title: neural tube organoids, 8 hrs post Day 2, N2B27+RA, biol rep 3 [S9914]

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

data_processing:
RNA-seq reads were trimmed using trimgalore v0.5.0
Ffiltered to remove abundant sequences using bowtie2 v2.3.4.1
Aligned to the Genome using star v2.6.0c
Summarized per gene with featureCounts (subread v1.6.2)
Assembly: GRCm38 genome (Ensembl release 94)
Supplementary files format and content: Tab delimited file of feature counts

source_name: neural tube organoid

growth_protocol: R1 mouse embryonic stem cell were embedded in Matrigel and differentiaed into neural tube organoids via clonal growth in N2B27 medium with antibiotics at 37C, 5% CO2.

extract_protocol:
RNA was harvested using RNeasy Micro Kit (Qiagen). 1.2 ug of total RNA was used for the construction of sequencing libraries.
RNAseq libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra Directional RNA Library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol:
Two days after differentation, the medium was replaced with N2B27 or N2B27+250 µM all-trans retinoic acid.
Neural tube organoids were extracted from the Matrigel with Cell Recovery solution at 0, 18, 30, 42, 54, 68, and 80 hrs post Day 2, and processed for RNA extraction.

value: neural tube organoid

value: mouse embryonic stem cell

value: WT

value: 3D neuroepithelial differentiation in Matrigel

tag: treatment condition

tag: time point

value: 8 hrs post Day 2


title: DRG neurons, sc-RNA seq batch 31

status: Public on Oct 01 2022

type: SRA

city: Beijing

first: Xi-Yin

last: Zhang

address: College Road

department: Neuroscience Research Institute

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Extract Barcode and UMI: umi_tools extract.
Trim TSO and PolyA: trim_TSO_polyA.pl, seqtk trimfq.
Mapping With STAR, add feature using featureCounts of subread
Sort and index bam file using Samtools
Assembly: Rnor_6.0.102
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell-id

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Dorsal root ganglia

growth_protocol: Specific pathogen-free (SPF) male Sprague-Dawley (SD) rats weighing 200 g were supplied by the Animal Center of Peking University Health Science Center. The animals were housed in an SPF laboratory in ventilated cages (IVC) (3-5 rats per cage) on a 12-hour light-dark cycle (lights on at 8:00 AM) with free access to food and water. All experiments were performed according to the guidelines of the Animal Care and Use Committee of Peking University, and efforts were made to minimize the discomfort of the animals.

extract_protocol:
A modified Smart-seq2 protocol developed by the Tang laboratory was used for single-cell RNA-seq. Briefly, acutely dissociated DRG neurons were plated on dishes as described previously. After 15 min, the DMEM was replaced with PBS, and a mouth pipette was then used to place each individual fluorescently labeled single DRG neuron into a volume of lysis buffer under a fluorescence microscope. Harvesting of the single DRG neurons from one rat was completed in 4 h, and the L4-5 DRG of at least 5 rats were harvested at each time point.
The reverse transcription reaction was performed with a TSO primer added at the 5’ end and with 25 nt oligo (dT) primer anchored with an 8 nt cell-specific barcode and 8 nt unique molecular identifiers (UMIs) added at the 3’ end. After reverse transcription, cDNAs were amplified by 15 cycles of PCR, during which the IS primer and the 3’P2 primer were added to the 5’ and 3’ ends of the cDNAs, respectively. The amplified cDNAs from single cells were pooled, purified using a DNA Clean & concentration-5 kit (Zymo Research, D4014) and AMPure XP beads (Beckman Coulter, A63882), and quantified using a Qubit dsDNA HS Assay Kit (Invitrogen, Q32854). To add biotin tags to the 3’ ends of the amplified cDNAs, biotinylated preindexed primers and IS primer were used to further amplify the PCR product through an additional 4 cycles of PCR. The biotinylated cDNAs were then sheared to approximately 300 bp using Covaris S2, and the 3’ termini of the cDNAs were captured using C1 beads (Dynabeads® Myone™ Streptavidin C1, Invitrogen, 65001). The RNA-seq library was constructed using a Kapa Hyper Prep Kit (KAPA Biosystems, KK8505), and short universal primers and QP2 primers were used in the last amplification. Finally, the genome and transcriptome libraries were subjected to 150 bp paired-end sequencing on an Illumina HiSeq 4000 platform (sequenced by Novogene).

treatment_protocol: Adult naïve rats were deeply anesthetized with 10% chloral hydrate and their bilateral L4-L5 DRGs were quickly dissected. Acute-dissociated DRG neurons were collected and resuspended in plating medium (DMEM containing 10% FBS) and then plated onto a 3.5-cm dish coated with poly-D-lysine. After 3 hours, the medium was replaced with Neurobasal medium supplemented with 2% B27 and 2 mM GlutaMAX-I. After 72 hours, the Neurobasal medium was replaced with PBS, and a mouth pipette was then used to place each single DRG neuron with neurites into a volume of lysis buffer under a microscope.

tag: tissue

value: Dorsal root ganglia

tag: cell type

value: Neurons

tag: strain

value: SD

tag: Sex

value: male

tag: numbers of_cells


title: mESC, Ctrl-preTreatment_noactivated, 1

city: SAN DIEGO

first: Anjana

last: Rao

state: CALIFORNIA

address: 9420 Athena CIRCLE, LA JOLLA

country: USA

institute: LA JOLLA INSTITUTE

description:
WGS_LowCov-Bulk_WT_preTAM-noActivated_r1
Whole Genome Sequencing (WGS) Low Coverage

library_source: genomic

data_processing:
WGS bulk low-coverage data was mapped to mm10 reference genome, using BSmap 2.74v allowing for maximum four mismatches (-v 4) and removing low-quality 3’ reads (-q 10).
Optical duplicate reads were removed Picard MarkDuplicates tool.
CNVkit (Talevich et. al 2016) was employed to detect copy number alterations (.cnn), in WGS, correcting for CG content and mappability bias. employing 500kb bins (or as indicated).
Assembly: mm10
Supplementary files format and content: .cnn.txt, sample genome coverage.

molecule: genomic DNA

organism: Mus musculus

source_name: mouse Embryonic Stem Cell

growth_protocol: mESC were cultured under 2i-conditions (CHIR99021 and PD0325901) using Mouse Embryonic Fibroblasts (MEFs) as feeders.

extract_protocol:
Samples were generated after sorting by CD326+/GFP+/Live/Thy1.2-/LiveDead dye- for Ctrl and TetiTKO mESCs and by CD326+/Live/Thy1.2-/LiveDead dye- for Dnmt TKO mESCs. Genomic DNA was extracted using PureLinkTM genomic DNA mini kit.
TruSeq DNA PCR-Free Sample Preparation kit (Illumina, 20015963).

treatment_protocol: mESCs were treated with tamoxifen (1µM) for 2.5 days, cultured for 4 additional days and then collected for the acute-deletion comparison. Monoclonal populations from TetiTKO and Ctrl mESC were maintained for 30 days in culture for long-term comparisons. DnmtTKO (germline Knock-out [non-inducible]) mESC samples were included as part of the long-term comparison.

tag: genotype

value: Cre/ERT2; Rosa26-LSL-H2b-Egfp

value: mouse Embryonic Stem Cell

tag: treatment

value: pre-treatment, not activated


title: neural tube organoids, 8 hrs post Day 2, N2B27+RA, biol rep 2 [S9913]

molecule: total RNA

tag: cell line


title: Wildtype biol rep 1

city: East Melbourne

first: Raymond

middle: CB

last: Wong

state: VIC

address: 32 Gisborne St

country: Australia

institute: Centre for Eye Research Australia

description:
100bp
ARPE_WT_1

data_processing:
Salmon v1.8
Salmon v1.8 was used for abundance estimates of transcripts
The Salmon pseudocounts were mapped to the GRCh38 genome assembly using the tximport v1.22.0 package
The gene count matrix was inputted to DESeq2 v1.34.0 for normalisation to make fair gene expression comparisons between samples
Assembly: GrCh38

organism: Homo sapiens

extract_protocol:
Total RNA of ARPE-19 cell lines was extracted using the Illustra RNAspin Mini Kit (GE Healthcare Life Sciences) according to manufacturer’s instructions
RNA quality was checked by bioanalyzer and the TruSeq Stranded mRNA kit (Illumina) was used to prepare transcriptome libraries according to manufacturer's instructions.

value: retinal pigment epithelial cells

value: wildtype

value: Regular maintenance

tag: time

value: Day 3


title: POLDIP2 KO biol rep 2

description:
100bp
ARPE_KO_2

value: POLDIP knockout


title: Female SERTfl/fll 3

city: Bronx

first: Ji

middle: Ying

last: Sze

state: NY

address: 1300 Morris Park Ave

department: Molecular Pharamcology

institute: Albert Einstein College of Medicine

data_processing:
Adaptor trimming
Alignment to genome
Remove duplicate reads
Create and compile counts matrix file
Assembly: mm10
Supplementary files format and content: txt file with raw counts matrix containing all samples

source_name: Dorsal hippocampus tissue pooled from four mice

extract_protocol:
RNA extraction was performed using Trizol (Thermo Fisher, 15596026)-chloroform, followed by cleanup and elution into RNAse-free water using the RNeasy Minelute Cleanup kit (Qiagen, 74204) per manufacturer instructions.
mRNA libraries were prepared using the Illumina Truseq RNA Library Prep Kit V2 (#RS-122-2001) per manufacturer instructions on 250 ng total RNA.

tag: age

value: Female

value: SERTfl/fl


title: DRG neurons, sc-RNA seq batch 30


title: Female SERTfl/fll 1

value: Dorsal hippocampus tissue pooled from four mice


title: DRG neurons, sc-RNA seq batch 29


title: Female SERTfl/fll 2


title: neural tube organoids, 8 hrs post Day 2, N2B27+RA, biol rep 1 [S9912]

value: neural tube organoid

value: mouse embryonic stem cell

value: WT

value: 3D neuroepithelial differentiation in Matrigel


title: neural tube organoids, 8 hrs post Day 2, N2B27, biol rep 3 [S9917]

value: 8 hrs post Day 2


title: Female SERTPyramid∆ 3

value: SERTPyramid


title: DRG neurons, sc-RNA seq batch 28-3

value: Dorsal root ganglia

value: Neurons

value: SD

value: male


title: PLIN2siRNA+6hOle+2day_3

city: New Haven

first: Haikuo

last: Li

state: CT

address: 55 Prospect St

institute: Washington University in St. Louis

data_processing:
Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software
Assembly: GRCh38.101
Supplementary files format and content: .sf file: Name;Length EffectiveLength;TPM;NumReads

source_name: Cell culture

extract_protocol:
Column-based RNA extraction
Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

value: Cell culture

value: RPTEC


title: PLIN2siRNA+6hOle+2day_2


title: PLIN2siRNA+6hOle+2day_1


title: mIMCD-3 subclone 5 rep4

city: Freiburg

first: Yong

address: Hugstetter Str. 49

department: Institute of Genetic Epidemiology

country: Germany

institute: Medical Center - University of Freiburg

data_processing:
Illumina Casava 1.8 software used for basecalling.
Remove reads containing adapters. Remove reads containing N > 10% (N represents the base cannot be determined). Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Reads were then aligned to mouse reference genome GRCm38 using STAR 2.7.3a with default parameters.
RSEM v1.3.1 was used to calculate gene expression values.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

source_name: mIMCD-3 subclone 5 rep4

growth_protocol: Cells were cultured with DMEM:F12 (LONZA, cat.no. BE12-719F), fetal bovine serum was added to a final concentration of 10% and penicillin/streptomycin (Sigma, P0781) with a final concentration of 1%.  Subculturing of cells was performed twice a week in a 1:10 ratio. Cells were maintained in a humidified incubator at 37°C and 10% CO2.

