title: LLC STM2457_rep 2

status: Public on Jan 31 2023

type: SRA

city: Wuhan

first: Haisheng

last: Yu

state: Hubei

address: 115, Donghu road, Wuchang district

department: Medical Research Institute

country: China

institute: Wuhan University

library_source: transcriptomic

data_processing:
After quality control, RNA-seq libraries were generated and sequenced on the BGISEQ platform with paired-end reads in the Beijing Genomics Institute (BGI).
For analysis of RNA-seq results, RNA-seq reads quality was estimated using FastQC (v0.11.9, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Feature Counts (v2.0.1, http://subread.sourceforge.net/) were applied to quantitate the transcriptome with the GTF annotation files.
After standardized data processing, R package DEGSeq2 (v1.28.1, https://bioconductor.org/packages/release/bioc/html/DESeq2.html) was used for differential analysis of gene expression data.
Assembly: RNA-seq reads were matched with the mouse genome GRCm38 by HISAT2 (v2.2.1, https://daehwankimlab.github.io/hisat2/).
Supplementary files format and content: tab-delimited csv files include RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Lung

growth_protocol: LLC cells were cultured with 10%  fetal bovine serum (FBS) DMEM and 1% antibiotics in humidified atmosphere with 5% CO2 37℃.

extract_protocol:
RNA was harvested using TRizolreagent (15596018, Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: LLC cells treated with DMSO and STM2457 (5 μM for 46 h).

tag: tissue

value: Lung

tag: cell line

value: Lewis lung carcinoma cells

tag: cell type

value: Cancer cell

tag: genotype

value: Wild type

tag: treatment

value: Treated with 5μM STM2457 for 46 hours


title: Spirosoma montanitarrae DY10T, UVC, 12 hr

city: seoul

first: Changyun

last: Cho

state: Not US or Canada

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Reads of each samples’ adaptor trimmed by Trim galore (version 0.6.7) for quality control.
Clean reads of the samples were aligned against the reference genome (Build: ASM198895v1) using Hisat2 (version 2.1.0).
HTSeq (version 0.12.4) was used to quantify the mapped reads per ORF.
Assembly: ASM198895v1
Supplementary files format and content: comma-delimited text files include read counts values for each Sample. The data consists of 6 columns, the first column represents the gene locus ID on the reference genome, and the 2nd to 6th columns represent the read counts obtained from each sample.

organism: Spirosoma montaniterrae

source_name: 12 hr

growth_protocol: The bacterial strain DY10T (KCTC 23999T) was grown at 25ºC in liquid nutrient-rich medium tryptone glucose yeast extract (TGY; 1% tryptone, 0.1% glucose and 0.5% yeast extract) or TGY agar plates.

extract_protocol:
The post-radiation cells of UVC were collected by centrifugation (17,500 × g for 5 min) at 5min, 1hr, 3hr and 12hr with washing and stored with RNAlater solution at -80ºC. Total RNA was isolated using the Ambion Ribopure-Yeast RNA kit, according to manufacturer's instructions.
Strand-specific RNA-seq library preparation and sequencing was carried out as a paid service by Somagenics Inc., Santa Cruz, California, USA. Paired-end reads (Illumina NextSeq 500 v2, 2 × 150 bp, 3 Gb average output per sample) were obtained from strain DY10T.

treatment_protocol: For the UVC treatment, the early stationary phase cells on TGY agar plates were exposed to 600 JM-2 of ultraviolet using an ultraviolet crosslinker (UVP, CX-2000, CA, USA) at 254nm.

tag: strain

value: 12 hr

value: UVC


title: Spirosoma montanitarrae DY10T, UVC, 3 hr

source_name: 3 hr

value: 3 hr


title: Spirosoma montanitarrae DY10T, UVC, 1 hr

source_name: 1 hr

value: 1 hr


title: LLC STM2457_rep 1


title: LLC STM2457_rep 3


title: Spirosoma montanitarrae DY10T, UVC, 5 min

source_name: 5 min

value: 5 min


title: LLC DMSO_rep 3

value: Treated with DMSO for 46 hours


title: Spirosoma montanitarrae DY10T, UVC, control

description: control

source_name: untreated

value: untreated

value: Untreated


title: LLC DMSO_rep 1


title: Mesenchymal stem cells, leukemia, rep 1

city: Nedlands

first: Anastasia

last: Hughes

state: WA

address: 15 Hospital Avenue

department: Cancer Centre

country: Australia

institute: Telethon Kids Institute

description: Leuk_1 FPKM

data_processing:
Data processing was performed by BGI Genomics. Quality control and filtering of data was conducted to remove reads containing the adaptor, unknown base N content greater than 5% and low-quality reads using SOAPnuke software (v1.5.2, BGI). Clean reads ranged between 57-74M per sample.
Clean reads were aligned to reference genome and genes (Mus_musculus, NCBI, version: GCF_000001635.26_GRCm38.p6) using HISAT2 (v2.0.4) and Bowtie2 (v2.2.5) respectively.
The gene expression level for each sample was calculated using RSEM (v1.2.8).
Assembly: NCBI Mus_musculus version:GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Excel file provides FPKM values for each sample

source_name: Bone marrow

extract_protocol:
BM was flushed out of the medullary cavity of femurs and tibias and discarded. The long bones were cut into small fragments with scissors, washed thrice with PBS, and incubated with 1.5mg/ml Collagenase Type 4 (Worthington Biochemical Corp.) and 0.1mg/ml DNase I (Sigma-Aldrich) in PBS supplemented with 10% fetal calf serum (FCS) at 37°C for 60 minutes under agitation. Bone digests were filtered through sterile 100mm cell strainers, and bone fragments were crushed gently using a mortar and pestle in PBS with 2% FCS to detach MSCs. Cells were washed from bone fragments with PBS, strained, and pooled into the bone digests. This was repeated 6 times to maximize the cell yield. Cells were pelleted and treated with Red Blood Cell Lysis Buffer (BD Biosciences), followed by washing and resuspension in 2% FCS/PBS. MSCs were isolated by fluorescent activated cell sorting (FACS). MSCs were identified as CD45-, TER119-, CD31-, Sca-1+, PDGFRa+. Total RNA was extracted from MSCs using the RNeasy Micro Kit (Qiagen). BGI genomics performed RNA sequencing.
RNA amplification was performed using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio). Quality control of amplification products was conducted prior to tagmentation-based library construction. Circularization and library quality control was performed prior to sequencing.

