat database from UCSC genome browser.
Ribo-lite data were trimmed with cutadapt (v1.14) with parameters: cutadapt --trim-n -a GATCGGAAGAGCACACGTCTG -a AGAGCACACGTCTG <input.file> | cutadapt -u 3 -a A{100} --no-indels -e 0.16666666666666666 - | cutadapt -O 8 --match-read-wildcards -g GTTCAGAGTTCTACAGTCCGACGATCSSS -m 18 - -o <output.file> , and the trimmed reads were sequentially mapped to human rRNAs sequences (hg19) using Bowtie2 (v2.2.2). Those aligned to rRNA were discarded, and the rest reads were mapped to transcriptome of hg19 using STAR (v2.5.3a). The gene expression level was then calculated by Cufflinks (v2.2.1) based on the annotation defined by hg19 refFlat database from the UCSC genome browser.
The paired-end Stacc–seq reads were aligned with the parameters: -t -q -p 96 -N 1 -L 25 -X 2000 --no-unal -x by Bowtie2 (v 2.2.5). All reads were aligned to either the human (hg19) or the Drosophila (dm6) (spike-in) reference genome.
Genome_build: hg19
Supplementary_files_format_and_content: The RNA FPKM tables including the FPKM of each gene for all the samples.
Supplementary_files_format_and_content: The BedGraph for Stacc-seq samples.


title: chr4KO-rep21

status: Public on Oct 08 2022

type: SRA

city: Tsukuba

first: Inoue

last: Kimiko

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

country: Japan

institute: RIKEN

description:
RLTR45-int putative null embryos
SMART-Seq HT kit
Raw.read.counts_KO.embryos.txt

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence using trimmomatic.
Trimmed sequence reads were mapped to the mouse genome build mm10 using STAR.
Read count extraction and normalization were performed using featureCounts and R, respectively.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw read counts for genes and transposal elements in each sample.

molecule: polyA RNA

organism: Mus musculus

source_name: Embryo

growth_protocol: C57BL/6N female mice at 4–20 weeks of age were superovulated by injection of 7.5 IU equine chorionic gonadotropin or anti-inhibin serum, followed 46–52 h later by injection of 7.5 IU human chorionic gonadotropin. Female mice were euthanized by cervical dislocation 16 h after the hCG injection, and then cumulus–oocyte complexes were collected from the ampullae of excised oviducts 16 h after the hCG injection, and placed in 100-μL droplets of human tubal fluid medium. For in vitro fertilization, spermatozoa were collected from the cauda epididymidis of adult DBA2 male mice and preincubated for at least 30 min in a 400-μL droplet of HTF. After preincubation, 3–5 μL of the sperm suspension was added to the oocyte cultures. At 3 h post-insemination, morphologically normal fertilized embryos were collected and cultured in potassium simplex optimized medium. For somatic cell nuclear transfer, cumulus cells used as nuclear donors were collected from wild-type and Xist heterozygous knockout female mice with a BDF1 (C57BL/6N ×DBA2) genetic background. Recipient oocytes were collected from BDF1 female mice following superovulation as above, and placed in KSOM droplets containing 0.1% bovine testicular hyaluronidase to remove cumulus cells. The cumulus-free oocytes were enucleated in Hepes-buffered KSOM containing 7.5 μg/mL cytochalasin B using a Piezo-driven pipette. After being cultured in fresh KSOM for 1 h, the enucleated oocytes were injected with cumulus cell nuclei in Hepes-buffered KSOM at room temperature. After 1 h culture, the injected oocytes were activated by culture in a Ca2+-free KSOM containing 3 mM strontium chloride and 5 μg/mL cytochalasin B for 1 h. The reconstructed oocytes were cultured in KSOM containing 5 μg/mL cytochalasin B for 5 h. After being washed thoroughly, SCNT-derived embryos were injected with 10 pL of 1500 ng/μL mouse Kdm4d mRNA at 5–6 h post-activation.

extract_protocol:
IVF- and SCNT-derived embryos were collected at 69–70 h post-insemination/activation, and washed twice in 0.05% bovine serum albumin in phosphate-buffered saline.
RNA-seq libraries were constructed by using SMART-Seq v4 kits or SMART-Seq HT kits.

tag: tissue

value: Embryo

tag: developmental stage

value: Morula

tag: genotype

value: Transfection of Cas9/gRNA targetting RLTR45-int on chr4

tag: treatment

value: IVF


title: B3-4B-1

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

country: China

institute: Fudan University

library_source: genomic

data_processing:
Library strategy: DAP-seq
Sequencing reads were cleaned with the fastp(version 0.20.0) and Trim Galore (version 0.4.4), which eliminated bases with low quality scores(< 25) and irregular GC contents, sequencing adapters, and short reads.
The remaining clean reads were mapped to the Chinese Spring (T. aestivum) genome with the Burrows–Wheeler Aligner(version 0.7.17-r1188).
The MACS(version 2.2.6) program was used to identify the read-enriched regions(peaks) based on the criteria: P < 1e−10. The peaks detected from samples introduced with Halo tag only were considered as non-specific bindings, and TF peaks overlapping with peaks detected from Halo samples were removed for subsequent analysis.
Genome_build: IWGSC RefSeq v1.1
Supplementary_files_format_and_content: peak files and bigwig files

molecule: genomic DNA

organism: Triticum aestivum

source_name: Triticum aestivum seedling

growth_protocol: 16h light, 8h dark, 22°C

extract_protocol:
Genomic DNA was extracted from leaves using Plant DNAzol Reagent(invitrogen). RNA was extracted using TRIzol.
Genomic DNA was fragmented. And then end repaired using the End-It kit(Lucigen) and A-tailed using Klenow(3'-5' exo-; NEB). Truncated Illumina Y-adapter was ligated to DNA using T4 DNA Ligase(Promega). Full length TF was cloned into pIX-Halo vector. Halo-tagged TF was expressed in vitro using TNT SP6 Coupled Wheat Germ Extract System(Promega). Halo-TF was immobilized by Magne HaloTag Beads(Promega) and then incubated with the DNA library. TF specific binding DNA was eluted for 10 min at 98°C and amplified with indexed Illumina primer using Phanta Max Super-Fidelity DNA Polymerase(Vazyme). Meanwhile, to capture background DNA which captured by Halo, pIX-Halo vector without TF cloned was expressed and incubated with the DNA library as well. The PCR product was purified using VAHTS DNA Clean Beads(Vazyme).

tag: dap antibody

value: Halo

tag: antibody manufacturer

value: Promega

tag: antibody catalog #

tag: cultivar

value: Chinese Spring


title: h_MII_10_Ribo_rep2

city: Peking

first: Zhuoning

last: Zou

address: 30 Shuangqing Rd

department: School of Life Sciences

institute: Tsinghua University

data_processing:
Library strategy: Ribo-seq
Illumina Casava1.8 software used for basecalling.
All RNA-seq data were trimmed by Trim Galore (v0.6.4) then mapped to transcriptome of mm9/hg19 by STAR (v2.5.3a). The gene expression level was calculated by Cufflinks (v2.2.1) based on the annotation of hg19 refFlat database from UCSC genome browser.
Ribo-lite data were trimmed with cutadapt (v1.14) with parameters: cutadapt --trim-n -a GATCGGAAGAGCACACGTCTG -a AGAGCACACGTCTG <input.file> | cutadapt -u 3 -a A{100} --no-indels -e 0.16666666666666666 - | cutadapt -O 8 --match-read-wildcards -g GTTCAGAGTTCTACAGTCCGACGATCSSS -m 18 - -o <output.file> , and the trimmed reads were sequentially mapped to human rRNAs sequences (hg19) using Bowtie2 (v2.2.2). Those aligned to rRNA were discarded, and the rest reads were mapped to transcriptome of hg19 using STAR (v2.5.3a). The gene expression level was then calculated by Cufflinks (v2.2.1) based on the annotation defined by hg19 refFlat database from the UCSC genome browser.
The paired-end Stacc–seq reads were aligned with the parameters: -t -q -p 96 -N 1 -L 25 -X 2000 --no-unal -x by Bowtie2 (v 2.2.5). All reads were aligned to either the human (hg19) or the Drosophila (dm6) (spike-in) reference genome.
Genome_build: hg19
Supplementary_files_format_and_content: The RNA FPKM tables including the FPKM of each gene for all the samples.
Supplementary_files_format_and_content: The BedGraph for Stacc-seq samples.

molecule: total RNA

organism: Homo sapiens

source_name: Oocyte

extract_protocol:
Ribo-lite was performed as previously described (Xiong et al., NCB, accepted), after removing the zona pellucida, oocytes or embryos extact preparation by detergent lysis, RNase I digestion, ultracentrifugation and size selection through polyacrylamide gel, RPFs were subjected to a small RNA-seq library preparation method (CATS, Diagenode).
Ribo-lite libraries were prepared using Ribo-lite developed in-house (accepted by NCB in principle), RPFs were subjected to a small RNA-seq library preparation method (CATS, Diagenode).

value: Oocyte

tag: cell type

value: MII oocyte

value: WT


title: MB3271_10X_sc_ATAC-seq

city: Cincinnati

first: Zaili

last: Luo

state: OH

address: 3333 Burnet Ave.

country: USA

institute: CCHMC

data_processing:
For scRNA-seq, According to the 10× CellRanger’s pipeline, the raw base call (BCL) files were demultiplexed into FASTQ files. The FASTQ files were aligned to the reference human genome GRCh38 (hg38) to generate raw gene-barcode count matrices. When clustering multiple samples together, we aggregated the multiple runs together to normalize on sequencing depth and re-computed the gene-barcode matrices.
For scATAC-seq, the data processing unit takes raw fastq files as input and outputs peak-by-cell count matrix, QC report and genome track files. It consists of the following modules: demultiplexing, adaptor trimming, read mapping, peak calling, cell calling, genome track file generation and quality control assessment. The downstream analysis unit consists of the following modules: dimension reduction, cell clustering, differential accessibility analysis, gene ontology analysis, TF motif enrichment analysis, TF footprinting analysis, linking regulatory DNA sequences with gene promoters, and integration of multiple datasets. We provide flexible options for most of analysis modules.
For Cut&run, Bam files were calculated using Bowtie 2 and transform to Bigwig file using esATAC in R.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: human MB tissue

growth_protocol: hNSCs and MB004 cells were cultured in complete NPC medium (Neurobasal medium containing B27 supplement, N2 supplement, 2 mM L-glutamine, 20 ng/ml EGF, 20 ng/ml bFGF, 2 mg/ml Heparin and 50 μg/ml BSA). Spheres were dissociated at a diameter of 100-200 μm and were changed with complete NPC medium every 3 days to maintain cell metabolic activity.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: no treatment for the 2 cell lines


title: chr4KO-rep19

description:
RLTR45-int putative non-null embryos
SMART-Seq HT kit
Raw.read.counts_KO.embryos.txt


title: MB004_HNRNPH1

data_processing:
Library strategy: Cut&run
For scRNA-seq, According to the 10× CellRanger’s pipeline, the raw base call (BCL) files were demultiplexed into FASTQ files. The FASTQ files were aligned to the reference human genome GRCh38 (hg38) to generate raw gene-barcode count matrices. When clustering multiple samples together, we aggregated the multiple runs together to normalize on sequencing depth and re-computed the gene-barcode matrices.
For scATAC-seq, the data processing unit takes raw fastq files as input and outputs peak-by-cell count matrix, QC report and genome track files. It consists of the following modules: demultiplexing, adaptor trimming, read mapping, peak calling, cell calling, genome track file generation and quality control assessment. The downstream analysis unit consists of the following modules: dimension reduction, cell clustering, differential accessibility analysis, gene ontology analysis, TF motif enrichment analysis, TF footprinting analysis, linking regulatory DNA sequences with gene promoters, and integration of multiple datasets. We provide flexible options for most of analysis modules.
For Cut&run, Bam files were calculated using Bowtie 2 and transform to Bigwig file using esATAC in R.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: human MB cell lines

tag: chip antibody


title: B3-4A-1


title: MB3076_10X_sc_ATAC-seq


title: HEK293T-hACE2-cov rep2

city: Duarte

first: Guihua

last: Sun

state: CA

address: 1500 East Duarte Rd.