extract_protocol:
RNA Isolation was performed 4 days after full confluency according to manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were harvested using 0.25 % Trypsin-EDTA (Gibco)

value: subclone 5


title: DRG neurons, sc-RNA seq batch 28-1


title: mIMCD-3 subclone 5 rep3

source_name: mIMCD-3 subclone 5 rep3


title: DRG neurons, sc-RNA seq batch 27


title: mIMCD-3 subclone 5 rep2

source_name: mIMCD-3 subclone 5 rep2


title: neural tube organoids, Day 2, biol rep 2 [S9911]

value: Day 2


title: DRG neurons, sc-RNA seq batch 26


title: NTsiRNA+6hOle+2day_3


title: neural tube organoids, Day 2, biol rep 1 [S9910]


title: mIMCD-3 subclone 5 rep1

source_name: mIMCD-3 subclone 5 rep1


title: NTsiRNA+6hOle+2day_2


title: DRG neurons, sc-RNA seq batch 25


title: POLDIP2 KO biol rep 1

description:
100bp
ARPE_KO_1

value: retinal pigment epithelial cells

value: POLDIP knockout

value: Regular maintenance

value: Day 3


title: mIMCD-3 subclone 4 rep4

source_name: mIMCD-3 subclone 4 rep4

value: subclone 4


title: neural tube organoids, Day 2, biol rep 3 [S10131]

value: neural tube organoid

value: mouse embryonic stem cell

value: WT


title: DRG neurons, sc-RNA seq batch 24


title: NTsiRNA+6hOle+2day_1


title: mIMCD-3 subclone 4 rep3

source_name: mIMCD-3 subclone 4 rep3


title: neural tube organoids, 78 hrs post Day 2, N2B27+RA, biol rep 3 [S10205]

value: 3D neuroepithelial differentiation in Matrigel

value: 78 hrs post Day 2


title: PLIN2siRNA+6hOle_3


title: neural tube organoids, 8 hrs post Day 2, N2B27, biol rep 2 [S9916]

value: 8 hrs post Day 2


title: neural tube organoids, 78 hrs post Day 2, N2B27+RA, biol rep 2 [S10204]


title: mIMCD-3 subclone 4 rep2

source_name: mIMCD-3 subclone 4 rep2


title: Input DNA, SUPT1 with overexpression of STAT5B wild type (WT), treated

city: Utrecht

first: Rico

last: Hagelaar

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

data_processing:
Raw reads were aligned to Hg38 using BWA, default settings
MACS2 was used for peakcalling. Narrow peak calling was used for transcription factors. Remainder of settings were left at default
Normalised BigWig files (bw) were created using BamCoverage of the Deeptools package, using the reads per genome coverage (RPCG) scaling factor
Genome_build: CRCh38
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: BigWig files; containing RPGC normalised values

source_name: SUPT-1 cell line

growth_protocol: SUPT-1 cells were cultured in RPMI-1640 medium (Gibco) supplemented with 1x Glutamax, 10% heat-inactivated fetal bovine serum (Gibco), 2% pencillin/streptomycin (Gibco) and 0,4% Fungizone (Gibco). Media for SUPT-1 cells was supplemented with 1-2 μg/mL puromycin for purification of doxycycline-inducible cells

extract_protocol:
20x10^6 cells were fixed and chromatin-immunoprecipitation (ChIP) was performed according to the manufacturer’s instructions (Simple ChIP Enzymatic Chromatin IP Kit, #9003, CST). Water bath sonification was performed for seven cycles (30 seconds on 30 seconds off), and DNA fragment size was validated by electrophoresis.
DNA library preparation was performed using the NEBNext Ultra II DNA Library Prep kit (New England Biolabs #E7103) with an additional 0,52X beads purification step.

treatment_protocol: Doxycycline-induced STAT5WT and STAT5BN642H SUPT-1 cells were cultured with or without 250µg/ml prednisolone for 16 hours

tag: overexpression

value: Wild type (WT)

value: 250ug/ml prednisolone for 16 hours


title: DRG neurons, sc-RNA seq batch 23

value: Dorsal root ganglia

value: Neurons

value: SD

value: male


title: DRG neurons, sc-RNA seq batch 22


title: PLIN2siRNA+6hOle_2

value: Cell culture

value: RPTEC


title: mIMCD-3 subclone 4 rep1

source_name: mIMCD-3 subclone 4 rep1


title: neural tube organoids, 8 hrs post Day 2, N2B27, biol rep 1 [S9915]


title: neural tube organoids, 78 hrs post Day 2, N2B27+RA, biol rep 1 [S10203]


title: DRG neurons, sc-RNA seq batch 21


title: mIMCD-3 subclone 3 rep4

source_name: mIMCD-3 subclone 3 rep4

value: subclone 3


title: neural tube organoids, 78 hrs post Day 2, N2B27, biol rep 3 [S10208]


title: NTsiRNA+6hOle_3


title: DRG neurons, sc-RNA seq batch 20


title: neural tube organoids, 78 hrs post Day 2, N2B27, biol rep 2 [S10207]


title: PLIN2siRNA+6hOle_1


title: seu-6, 1/2 MS+250mM Sorbitol, 6h, 10-day old whole seedlings,rep2

first: Xiaofeng

last: Fang

address: Hai dian

institute: Tsinghua University

data_processing:
RNA-seq reads were aligned to Arabidopsis reference genome (TAIR10) using Hisat2(v2.2.1).
Gene-level raw count data files were generated using HTseq-count (v0.13.5).
The raw count data was imported into Bioconductor package Deseq2 in R language to identify the differentially expressed genes.
Assembly: Genome_build: Arabidopsis reference genome (TAIR10).
Supplementary files format and content: Tab-delimited text files include raw counts of each gene for each sample.

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: All plants were grown under long photoperiod conditions (16 h light of 120 µmol m-2 s-1/8 h dark)

extract_protocol:
Total RNAs was extracted with the Trizol reagent. After DNA digestion, poly(A)+ RNAs were purified using Dynabeads mRNA Purification Kit (Invitrogen, USA).
RNA-seq libraries were constructed using NEXTflex RNA-Seq Kit (Bioo Scientific, USA). Briefly, RNAs were fragmented and the first strands and second strands of cDNAs were synthesized. After the addition of a single nucleotide “A”, cDNAs were subjected to adapter ligation. The products were purified with AMPure XP beads and then used as templates for PCR amplification.

treatment_protocol: Arabidopsis seedlings were transferred into liquid 1/2 MS medium or liquid 1/2 MS medium containing 300mM NaCl for 15 min, or liquid 1/2 MS medium containing 250mM sorbitol for 6 h.

value: whole seedling

value: seu-6 mutant

value: 1/2 MS+250mM Sorbitol 6 h


title: NTsiRNA+6hOle_1


title: mIMCD-3 subclone 3 rep2

source_name: mIMCD-3 subclone 3 rep2


title: seu-6, 1/2 MS+250mM Sorbitol, 6h, 10-day old whole seedlings,rep1


title: neural tube organoids, 78 hrs post Day 2, N2B27, biol rep 1 [S10206]

source_name: neural tube organoid

value: neural tube organoid

value: mouse embryonic stem cell


title: neural tube organoids, 66 hrs post Day 2, N2B27+RA, biol rep 3 [S10199]

value: WT

value: 3D neuroepithelial differentiation in Matrigel

value: 66 hrs post Day 2


title: NTsiRNA+6hOle_2


title: Col-0, 1/2 MS+250mM Sorbitol, 6h, 10-day old whole seedlings, rep2


title: mIMCD-3 subclone 2 rep4

source_name: mIMCD-3 subclone 2 rep4

value: subclone 2


title: NTsiRNA_3

value: NTsiRNA


title: Col-0, 1/2 MS+250mM Sorbitol, 6h, 10-day old whole seedlings, rep1


title: neural tube organoids, 66 hrs post Day 2, N2B27+RA, biol rep 2 [S10198]


title: mIMCD-3 subclone 2 rep3

source_name: mIMCD-3 subclone 2 rep3


title: NTsiRNA_2


title: mIMCD-3 subclone 2 rep2

source_name: mIMCD-3 subclone 2 rep2


title: seu-6, 1/2 MS, 6h,10-day old whole seedlings, rep2


title: neural tube organoids, 66 hrs post Day 2, N2B27, biol rep 3 [S10202]


title: NTsiRNA_1

source_name: Cell culture


title: mIMCD-3 subclone 3 rep3

source_name: mIMCD-3 subclone 3 rep3


title: neural tube organoids, 66 hrs post Day 2, N2B27+RA, biol rep 1 [S10197]


title: RNA-seq MV4:11 C10 rep3

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
Assembly: hg19
Supplementary files format and content: RNA-seq: tab-delimited text file include raw counts for each sample

growth_protocol: MV4:11 cells were grown in RPMI-1640 with 10% FBS and 10 U/ml Penicillin-Streptomycin. Cells were cultured at 37˚C and 5% CO2.

extract_protocol:
For RNA-seq, Cells were collected in Trizol and RNA was purified with Direct-Zol RNA Miniprep kit (Zymo) with on-column DNaseI treatment.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA-seq, cells were treated with 0.01% DMSO or 500 nM C16 or 100nM C10 for 3 days.

value: 100 nM C10 for 3 days


title: Col-0, 1/2 MS, 6h, 10-day old whole seedlings, rep2


title: mIMCD-3 subclone 1 rep4

source_name: mIMCD-3 subclone 1 rep4

value: subclone 1


title: mIMCD-3 subclone 2 rep1

source_name: mIMCD-3 subclone 2 rep1


title: RNA-seq MV4:11 C10 rep4


title: neural tube organoids, 66 hrs post Day 2, N2B27, biol rep 1 [S10200]


title: neural tube organoids, 66 hrs post Day 2, N2B27, biol rep 2 [S10201]


title: RNA-seq MV4:11 C10 rep1


title: mIMCD-3 subclone 3 rep1

source_name: mIMCD-3 subclone 3 rep1


title: neural tube organoids, 54 hrs post Day 2, N2B27+RA, biol rep 2 [S9937]

value: 54 hrs post Day 2


title: RNA-seq MV4:11 C10 rep2


title: seu-6, 1/2 MS+300mM NaCl, 15min, 14-day old whole seedlings, rep1

value: 1/2 MS+300mM NaCl 15 min


title: RNA-seq MV4:11 C16 rep4

value: 500 nM C16 for 3 days


title: Col-0, 1/2 MS, 6h, 10-day old whole seedlings, rep1


title: mIMCD-3 subclone 1 rep3

source_name: mIMCD-3 subclone 1 rep3


title: RNA-seq MV4:11 C16 rep3


title: Col-0, 1/2 MS+300mM NaCl, 15min, 14-day old whole seedlings, rep2


title: neural tube organoids, 54 hrs post Day 2, N2B27+RA, biol rep 3 [S9938]


title: scRNA-seq from Ramp1 knockout colon

city: Boston

first: Isaac

last: Chiu

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard medical school

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger, and Cell Ranger count QC summary report identified between 12,000-14,000 single cells in the samples.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Colon

extract_protocol:
Briefly, distal colon was collected from euthanized mice and flushed with ice cold PBS. Colons were cut into 0.5cm pieces and incubated on ice for 5 min in 10 mL of PBS containing 5 mM EDTA and 1 mM DTT. After shaking, the intestinal pieces were incubated at 37 ºC for 10 minutes in PBS containing 5 mM EDTA and 2% FBS. After vigorous shaking, the wash containing crypts was collected. This step was performed three times in total for colonic pieces and two times for ileal pieces with the epithelial fraction collected at the end of each wash. The crypt cells were pelleted and digested with 10 ml HBSS containing 8 mg Dispase II (Sigma) for 10 minutes at 37 ºC. Single epithelial cells were collected in PBS containing 2% FBS for flow cytometry staining and sorting.
scRNA-seq of colonic epithelial cells isolated from Nav1.8DTA mice, VillinCreRamp1 knockout mice and their littermate control mice was performed using 10X genomics following the user guide. Briefly, cells were counted on the LUNA-FX7 Automated Cell Counter (Logos Biosystems) using fluorescence detection for viability with an acridine orange/propidium iodide stain (Logos Biosystems). All samples had viability greater than 88% with concentration ranges from ~700-900 cells/µL. After counting, all samples were loaded into Chip G per the user guide from 10x Genomics. GEMs (Gel Beads-in-emulsions) were formed targeting 10,000 cells for each sample followed by immediate reverse transcription. The cDNA was cleaned from the GEM reagents, amplified for a total of 11 cycles and verified via TapeStation (Agilent Technologies). Amplified cDNA was diluted 1:6 and run on the 4200 TapeStation instrument using High Sensitivity D5000 tape and reagents (Agilent Technologies). The amplified cDNA was fragmented, end repaired, and A-tailed followed by adaptor ligation, and PCR amplification was run for a total of 11 cycles with each sample receiving a unique set of dual indices. Final libraries were diluted 1:10 and ran using the High Sensitivity D5000 tape and reagents on the 4200 TapeStation (Agilent Technologies). Libraries were quantified via Kapa qPCR using the Complete Universal Kit (Roche Sequencing Solutions) and the CFX96 Touch Real-Time PCR Detection System (Bio-Rad Laboratories). Libraries were sequenced on an Illumina NovaSeq S4 flow cell across one single lane (estimated reads per cell ~55,000) using the parameters outlined in the user guide (Read1: 28 bp, i7 index: 10 bp, i5 index: 10 bp, Read2: 90 bp).