treatment_protocol: Mice were intravenously injected with 1000 BCR-ABL1+ pre-B ALL cells via tail vein. Non-leukemic mice injected with plain phosphate-buffered saline (PBS) were used as controls. Leukemic mice were euthanised at endpoint (high leukemia burden) and controls were euthanised at the equivalent timepoint.

value: Mesenchymal stem cells

value: Bone marrow

tag: Sex

value: Female

tag: disease state

value: Leukemia


title: Mesenchymal stem cells, leukemia, rep 2

description: Leuk_2 FPKM


title: LLC DMSO_rep 2

value: Lung


title: Mesenchymal stem cells, control, rep 1

description: WT_1 FPKM

value: Control


title: Mesenchymal stem cells, control, rep 2

description: WT_2 FPKM


title: Leaves_natural_rep268

type: genomic

city: Guangzhou

first: Huixiao

last: Yang

state: Guangdong

address: No 233 1st Guangshan Road

institute: Guangdong Academy of Forestry

description: SAMPLE 268

hyb_protocol: Standard Illumina protocol

scan_protocol: SNP genotypes were called using GenomeStudio (Illumina Inc., San Diego,CA, USA) following standard genotyping and quality control procedures with no manual editing of clusters.

data_processing: The DNA samples were genotyped with the Eucalyptus EuCHIP60K chip, based on the Illumina Infinium technology being a total of 64,639 markers.

label: cy3 and cy5

molecule: genomic DNA

organism: Eucalyptus urophylla

source_name: leaves, natural condition, sampled at April, 2015

label_protocol: Standard Illumina protocol

growth_protocol:
The trees for this experiment were planted in a breeding gardern in Guangzhou under natural condition.
In 2008, the seeds of E. urophylla from 24 different sources were introduced into southern China through Commonwealth Scientific and Industrial Research Organisation (CSIRO), which comprised seed from 197 mother trees throughout the species’ entire natural distribution range. Among them, Thailand and Africa population belonged to cultivated species (Table S1). The minimum distance between individual trees was at least 50 m to avoid sampling close relatives. A map of the geographical locations of the 19 populations was created using software GenGis 2.5.037 (http://kiwi.cs.dal.ca/GenGIS/Main_Page) and free raster map data from Natural Earth (http://www.naturalearthdata.com/) (Fig. 1 and Table S1). Seeds were sown in a commercial nursery and were planted at the Experimental Farm of the Guangdong Academy of Forestry in Guangzhou District, Guangdong, China. The experimental site (23°22'N, 112°45'E, 45 m elevation) had a humid climate with an average annual rainfall of 1,400 mm and an average slope gradient of less than 25°. The population was planted in 2008 using 2m×3m spacing with 59 replications, and using a randomized complete block design with each family with one tree in each block. In the present study, 332 unrelated individuals included one or two originating from a different mother tree were used to assess genetic diversity and population structure that representing the entire geographic distribution of E. urophylla.

extract_protocol: Leaf tissue was collected at April, 2015. Total genomic DNA was extracted from 50 mg fresh individual plant leaves using a Plant Genomic DNA kit (Tiangen, Beijing, China) according to the manufacturer’s protocol.

treatment_protocol: Without treatment

tag: population

value: fresh leaves


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value: Thailand


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value: Africa


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title: Leaves_natural_rep365