department: Department of Neurodegenerative Diseases

institute: City of hope

data_processing:
Basecalls performed using CASAVA version 1.8
Cutadapt use to remove 3 nts at 5'end and 3' adaptor
miRge 2.0 was used for small RNA analysis
Genome_build: hg38
Supplementary_files_format_and_content: *mapped.csv (reads mapped to miRbase v22 by miRge 2)
Supplementary_files_format_and_content: *unmapped.csv (reads did not map to miRbase v22 by miRge 2)
Supplementary_files_format_and_content: *miR.Counts.csv (human miRNA count by miRge 2)

source_name: HEK293T-hACE2 cell line

extract_protocol:
Trizol extracted total RNA
Illumina small RNA library with modification
size fractionation of small RNA

treatment_protocol: MOI=1, infect for 72 hours

tag: cell line

value: human embryonic kidney cells

value: hACE2 overexpression

tag: infection


title: B3-2B-2


title: chr4KO-rep18


title: B3-2A-1


title: h_MI_19_Ribo_rep2

value: MI oocyte


title: h_ICM_15_Ribo_rep2

source_name: Preimplantation embryo

value: Preimplantation embryo

value: ICM


title: chr4KO-rep17


title: HEK293T-hACE2-cov rep1


title: h_ICM_10_Ribo_rep1


title: AP2-ERF-6D-1


title: AP2-RAV-4B-1


title: chr4KO-rep16


title: HEK293T-hACE2-mock rep1

value: mock


title: HEK293T-hACE2-mock rep2


title: AP2-ERF-6A-2


title: h_H1_hESC_500_Ribo_rep1

source_name: Embryonic stem cell

value: Embryonic stem cell


title: CEBPB_KD2 [RNA-seq]

city: Sendai

first: Hozumi

last: Motohashi

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University

data_processing:
Raw fastq sequencing files were aligned to the hg19 reference genome using STAR version 2.7.0d with the primary genome annotation in GENCODE Release 19.
FPKM calculation was performed by using StringTie version 2.1.4.
For differential expression analysis, the htseq-count command, a part of HTSeq package version 0.13.5, was used to count reads for each gene.
DESeq2 version 1.26.0 was used to identify differentially expressed genes based on the read counts.
Genome_build: hg19
Supplementary_files_format_and_content: A tab-delimited text file includes FPKM values for each sample and differential expression analysis results for each gene.

source_name: cancer cells

growth_protocol: A549 cells were incubated in the DMEM supplemented with 10% FBS and penicillin/streptomycin.The cells were cultured at 37oC under 5% CO2 and saturated humidity in 20% oxygen.

extract_protocol:
Total RNA was purified using RNeasy Mini Kit (Qiagen).
Total RNA from the A549 cells was used to prepare cDNA sequencing libraries using the SureSelect Strand-Specific RNA library preparation kit (Agilent Technologies). The libraries were quantified by qMiSeq and sequenced on a HiSeq2500  (Illumina) to generate 76-base single-end reads.

treatment_protocol: A549 cells were transfected with control siRNA or CEBPB siRNA-1, CEBPB siRNA-2. 24hrs after transfection, the culture medium was replaced with fresh DMEM supplemented with 10% FBS and penicillin/streptomycin. After additional 24 hrs, cell were harvested for RNA purification.

value: adeno carcinoma

value: lung tissue

value: CEBPB siRNA-2

value: A549 cells


title: h_H1_hESC_1000_Ribo_rep2


title: chr4KO-rep14

value: Embryo

value: Morula

value: Transfection of Cas9/gRNA targetting RLTR45-int on chr4

value: IVF


title: Control_2 [RNA-seq]

value: Control siRNA


title: chr4KO-rep20


title: AP2-ERF-6A-1

value: Halo

value: Promega

value: Chinese Spring


title: h_MI_4_Ribo_rep1

value: Oocyte

value: MI oocyte

value: WT


title: h_GV_18_Ribo_rep1

value: GV oocyte


title: AP2-ERF-5D-1


title: CEBPB_KD1 [RNA-seq]

value: CEBPB siRNA-1


title: AP2-ERF-5B-2


title: HEK293_1000_Ribo

source_name: Embryonic kidney 293 cell

value: Embryonic kidney 293 cell


title: AP2-ERF-5B-1


title: h_GV_16_Ribo_rep2


title: Control_1 [RNA-seq]

value: adeno carcinoma

value: lung tissue


title: chr4KO-rep11


title: chr4KO-rep12


title: Control_2_INPUT

data_processing:
Raw sequenced reads were mapped into hg19 using BWA 0.7.17.
Duplicated reads were marked by using SAMBLASTER version 0.1.26.
Duplicates and reads with mapping quality less than 6 were removed using SAMTools version 1.7.0.
PyMaSC version 0.3.2 was used to estimate a mean fragment length for each ChIPped sample.
Peaks were called with MACS2 version 2.2.7.1 with the following parameters: --SPMR --nomodel --extsize <mean_fragment_size>
Genome_build: hg19
Supplementary_files_format_and_content: Peak files (narrowPeak format) were generated by MACS2.
Supplementary_files_format_and_content: BigWig files were converted from bedGraph files by the bedGraphToBigWig command. They include the normalized (per 1M reads) depth of treat DNA fragment pileup calculated by MACS2.

extract_protocol:
Lysates were prepared from sonicated nuclei, and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEW ENGLAND BioLabs). The libraries were further purified and size-selected using an AMPure XP Kit (Beckman Coulter) and were quantified using a quantitative MiSeq (qMiSeq) method. Optimally diluted libraries were sequenced on a HiSeq2500 (Illumina) to generate 101-base single-end reads.

treatment_protocol: A549 cells were transfected with control siRNA or CEBPB siRNA-1, CEBPB siRNA-2. 24hrs after transfection, the culture medium was replaced with fresh DMEM supplemented with 10% FBS and penicillin/streptomycin. After additional 24 hrs, cell were harvested for chromatin precipitation.

tag: tissue source


title: h_8cell_3PN_22_Ribo_rep2

value: Preimplantation embryo


title: CEBPB_KD2_INPUT

value: CEBPB siRNA-2


title: chr4KO-rep15

value: Embryo

value: Morula


title: AP2-ERF-4B-2


title: CEBPB_KD1_INPUT


title: chr4KO-rep9

value: Transfection of Cas9/gRNA targetting RLTR45-int on chr4

value: IVF


title: h_8cell_2PN_22_Ribo_rep1


title: chr4KO-rep7


title: Control_1_INPUT

value: Control siRNA


title: AP2-DREB-5B-3

value: Halo

value: Promega


title: CEBPB_KD2_H3K27ac

value: H3K27ac  (MABI0309, MAB Institute)


title: h_2cell_3PN_22_Ribo_rep2


title: AP2-DREB-2D-1

value: Chinese Spring


title: h_4cell_2PN_22_Ribo_rep1

value: WT


title: chr4KO-rep13


title: AP2-DREB-1D-1


title: h_4cell_3PN_20_Ribo_rep2


title: chr4KO-rep6


title: Control_2_H3K27ac


title: h_2cell_2PN_21_Ribo_rep1


title: chr4KO-rep5


title: h_zygote_3PN_25_RNA_rep2

extract_protocol:
Oocytes, embryos (after removing the zona pellucida) or cells extact preparation by detergent lysis, and RNA-Seq libraries were prepared using Smart-Seq2 protocol with slightly modification.
RNA libraries were prepared for sequencing using Smart-seq2 protocols as previously described (Picelli et al., 2014).


title: chr4KO-rep10


title: AP2-DREB-1A-1


title: AP2-DREB-1B-1


title: chr4KO-rep4


title: AP2-ERF-3A-1


title: Control_1_H3K27ac


title: chr4KO-rep3


title: Hu1125_islet

description:
small RNA high throughput sequencing
Human islets and acinar cells miRNA count.xlsx

data_processing:
Basecalls performed using CASAVA version 1.8
cutadapt to remove three nucletide from 5' end
miRge
DEseq2

source_name: Islets

extract_protocol:
Trizol extractd total RNA
Modified illumina v1.5 protocol, 3 random nucleotide added to the end of the 5' adaptor

value: Primary cells

value: Pancreas


title: h_zygote_2PN_21_RNA_rep1


title: chr4KO-rep8


title: h_MII_9_RNA_rep1

value: Oocyte

value: MII oocyte


title: AP2-D


title: chr4KO-rep2


title: AP2-B


title: Hu1125_acinar

source_name: Acinar cells


title: Hu1123_islet


title: Alfin-4D-1


title: h_MII_10_RNA_rep2


title: chr4KO-rep1


title: Hu1123_acinar


title: Morula-SCNT-rep7

description:
SMART-Seq v4 kit
Raw.read.counts_IVF.SCNT.embryos.txt

value: Xist knockout, Kdm4d mRNA injection

value: SCNT


title: h_MI_19_RNA_rep2

value: MI oocyte


title: RNA-Seq MAP cells, Rosi3D 2

city: Indianapolis

first: Jisun

last: So

state: IN

address: 635 Barnhill Drive

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

data_processing:
Sequence reads were pre-processed by fastp for adaptor trimming and filtering, and then aligned to GrCM38/mm10 using STAR
Filtered reads were assigned to transcriptome and quantified by featureCounts.
Assembly: mm10
Supplementary files format and content: txt (a master matrix of raw counts from all samples)

source_name: Immortalized mouse adipocyte progenitor (MAP) cells

growth_protocol:
MAP cells were maintained in DMEM supplemented with 10% fetal bovine serm (FBS) and antibiotics.
Upon cell confluency (designated day 0, D0),  adipogenic differentation was induced with 5mg/ml insulin,  500uM isobutylmethylxanthine,  1uM dexamethasone, and  1uM rosiglitazone for 2 days.
MAP cells were then treatwed with 5mg/ml insulin and 1uM rosiglitazone for another 2 days for full differentiation.

extract_protocol:
RNA was harvested using TRIzol (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
The extracted RNA was first purified using the MinElute Cleanup Kit, and the RNA libraries for RNA-seq were prepared using the NEBNext rRNA Depletion Kit (New England BioLabs, Inc.) following manufacturer's protocols.

treatment_protocol: Adipocyte browning was induced by treating fully differentiated adipocytes (at day 7-8) with forskolin for 4 hours, 1 day, or 3 days or with rosiglitazone for 3 days.

