title: Tesits, NOD, rep2

status: Public on Sep 22 2023

city: Badalona

first: Tanya

last: Vavouri

state: BARCELONA

address: Ctra de Can Ruti, Cami de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

data_processing:
Adapter removed using cutadapt (v2.10) -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC -O 9 -j 0 -m 19 -M 36 --trimmed-only.
Reads filtered using fastq_quality_filter (FASTX Toolkit v0.0.14) -q 30 -p 90 -Q 33.
Reads mapped using bowtie (v1.2.3) --threads 4 -t -M 1 --best --strata -v 1 -q --seed 666.
Reads mapping to piRNA clusters counted using featureCounts (v2.0.1) -Q 1 -s 0 -O --minOverlap 18
Assembly: For strain C57BL/6J we used GRCm38/mm10, for strain CAST/EiJ we used CAST_EiJ_v1, for strain 129S1/SvlmJ we used 129S1_SvlmJ_v1, for strain C3HeB/FeJ we used C3H_HeJ_v1, for strain NOD we used NOD_ShiLtJ_v1 and for strain ICR we used GRCm38/mm10.
Supplementary files format and content: Comma separated text file of piRNA cluster normalized read counts in samples from outbred strain.
Supplementary files format and content: Comma separated text file of piRNA cluster normalized read counts in samples from inbred strains.

source_name: Testis

extract_protocol:
Total RNA was isolated using TRIzol® Reagent (Invitrogen) according to manufacturer's instructions
TruSeq small RNA protocol

value: Testis

tag: Sex

value: Male

value: NOD


title: rRNA Depleted totalRNA from liver from untreated FHH rats (replicate 1, sequencing batch 16)

status: Public on Oct 23 2023

type: SRA

city: Aurora

first: Laura

last: Saba

state: CO

address: 12850 E. Montview Blvd

department: Skaggs School of Pharmacy and Pharmaceutical Sciences

country: USA

institute: University of Colorado Anschutz Medical Campus

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: FHH_1_batch16
FHH_1

library_source: transcriptomic

data_processing:
Cutadapt (v1.9.1) trim Illumina adapter, quality, and length, parameters: -q 20 -m 20
Remove rRNA reads by alignment with bowtie2(v2.3.4.3) to rRNA
genome Alignment Hisat2 (v2.1.0)
Stringtie (v1.3.5) reconstruction
Run Aptardi (v1.4) on each strain reconstructed GTF
Merge aptardi output reconstruction Stringtie(v1.3.5)
Run RSEM (v1.3.1) on reconstruction
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Run RSEM(v1.3.1) on filtered reconstruction
Filter transcripts/genes from RSEM filtered transcriptome results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Apply a regularized log transformation of expected read counts from RSEM (rlog function in DESeq2 package of R)
Remove technical artifacts including batch effects using Removal of Unwanted Variance  (RUVg) with empirically-derived controls (RUVSeq package in R)
Assembly: Rn7.2
Supplementary files format and content: TSV batch corrected/normalized expression values
Supplementary files format and content: GTF of the reconstructed transcriptome

molecule: total RNA

organism: Rattus norvegicus

source_name: liver

extract_protocol:
RNA was collected from liver using the RNeasy Plus Universal Midi kits for RNA sequencing (Qiagen, Valencia, CA, USA).
Libraries were constructed using the Illumina TruSeq Stranded TotalRNA Kit (Illumina, San Diego, CA, USA).
rRNA depleted stranded totalRNA

treatment_protocol: Tissue frozen in RNA later.

tag: tissue

value: liver

tag: strain

value: FHH/EurMcwi

tag: batch

tag: treatment


title: rRNA Depleted totalRNA from liver from untreated BN rats (replicate 2, sequencing batch 18)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BN_2_batch18
BN_2

value: BN/NHsdMcwi


title: Testis, C3H, rep3

organism: Mus musculus

tag: genotype


title: Testis, C3H, rep2


title: Testis, BL6, rep2


title: Spermatogonia, CAST, rep2

source_name: Spermatogonia

value: Spermatogonia

value: CAST/EiJ


title: Testis, C3H, rep1


title: Testis, BL6, rep1


title: Spermatogonia, CAST, rep3


title: Spermatogonia, CAST, rep4


title: rRNA Depleted totalRNA from liver from untreated BN rats (replicate 1, sequencing batch 17)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BN_1_batch17
BN_1


title: Testis, 129, rep3


title: Tesits, NOD, rep1


title: TILD117_More-affected_TMA4-Run2_3mm

status: Public on Jun 04 2024

type: other

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

hyb_protocol: A total of 343 unique genes were included in the analysis of this dataset. 246 genes came from an early version of the Xenium human lung base panel (PD_336) and 97 genes from a custom designed panel (CVEVZD). The custom panel was curated based on human lung single cell analysis data (Habermann et al. 2020), selecting for genes useful in cell type identification and/or with suspected involvement in IPF. Gene panel probe hybridization occurred overnight for 18 hours at 50°C (Bio-Rad DNA Engine Tetrad 2). Subsequent washes the next day removed unbound probes. Ligase was added to circularize the paired ends of bound probes (2 hours at 37°C) and followed by enzymatic rolling circle amplification (2 hours at 30°C). Slides were washed in TE buffer before background fluorescence was chemically quenched; autofluorescence is a known issue in lung tissue as well as a byproduct of formalin-fixation (Davis et al. 2014). Following PBS and PBS-T washes, DAPI was used to stain sample nuclei. Finalized slides were stored in PBS-T in the dark at 4°C for ≤5 days until being loaded onto the Xenium Analyzer instrument. Stepwise Xenium FFPE preparation guidelines and buffer recipes can be found in 10X Genomics Demonstrated Protocol CG000578.

scan_protocol: Xenium Analyzer is fully automated. The user marks regions for analysis by manually selecting sample location on an initial low-resolution image. After loading consumable reagents and slides, internal sample and liquid handling mechanics control experiment progression. Data collection occurs in cycles of fluorescently labeled probe binding, image acquisition, and probe stripping. Localized points of fluorescence intensity detected during the rounds of imaging are then defined as potential RNA puncta. Each gene on the panel has a unique fluorescence pattern across the image channels. Puncta that match a specific pattern are then decoded and labeled according to the gene ID. All image FOVs (4240 x 2960 pixels) and associated detected transcripts are computationally stitched together via the DAPI-stained image. The data in this paper was acquired on instrument software version 1.1.2.4 and analysis version xenium-1.1.0.2. Detailed instructions on instrument operation and consumable preparation can be found in 10X Genomics’ Demonstrated Protocol CG000582.

data_processing:
Transcript-based niche embedding files (node_meta.csv and .npy files) were genetared using GraphSAGE.
Information about output files can be found here:
https://www.10xgenomics.com/support/in-situ-gene-expression/documentation/steps/onboard-analysis/understanding-xenium-outputs
Supplementary files format and content: HE_annotations.tar: This file contains geojson polygons of pathology annotations of regions mentioned in the paper for each sample as well as a csv assigning cells to the annotations they fall within.

molecule: other

organism: Homo sapiens

source_name: Lung, more affected

label_protocol: Deparaffinization and decrosslinking was performed to make subcellular RNA targets accessible (10X Genomics Demonstrated Protocol CG000580).

growth_protocol: A 5um section of each archived lung FFPE block was H&E stained and presented to a physician who identified areas of interest and labeled them as less or more fibrotic (LF or MF) relative to the sample. TMA blocks were designed in a 3x3 or 2x2 pattern for 3mm and 5mm cores, respectively. Sample cores were punched and placed manually using a “Quick-Ray Manual Tissue Microarrayer Full Set” and “Quick-Ray Molds”, according to the manufacturer’s directions. Empty core spaces were filled with core punches taken from blank paraffin blocks (VWR 76548-194). Once complete, blocks are placed face down on a clean glass slide and briefly heated in a warm drawer (~45°C) to slightly melt the paraffin together and even the block face. TMA blocks were then cooled to room temperature, removed from the slide, sealed, and stored at 4°C.

extract_protocol: Sectioning was performed at 5um on a Leica RM2135 with a water float temperature of 40°C. Sections were placed on Xenium slides (10X Genomics) and left to dry overnight. Slides were then stored in a sealed dessicator at room temperature for up to a maximum of 10 days.

treatment_protocol: All protocol workstations and equipment were cleaned using RNase Away (RPI 147002) followed by 70% Isopropanol. All reagents, including water, were molecular grade nuclease-free.

tag: age

tag: ethnicity

value: European

tag: status

value: Disease

value: Lung

tag: tma

tag: run

tag: punch size

tag: clinical diagnosis

value: ILD

tag: sample type


title: Spermatogonia, BL6, rep2


title: Spermatogonia, BL6, rep3


title: Testis, ICR, rep39

value: ICR


title: Testis, ICR, rep38


title: Spermatogonia, CAST, rep1


title: Testis, 129, rep2


title: Testis, ICR, rep35


title: Testis, ICR, rep37


title: Testis, 129, rep1


title: Testis, ICR, rep36


title: Testis, ICR, rep34


title: Testis, ICR, rep31


title: Testis, ICR, rep32


title: Testis, ICR, rep33


title: Testis, ICR, rep30


title: Spermatogonia, BL6, rep4


title: Testis, ICR, rep27


title: Testis, ICR, rep28


title: Spermatogonia, BL6, rep1


title: Testis, ICR, rep29


title: Testis, ICR, rep25


title: Testis, ICR, rep24


title: Testis, ICR, rep26


title: Testis, ICR, rep22


title: Testis, ICR, rep21


title: Testis, ICR, rep20


title: Testis, ICR, rep16


title: Testis, ICR, rep19


title: Testis, ICR, rep13


title: Testis, ICR, rep23


title: Testis, ICR, rep18


title: Testis, ICR, rep15


title: Testis, ICR, rep14


title: Testis, ICR, rep10


title: Testis, ICR, rep6


title: Testis, ICR, rep12


title: Testis, ICR, rep11


title: Testis, ICR, rep9


title: Testis, ICR, rep8


title: Testis, ICR, rep7


title: Testis, ICR, rep5


title: T2D4.5

status: Public on Aug 09 2023

city: Cleveland

first: Shanshan

last: Zhang

state: OH

address: 10900 Euclid Avenue

department: Department of Genome and Genetics

institute: Case Western Reserve University

description: scATAC-seq

library_source: genomic

data_processing:
none provided by the submitter
Genome_build: hg19

molecule: genomic DNA

source_name: human islet donor T2D4 plate5

extract_protocol: none provided by the submitter

value: no treat


title: T2D3.5

description: scATAC-seq

source_name: human islet donor T2D3 plate5


title: T2D4.2

description: scATAC-seq

source_name: human islet donor T2D4 plate2


title: T2D4.1

description: scATAC-seq

source_name: human islet donor T2D4 plate1


title: ChAR-seq ES replicate 1

city: Stanford

first: Aaron

middle: F

last: Straight

state: CA

address: 279 Campus Drive, B409A

department: Biochemistry

institute: Stanford University

library_source: other

data_processing:
*library strategy: ChAR-seq
Demultiplexed fastq files from the ChAR-seq data were processed using a custom Snakemake pipeline (https://github.com/straightlab/charseq-pipelines), outputting pairs files containing the RNA and DNA coordinates of each RNA(cDNA)-DNA chimeric read and relevant annotations for each RNA-DNA contact.
RNA-seq data was processed using a Snakemake pipeline mirroring the ChAR-seq pipeline, but all of the operations related to the DNA-side of the reads were skipped. In brief, demultiplexed fastq files were deduplicated, sequencing adapters were removed, paired mates were merged as described for ChAR-seq reads. Reads that aligned to a rRNA sequence by Bowtie2 were filtered out using Picard. Reads were aligned to hg38 using STAR and were annotated with tagtools using the Gencode V29 gene models. Reads with low mapping scores (STAR Q < 255), reads which could not be attributed to a single known gene or a single locus, and reads that overlapped with a locus on the ENCODE black were discarded.
For ATAC-seq data Illumina Nextera Adapters were removed using a custom Python script. Reads were aligned to the hg38 using Bowtie2. Duplicates were removed with Picard. Mitochondrial reads or reads with Bowtie2 MAPQ score < 30 were removed using SAMtools. All replicates were similar, so their alignment files were merged to increase library complexity (>100 million mapped reads per cell type) and produce a single bigwig file per cell type used to display the ATAC-seq tracks, and a single bam file to determine ATAC-seq peaks. ATAC-seq peaks were identified in each cell line using HMMRATAC v1.2.10.
Assembly: hg38
Supplementary files format and content: bed

source_name: embryo

growth_protocol: Human H9 ES cells were grown on matrigel in mTeSR1 medium in 5%C02 at 37°C

extract_protocol:
Cell extraction is described in detail in Limouse, C. et al in RNA-Chromatin Interactions: Methods Mol Biol. 2020;2161:115-142. doi:10.1007/978-1-0716-0680-3_10.
Library preparation is described in detail in Limouse, C. et al in RNA-Chromatin Interactions: Methods Mol Biol. 2020;2161:115-142. doi:10.1007/978-1-0716-0680-3_10.