description: SAMPLE 365


title: Leaves_natural_rep362

description: SAMPLE 362


title: Leaves_natural_rep363

description: SAMPLE 363


title: Leaves_natural_rep351

description: SAMPLE 351


title: Leaves_natural_rep353

description: SAMPLE 353


title: Leaves_natural_rep355

description: SAMPLE 355


title: Leaves_natural_rep361

description: SAMPLE 361


title: Leaves_natural_rep358

description: SAMPLE 358


title: Leaves_natural_rep357

description: SAMPLE 357


title: Leaves_natural_rep350

description: SAMPLE 350


title: Leaves_natural_rep352

description: SAMPLE 352


title: Leaves_natural_rep354

description: SAMPLE 354


title: Leaves_natural_rep356

description: SAMPLE 356


title: Leaves_natural_rep347

description: SAMPLE 347


title: Leaves_natural_rep345

description: SAMPLE 345


title: Leaves_natural_rep349

description: SAMPLE 349


title: Leaves_natural_rep346

description: SAMPLE 346


title: Leaves_natural_rep348

description: SAMPLE 348


title: Leaves_natural_rep343

description: SAMPLE 343


title: Leaves_natural_rep344

description: SAMPLE 344


title: Leaves_natural_rep342

description: SAMPLE 342


title: Leaves_natural_rep337

description: SAMPLE 337


title: Leaves_natural_rep339

description: SAMPLE 339


title: Leaves_natural_rep338

description: SAMPLE 338


title: Leaves_natural_rep334

description: SAMPLE 334


title: Leaves_natural_rep333

description: SAMPLE 333


title: Leaves_natural_rep332

description: SAMPLE 332


title: Leaves_natural_rep331

description: SAMPLE 331


title: Leaves_natural_rep328

description: SAMPLE 328


title: Leaves_natural_rep330

description: SAMPLE 330


title: Leaves_natural_rep335

description: SAMPLE 335


title: Leaves_natural_rep326

description: SAMPLE 326


title: Leaves_natural_rep327

description: SAMPLE 327


title: Leaves_natural_rep336

description: SAMPLE 336


title: Leaves_natural_rep323

description: SAMPLE 323


title: Leaves_natural_rep325

description: SAMPLE 325


title: Leaves_natural_rep329

description: SAMPLE 329


title: Leaves_natural_rep318

description: SAMPLE 318


title: Leaves_natural_rep321

description: SAMPLE 321


title: Leaves_natural_rep324

description: SAMPLE 324


title: Leaves_natural_rep322

description: SAMPLE 322


title: Leaves_natural_rep317

description: SAMPLE 317


title: Leaves_natural_rep316

description: SAMPLE 316


title: Leaves_natural_rep320

description: SAMPLE 320


title: Leaves_natural_rep319

description: SAMPLE 319


title: Leaves_natural_rep314

description: SAMPLE 314


title: Leaves_natural_rep313

description: SAMPLE 313


title: Leaves_natural_rep341

description: SAMPLE 341


title: Leaves_natural_rep312

description: SAMPLE 312


title: Leaves_natural_rep311

description: SAMPLE 311


title: Leaves_natural_rep307

description: SAMPLE 307


title: Leaves_natural_rep306

description: SAMPLE 306


title: Leaves_natural_rep305

description: SAMPLE 305


title: Leaves_natural_rep308

description: SAMPLE 308


title: Leaves_natural_rep309

description: SAMPLE 309


title: Leaves_natural_rep304

description: SAMPLE 304


title: Leaves_natural_rep301

description: SAMPLE 301


title: Leaves_natural_rep315

description: SAMPLE 315


title: Leaves_natural_rep340

description: SAMPLE 340


title: Leaves_natural_rep310

description: SAMPLE 310


title: dlrpa_2_liv_log_Input [I124a_2_liv_log]

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

country: USA

institute: University of Michigan

description:
processed data file:
WT_min_log_peaks.bedgraph

library_source: genomic

data_processing:
Adapter trimming: cutadapt 3.4
Quality trimming: TrimmomaticPE 0.39 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10
Alignment: bowtie2 v2.2.5 (arguments: --end-to-end –very-sensitive -I 0 -X 2000)
For Lrp ChIP samples – Occupancy quantitation (IPOD-HR pipeline v2.3.6)
For RNA polymerase ChIP samples – read counting with GenomicAlignments 1.26.0 (running under R 4.0.5)
For RNA polymerase ChIP samples – differential expression calling with deseq2 1.30.1 (running under R 4.0.5)
Genome_build: E. coli MG1655 (U00096.3)
Supplementary_files_format_and_content: bedgraph files of normalized occupancy (after subtraction of delta lrp signal)
Supplementary_files_format_and_content: csv files containing Deseq results

organism: Escherichia coli

source_name: Bacterial culture

growth_protocol: Cells were grown in M9 Minimal media (Min) or the same media supplemented with 0.2% each of L-leucine, L-isoleucine, and L-valine (LIV) at 37 degrees Celcius until OD600 = 0.2 (log-phase) or 12 hours after log-phase (stat phase) and crosslinked with 1% formaldehyde

extract_protocol:
Cell pellets were lysed and sonicated. Input samples were set aside and the remainder of each lysate was split in half where the Lrp-DNA complexes and RNAP-DNA complexes were isolated with their respective antibodies;  Neoclone W0023 (the RNA polymerase antibody),  lot # 2019G15-002, Lrp antibody is NeoClone custom antibody clone# 1G4D9A10, Lot# 2016E25-001.
ChIP-seq libraries were prepared for sequencing with the NEBNext UltraII DNA kit using an OpenTrons2 robot

tag: lineage

value: A

tag: biological replicate

tag: media

value: LIV

value: Log

tag: chip antibody


title: dC11b_2_liv_stat_Input [I144b_2_liv_stat]

description:
processed data file:
144b_liv_stat_LrpKOsub.bedgraph
144b_liv_stat_rnap_LrpKOsub.bedgraph

value: dC11 lrp at thyA

value: B

value: Stat


title: Leaves_natural_rep300

description: SAMPLE 300


title: Leaves_natural_rep297

description: SAMPLE 297


title: Leaves_natural_rep298

description: SAMPLE 298


title: Leaves_natural_rep303

description: SAMPLE 303


title: dC11b_1_liv_stat_Input [I144b_1_liv_stat]


title: dC11a_1_liv_stat_RNAPChIP [R144a_1_liv_stat]

description:
processed data file:
144a_liv_stat_rnap_LrpKOsub.bedgraph

value: RNAP


title: L136Ra_1_liv_stat_LrpChIP [L168a_1_liv_stat]

description:
processed data file:
168a_liv_stat_LrpKOsub.bedgraph
L136R_liv_stat_peaks.bedgraph

value: L136R lrp at thyA

value: Lrp


title: L136Ra_2_liv_log_Input [I168a_2_liv_log]

description:
processed data file:
168a_liv_log_LrpKOsub.bedgraph
168a_liv_log_rnap_LrpKOsub.bedgraph


title: Leaves_natural_rep286

description: SAMPLE 286


title: Leaves_natural_rep295

description: SAMPLE 295


title: L136Rb_1_liv_stat_Input [I168b_1_liv_stat]

description:
processed data file:
168b_liv_stat_LrpKOsub.bedgraph
168b_liv_stat_rnap_LrpKOsub.bedgraph


title: L136Ra_2_liv_stat_Input [I168a_2_liv_stat]

description:
processed data file:
168a_liv_stat_LrpKOsub.bedgraph
168a_liv_stat_rnap_LrpKOsub.bedgraph


title: Leaves_natural_rep299

description: SAMPLE 299


title: Leaves_natural_rep293

description: SAMPLE 293


title: Leaves_natural_rep296

description: SAMPLE 296


title: Leaves_natural_rep294

description: SAMPLE 294


title: Leaves_natural_rep302

description: SAMPLE 302

value: Lomblen


title: Leaves_natural_rep290

description: SAMPLE 290


title: Rich Media (YPD) Single Cell Gene Expression

city: New York

first: Christopher

last: Jackson

state: NY

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

description: 10x Genomics

data_processing:
Cellranger for standard demultiplexing and creation of gene count tables
fastqTomat0 for processing genotype barcodes, assigning them to cell reads, and removing doublets
Assembly: SacCer3 with custom UTR annotations
Supplementary files format and content: Processed data file is a compressed TSV file with 6829 gene expression count columns and 5 metadata columns (['Genotype', 'Genotype_Group', 'Replicate', 'Condition', 'tenXBarcode'], which indicate the specific biological replicate, the specific genotype, and the growth media) for 12482 single-cell observations in rows.

organism: Saccharomyces cerevisiae

source_name: pooled cells

growth_protocol: Yeast stored at -80C in 50% glycerol stocks in 96-well format. Thawed onto rich media (YPD) agar plates. Grown overnight in 96-well rich media (YPD) and pooled for treatment.