value: adipocyte progenitor cells

value: rosiglitazone treatment

tag: time


title: Hu1122_islet


title: Morula-SCNT-rep6

value: Embryo

value: Morula


title: RNA-Seq MAP cells, Rosi3D 3

value: Immortalized mouse adipocyte progenitor (MAP) cells


title: CEBPB_KD1_H3K27ac

value: adeno carcinoma

value: lung tissue

value: CEBPB siRNA-1


title: RNA-Seq MAP cells, FSK3D 3

value: forskolin treatment


title: h_ICM_10_RNA_rep1

value: Preimplantation embryo

value: ICM

value: WT


title: Hu1122_acinar

value: Primary cells

value: Pancreas


title: h_ICM_15_RNA_rep2


title: RNA-Seq MAP cells, Rosi3D 1


title: Morula-SCNT-rep4

value: Xist knockout, Kdm4d mRNA injection


title: Morula-SCNT-rep5

value: SCNT


title: Hu1121_islet


title: Hu1121acinar


title: h_H1_hESC_500_RNA_rep1

value: Embryonic stem cell


title: h_H1_hESC_1000_RNA_rep2


title: RNA-Seq MAP cells, FSK3D 1

value: adipocyte progenitor cells


title: Hu1120_islet


title: h_MI_4_RNA_rep1

value: Oocyte

value: MI oocyte


title: h_GV_18_RNA_rep1

value: GV oocyte


title: RNA-Seq MAP cells, FSK1D 3

value: Immortalized mouse adipocyte progenitor (MAP) cells


title: Hu1120_acinar


title: Hu1119_islet


title: RNA-Seq MAP cells, FSK1D 2


title: Morula-IVF-rep8

value: Embryo

value: Morula

value: IVF


title: h_GV_16_RNA_rep2


title: RNA-Seq MAP cells, FSK1D 1

value: forskolin treatment


title: Morula-IVF-rep7


title: HEK293_1000_RNA

value: Embryonic kidney 293 cell


title: Hu1119_acinar


title: Morula-IVF-rep6


title: Hu1117_islet


title: Morula-SCNT-rep3


title: Hu1117_acinar


title: RNA-Seq MAP cells, FSK4h 3


title: h_8cell_2PN_22_RNA_rep1

value: Preimplantation embryo


title: Morula-IVF-rep5

value: WT


title: h_8cell_3PN_22_RNA_rep2


title: RNA-Seq MAP cells, FSK4h 2


title: h_4cell_3PN_20_RNA_rep2


title: Morula-IVF-rep4


title: RNA-Seq MAP cells, FSK4h 1


title: RNA-Seq MAP cells, FSK3D 2


title: RNA-Seq MAP cells, Control 3

value: vehicle


title: Morula-IVF-rep3


title: Morula-SCNT-rep1


title: Morula-SCNT-rep2


title: Hu1116_acinar

value: Primary cells

value: Pancreas


title: h_2cell_3PN_22_RNA_rep2


title: RNA-Seq MAP cells, Control 2


title: RNA-Seq MAP cells, Control 1


title: Morula-IVF-rep2


title: h_2cell_2PN_21_RNA_rep1


title: Morula-IVF-rep1


title: h_4cell_2PN_22_RNA_rep1


title: Hu1116_islet


title: Brain tissue RESt-overexpressing mouse2

status: Public on Oct 07 2022

city: Houston

first: Bin

last: Liu

state: TX

address: 1515 Holcombe BLVD

department: epigenetics and molecular carcinogenesis

institute: University of Texas MD Anderson Cancer Center

data_processing:
Agilent GeneSpring GX11.5

Assembly: mm10
Supplementary files format and content: text file represents counts

source_name: Brain

extract_protocol: Total mRNAs were extracted, using TRIzol reagents (Invitrogen) according to the manufacturer’s instructions, from three sources: forebrains of E18.5 N- hRESTov/+ mice and their LSL-hREST littermates, striata of 2-month-old D-hRESTov/+ mice and their LSL-hREST littermates, and YFP-sorted brain cells of the D-hRESTov/+ mice and their LSL-hREST littermates.

value: Brain

value: Brain cells Neurons/Glia

value: RESt-overexpressing


title: Brain tissue RESt-overexpressing mouse3


title: Brain tissue RESt-overexpressing mouse1


title: Brain tissue wild type mouse3

value: wild type


title: Brain tissue wild type mouse2


title: Brain tissue wild type mouse1


title: Untreated HUVEC [SK02_Huvec_Unt]

type: RNA

city: bethesda

first: abdel

last: elkahloun

state: MD

address: 50 south dr

institute: nih

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix mouse GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing:
Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: Biotin

source_name: Untreated HUVEC

label_protocol: Per RNA labeling, 300 nanograms  of total RNA was used in conjunction with the Affymetrix recommended protocol GeneChip WT Terminal Labeling and Controls Kit (Cat#901525)

growth_protocol: Jurkat and JinB8 T cells {Reinhold, 1999 #16} were cultured using RPM1 1640 medium supplemented with 10% FBS (Gemini Bio, USA), glutamine and penicillin/streptomycin (Thermo Fischer Scientific, USA) as described previously {Kaur, 2011 #17}.

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Jurkat and JinB8 T cells were cultured in serum-free HITES medium as described previously {Kaur, 2011 #17}. In brief, ~1x106 Jurkat WT and JinB8 T cells were cultured overnight with 50 ml of HITES media using 175 cm2 flasks in triplicate for each cell type. Cells were centrifuged at 300 g for 5 minutes, and the conditioned media were transferred into new tubes. The cell free conditioned media was further centrifuged at 2000 g for 10 minutes to remove cell debris. The cell conditioned media of each flasks were concentrated using 15 ml amplicon with 10,000 MW cutoff to a volume of 1 ml. The concentrated media was pooled together and centrifuged at 16000 g for 30 minutes, and EVs were purified using Exo-spin Exosome Purification with size exclusion chromatography (SEC) from Cell Guidance System according to the manufacturer’s instructions. Conditioned media from Jurkat and JinB8 cells were prepared using HITES media as described in the EV extraction method. The size distribution of EVs was analyzed using the Nanoview platform from concentrated conditioned media derived from WT and JinB8 T cells.

value: HuVEC

value: Normal endothelial cell line

value: Untreated HUVEC


title: HUVEC treated with CD63+EVs derived from JINB9 [SK23_Huvec_JINB8_CD63]


title: HUVEC treated with only IgG [SK10_Huvec_IgGbeads]

source_name: HUVEC treated with only IgG

value: HUVEC treated with only IgG


title: Untreated HUVEC [SK03_Huvec_Unt]


title: HUVEC treated with MHC+EVs derived from Jurkat [SK16_Huvec_JK_MHC]


title: HUVEC treated with CD63+EVs derived from Jurkat [SK19_Huvec_JK_CD63]


title: HUVEC treated with CD63+EVs derived from JINB8 [SK22_Huvec_JINB8_CD63]


title: HUVEC treated with MHC+EVs derived from JINB12 [SK26_Huvec_JINB8_MHC]


title: HUVEC treated with MHC+EVs derived from JINB11 [SK25_Huvec_JINB8_MHC]


title: PAO1 SDS treated replicate 1

city: Singapore

first: Xianghui

address: 60 Nanyang Drive, SBS-01N-27

country: Singapore

institute: Nanyang Technological Univ. of Singapore

data_processing:
The raw reads from 48 samples were processed using cutadapt (version 1.2.1) with default parameters, except --overlap 10 -m 10 -q 20.
Each fastq file was mapped to rRNA sequences of the corresponding genomes (P. aeruginosa PAO1, P. protegens Pf-5 and K. pneumoniae KP-1 with GenBank accession numbers  NC_002516.2, CP000076.1 and CP012883.1 respectively)  or combined rRNA sequences from all the 3 genomes ( in case of mixed samples), using bowtie2 (version 2.2.6, running default parameters except -t -q -p 5 --un ). The unmapped reads from each sample were mapped to all the three genomes separately using bowtie2 (version 2.2.6, running default parameters except -t -q -p 5 --un ). Reads having multiple alignments within each genomes were removed (reads with "XS:i:" flag in the SAM file). The SAM files were further filtered for uniquely mapped reads (reads not mapping to muti-genomes ).
Transcript abundance estimation was subsequently performed by HTSeq v0.13.5 (Anders et al 2015) followed by differential expression analysis by DESeq2 v1.30.1 (Love et al 2014).  Genes with absolute value of log2 fold change (log2FC) ≥1 and adjusted p-value <=0.05 were considered as DEGs in comparative two-group analyses
Assembly: P. aeruginosa PAO1, P. protegens Pf-5 and K. pneumoniae KP-1 reference genomes (GenBank accession numbers:  AE004091, CP000076 and CP012883, respectively)
Supplementary files format and content: tab-delimited text files include RPKM values

organism: Pseudomonas aeruginosa PAO1

source_name: WT

growth_protocol: Bacteria were cultured in M9 minimal medium (48 mM Na2HPO4; 22 mM KH2PO4; 9 mM NaCl; 19 mM NH4Cl; 2 mM MgSO4; 0.1 mM CaCl2; and 0.04% w/v glucose) supplemented with 0.2% w/v casamino acids (supplemented M9 minimal medium).

extract_protocol:
Stabilized RNA from the biofilm was extracted from the cells using the RNeasy Protect Bacteria Mini Kit (Qiagen, Netherlands). Extracted RNA was treated with TURBO DNA-freeTM Kit (Ambion, USA) to remove any DNA before purification by RNA Clean & ConcentratorTM-5 (ZYMO Research Corporation, USA).
Libraries for total RNA were prepared using the TruSeq RNA Sample Preparation Kit (Illumina, USA) and sequenced on the HiSeq 2500 sequencer (Illumina, USA) according to the manufacturer's protocols.

treatment_protocol: Single and mixed species biofilms were cultivated in three-channel flow cells for 4, 5 and 6 d. Biofilms on day 4 were also treated with 0.1% w/v SDS as described (Lee et al 2014) (Table 1). Biomass from each flow cell was extracted by first flushing ice cold PBS through the channels several times followed by a validation of biomass removal efficiency by confocal laser scanning microscopy. Subsequently, the RNAprotect Bacteria reagent (Qiagen, Netherlands) was added immediately to the extracted biomass according to the protocols suggested by the manufacturer to stabilize the RNA before extraction.

tag: strain

value: SDS treated

tag: biol rep

value: replicate 1


title: PAO1 Day 6 Replicate 3

value: Day 6

value: Replicate 3


title: PAO1 SDS treated replicate 3

value: replicate 3


title: PAO1 SDS treated replicate 2

value: WT

value: replicate 2


title: PAO1 Day 6 Replicate 1

value: Replicate 1


title: PAO1 Day 6 Replicate 2

value: Replicate 2


title: PAO1 Day 5 Replicate 2

value: Day 5


title: PAO1 Day 5 Replicate 3


title: HUVEC treated with CD63+EVs derived from Jurkat [SK21_Huvec_JK_CD63]


title: HUVEC treated with CD63+EVs derived from JINB10 [SK24_Huvec_JINB8_CD63]


title: PAO1 Day 5 Replicate 1


title: HUVEC treated with MHC+EVs derived from Jurkat [SK18_Huvec_JK_MHC]


title: HUVEC treated with only IgG [SK11_Huvec_IgGbeads]


title: PAO1 Day 4 Replicate 3

value: Day 4


title: HUVEC treated with CD63+EVs derived from Jurkat [SK20_Huvec_JK_CD63]


title: HUVEC treated with MHC+EVs derived from JINB13 [SK27_Huvec_JINB8_MHC]


title: HUVEC treated with MHC+EVs derived from Jurkat [SK17_Huvec_JK_MHC]


title: Untreated HUVEC [SK01_Huvec_Unt]


title: HUVEC treated with only IgG [SK12_Huvec_IgGbeads]


title: PAO1 Day 4 Replicate 1


title: PAO1 Day 4 Replicate 2


title: MM.1S,Coculture1

city: Tianjin

first: Zhiqiang

address: 22 Qixiangtai Rd

department: Pathophysiology

institute: Tianjin Medical University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep(https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)[1] software. The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2/DEGseq/EdgeR[6]with Q value ≤ 0.05, DEGs with |log2FC|>1 and Q value <=0.05(DESeq2 or EdgeR) /Q value <= 0.001(DEGseq) were considered to be significantly different expressed genes). In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ≤0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools(https://github.com/tanghaibao/Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do).
All the alternative splice events that occurred in our sample were identified by using recently releases program rMATS(http：//rnaseq-mats.sourceforge.net/index.html). Only the isoforms that were similar to the reference or comprised novel splice junctions were considered, and the splicing differences were detected as exon inclusion, exclusion, alternative 5′, 3′, and intron retention events.
Assembly: GRCh38.p13
Supplementary files format and content: a matrix table  include RPKM values for each Sample

growth_protocol: MM.1S multiple myeloma cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from cells usingTRIzol®Reagent.
RNA-seq transcriptome librariy wa sprepared following TruSeqTMRNA sample preparation Kit from Illumina(SanDiego,CA) using 1μg of total RNA.