value: Colon

value: Epithelial cells

value: Baseline


title: neural tube organoids, 54 hrs post Day 2, N2B27+RA, biol rep 1 [S9936]


title: mIMCD-3 subclone 1 rep2

source_name: mIMCD-3 subclone 1 rep2


title: scRNA-seq from nociceptor control colon


title: seu-6, 1/2 MS+300mM NaCl, 15min, 14-day old whole seedlings, rep2

value: whole seedling

value: seu-6 mutant


title: neural tube organoids, 42 hrs post Day 2, N2B27+RA, biol rep 3 [S9932]

value: neural tube organoid

value: 42 hrs post Day 2


title: RNA-seq MV4:11 DMSO rep3

value: 0.01% DMSO for 3 days


title: RNA-seq MV4:11 C16 rep2


title: neural tube organoids, 54 hrs post Day 2, N2B27, biol rep 2 [S9940]

value: mouse embryonic stem cell

value: WT

value: 3D neuroepithelial differentiation in Matrigel


title: seu-6, 1/2 MS, 6h, 10-day old whole seedlings, rep1


title: Col-0, 1/2 MS+300mM NaCl, 15min, 14-day old whole seedlings, rep1


title: Col-0, 1/2 MS, 15min, 14-day old whole seedlings, rep2

value: 1/2 MS 15 min


title: mIMCD-3 subclone 1 rep1

source_name: mIMCD-3 subclone 1 rep1


title: neural tube organoids, 54 hrs post Day 2, N2B27, biol rep 1 [S9939]


title: RNA-seq MV4:11 DMSO rep2


title: scRNA-seq from Ramp1 control colon


title: seu-6, 1/2 MS, 15min, 14-day old whole seedlings, rep2


title: RNA-seq MV4:11 DMSO rep1


title: neural tube organoids, 54 hrs post Day 2, N2B27, biol rep 3 [S10196]


title: RNA-seq MV4:11 C16 rep1


title: T-7964-KO

city: Memphis

first: Liza

last: Makowski

state: Tennessee

address: 19 South Manassas St

department: Medicine- Heme Onc

institute: UTHSC

description: E0771-luciferase cells from PKC delta knockout

data_processing:
Fastqc was used to exclude poor quality samples.
STAR was used to align reads to transcriptome using a GRCm38.p4 genome build with Ensembl v86 gene annotation.
Salmon quantification in alignment-based mode was used to obtain transcript-level abundance.
Transcript-level abundance was imported into gene-level abundance with the R package tximport.
Genes with low expression were identified and filtered out from further analysis if total read counts for a given gene across all samples was less than ten.
Variance stabilizing transformations (VST) was performed using the DESeq2 R package.
Differential gene expression analysis was also conducted using  DESeq2.
Gene Ontology (GO) Enrichment Analysis tool and the Gene Set Enrichment Analysis (GSEA) software were used for pathway analysis.
VST normalized and transformed expression values were used for heirarchical clustering and plotting of heatmaps.
Assembly: GRCm38.p4
Ensembl v86
Supplementary files format and content: Salmon quant.sf files contain transcirpt level abundances.

source_name: Tumor - breast cancer

growth_protocol: E0771 cells were thawed from a 0.5 million cell aliquot stored in -80, plated and passed the same time for every injection. Each mouse received 250,000 cells in 25% matrigel in 1 syringe. Bone marrow cells were isolated from the femurs and tibias of PKC delta wiltype or knockout mice age-matched females and were cultured in complete RPMI media (5 x 105 million cells/mL) supplemented with 50µM β-mercaptoethanol, 10mM HEPES, 1mM MEM non-essential amino acids (all Thermo Fisher). Bone-marrow-derived macrophages (BMDMs) were obtained after 6 days of culture with M-CSF (50ng/mL). BMDMs were left unstimulated or further polarized to an M1-like phenotype (M1 BMDMs) with IFNγ (20ng/mL) and LPS (100ng/mL) or to an M2-like phenotype (M2 BMDMs) with IL-4 (20ng/mL) for 24 h. Bone-marrow dendritic cells (DCs) were obtained after 7 days of culture with FLT3L (100ng/mL) then left unstimulated or stimulated (DCstim) with LPS (100ng/mL) and anti-mouse agonistic CD40 monoclonal antibody (5μg/mL) for 24 h. Immature myeloid cells (iMCs) were obtained after culture with GM-CSF (40ng/mL) and IL-6 (40ng/mL).

extract_protocol:
RNA was extracted from tumor tissue using RNeasy mini kit (QIAGEN, Germantown, MD). The integrity of RNA was assessed using Agilent Bioanalyzer and samples with RIN >5.0 were used.
mRNA-seq libraries for the Illumina platform were generated and sequenced at GENEWIZ using the Illumina HiSeq 2x150bp configuration following manufacturer’s protocol.

treatment_protocol: Female mice were fed  high fat diet (HFD, D12492i – 60% kcal derived from fat from  Research Diets Inc., New Brunswick, NJ) from age 8 -26 weeks of age. E0771-luciferase cells (gift from Korkaya, Augusta University) were injected orthotopically into 4th mammary gland (250K in 25% matrigel). Three days after cell injection, IgG2a or anti-PD-1 intraperitoneal (IP) injections occured every 3 days until sacrifice at 21 days.

tag: primary mouse cells and tumor cells

value: E0771-luciferase cells

tag: mouse strain

value: PKC delta knockout


title: scRNA-seq from nociceptor knockout colon


title: RNA-seq MV4:11 DMSO rep4


title: neural tube organoids, 42 hrs post Day 2, N2B27+RA, biol rep 2 [S9931]


title: seu-6, 1/2 MS, 15min, 14-day old whole seedlings, rep1


title: Col-0, 1/2 MS, 15min, 14-day old whole seedlings, rep1


title: TF_5_2_wt

city: Schlieren, Zurich

first: Ruslan

last: Rust

state: Zurich

address: Wagistrasse 12

country: Switzerland

institute: University of Zurich

data_processing:
none provided by the submitter
Supplementary files format and content: counts

source_name: brain

extract_protocol: none provided by the submitter

value: brain

value: Stroke


title: neural tube organoids, 42 hrs post Day 2, N2B27+RA, biol rep 1 [S9930]


title: TF_4_3_delayed


title: HCT116_Spt5(1-820)KOW4-5_SE3minusTMPplusDoxy AviChIP

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description: Chromatin IP of Avi-Spt5(1-820) KOW4-5_SE3

data_processing:
Adapters were trimmed using cutadapt version 2.3
Reads were aligned using Bowtie2 version 2.3.2
PCR duplicates were removed UMI-tools v0.5.4
Read coordinates were collapsed to a single base pair coordinate corresponding to the RNA 3’ end
Assembly: hg19/hg38
Supplementary files format and content: BigWig/bam

growth_protocol: McCoy's 10% FCS, +200 ug/ml hygromycin, +1mg/ml G418+15 ug/ml blasticidin

extract_protocol:
Cross-linked chromatin was sonicated with a Covaris ME220 ultrasonicator
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, SPRI bead purification of ~200bp fragments, and amplification (15-18 cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

treatment_protocol: Avi-Spt5(1-820)KOW4-5_SE3 expression was induced with 2ug/ml doxycycline for 24 hrs

tag: growth conditions

value: McCoy's 10% FCS, +hygromycin, +G418-TMP

tag: antibody

value: Rabbit anti-avi-tag (GenScript A00674)


title: neural tube organoids, 42 hrs post Day 2, N2B27, biol rep 3 [S9935]

tag: treatment condition


title: HCT116_Spt5(1-820)KOW4-5_SA3minusTMPplusDoxy AviChIP

description: Chromatin IP of Avi-Spt5(1-820) KOW4-5_SA3

treatment_protocol: Avi-Spt5(1-820)KOW4-5_SA3 expression was induced with 2ug/ml doxycycline for 24 hrs


title: neural tube organoids, 42 hrs post Day 2, N2B27, biol rep 2 [S9934]

tag: time point


title: TF_5_5_delayed

tag: tissue


title: TF_5_3_wt


title: T-7869-WT

description: E0771-luciferase cells from PKC delta wildtype

value: PKC delta wiltype


title: neural tube organoids, 30 hrs post Day 2, N2B27+RA, biol rep 1 [S9926]

tag: cell type

value: 30 hrs post Day 2


title: TF_3_4_delayed


title: TF_3_5_delayed


title: T-7862-KO


title: HCT116_Spt5(1-820)CTR1_TE7_KOW4-5_SE3 AviChIP

description: Chromatin IP of Avi-Spt5(1-820) CTR1_TE7_KOW4-5_SE3

source_name: HCT116 Spt5-HA-dhfr pCW57AviSpt5(1-820)

treatment_protocol: Avi-Spt5(1-820) expression was induced with 2ug/ml doxycycline for 24 hrs


title: T-7963-KO


title: TF_3_3_delayed


title: T-7807-WT


title: TF_2_1_acute


title: HCT116_Spt5(1-820)CTR1_TE7minusTMPplusDoxy_pol IIChIP

description: Chromatin IP of RNA pol II

treatment_protocol: Avi-Spt5(1-820) CTR1_TE7 expression was induced with 2ug/ml doxycycline for 24 hrs

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)


title: HCT116_Spt5(1-820)CTR1_WTminusTMPplusDoxy_pol IIChIP

description: Chromatin IP of RNA pol II


title: HCT116_Spt5degron_minusTMP_pol IIChIP_DRB

description: Chromatin IP of RNA pol II

source_name: HCT116 Spt5-HA-dhfr

growth_protocol: McCoy's 10% FCS, +200 ug/ml hygromycin, +1mg/ml G418

value: McCoy's 10% FCS, +hygromycin, +G418-TMP+DRB


title: neural tube organoids, 30 hrs post Day 2, N2B27, biol rep 3 [S9929]

source_name: neural tube organoid

value: neural tube organoid


title: T-166-WT


title: TF_1_5_acute


title: Imm2_5Wt

value: Ctrl


title: T-7870-KO


title: neural tube organoids, 42 hrs post Day 2, N2B27, biol rep 1 [S9933]

value: 42 hrs post Day 2


title: HCT116_Spt5degron_minusTMP_pol IIChIP_2

description: Chromatin IP of RNA pol II


title: neural tube organoids, 30 hrs post Day 2, N2B27+RA, biol rep 2 [S10132]

value: mouse embryonic stem cell


title: T-121-WT


title: T-120-KO


title: Imm2_4Wt

value: WT


title: T-162-WT


title: neural tube organoids, 18 hrs post Day 2, N2B27+RA, biol rep 3 [S9920]

value: 3D neuroepithelial differentiation in Matrigel

value: 18 hrs post Day 2


title: neural tube organoids, 30 hrs post Day 2, N2B27, biol rep 2 [S9928]


title: neural tube organoids, 30 hrs post Day 2, N2B27, biol rep 1 [S9927]


title: T-119-WT

value: E0771-luciferase cells


title: HCT116_Spt5degron_minusTMP_pol IIChIP_1

description: Chromatin IP of RNA pol II

treatment_protocol: Spt5 degron depletion by trimethoprim withdrawal for 12hr?


