title: CUOP-2

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

institute: Cardiff University

data_processing:
Sequenced reads were mapped to a combined hg19 and NC_001526 whole genome using TopHat v2.0.13 with parameters --bowtie1
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using an in house tool.  In counting reads, at least 20 bases of a read had to map to the exon for that read to be counted and reads had to have the same orientation as the exon to be counted (i.e., taking into account strandedness information)
Genome_build: combined hg19 and NC_001526
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and transcript level count for each sample.

source_name: Tonsil sqamous cell carcinoma (cell line)

growth_protocol: The novel cell lines CUOP2 and CUOP3 were derived from oropharyngeal tumour biopsies that were obtained from patients prior to treatment for OPSCC at Cardiff and Vale University Health Board, from February 2013 to May 2014. The study was conducted with NHS Research Ethics Committee approval: Research Ethics Committee for Wales 13/WA/0002. Written informed consent was obtained for use of all patient samples. The study was performed in accordance with the Declaration of Helsinki. Fresh biopsies transported immediately to the laboratory and coarsely minced then incubated with Glasgow Modified Eagles Medium with 10% Fetal Bovine Serum, 10ng/ml Epidermal Growth Factor, 500 ng/ml Hydrocortisone, 0.1 nM Cholera toxin, and 1x Penicillin/Streptomycin (Sigma-Aldrich, Gillingham, UK). Cultures were supplemented with 60 Gy irradiated 3T3 fibroblasts (3T3 cells were removed prior to RNA extraction). All cell cultures were incubated at 37°C in 5% CO2. HPV status was assessed by p16 immunohistochemistry on the diagnostic biopsy, and HPV GP5/6 and E6 PCR on tumour DNA.UMSCC4 (HPV-negative, tonsil SCC), UMSCC6 (HPV-negative, base of tongue SCC), UMSCC19 (HPV-negative, base of tongue SCC), UMSCC74a (HPV-negative, base of tongue SCC), UMSCC47 (HPV-positive, lateral tongue SCC) cell lines were all obtained from the laboratory of Professor Thomas Carey (University of Michigan, USA). UPCISCC90 (HPV-positive, base of tongue SCC) was obtained from DSMZ (Braunschweig, Germany). These lines were obtained in October 2013 and were grown in DMEM with 10% Fetal Bovine Serum. The identities of these lines were confirmed by analysis of Short Tandem Repeat (STR) loci.

extract_protocol:
RNA was extracted using QiaAMP RNA Mini Kits, according to the manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA transcriptome sequencing was performed at the Beijing Genomics Institute. A 200 bp short-insert library was prepared. The TruSeq RNA-seq protocol was followed. Illumina HiSeq2000 (101PE) sequencing was used to generate 90 bp paired-end reads.

treatment_protocol: Cells were untreated (i.e. they were grown in standard conditions and then lysed on the plate)

tag: hpv status

value: HPV positive

tag: p53 status

value: p53 wild-type


title: UMSCC47

status: Public on Nov 28 2018

type: SRA

country: United Kingdom

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: Lateral tongue squamous cell carcinoma (cell line)


title: UPCISCC90

source_name: Base of tongue squamous cell carcinoma (cell line)


title: UMSCC4

value: HPV negative

value: p53 mutant


title: UMSCC6


title: UMSCC74a


title: UMSCC19


title: CUOP-3


title: yidC-induced (Test) Vs yidC-uninduced cells (Control) Replicate 2

type: RNA

city: Faridabad

first: Nisheeth

last: Agarwal

state: Haryana

address: 3rd Milestone, Faridabad-Gurugram Expressway

department: Infection and Immunity

country: India

institute: Translational Health Science and Technology Institute

description:
Biological replicate 2 of 3.
YidC_rep2

hyb_protocol: Labeled cDNAs and hybridization buffer (10X SSC, 50% Formamide and 0.2% SDS containing 10µg Salmon sperm DNA and 8µg yeast tRNA ) were added, and samples were applied to microarrays enclosed in hybridization chambers. After hybridization, slides were washed sequentially with buffers containing decreasing concentrations of SSC and SDS.

scan_protocol: Scanned on a GenePix 4000A microarray scanner (Axon Instruments). Images were quantified using GenePix Pro 7.2.22 software (Axon Instruments).

data_processing: For each channel, fluorescent intensity of individual spot was normalized with the sum of total intensities. Data were obtained from log2 of processed Red signal/processed Green signal.

label: alexa fluor 647

organism: Mycobacterium tuberculosis

source_name: Total RNA from ATc-treated test cells

label_protocol: 4 µg of total RNA were primed with 0.5 µg of random hexamer primer at 70°C for 10 min, then reversed transcribed at 46°C for 3 h in the presence of alexa fluor 647- or 555-aha-dCTP by using SuperScript Direct cDNA labeling system (Invitrogen) according to manufacturer's instructions.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: cells grown in 7H9-OADS medium containing 50ng/ml ATc for 4 days at 37°C

tag: strain

tag: treatment

value: transformed with pTetR-yidC

label: alexa fluor 555

source_name: Total RNA from ATc-treated control cells

value: transformed with pTetR


title: AD64

city: New York

first: Anthony

last: Romer

state: NY

address: 1150 St. Nicholas Ave

country: USA

institute: Columbia University

data_processing:
Base calling was performed using RTA (Illumina) software and bcl2fastq (version 1.8.4) coupled with adaptor trimming was used to convert BCL to fastq format.
Tophat (version 2.1.0) was used to map reads to the reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9)allowing for 4 mismatches and 10 maximum multiple hits.
Cufflinks (version 2.0.2) with default settings was used to estimate the relative expression level of genes and splice isoforms.
Statistics for differential gene expression were calculated using the R package Deseq.
Genome_build: mm9
Supplementary_files_format_and_content: Statitics for fold change differences in RNA expression between NEUROD1-/- and NEUROD1+/+ samples are found in Deseq csv file.

source_name: NEUROD1+/+ hESC derived D27 insulin-GFP+ cells

growth_protocol: Human embryonic stem cells, MEL-1 INSGFP/wt, were differentiated into pancreatic endocrine cells in culture.

extract_protocol:
After the directed differentiation of MEL-1 INSGFP/wt cells into pancreatic endocrine cells in culture, INS-GFP+ cells were isolated using a flow cytometer.  Total RNA from day 27 INS-GFP+ cells was extracted using Qiagen Rnaeasy kit micro kit.
An Illumina TruSeq RNA prep kit was used to generate cDNA libraries from total RNA (RIN>8).
Multiplexed libraries of cDNA were sequenced using an Illumina HiSeq2000 to yield roughly 30 million single-end 100bp reads.

tag: cell line/genotype

value: MEL-1 INSGFP/wt, NEUROD1+/+

tag: Stage

value: D27 islet cell stage

tag: cell type

value: Flow cytomertry sorted insulin-GFP+ cells


title: AD2

source_name: NEUROD1-/- hESC derived D27 insulin-GFP+ cells

value: MEL-1 INSGFP/wt, NEUROD1-/-


title: AD38


title: AD24


title: AD10


title: AD50


title: Ms Lung_SPC-cre TRF1flox/flox 9 Mon Tamox_ biological rep3

city: San Francisco

first: Paul

middle: John

last: Wolters

state: CA

address: 513 Parnassus Ave HSE 1355B

department: Pulmonary, Critical Care, Allergy and Sleep Medicine

institute: University of California, San Francisco

description: Gene expression after 9 months of tamoxifen treatment

hyb_protocol: Agilent hybridization protocol

scan_protocol: standard Agilent protocol

data_processing: standard Agilent protocol

organism: Mus musculus

source_name: Mouse Lung

label_protocol: Cyanine-3 (Cy3) labeled aRNA

extract_protocol: RNA was extracted using miRNAeasy mini kit (Qiagen, Hilden, Germany).

treatment_protocol: Mice were administered with Tamoxifen at 250 mg/kg body weight per week

tag: group name

value: Timepoint 2_T2

tag: tissue

value: Whole Lung

tag: age

value: 11 months


title: Ms Lung_SPC-cre TRF1flox/flox 9 Mon Tamox_ biological rep1


title: AD5


title: Ms Lung_SPC-cre TRF1flox/flox 3 Mon Tamox_ biological rep3

description: Gene expression after 3 months of tamoxifen treatment

value: Timepoint 1_T1

value: 5 months


title: yidC-induced (Test) Vs yidC-uninduced cells (Control) Replicate 3

description:
Biological replicate 3 of 3.
YidC_rep3


title: yidC-induced (Test) Vs yidC-uninduced cells (Control) Replicate 1

description:
Biological replicate 1 of 3.
YidC_rep1


title: Ikzf2

city: Bethesda

first: Michael

middle: C

last: Kelly

state: MD

address: 41 Center Drive

department: Center for Cancer Research

institute: NCI

description: Cochlea cells transfected with Anc80-Ikzf2 virus

data_processing:
R1 is cell barcode (16bp) followed by UMI (10bp)
R2 is cDNA insert [biological] (98bp)
I1 is the sample index (8bp), which was used for demultiplexing
10X Genomics cellranger v2.0.2 mkfastq to convert bcl files to fastqs and demultiplex
10X Genomics cellranger v2.0.2 count to convert cell barcodes, UMIs, and cDNA insert reads into gene expression matrix and bam file
Genome_build: mm10plusCustom.fa
Supplementary_files_format_and_content: HDF5 format raw gene expression matrix from 10X Genomics cellranger count v2.0.2 output

source_name: Cochlea

extract_protocol:
Oligo-dT reverse transcription
10X Genomics single cell 3' standard library prep

value: Ikzf2-transfected cochleae

value: cochlear cells


title: Ms Lung_SPC-cre TRF1flox/flox 3 Mon Tamox_ biological rep1


title: Ms Lung_TRF1flox/flox 9 Mon Tamox_biological rep3


title: Ms Lung_TRF1flox/flox 9 Mon Tamox_biological rep2


title: Ms Lung_SPC-cre TRF1flox/flox 9 Mon Tamox_ biological rep2


title: Ms Lung_SPC-cre TRF1flox/flox 3 Mon Tamox_ biological rep2


title: AD26


title: WT_PR82

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

description: counts.txt

data_processing:
All sequencing reads were quality controlled using FastQC v0.11.2. Illumina adapters were trimmed using Cutadapt v1.9.dev2, replicates were merged and aligned with their reference genome (UCSC mouse genome build mm10) using subread-align v1.4.6-p4. The BAM files from alignment were processed using featureCounts v1.4.6-p4 to obtain the counts per gene in all samples. Mus_musculus.GRCm38.83.gtf gene definition file was used. The differential expression analysis was performed using edgeR v3.18.1. Genes having counts per million less than 2 in all samples were excluded. Differentially expressed genes were defined using p-value < 0.01 and FDR-corrected p-value < 0.1 cutoffs. All bioinformatics analyses were conducted in R/Bioconductor computing environment v3.4.0.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text, counts

extract_protocol:
Lungs were removed, and RNA was harvested using Direct-zol RNA miniPrep plus kit from Zymo Research.
RNA-Seq library was prepared using the QuantSeq 3’ mRNA-Seq FWD sample preparation kit and sequenced on Illumina NextSeq 500 platform.
RNA-Seq libraries were pooled together to aim about 10-15M read passed filtered reads per sample.

value: lung

tag: genotype

value: wild type

tag: infection

value: influenza

tag: time

value: 6 days post influenza infection


title: WT_PR83

description: counts.txt


title: WT_PR86

description: counts.txt


title: WT_PR85

description: counts.txt


title: Ms Lung_TRF1flox/flox 9 Mon Tamox_biological rep1


title: WT_PR84

description: counts.txt


title: IS51

city: Rehovot

first: Idit

last: Shachar

address: Herzl 234

department: Immunology

country: Israel

institute: Weizmann Institute of science

hyb_protocol: 2ug ss cDNA in 80 ul total volume were hybridized to a Mouse Gene 2.0 ST using Affymetrix hybridization kit materials and hybridized for 17 hours at 45° at 60rpm. Post-hyb washes were done with Affymetrix wash solutions on the FS450 station using FS450_0007 protocol.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G

data_processing: The analysis was carried out using Partek Genome Suite software (Partek Inc., St. Louis, Missouri 63141, http://www.partek.com), using RMA.

label: biotin

source_name: CD84 activated M210B4

label_protocol: 200ng TotalRNA were used for labeling. cDNA samples were generated and labeled using Affymetrix WT-cDNA synthesis and labeling kit

growth_protocol: We isolated 200000 cells treated with either IgG1 or CD84 activating antibody for 24 hrs. Cells were grown at 37°C, 5% CO2 in starving (2% FCS) RPMI medium.

extract_protocol: Total RNA was isolated by PerfectPure RNA tissue kit (# 2302410, 5 PRIME, Germany) according to the manufacturer's instructions.

treatment_protocol: comparison of IgG1 to anti-CD84 activated M210B4 cells.