treatment_protocol: MM.1S multiple myeloma cells were harvested to cell pellets after being washed with PBS twice

value: multiple myeloma cell

value: coculture


title: MM.1S,Coculture2


title: Pf-5 SDS treated replicate 3

organism: Pseudomonas protegens Pf-5


title: MM.1S,mock2

value: Mock


title: MM.1S, bortezomib plus FeAc2, 12 hour

description: matrix txt _1.txt

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep(https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)[1] software. The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2/DEGseq/EdgeR[6]with Q value ≤ 0.05, DEGs with |log2FC|>1 and Q value <=0.05(DESeq2 or EdgeR) /Q value <= 0.001(DEGseq) were considered to be significantly different expressed genes). In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ≤0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools(https://github.com/tanghaibao/Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do).
All the alternative splice events that occurred in our sample were identified by using recently releases program rMATS(http：//rnaseq-mats.sourceforge.net/index.html). Only the isoforms that were similar to the reference or comprised novel splice junctions were considered, and the splicing differences were detected as exon inclusion, exclusion, alternative 5′, 3′, and intron retention events.
Assembly: GRCh38.p13
Supplementary files format and content: two matrix txt  include TPM values for each Sample

value: bortezomib plus FeAc


title: MM.1S,FeAc1, 12 hour

description: matrix txt _2.txt

value: FeAc


title: Pf-5 SDS treated replicate 2


title: MM.1S, bortezomib2, 12 hour

description: matrix txt _1.txt

value: bortezomib


title: MM.1S,FeAc2, 12 hour

description: matrix txt _2.txt


title: Pf-5 Day 5 Replicate 3


title: MM.1S,mock1


title: Pf-5 Day 6 Replicate 1


title: Sample 14

city: Stockholm

first: Volker

last: Lauschke

address: Solnavägen 9

country: Sweden

institute: Karolinska Institutet

data_processing:
Base calling and quality checks were performed using the RTA3.4.4 pipeline and Bcl2fastq (v2.20) conversion software (Illumina). Quality control, removal of genomic contaminants and ribosomal RNA, UMI-based read deduplication, transcript assembly and quantification using Stringtie were conducted using the nf-core/rnaseq
Assembly: GRCh38
Supplementary files format and content: FPKM expression values in tab-delimited text format

source_name: primary human hepatic cells

extract_protocol:
RNA was harvested using Quick RNA- minipre (Zymo). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBnext Ultra II Directional RNA library kit for illumina following manufacturer's protocols.

value: primary human hepatic cells

value: high glucose


title: Pf-5 SDS treated replicate 1

value: SDS treated

value: replicate 1


title: Pf-5 Day 6 Replicate 2

value: Day 6


title: MM.1S, bortezomib plus FeAc1, 12 hour

description: matrix txt _1.txt

value: WT


title: Pf-5 Day 5 Replicate 2


title: Pf-5 Day 5 Replicate 1


title: Pf-5 Day 6 Replicate 3

value: Replicate 3


title: Pf-5 Day 4 Replicate 3


title: MM.1S, vehicle control2, 12 hour

description: matrix txt _2.txt

value: Vehicle


title: Mixed SDS treated replicate 2

description: Mixed

organism:
Pseudomonas aeruginosa PAO1
Pseudomonas protegens Pf-5
Klebsiella pneumoniae KP-1

value: replicate 2


title: Sample 12


title: Pf-5 Day 4 Replicate 2

value: Replicate 2


title: MM.1S, vehicle control1, 12 hour

description: matrix txt _2.txt


title: Pf-5 Day 4 Replicate 1

value: Day 4

value: Replicate 1


title: Sample 13


title: Mixed SDS treated replicate 3

description: Mixed

value: replicate 3


title: Sample 11

value: low glucose


title: Mixed SDS treated replicate 1

description: Mixed


title: Sample 10


title: MM.1S, bortezomib1, 12 hour

description: matrix txt _1.txt

value: multiple myeloma cell


title: Sample 9


title: Mixed Day 6 Replicate 3

description: Mixed


title: Sample 8

source_name: primary human pancreatic islets

value: primary human pancreatic islets


title: Sample 6


title: Mixed Day 6 Replicate 1

description: Mixed


title: Mixed Day 6 Replicate 2

description: Mixed


title: Sample 7


title: Sample 5


title: Mixed Day 5 Replicate 3

description: Mixed

value: Day 5


title: Sample 4


title: Mixed Day 5 Replicate 2

description: Mixed


title: Mixed Day 4 Replicate 2

description: Mixed


title: Sample 1


title: Sample 2


title: Mixed Day 4 Replicate 3

description: Mixed


title: Mixed Day 4 Replicate 1

description: Mixed


title: Sample 3


title: Mixed Day 5 Replicate 1

description: Mixed


title: ET 5D-1

city: Anseong-si

first: Dasom

last: Choi

state: Gyeonggi-do

address: 4726, Seodong-daero

country: South Korea

institute: Chung-Ang University

description: replicate 1

data_processing:
Quality of raw reads were pre-checked using the FastQC software.
Cleaned reads with more than 95% (Q<30) were mapped to the kiwifruit genome (http://kiwifruitgenome.org/node/152174) using Tophat2 (2.0.12) with default parameters.
Mapped reads were then converted to digital counts using FeatureCounts and were analyzed using edgeR.
DEGs were identified based on an adjusted p-value <0.05 and an absolute log2 fold change ≥ 1.
Assembly: A. Chinensis reference genome (Red5) was obtained from Kiwifruit genome database (https://kiwifruitgenome.org/ftp/A_chinensis/Red5/v1.0/)
Supplementary files format and content: tab-delimited text files with raw gene counts for individual samples

organism: Actinidia deliciosa

source_name: flesh

extract_protocol:
Total RNAs were extracted using SpectrumTM Plant Total RNA kit (Sigma, USA) and treated with DNase I (NEB, USA).
RNA-seq libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., USA).

value: flesh

value: Hayward

value: ET


title: ET 7D-2

description: replicate 2


title: ET 3D-2

description: replicate 2


title: ET 5D-2

description: replicate 2


title: ET 7D-1

description: replicate 1


title: ET 7D-3

description: replicate 3


title: ET 5D-3

description: replicate 3


title: ET 3D-1

description: replicate 1


title: ET 0D-3

description: replicate 3


title: 1-MCP 7D-2

description: replicate 2


title: 1-MCP 7D-3

description: replicate 3


title: ET 0D-1

description: replicate 1


title: ET 0D-2

description: replicate 2


title: 1-MCP 5D-3

description: replicate 3


title: mLN_day300_2

city: Lausanne

first: Joern

last: Pezoldt

address: Station 19, SV 3818.A

department: SV

country: Switzerland

institute: EPFL

description:
mLN_day300_2
RCM_mLN_day300_scRNAseq.zip

data_processing:
Data were demultiplexed using Cell Ranger software (version 2.0.0) based on 8 bp 10X sample indexes and paired-end FASTQ files generated. The cell barcodes and transcript UMIs were processed as previously described (Zheng et al., 2017). Subsequently, read 2, which contains the transcript insert sequence, was aligned to mouse UCSC mm10 reference genome using STAR aligner with default parameters (Dobin and Gingeras, 2015). The alignment results were used to quantify the expression level of mouse genes and generation of gene-barcode matrix, which were further processed with Seurat (version 2.3.3). All cells received an identifier which was used as common meta-data throughout the analysis including differentiation trajectories and dynamic gene regulatory networks (see below).
All cells with less than 1,000 or more than 4,600 detected genes per cell were filtered out. Moreover, cells with more than 4.5 % read mapping to mitochondrial genes were removed yielding 15,659 cells passing QC. All cells across all developmental stages were subjected to canonical correlation analysis and regressed against the variables, number of UMIs, percent of mitochondrial reads, percent of ribosomal reads and scores for the proliferation S.Score and G2M.Score computed with CellCycleScoring(). t‑SNE dimensionality reduction was performed using the first 12 dimensions of the CCA and resolution set to 1.1. Only clusters (non-endothelial MC) with expression for Pecam < 1 were used for the further analysis amounting to 9,323 cells which were re-embedded as described above (resolution = 1.0). The perivascular mesenchymal cell (PvMC) cluster and clusters classified as adjacent cells were excluded and the remainder cells, numbering 5,658 mesenchymal cells were re-embedded as described above (resolution = 1.0). For subsetting the Prog. subset, 259 cells were re-embedded as described above (resolution = 0.5, dimsuse = 10). Gene ontology (GO) analysis was performed for differentially upregulated genes per cluster using TopGO (Alexa and Rahnenfuhrer, 2010).
Differentiation trajectories were analyzed using Monocle (version 2.18.0) (Trapnell et al., 2014). Unsupervised ordering was performed on the 5,658 mesenchymal cells using Monocle2’s DDRTree algorithm based on genes with a mean expression >0.1. The trajectory containing all mesenchymal cells, was split based on marker gene expression Vcam1 and Cd34 and the annotation of cells belonging to the ProgCxcl13+ or ProgCD34+ subset to distinct terminal branches. Two separate unsupervised orderings were performed as described above and are referred to as CD34+SC or FRC trajectory.
Gene regulatory networks were inferred with the dynGENIE3 algorithm, where the input expression values were based on ordering the genes according to physiological age per branch for each of the two trajectories being CD34+SC or FRC (Huynh-Thu and Geurts, 2018). The list of candidate TFs was derived from TFBS from ATAC-seq profiling or DMRs within the proximity of TFs. For network visualization with Cytoscape (version 3.6.0)(Shannon et al., 2003), only the top 500 links ranked by weight assigned by dynGENIE3 were used. Node centrality and betweenness were calculated with the degree and betweenness functions from the igraph (version 1.2.2) package.
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger processed fastq output yielding RMCs and gene annotation

source_name: gut-draining mesenteric lymph node

growth_protocol: Mice were housed under specific pathogen free conditions.

extract_protocol:
Single CD45‑CD24‑ cells were sorted by FACS ARIA III (BD) and collected in PBS containing 0.04 % w/v BSA at a density of 400 cells/μl. Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs)
Single Cell 3’ reagent kit v2 for reverse transcription, cDNA amplification and library construction (10xGenomics, Cat. #120236). The detailed protocol was provided by 10xGenomics. SimpliAmp Thermal Cycler was used for amplification and incubation steps (Applied Biosystems). Libraries were quantified by QubitTM 3.0 Fluometer (ThermoFisher) and quality checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent).
Sequencing was performed in paired-end mode (2 x 75 cycles) using NextSeq 500 sequencer (Illumina) to attain approximately 75,000 +/- 25,000 reads per single cell.

treatment_protocol: For stromal cell isolation, mLNs (small intestinal and colon/caecum-draining) were resected and digested in RPMI 1640 medium (Gibco, Cat. #72400021) containing 0.2 mg/ml collagenase P (Roche, Cat. #11213865001), 0.15 U/ml dispase (Roche, Cat. #4942078001) and 0.2 mg/ml DNase I (Roche, Cat. #4536282001) as described previously (Malhotra et al., 2012). After digestion, cells were kept at 4 °C in PBS containing 0.2 % BSA (Merck, Cat. #A2058) and 5 mM EDTA (Roth, Cat. #8043.1). CD45- cells were enriched by autoMACS separation after magnetic labeling of CD45+ cells using anti‑CD45‑APC followed by anti‑APC microbeads (Miltenyi Biotec, Cat. #130-090-855) or anti-CD45 Nanobeads (Biolegend, Cat. #480028). Subsequently, the CD45- fraction was stained using fluorochrome-coupled antibodies and used to sort CD45‑CD24‑CD31‑gp38+ FSCs (Aria II, 100 μm nozzle) and bulk CD45‑CD24‑ non-hematopoietic cells (Aria III, 70 μm nozzle) for RNA‑seq/ATAC‑seq and scRNA‑seq, respectively.