extract_protocol:
5mL of media (YPD: 4.25e7 cells/mL, MMD: 1.07e7 cells/mL) spun down, and cells resuspended in 1mL saturated ammonium sulfate (RNAlater). Cells washed once with 1mL RNAlater, and then stored overnight in -20C in 500 uL RNAlater.
Cells are processed into cDNA libraries using the 10X 3’ gene expression kit v3. Sequencing libraries are then further prepared and indexed from cDNA with the 10x 3’ gene expression kit v3. Genotype barcodes are extracted by PCR from cDNA libraries and indexed separately.

treatment_protocol: Pooled cells are washed with PBS and inoculated into 50mL of rich media (YPD) or minimal media (MMD) in 250mL baffled shake flasks. Pooled cells grown for 3h:30min and then treated with Beta-estradiol (1uM final concentration). Pooled cells grown for 30 additional minutes and then collected for sequencing.

value: pooled cells

value: rich media (YPD)


title: Leaves_natural_rep284

description: SAMPLE 284


title: Leaves_natural_rep288

description: SAMPLE 288


title: Rich Media (YPD) and Minimal Media (MMD) Single Cell Genotype Barcodes

description: 10x Genomics/Custom amplification

value: rich media (YPD) and minimal media (MMD)


title: Minimal Media (MMD) Single Cell Gene Expression

description: 10x Genomics

value: minimal media (MMD)


title: Leaves_natural_rep283

description: SAMPLE 283

value: fresh leaves


title: H1_D20_521_221_Plate_2_3

city: Singapore

first: Jing

last: Guo

state: State...

address: 8 Collage Road, DUKE-NUS Medical School, level 5

department: Center for Computational Biology

country: Singapore

institute: Duke-NUS Medical School

description: Human embryonic stem cells were cultured in wells coated with LN-521+LN-221 using nutristem medium.

data_processing:
RNA-Seq reads were aligned to hg38 (Ensembl Gene annotation build 79) using STAR 2.5.2b
Reads were quantified using featureCount v1.5.1
Ribosomal genes (Ensembl gene biotype “rRNA”) and mitochondrial genes were removed.
The gene level transcripts per million reads was computed from counts data.
Assembly: hg38 (Ensembl Gene annotation build 79)
Supplementary files format and content: tab-delimited text files include sample information, counts, and TPM values for each sample.

organism: Homo sapiens

source_name: Differentiated H1 Human Embryonic Stem Cells

growth_protocol: Cells were cultured in triplicates wells coated with LN-521 and LN-221. Cells at day 0 were cultured with Nutristem medium. Cells at Day 1 and 3 were cultured in RMPI 1640 with B27 without insulin supplement and CHIR99021. Cells at day 5 were cultured in RMPI 1640 with B27 without insulin supplement and IWP2. Cells at day 7 and 9 were cultured in RMPI 1640 with B27 without insulin supplement. Cells at day 11 to 90 were cultured in RPMI 1640 supplemented with CTS B-27 Supplement.

extract_protocol:
RNA extraction using Qiashredder (Qiagen; 79656) and RNeasy mini kit (Qiagen; 74106)
Libraries were constructed with TruSeq stranded total RNA library Prep Kit (Illumina).
Bulk RNA-seq on Illumina HiSeq 3000 for three biological replicates at each timepoint. Reads are pair-ended with 150bp length.

treatment_protocol: Pluripotent cells were seeded at 6 million cells into 10-cm2 dishes (ThermoFisher, 150464) coated with combination matrices of (3.33 mg/ml) LN-521 and (10 mg/ml) LN-221 on day 0 in 5ml of PBS. This protocol was based on our previous study(Yap et al., 2019b). At confluence (day 4), the cells were exposed to differentiation medium (RPMI 1640 (ThermoFisher, 11875-093) with B27 supplement without insulin (ThermoFisher, A1895601) and 10 mM of CHIR99021 (Tocris, 4423) for 24 hours. The next day (day 5), the medium was removed and replaced with differentiation medium. At day 7, the medium was changed to differentiation medium with the addition of 5 mM of IWP2 (Tocris, 3533) for 2 days. Wells were replaced with differentiation medium at day 9 and day 11. A 10-cm2 dish can generate ~ 20 million cells.

tag: biological replicates

tag: time

value: day 20


title: Leaves_natural_rep289

description: SAMPLE 289


title: Leaves_natural_rep287

description: SAMPLE 287


title: Leaves_natural_rep291

description: SAMPLE 291


title: H1_D9_521_221_Plate_2

value: day 9


title: H1_D4_521_221_Plate_5

value: day 4


title: H1_D11_521_221_Plate_2

value: day 11


title: Leaves_natural_rep292

description: SAMPLE 292


title: H1_D4_521_221_Plate_2


title: H1_D11_521_221_Plate_5


title: Leaves_natural_rep285

description: SAMPLE 285


title: H1_D20_521_221_Plate_6_1


title: H1_D20_521_221_Plate_2


title: H1_D11_521_221_Plate_6


title: dlrpb_1_liv_stat_LrpChIP [L124b_1_liv_stat]

value: LIV


title: H1_D9_521_221


title: dlrpb_1_liv_stat_Input [I124b_1_liv_stat]


title: dlrpa_1_liv_stat_LrpChIP [L124a_1_liv_stat]

value: A


title: H1_D0_3

source_name: Undifferentiated H1 Human Embryonic Stem Cells

value: day 0


title: dlrpb_2_min_stat_Input [I124b_2_min_stat]

value: B

value: Min

value: Stat


title: dlrpa_2_min_stat_LrpChIP [L124a_2_min_stat]

value: Lrp


title: dlrpa_2_min_stat_Input [I124a_2_min_stat]


title: dlrpb_1_min_stat_LrpChIP [L124b_1_min_stat]


title: dlrpa_1_min_stat_LrpChIP [L124a_1_min_stat]


title: H1_D0_2


title: H1_D4_521_221_Plate_1


title: dlrpb_1_liv_stat_RNAPChIP [R124b_1_liv_stat]

value: RNAP


title: H1_D9_521_221_Plate_6_1


title: dlrpa_1_liv_stat_Input [I124a_1_liv_stat]