value: Bone marrow stromal cell line

tag: cell line


title: IS52

source_name: lgG isotype control treated M210B4


title: WT_Mock_6

description: counts.txt

value: mock

value: 6 days post mock infection


title: WT_Mock_1

description: counts.txt


title: RIG_I_KO_Mock_5

description: counts.txt

value: RIG-I-/-


title: RIG_I_KO_Mock_3

description: counts.txt


title: RIG_I_KO_Mock_1

description: counts.txt


title: RIG_I_KO_Mock_4

description: counts.txt


title: RIG_I_KO_Mock_2

description: counts.txt


title: WT_PR81

description: counts.txt


title: Mavs_KO_PR84

description: counts.txt

value: mixed C57BL/6 and 129SvEv

value: MAVS-/-


title: Mavs_KO_PR85

description: counts.txt


title: WT_Mock_2

description: counts.txt


title: RIG_I_KO_Mock_6

description: counts.txt


title: WT_Mock_5

description: counts.txt


title: Mavs_KO_PR82

description: counts.txt


title: WT_Mock_3

description: counts.txt


title: MAVS_KO_Mock_6

description: counts.txt


title: MAVS_KO_Mock_2

description: counts.txt


title: MAVS_KO_Mock_3

description: counts.txt


title: MAVS_KO_Mock_4

description: counts.txt


title: MAVS_KO_Mock_1

description: counts.txt


title: MAVS_KO_Mock_5

description: counts.txt


title: Mavs_KO_PR86

description: counts.txt


title: KO_PR86

description: counts.txt


title: KO_PR85

description: counts.txt


title: KO_PR84

description: counts.txt


title: Mavs_KO_PR83

description: counts.txt


title: KO_PR83

description: counts.txt


title: Mavs_KO_PR81

description: counts.txt


title: KO_PR82

description: counts.txt


title: KO_PR81

description: counts.txt


title: Cell_10%_50ppm_rec_replicate 3 [nCeO2_Rec_009]

city: Nanjing

first: Junkang

last: Wu

state: Jiangsu

address: 2 Sipailou Street

department: Energy and environment

country: China

institute: Southeast University

description: Gene expression of CeO2 NP imapcted cells after recovery incubation

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity > 9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent N. europaea ATCC 19718 Microarrays (8x15K, Agilent Technologies) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37 °C with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software ( version 11.0.1.1, Agilent). Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 9 samples have flags in Present (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering (P≤0.05, Fold-change ≥ 2.0) .

organism: Nitrosomonas europaea ATCC 19718

source_name: Cell, 10%, 50ppm, rec, replicate 3

label_protocol: Sample labeling were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, USA) on the Agilent Array platform. Fluorescent cRNA was produced and labeled with Cy3-UTP using Quick Amp Labeling Kit, One-Color (Agilent Technologies, Inc., Palo Alto, CA, USA). The labeled cRNAs were then purified with RNeasy Mini Kit. The concentrations of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE) before hybridization onto the N. europaea ATCC 19718 Microarray (8x15K, Agilent Technologies).

growth_protocol: The studied N. europaea (ATCC 19718) was cultured  in a constantly stirred (100~150 rpm) chemostat bioreactor (3L working volume, 2.2 d hydraulic residence time (HRT)) in the dark at 25℃~28℃with the dissolved oxygen (DO) concentration in the reactor maintained at 2.0±0.10 mg/L by air aeration. The chemical composition of the cultivation medium was the same as we reported before (Yu and Chandran, 2010), and the medium pH in the reactor was controlled at 7.45±0.05 with a 40 % NaHCO3 solution as buffer automatically titrated with a pH controller (Meller, Taiwang, China).

extract_protocol: The cells were collected by centrifugation at 1, 3000 rpmm for 10 min. The pellet was immediately re-suspended in 1 mL Trizol solution (Invitrogen, Carlsbad, CA, USA) and stored at -80 °C. The total RNA was extracted with RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions. Total RNA was quantified using a NanoDrop-1000 spectrophotometer and quality control was accessed by electrophoresis on a denaturing agarose gel before microarray hybridization.

treatment_protocol: CeO2 NPs were introduced into the both bioreactor and the sterile feeding medium to reach the final concentration of 50 ppm. The cultures were sampled for microarray analysis when the ARA declined by 10% in the chemostat bioreactor. The sampled CeO2 NP impaired cells after removing NPs were further re-suspended in the fresh sterile medium for recovery incubation at 25°C for 12 h in the dark. After that cells were also subject to whole-genome microarray analysis.

tag: group


title: Cell_10%_50ppm_rec_replicate 2 [nCeO2_Rec_008]

source_name: Cell, 10%, 50ppm, rec, replicate 2

value: CeO2 NP imapcted cells after recovery incubation


title: Cell_10%_50ppm_rec_replicate 1 [nCeO2_Rec_007]

source_name: Cell, 10%, 50ppm, rec, replicate 1


title: Cell_10%_0ppm_con_replicate 2 [nCeO2_Con_002]

description: Gene expression of normal cells

source_name: Cell, 10%, 0ppm, con, replicate 2

value: normal cells


title: Cell_10%_0ppm_con_replicate 1 [nCeO2_Con_001]

description: Gene expression of normal cells

source_name: Cell, 10%, 0ppm, con, replicate 1


title: Cell_10%_50ppm_exp_replicate 1 [nCeO2_Exp_004]

description: Gene expression after exposure to 50ppm CeO2 NPs

source_name: Cell, 10%, 50ppm, exp, replicate 1

value: after exposure to 50ppm CeO2 NPs


title: Cell_10%_50ppm_exp_replicate 2 [nCeO2_Exp_005]

source_name: Cell, 10%, 50ppm, exp, replicate 2


title: Cell_10%_0ppm_con_replicate 3 [nCeO2_Con_003]

description: Gene expression of normal cells

source_name: Cell, 10%, 0ppm, con, replicate 3


title: Cell_10%_50ppm_exp_replicate 3 [nCeO2_Exp_006]

source_name: Cell, 10%, 50ppm, exp, replicate 3


title: SD rat (Control group), replicate 3

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

scan_protocol: Hybridization, scanning and washing were performed on Agilent’s Microarray Platform according to Agilent’s Standard Protocols. The array data were analyzed with Agilent Feature Extraction software.

data_processing: After global mean normalization, probes with intensity <400 were removed for further analysis. Significance Analysis of Microarrays (SAM) software was used to find differentially expressed genes (DEGs) with threshold set at fold change>1.5 and q-value<0.05.

organism: Rattus norvegicus

source_name: SD rat (Control group), replicate 3

label_protocol: RNA was amplified and labeled by using Agilent Low Input Quick Amp Labeling Kit.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen) according to the manufacture’s instructions. The quantity of RNA in each sample was assessed spectrophotometerically (NanoDrop Technologies) and RNA integrity was assessed by formaldehyde agarose gel electrophoresis.

treatment_protocol: Rats were treated with procainamide, and blood samples were drawn via venous sinus of eye at the end of treatment.

value: Sprague Dawley

tag: gender

value: Male

value: sterile water

source_name: SD rat (Control group), replicate 1


title: SD rat (Procainamide group), replicate 4

hyb_protocol: Hybridization, scanning and washing were performed on Agilent’s Microarray Platform according to Agilent’s Standard Protocols.

value: 40 mg/kg of procainamide


title: SD rat (Procainamide group), replicate 2


title: SD rat (Procainamide group), replicate 5


title: SD rat (Procainamide group), replicate 3


title: BN rat (Procainamide group), replicate 4

value: Brown Norway

source_name: BN rat (Control group), replicate 1


title: SD rat (Control group), replicate 2

source_name: SD rat (Control group), replicate 2


title: BN rat (Control group), replicate 2

source_name: BN rat (Control group), replicate 2


title: GFP

description: Cochlea cells transfected with Anc80-GFP virus

source_name: Cochlea

value: control-transfected cochleae

value: cochlear cells


title: SD rat (Control group), replicate 5

source_name: SD rat (Control group), replicate 5


title: BN rat (Procainamide group), replicate 3


title: BN rat (Control group), replicate 1


title: SD rat (Control group), replicate 4

source_name: SD rat (Control group), replicate 4


title: BN rat (Control group), replicate 4

source_name: BN rat (Control group), replicate 4


title: BN rat (Procainamide group), replicate 2


title: SD rat (Control group), replicate 1


title: BN rat (Procainamide group), replicate 1


title: SD rat (Procainamide group), replicate 1


title: Control 8

city: Bangalore

first: Ruchi

last: Jain

state: Karnataka

address: C V Raman Road

department: Molecular Reproduction Development and Genetics

institute: Indian Institute of Science

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was normalised using quantile normalisation in R software.

label: Biotin

source_name: Brain

label_protocol: Biotinylated cRNA were prepared with TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip.

extract_protocol: RNA was extracted with Trizol reagent, followed by purification with QIAGEN RNeasy mini kit as per the manufacturer's protocol. RNA integrity was checked using Agilent Bioanalyser.

value: Non-neoplastic brain tissue

value: Adult


title: BN rat (Control group), replicate 3

source_name: BN rat (Control group), replicate 3


title: Control 7

value: Female


title: Control 1


title: Control 5


title: Control 2


title: Control 3


title: Control 6


title: PT 17

tag: disease state

value: Glioblastoma

tag: grade

value: GBM WHO Grade IV tumour tissue

value: Peritumoural brain zone


title: PT 14

value: GBM WHO grade IV tumour tissue


title: PT 6


title: PT 8


title: PT 9


title: PT 4


title: PT 13


title: PT 12


title: PT 5


title: Control 4


title: Tumour Core 16

value: Tumour core


title: PT 15


title: PT 10


title: PT 1


title: Tumour Core 15


title: Tumour Core 17


title: Tumour Core 12


title: Tumour Core 13


title: Tumour Core 14


title: PT 7


title: PT 3


title: Tumour Core 11


title: Tumour Core 7


title: PT 11


title: Tumour Core 9


title: PT 2


title: PT 16


title: 16_h_dproQ_R2

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

description:
Ribo-Zero (Epidemiology) + fragmentation + standard cloning protocol
gene_wise_quantifications_combined_Human_uniquely_only.csv
gene_wise_quantifications_combined_Salmonella_uniquely_only.csv

data_processing:
Adaptor removal and quality trimming with cutadapt (version 1.13)
Read mapping with READemption (version 0.4.3)  and segemehl (0.2.20)
Feature quantification with READemption (version 0.4.3)
Genome_build: GRCh37, NC_016810.1, NC_017718.1, NC_017720.1
Supplementary_files_format_and_content: reads per feature in csv format (tabular separated)

organism:
Homo sapiens
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: HeLa cells in fected with S. Typhimurium

growth_protocol: Salmonella enterica serovar Typhimurium strain SL1344 (strain JVS-1574; (Stocker et al., 1983)) and a constitutively GFP-expressing derivative thereof (JVS-3858; (Papenfort et al., 2009)) are considered as wild-type. Chromosomal mutations were generated as previously described (Datsenko and Wanner, 2000), the respective resistance cassettes eliminated using the FLP helper plasmid pCP20 (Datsenko and Wanner, 2000) at 42°C, and the mutated alleles subsequently transduced into one of the wild-type backgrounds (GFP-negative or –positive, respectively) using P22 phage (Sternberg and Maurer, 1991). For plasmid transformation, the respective Salmonella strains were electroporated with ~10 ng of DNA.  Routinely, Salmonella strains were grown in liquid Lennox broth (LB) medium or on solid LB agar medium at 37°C. When appropriate, liquid or solid media were supplemented with 30 μg/mL chloramphenicol (Cm), 100 μg/mL ampicillin (Amp), 50 μg/mL kanamycin (Kan), or 0.02% (w/vol) L-arabinose (final concentrations).

extract_protocol:
mirVana kit
TruSeq-based (at Vertis Biotech. AG, Freising, Germany)

treatment_protocol: Infection assays were carried out as previously described (Westermann et al., 2016).

value: HeLa

value: proQ mutatnt

tag: time after infection


title: 16_h_WT_R1

tag: strain

value: wild type


title: 16_h_WT_R2


title: 08_h_WT_R2


title: E17ControlAR13

data_processing:
Base calling was performed using RTA (Illumina) software and bcl2fastq (version 1.8.4) coupled with adaptor trimming was used to convert BCL to fastq format.
Tophat (version 2.1.0) was used to map reads to the reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9)allowing for 4 mismatches and 10 maximum multiple hits.
Cufflinks (version 2.0.2) with default settings was used to estimate the relative expression level of genes and splice isoforms.
Statistics for differential gene expression were calculated using the R package Deseq.
Genome_build: mm9
Supplementary_files_format_and_content: Statistics for normalized RNA expression and fold changes in RNA expression between Neurod1 null and Neurod1+/+ control cells are found in Deseq csv file.

source_name: Neurod1 Het E17 pancreatic endocrine cells

extract_protocol:
Pancreata were dissected out of E17 mice and were digested into single cell suspensions using accutase. Neurog3-Cre+ Rosa Tomato+ lineage labeled cells were sorted by a flow cytometer and Rna was extracted using Qiagen Rnaeasy micro kit.
2.315 ng of RNA (RIN>8) was converted to cDNA and amplified using a NuGen Ovation RNA Amplification System V2 kit.
Multiplexed libraries of cDNA were sequenced using an Illumina HiSeq2000 to yield roughly 30 million single-end 100bp reads.

tag: strain/genotype

value: Neurod1floxed/wt; Neurog3Cre+; RosaTomato+; C56BL/J

tag: developmental stage

value: Flow cytometry sorted Neurog3-Cre+ Rosa Tomato+ cells


title: E17ControlAR19


title: E17ControlAR6


title: E17ND-koAR24

source_name: Neurod1 KO E17 pancreatic endocrine cells

value: Neurod1floxed/floxed; Neurog3Cre+; RosaTomato+; C56BL/J


title: E17ND-koAR17


title: 08_h_dproQ_R1


title: E17ND-koAR9


title: 00_h_WT_R2


title: Tumour Core 10

value: Male


title: 08_h_dproQ_R2


title: 08_h_WT_R1


title: E17ND-KOAR8


title: 00_h_dproQ_R2


title: 00_h_dproQ_R1


title: Tumour Core 5


title: Tumour Core 2


title: Tumour Core 4


title: 16_h_dproQ_R1


title: Tumour Core 8


title: Tumour Core 1


title: Tumour Core 6


title: E17ControlAR7


title: Lrp::kanR Rich stationary rep2-RNAseq

city: Ann Arbor

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr.