value: BALB/c

value: ex vivo isolated cells CD24-CD45-

value: gut-draining mesenteric lymph node

tag: housing

value: specific pathogen free


title: 1-MCP 5D-1

description: replicate 1

tag: tissue


title: mLN_day300_1

description:
mLN_day300_1
RCM_mLN_day300_scRNAseq.zip


title: 1-MCP 5D-2

description: replicate 2


title: ET 3D-3

description: replicate 3


title: 1-MCP 7D-1

description: replicate 1


title: pLN GF stromal cell

data_processing:
Data were demultiplexed using Cell Ranger software (version 2.0.0) based on 8 bp 10X sample indexes and paired-end FASTQ files generated. The cell barcodes and transcript UMIs were processed as previously described (Zheng et al., 2017). Subsequently, read 2, which contains the transcript insert sequence, was aligned to mouse UCSC mm10 reference genome using STAR aligner with default parameters (Dobin and Gingeras, 2015). The alignment results were used to quantify the expression level of mouse genes and generation of gene-barcode matrix, which were further processed with Seurat (version 4.0.1). All cells received an identifier which was used as common meta-data throughout the analysis including differentiation trajectories and dynamic gene regulatory networks (see below).
All cells with less than 750 or more than 4,000 detected genes per cell were filtered out. Moreover, cells with more than 7 % reads mapping to mitochondrial genes were removed yielding 18,045 cells passing QC. After filtering, data were default normalized and the 2,000 most variable genes identified. The expression levels of these genes were scaled before performing PCA. The following covariates were regressed out: number of UMIs, number of genes , percent of mitochondrial reads and percent of ribosomal reads. t SNE and UMAP dimensionality reduction was performed using the first 17 dimensions of the PCA and resolution set to 0.4.
Only non-endothelial SC clusters were used for the further analysis amounting to 14.307 cells which were re-embedded as described above (dimsuse = 20, resolution = 0.8).
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger processed fastq output yielding RMCs and gene annotation

source_name: speripheral skin-draining lymph node

growth_protocol: LNs of GF mice were harvested for stromal cell isolation.

extract_protocol:
Single CD45‑CD24‑ cells were sorted by FACS ARIA III (BD) and collected in PBS containing 0.04 % w/v BSA at a density of 400 cells/μl. Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs)
Single Cell 3’ reagent kit v2 for reverse transcription, cDNA amplification and library construction (10xGenomics, Cat. #120236). The detailed protocol was provided by 10xGenomics. SimpliAmp Thermal Cycler was used for amplification and incubation steps (Applied Biosystems). Libraries were quantified by QubitTM 3.0 Fluometer (ThermoFisher) and quality checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent).
Sequencing was performed in paired-end mode (2 x 75 cycles) using NextSeq 500 sequencer (Illumina) to attain approximately 100,000 +/- 25,000 reads per single cell.

treatment_protocol: For stromal cell isolation, LNs were resected and digested in RPMI 1640 medium (Gibco) containing 0.2 mg/ml collagenase D (Roche), 0.15 U/ml dispase (Roche) and 0.2 mg/ml DNase I (Roche). After digestion, cells were kept at 4°C in PBS containing 0.2 % BSA and 5 mM EDTA (Roth). CD45- cells were enriched by autoMACS separation after direct magnetic labeling of CD45+ cells using CD45 Nanobeads (Biolegend). Subsequently, the CD45- fraction was stained using fluorescence-coupled antibodies and used to sort bulk CD45-CD24- non-hematopoietic cells (Aria III, 70 μm nozzle) for scRNA‑seq.

value: pLN

tag: sorted cells

tag: condition

value: GF


title: mLN_day24

description:
mLN_day24
RCM_mLN_day24_scRNAseq.zip


title: mLN_day0

description:
mLN_day0
RCM_mLN_day0_scRNAseq.zip


title: 1-MCP 3D-1

description: replicate 1

tag: treatment


title: mLN_day10

description:
mLN_day10
RCM_mLN_day10_scRNAseq.zip


title: Stat1_4 (BRBseq)

data_processing:
Library strategy: BRB-seq
After sequencing and standard Illumina library demultiplexing, the fastq-files were aligned to the mouse reference genome mm10 (GRCm38) using STAR (version 2.7.3a), excluding multiple mapped reads.
Resulting BAM files were demultiplexed per sample using BRB-seqTools (version 1.4, https://github.com/DeplanckeLab/BRB-seqTools) and read-count matrices generated using HTSeq (version 0.12.4).
Raw read counts were converted to transcripts per kilobase of exon per million reads values. Protein-coding genes with at least 5 reads in at least two replicates were included in the analysis. The calculated read counts were further processed with DESeq2 for quantiﬁcation of differential gene expression (Love et al., 2014). Genes were considered as differentially expressed at log2(fold change) > 1.0 and an adjusted p-value of < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing the reads per gene per replicate per sample

growth_protocol: Murine C3H10T1/2 cells (ATCC Cat. No. CCL‑226) were seeded 12 h prior to transduction at confluence of 10-20%.

extract_protocol:
Direct-zol RNA kit (Zymo Research, Cat. #R2052) was used to extract RNA according to the manufacturer’s instruction.
3’end bulk mRNA cDNA library preparation and sequencing was performed following the BRB-seq strategy as previously described (Alpern et al., 2019). In brief, 20 ng of total RNA isolated from TF overexpressions from each sample was reverse transcribed using SuperScriptTM II Reverse Transcriptase (Lifetech, Cat. Cat. #18064014) with individual barcoded oligo-dT primers, featuring a 12-nt-long sample barcode (IDT). Double-stranded cDNA was generated by second strand synthesis via the nick translation method. To that end, a mix containing 2 μl of RNAse H (NEB, Cat. #M0297S), 1 μl of E. coli DNA ligase (NEB, Cat. #M0205 L), 5 μl of E. coli DNA Polymerase (NEB, Cat. #M0209 L), 1 μl of 10mM dNTP  (Thermo Fisher Scientific, Cat. #0181), 10 μl of 5x Second Strand Buffer (100 mM Tris, pH 6.9, [AppliChem, Cat. #A3452], 25 mM MgCl2 [Sigma, Cat. #M2670], 450 mM KCl [AppliChem, Cat. #A293], 0.8 mM β-NAD [Sigma, Cat. N1511], 60 mM (NH4)2SO4 [Fisher Scientific, Cat. #AC20587]), and 11 μl of water was added to 20 μl of ExoI-treated first-strand reaction on ice. The reaction was incubated at 16°C for 2.5 h. Full-length double-stranded cDNA was purified with 30 μl (0.6x) of AMPure XP magnetic beads (Beckman Coulter, Cat. #A63881) and eluted in 20 μl of water. cDNA concentration was measured using Qubit, and cDNA quality was assessed using a Fragment Analyzer (Agilent). cDNA was tagmented with in-house Tn5 (Picelli et al., 2014), and libraries were purified using AMPure XP magnetic beads (0.6X). The resulting libraries were profiled with a High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, Cat. #DNF-474) and measured with the Qubit dsDNA HS Assay Kit (Invitrogen, Cat. #Q32851)
Sequenced using the Illumina NextSeq 500 platform utilizing a BRB-seq custom primer and the High Output v2 kit (75 cycles) (Illumina, Cat. #FC-404-2005). The sequencing configuration is as follows: Read1 21cycles / index i7 8cycles / Read2 63c.

treatment_protocol: Transfection lentivirus containing supernatant was mixed at 1:1 ratio with fresh medium and 10 µl/ml polybrene (Sigma, Cat. #TR-1003-G) and added to the C3H10T1/2 to the plated adherent cells. Cells were then centrifuged at 1300 g for 30 min at 37°C, incubated with the respective lentivirus for 24 h and medium was exchanged after 24 h. After 48 h, transduced cells were selected using 2 µl/ml of puromycin (Thermo Fisher, Cat. #A1113803) for 72 h. Subsequent to puromycin selection medium was replaced and puromycin resistant cells permitted to recovered for 48 h. Then, medium containing 2 µl/ml doxycycline was added (Sigma, Cat. #D9891-1G) to induce TF expression. Medium with doxycycline was replenished every 48 h and doxocycline treatment maintained for 12 days.

tag: genotype

value: lentiviral Stat1 overexpression


title: 1-MCP 3D-2

description: replicate 2


title: 1-MCP 3D-3

description: replicate 3


title: Stat1_3 (BRBseq)


title: 1-MCP 0D-3

description: replicate 3


title: mLN_day56_1


title: Nfia_4 (BRBseq)

value: lentiviral Nfia overexpression


title: Nfia_3 (BRBseq)


title: Nfia_2 (BRBseq)


title: Stat1_2 (BRBseq)


title: 1-MCP 0D-1

description: replicate 1


title: mLN GF stromal cell

source_name: mesenteric lymph node

value: mLN


title: Control 7D-3

description: replicate 3

value: Control


title: Myc_3 (BRBseq)

value: lentiviral Myc overexpression


title: Myc_4 (BRBseq)


title: Myc_2 (BRBseq)


title: Nfia_1 (BRBseq)


title: Myc_1 (BRBseq)


title: Control 7D-1

description: replicate 1


title: Control 7D-2

description: replicate 2


title: Control 5D-2

description: replicate 2


title: Control 5D-3

description: replicate 3


title: 1-MCP 0D-2

description: replicate 2


title: EmptyVector_3 (BRBseq)

value: lentiviral emtpyVector overexpression


title: Stat1_1 (BRBseq)


title: Irf3_3 (BRBseq)

value: lentiviral Irf3 overexpression


title: EmptyVector_2 (BRBseq)


title: EmptyVector_4 (BRBseq)


title: Control 3D-3

description: replicate 3


title: Control 3D-2

description: replicate 2


title: Irf3_1 (BRBseq)


title: Irf2_3 (BRBseq)

value: lentiviral Irf2 overexpression


title: Irf2_2 (BRBseq)


title: Irf2_4 (BRBseq)


title: Irf3_2 (BRBseq)


title: Irf1_4 (BRBseq)

value: lentiviral Irf1 overexpression


title: Control 3D-1

description: replicate 1

value: flesh

value: Hayward


title: Irf1_3 (BRBseq)


title: Irf1_2 (BRBseq)


title: Irf1_1 (BRBseq)


title: Fos_4 (BRBseq)

value: lentiviral Fos overexpression


title: EmptyVector_1 (BRBseq)


title: Irf3_4 (BRBseq)


title: Fos_3 (BRBseq)


title: Control 0D-2

description: replicate 2


title: Fos_2 (BRBseq)


title: Control 5D-1

description: replicate 1


title: Fos_1 (BRBseq)


title: Control 0D-1

description: replicate 1


title: Irf2_1 (BRBseq)


title: Cebpa_2 (BRBseq)

value: lentiviral Cebpa overexpression


title: WT/pACYC, 42℃

city: Hohhot

first: Jiaxin

last: Qiao

address: Zhao Jun road

institute: Inner mongolia university

description: The three biological replicates were combined into a single test sample.

data_processing:
Raw data were filtered by the following standards, 1) removing reads with ≥ 10 % unidentified nucleotides (N); 2) removing reads with > 50 % bases having phred quality scores of ≤ 20; 3) removing reads aligned to the barcode adapter using FASTP (version 0.18.0). Quality trimmed reads were mapped to the reference genome using Bowtie2 (version 2.2.8) allowing no mismatches, reads mapped to ribosome RNA was removed. Repainted reads were aligned with the reference genome using Bowtie2 (version 2.2.8) to identify known genes and calculated gene expression by RSEM.
To evaluate reproducibility between samples, the correlation coefficient among replicas was calculated. Values closer to one indicated better reproducibility. Principle component analysis (PCA) was performed with the R package gmodels (http://www.rproject.org) to reveal the relationship between samples.
The gene expression level was further normalized by using the fragments per kilobase of transcript per million (FPKM) mapped reads method to eliminate the influence of different gene lengths and amount of sequencing data on the calculation of gene expression. The edgeR package (http://www.r-project.org/) was used to identify differentially expressed genes (DEGs) across samples with fold changes ≥ 2 and a false discovery rate-adjusted P (q value) < 0.05. DEGs were then subjected to enrichment analysis of GO function and KEGG pathways, and q values < 0.05 were used as the threshold.
The prediction of sRNA was conducted using Rockhopper (version 2.0.3) with the removal of sequences less than 50 bp. Candidate sRNAs were then screened against the sRNAMap database（version2009）and Rfam database （version13）for annotation. Secondary structures of sRNA were predicted by Vienna RNA packages (version 2.3.5). The sRNA expression level was normalized by using TPM values (transcripts per million). The edgeR package (http://www.r-project.org/) was used to identify differentially expressed sRNAs across samples with fold changes ≥ 2 and a false discovery rate-adjusted P (q value) < 0.05.
New Transcripts were predicted using Rockhopper (version 2.0.3). Cis-natural antisense transcripts (cis-NATs) are RNAs transcribed from the antisense strand of a gene locus, and are complementary to the RNA transcribed from the sense strand. According to the features, cis-NATs with overlap length to the known genes more than 30 bp were identified. Candidate cis-NATs were further verified using RNAplex (version 2.0.3) and cis-NATs with minimum free energy more than -30 kcal/mol were removed. Transcription start site (TSS), transcription termination site (TTS) and operons were revealed using Rockhopper After the identification of Untranslated Regions (UTR), Shine-Dalgarno sequence was predicted using RBSfinder with the parameter of rbs region length of 20 bp. ρ -independent terminator was identified using TransTermHP (version 2.09).
Assembly: NZ_CP009273.1
Supplementary files format and content: tab-delimited text file include FPKM values of each sample

organism: Escherichia coli

growth_protocol: Overnight cultures (LB medium) of WT/pACYC，WT/pdsrA，Δdps/pACYC and Δdps/pdsrA strains were diluted 5000-fold into fresh ABTG-CAA medium and were grown to mid-log phase (OD450=0.15~0.2) at 42 °C with shaking.