title: Imm2_4Rag

value: RAG


title: neural tube organoids, 18 hrs post Day 2, N2B27+RA, biol rep 2 [S9919]


title: neural tube organoids, 30 hrs post Day 2, N2B27+RA, biol rep 3 [S10133]


title: HCT116_Spt5degron_plusTMP_pol IIChIP_2

description: Chromatin IP of RNA pol II

growth_protocol: McCoy's 10% FCS, +200 ug/ml hygromycin, +1mg/ml G418+10 uM trimethoprim

value: McCoy's 10% FCS, +hygromycin, +G418+TMP


title: HCT116_Spt5degron_plusTMP_pol IIChIP_1

description: Chromatin IP of RNA pol II

treatment_protocol: control cells


title: MDSC-WT3

description: Bone marrow cells + GM-CSF+ IL-6 from PKC delta wiltype

source_name: Bone marrow

value: Bone marrow cells + GM-CSF+ IL-6


title: neural tube organoids, 18 hrs post Day 2, N2B27+RA, biol rep 1 [S9918]


title: HCT116_Spt5degron_minusTMP_Spt5ChIP

description: Chromatin IP of  Spt5

value: McCoy's 10% FCS, +hygromycin, +G418-TMP

value: Rabbit anti-Spt5 (aa703-1087)(Glover-Cutter et al NSMB 15:71, 2008)


title: Imm2_4NSG

value: brain

value: NSG


title: HCT116_Spt5degron_plusTMP_pol IIChIP_DRB

description: Chromatin IP of RNA pol II

value: McCoy's 10% FCS, +hygromycin, +G418+TMP+DRB

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)


title: MDSC-WT2

value: PKC delta wiltype


title: HCT116_Spt5degron_plusTMP_Spt5ChIP

description: Chromatin IP of  Spt5


title: neural tube organoids, 18 hrs post Day 2, N2B27, biol rep 3 [S9923]

value: neural tube organoid


title: Imm2_5m_1

value: Stroke


title: MDSC-KO3

description: Bone marrow cells + GM-CSF+ IL-6 from PKC delta knockout

value: PKC delta knockout


title: Imm2_4m_3


title: neural tube organoids, 18 hrs post Day 2, N2B27, biol rep 2 [S9922]

value: mouse embryonic stem cell

value: WT


title: Imm2_4f_1


title: neural tube organoids, 18 hrs post Day 2, N2B27, biol rep 1 [S9921]

value: 3D neuroepithelial differentiation in Matrigel

value: 18 hrs post Day 2


title: HCT116_Spt5(1-820)CTR1_TA7minusTMPplusDoxy_AviChIP

description: Chromatin IP of Avi-Spt5(1-820)CTR1_TA7

treatment_protocol: Avi-Spt5(1-820) CTR1_TA7 expression was induced with 2ug/ml doxycycline for 24 hrs

value: McCoy's 10% FCS, +hygromycin, +G418, +blasticidin, +doxycycline

value: Rabbit anti-avi-tag (GenScript A00674)


title: Imm2_3Wt

value: Ctrl


title: MDSC-KO2

value: Bone marrow cells + GM-CSF+ IL-6


title: MDSC-KO1


title: HCT116_Spt5(1-820)CTR1_WTminusTMPplusDoxy_AviChIP

description: Chromatin IP of Avi-Spt5(1-820)WT


title: mRNA B Zfp36l1 sKO 1

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

data_processing:
Quality of all libraries was checked by FastQC (v0.11.8) and FastqScreen (v0.13.0)
Reads were trimmed for poor quality and adaptor sequences using Trim Galore (0.5.0 dev) with default parameters, then mapped to the mouse GRCm38 genome build using Hisat2 (--dta --sp 1000,1000, including known-splicesite-infile from the GRCm38 v90 annotation release).
Mapped reads were imported into Seqmonk (v1.44.0), and raw read counts were generated for the GRCm38 v90 annotation release over mRNA features with merged isoforms, assuming paired end, unstranded libraries
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file containing gene names together with raw read counts generated over mRNA features using Seqmonk, for each sample

source_name: Spleen, peripheral and mesenteric LN

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen).
Libraries were generated using the RNA TruSeq V2 mRNA kit (Illumina), according to manufacturer's instructions

treatment_protocol: Naïve CD4+ T cells were isolated from pooled peripheral and mesenteric lymph nodes and spleen, with two mice per replicate, using the Miltenyi Biotech CD4+ CD62L+ T Cell Isolation Kit. T cells were cultured in RPMI1640 containing 10% FCS RPMI media with 10% FCS, 50 µM β-mercaptoethanol, 2mM Glutamine, penicillin/streptomycin and activated by crosslinking CD3ε on 2C11 monoclonal antibody coated tissue culture wells (10µg/ml), together with the 37.51 anti-CD28 monoclonal antibody as a hybridoma supernatant or purified antibody at 10µg/ml.

value: Spleen, peripheral and mesenteric LN

value: CD4+ T cells

tag: strain background

value: Zfp36l1fl/fl CD2-cre sKO

value: 9-11 weeks

value: Male


title: mRNA B Zfp36l1 sKO 2

value: 9 weeks

tag: Sex


title: Imm2_3NSG

value: brain

value: NSG


title: M2-WT3

description: Bone marrow macrophages polarized with IL-4 from PKC delta wiltype

value: PKC delta wiltype


title: HCT116_Spt5(1-820)CTR1_TE7minusTMPplusDoxy_AviChIP

description: Chromatin IP of Avi-Spt5(1-820)CTR1_TE7


title: mRNA B Ctrl 3

value: Zfp36l1fl/fl control

value: Female


title: Imm2_2Rag

value: RAG


title: M2-WT2

value: Bone marrow macrophages polarized with IL-4


title: Imm2_2NSG


title: Imm2_4m_4

value: Stroke


title: mRNA B Ctrl 2


title: HCT116_NelfAdegron_minusBNN

description: anti-pol II mNET-seq

data_processing:
Adapters were trimmed using cutadapt version 2.3
Reads were aligned using Bowtie2 version 2.3.2
PCR duplicates were removed UMI-tools v0.5.4
Read coordinates were collapsed to a single base pair coordinate corresponding to the RNA 3’ end
Assembly: hg19/hg38
Supplementary files format and content: BigWig/bam
Library strategy: anti-pol II mNET-seq

source_name: HCT116 NELFA-HA-FKBP

extract_protocol:
Pol II-associated nascent RNA was isolated by IP
10-20ng of RNA was used with the QIAseq miRNA  kit (#331565)

value: McCoy's 10% FCS, +hygromycin, +G418

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)


title: MDSC-WT1

value: Bone marrow cells + GM-CSF+ IL-6


title: HCT116_Spt6degron_minusTMP_3

description: anti-pol II mNET-seq

source_name: HCT116 Spt6-HA-dhfr


title: Imm2_2m_5

value: WT


title: M2-WT1


title: mRNA A Zfp36 sKO 3

value: Spleen, peripheral and mesenteric LN

value: CD4+ T cells

value: Zfp36fl/fl CD4-cre sKO

value: 17-19 weeks

value: pooled male and female


title: Imm2_2m_3

value: brain


title: M2-KO2

description: Bone marrow macrophages polarized with IL-4 from PKC delta knockout

value: PKC delta knockout


title: HCT116_Spt6degron_plusTMP_3

description: anti-pol II mNET-seq


title: mRNA B Ctrl 1

value: 11 weeks


title: HCT116_Spt6degron_plusTMP_2

description: anti-pol II mNET-seq


title: HCT116_Spt6degron_minusTMP_2

description: anti-pol II mNET-seq


title: mRNA A Zfp36 sKO 1

value: 19 weeks


title: HCT116_Spt6degron_minusTMP_1

description: anti-pol II mNET-seq


title: HCT116_NelfAdegron_plusBNN

description: anti-pol II mNET-seq


title: Imm2_1NSG

value: NSG

value: Ctrl


title: M2-KO3

value: Bone marrow macrophages polarized with IL-4


title: mRNA A Ctrl 2

value: Zfp36fl/fl control

value: Female


title: HCT116_Spt6degron_plusTMP_1

description: anti-pol II mNET-seq

value: McCoy's 10% FCS, +hygromycin, +G418

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)


title: mRNA A Zfp36 sKO 2

value: Male


title: Imm2_1m_3

value: Stroke


title: mRNA A Ctrl 1

value: Spleen, peripheral and mesenteric LN

value: CD4+ T cells


title: HCT116_Spt5(1-820)CTR1_WTplusDoxyplusDRBminusTMP_2

description: anti-pol II mNET-seq

value: McCoy's 10% FCS, +hygromycin, +G418, +blasticidin, +doxycycline+DRB


title: Imm2_1Wt

value: WT


title: MIHSCF_18

city: Qingdao

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

data_processing:
library strategy: 16S rDNA seq
Illumina HiSeq software used for basecalling.
Take the method of removing low quality by window, the specific operation is as follows: set a window of 25 bp, if the average quality value of the window is less than 20, the back-end bases will be truncated from the window; the read length after truncation is lower than the original read length For 75%, remove the entire sequence.
Remove linker contamination of reads (default adapter sequence and read sequence have an overlap of 15 bp, set to 15 bp, and allow the number of mismatches to be 3);
Remove reads containing N;Remove low-complexity reads (default reads with continuous base length ≥10 are low-complexity reads) finally, get the Cleandata
Splice the reads into tags through the overlap relationship between the reads; cluster the tags into OTUs and compare them with the database, and annotate species; based on the OTU and annotation results, perform sample species complexity analysis, analysis of species differences between groups, and association analysis. Model prediction, etc.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression

source_name: small intestinal

extract_protocol:
small intestinal were removed, than quikly removed the contents and frozen in the luquid nitrogen, and extract the total DNA to analyze the microbial diversity
16S rDNA libraries were prepared for sequencing using standard IlluminaHiSeq protocols

tag: strain

value: ICR

value: small intestinal

value: 10 weeks

value: High fat diet & STZ+control-FMT


title: M1-WT3

description: Bone marrow macrophages polarized with LPS+IFNγ from PKC delta wiltype

value: PKC delta wiltype


title: Imm2_1Rag

value: brain

tag: genotype

value: RAG

value: Ctrl


title: M1-WT2

value: Bone marrow macrophages polarized with LPS+IFNγ

tag: treatment


title: M1-KO3

description: Bone marrow macrophages polarized with LPS+IFNγ from PKC delta knockout

value: PKC delta knockout


title: M1-WT1


title: Imm2_1f_2

value: NSG


title: DCstim-WT3

description: Bone marrow dendritic cells stimulated with LPS+ agonistic αCD40 mAb from PKC delta wiltype


title: MIHSCF_20


title: HCT116_Spt5degron_plusTMPplusDRB

description: anti-pol II mNET-seq

tag: cell line

value: McCoy's 10% FCS, +hygromycin, +G418, +DRB

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)


title: MIHSCF_11


title: HCT116_Spt5(1-820)CTR1_WTplusDoxyplusDRBminusTMP_1

description: anti-pol II mNET-seq


title: M1-KO2


title: M1-KO1


title: S16_M_L

city: BOULDER

first: Winona

last: Booher

address: 5441 White place

department: Institute for Behavioral Genetics

institute: University of Colorado Boulder

data_processing:
Alignment to the reference genome (hisat2; v2.2.1).
Gene-level estimates of aundance were derived using RNA-seq by Expectation-Maximization (RSEM; v1.2.31).
RSEM output filtered for genes with an expected read count of zero across all samples and those genes were removed.
Raw reads were normalized and quantified (DESeq2; v1.30.1).
Identified strain effects (dependent or independent of sex) on gene expression by performing a likelihood ratio test (LRT) using DESeq2 (v1.30.1)
Assembly: mm10
Supplementary files format and content: Single csv file that includes a matrix of the expression abundance of 31,960 genes X 16 samples. Values are the DESeq2 normalized output for each full transcript (transcripts with 0 counts across all 16 samples were removed).