department: Biological Chemistry

institute: University of Michigan

description:
KO_RDM_stat_171
RDM_stat_wt_vs_ko_wald_test.csv
RDM_stat_tpm_estimates.tsv

data_processing:
pre-processing RNA-Seq: Sequencing adapters were removed from all sequences using CutAdapt version 1.8.1 (Martin 2011) with parameters --quality-base=33 -a AGATCGGAAGAGC -A AGATCGGAAGAGC -n 3 -m 20 --mask-adapter --match-read-wildcards. Low quality reads were trimmed with Trimmomatic version 0.32 (Bolger et al. 2014) using the parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20. For all samples, remaining ribosomal reads were removed from analysis (details in the publication).
Wald Test RNA-seq: Gene-centric quantification of RNA expression for all samples was performed using kallisto version 0.43.0 (Bray et al. 2016) with the arguments: quant -t 4 -b 100 --rf-stranded. wald_test.csv files represent a Wald test calculated using sleuth (Pimento et al. 2017) performed on the genotype term of a simple model where transcript_abundance ~ genotype for each condition and time point combination seperately. The lrp::kanR genotype is considered the baseline in this model.
TPM estimates RNA-seq: log2(WT/KO) TPM ratios were calculated from the TPM estimates given by kallisto run as described in the Wald Test RNA-seq step above. Percentile-based 95% confidence intervals are estimated from 100 bootstrap replicates of the log2(WT/KO) TPM ratios (details in publication)
pre-processing ChIP-Seq: Sequencing adapters were removed from all sequences using CutAdapt version 1.8.1 (Martin 2011) with parameters -a AGATCGGAAGAGC -A AGATCGGAAGAGC -n 3 -m 20 --mask-adapter --match-read-wildcards. Low quality reads were trimmed with Trimmomatic version 0.32 (Bolger et al.2014)  using the parameters TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20.
Lrp WT - lrp::kanR ChIP-signal: Median-normalized WT log2(Extracted/Input) - KO(Extracted/Input) signal at every 10 bp is reported for each combination of WT and KO replicates for each time and condition. (details in publication)
Robust-Z ChIP summary signal: Each subtracted replicate in the step above was converted to a Robust-Z score and average between replicates for each time and condition combination to give a final summary signal (details in publication)
Lrp ChIP peaks: High-confidence Lrp binding regions were called through the use of three filters: 1. technical reproducibility estimated by bootstrap replicates sampled from raw reads. 2. biological signal estimated from the Lrp WT- lrp::kanR ChIP signal. 3. Biological reproducibility estimated from the IDR (Li et al. 2011)  between biological replicates. (details in publication)
Genome_build: E.coli MG1655 U00096.2 modified to match ATCC47076 strain as reported by Freddolino et al. 2012. All genome annotations were taken from RegulonDB version 9.4 (Gama-Castro S et al. 2016) with genome coordinates converted appropriately
Supplementary_files_format_and_content: Files ending in wald_test.csv: Results of Wald test as described in the Wald Test RNA-seq data processing step for each time and condition combination in the file name. Files are in csv format
Files ending in log2_wt_ko_ratio.tsv: Results of the log2(WT/KO) expression estimates. RNA-seq data processing step for each time and condition combination in the file name. Files are in tab seperated format (tsv). Column 1 is the estimate. Columns 2 and 3 represent a conservative percentile based 95% confidence interval.
Files ending in actual.bedgraph.gz: Results of Lrp WT- lrp::kanR ChIP-signal data processing step for the appropriate combination of WT and lrp::kanR replicates in the file name. Lines include a one 1bp entry for each location reported. Locations resulting in a NaN, inf, or -inf were not included in each .bedgraph
Files ending in robust_z.bedgraph.gz: Results of the Robust-Z ChIP summary signal data processing step for the appropriate combination of time and condition in the file name. Lines include a one 1bp entry for each location reported. Locations resulting in a NaN, inf, or -inf were not included in each .bedgraph
Files ending in peaks.bed.gz: Results of the Lrp ChIP peaks data processing step for each time and condition combination in the file name. Peaks are in .bed6+4 format with ATCC47076 as the chromosome name. The score (fifth) field is the maximum robustZ score found in the peak.The additional 4 fields include: 7. Maximum -log10(qvalue) for the technical filter 8. maximum -log10(qvalue) for the biological filter and 9. maximum -log10(qvalue) for the idr reproducibility filter. 10. peak 0-based offset from start where maximum robustZ score occured. In all cases where -log10(qvalue) resulted in an +infinite value (i.e. when qvalue = 0)  the -log10(qvalue) was truncated to the next highest finite -log10(qvalue) in the dataset for that filter.
Files ending in abundance.tsv: Results of quantification of each individual RNA sample from kallisto

organism: Escherichia coli

source_name: Culture lysate

growth_protocol: Cells isolated from a single colony were grown in liquid culture at 37C until harvest.

extract_protocol:
RNA was harvested using Qiagen RNAProtect. RNA was isolated, and rRNA depletion was performed according to the Illumina Ribo-Zero rRNA Removal Kit for Bacteria.
Specific Lrp-DNA complexes were isolated using a monoclonal antibody developed against Lrp, and DNA was isolated by phenol-chloroform extraction.
DNA was preprared for sequencing using the NEBNext DNA Library Prep Kit.  RNA was prepared fro sequencing using the NEBNext Ultra Directionaly RNA Library Prep Kit.

treatment_protocol: Cells were cross-linked by addition of 1% formaldehyde.

tag: media

value: MOPS rich defined media + glycerol

tag: time of harvest

value: stationary phase


title: Lrp::kanR Rich stationary rep1-RNAseq

description:
KO_RDM_stat_169
RDM_stat_wt_vs_ko_wald_test.csv
RDM_stat_tpm_estimates.tsv


title: Lrp::kanR Rich transition point rep2-RNAseq

description:
KO_RDM_mid_153
RDM_mid_wt_vs_ko_wald_test.csv
RDM_mid_tpm_estimates.tsv

value: transition point


title: ControlARC10

data_processing:
Base calling was performed using RTA (Illumina) software and bcl2fastq (version 1.8.4) coupled with adaptor trimming was used to convert BCL to fastq format.
Tophat (version 2.1.0) was used to map reads to the reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9)allowing for 4 mismatches and 10 maximum multiple hits.
Cufflinks (version 2.0.2) with default settings was used to estimate the relative expression level of genes and splice isoforms.
Statistics for differential gene expression were calculated using the R package Deseq.
Genome_build: mm9
Supplementary_files_format_and_content: Normalized gene expression data and statistics for fold change differences in RNA expression between NEUROD1 beta cell specific knock out and control adult mouse islets are found in Deseq csv file.

source_name: Control 12 week islets

extract_protocol:
Pancreata were dissected from 12 week Neurod1-Floxed/Floxed; Rip-Cre+ and Neurod1-Floxed/Floxed mice. Pancreata were digested with Collagenase P and endocrine islets were isolated using a Histopaque gradient followed by picking islets with a micro pipette.  Total islet Rna was extracted using a Qiagen Rnaeasy mini kit.
An Illumina TruSeq RNA prep kit was used to generate cDNA libraries from total RNA (RIN>8).
Multiplexed libraries of cDNA were sequenced using an Illumina HiSeq2000 to yield roughly 30 million single-end 100bp reads.

tag: genotype/strain

value: Neurod1-floxed/floxed; C56BL/J

value: 12 week

tag: cell type

value: isolated pancreatic islets


title: PP9

city: Shanghai

first: Xiaochun

last: Xue

address: 168 Changhai Road

department: Department of Pharmacy

institute: Changhai Hospital, Second Military Medical University

description: IonXpressRNA_004_R_2015_04_21_12_12_10_sn247770157_NOV-86-XXC2_Auto_sn247770157_NOV-86-XXC2_119

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.8 mapping to reference genome
count counting
Genome_build: GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: psoriasis vulgaris patient_skin

extract_protocol:
Total RNA was extracted from skins by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >6.0 is right for cDNA library construction.
Ion  Proton Sequencing Protocol

tag: participant condition

value: psoriasis vulgaris patient

tag: age (years)

value: male

tag: sampling location

value: limb

tag: tissue

value: skin


title: Lrp::kanR Rich transition point rep1-RNAseq

description:
KO_RDM_mid_146
RDM_mid_wt_vs_ko_wald_test.csv
RDM_mid_tpm_estimates.tsv

tag: genotype


title: Lrp::kanR Rich logarithmic rep2-RNAseq

description:
KO_RDM_log_171
RDM_log_wt_vs_ko_wald_test.csv
RDM_log_tpm_estimates.tsv

value: logarithmic phase


title: PP6

description: IonXpressRNA_001_R_2015_04_20_18_02_37_sn247770157_NOV-85-LXY1_Auto_sn247770157_NOV-85-LXY1_118

value: female

value: trunk


title: Tumour Core 3

value: Glioblastoma

value: GBM WHO grade IV tumour tissue

value: Tumour core

tag: age

value: Adult


title: ControlARC16


title: ND-koARM5

source_name: Neurod1 beta cell specific KO 12 week islets


title: ControlARC7


title: ND-koARM4


title: PP5

description: IonXpressRNA_008_R_2015_04_20_18_02_37_sn247770157_NOV-85-LXY1_Auto_sn247770157_NOV-85-LXY1_118

tag: gender


title: PP8

description: IonXpressRNA_003_R_2015_04_21_12_12_10_sn247770157_NOV-86-XXC2_Auto_sn247770157_NOV-86-XXC2_119


title: PP4

description: IonXpressRNA_007_R_2015_04_20_18_02_37_sn247770157_NOV-85-LXY1_Auto_sn247770157_NOV-85-LXY1_118


title: PP20

description: IonXpressRNA_009_R_2015_08_25_11_17_10_sn247770157_NOV-175-LXY2_Auto_sn247770157_NOV-175-LXY2_217


title: PP3

description: IonXpressRNA_007_R_2015_04_22_00_01_46_user_NOV-312-XXC4_Auto_user_NOV-312-XXC4_337


title: Lrp::kanR Minimal+LIV stationary rep2-RNAseq

description:
KO_minLIV_stat_163
minLIV_stat_wt_vs_ko_wald_test.csv
minLIV_stat_tpm_estimates.tsv

value: MOPS minimal media + LIV + glycerol


title: ND-koARM6


title: Lrp::kanR Minimal+LIV stationary rep1-RNAseq

description:
KO_minLIV_stat_151
minLIV_stat_wt_vs_ko_wald_test.csv
minLIV_stat_tpm_estimates.tsv

value: stationary phase


title: Cello2

city: Baltimore

first: yang

last: song

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse GRCm38 reference using the TopHat splice-aware aligner
Reads counts were calculated for each sample.
Differential expression of genes were computed between wild type and mutant samples
Genome_build: M. musculus (GRCm38)
Supplementary_files_format_and_content: tab-delimited text files include counts per million reads (CPM) for each sample

growth_protocol: Room temperature 18-23°C, 40-60% humidity, 12 hour light/dark cylce

extract_protocol:
RNA was extracted from the dissected cochlea of P8 wildtype and Ikzf2cello/cello littermates using the Direct-zol™ RNA MiniPrep Plus kit per the manufacturer's instructions
Libraries were prepared using the TruSeq RNA Sample Prep kit (Illumina) following the manufacturer's instructions

value: whole cochlea


title: PP17

description: IonXpressRNA_005_R_2015_08_24_20_19_46_sn247770157_NOV-174-LXY1_Auto_sn247770157_NOV-174-LXY1_216


title: Wild-type2


title: PP2

description: IonXpressRNA_006_R_2015_04_21_12_12_10_sn247770157_NOV-86-XXC2_Auto_sn247770157_NOV-86-XXC2_119


title: Cello1


title: Lrp::kanR Minimal+LIV transition point rep2-RNAseq

description:
KO_minLIV_mid_165
minLIV_mid_wt_vs_ko_wald_test.csv
minLIV_mid_tpm_estimates.tsv

value: transition point


title: PP7

description: IonXpressRNA_002_R_2015_04_20_18_02_37_sn247770157_NOV-85-LXY1_Auto_sn247770157_NOV-85-LXY1_118


title: PP16

description: IonXpressRNA_003_R_2015_08_24_20_19_46_sn247770157_NOV-174-LXY1_Auto_sn247770157_NOV-174-LXY1_216


title: Lrp::kanR Rich logarithmic rep1-RNAseq

description:
KO_RDM_log_159
RDM_log_wt_vs_ko_wald_test.csv
RDM_log_tpm_estimates.tsv

value: MOPS rich defined media + glycerol


title: Lrp::kanR Minimal+LIV transition point rep1-RNAseq

description:
KO_minLIV_mid_156
minLIV_mid_wt_vs_ko_wald_test.csv
minLIV_mid_tpm_estimates.tsv


title: Lrp::kanR Minimal+LIV logarithmic rep2-RNAseq

description:
KO_minLIV_log_163
minLIV_log_wt_vs_ko_wald_test.csv
minLIV_log_tpm_estimates.tsv


title: Wild-type1


title: PP14

description: IonXpressRNA_001_R_2015_08_24_20_19_46_sn247770157_NOV-174-LXY1_Auto_sn247770157_NOV-174-LXY1_216