extract_protocol:
Total RNA was extracted by TRIzol-based method (Life Technologies, CA, USA).
Firstly, the rRNA was depleted from 1 microgram of total RNA using illumina MRZB12424 Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina, San Diego, CA, USA ). Then, the first-strand cDNA was synthesized using ProtoScript Ⅱ Reverse Transcriptase (New England BioLabs, Ipswich, MA, USA) at 25 °C for 10 min; 42 °C for 15 min; 70 °C for 15 min. The second-strand cDNA was synthesized using NEBNext Second Strand Synthesis Reaction Buffer and dATP, dGTP, dCTP, dUTP mix (New England BioLabs, Ipswich, MA, USA) at 16 °C for 1 h. Resulted cDNA was  purified with Agencourt AMPure XP beads (Beckman Coulter, Brea, CA) and end repaired with NEBNext End Repair Reaction Buffer and Enzyme Mix (New England BioLabs, Ipswich, MA, USA) at 20 °C for 30 min; 65 °C for 30 min. Sequencing adapters were ligated using NEBNext Adaptor for Illumina (New England BioLabs, Ipswich, MA, USA) at 20 °C for 15 min. The second-strand cDNA was then degraded using the USER enzyme mix (New England BioLabs, Ipswich, MA, USA) at 37 °C for 15 min and the product was purified by Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). Finally, the clustering of the index-coded samples was performed on a cBot Cluster Generation System using NEBNext Q5 Hot Start HiFi PCR Master Mix(New England Biolabs, Ipswich, MA, USA).
After cluster generation, sequencing was performed using the Illumina Novaseq 6000 platform with pair-end 150 base reads.

treatment_protocol: Cells cultured to OD450=0.15-0.2 were collected by centrifugation, frozen using liquid nitrogen, and then stored at -80 °C for subsequent total RNA extraction.

value: bacterial cells

value: WT, transformed empty pACYC vector

tag: growth condition

value: 42C, ABTG-CAA medium


title: Atf4_4 (BRBseq)

value: lentiviral Atf4 overexpression


title: WT/pdsrA, 42℃

value: WT, dsrA over expression


title: Atf4_3 (BRBseq)


title: Atf4_2 (BRBseq)


title: Δdps/pdsrA, 42℃

value: dps knockout, dsrA over expression


title: Cebpa_1 (BRBseq)


title: Control 0D-3

description: replicate 3


title: Single, control tumor (P815-M), dark, 6 days, biol rep 2

city: shenzhen

first: chen

last: rui

address: 1088 Xueyuan Avenue, Shenzhen 518055, P.R. China

institute: sustech

data_processing:
For RNA sequencing preprocessing, the sequences and annotations of the knock-in genes were added into the mouse mm10 reference genome to build the reference genome for engineered murine tumor cells. Raw FASTQ sequencing reads were filtered and corrected by the Fastp (v0.20.1) with default parameters to get the clean reads and quality reports. Clean reads were splice-aware aligned to the reference genome using STAR (v2.7.9a) and counted using HTSeq (v0.13.5) with default parameters. The counts of the mitochondrial genes in all samples were removed. The ComBat-seq tool in the sva R package (v3.40.0) was used to adjust the batch effect in the counts.
For differential gene expression and enrichment analysis, the genes with a total count < 10 reads were removed prior to identifying differentially expressed genes using DESeq2 R package (v1.32.0) and IHW R package (v1.20.0) with default parameters. Genes are considered significantly differentially expressed if the Benjamini-Hochberg adjusted p-value ≤ 0.05 and the absolute value of the Log2 Fold Change ≥ 1. The differentially expressed genes between the P815-IFNγ and P815-M in the light group were filtered with the genes that were also identified differentially in the dark group. Moreover, the differentially expressed genes in P815-IFNγ tumors between the light and dark groups were filtered with the genes that were also identified differentially in P815-M tumors between the light and dark groups. The GO Enrichment Analysis of the filtered differentially gene sets for the biological process was conducted using clusterProfiler R package (v4.0.5) with the qvalueCutoff = 0.05.
Assembly: mm10
Supplementary files format and content: The files with the suffix 'hcg.txt' contains the gene counts for each library. The file is three columns. The first and second columns is the gene id. The third column is the gene counts.

source_name: Tumor

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Engineered P815-IFNγ or control P815-M cells were collected, washed, and suspended in 100 μL PBS, and subsequently implanted subcutaneously into the backs of DBA/2 mice to establish single-tumor bearing mice. Seven days later, all experimental mice were randomly assigned to groups that were illuminated with (light group, n = 3) or without blue light (dark group; n = 3). Subsequently, the mice in the light group were housed individually in light-controlled cages with free water and food supply. After 6 days of illumination, all the mice were sacrificed, and the tumor tissues were removed for RNA extraction.

value: Tumor

value: mastocytoma  cell

value: without illumination


title: Single, control tumor (P815-M), dark, 6 days, biol rep 1


title: Single, control tumor (P815-M), dark, 6 days, biol rep 3


title: Single, control tumor (P815-M), illumination, 6 days (12/12h light/dark cycle), biol rep 2

value: illumination with blue light


title: Single, control tumor (P815-M), illumination, 6 days (12/12h light/dark cycle), biol rep 1


title: Cebpa_3 (BRBseq)


title: RPTEC_3D_D31_rep3

city: Atlanta

first: Shuichi

last: Takayama

state: GA

address: 950 Atlantic Dr NW

department: Biomedical Engineering

institute: Georgia Institute of Technology

description:
Day 31 organoid rep3
RPTEC_3D_D31_3

data_processing:
FASTQ files provided by Emory Integrated Genomics Core were first downloaded to Georgia Tech’s high-performance computing cluster called Partnership for an Advanced Computing Environment (PACE). Quality control was then performed using FastQC.
Upon passing quality requirements, the reads were aligned using STAR. A custom Python script was written to generate a gene count matrix.
Genes with less than 0.5 CPM in at least 3 samples were eliminated. Differential gene expression analysis was conducted using the EdgeR package in R. PCA analysis was performed to examine the samples for possible outliers prior to further analysis. The counts were normalized based on library size using the default TMM method from EdgeR. A comparison was run between the two groups through GLM, and LRT to identified statistically significant differential expressions. The cutoff for significance was set at under an alpha value of 0.05 for the adjusted p-value, and the log2 fold change of ±1.
Assembly: hg38
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

source_name: RPTEC organoid

growth_protocol: 2D RPTEC cells were grown in 6-well plates until 95% confluence was achieved. RPTEC organoids were grown in hanging drop culture. Organoids were seeded with 3000 cells, 2.5% fetal bovine serum (FBS), 110-130 ug/mL Matrigel, and 0.24% Methylcellulose. 2D cells and organoids were maintained in renal epithelial cell basal media (ATCC) supplemented with 0.5% fetal bovine serum (FBS), 10 nM triiodothyronine, 10 ng/mL epidermal growth factor (EGF), 100 ng/mL hydrocortisone hemisuccinate, 5 ug/mL insulin, 1.0 µM epinipherine, 5 µg/mL transferrin, 2.4 mM L-glutamine, and 1% penicillin-streptomycin (pen-strep).

extract_protocol:
Cells/organoids were lysed in RLT buffer, then processed for RNA extraction, or flash frozen, and stored in -80oC until future extraction. RNA was isolated using the Quick-RNA Microprep Kit (Zymo Research)
The cDNA was generated using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio). The final sequencing library was made using the Nextera XT kit (Illumina). The library construction used Nextera XT chemistry which tagmented 200pg of DNA and added adapters in one step. The fragmented and tagged DNA was then PCR amplified for 12 cycles to incorporate dual-indexing sequencing adapters to generate the final library. A combination of both concentration and library size patterning was used as QC metrics to determine the success of the assay. The UV Qubit fluorometer quantitation step determined the concentration of the library. The Bio/Fragment Analyzer trace revealed the size distribution and concentration of the final sequencing library. Based on these three parameters we assigned library scores to each library. Libraries with a pass score were then used for sequencing in NextSeq 550.

treatment_protocol: The 2D cells and organoids did not undergo any treatment protocols.

value: renal proximal tubule epithelial cell organoids

tag: culture method


title: RPTEC_3D_D31_rep2

description:
Day 31 organoid rep2
RPTEC_3D_D31_2


title: RPTEC_3D_D31_rep1

description:
Day 31 organoid rep1
RPTEC_3D_D31_1


title: RPTEC_2D_rep2

description:
2D rep2
RPTEC_2D_2

source_name: RPTEC

value: renal proximal tubule epithelial cells (RPTECs)


title: Single, enigneered tumor (P815-IFNγ), dark, 6 days, biol rep 3


title: Single, enigneered tumor (P815-IFNγ), dark, 6 days, biol rep 1


title: Single, enigneered tumor (P815-IFNγ), illumination, 6 days (12/12h light/dark cycle), biol rep 3


title: Single, enigneered tumor (P815-IFNγ), dark, 6 days, biol rep 2


title: RPTEC_2D_rep3

description:
2D rep3
RPTEC_2D_3


title: Δdps/pACYC, 42℃

value: dps knockout, transformed empty pACYC vector


title: Atf4_1 (BRBseq)


title: Single, enigneered tumor (P815-IFNγ), illumination, 6 days (12/12h light/dark cycle), biol rep 2


title: Single, enigneered tumor (P815-IFNγ), illumination, 6 days (12/12h light/dark cycle), biol rep 1


title: SRI_40109_8h_1

city: Birmingham

first: Anupam

last: Agarwal

state: AL

address: 703 19th St S

institute: University of Alabama at Birmingham

data_processing:
STAR alignment
Assembly: hg18
Supplementary files format and content: counts

extract_protocol: RNA was isolated according to manufacturer's instructions with Trizol

value: SRI-40109_8 hours

value: kidney

value: 8 hours


title: SRI_37618_8h_1

value: SRI-37618_8 hours


title: SRI_37618_8h_2


title: Broxaldine_8h_2

value: broxaldine_8 hours


title: SRI_40109_8h_2


title: Single, control tumor (P815-M), illumination, 6 days (12/12h light/dark cycle), biol rep 3


title: Hemin_8h_2

value: hemin treated_8 hours


title: Broxaldine_8h_1


title: Hemin_8h_1


title: Vehicle_8h_1

value: vehicle (DMSO)_8


title: RPTEC_2D_rep1

description:
2D rep1
RPTEC_2D_1


title: SRI_40109_4h_1

value: SRI-40109_4 hours

value: 4 hours


title: SRI_40109_4h_2


title: Vehicle_8h_2


title: MDA-MB-231 sgMLL3, H3K4me3, biological replicate2

city: Bronx

first: Jihong

last: Cui

state: NY

address: 1301 Morris Park Avenue, Room 108/114

institute: Albert einstein college of medicine

data_processing:
Basecalls were performed using bcl2fastq.
The raw read were quality assessed using FastQC v0.11.9, then quality trimmed using Trimmomatic 0.40 with illumina adaptor file and default values.
The surviving paired reads post quality trimming were then aligned against the human reference genome (GRCh38) with bwa-mem(arXiv:1303.3997v2), then sorted and indexed with samtools.The resulting BAM alignments were then processed through PICARD (https://github.com/broadinstitute/picard) tools for ‘MarkDuplicates’.
BigWig files were generated from the Markduplicated bam files using bamCoverage with RPKM normalization. The resulting BigWig files were then passed to computeMatrix, which generates a matrix of scores per genomic region for visualization.
Peaks were called using MACS2 with a p value of 1e-3. Super-enhancers were identified using ROSE based on H3K27ac ChIP-seq signals. The peak annotation was also taken from ROSE output.
Assembly: GRCh38/hg38
Supplementary files format and content: bigWig

growth_protocol: Cells were cultured in DMEM medium with 10%FBS.