treatment_protocol: Cells were defferentiated into Definitive Endoderm by treatment with 10 µM Y27632 on day 0, and their media was replaced on day 1 with DE induction Media A (Gibco Cat# A3062601), and on day 2 with DE induction Media B (Gibco Cat# A3062601). On day 3, cells were harvested for ChAR-seq.

value: embryo

tag: cell line

tag: cell type

value: embryonic stem cell

value: ES wild type


title: Testis, ICR, rep4

value: Testis


title: T2D3.4

description: scATAC-seq

source_name: human islet donor T2D3 plate4


title: D429F02_D493F01_D557F01_D610F01_Hi-C p50_PD-D2-24h

status: Public on Sep 17 2023

city: Paris

first: Héloïse

last: Muller

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: Hi-C

data_processing:
Library were sequenced on Novaseq.
Adapter sequences were trimmedfrom reads using trimgalore.
Hi-C reads were processed and filtered using the HiCPro suite.
Matrices files have been generated using the cooler suite and format.
Assembly: Bmori_v3 or Bmori_4
Supplementary files format and content: multi-resolution cooler

organism: Bombyx mori

source_name: full embryo

growth_protocol: 20-30 p50 diapaused eggs harvest after release at 25°C

extract_protocol:
Eggs were glued in a Petri dish filled with 3% formaldehyde before chorions were poked with a fine needle to allow embryos fixation for 30 min. After quenching, embryos were dissected out of chorion with fine forceps before frozen at -80°C and processed with Arima-HiC+ kit from Arima genomics.
Sequencing libraries were prepared using the KAPA HyperPrep Library Preparation Kit complemented with Illumina TruSeq DNA UD Indexes. Libraries were amplified using 8-14 cycles on the thermocycler. Post amplification libraries were size selected at 250-600bp in length using SPRIselect beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity screenTapes.

value: full embryo

tag: time


title: Testis, ICR, rep3

tag: Sex

value: Male


title: Testis, ICR, rep2

tag: tissue


title: T2D2.6

description: scATAC-seq

source_name: human islet donor T2D2 plate6


title: T2D3.2

description: scATAC-seq

source_name: human islet donor T2D3 plate2


title: T2D4.4

description: scATAC-seq

source_name: human islet donor T2D4 plate4


title: ChAR-seq DE replicate 1

value: DE wild type

value: endodermal differentiation


title: T2D3.1

description: scATAC-seq

source_name: human islet donor T2D3 plate1


title: Testis, ICR, rep1


title: T2D2.3

description: scATAC-seq

source_name: human islet donor T2D2 plate3


title: T2D3.3

description: scATAC-seq

source_name: human islet donor T2D3 plate3


title: Testis, ICR, rep17

source_name: Testis


title: T2D2.4

description: scATAC-seq

source_name: human islet donor T2D2 plate4


title: T2D4.3

description: scATAC-seq

source_name: human islet donor T2D4 plate3


title: ChAR-seq DE replicate 2


title: T2D1.1

description: scATAC-seq

source_name: human islet donor T2D1 plate1


title: T2D2.2

description: scATAC-seq

source_name: human islet donor T2D2 plate2


title: T2D2.1

description: scATAC-seq

source_name: human islet donor T2D2 plate1


title: HT7.4

description: scATAC-seq

source_name: human islet donor HT7 plate4


title: HT7.2

description: scATAC-seq

source_name: human islet donor HT7 plate2


title: ChAR-seq ES replicate 2

source_name: embryo


title: HT6.2

description: scATAC-seq

source_name: human islet donor HT6 plate2


title: T2D2.5

description: scATAC-seq

source_name: human islet donor T2D2 plate5


title: HT6.1

description: scATAC-seq

source_name: human islet donor HT6 plate1


title: T2D1.2

description: scATAC-seq

source_name: human islet donor T2D1 plate2


title: HT5.3

description: scATAC-seq

source_name: human islet donor HT5 plate3


title: HT6.3

description: scATAC-seq

source_name: human islet donor HT6 plate3


title: HT4.4

description: scATAC-seq

source_name: human islet donor HT4 plate4


title: HT4.6

description: scATAC-seq

source_name: human islet donor HT4 plate6


title: HT5.2

description: scATAC-seq

source_name: human islet donor HT5 plate2


title: HT4.7

description: scATAC-seq

source_name: human islet donor HT4 plate7


title: HT4.2

description: scATAC-seq

source_name: human islet donor HT4 plate2


title: HT7.3

description: scATAC-seq

source_name: human islet donor HT7 plate3


title: HT5.1

description: scATAC-seq

source_name: human islet donor HT5 plate1


title: HT5.4

description: scATAC-seq

source_name: human islet donor HT5 plate4


title: HT4.3

description: scATAC-seq

source_name: human islet donor HT4 plate3


title: HT4.1

description: scATAC-seq

source_name: human islet donor HT4 plate1


title: HT3.1

description: scATAC-seq

source_name: human islet donor HT3 plate1


title: HT2.2

description: scATAC-seq

source_name: human islet donor HT2 plate2


title: HT3.2

description: scATAC-seq

source_name: human islet donor HT3 plate2


title: HT7.1

description: scATAC-seq

source_name: human islet donor HT7 plate1


title: HT2.1

description: scATAC-seq

source_name: human islet donor HT2 plate1


title: HT1.2

description: scATAC-seq

source_name: human islet donor HT1 plate2


title: HT1.4

description: scATAC-seq

source_name: human islet donor HT1 plate4


title: HT1.5

description: scATAC-seq

source_name: human islet donor HT1 plate5


title: rRNA Depleted total RNA from whole brain from untreated WAG rats (replicate 2, sequencing batch 16)

status: Public on Aug 04 2023

data_processing:
Cutadapt (v1.9.1) trim Illumina adapter, quality, and length, parameters: -q 20 -m 20
Remove rRNA reads by alignment with bowtie2(v2.3.4.3) to rRNA
genome Alignment Hisat2 (v2.1.0)
Stringtie (v1.3.5) reconstruction
Run Aptardi (v1.4) on each strain reconstructed GTF
Merge aptardi output reconstruction Stringtie(v1.3.5)
Run RSEM (v1.3.1) on reconstruction
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Run RSEM(v1.3.1) on filtered reconstruction
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Apply a regularized log transformation of expected read counts from RSEM (rlog function in DESeq2 package of R)
Remove technical artifacts including batch effects using Removal of Unwanted Variance  (RUVg) with empirically-derived controls (RUVSeq package in R)
Assembly: Rn7.2
Supplementary files format and content: TSV batch corrected/normalized expression values and GTF of the reconstructed transcriptome

source_name: whole brain

extract_protocol:
RNA was collected from whole brain using the RNeasy Plus Universal Midi kits for RNA sequencing (Qiagen, Valencia, CA, USA).
Libraries were constructed using the Illumina TruSeq Stranded total RNA Kit (Illumina, San Diego, CA, USA).
rRNA depleted stranded total RNA

tag: strain

value: WAG/RijCrl

tag: extraction protocol

value: whole brain


title: HT1.3

description: scATAC-seq

source_name: human islet donor HT1 plate3

tag: treatment


title: HT1.1

description: scATAC-seq

source_name: human islet donor HT1 plate1


title: rRNA Depleted total RNA from whole brain from untreated WAG rats (replicate 1, sequencing batch 15)

tag: batch

value: RNA was collected from whole brain using the RNeasy Plus Universal Midi kits for RNA sequencing (Qiagen, Valencia, CA, USA).


title: HT4.5

description: scATAC-seq

source_name: human islet donor HT4 plate5


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 4, sequencing batch 17)

value: SHR/OlaIpcv


title: rRNA Depleted total RNA from whole brain from untreated WAG rats (replicate 3, sequencing batch 16)


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 4, sequencing batch 16)


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 4, sequencing batch 15)


title: rRNA Depleted total RNA from whole brain from untreated MWF rats (replicate 3, sequencing batch 17)

value: MWF/Hsd


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 3, sequencing batch 6)


title: rRNA Depleted total RNA from whole brain from untreated MWF rats (replicate 1, sequencing batch 15)


title: rRNA Depleted total RNA from whole brain from untreated PVG rats (replicate 3, sequencing batch 17)

value: PVG/Seac


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 1, sequencing batch 15)


title: rRNA Depleted total RNA from whole brain from untreated PVG rats (replicate 2, sequencing batch 17)


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 1, sequencing batch 16)


title: rRNA Depleted total RNA from whole brain from untreated PVG rats (replicate 1, sequencing batch 16)


title: rRNA Depleted total RNA from whole brain from untreated M520 rats (replicate 3, sequencing batch 17)


title: rRNA Depleted total RNA from whole brain from untreated M520 rats (replicate 1, sequencing batch 15)


title: rRNA Depleted total RNA from whole brain from untreated M520 rats (replicate 2, sequencing batch 16)


title: rRNA Depleted total RNA from whole brain from untreated LH rats (replicate 2, sequencing batch 17)

value: LH/MavRrrc


title: HT1.6

description: scATAC-seq

source_name: human islet donor HT1 plate6


title: rRNA Depleted total RNA from whole brain from untreated LH rats (replicate 3, sequencing batch 17)


title: rRNA Depleted total RNA from whole brain from untreated LEXF1C rats (replicate 3, sequencing batch 16)


title: rRNA Depleted total RNA from whole brain from untreated LH rats (replicate 1, sequencing batch 16)


title: rRNA Depleted total RNA from whole brain from untreated LEXF1C rats (replicate 2, sequencing batch 15)


title: rRNA Depleted total RNA from whole brain from untreated MWF rats (replicate 2, sequencing batch 16)


title: rRNA Depleted total RNA from whole brain from untreated LEXF10A rats (replicate 3, sequencing batch 16)


title: rRNA Depleted total RNA from whole brain from untreated LEXF10A rats (replicate 1, sequencing batch 15)


title: rRNA Depleted total RNA from whole brain from untreated LEXF10A rats (replicate 2, sequencing batch 15)


title: rRNA Depleted total RNA from whole brain from untreated GK rats (replicate 1, sequencing batch 16)

value: GK/FarMcwi


title: rRNA Depleted total RNA from whole brain from untreated GK rats (replicate 2, sequencing batch 17)


title: rRNA Depleted total RNA from whole brain from untreated FXLE20 rats (replicate 2, sequencing batch 15)


title: rRNA Depleted total RNA from whole brain from untreated FXLE15 rats (replicate 2, sequencing batch 15)


title: rRNA Depleted total RNA from whole brain from untreated FXLE15 rats (replicate 3, sequencing batch 17)


title: rRNA Depleted total RNA from whole brain from untreated FXLE12 rats (replicate 3, sequencing batch 16)


title: rRNA Depleted total RNA from whole brain from untreated FXLE15 rats (replicate 1, sequencing batch 15)


title: rRNA Depleted total RNA from whole brain from untreated FHH rats (replicate 3, sequencing batch 17)

value: FHH/EurMcwi


title: rRNA Depleted total RNA from whole brain from untreated FXLE12 rats (replicate 2, sequencing batch 15)


title: rRNA Depleted total RNA from whole brain from untreated FHH rats (replicate 1, sequencing batch 15)


title: rRNA Depleted total RNA from whole brain from untreated BN rats (replicate 2, sequencing batch 17)

value: BN/NHsdMcwi


title: rRNA Depleted total RNA from whole brain from untreated BN rats (replicate 1, sequencing batch 16)


title: rRNA Depleted total RNA from whole brain from untreated FXLE12 rats (replicate 1, sequencing batch 15)


title: Colonic tumor, KrasG12D_K104Q_3

status: Public on Jun 01 2023

city: Boston

first: Bing

last: Shui

state: MA

address: 360 Longwood Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

data_processing:
Salmon (salmon v0.14.1) pseudo-aligner was used for sequencing alignment and read count, with the Ensembl mm10 genome (Mus_musculus.GRCm38) as reference, using the following parameter: -l A --seqBias --useVBOpt --validateMappings
Normalized count was obtained using DESeq2, normalized across all samples from the same model
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample
Supplementary files format and content: Table with differential analysis result from DESeq2 for every gene (KrasG12D vs KrasWT, KrasG12DK104Q vs KrasG12D, KrasG12DK104Q vs KrasWT)

source_name: Colonic tumor

growth_protocol: Control and experimental mice were housed until 8-12 weeks old

extract_protocol:
Colonic tumors were resected from animals that reached humane end points. Scraped tissues were flash frozen in liquid nitrogen and stored at -80ºC. Frozen samples were powderized in liquid nitrogen with a tissue homogenizer. RNA was extracted using the RNeasy Plus Universal kit from Qiagen, following the manufacturer's instructions. RNA concentration and quality were evaluated in Agilent Bioanalyzer/TapeStation.
1µg of RNA was used for RNA-Seq library preparation using Truseq Strand Specific Large Insert RNA Sequencing Unaligned v1. Library construction was performed by the Genomics platform team at the Broad Institute.