title: Cdk12△_Clone36_plusDox_3E8_rep2_ChIPseq

city: Cambridge

first: Sara

middle: Jane

last: Dubbury

state: MA

address: 500 Main Street, 76-417

department: Koch Institute

institute: MIT

description: NFH36plus_3E8_merge_sorted_bigwig_normalized.bw

library_source: genomic

data_processing:
Raw RNA-seq reads were mapped using STAR aligner version 2.4.1d49 with the parameters:  STAR --runMode alignReads --runThreadN 2 --genomeDir UCSC_mm9 --twopassMode Basic --sjdbOverhang 74  --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 70 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMstrandField intronMotif --outFilterType BySJout
Gene-level quantification was performed using Rsem version 1.2.2650 and EBSeq version 1.10.151 using the UCSC mm9 genome annotation with four independent replicates each (2x technical replicates of 2x independent clones) for Cdk12-expressing and Cdk12-depleted samples at 24 and 48 hours post dox-withdrawal.   Parameters:  rsem-calculate-expression --forward-prob 0.5 --output-genome-bam -p 2 --paired-end  UCSC_mm9   Rsem analysis was followed by read-count matrix assembly and standard EBSeq differential expression analysis.  Gene-level and quantification was also performed using DESeq 1.22.1 to obtain independent validation as well as to derive an adjusted p value for use in gene expression volcano plots. Gene expression differences at the total gene level were considered significant if the posterior probability of differential expression (PPDE) as determined by EBSeq > 0.95. Genes that exhibited statistically significant changes in response to doxycycline alone were excluded from the set of Cdk12-affected genes. Gene expression data is provided in the processed data.
Raw ChIP-sequencing reads were mapped using bwa mem v. 0.7.12-r1039 [https://github.com/lh3/bwa] and the following mapping commands:  bwa   aln -o 0 -t16 /home/Genomes/bwa_indexes/mm10.fa File_1_sequence.fastq -f output_1_sequence.sai;  bwa   aln -o 0 -t16 /home/Genomes/bwa_indexes/mm10.fa File_2_sequence.fastq -f output_2_sequence.sai;  bwa   sampe -f output_file.sam  /home/Genomes/bwa_indexes/mm10.fa output_1_sequence.sai output_2_sequence.sai File_1_sequence.fastq File_2_sequence.fastq
ChIP sequencing: (1) The bam files for both biological replicates from each condition/antibody were merged using samtools (v.1.3). (2) The merged bam files were converted to bedgraphs normalized by total mapped reads iusing bedtools/2.20.1 genomecov. (3) The bedgraphs were converted into bigWigs using ucsc-tools/20120530.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP sequencing data is processed here as bigwig files normalized by mapped reads. RNA seuqenicng data is processed here as total gene expression changes upon loss of Cdk12 after 24 or 48 hous.

molecule: genomic DNA

source_name: Embryonic Stem Cells

growth_protocol: V6.5 (C57Bl/6-129) mESCs and derived cell lines were cultured on 0.2% gelatin-coated tissue culture plates in ES media (HEPES-buffered DMEM (Thermo Fisher) supplemented with 15% FBS (Hyclone), 1000U/mL LIF (Millipore), non-essential amino acids, L-glutamine, BME, penicillin, and streptomycin). Cdk12∆ clones were maintained in 1ug/mL doxycycline (dox) (Sigma) in ES media (changed daily) to sustain complementing levels of Cdk12. To investigate Cdk12 loss, cells were washed at time zero with HBS and switched to ES media without dox for 24 or 48 hours. For the RNA sequencing experiment, parental Cdk12 Floxed cells (V6.5 mouse embryonic stem cells with homoqygous LoxP sites flanking Cdk12 exon 4 without introduction of the Dox-inducbile transgene) were pretreated with Dox for 17 days and then either harvested in Dox or harvested after withdrawal of Dox for 24 or 48 hours to serve as a control for gene expression changes caused by long-term Dox treatment followed by short term withdrawal.

extract_protocol:
RNA Sequencing: Total RNA was harvested using Trizol Reagent (Thermo Fischer) following the manufacturer's protocol and subsequently DNase treated with Turbo DNase (Thermo Fishcer) under standard reaction conditions. RNA quality was assessed by the Agilent 2100 BioAnalyzer and only samples with a RIN value >= 9 were used for library preparation. ChIP sequencing: We modified a high resolution, micrococcal nuclease (MNase) digestion-based ChIP methodology (Skene, P. J. & Henikoff, S. A simple method for generating high-resolution maps of genome-wide protein binding. eLife 4, 1–9 (2015).; Skene, P. J., Hernandez, A. E., Groudine, M. & Henikoff, S. The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1. eLife 3, 1–19 (2014).) Briefly, 48 hours before cells were harvested, 10e6 CDK12 cells were plated in 15 cm dishes either in +dox or –dox ES media. Cells were crosslinked directly in media on the plate in 1% methanol-free formaldehyde (Thermo Fisher) for 10 minutes at room temperature. Crosslinking was quenched with 250mM glycine. Cells were washed 3x in 10mL chilled PBS and harvested by scraping. Cells were pelleted, washed in 10mL chilled PBS, and pelleted again. PBS was aspirated off the cells and the pellets were flash frozen in liquid nitrogen and stored at -80 degrees C. Pellets were thawed on ice and resuspended in 0.9mL of ChIP Lysis Buffer (1% SDS, 10mM EDTA, 50mM Tris-HCL pH7.5) supplemented with 1x cOmplete Protease Inhibitors (Roche) and 1x Halt Phosphatase Inhibitors (Thermo Fisher) and lysed for 10 minutes at room temperature. Pellets were diluted in 8.1mL of ChIP Dilution Buffer (1% TritonX-100, 2mM EDTA, 150mM NaCl, 20mM Tris-HCl ph7.5) supplemented with 1x cOmplete Protease Inhibitors (Roche) and 1x Halt Phosphatase Inhibitors (Thermo Fisher) and 3mM CaCl2. Each tube was pre-warmed at 37 degrees C for 2 minutes. 12 Units of micrococcal nuclease (MNase, Sigma) were added per tube and samples were digested for 30 min at 37 degrees C with rotation. The digestion reaction was quenched with the addition of 180uL 500mM EDTA and 360uL 500mM EGTA per tube. Samples were sonicated in 15mL polystyrene tubes in a BioRupter (Diagenode) for 20 cycles on high (1 cycle = 30 seconds ON/30 seconds OFF). Samples were cleared by centrifugation (max speed, 4 degrees C, 10min). Soluble material was transferred to a new tube and each sample (one pellet) was split into four 1.8mL parts. Lysate was incubated overnight at 4 degrees C plus rotation with 10ug or 10uL of acites fluid of the following antibodies: Total RNAPII (8WG16 and Rpb3), RNAPII CTD Ser2p (H5 and 3E10), and RNAPII CTD Ser5p (H14 and 3E8). After the overnight incubation, the IPs were incubated for 2 hours at 4°C as follows: The 8WG16 and Rpb3 IPs were incubated with 100uL of Protein G Dynabeads (Thermo Fisher). The H5 and H14 IPs were incubated with 100uL of Protein G Dynabeads pre-conjugated overnight with 20ug goat anti-mouse IgM (Thermo Fisher 31172) in Bead Preparation Solution (9 ChIP Dilution Buffer: 1 ChIP Lysis Buffer). The 3E10 IP was incubated with 100uL of Protein G Dynabeads pre-conjugated with 20ug goat anti-rat IgG (Thermo Fisher 31226). IPs were washed as follows 2 x 2mL LB3 (20mM Tris-HCl pH7.5, 150mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100); 1x 2mL LB3+ (20mM Tris-HCl pH7.5, 500mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100); 1x 2mL Lithium Chloride Buffer (10mM Tris-HCl, pH 7.5, 250mM LiCl, 1mM EDTA, 1% NP-40), and 1x 2mL TE+50mM NaCl (10mM Tris-HCl, pH 7.5, 1mM EDTA, 50mM NaCl). After washing, beads were resuspended in 200uL of Extraction Buffer (50 mM Tris pH 8, 10mM EDTA, 5mM EGTA, 1% SDS). For WCE control, 100uL of soluble input material was added to 100uL of Extraction buffer. Samples were incubated overnight at 65°C +1000rpm shaking to elute IP and reverse crosslinks. 200uL of eluted samples was cleared of beads and added to 200uL TE pH 8. Samples were digested with 0.2mg/mL RNaseA for 1 hour at 37°C. 7 uL of CaCl2 solution (10mM Tris-HCl, pH 8 and 300mM CaCl2) and 4uL of 20mg/mL proteinase K were added to each sample and incubated for 1 hour at 55°C. Samples were extracted 1 x phenol:chloroform followed by 1 x chloroform and precipitated overnight at -80 degrees C with a standard NaCl, ethanol, and glycogen DNA precipitation. Pellets were washed 2x 1mL 70% ethanol, dried, and resuspended in 70uL 0.1x TE pH 8.
RNA Sequencing: Libraries were made from 1ug of total RNA input using the TruSeq Stranded mRNA Library Prep Kit (Illumina RS-122-2102) with multiplexing barcodes, following the standard protocol with the following specifications: (1) 5 min RNA fragmentation time, (2) Superscript III (Thermo Fisher) was used for reverse transcription, (3) 15 cycles of PCR were used during the library amplification step, and (4) AMPure beads (Beckman Coulter) were used to size select/purify the library post PCR amplification instead of gel size selection. ChIP Sequencing: All of the ChIP material (70 uL resuspended) or 200ng of input material (WCE) was used to prepare libraries. Sample DNA was end-repaired for 30 min at 20°C in a 100uL reaction: 1x T4 DNA Ligase Buffer (New England Biolabs, NEB), 0.4 mM dNTPs (NEB), 15 U of T4 DNA Polymerase (NEB), 5 U of Klenow enzyme (NEB), 50 U of T4 PNK (NEB). Samples were purified by Invitrogen Purelink Kit (Thermo Fisher) following standard conditions and eluted in 33uL. 32uL of purified product was A-tailed for 37°C for 30 min in a 50uL reaction with 1x NEB Buffer 2, 2 uM dATP (NEB), and 15 U of Klenow exo- (NEB). Samples were purified by Invitrogen Purelink Kit and eluted in 11uL. Illumina genomic adapters were ligated onto 10uL of the purified product for 15min at 20°C in the following 50uL reaction with 1x Quick Ligase Buffer (NEB), 400nM of Y-shaped Adapter Oligo, and 5uL of Quick Ligase. The reaction was cleaned up by a double size selection with AMPure beads as described by the manufacturer with the initial size selection using a 0.9x AMPure ratio and keeping the supernatant (to select against large products – mononucleosomes and larger) followed by a 1.8x AMPure selection keeping the bead bound material (to select against adapter dimers and free adapters). Note: When switching between first and second size selection, we used the following formula provided by the manufacturer to calculate the amount of additional beads to add: (second ratio-first ratio)*volume transferred. Illumina adapter oligos were added to the size selected product in a 50 uL PCR reaction with 200uM dNTPs (NEB), 1x High Fidelity Phusion Buffer (NEB), 1uL Phusion Polymerase (NEB), 0.5uM forward Illumina oligo adapter, and 0.5uM reverse Illumina oligo adapter with 16x cycles of standard Phusion PCR conditions (annealing: 65°C 30 sec and extension: 72°C 30 sec). PCR products were AMPure purified (1.8x ratio) according to manufacturer guidelines. Libraries were run on the BioAnalyzer. Libraries with adapter dimer contamination were repurified with extra AMPure selections until adapter dimer contamination disappeared.

tag: cell line

tag: mouse strain

value: Embryonic Stem Cells

tag: clone number

tag: dox treatment

value: +Dox

tag: primary antibody

tag: secondary antibody

tag: barcode

value: AATGGTAGAGAG

tag: rin value


title: PP15

description: IonXpressRNA_002_R_2015_08_25_11_17_10_sn247770157_NOV-175-LXY2_Auto_sn247770157_NOV-175-LXY2_217

value: psoriasis vulgaris patient

value: male


title: Lrp::kanR Minimal+LIV logarithmic rep1-RNAseq

description:
KO_minLIV_log_151
minLIV_log_wt_vs_ko_wald_test.csv
minLIV_log_tpm_estimates.tsv

tag: strain

tag: media

tag: time of harvest

value: logarithmic phase


title: PP13

description: IonXpressRNA_015_R_2015_08_27_19_08_22_sn247770157_NOV-177-ACR2_Auto_sn247770157_NOV-177-ACR2_221

tag: participant condition

tag: age (years)

value: skin


title: C54-2

first: Kai

last: Xu

address: No.2901, Beidi Rd.

institute: Shanghai Agrobiological Gene Center

description: Gene expression data from leaves under normal condition

data_processing:
Raw data of fastq were firstly processed through perl scripts to remove the contaminated reads for adapters and the low quality reads
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.1p2, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Genome_build: Oryza_sativa.IRGSP-1.0.dna.toplevel.fa

organism: Oryza sativa

source_name: osbzip62 mutant, normal conditions, replicate2

growth_protocol: The seedlings were grown with the liquid culture solution in grow chamber with a 16h light (28C)/8h dark(24C) photoperiod.

extract_protocol:
Total RNA was extracted using Trizol Reagent (Life Technologies)  following the manufacturer's instructions.
We used the qualified RNA samples for library construction following the specifications of the TruSeq® RNA Sample Preparation v2 Guide (Illumina)

tag: tissue

value: leaves

tag: genotype/variation

value: OsbZIP62 CRISPR mutant

tag: Stage

value: four-leaf stage


title: Cdk12△_Clone36_minusDox_H14_rep2_ChIPseq

description: NFH36minus_H14_merge_sorted_bigwig_normalized.bw

treatment_protocol: Cdk12∆ clones were maintained in 1ug/mL doxycycline (dox) (Sigma) in ES media (changed daily) to sustain complementing levels of Cdk12. To investigate Cdk12 loss, cells were washed at time zero with HBS and switched to ES media without dox for 24 or 48 hours.