extract_protocol:
Around 2 x 107 cells and two biological repeats per genotype were used for ChIP-seq experiment. Crosslinking was performed with 1% formaldehyde (Sigma, F1635) at 37°C for 10 min. A final concentration of 125 mM glycine was added for 5 minutes at room temperature to quench formaldehyde crosslinking. Cells were washed with cold PBS and harvested on ice. Cells were lysed with 1ml of SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH8) in the presence of protease inhibitor (Roche, cat#11836170001) and phosphatase inhibitor (Thermo, cat#78427). Cells were sonicated using the Branson Sonifier 250 (Branson Ultrasonics 101063588) with a 20% amplitude setting for 5 min 30 s with 10 s of on and off intervals. After sonication, 1 ml of ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH8, 167 mM NaCl) with proteinase and phosphatase inhibitor was added to prevent SDS precipitation. After centrifugation at 14,000 rpm for 10 min at 4°C, 2 ml of supernatant were transferred to a 15 ml falcon tube and diluted with 3 ml of ChIP dilution buffer containing proteinase and phosphatase inhibitor.  50 μl of Dynabeads (Thermo Fisher Scientific 10009D), which were previously blocked with 1% BSA, were added to samples and incubated at 4°C with rotation for 1 hour. After pre-clearing, Dynabeads beads were removed. The supernatant was transferred to new 15 ml falcon tubes and 100 μl out of 5 ml volume was collected as 2% input. Antibodies were added to the pre-cleared samples for overnight incubation at 4°C with rotation. 200 μl of Dynabeads that were previously blocked with 1% BSA, were added to the sample and incubated for 6 hours at 4°C with rotation. After incubation, beads were collected and washed at 4°C with rotation following the procedure: 5 min with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH8, 150 mM NaCl), twice 5 min with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH8, 500 mM NaCl) and twice 5 min with TE buffer (10 mM Tris-HCl pH8, 1 mM EDTA). After washing, beads were resuspended in 250 μl of elution buffer (1% SDS, 0.1 M NaHCO3) and incubated at 60°C for 30 min using a thermomixer (850 rpm). The supernatant was transferred to new tubes and 5 M NaCl was added for overnight de-crosslinking at 65°C. 10 μl of 0.5 M EDTA, 20 μl of 1 M Tris-HCl (pH 6.5) and 1 μl of proteinase K (20 mg/ml, NEB, P8107S) were added and incubated at 45°C for 1 hour for de-crosslinking. ChIP-DNA was isolated by using the QIAquick PCR purification kit (QIAGEN, 28104).
Libraries were prepared using the NEBNext® Ultra II DNA Library Prep Kit (NEB, E7103S) and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1; NEB, E7335S). Samples were pooled and submitted to MSKCC Integrated Genomics Operation core for sequencing. Libraries were run over one lane of a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina).

treatment_protocol: No treatment

value: Breast cancer cell line

value: H3K4me3 (clone C42D8, Cell Signaling Technology, 9751s, 2 μg per sample)


title: MDA-MB-231 sgMLL3, H3K27ac, biological replicate1

value: H3K27ac (Polyclonal, Active Motif, 39133, 2 μg per sample)


title: Broxaldine_4h_2

value: broxaldine_4 hours


title: MDA-MB-231 sgMLL3, H3K27ac, biological replicate2


title: SRI_37618_4h-1

value: SRI-37618_4 hours


title: Broxaldine_4h_1


title: MDA-MB-231 sgMLL3, H3K4me3, biological replicate1


title: MDA-MB-231 sgMLL3, H3K4me1, biological replicate2

value: H3K4me1 (clone D1A9, Cell Signaling Technology, cat#5326s, 2 μg per sample)


title: MDA-MB-231 sgMLL3, H3K4me1, biological replicate1


title: Hemin_4h_2

value: hemin treated_4 hours


title: NexCre:Atg7f/f [ko_2]

city: Tsukuba

first: Fuminori

last: Tsuruta

address: 1-1-1 Tennodai

institute: University of Tsukuba

hyb_protocol: DNA samples were hybridized at 45°C for 17 hours on Mouse Exon 1.0 ST arrays and the samples were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with the Gene Spring 12.6 software.

label: Biotin Allonamide Triphosphate

label_protocol: Biotinylated fragmented DNA were prepared according to the GeneChip WT Terminal Labeling and Hybridization kit protocol (Affymetrix).

extract_protocol: Isogen II extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The tissues were collected after dissecting mice according to the university guidelines for animal care and use.

value: Brain

tag: age


title: 7g/kg EtOH Gavage 3

city: Rockville

first: Bryan

last: Mackowiak

address: 5625 Fishers Lane, 2S12

institute: NIH

hyb_protocol: Blocking buffer and Hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2600D scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software. Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: Mouse liver 7g/kg EtOH binge

label_protocol: cDNA was generated with SuperScript® Indirect cDNA Labeling Core kit (Invitrogen) and labeled with Cy3/Cy5-mono reactive dye pack (GE healthcare), and the labeled cDNA was purified with Qiagen kit (#28004)

extract_protocol: Total RNA extracted using Trizol from liver and purified with QIAGEN kit (#74104) following manufacturer's instructions.

treatment_protocol: Collected tissues from fresh liver

tag: gender

value: Male

value: Liver

source_name: Ambion Mouse Assorted Total RNA

value: liver


title: Hemin_4h_1

value: kidney


title: NexCre:Atg7+/+ [wt_3]


title: NexCre:Atg7+/+ [wt_1]


title: 5g/kg EtOH Gavage 3

source_name: Mouse liver 5g/kg EtOH binge


title: 7g/kg EtOH Gavage 2


title: 5g/kg EtOH Gavage 4


title: 5g/kg EtOH Gavage 2


title: 7g/kg EtOH Gavage 1


title: MDA-MB-231 sgMLL3, input, biological replicate2

tag: cell type

tag: chip antibody


title: NexCre:Atg7f/f [ko_3]


title: Control isocaloric maltose gavage 3 (equivalent to 5g/kg EtOH) 3

source_name: Mouse liver isocaloric maltose binge (equivalent to 5g/kg EtOH)


title: NexCre:Atg7+/+ [wt_2]


title: NexCre:Atg7f/f [ko_1]


title: Control isocaloric maltose gavage 1 (equivalent to 5g/kg EtOH) 1


title: 5g/kg EtOH Gavage 1


title: Control isocaloric maltose gavage 2 (equivalent to 5g/kg EtOH) 2


title: Veh_4h_2

value: vehicle (DMSO)_4

tag: cell line


title: Veh_4h_1


title: Tumor cell mix 1, replicate B, scRNAseq, hashtag library

city: Bethesda

first: Robert

last: Seder

address: 40 Convent Dr

department: VRC

institute: NIAID, NIH

library_source: transcriptomic single cell

data_processing:
Cell Ranger
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Spleens were mechanically dissociated and then filtered through a 70μm cell strainer to isolate a single cell suspension. Tumors were mechanically dissociated in a cocktail containing RPMI, DNase1, and collagenase D using gentlemacs C tubes, followed by incubation at 37C in an incubator for 30 minutes and then filtering the cell suspension through a 70μm cell strainer. Isolated single cell suspensions were then stained with hashtag antibodies and cell surface antibodies for FACS. Isolated Live, CD45+, CD11b+, CD11c+ cell were used as the input for the 10X genomics chromium platform using a 5' sequencing kit and protocol.
Library construction was performed according to manufacturers instructions (10X genomics, 5' kit version 2)

value: Tumor

value: Mixed


title: Tumor cell mix 2, replicate B, scRNAseq, hashtag library


title: Tumor cell mix 2, replicate A, scRNAseq, hashtag library


title: MDA-MB-231 sgNT1, H3K27ac, biological replicate2


title: No_treatment2

value: no treatment


title: MDA-MB-231 sgNT1, H3K27ac, biological replicate1


title: MDA-MB-231 sgMLL3, input, biological replicate1


title: Tumor cell mix 1, replicate A, scRNAseq, hashtag library


title: No_treatment1


title: Ethanol-exposed Affected

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description: 10X Genomics 3' GEM Reagent Kit v3.1

data_processing:
Base-calling was performed by Psomagen using Illumina software.
Fastq files were filtered, aligned with combined hg38 and mm10 reference index, and assigned to barcodes using 10X Genomics cellranger software v 4.0.0
Counts files (filtered_feature_bc_matrix.h5) were loaded into Seurat v 4.0.2 for sample merging, filtering, clustering and analysis of gene expression
Seurat clusters containing mouse glia (matching mm10 genome) were removed, leaving only human (matching hg38).
Assembly: hg38
Supplementary files format and content: Output from combined Seurat data object with the GetAssay(slot="counts") command.  File is tab-delimited text file containing counts for sample-barcodes x genes. Column names consist of <sample name>_<subject code>_<barcode>

source_name: Excitatory neurons plated on primary mouse glia

growth_protocol: Excitatory (Ngn2) neurons were prepared by lentiviral induction of pluripotent stem cells and grown on mouse primary glia in Neurobasal medium. Cultures were harvested 4 weeks after induction.

extract_protocol:
For each cell line, two wells of a six well plate was plated with mixed cultures at 2x106 iNs and 2.5 x 105 glia/well.  On day 40, cells were dissociated with TrypLE (Thermo Fisher) for 5 min at 37°C, which preferentially releases neurons from glia. Cells were washed twice with 1X HBSS (Thermo Fisher), resuspended at 1200 cells/ml in 1% BSA/1X PBS and placed on ice.
Single-cell cDNA libraries were generated using the Chromium Next GEM Single Cell 3’ GEM Reagent Kits v3.1 (10X Genomics).  Approximately 2x104dissociated cells were loaded onto a cassette in the Chromium Controller with accompanying reagents to generate Gel Beads in Emulsions (GEMs). These were reverse transcribed to single-cell cDNA libraries before the oil emulsion was disrupted and cDNA purified using Dynabeads MyOne Silane (Thermo Fisher). cDNA was amplified by PCR for 11 cycles and purified using SPRIselect reagent (Beckman-Coulter).  cDNA fragmentation, A-tailing, and end repair was performed followed by adapter ligation for paired-end sequencing.  An additional 12 cycles of PCR were performed to incorporate the sample index sequences and to amplify the libraries before purification and sequencing.

treatment_protocol: Intermittent ethanol exposure (IEE) replaced half the culture medium daily with fresh medium containing 40 mM ethanol, to account for daily evaporation.