title: dlrpa_2_liv_stat_RNAPChIP [R124a_2_liv_stat]


title: dlrpa_2_liv_stat_Input [I124a_2_liv_stat]


title: H1_D0_1


title: dlrpa_2_min_stat_RNAPChIP [R124a_2_min_stat]


title: dlrpb_1_liv_log_RNAPChIP [R124b_1_liv_log]

value: Log


title: dlrpa_1_liv_stat_RNAPChIP [R124a_1_liv_stat]


title: dlrpb_2_min_stat_LrpChIP [L124b_2_min_stat]


title: dlrpb_1_liv_log_Input [I124b_1_liv_log]


title: dlrpb_1_min_stat_Input [I124b_1_min_stat]


title: dlrpa_2_liv_stat_LrpChIP [L124a_2_liv_stat]


title: dlrpa_2_liv_log_LrpChIP [L124a_2_liv_log]


title: dlrpa_1_liv_log_LrpChIP [L124a_1_liv_log]


title: dlrpa_1_liv_log_RNAPChIP [R124a_1_liv_log]


title: dlrpa_1_min_stat_Input [I124a_1_min_stat]


title: dlrpb_1_min_stat_RNAPChIP [R124b_1_min_stat]


title: dlrpb_2_min_log_RNAPChIP [R124b_2_min_log]


title: dlrpa_1_min_stat_RNAPChIP [R124a_1_min_stat]


title: dlrpb_2_min_stat_RNAPChIP [R124b_2_min_stat]


title: dlrpa_2_liv_log_RNAPChIP [R124a_2_liv_log]


title: dlrpa_1_min_log_RNAPChIP [R124a_1_min_log]


title: dlrpb_1_min_log_Input [I124b_1_min_log]


title: dlrpa_2_min_log_Input [I124a_2_min_log]


title: dlrpa_1_min_log_Input [I124a_1_min_log]


title: dC11a_2_liv_stat_RNAPChIP [R144a_2_liv_stat]

value: dC11 lrp at thyA


title: dlrpb_1_liv_log_LrpChIP [L124b_1_liv_log]


title: dC11a_1_liv_stat_LrpChIP [L144a_1_liv_stat]

description:
processed data file:
144a_liv_stat_LrpKOsub.bedgraph
dC11_liv_stat_peaks.bedgraph


title: dC11a_2_liv_stat_LrpChIP [L144a_2_liv_stat]


title: dC11b_2_liv_stat_LrpChIP [L144b_2_liv_stat]

description:
processed data file:
144b_liv_stat_LrpKOsub.bedgraph
dC11_liv_stat_peaks.bedgraph


title: dC11a_2_liv_stat_Input [I144a_2_liv_stat]

description:
processed data file:
144a_liv_stat_LrpKOsub.bedgraph
144a_liv_stat_rnap_LrpKOsub.bedgraph


title: dlrpb_2_min_log_LrpChIP [L124b_2_min_log]


title: dC11b_1_min_stat_RNAPChIP [R144b_1_min_stat]

description:
processed data file:
144b_min_stat_rnap_LrpKOsub.bedgraph


title: dlrpa_1_min_log_LrpChIP [L124a_1_min_log]


title: dlrpb_2_min_log_Input [I124b_2_min_log]


title: dC11b_2_min_stat_RNAPChIP [R144b_2_min_stat]


title: dlrpb_1_min_log_LrpChIP [L124b_1_min_log]


title: dC11b_2_liv_stat_RNAPChIP [R144b_2_liv_stat]

description:
processed data file:
144b_liv_stat_rnap_LrpKOsub.bedgraph


title: dC11b_1_liv_stat_RNAPChIP [R144b_1_liv_stat]


title: dC11a_1_min_stat_RNAPChIP [R144a_1_min_stat]

description:
processed data file:
144a_min_stat_rnap_LrpKOsub.bedgraph


title: dC11b_1_liv_stat_LrpChIP [L144b_1_liv_stat]


title: dlrpa_2_min_log_LrpChIP [L124a_2_min_log]


title: dC11a_1_liv_stat_Input [I144a_1_liv_stat]


title: dlrpa_2_min_log_RNAPChIP [R124a_2_min_log]


title: dlrpa_1_liv_log_Input [I124a_1_liv_log]


title: dC11b_2_min_stat_Input [I144b_2_min_stat]

description:
processed data file:
144b_min_stat_LrpKOsub.bedgraph
144b_min_stat_rnap_LrpKOsub.bedgraph


title: dC11a_2_min_stat_LrpChIP [L144a_2_min_stat]

description:
processed data file:
144a_min_stat_LrpKOsub.bedgraph
dC11_min_stat_peaks.bedgraph


title: dC11b_2_liv_log_LrpChIP [L144b_2_liv_log]

description:
processed data file:
144b_liv_log_LrpKOsub.bedgraph
dC11_liv_log_peaks.bedgraph


title: dC11b_1_liv_log_Input [I144b_1_liv_log]

description:
processed data file:
144b_liv_log_LrpKOsub.bedgraph
144b_liv_log_rnap_LrpKOsub.bedgraph


title: dC11b_1_liv_log_RNAPChIP [R144b_1_liv_log]

description:
processed data file:
144b_liv_log_rnap_LrpKOsub.bedgraph


title: dC11b_2_liv_log_Input [I144b_2_liv_log]


title: dC11a_2_min_stat_RNAPChIP [R144a_2_min_stat]


title: dC11a_1_min_stat_Input [I144a_1_min_stat]

description:
processed data file:
144a_min_stat_LrpKOsub.bedgraph
144a_min_stat_rnap_LrpKOsub.bedgraph


title: dC11a_2_liv_log_LrpChIP [L144a_2_liv_log]

description:
processed data file:
144a_liv_log_LrpKOsub.bedgraph
dC11_liv_log_peaks.bedgraph


title: dC11a_1_min_stat_LrpChIP [L144a_1_min_stat]


title: dC11b_1_min_stat_LrpChIP [L144b_1_min_stat]

description:
processed data file:
144b_min_stat_LrpKOsub.bedgraph
dC11_min_stat_peaks.bedgraph


title: dC11a_1_liv_log_RNAPChIP [R144a_1_liv_log]