source_name: Brain

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini kits. Quantity and quality were determined using a NanoDrop™ spectrophotometer and an Agilent 2100 BioAnalyzer. Samples were enriched for poly-A RNA using the Invitrogen Dynabeads mRNA Purification kit.
Paired-end (2x150, expected size of 300 bp), strand-specific, cluster-ready libraries were prepared from the poly-A enriched RNA using the NEBNext Ultra II RNA Library Prep kit.

treatment_protocol: Mice were euthanized at postnatal day 70 and hippocampi were collected immediately.

tag: strain name

value: Low Activity

value: Male

value: postnatal day 70

value: Hippocampi


title: DCstim-WT2

value: Bone marrow dendritic cells stimulated with LPS+ agonistic αCD40 mAb


title: MIHSCF_13

value: ICR

value: small intestinal

tag: age


title: HCT116_Spt5degron_plusTMPplusDRB_2

description: anti-pol II mNET-seq


title: S15_M_L


title: HCT116_Spt5degron_plusTMPplusDRB_1

description: anti-pol II mNET-seq


title: DCstim-WT1


title: MIHSCF_5

value: 10 weeks

value: High fat diet & STZ+control-FMT


title: S12_F_L

value: Female


title: MIHSCF_10


title: Imm2_1f_1

value: brain

value: Stroke


title: Dcstim-KO2

description: Bone marrow dendritic cells stimulated with LPS+ agonistic αCD40 mAb from PKC delta knockout


title: MIHSCF_7


title: S11_F_L


title: HCT116_Spt5(1-820)CTR1_WTminusTMPplusDoxy_DRB15min

description: anti-pol II mNET-seq

value: McCoy's 10% FCS, +hygromycin, +G418, +blasticidin, +doxycycline+DRB


title: Dcstim-KO3

value: PKC delta knockout


title: MIHSCF_4


title: HCT116_Spt5(1-820)KOW4-5_SE3plusDoxyminusTMP_1

description: anti-pol II mNET-seq

value: McCoy's 10% FCS, +hygromycin, +G418, +blasticidin, +doxycycline


title: HCT116_Spt5(1-820)KOW4-5_SA3plusDoxyminusTMP_2

description: anti-pol II mNET-seq


title: MIHSCF_1


title: Dcstim-KO1


title: DC-WT3

description: Bone marrow dendritic cells from PKC delta wiltype

value: Bone marrow dendritic cells

value: PKC delta wiltype


title: S14_M_L

value: Low Activity


title: DC-WT2


title: HCT116_Spt5(1-820)KOW4-5_SA3plusDoxyminusTMP_1

description: anti-pol II mNET-seq

extract_protocol:
SA3
10-20ng of RNA was used with the QIAseq miRNA  kit (#331565)

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)


title: S9_F_L

value: postnatal day 70


title: MIHSCF_2


title: S13_M_L

value: Male

value: Hippocampi


title: HCT116_Spt5(1-820)CTR1_WTplusTMPminusDoxy_DRB15min

description: anti-pol II mNET-seq


title: HCT116_Spt5degron_Spt5(1-820)CTR1_TE7_KOW4-5_SE3

description: anti-pol II mNET-seq

source_name: HCT116 Spt5-HA-dhfr Spt5(1-820)KOW4-5_SE3 CTR1_TE7

treatment_protocol: Avi-Spt5(1-820) KOW4-5SE3 CTR1_TE7 expression was induced with 2ug/ml doxycycline for 24 hrs


title: MIHSAF_20

value: ICR

value: High fat diet & STZ+AOS10mg/kg-FMT


title: HCT116_Spt5(1-820)KOW4-5_SE3plusDoxyminusTMP_2

description: anti-pol II mNET-seq


title: DC-WT1


title: S8_M_H

value: High Activity


title: S7_M_H


title: HCT116_Spt5(1-820)CTR1_TE7minusTMPplusDoxy_2

description: anti-pol II mNET-seq


title: DC-KO3

description: Bone marrow dendritic cells from PKC delta knockout


title: HCT116_Spt5(1-820)CTR1_TE7minusTMPplusDoxy_1

description: anti-pol II mNET-seq


title: HCT116_Spt5(1-820)CTR1_TA7minusTMPplusDoxy_2

description: anti-pol II mNET-seq


title: S6_M_H


title: MIHSAF_18

value: small intestinal

value: 10 weeks


title: MIHSAF_17


title: DC-KO2


title: S5_M_H


title: MIHSAF_15


title: DC-KO1


title: S4_F_H

value: Female


title: MIHSAF_14


title: BMDM-WT3

description: Bone marrow macrophages from PKC delta wiltype

value: Bone marrow macrophages


title: HCT116_Spt5(1-820)CTR1_TA7minusTMPplusDoxy_1

description: anti-pol II mNET-seq


title: S10_F_L


title: MIHSAF_7


title: BMDM-WT2


title: S2_F_H


title: MIHSAF_6


title: S1_F_H


title: HCT116_Spt5(1-820)CTR1_WTminusTMPplusDoxy_1

description: anti-pol II mNET-seq


title: BMDM-WT1


title: HCT116_Spt5degron_minusTMP_2

description: anti-pol II mNET-seq

value: McCoy's 10% FCS, +hygromycin, +G418


title: BMDM-KO3

description: Bone marrow macrophages from PKC delta knockout

value: PKC delta knockout


title: MIHSAF_3


title: Spt5KD_F_2

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

data_processing:
The reference genome (GRCm38.dna.primary_assembly.fa) and annotation files (GRCm38.101.gtf) were modified by concatenating the mouse genome with ERCC (source: Thermofisher) and the construct ‘pGEMHE-mCherry-mTrim21’ fasta and gtf files, respectively. The endogenous Trim21 locus was masked using bedtools (version 2.29.0).
The modified reference fasta file was used to prepare STAR index files using rsem-prepare-reference (rsem version 1.3.3). Paired-end reads were aligned using STAR (version 2.7.6a) with parameters --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate.
Downstream analysis was carried out on read counts per gene calculated by STAR.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab files of read counts per gene

source_name: 2-cell embryo

extract_protocol:
Zygotes were collected at 17h post hCG injection and cultured with or without BAY1251152 (Cdk9in or Noinject), or subjected to Trim-Away for SPT5 (Spt5KD), NELF-E (NelfEKD) or IgG. Embryos were cultured until 46h post hCG, washed in PBS and flash-frozen in lysis buffer.
Libraries for single embryo RNA-seq were prepared with Smart-Seq2 protocol (PMID: 24385147). The quality of the libraries was assessed using a 2100 Bioanalyzer (Agilent). Samples were paired-end sequenced at PE150 on an Illumina NovaSeq 6000 platform.

tag: protocol

value: RNA-seq

value: Spt5 Trim-Away


title: MIHSAF_4


title: HCT116_Spt5degron_plusTMP_2

description: anti-pol II mNET-seq


title: BMDM-KO1

tag: primary mouse cells and tumor cells


title: MIHSA10_10

value: High fat diet & STZ+AOS10mg/kg


title: BMDM-KO2

tag: mouse strain


title: HCT116_Spt5degron_plusTMP_1

description: anti-pol II mNET-seq

tag: growth conditions


title: MIHSAF_1


title: Spt5KD_E_3


title: Spt5KD_F_1


title: Spt5KD_E_2


title: R597-9-245-T27

city: Houston

first: Khandan

last: Keyomarsi

state: TX

address: 1515 Holcombe Blvd

department: Experimental Radiation Onc

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Paired-end reads in fastq format were initially checked for read quality using FastQC 0.11.8
Sequence reads were mapped to the mouse reference genome (Gencode GRCm38) using TopHat 2.1.1 (parameter: --library-type=fr-firststrand)
The BAM file with mapped reads for each sample was sorted and then used as an input for HTSeq 0.11.0 in order to generate read count data on gene level (parameters: -s reverse  -m union)
Assembly: GRCm38
Supplementary files format and content: raw read count data generated by htseq-count 0.11.0 for each sample

source_name: mammary tumors

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq stranded protocol.

value: mammary tumors

value: C57BL/6J X BALB/cJ F1 hybrid

tag: gender


title: MIHSA10_9


title: S3_F_H

value: postnatal day 70


title: HCT116_Spt5degron_minusTMP_1

description: anti-pol II mNET-seq

tag: antibody

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)


title: MIHSA10_8


title: HEK293_AvitagRpb1WT_1

description: anti-pol II mNET-seq

source_name: HEK293 Flp-in T-REx pcDNA5 Avitag Rpb1 WT

growth_protocol: DMEM 10% FCS, +200 ug/ml hygromycin, +6.5 ug/ml blasticidin, +pen/strep

treatment_protocol: Avi Rpb1 expression was induced with 2ug/ml doxycycline for 24 hrs, followed by treatment with 2 mM DMOG for 16 hrs

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline

value: Rabbit anti-avi-tag (GenScript A00674)


title: R597-8-245-T24


title: HEK293_AvitagRpb1WT_2

description: anti-pol II mNET-seq


title: HCT116_Spt5(1-820)CTR1_WTminusTMPplusDoxy_2

description: anti-pol II mNET-seq

value: McCoy's 10% FCS, +hygromycin, +G418, +blasticidin, +doxycycline


title: MIHSA10_7

value: ICR


title: Spt5KD_D_4


title: R597-6-245-T20


title: MIHSA10_6

value: small intestinal


title: Osteoclast GIP Donor 8

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

data_processing:
RNA-seq reads were aligned to GRCh38 genome using STAR aligner and default settings.
Gene expression was quantified using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with the options -count exons -condenseGenes -noCondensing -noadj. Normalization and differential expression analysis was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550) comparing GIP treated cells to control ones (pval_gip_vs_ctr; logFC_gip_vs_ctr).
Assembly: GRCh38
Supplementary files format and content: Txt file containing raw counts, DEseq2 derived normalized and rlog transformed counts as well as p values and logFC for GIP treatment versus ctrl

source_name: Osteoclast day 10 in vitro Donor 8

growth_protocol: Primary human osteoclasts were differentiated from human CD14+ monocytes isolated from buffy coats obtained from anonymous blood donations as previously described (Herrild D M H, et al. 2015. Bone Research 3: 15032) . Monocytes were seeded in T75 cell culture flasks (5 x 106 cells/flask) in α-minimal essential medium (αMEM, Gibco) with 10% fetal bovine serum (FBS, Gibco), 1% penicillin/streptomycin (Gibco) and stimulated with 25 ng/mL macrophage colony-stimulating factor (MCSF, R&D Systems). After two days, media was replaced with fresh media containing MCSF and receptor activator of nuclear κB (RANKL) (25 ng/mL each, R&D Systems), and media refreshed every 2-3 days thereafter until a total of seven days stimulation with RANKL. Microscopic validation of the presence of multinucleated cells was performed before cells were used for experiments. All cells were maintained at 37oC, 5% CO2.

extract_protocol:
RNA was extracted from cultured cells using Trizol combined with Econo Spin columns (Epoch Life Sciences).
RNA-seq was performed according to manufacturer’s instructions (TruSeq 2, Illumina) using 1 µg RNA for preparation of cDNA libraries.

treatment_protocol: At day 10 of differentiation, media with or without 10 nM GIP was added for 4 hours after which cells were harvested using TRIzol.