value: Colonic tumor

tag: genotype


title: rRNA Depleted total RNA from whole brain from untreated BN rats (replicate 3, sequencing batch 17)


title: rRNA Depleted total RNA from whole brain from untreated FHH rats (replicate 2, sequencing batch 16)


title: Colonic tumor, KrasG12D_2


title: Colonic tumor, KrasG12D_K104Q_2


title: rRNA Depleted total RNA from whole brain from untreated LEXF1C rats (replicate 1, sequencing batch 15)


title: Colonic tumor, KrasG12D_3


title: Colonic tumor, KrasG12D_K104Q_1


title: rRNA Depleted total RNA from whole brain from untreated GK rats (replicate 3, sequencing batch 17)


title: rRNA Depleted total RNA from whole brain from untreated FXLE20 rats (replicate 1, sequencing batch 15)


title: STINGseq-v2_cDNA-B

status: Public on Mar 22 2023

city: New York

first: John

middle: A

last: Morris

state: New York

address: 101 Avenue of the Americas, 4th Floor

institute: New York Genome Center

data_processing:
cDNA reads were mapped to the human genome (hg38, ensembl v96). cDNA, HTO, ADT, and GDO reads were quantified using 10x Cell Ranger v.6.0.0 to generate UMI count matrices.
Cells were demultiplexed based on their HTO counts into their singlets after normalization (centered log ratio transformation) using the HTOdemux function in Seurat v.4.0.1.
For STINGseq-v1 and STINGseq-v2, gRNAs per cell were identitied with the 10x Cell Ranger v.6.0.0 determined threshold (with a minimum UMI = 3 threshold applied). For BeeSTINGseq, we tested each gRNA at UMI thresholds from 1-5.
Assembly: hg38
Supplementary files format and content: Processed data provided in standard UMI count matrix format for cDNA, GDO, HTO, and ADT modalities. Each sample has three files separated into features, barcodes and a sparse matrix file. STINGseq-v1 and STINGseq-v2 GDO files have the UMI threshold files included.

molecule: polyA RNA

source_name: Human erythroleukemic cell line, K562, expressing KRAB-dCas9-MeCP2

extract_protocol:
For STINGseq-v1, we ran one lane of a 10x Genomics 5’ kit (Chromium Single Cell Immune Profiling Solution v1.0, 1000014, 1000020, 1000151) with cell hashing performed using four hashtag-derived oligonucleotides (HTOs). For STINGseq-v2, we ran four lanes of a 10x Genomics 5' kit (Chromium Next GEM Single Cell 5' Kit v2 1000265) with cell hashing performed using eight HTOs. For BeeSTINGseq, we ran three lanes of a 10x Genomics 5’ v2 kit (Chromium Next GEM Single Cell 5' Kit v2 1000265) with cell hashing performed using nine HTOs.
Gene expression (cDNA), hashtags (HTOs), guide RNA (Guide-derived oligos, GDOs) libraries, and oligo-tagged antibodies (ADTs) were constructed by following 10x Genomics and ECCITE-seq protocols. We sequenced all cDNA, HTO, GDO, and ADT libraries with  a NextSeq 500 or NovaSeq 6000 (Illumina).
ECCITE-seq sequencing strategy, with the following read recipe: R1 = 26; i7 = 8; R2 = 57


title: 205624640173_R03C01

status: Public on Feb 08 2023

type: genomic

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg, Intitute of Pathology

description:
Methylation data from tumor sample
Sample 252

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
processed data file includes: Average Beta

source_name: PCA

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

value: tumor

tag: tissue preparation

value: FFPE


title: 200772280002_R03C01

description:
Methylation data from tumor sample
Sample 142

source_name: PINB


title: 205624640173_R04C01

description:
Methylation data from tumor sample
Sample 132


title: Colonic tumor, WT_2

value: K-RAS-WT


title: Colonic tumor, WT_1


title: 205624640173_R02C01

description:
Methylation data from tumor sample
Sample 131


title: 205624640136_R06C01

description:
Methylation data from tumor sample
Sample 129

source_name: MG


title: 205624640136_R04C01

description:
Methylation data from tumor sample
Sample 128


title: 205624640113_R07C01

description:
Methylation data from tumor sample
Sample 124


title: 205624640136_R01C01

description:
Methylation data from tumor sample
Sample 126


title: 205624640136_R07C01

description:
Methylation data from tumor sample
Sample 130


title: 205624640113_R06C01

description:
Methylation data from tumor sample
Sample 123


title: 205624640113_R05C01

description:
Methylation data from tumor sample
Sample 122


title: 205624640113_R03C01

description:
Methylation data from tumor sample
Sample 121


title: Colonic tumor, KrasG12D_1


title: 205624640136_R08C01

description:
Methylation data from tumor sample
Sample 120


title: Castration-resistant prostate cancer [CRPC #3]

status: Public on Jan 15 2023

city: Shanghai

first: Zehua

last: Ma

address: Pujian road 160

country: China

institute: Shanghai Jiaotong university

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were converted to FASTQ files with Illumina bcl2fastq, version 2.19.1, and data were aligned to the human genome reference se_x0002_quence (GRCH38)
The CellRanger (10X Genomics, 2.1.1 version) analysis pipeline was used for sample demultiplexing, barcode processing and single-cell 3′ gene counting to generate a digital gene-cell matrix from these data.
Cell Ranger filters any barcode that contains less than 10% of the 99th percentile of total UMI counts per barcode, as these are considered to be associated with low quality cell barcodes
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: primary prostate cancer

extract_protocol:
Tumor tissues were ressected by biopsy surgery and transported in DMEM/F12 medium on ice to the laboratory within an hour. For scRNA-seq, the tissues were dissociated into single cells suspensions using digestion buffer (DMEM/F12 Medium+ 2 mg/ml of collagenase IV + 100 IU/ml DNase I), and single cell GEMs were generated by 10X genomics Chromium Controller. cDNA library was constructed following the manufacture’s protocol.
The cell suspension of each sample was run in the Chromium Controller with appropriate reagents to generate single cell gel bead-in-emulsions (GEMs) for sample and cell barcoding. The libraries were then pooled and sequenced on a NovaSeq 6000 (Illumina) at a depth of ~400 M reads per sample.

treatment_protocol: CSPC recevied no treatment, CRPC received ADT and androgen receptor antagonist

value: primary prostate cancer

tag: age

value: Male

value: Goserelin+Enzalutamide


title: 205624640136_R05C01

description:
Methylation data from tumor sample
Sample 119


title: Castration-resistant prostate cancer [CRPC #2]


title: Colonic tumor, WT_3


title: Castration-resistant prostate cancer [CRPC #1]


title: 205624640113_R08C01

description:
Methylation data from tumor sample
Sample 125


title: circ_0001400_pulldown_antisense_2

status: Public on Dec 19 2022

city: Bethesda

first: Joseph

middle: M

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Assembly: GRCh38

source_name: KSHV-infected HUVEC + control siRNA Rep.2

growth_protocol: 293T cells are cultured in DMEM +10%FBS, Penicillin, Sptreptomycin.

extract_protocol:
Cells are incubated with 5 mg psoralen-TEG-azide (Berry) for 20 minutes at 37°C followed by exposure to long-wavelength UV for 10 minutes. Cells were lysed with Trizol and RNA was extracted by Direct-zol (Zymo) with on-column DNAse I digestion following the manufacturer's instruction. RNA was then incubated with 100pmol biotinylated DNA oligos (IDT) either complemetary to circ_0001400 or same strand as circRNA (control) for 6 hours. RNAs are captured with 100 μl Dynabeads MyOne Streptavidin C1 and exposed to short-wavelength UV.
SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA), and Illumina Nextera XT library was used for sequencing library preparation.
RNA pulldown

treatment_protocol: 4 Million 293T cells are transfected with 2ug of circ_0001400 expressing plasmid with Transporter4 reagent for 24 hours.

value: Human epithelial cell line

tag: probe

value: circ_0001400-specific probe


title: KSHV-infected HUVEC + circ_0001400 lentivirus Rep.3

data_processing: Illumina Casava1.7 software used for basecalling.

source_name: Human primary endothelial cell

growth_protocol: All HUVECs are cultured in EGM2 media.

extract_protocol:
Cells are lysed with Trizol and RNA was extracted by Direct-zol (Zymo) with on-column DNAse I digestion following the manufacturer's instruction.
Illumina, strand-specific RNA-seq with PolyA selection

treatment_protocol: For siRNAs, 20nM fianl of siRNAs (ON-TARGETplus) was added day before the infection, and KSHV (BAC16) was added at MOI of 1.0. For lentivirus, MOI 1.0 of both KSHV and lentivirus (VecotrBuilder) was added. In all samples, media was replaced day after infection and RNA was collected 3 days post infection.

value: HUVEC

tag: virus infection

value: KSHV (BAC16), 3dpi

value: lentivirus (hsa_circ_0001400)


title: circ_0001400_pulldown_sense_1

source_name: KSHV-infected HUVEC + control si_circ_0001400 Rep.1

value: control probe


title: circ_0001400_pulldown_antisense_1

source_name: KSHV-infected HUVEC + control siRNA Rep.1


title: KSHV-infected HUVEC + circ_0001400 lentivirus Rep.1


title: circ_0001400_pulldown_sense_3

source_name: KSHV-infected HUVEC + control si_circ_0001400 Rep.3


title: KSHV-infected HUVEC + control si_circ_0001400 Rep.3

value: siRNA (against hsa_circ_0001400)


title: KSHV-infected HUVEC + control si_circ_0001400 Rep.1


title: KSHV-infected HUVEC + control si_circ_0001400 Rep.2


title: Akata (-) Rep. 2

type: RNA

description: circular RNA

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The microarray slides were scanned with an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package.

label: biotin

source_name: Burkitt's lymphoma cell line

label_protocol: Total RNA from each sample was treated with RNase R to enrich circular RNA. The enriched circular RNA was reverse transcribed with random primers containing a T7 promoter. The cRNA was linearly amplified and Cy3 labeled by in vitro T7 polymerase transcription using Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

growth_protocol: Akata cells were cultured in RPMI with 10%FBS, penicillin, and streptomycin. Cell concentrations was maintained under 1 million cell/ml.

extract_protocol: Trizol and Direct-zol RNA miniprep kit (Zymo) were used to extract total RNA.

treatment_protocol: No treatment was applied.

value: EBV negative

value: Akata


title: KSHV-infected HUVEC + control siRNA Rep.3

value: siRNA (non-targeting)


title: circ_0001400_pulldown_antisense_3

source_name: KSHV-infected HUVEC + control siRNA Rep.3


title: Akata (+) Rep. 2

description: circular RNA

value: EBV positive


title: Akata (-) Rep. 3

description: circular RNA


title: KSHV-infected HUVEC + circGFP lentivirus Rep.2

value: lentivirus (circGFP)


title: KSHV-infected HUVEC + control siRNA Rep.1


title: Akata (+) Rep. 1

description: circular RNA


title: Akata (-) Rep. 1

description: circular RNA


title: PRO-cap from HCT116 (ENCLB566XSC)

status: Public on Dec 04 2022

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR273JQN/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in SUPT16H_U.
experiment encode accession: ENCSR273JQN
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB566XSC
spikeins used: The drosophila spike-in reference used for alignment