description:
processed data file:
144a_liv_log_rnap_LrpKOsub.bedgraph


title: dC11a_2_liv_log_Input [I144a_2_liv_log]

description:
processed data file:
144a_liv_log_LrpKOsub.bedgraph
144a_liv_log_rnap_LrpKOsub.bedgraph


title: dlrpb_1_min_log_RNAPChIP [R124b_1_min_log]

description:
processed data file:
WT_min_log_peaks.bedgraph


title: dC11b_1_min_stat_Input [I144b_1_min_stat]


title: dC11a_2_min_stat_Input [I144a_2_min_stat]


title: dC11b_2_min_stat_LrpChIP [L144b_2_min_stat]


title: dC11b_2_min_log_LrpChIP [L144b_2_min_log]

description:
processed data file:
144b_min_log_LrpKOsub.bedgraph
dC11_min_log_peaks.bedgraph


title: dC11b_2_liv_log_RNAPChIP [R144b_2_liv_log]


title: dC11b_2_min_log_Input [I144b_2_min_log]

description:
processed data file:
144b_min_log_LrpKOsub.bedgraph
144b_min_log_rnap_LrpKOsub.bedgraph


title: dC11b_1_min_log_LrpChIP [L144b_1_min_log]


title: dC11b_1_liv_log_LrpChIP [L144b_1_liv_log]


title: dC11b_2_min_log_RNAPChIP [R144b_2_min_log]

description:
processed data file:
144b_min_log_rnap_LrpKOsub.bedgraph


title: dC11a_2_liv_log_RNAPChIP [R144a_2_liv_log]


title: dC11a_1_liv_log_LrpChIP [L144a_1_liv_log]


title: dC11b_1_min_log_Input [I144b_1_min_log]


title: dC11b_1_min_log_RNAPChIP [R144b_1_min_log]


title: dC11a_2_min_log_LrpChIP [L144a_2_min_log]

description:
processed data file:
144a_min_log_LrpKOsub.bedgraph
dC11_min_log_peaks.bedgraph


title: dC11a_2_min_log_RNAPChIP [R144a_2_min_log]

description:
processed data file:
144a_min_log_rnap_LrpKOsub.bedgraph


title: L136Rb_2_liv_stat_RNAPChIP [R168b_2_liv_stat]

description:
processed data file:
168b_liv_stat_rnap_LrpKOsub.bedgraph
L136R_liv_stat_deseq.csv

value: L136R lrp at thyA


title: dC11a_1_liv_log_Input [I144a_1_liv_log]


title: dC11a_1_min_log_LrpChIP [L144a_1_min_log]


title: dC11a_2_min_log_Input [I144a_2_min_log]

description:
processed data file:
144a_min_log_LrpKOsub.bedgraph
144a_min_log_rnap_LrpKOsub.bedgraph


title: dC11a_1_min_log_Input [I144a_1_min_log]


title: L136Rb_2_liv_stat_LrpChIP [L168b_2_liv_stat]

description:
processed data file:
168b_liv_stat_LrpKOsub.bedgraph
L136R_liv_stat_peaks.bedgraph


title: L136Ra_1_liv_stat_Input [I168a_1_liv_stat]

description:
processed data file:
168a_liv_stat_LrpKOsub.bedgraph
168a_liv_stat_rnap_LrpKOsub.bedgraph


title: L136Ra_2_liv_stat_RNAPChIP [R168a_2_liv_stat]

description:
processed data file:
168a_liv_stat_rnap_LrpKOsub.bedgraph
L136R_liv_stat_deseq.csv


title: dC11a_1_min_log_RNAPChIP [R144a_1_min_log]


title: L136Ra_1_liv_stat_RNAPChIP [R168a_1_liv_stat]


title: L136Rb_1_liv_stat_LrpChIP [L168b_1_liv_stat]


title: L136Rb_2_min_stat_RNAPChIP [R168b_2_min_stat]

description:
processed data file:
168b_min_stat_rnap_LrpKOsub.bedgraph
L136R_min_stat_deseq.csv


title: L136Ra_2_liv_stat_LrpChIP [L168a_2_liv_stat]

description:
processed data file:
168a_liv_stat_LrpKOsub.bedgraph
L136R_liv_stat_peaks.bedgraph


title: L136Rb_2_min_stat_LrpChIP [L168b_2_min_stat]

description:
processed data file:
168b_min_stat_LrpKOsub.bedgraph
L136R_min_stat_peaks.bedgraph


title: L136Rb_2_liv_stat_Input [I168b_2_liv_stat]

description:
processed data file:
168b_liv_stat_LrpKOsub.bedgraph
168b_liv_stat_rnap_LrpKOsub.bedgraph


title: L136Rb_2_min_stat_Input [I168b_2_min_stat]

description:
processed data file:
168b_min_stat_LrpKOsub.bedgraph
168b_min_stat_rnap_LrpKOsub.bedgraph


title: L136Rb_1_min_stat_RNAPChIP [R168b_1_min_stat]


title: L136Ra_1_min_stat_RNAPChIP [R168a_1_min_stat]

description:
processed data file:
168a_min_stat_rnap_LrpKOsub.bedgraph
L136R_min_stat_deseq.csv


title: L136Rb_1_min_stat_Input [I168b_1_min_stat]


title: L136Ra_2_min_stat_RNAPChIP [R168a_2_min_stat]


title: L136Rb_1_min_stat_LrpChIP [L168b_1_min_stat]


title: L136Rb_1_liv_stat_RNAPChIP [R168b_1_liv_stat]


title: L136Rb_2_liv_log_LrpChIP [L168b_2_liv_log]

description:
processed data file:
168b_liv_log_LrpKOsub.bedgraph
L136R_liv_log_peaks.bedgraph


title: L136Ra_2_min_stat_Input [I168a_2_min_stat]

description:
processed data file:
168a_min_stat_LrpKOsub.bedgraph
168a_min_stat_rnap_LrpKOsub.bedgraph


title: L136Ra_1_min_stat_Input [I168a_1_min_stat]


title: L136Ra_2_min_stat_LrpChIP [L168a_2_min_stat]

description:
processed data file:
168a_min_stat_LrpKOsub.bedgraph
L136R_min_stat_peaks.bedgraph


title: L136Rb_2_liv_log_Input [I168b_2_liv_log]