tag: cell type

tag: genotype

value: -Dox 48hrs

value: Gt anti-ms IgM (Thermo 31172)

value: TACCGCTCTCTC


title: C54-1

source_name: osbzip62 mutant, normal conditions, replicate1


title: NIP-3

source_name: wild-type rice (Nipponbare) leaves,normal conditions, replicate 3

value: wild type


title: C54-3

source_name: osbzip62 mutant, normal conditions, replicate3


title: NIP-2

source_name: wild-type rice (Nipponbare) leaves,normal conditions, replicate 2


title: Lrp::kanR Minimal stationary rep1-RNAseq

description:
KO_min_stat_149
min_stat_wt_vs_ko_wald_test.csv
min_stat_tpm_estimates.tsv

value: MOPS minimal media + glycerol

value: stationary phase


title: PP12

description: IonXpressRNA_010_R_2015_08_25_11_17_10_sn247770157_NOV-175-LXY2_Auto_sn247770157_NOV-175-LXY2_217

tag: gender

tag: sampling location

value: limb


title: NIP-1

source_name: wild-type rice (Nipponbare) leaves,normal conditions, replicate 1


title: Lrp::kanR Minimal stationary rep2-RNAseq

description:
KO_min_stat_161
min_stat_wt_vs_ko_wald_test.csv
min_stat_tpm_estimates.tsv


title: PP10

description: IonXpressRNA_014_R_2015_08_25_11_17_10_sn247770157_NOV-175-LXY2_Auto_sn247770157_NOV-175-LXY2_217

value: trunk


title: Lrp::kanR Minimal transition point rep1-RNAseq

description:
KO_min_mid_155
min_mid_wt_vs_ko_wald_test.csv
min_mid_tpm_estimates.tsv

value: transition point


title: OE1-3

source_name: OsbZIP62-VP64-overexpressing rice leaves,normal conditions, replicate 3

value: OsbZIP62-VP64 overexpression


title: Cdk12△_Clone36_minusDox_InputControl

description: NFH36minus_negContIPs_merge_sorted_bigwig_normalized.bw

tag: cell line

tag: mouse strain

value: Embryonic Stem Cells

tag: clone number

tag: dox treatment

value: GCAGCGTCTCTC


title: PP11

description: IonXpressRNA_007_R_2015_08_25_11_17_10_sn247770157_NOV-175-LXY2_Auto_sn247770157_NOV-175-LXY2_217

value: psoriasis vulgaris patient

value: male


title: Lrp::kanR Minimal transition point rep2-RNAseq

description:
KO_min_mid_164
min_mid_wt_vs_ko_wald_test.csv
min_mid_tpm_estimates.tsv


title: OE1-2

source_name: OsbZIP62-VP64-overexpressing rice leaves,normal conditions, replicate 2

value: leaves


title: Cdk12△_Clone36_minusDox_negContIP_antiRatIgG_ChIPseq

tag: primary antibody

tag: secondary antibody

value: Gt anti-rat IgG (Thermo 31226)

tag: barcode

value: CGTTATTCTCTC

tag: rin value


title: Cdk12△_Clone36_minusDox_negContIP_antiMsIgM_ChIPseq

value: -Dox 48hrs

value: AAGCTCCACACA


title: Lrp::kanR Minimal logarithmic rep2-RNAseq

description:
KO_min_log_161
min_log_wt_vs_ko_wald_test.csv
min_log_tpm_estimates.tsv

tag: strain

tag: media

tag: time of harvest

value: logarithmic phase


title: OE1-1

source_name: OsbZIP62-VP64-overexpressing rice leaves,normal conditions, replicate 1

tag: tissue

tag: genotype/variation

value: four-leaf stage


title: Cdk12△_Clone36_minusDox_3E8_rep2_ChIPseq

description: NFH36minus_3E8_merge_sorted_bigwig_normalized.bw

tag: cell type

value: AAGCTCTCTCTC


title: PP1

description: IonXpressRNA_005_R_2015_04_21_12_12_10_sn247770157_NOV-86-XXC2_Auto_sn247770157_NOV-86-XXC2_119

tag: participant condition

tag: age (years)

value: female

value: skin


title: NN19

description: IonXpressRNA_008_R_2015_08_25_11_17_10_sn247770157_NOV-175-LXY2_Auto_sn247770157_NOV-175-LXY2_217

source_name: healthy volunteer_skin

value: healthy volunteer

tag: gender

tag: sampling location

value: trunk


title: Cdk12△_Clone36_plusDox_3E10_rep2_ChIPseq

description: NFH36plus_3E10_merge_sorted_bigwig_normalized.bw

tag: cell line

tag: mouse strain

tag: genotype

value: +Dox

value: GGCAACAGAGAG


title: Lrp::kanR Minimal logarithmic rep1-RNAseq

description:
KO_min_log_149
min_log_wt_vs_ko_wald_test.csv
min_log_tpm_estimates.tsv

value: MOPS minimal media + glycerol


title: WT Rich stationary rep2-RNAseq

description:
WT_RDM_stat_170
RDM_stat_wt_vs_ko_wald_test.csv
RDM_stat_tpm_estimates.tsv

value: wild type

value: MOPS rich defined media + glycerol

value: stationary phase


title: NN12

description: IonXpressRNA_014_R_2015_04_22_00_01_46_user_NOV-312-XXC4_Auto_user_NOV-312-XXC4_337

value: male

value: limb


title: WT-3

description: Gene expression data from leaves under normal condition

source_name: wild-type rice (Kitaake) leaves,normal conditions, replicate 3

value: leaves

tag: Stage


title: Cdk12△_Clone36_minusDox_H14_rep1_ChIPseq

description: NFH36minus_H14_merge_sorted_bigwig_normalized.bw

value: Embryonic Stem Cells

tag: clone number

tag: dox treatment

value: -Dox 48hrs

tag: primary antibody

tag: secondary antibody

value: Gt anti-ms IgM (Thermo 31172)

value: TCCGGGTCTCTC


title: Cdk12△_Clone36_minusDox_3E8_rep1_ChIPseq

tag: barcode

value: TCCGGGCACACA

tag: rin value


title: WT-2

source_name: wild-type rice (Kitaake) leaves,normal conditions, replicate 2

tag: tissue

value: four-leaf stage


title: NN13

description: IonXpressRNA_003_R_2015_04_22_00_01_46_user_NOV-312-XXC4_Auto_user_NOV-312-XXC4_337

value: healthy volunteer

value: skin


title: WT-1

source_name: wild-type rice (Kitaake) leaves,normal conditions, replicate 1

tag: genotype/variation


title: WT Rich stationary rep1-RNAseq

description:
WT_RDM_stat_168
RDM_stat_wt_vs_ko_wald_test.csv
RDM_stat_tpm_estimates.tsv

source_name: Culture lysate

tag: strain

tag: media

tag: time of harvest


title: Cdk12△_Clone36_minusDox_3E10_rep2_ChIPseq

description: NFH36minus_3E10_merge_sorted_bigwig_normalized.bw

tag: cell type

value: Gt anti-rat IgG (Thermo 31226)

value: GGATCTCACACA


title: Cdk12△_Clone36_minusDox_negContIP_msIgG2a_IsotypeControl_ChIPseq

value: mouse IgG2a [MOPC-173] Isotype Control (Abcam ab18413)

value: CTTAAATCTCTC


title: WT_Mock_4

description: counts.txt

value: lung

value: wild type

tag: infection

value: mock

tag: time

value: 6 days post mock infection


title: NN11

description: IonXpressRNA_007_R_2015_04_23_12_26_07_sn247770157_NOV-88-XXC3_Auto_sn247770157_NOV-88-XXC3_121

tag: participant condition

tag: age (years)

tag: gender

value: female

tag: sampling location

value: trunk


title: NN10

description: IonXpressRNA_006_R_2015_04_22_00_01_46_user_NOV-312-XXC4_Auto_user_NOV-312-XXC4_337

value: male


title: WT Rich transition point rep2-RNAseq

description:
WT_RDM_mid_152
RDM_mid_wt_vs_ko_wald_test.csv
RDM_mid_tpm_estimates.tsv

tag: genotype

value: MOPS rich defined media + glycerol

value: transition point


title: Cdk12△_Clone36_minusDox_3E10_rep1_ChIPseq

tag: cell line

tag: mouse strain

value: Embryonic Stem Cells

tag: clone number

tag: dox treatment

value: -Dox 48hrs

tag: primary antibody

value: GGATCTTCTCTC


title: Cdk12△_Clone36_minusDox_H5_rep2_ChIPseq

description: NFH36minus_H5_merge_sorted_bigwig_normalized.bw

value: H5 (Abcam Ab24758)

tag: secondary antibody

value: Gt anti-ms IgM (Thermo 31172)

tag: barcode

value: GTAACACACACA

tag: rin value


title: WT Rich transition point rep1-RNAseq

description:
WT_RDM_mid_147
RDM_mid_wt_vs_ko_wald_test.csv
RDM_mid_tpm_estimates.tsv

tag: strain

tag: media

tag: time of harvest


title: cKO-3

first: Fangzhou

last: Lou

address: 280 South Chongqing Road

department: Shanghai Institute of Immunology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
The adaptor sequences were trimmed from the raw paired-end reads, and RNA de novo assembly was achieved using the Trinity platform (http://trinityrnaseq.sourceforge.net/).
Unisequences were predicted and annotated using local BLASTX programs against the NCBI nr/nt, SwissProt, STRING and Cluster of Orthologous Groups (COG) databases (10-5-value cutoff).
The read counts were further normalized into FPKM values, and the fold changes were calculated using RSEM software (http://deweylab.biostat.wisc.edu/rsem/).
DEGs were identified using the edgeR software package (http://www.bioconductor.org/packages/elease/bioc/tml/edgeR.html).
Genome_build: mm8
Supplementary_files_format_and_content: The xls file includes FPKM values for each sample.

source_name: skin

extract_protocol:
Skin was quick-frozen and pulverized. Total RNA was extracted with Trizol reagent.
cDNA library was prepared using a TruSeq RNA sample preparation kit (Illumina cat. FC-122-1001) according to the manufacturer’s instructions. Briefly, mRNA was pulled-down with Oligo(dT) magnetic beads, fragmented, and reverse-transcribed with random hexamers. The resulted cDNA was used for second strand synthesis.

tag: genetic background

tag: age

value: 17 weeks


title: NN8

description: IonXpressRNA_005_R_2015_04_23_12_26_07_sn247770157_NOV-88-XXC3_Auto_sn247770157_NOV-88-XXC3_121

tag: participant condition

value: healthy volunteer

tag: age (years)

tag: tissue

value: skin


title: cKO-2


title: WT Rich logarithmic rep1-RNAseq

description:
WT_RDM_log_158
RDM_log_wt_vs_ko_wald_test.csv
RDM_log_tpm_estimates.tsv

tag: genotype

value: wild type

value: logarithmic phase


title: NN7

description: IonXpressRNA_004_R_2015_04_21_03_36_33_user_NOV-311-XXC3_Auto_user_NOV-311-XXC3_336

tag: gender

tag: sampling location


title: WT Rich logarithmic rep2-RNAseq

description:
WT_RDM_log_170
RDM_log_wt_vs_ko_wald_test.csv
RDM_log_tpm_estimates.tsv


title: PP6fl/fl-3


title: PP6fl/fl-2


title: Cdk12△_Clone36_minusDox_Rpb3_rep2_ChIPseq

description: NFH36minus_Rpb3_merge_sorted_bigwig_normalized.bw

tag: cell line

tag: mouse strain

tag: cell type

tag: clone number

value: Rpb3 (Bethyl A303-771A)

value: CATCACCACACA


title: WT Minimal+LIV stationary rep2-RNAseq

description:
WT_minLIV_stat_162
minLIV_stat_wt_vs_ko_wald_test.csv
minLIV_stat_tpm_estimates.tsv

value: MOPS minimal media + LIV + glycerol

value: stationary phase


title: NN1

description: IonXpressRNA_001_R_2015_04_21_03_36_33_user_NOV-311-XXC3_Auto_user_NOV-311-XXC3_336

value: female

value: limb


title: WT Minimal+LIV stationary rep1-RNAseq

description:
WT_minLIV_stat_150
minLIV_stat_wt_vs_ko_wald_test.csv
minLIV_stat_tpm_estimates.tsv


title: Cdk12△_Clone36_minusDox_8WG16_rep2_ChIPseq

description: NFH36minus_8WG16_merge_sorted_bigwig_normalized.bw

value: Embryonic Stem Cells

tag: dox treatment

tag: primary antibody

value: 8WG16 (Abcam ab817)

tag: secondary antibody

tag: barcode

value: ACGGTGCACACA


title: NN5

description: IonXpressRNA_003_R_2015_04_21_03_36_33_user_NOV-311-XXC3_Auto_user_NOV-311-XXC3_336

value: male


title: WT Minimal+LIV transition point rep2-RNAseq

description:
WT_minLIV_mid_166
minLIV_mid_wt_vs_ko_wald_test.csv
minLIV_mid_tpm_estimates.tsv