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H

tag: line

value: cell line

tag: biosample encode accession

tag: organism

value: Homo sapiens

value: male

tag: health state

value: colorectal carcinoma

tag: dev stage

value: adult

value: 48 year

tag: lab

value: Erez Aiden, Baylor

tag: source

value: Dr. Masato Kanemaki

tag: link

value: ENCBS984MQX at ENCODE; https://www.encodeproject.org/ENCBS984MQX/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: PRO-cap from HCT116 (ENCLB449DCR)

description:
https://www.encodeproject.org/experiments/ENCSR273JQN/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in SUPT16H_U.
experiment encode accession: ENCSR273JQN
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB449DCR
spikeins used: The drosophila spike-in reference used for alignment

tag: Sex

value: ENCBS465EAG at ENCODE; https://www.encodeproject.org/ENCBS465EAG/


title: H3K27me3_wt_21-24hr_rep3_#6

status: Public on Nov 09 2022

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz

institute: Max Planck Institute of Biochemistry

data_processing:
Reads from fastq files were aligned to the dm6 genome (and to the D. pseudoobscura dp3 genome for subsequent normalization) using STAR (Dobin et al., 2013). Only sequences that mapped uniquely to the genome with a maximum of two mismatches were considered for further analyses.
Bam files were used as inputs to run Bioconductor packages.
The STAN Bioconductor package (Zacher et al., 2014) was used to define the location of H3K36me2 enriched-regions and H3K27me3 enriched-regions.
The proportion of D. pseudoobscura reads as compared to D. melanogaster reads in input and in samples was used to normalize the ChIP-seq datasets for histone marks in embryos. Reference samples for normalization with D. pseudoobscura chromatin are indicated. Other samples were normalized based on total read number per million reads. Normalization factor for each sample is indicated.
Assembly: dm6
Supplementary files format and content: Normalized bigwig files (bin size = 1) were generated with deepTools (Ramirez et al., 2016).

organism: Drosophila melanogaster

source_name: 21-24hr old embryos

growth_protocol: Drosophila embryos and larvae were grown on standard medium at 25˚C

extract_protocol:
Lysates were clarified from sonicated fixed nuclei (for embryos) and from sonicated fixed hand-dissected imaginal disc tissues (for 3rd instar larvae). Histone/Protein-DNA complexes were isolated with antibody. D. pseudoobscura chromatin was spiked in at a 1:5 ratio of dm / dp chromatin before the addition of the antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq kit.

tag: tissue

value: 21-24hr old embryos

value: wt

tag: antibodies

value: H3K27me3 (Cell Signaling (#9733))

tag: normalization factor


title: circ_0001400_pulldown_sense_2

source_name: KSHV-infected HUVEC + control si_circ_0001400 Rep.2

tag: cell type

value: Human epithelial cell line

tag: cell line

value: control probe


title: KSHV-infected HUVEC + circ_0001400 lentivirus Rep.2

value: HUVEC

value: KSHV (BAC16), 3dpi

tag: treatment

value: lentivirus (hsa_circ_0001400)


title: KSHV-infected HUVEC + circGFP lentivirus Rep.3

value: lentivirus (circGFP)


title: KSHV-infected HUVEC + circGFP lentivirus Rep.1


title: H3K27me3_SceI48A_21-24hr_rep2_#6

tag: genotype


title: H3K27me3_wt_21-24hr_rep2_#1


title: H3K27me3_Asx0_21-24hr_rep1_#8


title: rRNA Depleted total RNA from whole brain from untreated FXLE20 rats (replicate 3, sequencing batch 16)

source_name: whole brain

tag: strain

tag: batch

tag: extraction protocol

value: RNA was collected from whole brain using the RNeasy Plus Universal Midi kits for RNA sequencing (Qiagen, Valencia, CA, USA).

value: whole brain


title: KSHV-infected HUVEC + control siRNA Rep.2

tag: virus infection

value: siRNA (non-targeting)


title: H2Aub1_wt_21-24hr_rep2_#8

value: H2Aub1 (cell signaling (#8240))


title: H2Aub1_SceI48A_21-24hr_rep2_#7


title: H2Aub1_wt_21-24hr_rep1_#1


title: H2Aub1_SceI48A_21-24hr_rep1_#6


title: H2Aub1_Asx0_21-24hr_rep1_#8


title: H2Aub1_wt_21-24hr_rep4_#6


title: P11W6

status: Public on Oct 14 2022

city: Ramat Gan

first: Nissan

last: Yissachar

address: Bar-Ilan University

country: Israel

institute: Bar-Ilan University

data_processing: Gut microbiome composition was analyzed by 16S rRNA gene sequencing of IBS patients’ fecal samples collected at 0, 3 and 6 weeks under low-FODMAP diet.

organism: human gut metagenome

source_name: bacteria

extract_protocol:
DNA was extracted from all fecal samples using the Mobio PowerSoil DNA extraction kit, as described by the manufacturer (MoBio, Carlsbad, CA). DNA concentrations were measured by nanodrop, and 20 ng of DNA was used for 16S library preparation
Library preparation and sequencing were performed by HyLabs Ltd (Israel), as follows: 16S libraries for Illumina sequencing were prepared using a two-step PCR protocol. In the first PCR, primers containing tails were used to amplify the V4 region of the 16S rRNA gene. The Access Array primers for Illumina (Fluidigm) were used in the second PCR to add the adaptor and index sequences to each sample. After the second PCR, the reactions were cleaned using Kapa Pure beads (Roche) to remove unincorporated primers and any primer-dimer produced. The concentration of each library was measured by Qubit (Life Technologies) using the Denovix ds DNA HS assay (Deonvix) and then the samples were combined in equal amounts to a single pool.

tag: biology sample

value: human fecal sample

value: low-FODMAP diet

tag: time

value: 6 weeks under low-FODMAP diet

value: female

value: bacteria


title: P10W6

value: male


title: P10W0

value: without treatment

value: 0 weeks under low-FODMAP diet


title: P11W3

value: 3 weeks under low-FODMAP diet


title: P9W6


title: P9W0


title: P9W3


title: H3K27me3_wt_21-24hr_rep1_#8

value: 21-24hr old embryos

value: wt

value: H3K27me3 (Cell Signaling (#9733))


title: H3K27me3_SceI48A_21-24hr_rep1_#8


title: P8W3


title: P8W0


title: H2Aub1_wt_21-24hr_rep5_#7


title: P7W0


title: P6W6


title: P11W0


title: P4W6


title: P10W3


title: P2W0


title: P1W3


title: P6W3


title: 205624640136_R03C01

description:
Methylation data from tumor sample
Sample 127

value: tumor

tag: tissue preparation

value: FFPE


title: P3W6


title: P1W0


title: P3W3


title: P6W0


title: P1W6


title: P2W3


title: experiment 2  Bifidobacterium adolescentis 2

data_processing:
Reads were aligned to the Mus musculus reference genome GRCm38 using STAR (version 020201) (Dobin et al., 2013), and quantification of reads was performed using htseq-count (version 0.12.4) (Anders et al., 2015) and a list of genes (Ensembl gtf file) (Howe et al., 2021). Differential gene expression analysis was then performed using DESeq2 as described above.
Assembly: GRCm38
Supplementary files format and content: Table S4: Differential gene expression analysis, comparing colonic transcriptional responses to ex-vivo infusion of B. adolescentis versus sterile medium, at 2h post-stimulation
Supplementary files format and content: Normalized counts for table S4

source_name: colon

extract_protocol:
The Illumina TruSeq stranded mRNA library prep kit (#20020594) was used for library generation, and next generation sequencing was performed in the Bar-Ilan University scientific equipment center using the Illumina NextSeq platform (NextSeq 500 High Output v2 kit (#FC-404-2005)).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: colon

value: C57BL/6 strain

tag: age

value: 14 days ols

value: WT

value: Bifidobacterium adolescentis


title: P7W3

value: human fecal sample

value: low-FODMAP diet


title: experiment 2  Bifidobacterium adolescentis 1


title: experiment 2 control 2

value: contol


title: P4W0 #1

value: female

value: bacteria


title: P4W0 #2

value: without treatment

value: 0 weeks under low-FODMAP diet


title: experiment 1 Bifidobacterium adolescentis 1


title: experiment 1 control 2


title: P6W6 repeat 1

data_processing:
Reads were aligned to the Mus musculus reference genome GRCm38 using STAR (version 020201) (Dobin et al., 2013), and quantification of reads was performed using htseq-count (version 0.12.4) (Anders et al., 2015) and a list of genes (Ensembl gtf file) (Howe et al., 2021). Differential gene expression analysis was then performed using DESeq2 as described above.
Assembly: GRCm38
Supplementary files format and content: Table S2: Differential gene expression analysis, comparing early (2h) colonic transcriptional responses to ex-vivo infusion of post-diet versus pre-diet microbiota from clinically responding patients
Supplementary files format and content: Normalized counts for table S2

value: patient 6 post (week 6)


title: experiment 2 control 1


title: Akata (+) Rep. 3

description: circular RNA

value: EBV positive

value: Akata


title: P2W6

value: 6 weeks under low-FODMAP diet

value: male


title: P6W0 repeat 2

value: colon

value: patient 6 pre (week 0)


title: experiment 1 control 1

value: C57BL/6 strain

value: 14 days ols


title: P6W6 repeat 2

value: WT


title: P4W0 repeat 2

value: patient 4 pre (week 0)


title: P3W6 repeat 2

value: patient 3 post (week 6)


title: P4W6 repeat 1

value: patient 4 post (week 6)


title: P3W6 repeat 1


title: P3W0 repeat 1

value: patient 3 pre (week 0)


title: P1W6 repeat 2

value: patient 1 post (week 6)


title: P4W0 repeat 1


title: P3W0 repeat 2


title: P3W0

value: human fecal sample

value: without treatment

value: female

value: bacteria


title: P1W0 repeat 2

value: patient 1 pre (week 0)


title: P4W6 repeat 2


title: P1W0 repeat 1


title: 21-015

status: Public on Oct 12 2022

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University

data_processing:
Expression counts determined by spaceranger and reference genome hg38.
The remaining processing and normalization steps described on the paper were not performed on the provided processed data.
Assembly: Hg38
Supplementary files format and content: Compressed file with outputs from spaceranger in a tar.gz file, high resolution image on tiff.

source_name: Kidney

extract_protocol:
Four reference tissues (18-0006, 19-F52, 19-M61, 19-M32) from deceased donor nephrectomies and one  CKD biopsy specimen (20-13437) were obtained from the biopsy biobank cohort of Indiana (BBCI) (PMID:32336487). All remaining samples were provided by the Kidney Precision Medicine Project. All samples were frozen on OCT within 24 h. 10 um of tissue was cut on a cryotome and placed on a 10x Visium capture slide. RNA was extracted according to the manufacturer's protocol.
CG000239_VisiumSpatialGeneExpression_UserGuide_RevD, 10X Genomics

tag: disease

value: Reference

tag: tissue source

value: Nephrectomy

tag: storage

value: OCT at -80C

tag: gender

value: F

tag: median umis per spot

tag: median genes per spot


title: 21-019

value: M


title: P8W6

value: low-FODMAP diet

value: 6 weeks under low-FODMAP diet

tag: Sex

value: male

tag: cell type


title: P1W6 repeat 1

tag: tissue

value: colon

value: C57BL/6 strain

value: 14 days ols

tag: genotype

value: WT

tag: treatment


title: retina barcodes rep2 [scMPPRA]

status: Public on Oct 06 2022

city: St. Louis

first: SIQI

last: ZHAO

state: MO

address: Campus Box 8232 4515 McKinley Ave.