description:
processed data file:
168b_liv_log_LrpKOsub.bedgraph
168b_liv_log_rnap_LrpKOsub.bedgraph


title: L136Rb_1_liv_log_RNAPChIP [R168b_1_liv_log]

description:
processed data file:
168b_liv_log_rnap_LrpKOsub.bedgraph
L136R_liv_log_deseq.csv


title: L136Ra_1_liv_log_LrpChIP [L168a_1_liv_log]

description:
processed data file:
168a_liv_log_LrpKOsub.bedgraph
L136R_liv_log_peaks.bedgraph


title: L136Ra_2_liv_log_LrpChIP [L168a_2_liv_log]


title: L136Ra_1_liv_log_RNAPChIP [R168a_1_liv_log]

description:
processed data file:
168a_liv_log_rnap_LrpKOsub.bedgraph
L136R_liv_log_deseq.csv


title: L136Rb_2_min_log_RNAPChIP [R168b_2_min_log]

description:
processed data file:
168b_min_log_rnap_LrpKOsub.bedgraph
L136R_min_log_deseq.csv


title: L136Rb_2_min_log_LrpChIP [L168b_2_min_log]

description:
processed data file:
168b_min_log_LrpKOsub.bedgraph
L136R_min_log_peaks.bedgraph


title: L136Ra_1_liv_log_Input [I168a_1_liv_log]

description:
processed data file:
168a_liv_log_LrpKOsub.bedgraph
168a_liv_log_rnap_LrpKOsub.bedgraph


title: L136Rb_1_liv_log_Input [I168b_1_liv_log]


title: L136Ra_2_liv_log_RNAPChIP [R168a_2_liv_log]


title: L136Rb_2_min_log_Input [I168b_2_min_log]

description:
processed data file:
168b_min_log_LrpKOsub.bedgraph
168b_min_log_rnap_LrpKOsub.bedgraph


title: L136Ra_1_min_stat_LrpChIP [L168a_1_min_stat]


title: L136Rb_1_min_log_RNAPChIP [R168b_1_min_log]


title: L136Rb_1_min_log_Input [I168b_1_min_log]


title: L136Ra_2_min_log_Input [I168a_2_min_log]

description:
processed data file:
168a_min_log_LrpKOsub.bedgraph
168a_min_log_rnap_LrpKOsub.bedgraph


title: L136Rb_1_min_log_LrpChIP [L168b_1_min_log]


title: L136Rb_2_liv_log_RNAPChIP [R168b_2_liv_log]


title: D114Eb_2_liv_stat_RNAPChIP [R142b_2_liv_stat]

description:
processed data file:
142b_liv_stat_rnap_LrpKOsub.bedgraph
D114E_liv_stat_deseq.csv

value: D114E lrp at thyA


title: L136Ra_1_min_log_LrpChIP [L168a_1_min_log]

description:
processed data file:
168a_min_log_LrpKOsub.bedgraph
L136R_min_log_peaks.bedgraph


title: L136Rb_1_liv_log_LrpChIP [L168b_1_liv_log]


title: D114Eb_2_liv_stat_LrpChIP [L142b_2_liv_stat]

description:
processed data file:
142b_liv_stat_LrpKOsub.bedgraph
D114E_liv_stat_peaks.bedgraph


title: D114Eb_1_liv_stat_RNAPChIP [R142b_1_liv_stat]


title: D114Eb_1_liv_stat_LrpChIP [L142b_1_liv_stat]


title: L136Ra_1_min_log_Input [I168a_1_min_log]


title: D114Eb_1_liv_stat_Input [I142b_1_liv_stat]

description:
processed data file:
142b_liv_stat_LrpKOsub.bedgraph
142b_liv_stat_rnap_LrpKOsub.bedgraph


title: D114Eb_2_liv_stat_Input [I142b_2_liv_stat]


title: D114Ea_2_liv_stat_RNAPChIP [R142a_2_liv_stat]

description:
processed data file:
142a_liv_stat_rnap_LrpKOsub.bedgraph
D114E_liv_stat_deseq.csv


title: L136Ra_2_min_log_RNAPChIP [R168a_2_min_log]

description:
processed data file:
168a_min_log_rnap_LrpKOsub.bedgraph
L136R_min_log_deseq.csv


title: L136Ra_2_min_log_LrpChIP [L168a_2_min_log]


title: D114Ea_2_liv_stat_LrpChIP [L142a_2_liv_stat]

description:
processed data file:
142a_liv_stat_LrpKOsub.bedgraph
D114E_liv_stat_peaks.bedgraph


title: D114Ea_2_liv_stat_Input [I142a_2_liv_stat]

description:
processed data file:
142a_liv_stat_LrpKOsub.bedgraph
142a_liv_stat_rnap_LrpKOsub.bedgraph


title: L136Ra_1_min_log_RNAPChIP [R168a_1_min_log]


title: D114Ea_1_liv_stat_LrpChIP [L142a_1_liv_stat]


title: D114Eb_2_min_stat_LrpChIP [L142b_2_min_stat]

description:
processed data file:
142b_min_stat_LrpKOsub.bedgraph
D114E_min_stat_peaks.bedgraph


title: D114Eb_1_min_stat_Input [I142b_1_min_stat]

description:
processed data file:
142b_min_stat_LrpKOsub.bedgraph
142b_min_stat_rnap_LrpKOsub.bedgraph


title: D114Eb_1_min_stat_RNAPChIP [R142b_1_min_stat]

description:
processed data file:
142b_min_stat_rnap_LrpKOsub.bedgraph
D114E_min_stat_deseq.csv


title: D114Ea_2_min_stat_Input [I142a_2_min_stat]

description:
processed data file:
142a_min_stat_LrpKOsub.bedgraph
142a_min_stat_rnap_LrpKOsub.bedgraph


title: D114Ea_1_min_stat_RNAPChIP [R142a_1_min_stat]

description:
processed data file:
142a_min_stat_rnap_LrpKOsub.bedgraph
D114E_min_stat_deseq.csv


title: D114Ea_2_min_stat_RNAPChIP [R142a_2_min_stat]


title: D114Ea_1_min_stat_LrpChIP [L142a_1_min_stat]