tag: strain

tag: media

tag: time of harvest

value: transition point


title: Cdk12△_Clone36_minusDox_Rpb3_rep1_ChIPseq

value: -Dox 48hrs

value: CATCACTCTCTC

tag: rin value


title: IMCD3_Pcm1_KO_rep2

city: Istanbul

first: seref

last: gul

address: Yalikoy Mh., Beykoz

department: Institute of Life Sciences and Biotechnology

country: Turkey

institute: Bezmialem Vakif University

data_processing:
The fluorescent images were processed into sequences, and base calling and quality value calculations were performed using the Illumina data processing pipeline (v1.5). FastQC (v0.11.5) was utilized to evaluate the initial quality of the reads.
Adaptor sequence and low-quality bases (quality score < Q30) were trimmed from the sequence reads by using Trimmomatic (v0.35).
Clean high quality data were mapped to the reference hg38 genome for human cells, and  to GRCm38.p5 genome for mouse cells via STAR  aligner (v2.5.3) with the following options --outSJfilterReads Unique --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate.
Fragments per kilobases of exons per million mapped read (FPKM) and fold changes were calculated using the Cuffdiff command from the Cufflinks suite. Quartile library normalization and pooled dispersion estimation methods were performed for the differential expression analysis. We used a minimum alignment count of 10, false discovery rate (FDR) < 0.05 and the absolute value of |Fold change| ≥ 2 as the threshold to judge significant differences in gene expression. To identify differentially expressed genes (DEGs) in WT and KO samples, the FPKM values for each gene (in KO samples) were compared to controls (WT sample) of each subject.
DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/) was utilized to test the statistical enrichment of the significantly (p-val < 0.05) differentially expressed genes in KEGG pathways and GO enrichment analysis.
Genome_build: hg38 for human  GRCm38.p5 for mouse cells
Supplementary_files_format_and_content: Tab-delimited text files for all genes having differential expression, p-val and q-val data obtained as a result of comparing WT vs KO cells (RPEI and IMCD3 samples), e.g. RPEI_gene_exp_diff.csv and IMCD3_gene_exp_diff.csv

source_name: inner medullary collecting duct cells

extract_protocol:
Total RNA from the fibroblast cell lines was extracted using the RNeasy Mini Kit (Qiagen, USA) protocol according to manufacturer’s instructions including the DNase I treatment.
After checking the quality and quantity of total RNA via 2100 BioAnalyzer, RNA-seq library preparation was performed using TruSeq mRNA Sample Preparation Kit (Illumina, USA) according to the manufacturer’s instructions. Paired-end sequencing was performed for the two cDNA libraries (two biological replicates) for each condition in Illumina HiSeq sequencing platform. All sequence data were PE 2x100 bp. Illumina data processing pipeline (v1.5) was utilized to perform the image processing, base calling, and quality calculation. High quality reads were saved in FASTQ format.

value: inner medullary collecting duct cells

tag: passage


title: IMCD3_Pcm1_KO_rep1


title: Cdk12△_Clone36_minusDox_H5_rep1_ChIPseq

source_name: Embryonic Stem Cells

value: H5 (Abcam Ab24758)

value: Gt anti-ms IgM (Thermo 31172)

value: GTAACATCTCTC


title: Cdk12△_Clone36_minusDox_8WG16_rep1_ChIPseq

value: ACGGTGTCTCTC


title: WT Minimal+LIV transition point rep1-RNAseq

first: Peter

description:
WT_minLIV_mid_157
minLIV_mid_wt_vs_ko_wald_test.csv
minLIV_mid_tpm_estimates.tsv

value: wild type


title: IMCD3_WT_rep2

value: Wild type


title: IMCD3_WT_rep1


title: Cdk12△_Clone36_plusDox_InputControl

description: NFH36plus_negContIPs_merge_sorted_bigwig_normalized.bw

value: +Dox

value: TACCGCAGAGAG


title: WT Minimal+LIV logarithmic rep2-RNAseq

description:
WT_minLIV_log_162
minLIV_log_wt_vs_ko_wald_test.csv
minLIV_log_tpm_estimates.tsv

value: MOPS minimal media + LIV + glycerol

value: logarithmic phase


title: Cdk12△_Clone36_plusDox_negContIP_antiRatIgG_ChIPseq

value: Embryonic Stem Cells

value: Gt anti-rat IgG (Thermo 31226)

value: GCAGCGAGAGAG


title: 8d-2_IP

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse GRCm38 reference using the TopHat splice-aware aligner
Reads counts were calculated for each sample.
Differential expression of genes were computed between wild type and mutant samples
Genome_build: M. musculus (GRCm38)
Supplementary_files_format_and_content: tab-delimited text files include read counts per million (CPM) for each sample

growth_protocol: Room temperature 18-23°C, 12 hour light/dark cylce

extract_protocol:
The outer hair cell translatome was enriched for by ribosome immunoprecipitation using an HA antibody (see protocol outlined in Sanz et al., 2009)
Libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer's instructions

treatment_protocol: Tamoxifen injection to induce PrestinCreERT2 recombination (3mg/40g body weight in mice younger than 21 days, 9mg/40g body weight in mice 21 days or older)

tag: developmental stage

tag: tissue

value: outer hair cells (enriched)

tag: antibody

value: HA

tag: molecule subtype

value: Translated mRNAs


title: 8d-2_input

value: whole cochlea

value: total RNA


title: WT Minimal+LIV logarithmic rep1-RNAseq

description:
WT_minLIV_log_150
minLIV_log_wt_vs_ko_wald_test.csv
minLIV_log_tpm_estimates.tsv

tag: genotype


title: 8d-1_IP


title: Cdk12△_Clone36_plusDox_negContIP_antiMsIgM_ChIPseq

tag: cell line

tag: mouse strain

value: Gt anti-ms IgM (Thermo 31172)

value: CTTAAAAGAGAG


title: Cdk12△_Clone36_plusDox_negContIP_msIgG2a_IsotypeControl_ChIPseq

tag: cell type

tag: clone number

value: mouse IgG2a [MOPC-173] Isotype Control (Abcam ab18413)

value: CGTTATAGAGAG


title: WT Minimal stationary rep1-RNAseq

description:
WT_min_stat_148
min_stat_wt_vs_ko_wald_test.csv
min_stat_tpm_estimates.tsv

value: wild type

value: MOPS minimal media + glycerol

value: stationary phase


title: WT Minimal stationary rep2-RNAseq

description:
WT_min_stat_160
min_stat_wt_vs_ko_wald_test.csv
min_stat_tpm_estimates.tsv


title: WT Minimal transition point rep2-RNAseq

description:
WT_min_mid_167
min_mid_wt_vs_ko_wald_test.csv
min_mid_tpm_estimates.tsv

value: transition point


title: Cdk12△_Clone36_plusDox_3E8_rep1_ChIPseq

description: NFH36plus_3E8_merge_sorted_bigwig_normalized.bw

tag: dox treatment

value: +Dox

tag: primary antibody

value: AAGCTCGTGTGT


title: 8d-1_input


title: WT Minimal transition point rep1-RNAseq

description:
WT_min_mid_154
min_mid_wt_vs_ko_wald_test.csv
min_mid_tpm_estimates.tsv


title: 6w-2_input

value: 6 weeks


title: 6w-2_IP


title: Cdk12△_Clone36_plusDox_H14_rep2_ChIPseq

description: NFH36plus_H14_merge_sorted_bigwig_normalized.bw

value: Embryonic Stem Cells

tag: secondary antibody

tag: barcode

value: TCCGGGGTGTGT


title: WT Minimal logarithmic rep1-RNAseq

description:
WT_min_log_148
min_log_wt_vs_ko_wald_test.csv
min_log_tpm_estimates.tsv

tag: strain

tag: media

value: logarithmic phase


title: Cdk12△_Clone36_plusDox_3E10_rep1_ChIPseq

description: NFH36plus_3E10_merge_sorted_bigwig_normalized.bw

value: Gt anti-rat IgG (Thermo 31226)

value: GGATCTAGAGAG

tag: rin value


title: Cdk12△_Clone36_plusDox_H5_rep2_ChIPseq

description: NFH36plus_H5_merge_sorted_bigwig_normalized.bw

value: H5 (Abcam Ab24758)

value: GTAACAGTGTGT


title: Cdk12△_Clone36_plusDox_H14_rep1_ChIPseq

value: Gt anti-ms IgM (Thermo 31172)

value: TCCGGGAGAGAG


title: WT Minimal logarithmic rep2-RNAseq

description:
WT_min_log_160
min_log_wt_vs_ko_wald_test.csv
min_log_tpm_estimates.tsv

tag: time of harvest


title: 6w-1_input

tag: developmental stage

value: whole cochlea

value: total RNA


title: 6w-1_IP

tag: tissue

value: outer hair cells (enriched)

value: HA

value: Translated mRNAs


title: High-NaCl diet rep1

city: Portland

first: David

last: Ellison

state: OR

address: 3181 SW Sam Jackson Park Rd CR145

institute: Oregon Health and Science University

data_processing:
Base Calling: Sanger/Illumina 1.9
QA /QC FastQC
Trimming:Fastx_toolkit
Alignment: Subread to mm10
Quantification: featureCounts
edgeR: Differential Expression analysis and normalization
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts: Tab delimited file for each sample and raw counts of transcripts
Supplementary_files_format_and_content: Counts and Analysis: Xlsx file with CPM and results of differential Expression Analysis

source_name: Mouse kidney

extract_protocol: RNA was extracted with Qiazol lysis reagent, followed by clean-up and gDNA eliminator treatment with QIAGEN RNeasy Plus Universal Mini Kit. Quality control was performed using an Agilent 2100 Bioanalyzer.

treatment_protocol: Mice were fed either high-NaCl (2.4% sodium, TD.90230 Envigo) or low-NaCl (0.01-0.02% sodium, TD.90228) diet for 5 days prior to isolation of collecting duct cells.

tag: diet

value: High-NaCl diet

tag: Sex

value: Male

value: Kidney


title: High-NaCl diet rep3


title: Lrp::kanR Rich stationary rep2-ChIPseq input

description:
KO_RDM_stat_I123
RDM_stat_called_peaks.bed.gz
RDM_stat_actual_10bp_robust_z.bedgraph.gz
RDM_stat_actual_10bp_WT_RDM_stat_E101_Sub_KO_RDM_stat_E123_actual.bedgraph.gz
RDM_stat_actual_10bp_WT_RDM_stat_E105_Sub_KO_RDM_stat_E123_actual.bedgraph.gz

tag: genotype

value: MOPS rich defined media + glycerol

value: stationary phase

tag: chip antibody


title: 28d-2_IP

tag: antibody

tag: molecule subtype


title: Low-NaCl diet rep3

value: Low-NaCl diet


title: Cdk12△_Clone36_plusDox_H5_rep1_ChIPseq

tag: cell line

tag: mouse strain

tag: cell type

value: Embryonic Stem Cells

tag: clone number

value: +Dox

value: GTAACAAGAGAG


title: 28d-2_input


title: Lrp::kanR Rich stationary rep1-ChIPseq input

description:
KO_RDM_stat_I115
RDM_stat_called_peaks.bed.gz
RDM_stat_actual_10bp_robust_z.bedgraph.gz
RDM_stat_actual_10bp_WT_RDM_stat_E101_Sub_KO_RDM_stat_E115_actual.bedgraph.gz
RDM_stat_actual_10bp_WT_RDM_stat_E105_Sub_KO_RDM_stat_E115_actual.bedgraph.gz


title: Lrp::kanR Rich transition point rep2-ChIPseq input

description:
KO_RDM_mid_I153
RDM_mid_called_peaks.bed.gz
RDM_mid_actual_10bp_robust_z.bedgraph.gz
RDM_mid_actual_10bp_WT_RDM_mid_E147_Sub_KO_RDM_mid_E153_actual.bedgraph.gz
RDM_mid_actual_10bp_WT_RDM_mid_E152_Sub_KO_RDM_mid_E153_actual.bedgraph.gz

value: transition point


title: Low-NaCl diet rep2


title: Low-NaCl diet rep1


title: 28d-1_IP


title: Cdk12△_Clone36_plusDox_Rpb3_rep2_ChIPseq

description: NFH36plus_Rpb3_merge_sorted_bigwig_normalized.bw

tag: dox treatment

tag: primary antibody

value: Rpb3 (Bethyl A303-771A)

tag: secondary antibody

tag: barcode

value: CATCACGTGTGT


title: Cdk12△_Clone36_plusDox_Rpb3_rep1_ChIPseq

value: CATCACAGAGAG

tag: rin value


title: 28d-1_input

tag: developmental stage

value: whole cochlea

value: total RNA


title: Cdk12△_Clone36_plusDox_8WG16_rep2_ChIPseq

description: NFH36plus_8WG16_merge_sorted_bigwig_normalized.bw

value: 8WG16 (Abcam ab817)

value: ACGGTGGTGTGT


title: 14d-2_IP

tag: tissue

value: outer hair cells (enriched)

value: HA

value: Translated mRNAs


title: Lrp::kanR Rich logarithmic rep2-ChIPseq input

description:
KO_RDM_log_I117
RDM_log_called_peaks.bed.gz
RDM_log_actual_10bp_robust_z.bedgraph.gz
RDM_log_actual_10bp_WT_RDM_log_E40_Sub_KO_RDM_log_E117_actual.bedgraph.gz
RDM_log_actual_10bp_WT_RDM_log_E9_Sub_KO_RDM_log_E117_actual.bedgraph.gz

tag: strain

tag: media

value: MOPS rich defined media + glycerol

tag: time of harvest

value: logarithmic phase


title: High-NaCl diet rep2

tag: diet

value: High-NaCl diet

tag: Sex

value: Male

value: Kidney


title: Cdk12△_Clone36_plusDox_8WG16_rep1_ChIPseq

value: Embryonic Stem Cells

tag: genotype

value: +Dox

value: ACGGTGAGAGAG


title: 14d-2_input

tag: antibody

tag: molecule subtype


title: Lrp::kanR Rich logarithmic rep1-ChIPseq input

description:
KO_RDM_log_I113
RDM_log_called_peaks.bed.gz
RDM_log_actual_10bp_robust_z.bedgraph.gz
RDM_log_actual_10bp_WT_RDM_log_E40_Sub_KO_RDM_log_E113_actual.bedgraph.gz
RDM_log_actual_10bp_WT_RDM_log_E9_Sub_KO_RDM_log_E113_actual.bedgraph.gz

tag: chip antibody


title: 14d-1_IP


title: 19: RLTR6_bait2_Bl6_Bcells_rep1

city: La Jolla

first: Ramya

last: Raviram

address: 9500 Gilman Drive

institute: University of California San Diego

data_processing:
Library strategy: 4C-Seq
Reads were mapped to mm10 or hg19 using bowtie2.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of raw 4C-Seq signal and BED file of observed baits

source_name: Splenic B cells

growth_protocol: ES cells were obtained from the ATCC cell line #CRL-1821 and were derived from a 129/Ola mouse strain. Mouse embryonic fibroblasts were prepared from E13.5 embryos of the 129S1 strain. Embryos were isolated from timed-matings and dissociated using trypsin after removal of internal organs and decapitation. Cells were cultured for 2 passages before 4C material preparation. Resting mature splenic B cells were isolated a using magnetic beads for CD43 depletion from either C57/Bl6 Taconic mice (C57BL/6NTac) or from 129S6 mice also from Taconic (129S6/SvEvTac).