department: Genetics

institute: Washington University in St. Louis

description:
Demultiplexed barcodes
retina_pBC_exp_rep2.csv

data_processing:
scRNA-seq data was processed with Cell Ranger 6.0.1; Barcodes were extracted by fuzzy match the 8 bp before and after the barcode region, wrong length barcodes were removed. Barcodes attached to wrong cell barcode determiend by Cell Ranger were removed.
Assembly: mm10
Supplementary files format and content: single-cell RNA-seq processed expression using Cell Ranger is stored in .mtx.gz files. scMPRA barcodes counts per cell are stored in pBC_exp.csv
Library strategy: Massively Parallel Reporter Assay

source_name: Retina

growth_protocol: Retinas from newborn mice were dissected, cultured, and electroporated as described in White et al. For each replicate experiment, three retinas were electroporated with 0.5 μg/μL of the Gnb3 promoter variant library, and co-electroporated with 0.5 μg/μL of a plasmid in which the Rhodopsin promoter drives the dsRED fluorophore. Electroporated retinas were harvested and dissociated as in Murphy et al.42 with modifications as outlined below.

extract_protocol:
To quantify the cBC-rBC pairs, we performed separate PCRs using primers specifically targeting the reporter gene to improve barcode recovery efficiencies. Because the 10x protocol only uses 1/4 of the generated cDNA, we separately amplified the barcodes from another 1/4 of the pellet cleanup. We first used Q5 (New England BioLabs M0515) polymerase to amplify the region containing the cBC-rBC pairs with SCARED P17 and SCARED P18 with 10 cycles. The sample was divided equally into eight PCR reactions, each with 50 μl of total volume to reduce possible jackpotting. The product was then purified with the Monarch PCR&DNA Cleanup kit (New England BioLabs T1030L), and eluted with 20 μl of ddH2O. We then added sequencing adapters using an additional two rounds of PCR. The first adapter PCR was performed with SCARED P21 and SCARED PP2 with a total of 10 ng of product from the barcode PCR. Again, we pooled eight PCR reactions, each with 50 μl of total volume and 10 PCR cycles. The PCR product was purified using the Monarch PCR&DNA Cleanup kit (New England BioLabs T1030L). For the last PCR, to add the P5 and P7 Illumina adapters, we used the primers SCARED P45, SCARED PP3 with 10ng of product and pooled eight PCR reactions, each with 50 μl of total volume and 10 PCR cycles.
scRNA-seq and scMPRA are extracted using 10X protocol

value: Retina

tag: strain

value: postnatal day 8


title: RNA-seq ESC 0h biol rep 2

status: Public on Oct 01 2022

city: Baltimore

last: Beer

address: 733 N. Broadway

department: Biomedical Engineering and Genetic Medicine

institute: Johns Hopkins University

data_processing:
RNA-seq: We alignned reads to hg38 with STAR_2.5.1b and quantified transcripts with RSEM v1.2.23.
Assembly: hg38
Supplementary files format and content: bigwig, hic, barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, expr_table.tsv.gz, gRNA_table.tsv.gz

extract_protocol:
RNA-seq:  Total RNA was extracted using Quick-RNA MiniPrep kits (ZYMO research; R1055).  cDNA was produced by using High Capacity cDNA Reverse Transcription Kit (AppliedBiosystems; 4368817)
RNA-seq: 500ng of total RNA underwent polyA selection and TruSeq library preparation following Illumina (TruSeq Stranded mRNA LT Kit; RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 or NovaSeq 6000 platform in a PE50 run, using the HiSeq 3000/4000 SBS Kit or NovaSeq 6000 SP or S2 Reagent Kit (100 Cycles) (Illumina).

tag: cell line

value: hESC

value: idCas9-KRAB SOX17eGFP/+

value: ESC-DE differentiation


title: RNA-seq ESC 0h biol rep 3


title: RNA-seq ESC 0h biol rep 1


title: Y_58P_D3_Mock

status: Public on Aug 03 2022

city: Chapel Hill

first: Takafumi

last: Kato

state: NC

address: 125 Mason Farm Rd, 7230-K Marsico Hall CB #7248

department: Marsico Lung Institute

institute: University of North Carolina

description: mRNA

data_processing:
Illumina bcl2fastq v2.19 used for basecalling.
Sequence reads in FASTQ files were mapped to GRCh38 reference genome with GENCODE 37 gene annotation by STAR, and gene expression estimates were derived from StringTie using default parameters.
Assembly: GRCh38
Supplementary files format and content: select_14codes_grch38gc37hG_geneCount.txt: Tab-delimited text file includes gene counts for each Sample.
Supplementary files format and content: select_14codes_grch38gc37hG_gene_tpm.txt: Tab-delimited text file includes TPM values for each Sample.

source_name: Primary bronchial airway epithelial cells

growth_protocol: Human bronchial epithelial (HBE) cells were obtained from freshly isolated large airway epithelium of non-smoker lung transplant donors with lungs unsuitable for transplant. Isolated HBE cells were expanded using a modified conditional reprogramming cell culture. The cells were seeded onto 12mm Transwell inserts at 0.25 million cells per insert. The cells were cultured under submerged condition until confluence. Then they were cultured under air-liquid interface (ALI) culture until full-differentiation confirmed by ciliation under light microscopic examination.

extract_protocol:
Cell culture membranes were kept in TRI Reagent and the RNA extracted according to the manufacturer’s instructions. RNA concentrations were determined using a NanoDrop-8000 spectrophotometer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The HBE cells were inoculated with SARS-CoV-2 (D614G strain) at MOI=0.5 for two hours. The cells were maintained under ALI culture until 1-, 3- 7- and 14-day post inoculation. RNAs were extracted from the cell lysates.

value: Human bronchial epithelial (HBE) cells

value: Y

value: Male

value: Mock

tag: time point

tag: titer


title: Y_58P_D3_Virus

description: mRNA


title: Y_58P_D14_Mock

description: mRNA


title: Y_49O_D7_Mock

description: mRNA

value: Female


title: Y_49O_D3_Virus

description: mRNA


title: P6W0 repeat 1

value: patient 6 pre (week 0)


title: Y_49O_D14_Mock

description: mRNA


title: Y_49O_D14_Virus

description: mRNA


title: Y_48G_D7_Virus

description: mRNA


title: Y_49O_D1_Virus

description: mRNA


title: Y_48G_D7_Mock

description: mRNA


title: Y_48G_D14_Virus

description: mRNA


title: Y_58P_D14_Virus

description: mRNA


title: Y_48G_D3_Virus

description: mRNA


title: Y_37O_D7_Virus

description: mRNA


title: Y_37O_D7_Mock

description: mRNA


title: Y_48G_D1_Mock

description: mRNA


title: Y_48G_D14_Mock

description: mRNA


title: Y_37O_D3_Mock

description: mRNA


title: Y_58P_D7_Virus

description: mRNA


title: Y_48G_D1_Virus

description: mRNA


title: Y_58P_D7_Mock

description: mRNA


title: Y_37O_D14_Virus

description: mRNA


title: Y_37O_D14_Mock

description: mRNA


title: Y_49O_D7_Virus

description: mRNA


title: Y_58P_D1_Virus

description: mRNA


title: Y_37O_D1_Mock

description: mRNA


title: M_9N_D7_Virus

description: mRNA

value: M


title: M_9N_D7_Mock

description: mRNA


title: Y_37O_D1_Virus

description: mRNA


title: M_9N_D3_Mock

description: mRNA


title: M_9N_D3_Virus

description: mRNA


title: M_9N_D14_Mock

description: mRNA


title: Y_48G_D3_Mock

description: mRNA


title: M_9N_D14_Virus

description: mRNA


title: M_9N_D1_Virus

description: mRNA


title: Y_49O_D1_Mock

description: mRNA


title: M_74K_D7_Mock

description: mRNA


title: M_74K_D3_Mock

description: mRNA


title: M_74K_D14_Virus

description: mRNA


title: M_74K_D14_Mock

description: mRNA


title: M_74K_D1_Mock

description: mRNA


title: M_74K_D3_Virus

description: mRNA


title: M_74K_D1_Virus

description: mRNA


title: M_25O_D7_Virus

description: mRNA


title: M_25O_D7_Mock

description: mRNA


title: M_25O_D14_Virus

description: mRNA


title: M_25O_D3_Mock

description: mRNA


title: M_25O_D14_Mock

description: mRNA


title: M_25O_D1_Virus

description: mRNA


title: M_9N_D1_Mock

description: mRNA


title: M_19O_D7_Virus

description: mRNA


title: M_19O_D7_Mock

description: mRNA


title: M_19O_D3_Virus

description: mRNA


title: M_19O_D1_Virus

description: mRNA


title: M_19O_D3_Mock

description: mRNA


title: M_19O_D14_Mock

description: mRNA


title: M_74K_D7_Virus

description: mRNA


title: M_19O_D14_Virus

description: mRNA


title: M_10H_D7_Virus

description: mRNA


title: M_25O_D3_Virus

description: mRNA


title: M_10H_D7_Mock

description: mRNA


title: M_10H_D3_Virus

description: mRNA


title: M_10H_D3_Mock

description: mRNA


title: M_10H_D14_Virus

description: mRNA


title: M_10H_D1_Mock

description: mRNA


title: E_5I_D3_Virus

description: mRNA

value: E


title: E_5I_D7_Mock

description: mRNA


title: M_19O_D1_Mock

description: mRNA


title: E_5I_D3_Mock

description: mRNA


title: E_5I_D7_Virus

description: mRNA


title: E_5I_D1_Mock

description: mRNA


title: E_5I_D14_Virus

description: mRNA


title: E_5I_D1_Virus

description: mRNA


title: E_3N_D7_Virus

description: mRNA


title: M_10H_D1_Virus

description: mRNA


title: E_3N_D7_Mock

description: mRNA


title: E_3N_D14_Virus

description: mRNA


title: E_3N_D1_Mock

description: mRNA


title: E_35K_D7_Virus

description: mRNA


title: E_3N_D3_Mock

description: mRNA


title: E_35K_D7_Mock

description: mRNA


title: E_3N_D14_Mock

description: mRNA


title: E_3N_D1_Virus

description: mRNA


title: E_3N_D3_Virus

description: mRNA


title: E_35K_D3_Mock

description: mRNA


title: E_35K_D14_Mock

description: mRNA


title: M_10H_D14_Mock

description: mRNA


title: E_35K_D3_Virus

description: mRNA


title: E_35K_D14_Virus

description: mRNA


title: E_35K_D1_Mock

description: mRNA


title: M_25O_D1_Mock

description: mRNA


title: E_35K_D1_Virus

description: mRNA


title: E_26P_D3_Virus

description: mRNA


title: E_26P_D3_Mock

description: mRNA


title: E_26P_D14_Virus

description: mRNA


title: E_26P_D14_Mock

description: mRNA


title: E_26P_D1_Virus

description: mRNA


title: E_10G_D7_Mock

description: mRNA


title: E_10G_D7_Virus

description: mRNA


title: E_10G_D3_Mock

description: mRNA


title: E_10G_D14_Virus

description: mRNA


title: E_10G_D14_Mock

description: mRNA


title: E_10G_D1_Mock

description: mRNA


title: E_10G_D1_Virus

description: mRNA


title: ACT 0.25 h, rep3

status: Public on Jul 20 2022

city: Pasadena

first: Zikun

last: Zhu

address: 1200 E California Blvd

institute: California Institute of Technology

data_processing:
Library strategy: ribosome profiling
For replicates 1 and 2, pair-end reads were merged using PEAR and adaptor sequences (ATCGT for rep1; AGCTA for rep2) were trimmed from sequencing reads using Cutadapt. Each read is flanked by 2- and 5-nt unique molecular identifiers at the 5ʹ and 3ʹ ends, which are also removed. Raw data files contain the reads that have been demultiplexed and trimmed.
For replicate 3, adaptor sequence (CTGTAGGCACCATCAATTCGTATGCCGTCTTCTGCTTG) was trimmed from sequencing reads using Cutadapt.
Ribosomal RNAs reads were removed by alignment using Bowtie.
Remaining reads were mapped to bacterial genome using Bowtie.
Ribosome density was assigned to 14-nt upstream of the 3’-end of reads using reads with size range 15–45 nt
Assembly: ASM584v2
Supplementary files format and content: Tab-delimited text files include: Column1: strand; Column2: genomic position; Column3: normalizeds ribosome reads (RPM); Column4: counts of ribosome reads.