value: Osteoclast day 10 in vitro

value: GIP 4hrs (10nM)


title: Osteoclast GIP Donor 7

source_name: Osteoclast day 10 in vitro Donor 7


title: R597-5-245-T17

value: Female


title: Spt5KD_D_3


title: Spt5KD_D_2


title: Osteoclast GIP Donor 6

source_name: Osteoclast day 10 in vitro Donor 6


title: MIHSA10_5

value: 10 weeks


title: R597-4-245-T14


title: MIHSA10_4


title: Spt5KD_D_1


title: R597-3-245-T5


title: Spt5KD_C_3


title: Osteoclast GIP Donor 5

source_name: Osteoclast day 10 in vitro Donor 5


title: R597-2-245-T4


title: Spt5KD_E_1


title: MIHSA10_3


title: R597-7-245-T21


title: MIHSA10_1


title: Spt5KD_C_2


title: MIHSA10_2


title: MIHS_19

value: High fat diet & STZ


title: Osteoclast GIP Donor 4

source_name: Osteoclast day 10 in vitro Donor 4


title: Spt5KD_C_1

value: RNA-seq


title: R597-1-245-T1


title: Osteoclast GIP Donor 3

source_name: Osteoclast day 10 in vitro Donor 3


title: Osteoclast GIP Donor 1

source_name: Osteoclast day 10 in vitro Donor 1


title: Osteoclast GIP Donor 2

source_name: Osteoclast day 10 in vitro Donor 2


title: Spt5KD_B_3

value: Spt5 Trim-Away


title: Osteoclast ctrl Donor 8

value: ctrl


title: MIHS_18


title: Spt5KD_B_1


title: MIHS_17


title: kidney, mut3

city: Vienna

first: Irina

last: Poverennaya

state: Österreich

address: Spitalgasse 4 / Medizinishe Universitat Wien, Zentrum fur Hirnforschung

department: Neuroimmunology

institute: Medical University of Vienna

data_processing:
Raw files were processed, mapped, and counted to the Cell Ranger mm10-2020-A genome and its corresponding annotation by Cell Ranger version 4.0.0.
The output count matrices for each sample were further processed with the Seurat package pipeline (v.3.2.2.9001)
Assembly: Cell Ranger mm10-2020-A genome
Supplementary files format and content: h5datasets with raw gene expression counts filtered by CellRanger; merged count matrix, its annotation and UMAP coordinates

source_name: kidney

extract_protocol:
Control and mutant littermate mice (both male and female) were used for single-cell transcriptomic and morphological analysis of the adult kidney. Mice were anesthetized with isoflurane overdose and transcardially perfused with PBS. Kidneys were dissected out. One kidney per mouse was fixed in 4% PFA at 4°C overnight to be used for morphological analysis (see section: Adult kidney preparation for micro-computed tomography). The second kidney was chopped in small pieces and digested with 2 mg/ml collagenase P for 10 min at 37°C, an equal volume of 0,10% trypsin/EDTA was added and tissue was digested for an additional 10 min at 37°C. Following enzymatic digestion, tissue was triturated using a wide-bore pipette tip and clumps were mechanically dissociated using a 100 µm mesh and a syringe plunger.
Cell suspensions were washed with PBS/10% FBS twice and resuspended at a concentration of 1,000 cells/µl for processing with a 10X controller. 10x Genomics Chromium Single Cell 3ʹ protocol for Reagent Kits v3 was used for library preparation.

value: kidney

value: mutant

value: pooled male and female


title: kidney, wt3

value: wildtype


title: kidney, wtF

value: female


title: Osteoclast ctrl Donor 7


title: MIHS_16


title: kidney, mutM

value: male


title: Osteoclast ctrl Donor 6


title: MIHS_15


title: Spt5KD_A_2


title: kidney, mutF


title: Osteoclast ctrl Donor 5


title: MIHS_14


title: AstroCCM3KO_04

city: La Jolla

first: Miguel

middle: Alejandro

last: Lopez-Ramirez

state: Ca

address: 9500 Gilman Dr

department: Medicine

institute: University of California, San Diego

description:
Ribosome bound RNA
Ribo-Seq

data_processing:
Data was processed using the systempipeR workflow.
RNA reads were aligned to the GRCm39 genome assembly using hisat2.
Differential gene expression was calculated using EdgeR.
Assembly: GRCm39 release 104

growth_protocol: NA: cells isolated from tissue samples.

extract_protocol:
Brain tissue was harvested from animals and either homogenized in TRIzol solution for RNAseq analysis, Brain microvascular endothelial cells were isolated, or Astrocyte tagged ribosomes were isolated as previously described (PMID: 24810037). RNA from brain tissue, brain microvascular endothelial cells, or ribisome purified RNA from Astrocytes was then purified using TRIzol according to the manufacturer’s instructions.
Following isolation, RNA quality was assessed using an Agilent Tapestation 4200. Only samples with with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries using the Illumina Stranded mRNA Prep according to the manufacturer’s insturctions.

treatment_protocol: NA: Differential expression resulted from genetically modified animals in the absence of treatment.

value: Brain

value: Male

value: Astrocyte


title: MIHS_11

value: ICR

value: small intestinal


title: AstroCCM3KO_03

description:
Ribosome bound RNA
Ribo-Seq


title: Osteoclast ctrl Donor 4

value: Osteoclast day 10 in vitro


title: Osteoclast ctrl Donor 3


title: Spt5KD_A_1


title: Noinject_C_3

value: No injection


title: Noinject_C_2


title: Spt5KD_B_2


title: AstroCCM3Flox_03

description:
Ribosome bound RNA
Ribo-Seq


title: Noinject_C_1


title: AstroCCM3KO_02

description:
Ribosome bound RNA
Ribo-Seq


title: Osteoclast ctrl Donor 1


title: MIHS_9

value: 10 weeks

value: High fat diet & STZ


title: MIHS_7


title: MIHS_2


title: Spt5KD_A_3

value: RNA-seq

value: Spt5 Trim-Away


title: AstroCCM3Flox_02

description:
Ribosome bound RNA
Ribo-Seq


title: Noinject_B_3


title: BM_NK

city: Leiden

first: Janine

last: Melsen

address: Albinusdreef 2

department: Pediatrics

institute: LUMC

data_processing:
Cell ranger count  (software v3.0.2, 10x Genomics,) was used to align the sequences to the human genome (hg38) and the antibodies. The force cells =7000 argument was used.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: cell-associated barcodes, features.tsv.gz: genes and proteins, matrix.mtx.gz: UMI count matrix, filtered_feature_bc_matrix.h5: compressed format UMI count matrix of cell-associated barcodes

source_name: bone marrow

growth_protocol: Residual fresh bone marrow from one healthy donor was used for single-cell RNA sequencing

extract_protocol:
The NK-enriched cell suspension was loaded on a Chromium Single Cell Chip (10x Genomics, Pleasanton, CA, USA) to encapsulate 10,000 cells with barcoded beads. Library preparation of the mRNA and cell surface bounded antibodies was performed by using the Single Cell 3’ solution v3 (10x Genomics), according to manufacturer’s instructions.
The libraries were pooled, and sequencing was performed on one lane of the Illumina NovaSeq 6000 system (Illumina, San Diego, CA, USA).

treatment_protocol: The bone marrow aspirate was collected in an EDTA tube. Mononuclear cells were isolated by Ficoll-Isopaque (Leiden University Medical Center Pharmacy, Leiden, NL) density gradient centrifugation and NK and progenitor cells were enriched using the Mojosort untouched NK cell isolation kit (Biolegend, San Diego, CA, USA) according to manufacturers’ instructions. Anti-CD34 was not included in this kit, enabling enrichment of NK progenitor cells. Enriched cells were incubated with Fc block (eBioscience, San Diego, CA USA), after which cells were labeled with 1µg/ml oligonucleotide conjugated antibodies specific for CD34,  CD117, CD56 and CXCR6 (TotalSeq-A, Biolegend, Table S2).

value: bone marrow

value: NK and progenitor cells

tag: method

value: negatively enriched (magnetically)


title: Noinject_B_2


title: MIcon_12

tag: tissue

value: control


title: MIcon_11


title: MBECsCCM3KO_04

description:
mRNA
RNA-Seq

tag: cell type

value: Brain Microvascular Endothelial


title: Noinject_B_1


title: hAECs, Donor 4 - IL17+Dexamethasone

city: Groningen

first: Reinoud

last: Gosens

address: Antonius Deusinglaan 1

department: Molecular Pharmacology

institute: University of Groningen

data_processing:
Library preparation was checked by calculating ribosomal (and globin) content.
Checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw dataset was determined using quality control tools (FstQC v0.34 and FastQA).
Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic v0.30.
To align the reads of each sample, the  human reference GRCh37.75 was used. Data was analyzed with DESEQ2 in R studio v1.4.1106
Assembly: GRCh37.75
Supplementary files format and content: Count files

source_name: primary human airway epithelial cells (hAECs)

growth_protocol: For experiments in ALI cultured cells, cells from passage 1-2 were grown submerged on collagen-coated Transwell inserts until confluence, after which they were cultured at an air-liquid interface (ALI) and differentiated for two weeks in B/D medium (1:1), which is a mixture of DMEM [Gibco] and bronchial epithelial growth medium (BEGM) [Lonza], supplemented with 0.4% [w/v] bovine pituitary extract [BPE], 0.5 ng/ml epidermal growth factor [EGF], 5 µg/ml insulin, 10 µg/ml transferrin, 1 µM hydrocortisone, 6.5 ng/ml T3, 0.5 µg/ml epinephrine [all from Lonza], 15 ng/ml retinoic acid [Sigma chemical] 1.5 µg/ml bovine serum albumin [Sigma chemical] 0.5 mM sodium pyruvate [Gibco], 20 U/ml penicillin and 20 µg/ml streptomycin [Gibco]52. Cells were exposed to 10 nM of Dexamethasone (Sigma-aldrich D4902), 10 ng/ml of recombinant human IL-17A (R&D 7955-IL-025/CF), or the combination of IL-17A and Dexamethasone that was added to the basal medium during two weeks of differentiation. ALI cultures were maintained for 14 days at 37°C in a humidified atmosphere of 5% CO2. Medium and stimuli were refreshed three times per week. The apical side of the epithelial cells was washed with phosphate buffer saline (PBS) at the same time. After two weeks, cells were collected for RNA analysis or used for barrier function experiments, mucus was collected for volume measurement, and basal medium was collected for cytokine analysis.

extract_protocol:
Total RNA was isolated using the RNA purification kit NucleoSpin RNA (Macherey-Nagel 740955, Germany) according to the manufacturer’s guide. Cells were lysed by adding a mixture of buffer RA1 and dithiothreitol (Sigma-Aldrich, 3483-12-3). The yield of the isolated RNA was then measured using the NanoDrop 1000 spectrophotometer.
RNA-seq was conducted using the Illumina NovaSeq 6000 sequencer by GenomeScan (https://www.genomescan.nl/). The procedure included data quality control, adapter trimming, alignment of short reads and feature counting. Library preparation was checked by calculating ribosomal (and globin) content. Checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw dataset was determined using quality control tools (FstQC v0.34 and FastQA). Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic v0.30. To align the reads of each sample, the human reference GRCh37.75was used. Data was analyzed with DESEQ2 in R studio v1.4.1106.

tag: individual

value: DonorID 4

tag: dexamethasone

value: Yes


title: hAECs, Donor 4 - Dexamethasone

value: primary human airway epithelial cells (hAECs)

value: No


title: MIcon_10

first: Yong

source_name: small intestinal

tag: strain

value: ICR


title: Osteoclast ctrl Donor 2

value: ctrl


title: Noinject_A_4


title: MBECsCCM3KO_02

description:
mRNA
RNA-Seq

source_name: Brain

value: Brain

tag: Sex

value: Male

tag: genotype


title: Noinject_A_3

tag: treatment

value: No injection


title: hAECs, Donor 4 - IL17


title: MIcon_9

value: small intestinal

value: 10 weeks


title: MBECsCCM3KO_01

description:
mRNA
RNA-Seq


title: Noinject_A_2

value: RNA-seq


title: hAECs, Donor 4 - Control


title: AstroCCM3Flox_01

description:
Ribosome bound RNA
Ribo-Seq

value: Astrocyte


title: MBECsCCM3Flox_04

description:
mRNA
RNA-Seq


title: hAECs, Donor 3 - Dexamethasone

value: DonorID 3


title: Noinject_A_1


title: MIcon_8


title: MIcon_5


title: MIcon_4


title: MBECsCCM3Flox_03

description:
mRNA
RNA-Seq


title: hAECs, Donor 3 - IL17+Dexamethasone


title: hAECs, Donor 3 - IL17


title: MBECsCCM3KO_03

description:
mRNA
RNA-Seq


title: MBECsCCM3Flox_02

description:
mRNA
RNA-Seq


title: NelfEKD_C_1

value: NELF-E Trim-Away


title: hAECs, Donor 3 - Control


title: MIcon_3

value: control


title: MIcon_2


title: NelfEKD_C_2


title: hAECs, Donor 2 - IL17+Dexamethasone

value: DonorID 2


title: NelfEKD_B_2


title: MIA10_10


title: hAECs, Donor 2 - IL17


title: PBDE 13

city: Los Angeles

first: Donald

middle: M.