extract_protocol:
Starting material for each sample was 10 million cells. Cells were fixed with 2% formaldehyde and digested in situ with Dpn2. Following cell-lysis DNA fragments were diluted to favor proximity-mediated ligation. Concatemers of DNA fragment ligations were subsequently digested with Csp6I and religated upon dilution.
Adaptors were introduced in the gene-specific inverse PCR step. 4C template was then amplified by thirty PCR cycles using 1μg of DNA divided by ten 50ul PCR reactions.

treatment_protocol: ES cells and MEFs were grown for two passages before 4C material preparation. Splenic B cells were used right after isolation

value: Splenic B cells

value: Wild-type


title: 17: RLTR6_bait1_129_ES

source_name: Embryonic stem cells

value: Embryonic stem cells


title: 18: RLTR6_bait2_129_ES


title: Lrp::kanR Minimal+LIV stationary rep1-ChIPseq input

description:
KO_minLIV_stat_I114
minLIV_stat_called_peaks.bed.gz
minLIV_stat_actual_10bp_robust_z.bedgraph.gz
minLIV_stat_actual_10bp_WT_minLIV_stat_E100_Sub_KO_minLIV_stat_E114_actual.bedgraph.gz
minLIV_stat_actual_10bp_WT_minLIV_stat_E104_Sub_KO_minLIV_stat_E114_actual.bedgraph.gz

value: MOPS minimal media + LIV + glycerol

value: stationary phase


title: 16: MuLV_bait1_129_ES


title: Cdk12△_Clone36_minusDox48hrs_rep2_RNAseq

tag: cell line

tag: mouse strain

tag: cell type

tag: clone number

value: -Dox 48hrs

value: GGCTAC


title: Cdk12△_Clone36_minusDox24hrs_rep2_RNAseq

tag: dox treatment

value: -Dox 24hrs

tag: barcode

value: TAGCTT


title: Cdk12△_Clone36_plusDox_rep2_RNAseq

value: GATCAG

tag: rin value


title: 14d-1_input

tag: developmental stage

tag: tissue

value: whole cochlea

value: total RNA


title: 10w-3_IP

value: 10 weeks

value: outer hair cells (enriched)

value: HA

value: Translated mRNAs


title: Lrp::kanR Minimal+LIV transition point rep2-ChIPseq input

description:
KO_minLIV_mid_I165
minLIV_mid_called_peaks.bed.gz
minLIV_mid_actual_10bp_robust_z.bedgraph.gz
minLIV_mid_actual_10bp_WT_minLIV_mid_E156_Sub_KO_minLIV_mid_E165_actual.bedgraph.gz
minLIV_mid_actual_10bp_WT_minLIV_mid_E166_Sub_KO_minLIV_mid_E165_actual.bedgraph.gz

tag: strain

tag: media

value: transition point


title: 00_h_WT_R1

description:
Ribo-Zero (Epidemiology) + fragmentation + standard cloning protocol
gene_wise_quantifications_combined_Human_uniquely_only.csv
gene_wise_quantifications_combined_Salmonella_uniquely_only.csv

source_name: HeLa cells in fected with S. Typhimurium

value: HeLa

value: wild type

tag: time after infection


title: 15: MuLV_bait1_Bl6_Bcells_rep2

value: Splenic B cells

value: Wild-type


title: Lrp::kanR Rich transition point rep1-ChIPseq input

description:
KO_RDM_mid_I146
RDM_mid_called_peaks.bed.gz
RDM_mid_actual_10bp_robust_z.bedgraph.gz
RDM_mid_actual_10bp_WT_RDM_mid_E147_Sub_KO_RDM_mid_E146_actual.bedgraph.gz
RDM_mid_actual_10bp_WT_RDM_mid_E152_Sub_KO_RDM_mid_E146_actual.bedgraph.gz

value: MOPS rich defined media + glycerol

tag: time of harvest


title: Lrp::kanR Minimal+LIV transition point rep1-ChIPseq input

description:
KO_minLIV_mid_I157
minLIV_mid_called_peaks.bed.gz
minLIV_mid_actual_10bp_robust_z.bedgraph.gz
minLIV_mid_actual_10bp_WT_minLIV_mid_E156_Sub_KO_minLIV_mid_E157_actual.bedgraph.gz
minLIV_mid_actual_10bp_WT_minLIV_mid_E166_Sub_KO_minLIV_mid_E157_actual.bedgraph.gz

tag: genotype

value: MOPS minimal media + LIV + glycerol


title: Cdk12△_Clone28_minusDox24hrs_rep2_RNAseq

value: Embryonic Stem Cells

value: TTAGGC


title: 13: MuLV_bait1_129_Bcells_rep2


title: Lrp::kanR Minimal+LIV logarithmic rep2-ChIPseq input

description:
KO_minLIV_log_I116
minLIV_log_called_peaks.bed.gz
minLIV_log_actual_10bp_robust_z.bedgraph.gz
minLIV_log_actual_10bp_WT_minLIV_log_E13_Sub_KO_minLIV_log_E116_actual.bedgraph.gz
minLIV_log_actual_10bp_WT_minLIV_log_E21_Sub_KO_minLIV_log_E116_actual.bedgraph.gz

value: logarithmic phase


title: Cdk12△_Clone28_plusDox_rep2_RNAseq

value: +Dox

value: ATCACG


title: Lrp::kanR Minimal+LIV stationary rep2-ChIPseq input

description:
KO_minLIV_stat_I122
minLIV_stat_called_peaks.bed.gz
minLIV_stat_actual_10bp_robust_z.bedgraph.gz
minLIV_stat_actual_10bp_WT_minLIV_stat_E100_Sub_KO_minLIV_stat_E122_actual.bedgraph.gz
minLIV_stat_actual_10bp_WT_minLIV_stat_E104_Sub_KO_minLIV_stat_E122_actual.bedgraph.gz

value: stationary phase


title: Lrp::kanR Minimal+LIV logarithmic rep1-ChIPseq input

description:
KO_minLIV_log_I112
minLIV_log_called_peaks.bed.gz
minLIV_log_actual_10bp_robust_z.bedgraph.gz
minLIV_log_actual_10bp_WT_minLIV_log_E13_Sub_KO_minLIV_log_E112_actual.bedgraph.gz
minLIV_log_actual_10bp_WT_minLIV_log_E21_Sub_KO_minLIV_log_E112_actual.bedgraph.gz


title: 10w-2_input

value: 10 weeks

value: whole cochlea

tag: antibody

value: total RNA


title: Cdk12Flox_minusDox48hrs_rep2_RNAseq

value: Cdk12 Fl/Fl; Cdk12 Tg-

value: -Dox 48hrs

value: GTGAAA


title: Cdk12Flox_minusDox24hrs_rep2_RNAseq

value: -Dox 24hrs

value: GTCCGC


title: Lrp::kanR Minimal stationary rep2-ChIPseq input

description:
KO_min_stat_I98
min_stat_called_peaks.bed.gz
min_stat_actual_10bp_robust_z.bedgraph.gz
min_stat_actual_10bp_WT_min_stat_E103_Sub_KO_min_stat_E98_actual.bedgraph.gz
min_stat_actual_10bp_WT_min_stat_E99_Sub_KO_min_stat_E98_actual.bedgraph.gz

value: MOPS minimal media + glycerol


title: 10: IAPEz_bait1_129_ES

value: Embryonic stem cells

value: Wild-type


title: 10w-1_input

tag: molecule subtype


title: 10w-1_IP

value: outer hair cells (enriched)

value: HA

value: Translated mRNAs


title: Lrp::kanR Minimal stationary rep1-ChIPseq input

description:
KO_min_stat_I102
min_stat_called_peaks.bed.gz
min_stat_actual_10bp_robust_z.bedgraph.gz
min_stat_actual_10bp_WT_min_stat_E103_Sub_KO_min_stat_E102_actual.bedgraph.gz
min_stat_actual_10bp_WT_min_stat_E99_Sub_KO_min_stat_E102_actual.bedgraph.gz

tag: chip antibody


title: Cdk12△_Clone28_minusDox48hrs_rep2_RNAseq

tag: cell line

value: Embryonic Stem Cells

value: ACTTGA


title: Cdk12Flox_plusDox_rep2_RNAseq

tag: mouse strain

value: +Dox

value: AGTTCC


title: 10w-3_input

value: 10 weeks

value: whole cochlea


title: 8: EtnERV_bait2_129_ES


title: Lrp::kanR Minimal transition point rep2-ChIPseq input

description:
KO_min_mid_I164
min_mid_called_peaks.bed.gz
min_mid_actual_10bp_robust_z.bedgraph.gz
min_mid_actual_10bp_WT_min_mid_E154_Sub_KO_min_mid_E164_actual.bedgraph.gz
min_mid_actual_10bp_WT_min_mid_E167_Sub_KO_min_mid_E164_actual.bedgraph.gz

value: transition point


title: Cdk12△_Clone36_minusDox48hrs_rep1_RNAseq

tag: cell type

value: -Dox 48hrs

value: CCGTCC


title: Cdk12△_Clone36_minusDox24hrs_rep1_RNAseq

tag: clone number

value: -Dox 24hrs

value: ATGTCA


title: Cdk12△_Clone36_plusDox_rep1_RNAseq

tag: dox treatment

value: AGTCAA


title: Lrp::kanR Minimal logarithmic rep2-ChIPseq input

description:
KO_min_log_I25
min_log_called_peaks.bed.gz
min_log_actual_10bp_robust_z.bedgraph.gz
min_log_actual_10bp_WT_min_log_E11_Sub_KO_min_log_E25_actual.bedgraph.gz
min_log_actual_10bp_WT_min_log_E42_Sub_KO_min_log_E25_actual.bedgraph.gz

value: MOPS minimal media + glycerol

value: logarithmic phase


title: 14: MuLV_bait1_Bl6_Bcells_rep1

value: Splenic B cells

value: Wild-type


title: 7: EtnERV_bait1_129_MEFs_rep2

source_name: Embryonic fibroblasts

value: Embryonic fibroblasts


title: Lrp::kanR Minimal logarithmic rep1-ChIPseq input

description:
KO_min_log_I23
min_log_called_peaks.bed.gz
min_log_actual_10bp_robust_z.bedgraph.gz
min_log_actual_10bp_WT_min_log_E11_Sub_KO_min_log_E23_actual.bedgraph.gz
min_log_actual_10bp_WT_min_log_E42_Sub_KO_min_log_E23_actual.bedgraph.gz


title: 6: EtnERV_bait1_129_MEFs_rep1


title: 10w-2_IP

value: outer hair cells (enriched)

value: HA

value: Translated mRNAs


title: 12: MuLV_bait1_129_Bcells_rep1


title: 5: ETnERV_bait1_Bl6_Bcells_rep3


title: WT Rich stationary rep2-ChIPseq input

description:
WT_RDM_stat_I105
RDM_stat_called_peaks.bed.gz
RDM_stat_actual_10bp_robust_z.bedgraph.gz
RDM_stat_actual_10bp_WT_RDM_stat_E105_Sub_KO_RDM_stat_E115_actual.bedgraph.gz
RDM_stat_actual_10bp_WT_RDM_stat_E105_Sub_KO_RDM_stat_E123_actual.bedgraph.gz

value: wild type

value: MOPS rich defined media + glycerol

value: stationary phase


title: 9: IAPEz_bait1_Bl6_Bcells


title: 4: ETnERV_bait1_Bl6_Bcells_rep2


title: 11: IAPEz_bait2_129_ES

value: Embryonic stem cells


title: WT Rich stationary rep1-ChIPseq input

description:
WT_RDM_stat_I101
RDM_stat_called_peaks.bed.gz
RDM_stat_actual_10bp_robust_z.bedgraph.gz
RDM_stat_actual_10bp_WT_RDM_stat_E101_Sub_KO_RDM_stat_E115_actual.bedgraph.gz
RDM_stat_actual_10bp_WT_RDM_stat_E101_Sub_KO_RDM_stat_E123_actual.bedgraph.gz