organism: Escherichia coli

source_name: ACT 0.25 h, rep3

growth_protocol: CAG12184 were grown at 37 ˚C in SILAC medium (48 mM Na2HPO4, 22 mM KH2PO4, 8 mM NaCl, 19 mM NH4Cl, 2 mM MgSO4, 0.1 mM CaCl2, 0.4% glucose, 40 µg/mL each of Ser, Thr, Val, Phe, Ile, Leu, Tyr, His, Met, Trp, Lys, and Arg).

extract_protocol:
Frozen cells were mixed with 0.5 mL of Lysis buffer (50 mM Hepes-KOH, 100 mM NaCl, 10 mM MgCl2, 5 mM CaCl2,  0.4% Triton X-100, 0.1% NP-40, 1 mM chloramphenicol, 1 mM PMSF, 50 U/mL DNaseI, pH 7.0) and lysed via mixer milling. Polysomes were digested with MNase (3750 U/1 mg RNA) and purified through a sucrose cushion. RNA was extracted using Direct-zol kit. Ribosome-protected fragment were size selected and converted into a cDNA library for sequencing.
Libraries are prepared as described in (Mohammad and Buskirk, 2019) with modifications.

treatment_protocol: Cells were treated with 4 µg/mL ACT when OD600 reached 0.4. At indicated time points, 200 mL of cell culture were harvested by rapid filtration through nitrocellulose membrane with 0.2 mm pores and flash-frozen in liquid nitrogen.

value: 4 ug/mL ACT, 0.25 h


title: untreated, rep3

source_name: untreated, rep3

value: untreated


title: ACT 0.5 h, rep3

source_name: ACT 0.5 h, rep3

value: 4 ug/mL ACT, 0.5 h


title: ACT 1.5 h, rep2

source_name: ACT 1.5 h, rep2

value: 4 ug/mL ACT, 1.5 h


title: ACT 1.5 h, rep3

source_name: ACT 1.5 h, rep3


title: ACT 1.5 h, rep1

source_name: ACT 1.5 h, rep1


title: untreated, rep2

source_name: untreated, rep2


title: E_26P_D7_Virus

description: mRNA


title: ACT 0.25 h, rep2

source_name: ACT 0.25 h, rep2


title: E_26P_D7_Mock

description: mRNA


title: E_26P_D1_Mock

description: mRNA


title: ACT 0.5 h, rep1

source_name: ACT 0.5 h, rep1


title: untreated, rep1

source_name: untreated, rep1


title: WT membrane monosomes, rep1, CCCP

status: Public on May 16 2022

data_processing:
Library strategy: Ribo-Seq
Adaptor sequences (CTGTAGGCACCATCAATTCGTATGCCGTCTTCTGCTTG) were trimmed from sequencing reads using Cutadapt.
Ribosomal RNAs reads were removed by alignment using Bowtie.
Remaining reads were mapped to bacterial genome using Bowtie.
Ribosome density was assigned to 14-nt upstream of the 3’-end of reads using reads with size range 15–45 nt
Genome_build: ASM1024v1
Supplementary_files_format_and_content: Tab-delimited text files include: Column1: strand; Column2: genomic position; Column3: normalizeds ribosome reads (RPM); Column4: counts of ribosome reads.

source_name: WT membrane monosomes, CCCP

growth_protocol: E. coli cells were grown in LB medium at 37 °C to an OD600 of 0.4 .

extract_protocol:
Polysomes were digested with MNase (3750 U/1 mg RNA), purified through a sucrose cushion, and affinity purified via streptavidin magnetic beads . RNA from total monosomes and SecA-bound monosomes was extracted using Direct-zol kit. Ribosome-protected fragment were size selected and converted into a cDNA library for sequencing.
Libraries are prepared as described in (Mohammad and Buskirk, 2019) with modifications.

treatment_protocol: The cells were harvested by rapid filtration, followed by flash freezing in liquid nitrogen. Frozen cells were mixed with 1 mL frozen Lysis Buffer and lysed by mixer milling (2 min, 25 Hz, Retsch). Frozen lysed cell powder was thawed in the presence of 20mM EDC. The crosslinking reaction was quenched with 20 mM glycine, 100 mM Tris pH 8.0, 4 mM NaHCO3.

tag: genotype/variation

value: SecA-Thrombin-Avi

value: 50uM CCCP in medium during filtration


title: WT membrane monosomes, rep2, CCCP


title: WT cytosolic monosomes, rep2, CCCP

source_name: WT cytosolic monosomes, CCCP


title: WT cytosolic monosomes, rep1, CCCP


title: ACT 0.25 h, rep1

source_name: ACT 0.25 h, rep1


title: WT SecA interactome, rep2, CCCP

source_name: WT SecA interactome, CCCP


title: E_10G_D3_Virus

description: mRNA


title: WT total translatome, rep2, CCCP

source_name: WT total translatome, CCCP


title: secA∆ZnBD total translatome, rep2

source_name: secA∆ZnBD total translatome

value: SecAdeltaZnBD-Thrombin-Avi


title: secA∆ZnBD total translatome, rep1


title: secA∆ZnBD SecA interactome, rep1

source_name: secA∆ZnBD SecA interactome


title: ACT 0.5 h, rep2

source_name: ACT 0.5 h, rep2


title: WT total translatome, rep1, CCCP


title: WT SecA interactome, rep1, AcrB and OppC mutants

source_name: WT SecA interactome, AcrB and OppC mutants


title: WT total translatome, rep2

source_name: WT total translatome


title: secA∆ZnBD SecA interactome, rep2


title: WT SecA interactome, rep1

source_name: WT SecA interactome


title: WT SecA interactome, rep2


title: WT total translatome, rep2, AcrB and OppC mutants

source_name: WT total translatome, AcrB and OppC mutants


title: WT total translatome, rep1, AcrB and OppC mutants


title: WT SecA interactome, rep2, AcrB and OppC mutants


title: WT membrane monosomes, rep2

source_name: WT membrane monosomes


title: WT membrane monosomes, rep1


title: WT cytosolic monosomes, rep1

source_name: WT cytosolic monosomes


title: ∆secB total translatome, rep1

source_name: ∆secB total translatome

value: deltasecB::Kan SecA-Thrombin-Avi


title: ∆secB total translatome, rep2


title: WT cytosolic monosomes, rep2


title: ∆secB SecA interactome, rep2

source_name: ∆secB SecA interactome


title: ∆secB SecA interactome, rep1


title: ∆tig total translatome, rep1

source_name: ∆tig total translatome

value: deltatig::Kan SecA-Thrombin-Avi


title: ∆tig SecA interactome, rep2

source_name: ∆tig SecA interactome


title: ∆tig SecA interactome, rep1


title: KrasG12D_8 (crc)

status: Public on May 13 2022

data_processing:
Salmon (salmon v0.14.1) pseudo-aligner was used for sequencing alignment and read count, with the Ensembl mm10 genome (Mus_musculus.GRCm38) as reference, using the following parameter: -l A --seqBias --useVBOpt --validateMappings
Normalized count was obtained using DESeq2, normalized across all samples from the same model
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample
Supplementary_files_format_and_content: Table with differential analysis result from DESeq2 for every gene (KrasG12D vs KrasWT)

source_name: Colonic tumor

extract_protocol:
Animals were sacrified when they became moribund.Tumor lawns along colon were resected or scraped using a razor blade. Tumor tissues were flash frozen in liquid nitrogen and stored at -80ºC. Frozen samples were powderized in liquid nitrogen with a tissue homogenizer. RNA was extracted using the RNeasy Plus Universal kit from Qiagen, following the manufacturer's instructions. RNA concentration and quality were evaluated in Agilent Bioanalyzer/TapeStation.
1µg of RNA was used for RNA-Seq library preparation. Poly-A enrichment was performed to increase mRNA amount in the input RNA. RNA-Seq library was prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® following the manufacturer's instructions.

treatment_protocol: Enema of the 8-12 weeks old animals were performed using 4-hydroxytamoxifen (4-OHT, 5mg/ml in 100% ethanol) to induce colonic tumor formation.

value: Colonic tumor

tag: model

value: Experimental

tag: batch

value: G12D (K-ras allele)


title: WT total translatome, rep1


title: KrasG12D_7 (crc)


title: KrasG12D_2 (crc)


title: KrasG12D_4 (crc)


title: KrasWT_8 (crc)

value: Control

value: WT (K-ras allele)


title: KrasG12D_5 (crc)


title: KrasG12D_1 (crc)


title: KrasG12D_3 (crc)


title: KrasWT_6 (crc)


title: KrasWT_7 (crc)


title: KrasWT_5 (crc)


title: ∆tig total translatome, rep2


title: KrasWT_2 (crc)


title: KrasWT_4 (crc)


title: KrasWT_1 (crc)


title: KrasWT_3 (crc)


title: KrasG12D_4 (ce)

data_processing:
Salmon (salmon v0.14.1) pseudo-aligner was used for sequencing alignment and read count, with the Ensembl mm10 genome (Mus_musculus.GRCm38) as reference, using the following parameter: -l A --seqBias --useVBOpt --validateMappings
Normalized count was obtained using DESeq2, normalized across all samples from the same model
Genome_build: mm10
Supplementary_files_format_and_content: RNA_ce_raw_gene_counts.csv (raw counts)
Supplementary_files_format_and_content: RNA_ce_normalized_raw_gene_counts.csv (normalized counts)
Supplementary_files_format_and_content: RNA_ce_Differential Analysis.csv (differential analysis)

source_name: Colonic epithelium

extract_protocol:
Distal colon was scraped using a razor blade to enrich for colonic epithelium. Scraped tissues were flash frozen in liquid nitrogen and stored at -80ºC. Frozen samples were powderized in liquid nitrogen with a tissue homogenizer. RNA was extracted using the RNeasy Plus Universal kit from Qiagen, following the manufacturer's instructions. RNA concentration and quality were evaluated in Agilent Bioanalyzer/TapeStation.
1µg of RNA was used for RNA-Seq library preparation. Poly-A enrichment was performed to increase mRNA amount in the input RNA. RNA-Seq library was prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® following the manufacturer's instructions.

value: Colonic epithelium


title: KrasG12D_3 (ce)


title: KrasG12D_2 (ce)


title: Fabp_2 (ce)


title: Fabp_3 (ce)


title: KrasG12D_1 (ce)


title: HEAP mRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 6 (HVAK_mRNA6)

data_processing:
STAR (2.5.2b) aligner was used for sequencing alignment, with the Ensembl mm10 genome (Mus_musculus.GRCm38) as reference, using the following parameter: --alignIntronMin 70 --alignIntronMax 100000  --outFilterMultimapNmax 1 \   --outFilterMultimapScoreRange 0 --outFilterMismatchNmax 5  --outSAMtype BAM SortedByCoordinate. CLIPanalyze (0.0.10) was used for peak calling.
miRNA alignment and quantification was performed using Seqcluster (1.2.4a7).
Differential analysis and normalized counts of the peaks were obtained using DESeq2, normalized across all samples from the same model
Differential analysis and normalized counts of the miRNA were obtained using "isomiRs" R package, normalized across all samples from the same model
Genome_build: mm10
Supplementary_files_format_and_content: BED file of filtered peaks called from HF samples alone
Supplementary_files_format_and_content: BED file of filtered peaks called from HFK samples alone
Supplementary_files_format_and_content: BED file of filtered peaks merging HF and HFK peaks
Supplementary_files_format_and_content: miRNA_differential_analysis.csv (differential analysis of Ago2-bound miRNA (KrasG12D vs KrasWT))
Supplementary_files_format_and_content: miRNA_normalized_counts.csv (normalized counts of Ago2-bound miRNA)
Supplementary_files_format_and_content: Peak_differential_analysis.csv (differential analysis of counts in HEAP peaks (KrasG12D vs KrasWT))
Supplementary_files_format_and_content: Peak_information.csv (Information (Location, target information, and matching miRNA) of filtered peaks)
Supplementary_files_format_and_content: Peak_normalized_counts.csv (normalized counts in HEAP peaks)