last: Lamkin

state: CA

address: 300 UCLA Medical Plaza, Room 3160

department: Semel Institute for Neuroscience

institute: UCLA

data_processing:
Illumina HiSeq Control Software 3.4.0 used for basecalling
STAR 2.5.3a used for alignment
STAR 2.5.3a used for normalized abundance measurement
Assembly: GRCm38 GencodeM15
Supplementary files format and content: tab-delimited text files include log2-transformed CPM values for each Sample

source_name: left 4th mammary tissue

extract_protocol:
Mammary tissues were dissected, flash frozen, and stored at -80 C until being dissociated in RLT lysis buffer (supplemented with beta-mercaptoethanol) with a bead mill (Qiagen TissueLyser LT). Lysates were then processed with Qiagen Rneasy Mini Kit, utilizing qiashredder tubes for homogenization and on-column DNAse
Lexogen QuantSeq 3' FWD

value: left 4th mammary tissue

tag: experiment #

tag: replicate

value: BDE-47 in PEG300, 1%DMSO


title: NelfEKD_B_1

source_name: 2-cell embryo

tag: protocol


title: hAECs, Donor 2 - Control

value: primary human airway epithelial cells (hAECs)


title: PBDE 14


title: PBDE 12


title: NelfEKD_A_2


title: NelfEKD_A_4


title: hAECs, Donor 1 - Dexamethasone

value: DonorID 1

value: Yes

value: No


title: MIA10_8

value: ICR

tag: age


title: MIA10_9


title: NelfEKD_A_1


title: PBDE 10


title: MIA10_7


title: PBDE 15


title: PBDE 9


title: NelfEKD_B_3


title: hAECs, Donor 2 - Dexamethasone


title: hAECs, Donor 1 - IL17+Dexamethasone


title: IgG_E_2

value: IgG Trim-Away


title: MIA10_6


title: hAECs, Donor 1 - IL17


title: Control 8

value: PEG300, 1%DMSO


title: MIcon_1

value: small intestinal


title: IgG_E_1


title: MIA10_5

value: 10 weeks


title: Control 7


title: PBDE 11


title: IgG_D_2

value: RNA-seq


title: IgG_D_3


title: MIA10_4


title: IgG_D_1


title: Control 5


title: Control 6


title: MIA10_2

value: AOS 10mg/kg


title: MIA10_3


title: IgG_C_2


title: Control 3


title: IgG_C_3


title: Control 4


title: MCOHSCF_18

source_name: colon

extract_protocol:
COLON were removed, than quikly removed the contents and frozen in the luquid nitrogen, and extract the total DNA to analyze the microbial diversity
16S rDNA libraries were prepared for sequencing using standard IlluminaHiSeq protocols

value: colon

value: High fat diet & STZ+control-FMT


title: Control 1


title: IgG_C_1


title: IgG_B_3


title: MCOHSCF_13


title: MCOHSCF_11


title: hAECs, Donor 1 - Control


title: MCOHSCF_10


title: IgG_B_1


title: IgG_A_3


title: MCOHSCF_7


title: MIA10_1


title: MCOHSCF_5


title: IgG_A_2


title: IgG_A_1


title: MCOHSCF_4


title: Cdk9in_E_2

value: Cdk9 inhibitor (BAY1251152)


title: Control 2


title: MCOHSCF_20


title: MCOHSCF_2


title: IgG_B_2


title: Cdk9in_E_1


title: MCOHSAF_20

value: High fat diet & STZ+AOS10mg/kg-FMT


title: Cdk9in_D_3


title: MCOHSCF_1


title: N0475_Circ-INSR-siRNA-2

city: hannover

first: Dongchao

last: LU

state: Deutschland

address: Carl-Neuberg-Str. 1,

institute: Hannover medical school

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.17.1.14
nfcore/rnaseq (v1.3), pipeline: Nextflow (v18.10.1), FastQC (v0.11.4), TrimGalore ((version 0.4.1), STAR (version 2.5.0c), RSeQC (v3.0.0), dupRadar, Preseq (v2.0.3), featureCounts (v1.6.4), StringTie (v1.3.5), Sample_correlation, MultiQC (v1.7)
Assembly: UCSC, build mm10
Supplementary files format and content: tab-delimited text files of raw read counts from each sample.

extract_protocol:
HL-1 were harvested and RNA were isolated with miRNeasy mini kit (Qiagen). 500ng of total RNA was used for mRNA enrichment procedure with NEBNext PolyA mRNA magnetic Isolation Module.
Stranded cDNA library was generated using using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina with an additional purification step using Agencourt® AMPure® XP Beads. cDNA libraries were barcoded by dual indexing approach with NEBNext Multiplex Oligos for Illumina - 96 Unique Dual Index Primer Pairs.

tag: cell line

value: Circ-INSR siRNA

value: Circular RNA-INSR knockdown


title: N0474_Circ-INSR-siRNA-1


title: N0473_nc-siRNA-3

value: control


title: N0476_Circ-INSR-siRNA-3


title: Cdk9in_D_1


title: MCOHSAF_17


title: Cdk9in_D_2


title: MCOHSAF_18


title: N0472_nc-siRNA-2


title: RNA_X2_cells_Distal_polyadenylation sites_Rep1

type: RNA

city: Bangalore

first: Dasaradhi

last: Palakodeti

state: Karnataka

address: GKVK Campus, Bellary road

department: TAS

country: India

institute: inStem, NCBS

description: We isolated RNA from FACS sorted cells and gene expression analysis was done.

hyb_protocol: Agilent’s In situ Hybridzation kit 5190-6420 was used for hybridization

scan_protocol: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 072436_D_F_20150113) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.Background detrend ( On(FeatNCRange, LoPass)), saturation value 65526.

data_processing:
The images were manually verified and found to be devoid of uneven hybridization, streaks, blobs and other artifacts. Hybridization across the slide was good based on number of feature that were “g is PosAndSignif” which indicates feature is positive and significantly above background.The microarray images were overall clean, uniform intensity and with very low background noise.
We used backgroundCorrect(data,method=normexp) from limma & vsn(data) from arrayQualityMetrics to normalize the data.

organism: Schmidtea mediterranea

source_name: X2 cells, Distal peaks

label_protocol: OligodT primer with T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis).Agilent’s Quick-Amp labeling Kit (p/n:5190-0442) was used for labelling

extract_protocol: We isolated mRNA through oligodT probes from different samples and used as input for the microarray experiment. Qiagen’s RNeasy minikit Cat#74106 was used.

treatment_protocol: No specific treatment was done to the isolated RNA

value: X2 (Progenitor cells)

value: Sexual


title: RNA_X1_cells_Distall_polyadenylation sites_Rep2

source_name: X1 cells, Distal peaks

value: X1 (Stem cells)


title: RNA_Xins_cells_Distal_polyadenylation sites_Rep2

source_name: Xins cells, Distal peaks

value: Xins (Differentiated cells)


title: RNA_Xins_cells_Distal_polyadenylation sites_Rep1


title: RNA_X2_cells_Distal_polyadenylation sites_Rep2


title: RNA_X1_cells_Distal_polyadenylation sites_Rep1


title: MCOHSAF_15

value: ICR


title: Cdk9in_C_3


title: Cdk9in_C_2


title: Cdk9in_B_3


title: dcp5-1 T60 rep3

city: Shenzhen

first: Yinpeng

last: Xie

state: Guangdong

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

description: Sample 12-d60#2

data_processing:
Bowtie for alignment, v2, default parameter
Cufflink for expression profiling, V2.1.0, default parameter
Assembly: TAIR10

source_name: seedling

growth_protocol: Sueface sterilized seeds were imbibed in water at 4 °C for 3 days and germinated on 1x MS agar at standard condition (16h ligth/8h dark, 22 °C) for 5 days

extract_protocol:
Total RNA were extracted from each input lysate.
stander Illumina mRNA-seq protocol

treatment_protocol: Seedlings were rested in 1 x MS liquid medium for 30 min and subjected to 1 x MS liquid  medium supplie with 150 mM NaCl for 0 or 60 min

value: 60 min with 150 mM NaCl


title: Cdk9in_B_2


title: dcp5-1 T60 rep2

description: Sample 11-d60#1


title: MCOHSAF_7


title: MCOHSAF_6


title: dcp5-1 T60 rep1

description: Sample 10-d60#0


title: Cdk9in_B_1


title: MCOHSAF_3


title: dcp5-1 T0 rep2

description: Sample 8-d0#1

value: 0 min with 150 mM NaCl


title: Cdk9in_A_2


title: MCOHSAF_1

value: 10 weeks


title: dcp5-1 T0 rep1

description: Sample 7-d0#0


title: MCOHSAF_4


title: Cdk9in_A_4

value: RNA-seq


title: Cdk9in_A_1


title: MCOHSA10_10

value: High fat diet & STZ+AOS10mg/kg


title: Col-0 T60 rep3

description: Sample 6-W60#2


title: Col-0 T60 rep2

description: Sample 5-W60#1


title: MCOHSA10_9

value: colon


title: N0471_nc-siRNA-1


title: MCOHSAF_14


title: ES_ChIP_S5P_1

data_processing:
The mouse reference genome and annotations were downloaded from Ensembl (version GRCm38.dna.primary_assembly.fa and GRCm38.101.gtf).
Paired-end sequencing reads were trimmed using cutadapt (version 3.4) with parameters -a CTGTCTCTTATA -A CTGTCTCTTATA --pair-filter=any --minimum-length=20.
Trimmed reads were mapped to the reference genome using bowtie2 (version 2.3.5) with parameters --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant -I 10 -X 500.
Aligned reads were filtered by quality using samtools (version 1.3) with parameter -q 12. Read pairs were read in to R (version 3.6.3) using readGAlignmentPairs from the GenomicAlignment package (version 1.22.0) and fragments were filtered for fragments that have both unique start and end positions.
Coverage vectors were created using the coverage function from GenomicRanges package (version 1.38.0) and were normalized by the number of fragments and multiplied by a million. Normalized coverage were exported as bigwig files using the rtracklayer package (version 1.46.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: bigwig files of normalized coverage

source_name: mES-cells

extract_protocol:
ES cells were fixed with 1% formaldehyde in DMEM at 37 °C for 10 min, neutralized in DMEM containing 125 mM glycine at room temperature for 5 min and washed with PBS three times. Fixed cells were collected with 2ml soft lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA and 0.1% NP-40 10% Glycerol) and centrifuged at 3000 rpm for 15 min. The cell pellet was resuspended in 100µl SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.0), and sonicated. Soluble chromatin was diluted in 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.0, 167mM NaCl) and incubated with 2µg anti-Pol II Ser5P (Abcam, ab5131), anti-Pol II Ser2P (Abcam, ab5095) antibodies or IgG at 4 °C overnight. Bound chromatin was purified on magnetic beads after washings in low salt buffer (20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% SDS, 1% Triton X-100), high salt buffer (20 mM Tris-HCl, pH 8.0 ,2 mM EDTA, 500 mM NaCl, 0.1% SDS, 1% Triton X-100) and LiCl buffer (250 mM LiCl, 1% NP-40, 1% sodium deoxycholate). Chromatin was eluted in 1% SDS, 100mM NaHCO3 at 65 °C, reverse-crosslinked and was purified by phenol-chloroform extraction.
ChIP–seq libraries were prepared using a NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and the library quality was assessed using a 2100 Bioanalyzer (Agilent). Samples were paired-end sequenced at PE150 on an Illumina Hiseq 4000.

value: ChIP-seq

tag: assay

value: S5P (Abcam, ab5131)


title: MCOHSA10_8


title: Col-0 T0 rep2

description: Sample 2-W0#1


title: ES_ChIP_S5P_2


title: ES_ChIP_S5P_3


title: MCOHSA10_6


title: Whole blood of PR-after treatment

city: Jinan

first: Wenxiong

last: Sun

address: No.107 West Wenhua Road, Jinan, 250001, China

institute: Qilu Hospital, Cheeloo College of Medicine, Shandong University

description: After treatment with anti-PD-L1 and TGF-β bifunctional fusion protein.