title: Cdk12△_Clone28_minusDox24hrs_rep1_RNAseq

value: Embryonic Stem Cells

tag: barcode

value: CAGATC


title: WT Rich transition point rep2-ChIPseq input

description:
WT_RDM_mid_I152
RDM_mid_called_peaks.bed.gz
RDM_mid_actual_10bp_robust_z.bedgraph.gz
RDM_mid_actual_10bp_WT_RDM_mid_E152_Sub_KO_RDM_mid_E146_actual.bedgraph.gz
RDM_mid_actual_10bp_WT_RDM_mid_E152_Sub_KO_RDM_mid_E153_actual.bedgraph.gz

value: transition point


title: WT Rich transition point rep1-ChIPseq input

description:
WT_RDM_mid_I147
RDM_mid_called_peaks.bed.gz
RDM_mid_actual_10bp_robust_z.bedgraph.gz
RDM_mid_actual_10bp_WT_RDM_mid_E147_Sub_KO_RDM_mid_E146_actual.bedgraph.gz
RDM_mid_actual_10bp_WT_RDM_mid_E147_Sub_KO_RDM_mid_E153_actual.bedgraph.gz


title: Cdk12△_Clone28_plusDox_rep1_RNAseq

value: +Dox

value: GCCAAT

tag: rin value


title: Cdk12Flox_minusDox48hrs_rep1_RNAseq

value: Cdk12 Fl/Fl; Cdk12 Tg-

value: -Dox 48hrs

value: ACAGTG


title: Cdk12Flox_minusDox24hrs_rep1_RNAseq

value: -Dox 24hrs

value: TGACCA


title: WT Rich logarithmic rep2-ChIPseq input

description:
WT_RDM_log_I9
RDM_log_called_peaks.bed.gz
RDM_log_actual_10bp_robust_z.bedgraph.gz
RDM_log_actual_10bp_WT_RDM_log_E9_Sub_KO_RDM_log_E113_actual.bedgraph.gz
RDM_log_actual_10bp_WT_RDM_log_E9_Sub_KO_RDM_log_E117_actual.bedgraph.gz

value: logarithmic phase


title: 2W_STR_uninjured_rep5

city: Livermore

first: Aimy

last: Sebastian

address: 7000 East Ave

institute: Lawrence Livermore National Laboratory

data_processing:
Sequenced reads were mapped to mouse genome mm10 using TopHat (version 2.0.11)
After read mapping, ‘featureCounts’ from Rsubread package (version 1.22.2) was used to generate gene-wise read counts.
Genes were filtered from downstream analysis if they did not have a CPM (counts per million mapped fragments) value of at least 2 in at least five libraries
RUVseq was used to normalize the data using 25 housekeeping genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 CPM values for each sample .

source_name: 2W_STR_uninjured_knee joint

extract_protocol:
Total RNA was purified using RNeasy Mini Kit (QIAGEN Inc, Germantown, MD, USA) according to manufacturer’s protocol.
Poly(A)+-enriched cDNA libraries were generated using the Illumina TruSeq Sample Preparation kit (Illumina Inc, Hayward, CA, USA)  according to manufacturer’s protocol.

treatment_protocol: Right knee joints of 10 weeks old STR/ort, C57BL/6 and MRL/MpJ mice were injured using a compressive load of 10-12N. Injured and uninjured (contralateral) joints were collected at 0-day [before injury], 1-day, 1-week, and 2-weeks post-injury. Subsequently, joints were dissected and cut at the base edges of femoral and tibial joint regions with small traces of soft tissues to preserve the intact knee joint.  Dissected joints were then cut into small pieces and submerged in RNA Later (Qiagen) and stored at 4 ̊C until processing.

value: STR/ort

tag: age

value: 10 Weeks

tag: susceptibility to ptoa

value: highly susceptible

value: Knee joints

tag: treatment

value: Uninjured

tag: sample collection

value: 2-weeks post-injury

tag: experimental batch


title: 1: ETnERV_bait1_129_Bcells_rep1

tag: tissue

value: Splenic B cells

value: Wild-type


title: Cdk12△_Clone28_minusDox48hrs_rep1_RNAseq

value: Embryonic Stem Cells

tag: genotype

value: CTTGTA


title: WT Rich logarithmic rep1-ChIPseq input

description:
WT_RDM_log_I40
RDM_log_called_peaks.bed.gz
RDM_log_actual_10bp_robust_z.bedgraph.gz
RDM_log_actual_10bp_WT_RDM_log_E40_Sub_KO_RDM_log_E113_actual.bedgraph.gz
RDM_log_actual_10bp_WT_RDM_log_E40_Sub_KO_RDM_log_E117_actual.bedgraph.gz

tag: strain

value: wild type

tag: media

value: MOPS rich defined media + glycerol

tag: time of harvest


title: Ski-WT SLAM Cell47

city: Cincinnati

first: H. Leighton

last: Grimes

state: OH

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

institute: Cincinnati Childrens Hospital Medical Center

description:
061016_Cell95-E9
Ski-WT SLAM

data_processing:
RNA reads were aligned to the reference mm9 mouse genome using Bowtie2.
Single-cell RNA-Seq data were analyzed using RSEM to estimate transcripts per million mapped reads (TPM) for all genes.
Differentially expressed genes were identified using AltAnalyze using a FDR adjusted empirical Bayes moderated t-test p<0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values

source_name: Bone marrow

extract_protocol:
cDNA Synthesis: Fluidigm C1 protocol
Nextera XT DNA Library Preparation Kit (Illumina)
150bp Paired-End, 150 million reads/96 cell library
Bone marrow was extracted by crushing hindlimbs isolated from mice immediately following euthanasia. The single cell suspension was enriched using CD117 Microbeads on an AutoMACS Pro (Mitenyi) and stained with fluorchome-conjugated antibodies for FACS-sorting of Cd45.2+ Lineage- c-Kit+ Sca-1+ Cd48- Cd150+ bone marrow cells. Single cells were separated using the Fluidigm C1 system and lysed on chip for subsequent reverse transcription.
cDNA was made with the SMARTer mRNA-Seq Kit (Clontech) and libraries were constructed using the Nextera XT DNA Library Preparation Kit (Illumina).

value: Fetal liver derived HSC - transplanted for 6 months

tag: genotype/variation

value: Ski-WT


title: WT Minimal+LIV stationary rep2-ChIPseq input

description:
WT_minLIV_stat_I104
minLIV_stat_called_peaks.bed.gz
minLIV_stat_actual_10bp_robust_z.bedgraph.gz
minLIV_stat_actual_10bp_WT_minLIV_stat_E104_Sub_KO_minLIV_stat_E114_actual.bedgraph.gz
minLIV_stat_actual_10bp_WT_minLIV_stat_E104_Sub_KO_minLIV_stat_E122_actual.bedgraph.gz

value: MOPS minimal media + LIV + glycerol

value: stationary phase

tag: chip antibody


title: Cdk12Flox_plusDox_rep1_RNAseq

tag: cell line

tag: mouse strain

tag: cell type

value: Cdk12 Fl/Fl; Cdk12 Tg-

value: +Dox

value: CGATGT


title: Ski-WT SLAM Cell48

description:
061016_Cell96-F9
Ski-WT SLAM


title: 2W_STR_uninjured_rep3

value: STR/ort

value: 10 Weeks

value: highly susceptible


title: WT Minimal+LIV transition point rep2-ChIPseq input

description:
WT_minLIV_mid_I166
minLIV_mid_called_peaks.bed.gz
minLIV_mid_actual_10bp_robust_z.bedgraph.gz
minLIV_mid_actual_10bp_WT_minLIV_mid_E166_Sub_KO_minLIV_mid_E157_actual.bedgraph.gz
minLIV_mid_actual_10bp_WT_minLIV_mid_E166_Sub_KO_minLIV_mid_E165_actual.bedgraph.gz

value: transition point


title: Ski-WT SLAM Cell45

description:
061016_Cell93-E8
Ski-WT SLAM


title: 2W_STR_uninjured_rep4

value: Knee joints

value: Uninjured

value: 2-weeks post-injury


title: 2W_STR_uninjured_rep2


title: Ski-WT SLAM Cell44

description:
061016_Cell92-D8
Ski-WT SLAM


title: Lrp::kanR Minimal transition point rep1-ChIPseq input

description:
KO_min_mid_I155
min_mid_called_peaks.bed.gz
min_mid_actual_10bp_robust_z.bedgraph.gz
min_mid_actual_10bp_WT_min_mid_E154_Sub_KO_min_mid_E155_actual.bedgraph.gz
min_mid_actual_10bp_WT_min_mid_E167_Sub_KO_min_mid_E155_actual.bedgraph.gz

value: MOPS minimal media + glycerol


title: 2W_STR_uninjured_rep1


title: 3: ETnERV_bait1_Bl6_Bcells_rep1

value: Splenic B cells

value: Wild-type


title: 2: ETnERV_bait1_129_Bcells_rep2


title: WT Minimal+LIV logarithmic rep2-ChIPseq input

description:
WT_minLIV_log_I21
minLIV_log_called_peaks.bed.gz
minLIV_log_actual_10bp_robust_z.bedgraph.gz
minLIV_log_actual_10bp_WT_minLIV_log_E21_Sub_KO_minLIV_log_E112_actual.bedgraph.gz
minLIV_log_actual_10bp_WT_minLIV_log_E21_Sub_KO_minLIV_log_E116_actual.bedgraph.gz

value: wild type

value: logarithmic phase


title: Ski-WT SLAM Cell42

description:
061016_Cell90-A8
Ski-WT SLAM

value: Fetal liver derived HSC - transplanted for 6 months

value: Ski-WT


title: 2W_STR_injured_rep5

source_name: 2W_STR_injured_knee joint

value: Injured


title: 2W_STR_injured_rep4


title: WT_SPI-2_R3

description:
Ribo-Zero (Bacteria) + fragmentation + standard cloning protocol
gene_wise_quantifications_combined.csv

data_processing:
Adaptor removal and quality trimming with cutadapt (version 1.13)
Read mapping with READemption (version 0.4.3)  and segemehl (0.2.20)
Feature quantification with READemption (version 0.4.3)
Genome_build: NC_016810.1, NC_017718.1, NC_017720.1
Supplementary_files_format_and_content: reads per feature in csv format (tabular separated)

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: S. Typhimurium_in-vitro conditions

growth_protocol: Salmonella enterica serovar Typhimurium strain SL1344 (strain JVS-1574; (Stocker et al., 1983)) and a constitutively GFP-expressing derivative thereof (JVS-3858; (Papenfort et al., 2009)) are considered as wild-type. Chromosomal mutations were generated as previously described (Datsenko and Wanner, 2000), the respective resistance cassettes eliminated using the FLP helper plasmid pCP20 (Datsenko and Wanner, 2000) at 42°C, and the mutated alleles subsequently transduced into one of the wild-type backgrounds (GFP-negative or –positive, respectively) using P22 phage (Sternberg and Maurer, 1991). For plasmid transformation, the respective Salmonella strains were electroporated with ~10 ng of DNA. The complete lists of bacterial strains and plasmids used in this study are provided in Supplementary Tables S5 and S6. Routinely, Salmonella strains were grown in liquid Lennox broth (LB) medium or on solid LB agar medium at 37°C. When appropriate, liquid or solid media were supplemented with 30 μg/mL chloramphenicol (Cm), 100 μg/mL ampicillin (Amp), 50 μg/mL kanamycin (Kan), or 0.02% (w/vol) L-arabinose (final concentrations).

extract_protocol:
TRIzol
TruSeq-based (at Vertis Biotech. AG, Freising, Germany)

treatment_protocol: Infection assays were carried out as previously described (Westermann et al., 2016). To avoid loss of the proQ overexpression plasmid (and the respective empty control vector) during intracellular bacterial growth, we performed HeLa infection assays in the presence or absence of the respective selection marker (ampicillin) in the host cell medium.

value: WT

tag: medium

value: SPI-2 inducing


title: WT Minimal+LIV logarithmic rep1-ChIPseq input

description:
WT_minLIV_log_I13
minLIV_log_called_peaks.bed.gz
minLIV_log_actual_10bp_robust_z.bedgraph.gz
minLIV_log_actual_10bp_WT_minLIV_log_E13_Sub_KO_minLIV_log_E112_actual.bedgraph.gz
minLIV_log_actual_10bp_WT_minLIV_log_E13_Sub_KO_minLIV_log_E116_actual.bedgraph.gz

value: MOPS minimal media + LIV + glycerol


title: Ski-WT SLAM Cell46

description:
061016_Cell94-B9
Ski-WT SLAM


title: WT Minimal stationary rep2-ChIPseq input

description:
WT_min_stat_I99
min_stat_called_peaks.bed.gz
min_stat_actual_10bp_robust_z.bedgraph.gz
min_stat_actual_10bp_WT_min_stat_E99_Sub_KO_min_stat_E102_actual.bedgraph.gz
min_stat_actual_10bp_WT_min_stat_E99_Sub_KO_min_stat_E98_actual.bedgraph.gz

value: stationary phase


title: WT_SPI-2_R2


title: 2W_STR_injured_rep3

value: STR/ort

value: 10 Weeks

value: highly susceptible


title: Ski-WT SLAM Cell41

description:
061016_Cell89-H7
Ski-WT SLAM


title: WT Minimal stationary rep1-ChIPseq input

description:
WT_min_stat_I103
min_stat_called_peaks.bed.gz
min_stat_actual_10bp_robust_z.bedgraph.gz
min_stat_actual_10bp_WT_min_stat_E103_Sub_KO_min_stat_E102_actual.bedgraph.gz
min_stat_actual_10bp_WT_min_stat_E103_Sub_KO_min_stat_E98_actual.bedgraph.gz