extract_protocol:
Animals were sacrified when they became moribund.Tumor lawns along colon were resected or scraped using a razor blade. Tissue was minced on ice and UV-crosslinked (400mJ/cm2, 3X). Scraped tissues were flash frozen in liquid nitrogen and stored at -80ºC. Frozen samples were powderized in liquid nitrogen with a tissue homogenizer before library prep.
Published protocl was followed (PMID: 32497496). In short, Halo-Ago2/mRNA/miRNA complex was pulled-down from tissue lysate. Ago2 was digested to release miRNA and mRNA. RNA was then used for library construction. RNA extracted from Input lysate without Halo-Ago2 pulldown was used for Input Control library construction.
HEAP (CLIP-Seq)

tag: library type

value: mRNA

tag: pulldown reagent

value: HaloLink™ Resin (Promega G1914, Lot 0000257900)


title: Fabp_1 (ce)


title: HEAP miRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 6 (HVAK_miRNA6)

value: miRNA


title: HEAP IC library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 5 (HVAK_IC5)

value: IC

value: none (input)


title: HEAP IC library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 4 (HVAK_IC4)


title: HEAP miRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 4 (HVAK_miRNA4)


title: HEAP IC library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 3 (HVAK_IC3)


title: HEAP mRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 5 (HVAK_mRNA5)


title: HEAP mRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 4 (HVAK_mRNA4)


title: HEAP miRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 5 (HVAK_miRNA5)


title: KrasG12D_6 (crc)


title: Fabp_4 (ce)


title: HEAP mRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 1 (HVAK_mRNA1)


title: HEAP miRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 3 (HVAK_miRNA3)


title: HEAP miRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 2 (HVAK_miRNA2)


title: HEAP miRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 1 (HVAK_miRNA1)


title: HEAP IC library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 6 (HVA_IC6)


title: HEAP IC library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 1 (HVAK_IC1)


title: HEAP mRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 2 (HVAK_mRNA2)


title: HEAP IC library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 6 (HVAK_IC6)


title: HEAP IC library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 2 (HVAK_IC2)


title: HEAP mRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 5 (HVA_mRNA5)


title: HEAP IC library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 5 (HVA_IC5)


title: HEAP IC library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 4 (HVA_IC4)


title: Y_49O_D3_Mock

description: mRNA

source_name: Primary bronchial airway epithelial cells

value: Human bronchial epithelial (HBE) cells

value: Y

value: Female

value: Mock


title: HEAP miRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 5 (HVA_miRNA5)


title: HEAP mRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 4 (HVA_mRNA4)


title: HEAP mRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 6 (HVA_mRNA6)


title: HEAP miRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 4 (HVA_miRNA4)


title: HEAP mRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl); K-Ras-G12D/+, rep 3 (HVAK_mRNA3)


title: HEAP IC library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 2 (HVA_IC2)


title: HEAP miRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 3 (HVA_miRNA3)


title: HEAP mRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 3 (HVA_mRNA3)


title: HEAP mRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 2 (HVA_mRNA2)


title: HEAP IC library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 3 (HVA_IC3)


title: HEAP mRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 1 (HVA_mRNA1)


title: HEAP miRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 2 (HVA_miRNA2)


title: HEAP miRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 6 (HVA_miRNA6)


title: HEAP IC library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 1 (HVA_IC1)


title: HEAP mRNA library, Halo-Ago2/+; Fabp-Cre/+; K-Ras-G12D/+, rep 3 (HFK_mRNA3)

extract_protocol:
Distal colon was scraped using a razor blade to enrich for colonic epithelium. Tissue was minced on ice and UV-crosslinked (400mJ/cm2, 3X). Scraped tissues were flash frozen in liquid nitrogen and stored at -80ºC. Frozen samples were powderized in liquid nitrogen with a tissue homogenizer before library prep.
Published protocl was followed (PMID: 32497496). In short, Halo-Ago2/mRNA/miRNA complex was pulled-down from tissue lysate. Ago2 was digested to release miRNA and mRNA. RNA was then used for library construction. RNA extracted from Input lysate without Halo-Ago2 pulldown was used for Input Control library construction.
HEAP (CLIP-Seq)


title: HEAP miRNA library, Halo-Ago2/+; Fabp-Cre/+; K-Ras-G12D/+, rep 3 (HFK_miRNA3)


title: HEAP IC library, Halo-Ago2/+; Fabp-Cre/+; K-Ras-G12D/+, rep 3 (HFK_IC3)


title: HEAP miRNA library, Halo-Ago2/+; Villin-CreER/+; Apc(fl/fl), rep 1 (HVA_miRNA1)


title: HEAP IC library, Halo-Ago2/+; Fabp-Cre/+; K-Ras-G12D/+, rep 1 (HFK_IC1)


title: HEAP IC library, Halo-Ago2/+; Fabp-Cre/+; K-Ras-G12D/+, rep 2 (HFK_IC2)


title: HEAP mRNA library, Halo-Ago2/+; Fabp-Cre/+; K-Ras-G12D/+, rep 1 (HFK_mRNA1)


title: HEAP mRNA library, Halo-Ago2/+; Fabp-Cre/+; K-Ras-G12D/+, rep 2 (HFK_mRNA2)


title: HEAP miRNA library, Halo-Ago2/+; Fabp-Cre/+; K-Ras-G12D/+, rep 1 (HFK_miRNA1)


title: HEAP IC library, Halo-Ago2/+; Fabp-Cre/+, rep 3 (HF_IC3)


title: HEAP mRNA library, Halo-Ago2/+; Fabp-Cre/+, rep 3 (HF_mRNA3)


title: Y_37O_D3_Virus

description: mRNA

value: Male


title: HEAP IC library, Halo-Ago2/+; Fabp-Cre/+, rep 2 (HF_IC2)


title: HEAP IC library, Halo-Ago2/+; Fabp-Cre/+, rep 1 (HF_IC1)


title: HEAP mRNA library, Halo-Ago2/+; Fabp-Cre/+, rep 2 (HF_mRNA2)


title: HEAP mRNA library, Halo-Ago2/+; Fabp-Cre/+, rep 1 (HF_mRNA1)


title: HEAP miRNA library, Halo-Ago2/+; Fabp-Cre/+, rep 1 (HF_miRNA1)


title: Kras_tumor_rep1

description:
ATAC_crc_Kras-WT_merged.csv
ATAC_crc_normalized_count.csv
ATAC_peaks_crc.bed

data_processing:
Bcbio ATAC-Seq pipeline was used for alignment and peak calling (https://bcbio-nextgen.readthedocs.io/en/latest/contents/atac.html), with the Ensembl mm10 genome (Mus_musculus.GRCm38) as reference. BWA was used as the aligner and MACS2 was used for peak calling. Defalt parameters of Bcbio pipeline was used.
NarrowPeaks from Nucleosome-free (NF) fraction merged across all samples and peaks within 500bp were merged into a single peak. CHIPseeker(1.28.3) was used for peak annotation and filtering (filtered for peaks within 1000bp of the Transcription start site). Peaks within the blacklisted regions were removed (mm10-blacklist.v2.bed.gz from https://github.com/Boyle-Lab/Blacklist/tree/master/lists). Differential analysis was performed using DESeq2. Normalized count was obtained using DESeq2, normalized across all samples from the same model
Genome_build: mm10
Supplementary_files_format_and_content: Table with differential analysis result from DESeq2 for every peak (KrasG12D vs KrasWT), merged
Supplementary_files_format_and_content: Matrix table with normalized counts for every peak and every sample, annotated with the associated gene for each peak
Supplementary_files_format_and_content: BED file containing locations of all filtered peaks
Supplementary_files_format_and_content: BigWig file of each NF-sample, rescaled using sizeFactors generated from DESeq2

extract_protocol:
For colonic epithelium, distal colon was scraped using a razor blade to enrich for colonic epithelium. For colonic tumor, animals were sacrified when they became moribund. Tumor lawns along colon were resected or scraped using a razor blade. Harvested tissues were flash frozen in liquid nitrogen and stored at -80ºC. Nuclei isolation was performed using ActiveMotif ATAC-Seq kit following manufacturer's protocol.
100,000 nuclei was used for ATAC-Seq library preparation. ATAC-Seq library was prepared using ActiveMotif ATAC-Seq kit following the manufacturer's instructions.

treatment_protocol: Enema of the 8-12 weeks old tumor model animals were performed using 4-hydroxytamoxifen (4-OHT, 5mg/ml in 100% ethanol) to induce colonic tumor formation.


title: Kras_tumor_rep2


title: HEAP miRNA library, Halo-Ago2/+; Fabp-Cre/+; K-Ras-G12D/+, rep 2 (HFK_miRNA2)


title: WT_colon_rep3

description:
ATAC_ce_Kras-WT_merged.csv
ATAC_ce_normalized_count.csv
ATAC_peaks_ce.bed


title: WT_tumor_rep1


title: Kras_colon_rep1


title: WT_colon_rep2


title: Kras_colon_rep2


title: WT_colon_rep1


title: HEAP miRNA library, Halo-Ago2/+; Fabp-Cre/+, rep 3 (HF_miRNA3)


title: HEAP miRNA library, Halo-Ago2/+; Fabp-Cre/+, rep 2 (HF_miRNA2)


title: Kras_tumor_rep3


title: WT_tumor_rep3


title: WT_tumor_rep2


title: WT SecA interactome, rep1, CCCP

source_name: WT SecA interactome, CCCP

value: SecA-Thrombin-Avi

value: 50uM CCCP in medium during filtration


title: peripheral blood (9611518155_R01C01)

status: Public on Apr 22 2022

city: Munich

first: Binder

last: Elisabeth

address: Kraepelinstr. 2+10

institute: Max-Planck-Institute Psychiatry

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner setting

data_processing:
The Bioconductor R package minfi was used for the quality control of DNAm data. Failed probes based on a detection P-value larger than 0.01 in >50% of the samples as well and non-specific binding probes a nd probes on X and Y chromosome were removed.
We also excluded probes if single nucleotide polymorphisms (SNPs) were documented in the interval for which the Illumina probe is designed to hybridize. Probes located close (10 bp from query site) to a SNP which had a minor allele frequency of ≥0.05, as reported in the 1,000 Genomes Project, were also removed
The data were then normalized with functional normalization. Batch effects were identified using the Empirical Bayes’ method ComBat . Batch corrected M-values after ComBat were used for all further statistical analyses

label: Cy3, Cy5

source_name: peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from peripheral blood

tag: panic disorder case (1)-control(0)

tag: age

tag: genetic sex

tag: weighted life events


title: peripheral blood (9259684097_R03C02)


title: peripheral blood (9611518027_R03C01)


title: peripheral blood (9588557114_R03C01)


title: peripheral blood (9259684107_R05C01)


title: peripheral blood (9588557079_R05C01)


title: peripheral blood (9611518155_R01C02)


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title: peripheral blood (9611518048_R04C02)


title: peripheral blood (9259684060_R01C01)


title: peripheral blood (9611518050_R02C02)


title: peripheral blood (9611518046_R01C01)


title: peripheral blood (9588557058_R06C02)


title: peripheral blood (9588557114_R01C02)


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title: peripheral blood (9259684107_R04C01)


title: peripheral blood (9611518103_R05C01)


title: peripheral blood (9611518103_R04C02)


title: peripheral blood (9588557082_R01C02)


title: peripheral blood (9259684097_R03C01)


title: peripheral blood (9588557058_R01C01)


title: peripheral blood (9611518155_R06C01)


title: peripheral blood (9588557080_R03C02)


title: peripheral blood (9588557080_R05C01)


title: peripheral blood (9611518026_R05C01)


title: peripheral blood (9611518020_R06C01)


title: peripheral blood (9588557082_R05C02)


title: peripheral blood (9482800102_R02C01)


title: peripheral blood (9259684062_R03C02)


title: peripheral blood (9588557082_R01C01)


title: peripheral blood (9588557079_R04C02)


title: peripheral blood (9588557080_R02C01)


title: peripheral blood (9259684060_R05C01)


title: peripheral blood (9259684062_R05C01)


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title: peripheral blood (9611518027_R02C01)


title: peripheral blood (9588557083_R04C02)


title: peripheral blood (9588557058_R05C02)


title: peripheral blood (9259684060_R05C02)


title: peripheral blood (9588557051_R01C01)


title: peripheral blood (9482800102_R02C02)


title: peripheral blood (9588557082_R06C01)


title: peripheral blood (9611518105_R02C01)


title: peripheral blood (9611518026_R02C01)