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that. Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. padj<0.05 and |log2(foldchange)| > 1 were set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package (3.8.1), in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package (3.8.1) to test the statistical enrichment of differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases. DO pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DisGeNET database integrates human disease-related genes. DisGeNET pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler R package (3.8.1) to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNET pathway.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: gene.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: Whole blood

extract_protocol:
Take the patient's blood, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
NEBNext® Ultra RNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: patient

value: PR

tag: diagnosis

value: Recurrent cervical cancer

value: Female

value: Whole blood

value: anti-PD-L1 and TGF-beta bifunctional fusion protein

tag: treatment response

value: Partial response


title: MCOHSA10_7

tag: tissue


title: Col-0 T0 rep3

description: Sample 3-W0#2


title: Col-0 T0 rep1

description: Sample 1-W0#0


title: MCOHSA10_4


title: ES_ChIP_S2P_3

value: S2P (Abcam, ab5095)


title: dcp5-1 T0 rep3

description: Sample 9-d0#2


title: MCOHSA10_3


title: Whole blood of PD-after treatment

value: PD

value: Progressive disease


title: ES_ChIP_S2P_2


title: MCOHSA10_5

value: ICR


title: ES_ChIP_S2P_1


title: ES_ChIP_Input_3

value: Input


title: Whole blood of PR-before treatment

value: Untreated


title: bm-MPC_Adipogenic differentiation media with TGFB1 + TAK1 inhibitor_48hrs_rep2

city: London

first: Jina

last: Kum

state: ON

address: 1151 Richmond Street

country: Canada

institute: Western University

description: TGFB1 (10 ng/mL) + TAK1 inhibitor (10 umol/L)

hyb_protocol: 5.5 ug cDNA is fragmented and labelled, and a volume that should be equivalent to 2.3 ug of fragmented and labelled ss-cDNA is hybridized to the Clariom S Human Array. The GeneChip Fluidics Station 450 is used to stain and wash the arrays.

scan_protocol: Scanning is performed on the GeneChip Scanner 3000.

data_processing:
SST-RMA gene-level probeset summary with standard settings of the Thermo Fisher Scientific Transcriptome Analysis Console (TAC) software.
Normalized data matrix contains: TAC (4.0.2.15) Tukey biweight average of the expression levels of the probe selection region/junction probeset for samples from condition.

label: Biotin

source_name: Human bm-MPCs, Adipogenic differentiation media with TGFB1 + TAK1 inhibitor, 48 hours

label_protocol: 100 ng input RNA to cRNA to cDNA. Samples are processed using the Applied Biosystems WTPlus reagent kit.

growth_protocol: Human mesenchymal progenitor cells derived from bone marrow mononuclear cells were seeded on tissue culture plates in low glucose Dulbecco’s Modified Eagle Medium, supplemented with 10% fetal bovine serum and 1X PSF.

extract_protocol: Total RNA was isolated using RNeasy Mini Plus Kit (Qiagen)

treatment_protocol: To induce adipogenic differentiation, bm-MPCs were plated at a density of 40,000 cells/cm^2.  The next day, cells were exposed to adipogenesis-inducing media (ADP) for 48 hours.

value: Bone marrow

tag: cell type

value: bone marrow-derived mesenchymal progenitor cells


title: ES_ChIP_Input_1


title: ES_ChIP_Input_2


title: Col-0 T60 rep1

description: Sample 4-W60#0

value: 60 min with 150 mM NaCl


title: bm-MPC_Adipogenic differentiation media with TGFB1 + TAK1 inhibitor_48hrs_rep1

value: TGFB1 (10 ng/mL) + TAK1 inhibitor (10 umol/L)


title: ES_ChIP_IgG_3

value: ChIP-seq

value: IgG


title: Whole blood of PD-before treatment

value: Recurrent cervical cancer


title: bm-MPC_Adipogenic differentiation media_48hrs_rep2

description: ADP

source_name: Human bm-MPCs, Adipogenic differentiation media, 48 hours

value: ADP


title: bm-MPC_Adipogenic differentiation media with TGFB1_48hrs_rep2

description: TGFB1 (10 ng/mL)

source_name: Human bm-MPCs, Adipogenic differentiation media with TGFB1, 48 hours

value: TGFB1 (10 ng/mL)


title: T24-si-circSLC38A1-2 RNA-seq

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

institute: The Second Hospital of Shandong University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
STAR is used to align clean reads to reference genome. STAR outperforms other aligners by a factor of >50 in mapping speed, while at the same time improving alignment sensitivity and precision.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
GO and KEGG enrichment analysis of differentially expressed genes
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human bladder cancer cells

extract_protocol:
Total RNAs extracted from cells were using Trizol reagent (Thermo Fisher Scientific，15596018).
NEBNext UltraTM RNA Library Prep Kit（NEB #E7490）was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Cells were treated with a control scramble (scr) siRNA or a siRNA that specifically knock down the expression of circSLC38A1.

value: Human bladder cancer cells

value: si-circSCL38A1 transfection


title: MCOHS_18

data_processing:
library strategy: 16S rDNA seq
Illumina HiSeq software used for basecalling.
Take the method of removing low quality by window, the specific operation is as follows: set a window of 25 bp, if the average quality value of the window is less than 20, the back-end bases will be truncated from the window; the read length after truncation is lower than the original read length For 75%, remove the entire sequence.
Remove linker contamination of reads (default adapter sequence and read sequence have an overlap of 15 bp, set to 15 bp, and allow the number of mismatches to be 3);
Remove reads containing N;Remove low-complexity reads (default reads with continuous base length ≥10 are low-complexity reads) finally, get the Cleandata
Splice the reads into tags through the overlap relationship between the reads; cluster the tags into OTUs and compare them with the database, and annotate species; based on the OTU and annotation results, perform sample species complexity analysis, analysis of species differences between groups, and association analysis. Model prediction, etc.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression

value: colon

value: 10 weeks

value: High fat diet & STZ


title: MCOHSA10_1

value: ICR

value: High fat diet & STZ+AOS10mg/kg


title: MCOHS_17


title: T24-si-circSLC38A1-3 RNA-seq


title: bm-MPC_Control growth media_48hrs_rep2

description: Control media

source_name: Human bm-MPCs, control growth media, 48 hours

value: Control media


title: T24-si-NC-3 RNA-seq

value: control scramble siRNA transfection


title: bm-MPC_Adipogenic differentiation media with TGFB1_48hrs_rep1

description: TGFB1 (10 ng/mL)

value: Bone marrow

value: bone marrow-derived mesenchymal progenitor cells


title: T24-si-NC-2 RNA-seq


title: ES_ChIL100C_S5P_3

data_processing:
Library strategy: ChIL-seq
The mouse reference genome and annotations were downloaded from Ensembl (version GRCm38.dna.primary_assembly.fa and GRCm38.101.gtf).
Paired-end sequencing reads were trimmed using cutadapt (version 3.4) with parameters -a CTGTCTCTTATA -A CTGTCTCTTATA --pair-filter=any --minimum-length=20.
Trimmed reads were mapped to the reference genome using bowtie2 (version 2.3.5) with parameters --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant -I 10 -X 500.
Aligned reads were filtered by quality using samtools (version 1.3) with parameter -q 12. Read pairs were read in to R (version 3.6.3) using readGAlignmentPairs from the GenomicAlignment package (version 1.22.0) and fragments were filtered for fragments that have both unique start and end positions.
Coverage vectors were created using the coverage function from GenomicRanges package (version 1.38.0) and were normalized by the number of fragments and multiplied by a million. Normalized coverage were exported as bigwig files using the rtracklayer package (version 1.46.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: bigwig files of normalized coverage

extract_protocol:
ChIL-seq was performed following a modified protocol of the original ChIL-seq (PMID: 30532068). For ES cells, 100 or 1000 cells were plated on gelatin coated 96-well plates and let to attach for 16h in culture. Cells were then fixed with 1% formaldehyde in DMEM for 5 min and permeabilized with 1% Triton X-100 in PBS for 20min. Embryos were fixed using the same procedure. Samples were incubated in 2% BSA in PBS with anti-Pol II Ser5P (Abcam, ab5131) or anti-Pol II Ser2P (Abcam, ab5095) at 2μg/ml for 6h at room temperature, washed three times in 0.5% BSA in PBS and then incubated at 4 °C overnight in 2% BSA in PBS containing 500mM NaCl and the ChIL probe at 2μg/ml. After washing in PBS for ES-cells or PBS containing 0.1% BSA for embryos, samples were incubated in 50 µl Tn5 solution (50mM HEPES-KOH, pH 7.2, 0.1M NaCl, 0.1mM EDTA, 1mM dithiothreitol, 0.1% Triton X-100 and 10% glycerol) containing 0.5µl HActive™ Tn5 transposase (Glow Biologics, GBRP-TN5) for 10min at room temperature. Tn5-MEDS-B oligo (2 µM) was then added at 0.5 µl per well in 1× dialysis buffer (50mM HEPES-KOH, pH 7.2, 0.1M NaCl, 0.1mM EDTA, 1mM dithiothreitol, 0.1% Triton X-100 and 10% glycerol) and incubated for 60min at room temperature. Samples were then washed in 1× dialysis buffer and three times in PBS for ES-cells or PBS containing 0.1% BSA for embryos, incubated in 100 µl 1× TAPS-DMF buffer (10mM TAPS-NaOH, pH 8.5, 5mM MgCl2 and 10% N,N-dimethylformamide) for 1h at 37 °C, and washed at three times in PBS for ES-cells or PBS containing 0.1% BSA for embryos. To stop the Tn5 reaction, cells were incubated in 100 µl 0.2% SDS for 10min at room temperature or embryos were incubated in 0.1% BSA/PBS containing 50mM EDTA at 50 °C for 30 min. After washing at three times in PBS for ES-cells or PBS containing 0.1% BSA for embryos, samples were incubated in 50 µl reaction mixture (200U T4 DNA ligase, NEB, and 1.5U T4 DNA polymerase, NEB, in 1× T4 DNA ligase reaction buffer containing 0.1 mM dNTP) for 30min at room temperature. After discarding the solution, for ES cells, 100µl 0.2% SDS were added to remove DNA-bound enzymes, followed by incubation for 10min at room temperature and three washes in PBS. For embryos, 0.1% BSA/PBS containing 50mM EDTA was added for 30 min at 50 °C, and then washed at three times in 0.1% BSA/PBS. In situ transcription was then carried out using T7 RNA polymerase (800U per well; NEB) for 20h at 37 °C. The samples were treated with DNase I (2.5U per well; Thermo) for 30min at 37 °C and RNA was extracted using a Qiagen MinElute Cleanup kit.
Purified RNA was reverse-transcribed with SMARTScribe reverse transcriptase (Takara) following the manufacturer’s instructions and the resulting cDNA was amplified by Prime star GXL (Takara) by 14 cycles for 1000 cells with anti-Pol II Ser5P antibody, 15 cycles for 1000 cells with anti-Pol II Ser2P antibody, 16 cycles for 100 cells or embryos with anti-Ser5P antibody, or 17 cycles for 100 cells or embryos with anti-Ser2P antibody. After amplification, small fragments (<150bp) were removed using Gene read Size selection kit (Qiagen) and large size of fragments (>600bp) were removed using AMPure XP beads (Beckman Coulter). The amplified DNA was purified using AMPure XP beads and the quality of the libraries was assessed using a Bioanalyzer 2100 (Agilent Technologies). Samples were paired-end sequenced at PE150 on an Illumina NovaSeq 6000 platform

value: ChIL-seq

value: S5P (Abcam, ab5131)


title: bm-MPC_Adipogenic differentiation media_48hrs_rep1

description: ADP


title: MCOHS_16


title: MCOHS_15


title: ES_ChIL100C_S5P_2


title: T24-si-circSLC38A1-1 RNA-seq


title: T24-si-NC-1 RNA-seq


title: MCOHSA10_2


title: ES_ChIL100C_S5P_1


title: MCOHS_19