tag: sample type

value: iPSC-derived neuron culture

value: minor allele of KCNJ6 haplotype


title: MDA-MB-231 sgNT1, H3K4me3, biological replicate2

value: Breast cancer cell line

value: H3K4me3 (clone C42D8, Cell Signaling Technology, 9751s, 2 μg per sample)


title: Spleen cell mix 2, replicate A, scRNAseq, hashtag library

source_name: Spleen

value: Spleen


title: MDA-MB-231 sgNT1, H3K4me3, biological replicate1


title: Spleen cell mix 1, replicate A, scRNAseq, hashtag library


title: Untreated Affected

description: 10X Genomics 3' GEM Reagent Kit v3.1


title: Spleen cell mix 1, replicate B, scRNAseq, hashtag library


title: Ethanol-exposed Control

description: 10X Genomics 3' GEM Reagent Kit v3.1

value: major allele of KCNJ6 haplotype


title: Untreated Control

description: 10X Genomics 3' GEM Reagent Kit v3.1


title: MDA-MB-231 sgNT1, input, biological replicate2


title: MDA-MB-231 sgNT1, input, biological replicate1


title: MDA-MB-231 sgNT1, H3K4me1, biological replicate1

value: H3K4me1 (clone D1A9, Cell Signaling Technology, cat#5326s, 2 μg per sample)


title: Tumor cell mix 1, replicate B, scRNAseq, gene expression


title: Tumor cell mix 2, replicate A, scRNAseq, gene expression


title: UN iN culture 472

data_processing:
Base calling was done by sequencing vendor using Illumina software
Raw fastq files were filtered for quality and trimmed using FASTP software v0.12.2
Filtered fastq files were aligned with HISAT2 v2.2.0 using a mixed, indexed genome reference containing both human (hg38) and mouse (mm10)
Human-specific sequencing reads were selected those with the primary alignment matching human genome. Selected reads were re-aligned with HISAT2 and hg38 genome.
Sam files were converted to bam, sorted, and indexed using samtools v1.3.1
Alignments were deduplicated using Picard
Gene-level counts were produced using R/Rsubread function featureCounts using the GRCh38.gtf downloaded from Ensembl
Counts were modeled in DESeq2. Normalized counts were exported for the Processed Data File.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated values (tsv), Normalized counts

source_name: iPSC-derived induced neurons (iN)

growth_protocol: Human neurons are grown on mouse glia in Neurobasal Plus (ThermoFisher) with B27 Plus supplement (ThermoFisher).  Neurons are harvested at least 30 days after induction with Ngn2.

extract_protocol:
Total cellular RNA was prepared using a Zymo Quick-RNA Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Excitatory iN

tag: cell line id

tag: group

value: UN

tag: Sex

value: M


title: Tumor cell mix 1, replicate A, scRNAseq, gene expression


title: UN iN culture 384


title: MDA-MB-231 sgMLL3 #2, biological replicate 2

data_processing:
Base calling were conducted by illumina HiSeq Control Software.
After investigating the quality of raw data by FASTQC, RNA-seq reads were aligned using STAR (version 2.4.0) to the reference human genome (GRCh38.p13) with Ensembl annotation (gencode.v33).
featureCounts (v1.5.0) was used to generate raw counts from aligned reads.
DESeq2 (v1.30.1) R package was applied to analyze the differential expression.
Matrix table with raw gene counts for every gene and every sample generated by featureCounts.
Assembly: GRCh38/hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: breast cancer cell

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium with 10%FBS.

extract_protocol:
RNA was extracted using Quick-RNA microprep kit (Cat# R1050).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Triple-negative breast cancer line MDA-MB-231

value: Beast

value: MLL3-knock out


title: MDA-MB-231 sgMLL3 #1, biological replicate 1


title: UN iN culture 420

value: F


title: Spleen cell mix 2, replicate B, scRNAseq, gene expression


title: Spleen cell mix 2, replicate B, scRNAseq, hashtag library


title: AF iN culture 351

value: AF


title: AF iN culture 233


title: MDA-MB-231 sgNT #3, biological replicate 3

value: Wilde type


title: MDA-MB-231 sgNT1, H3K4me1, biological replicate2


title: Spleen cell mix 2, replicate A, scRNAseq, gene expression

value: Mixed


title: MDA-MB-231 sgNT #2, biological replicate 2

value: no treatment


title: Spleen cell mix 1, replicate B, scRNAseq, gene expression


title: AF iN culture 246


title: Tumor cell mix 2, replicate B, scRNAseq, gene expression

value: Tumor


title: AF iN culture 376


title: sgNT CD44+CD104-/low, biological replicate 3 [sgNT M3]

extract_protocol:
Cells were sorted based on the level of CD104. RNA was extracted using Quick-RNA microprep kit (Cat# R1050).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For Foskolin treament, cells were treated with 10 μM foskolin for 14 days. Medium was freshed every 2 days.

value: Forskolin 10 μM for 14 days


title: sgNT CD44+CD104-/low, biological replicate 2 [sgNT M2]


title: MDA-MB-231 sgMLL3 #3, biological replicate 3


title: sgNT CD44+CD104-/low, biological replicate 1 [sgNT M1]


title: sgNT CD44+CD104high, biological replicate 3 [sgNT E/M3]


title: VCaP_CRPC_PolyRb_rep2

city: Quebec City

first: Samer

last: Hussein

state: Quebec

address: 9 rue Mcmahon

department: Departement of medecine

country: Canada

institute: CHU de Québec - Université Laval

description: heavy polysome-bound RNA

data_processing:
The reads were aligned to the GRCh37 (hg19) human genome (Ensembl release 75), provided as reference fasta file "genome.fa", using STAR (v2.7.5)
Read alignments were merged and disambiguated, and a single BAM file output per library or sample was used. BAM files were then additionally filtered to remove reads with a mapping quality (MAPQ) less than 13, and all ribosomal and mitochondrial RNA reads.
Alignments were assembled using Cufflinks (v2.2.1) using the –g parameter to construct a genome annotation file against the reference gene model (Ensembl release 75) and to identify novel transcripts
Raw read counts were obtained by mapping reads at the gene level using the Cufflinks assembled transcript annotation file with the featureCounts tool from the SubRead package (version 2.0.0) using the exon counting mode
EdgeR R-package (v3.12.1) was then used to normalize the data, calculate transcript abundance (as counts per million reads (CPM)) and perform statistical analysis
Genome_build: hg19
Supplementary_files_format_and_content: Excel table (.xlsx) containing CPM values for each gene and sample, and EdgeR normalization output.

source_name: Prostate cancer cell line

growth_protocol: VCaP, VCaP-CRPC and VCaP-ER (Enzalutamide-resistant cell line) were cultivated in DMEM F12 10% FBS with 1mM sodium pyruvate. ENZ-resistant cell lines were maintained in 10 µM ENZ (enzalutamide).

extract_protocol:
Total RNA: VCaP, VCaP-CRPC and VCaP-ER were flash frozen on dry ice, and RNA was harvested using Trizol reagent according to the manufacturer's instructions.
Polysomes RNA: VCaP-CRPC and VCaP-ER were incubated in a cytoplasmic lysis buffer and nuclei were excluded by centrifugation. Cytoplasmic RNA was then loaded on a sucrose gradient and ultracentrifuged to allow for sorting according to the number of associated ribosomes. RNA fractions corresponding to 3 ribosomes or more (Heavy polysomes) were pooled and harvested using Phenol/chloroform extraction.
Paired-ends RNA libraries were constructed from 0.2 ug of RNA in accordance with the TruSeq stranded mRNA kit protocol (Illumina; # 20020594) and TruSeq RNA Single Indexes Set A and B (Illumina, # 20020492 and 20020493).

treatment_protocol: VCaP-ER were cultivated with ENZ (10uM)

tag: media

value: DMEM F12 media + 10% FBS


title: VCaP_CRPC_PolyRb_rep1

description: heavy polysome-bound RNA


title: VCaP_ER_rep2

description: polyA RNA

value: DMEM F12 media + 10% FBS + Enzalutamide (10uM)


title: sgNT CD44+CD104high, biological replicate 2 [sgNT E/M2]

tag: tissue


title: Morulae, 10% EtOH sire, EM29

city: College Station

first: Michael

last: Golding

state: Texas

address: Veterinary Research Building, Bldg 1197, Rm 334, 588 Raymond Stotzer Pkwy

department: Veterinary Physiology & Pharmacology

institute: Texas A&M University

data_processing:
Fast QC/Multi QC
Trim universal Illumina adapters
Fast QC/Multi QC
Mapping genome
counts file, DESeq2
Assembly: GRCm39/mm39
Supplementary files format and content: featureCounts, tabular file

source_name: embryo

growth_protocol: Nakagata IVF protocol with CARD media

extract_protocol:
Quick Biololgy Inc. RNA isolation protocol
Quick Biololgy Inc. library construction protocol
Illumina sequencing of 15Mpair reads

value: embryo

tag: strain

tag: developmental stage

value: Morula stage embryos

value: 10% EtOH


title: sgNT CD44+CD104high, biological replicate 1 [sgNT E/M1]

tag: treatment


title: VCaP_ER_rep1

description: polyA RNA


title: VCaP_CRPC_rep2

description: polyA RNA


title: Morulae, control sire, C27

value: Control


title: MDA-MB-231 sgNT #1, biological replicate 1

tag: genotype


title: Morulae, 10% EtOH sire, EM12


title: Morulae, control sire, C11


title: Neanderthal_updated_pool2B_output_rep1

city: Providence

first: William

last: Fairbrother

state: RI

address: 70 Ship St.

department: Molecular Biology, Cell Biology, and Biochemistry

institute: Brown University

data_processing:
Alignment of MaPSy input/output paired-end reads to either input/output custom reference genomes with STAR (2.7.9a) with parameters (--runThreadN 8 --genomeDir [DIR] --readFilesIn [FASTQ_R1] [FASTQ_R2] --readFilesCommand zcat -c --outSAMtype BAM Unsorted --outFileNamePrefix [PREFIX] --alignIntronMax 1 --outFilterMismatchNmax 5 --alignEndsType EndToEnd --outFilterMultimapNmax 1)
Get unique reads with samtools view (1.7) with parameters (-@ 16 -hbq 10 [BAM_UNSORTED] >| [BAM_UNIQUE]])
Sort reads with samtools sort (1.7) with parameters (-@ 16 -o [BAM_SORTED] [BAM_UNSORTED])
Index reads with samtools index (1.7) with parameters (-@ 16 -b [BAM_SORTED])
Count reads with samtools idxstats (1.7) with parameters ([BAM_SORTED] >| [IDXSTATS])
Join read counts by seq id to reference table
genome build: Custom minigene reference genomes based on hg19 (neanderthal_updated_input.fasta.gz for input libraries, neanderthal_updated_output.fasta.gz for output libraries)
processed data files format and content: txt - samtools idxstats read counts

source_name: HEK 293T cells

extract_protocol:
Forty-eight hours after transfection, RNA was extracted using TRIzol (ThermoFisher) and DNase treated (Invitrogen). Random 9-mers were used to generate cDNA with SuperScript IV Reverse Transcriptase (Invitrogen) followed by 25 cycles of PCR amplification (GoTaq, Promega), resulting in output libraries of spliced exon inclusion and exon skipped species.
Primers were designed to amplify the region of the input and output library sequences immediately surrounding the variable region of interest. For the input libraries, the primers matched AD81 and ACTN1 intronic regions, and for the output libraries, the primers matched exonic regions of AD81 and ACTN1. Replicates were identified using NEXTflex DNA Barcodes (PerkinElmer).

treatment_protocol: The input library was transfected into human embryonic kidney HEK 293T cells obtained from the American Type Culture Collection (ATCC CRL-316) in three cell culture replicates using Lipofectamine 3000 (Invitrogen) in a 6-well plate.

value: HEK 293T cells

value: wildtype


title: Morulae, 6% EtOH sire, M215

value: 6% EtOH


title: VCaP_rep2

description: polyA RNA

value: VCaP


title: Neanderthal_updated_pool2B_output_rep2


title: VCaP_ER_PolyRb_rep1

description: heavy polysome-bound RNA


title: VCaP_ER_PolyRb_rep2

description: heavy polysome-bound RNA


title: Morulae, 10% EtOH sire, EM14


title: VCaP_rep1

description: polyA RNA


title: Spleen cell mix 1, replicate A, scRNAseq, gene expression

value: Spleen


title: Neanderthal_updated_pool2B_output_rep3


title: Morulae, control sire, C9