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title: peripheral blood (9482800102_R06C01)


title: peripheral blood (9588557083_R01C01)


title: peripheral blood (9588557080_R01C02)


title: peripheral blood (9611518051_R06C01)


title: peripheral blood (9588557083_R02C01)


title: peripheral blood (9588557058_R03C01)


title: peripheral blood (9588557114_R05C01)


title: peripheral blood (9611518016_R06C02)


title: peripheral blood (9611518155_R02C01)


title: peripheral blood (9588557082_R02C01)


title: peripheral blood (9611518155_R05C01)


title: peripheral blood (9259684097_R06C02)


title: peripheral blood (9611518025_R06C02)


title: peripheral blood (9611518025_R02C02)


title: peripheral blood (9588557079_R03C02)


title: peripheral blood (9588557079_R06C01)


title: peripheral blood (9611518005_R03C01)


title: peripheral blood (9611518027_R04C01)


title: peripheral blood (9611518105_R06C02)


title: peripheral blood (9611518046_R06C01)


title: peripheral blood (9588557083_R04C01)


title: peripheral blood (9611518105_R06C01)


title: peripheral blood (9588557114_R04C02)


title: peripheral blood (9611518103_R02C02)


title: peripheral blood (9611518048_R01C02)


title: peripheral blood (9611518019_R05C01)


title: peripheral blood (9588557051_R02C01)


title: peripheral blood (9588557051_R04C01)


title: peripheral blood (9611518051_R05C02)


title: peripheral blood (9611518050_R03C02)


title: peripheral blood (9611518103_R06C02)


title: peripheral blood (9611518048_R03C02)


title: peripheral blood (9259684097_R02C01)


title: peripheral blood (9611518155_R06C02)


title: peripheral blood (9259684062_R02C02)


title: peripheral blood (9611518105_R05C02)


title: peripheral blood (9588557114_R04C01)


title: peripheral blood (9611518019_R02C01)


title: peripheral blood (9611518019_R06C02)


title: peripheral blood (9588557051_R02C02)


title: peripheral blood (9611518046_R03C01)


title: peripheral blood (9611518016_R05C01)


title: peripheral blood (9611518103_R05C02)


title: peripheral blood (9259684097_R05C02)


title: peripheral blood (9611518103_R01C01)


title: peripheral blood (9259684062_R01C01)


title: peripheral blood (9611518050_R03C01)


title: peripheral blood (9611518016_R05C02)


title: peripheral blood (9611518048_R06C01)


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title: peripheral blood (9482800102_R01C02)


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title: peripheral blood (9611518025_R03C01)


title: peripheral blood (9611518050_R05C01)


title: peripheral blood (9588557083_R03C01)


title: peripheral blood (9588557051_R06C02)


title: peripheral blood (9611518006_R01C01)


title: peripheral blood (9611518051_R01C02)


title: peripheral blood (9259684107_R02C02)


title: peripheral blood (9588557051_R04C02)


title: peripheral blood (9611518048_R06C02)


title: peripheral blood (9611518027_R02C02)


title: peripheral blood (9611518020_R01C01)


title: peripheral blood (9611518025_R06C01)


title: peripheral blood (9611518105_R01C01)


title: peripheral blood (9611518005_R02C01)


title: peripheral blood (9611518105_R03C01)


title: peripheral blood (9588557079_R04C01)


title: peripheral blood (9588557080_R04C02)


title: peripheral blood (9611518155_R04C01)


title: peripheral blood (9611518016_R06C01)


title: peripheral blood (9611518006_R06C02)


title: peripheral blood (9588557114_R01C01)


title: peripheral blood (9611518020_R04C01)


title: peripheral blood (9588557051_R03C02)


title: peripheral blood (9588557080_R05C02)


title: peripheral blood (9588557058_R03C02)


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title: peripheral blood (9611518050_R06C02)


title: peripheral blood (9611518006_R03C01)


title: peripheral blood (9611518016_R03C01)


title: peripheral blood (9588557058_R02C02)


title: peripheral blood (9259684097_R02C02)


title: peripheral blood (9588557080_R04C01)


title: peripheral blood (9588557082_R02C02)


title: peripheral blood (9611518019_R01C02)


title: peripheral blood (9611518027_R01C02)


title: peripheral blood (9611518025_R05C01)


title: peripheral blood (9588557051_R01C02)


title: peripheral blood (9259684062_R03C01)


title: peripheral blood (9588557114_R03C02)


title: peripheral blood (9611518020_R05C02)


title: peripheral blood (9588557083_R05C01)


title: peripheral blood (9611518027_R05C02)


title: peripheral blood (9611518020_R02C02)


title: peripheral blood (9259684060_R04C02)


title: peripheral blood (3999840047_R01C01)

value: F


title: peripheral blood (9611518019_R03C02)


title: peripheral blood (9611518008_R06C02)


title: peripheral blood (9989536109_R05C01)


title: peripheral blood (9989536118_R05C02)


title: peripheral blood (3999840162_R04C01)


title: peripheral blood (9989536146_R06C01)

value: M


title: peripheral blood (9588557079_R03C01)


title: peripheral blood (9611518026_R04C02)


title: peripheral blood (9611518008_R01C01)


title: peripheral blood (9611518025_R03C02)


title: peripheral blood (9259684060_R02C02)


title: peripheral blood (9989536066_R06C01)


title: peripheral blood (9989536146_R02C02)


title: peripheral blood (3999840166_R04C01)


title: peripheral blood (9989536025_R05C01)


title: peripheral blood (9588557083_R05C02)


title: peripheral blood (9611518006_R01C02)


title: peripheral blood (9989536044_R03C01)


title: peripheral blood (9588557083_R06C02)


title: peripheral blood (9588557083_R03C02)


title: peripheral blood (9611518103_R02C01)


title: peripheral blood (9989536117_R06C01)


title: peripheral blood (9588557082_R04C01)


title: peripheral blood (3999840037_R05C02)


title: peripheral blood (9989536110_R04C01)


title: peripheral blood (9989536109_R02C01)


title: peripheral blood (9989536117_R02C01)


title: peripheral blood (3999840128_R04C02)


title: peripheral blood (9611518016_R04C02)


title: peripheral blood (3999840095_R01C02)


title: peripheral blood (3999840132_R02C02)


title: peripheral blood (3999840071_R06C02)


title: peripheral blood (3999840055_R05C01)


title: peripheral blood (3999840140_R01C02)


title: peripheral blood (3999840035_R01C02)


title: peripheral blood (3999840061_R03C01)


title: peripheral blood (3999840128_R02C02)


title: peripheral blood (9989536118_R06C01)


title: peripheral blood (9611518008_R02C02)


title: peripheral blood (3999840057_R01C01)


title: peripheral blood (3999840158_R04C01)


title: peripheral blood (9989536093_R05C01)


title: peripheral blood (9611518048_R05C01)


title: peripheral blood (9989536044_R04C02)


title: peripheral blood (9989536100_R03C01)


title: peripheral blood (9989536078_R03C01)


title: peripheral blood (3999840088_R01C01)


title: peripheral blood (3999840047_R01C02)


title: peripheral blood (3999840098_R06C02)


title: peripheral blood (9989536096_R02C02)


title: peripheral blood (9989536077_R05C02)


title: peripheral blood (3999840035_R06C02)


title: peripheral blood (9989536126_R01C01)


title: peripheral blood (3999840161_R02C01)


title: peripheral blood (9989536093_R03C02)


title: peripheral blood (9989536112_R03C01)


title: peripheral blood (9989536075_R03C02)


title: peripheral blood (9989536114_R04C02)


title: peripheral blood (3999840056_R01C02)


title: peripheral blood (3999840056_R05C01)


title: peripheral blood (3999840056_R06C02)


title: peripheral blood (3999840037_R03C01)


title: peripheral blood (3999840150_R05C01)


title: peripheral blood (3999840057_R02C01)


title: peripheral blood (3999840071_R04C02)


title: peripheral blood (3999840162_R06C01)


title: peripheral blood (9989536134_R02C01)


title: peripheral blood (9989536110_R03C02)


title: peripheral blood (9989536134_R03C01)


title: peripheral blood (3999840166_R03C01)


title: peripheral blood (9989536119_R05C01)


title: peripheral blood (3999840057_R04C02)


title: peripheral blood (9989536134_R06C01)


title: peripheral blood (9989536137_R04C01)


title: peripheral blood (3999840071_R02C02)


title: peripheral blood (9989536137_R06C01)


title: peripheral blood (9989536091_R01C02)


title: peripheral blood (3999840047_R06C01)


title: peripheral blood (3999840132_R02C01)


title: peripheral blood (9989536114_R03C01)


title: peripheral blood (9989536120_R03C02)


title: peripheral blood (3999840150_R04C02)


title: peripheral blood (9989536116_R03C02)


title: peripheral blood (9989536075_R05C01)


title: peripheral blood (9989536117_R05C02)


title: peripheral blood (3999840095_R03C02)


title: peripheral blood (3999840159_R04C02)


title: peripheral blood (9989536077_R06C02)


title: peripheral blood (3999840070_R06C02)


title: peripheral blood (3999840061_R01C02)


title: peripheral blood (3999840162_R01C02)


title: peripheral blood (9989536117_R04C02)


title: peripheral blood (3999840072_R06C01)


title: peripheral blood (9989536044_R04C01)


title: peripheral blood (3999840103_R04C02)


title: peripheral blood (3999840098_R02C02)


title: peripheral blood (9989536114_R06C01)


title: peripheral blood (9989536066_R03C02)


title: peripheral blood (9989536146_R01C01)


title: peripheral blood (3999840150_R02C01)


title: peripheral blood (3999840095_R05C02)


title: peripheral blood (9989536027_R01C01)


title: rRNA Depleted total RNA from liver from untreated WKY rats (replicate 3, sequencing batch 10)

status: Public on Apr 01 2022

city: Aurora

first: Laura

last: Saba

address: 12850 E. Montview Blvd

institute: University of Colorado Anschutz Medical Campus

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: WKY_3_batch10
HRDPv5 Sample Name: WKY-NCrl_3_batch10
WKY_3

data_processing:
Cutadapt (v1.9.1) trim Illumina adapter, quality, and length, parameters: -q 20 -m 20
Remove rRNA reads by alignment with bowtie2(v2.3.4.3) to rRNA
genome Alignment Hisat2 (v2.1.0)
Stringtie (v1.3.5) reconstruction
Run Aptardi (v1.4) on each strain reconstructed GTF
Merge aptardi output reconstruction Stringtie(v1.3.5)
Run RSEM (v1.3.1) on reconstruction
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Run RSEM(v1.3.1) on filtered reconstruction
Filter transcripts/genes from RSEM filtered transcriptome results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Apply a regularized log transformation of expected read counts from RSEM (rlog function in DESeq2 package of R)
Remove technical artifacts including batch effects using Removal of Unwanted Variance  (RUVg) with empirically-derived controls (RUVSeq package in R)
Assembly: Rn7.2
Supplementary files format and content: TSV batch corrected/normalized expression values
Supplementary files format and content: GTF of the reconstructed transcriptome

source_name: liver

extract_protocol:
RNA was collected from liver using the RNeasy Plus Universal Midi kits for RNA sequencing (Qiagen, Valencia, CA, USA).
Libraries were constructed using the Illumina TruSeq Stranded total RNA Kit (Illumina, San Diego, CA, USA).
rRNA depleted stranded total RNA

value: liver

value: WKY/NCrl

tag: Sex

value: male


title: peripheral blood (9989536013_R02C02)


title: peripheral blood (9989536119_R05C02)


title: rRNA Depleted total RNA from liver from untreated WKY rats (replicate 2, sequencing batch 8)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: WKY_2_batch8
HRDPv5 Sample Name: WKY-NCrl_2_batch8
WKY_2

tag: tissue


title: rRNA Depleted total RNA from liver from untreated WKY rats (replicate 1, sequencing batch 8)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: WKY_1_batch8
HRDPv5 Sample Name: WKY-NCrl_1_batch8
WKY_1


title: peripheral blood (3999840103_R04C01)


title: rRNA Depleted total RNA from liver from untreated SS rats (replicate 3.2, sequencing batch 10)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: SS-JrHsd_3_batch10
SS_3.2

value: SS/JrHsdMcwi


title: rRNA Depleted total RNA from liver from untreated SS rats (replicate 2, sequencing batch 10)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: SS-JrHsd_2_batch10
SS_2