description:
processed data file:
142a_min_stat_LrpKOsub.bedgraph
D114E_min_stat_peaks.bedgraph


title: D114Eb_1_min_stat_LrpChIP [L142b_1_min_stat]


title: D114Eb_2_liv_log_Input [I142b_2_liv_log]

description:
processed data file:
142b_liv_log_LrpKOsub.bedgraph
142b_liv_log_rnap_LrpKOsub.bedgraph


title: D114Eb_2_liv_log_LrpChIP [L142b_2_liv_log]

description:
processed data file:
142b_liv_log_LrpKOsub.bedgraph
D114E_liv_log_peaks.bedgraph


title: D114Ea_1_liv_stat_RNAPChIP [R142a_1_liv_stat]


title: D114Ea_1_min_stat_Input [I142a_1_min_stat]


title: D114Ea_2_liv_log_Input [I142a_2_liv_log]

description:
processed data file:
142a_liv_log_LrpKOsub.bedgraph
142a_liv_log_rnap_LrpKOsub.bedgraph


title: D114Eb_1_liv_log_LrpChIP [L142b_1_liv_log]


title: D114Ea_1_liv_stat_Input [I142a_1_liv_stat]


title: D114Eb_1_liv_log_Input [I142b_1_liv_log]


title: D114Eb_1_liv_log_RNAPChIP [R142b_1_liv_log]

description:
processed data file:
142b_liv_log_rnap_LrpKOsub.bedgraph
D114E_liv_log_deseq.csv


title: D114Ea_2_liv_log_LrpChIP [L142a_2_liv_log]

description:
processed data file:
142a_liv_log_LrpKOsub.bedgraph
D114E_liv_log_peaks.bedgraph


title: D114Eb_2_min_stat_RNAPChIP [R142b_2_min_stat]


title: D114Ea_2_liv_log_RNAPChIP [R142a_2_liv_log]

description:
processed data file:
142a_liv_log_rnap_LrpKOsub.bedgraph
D114E_liv_log_deseq.csv


title: D114Ea_1_liv_log_RNAPChIP [R142a_1_liv_log]


title: D114Ea_1_liv_log_LrpChIP [L142a_1_liv_log]


title: D114Ea_2_min_stat_LrpChIP [L142a_2_min_stat]


title: D114Eb_2_min_log_LrpChIP [L142b_2_min_log]

description:
processed data file:
142b_min_log_LrpKOsub.bedgraph
D114E_min_log_peaks.bedgraph


title: D114Eb_2_min_log_RNAPChIP [R142b_2_min_log]

description:
processed data file:
142b_min_log_rnap_LrpKOsub.bedgraph
D114E_min_log_deseq.csv


title: D114Eb_2_liv_log_RNAPChIP [R142b_2_liv_log]


title: D114Ea_1_min_log_RNAPChIP [R142a_1_min_log]

description:
processed data file:
142a_min_log_rnap_LrpKOsub.bedgraph
D114E_min_log_deseq.csv


title: D114Eb_2_min_log_Input [I142b_2_min_log]

description:
processed data file:
142b_min_log_LrpKOsub.bedgraph
142b_min_log_rnap_LrpKOsub.bedgraph


title: D114Eb_1_min_log_Input [I142b_1_min_log]


title: D114Ea_2_min_log_Input [I142a_2_min_log]

description:
processed data file:
142a_min_log_LrpKOsub.bedgraph
142a_min_log_rnap_LrpKOsub.bedgraph


title: D114Ea_2_min_log_RNAPChIP [R142a_2_min_log]


title: D114Ea_1_min_log_LrpChIP [L142a_1_min_log]

description:
processed data file:
142a_min_log_LrpKOsub.bedgraph
D114E_min_log_peaks.bedgraph


title: WTb_1_liv_stat_LrpChIP [L123b_1_liv_stat]

description:
processed data file:
123b_liv_stat_LrpKOsub.bedgraph
WT_liv_stat_peaks.bedgraph

value: WT lrp at thyA


title: WTb_2_liv_stat_RNAPChIP [R123b_2_liv_stat]

description:
processed data file:
123b_liv_stat_rnap_LrpKOsub.bedgraph
WT_liv_stat_deseq.csv


title: WTa_2_liv_stat_RNAPChIP [R123a_2_liv_stat]

description:
processed data file:
123a_liv_stat_rnap_LrpKOsub.bedgraph
WT_liv_stat_deseq.csv


title: WTa_2_liv_stat_Input [I123a_2_liv_stat]

description:
processed data file:
123a_liv_stat_LrpKOsub.bedgraph
123a_liv_stat_rnap_LrpKOsub.bedgraph


title: WTa_2_liv_stat_LrpChIP [L123a_2_liv_stat]

description:
processed data file:
123a_liv_stat_LrpKOsub.bedgraph
WT_liv_stat_peaks.bedgraph


title: WTb_1_liv_stat_Input [I123b_1_liv_stat]

description:
processed data file:
123b_liv_stat_LrpKOsub.bedgraph
123b_liv_stat_rnap_LrpKOsub.bedgraph


title: WTb_2_liv_stat_LrpChIP [L123b_2_liv_stat]


title: WTb_2_liv_stat_Input [I123b_2_liv_stat]


title: D114Eb_2_min_stat_Input [I142b_2_min_stat]

description:
processed data file:
142b_min_stat_LrpKOsub.bedgraph
142b_min_stat_rnap_LrpKOsub.bedgraph


title: D114Ea_1_liv_log_Input [I142a_1_liv_log]

description:
processed data file:
142a_liv_log_LrpKOsub.bedgraph
142a_liv_log_rnap_LrpKOsub.bedgraph


title: WTa_1_liv_stat_LrpChIP [L123a_1_liv_stat]


title: WTa_1_liv_stat_RNAPChIP [R123a_1_liv_stat]


title: WTb_1_liv_stat_RNAPChIP [R123b_1_liv_stat]


title: D114Eb_1_min_log_RNAPChIP [R142b_1_min_log]


title: D114Eb_1_min_log_LrpChIP [L142b_1_min_log]


title: WTa_1_liv_stat_Input [I123a_1_liv_stat]


title: D114Ea_2_min_log_LrpChIP [L142a_2_min_log]


title: WTb_2_min_stat_LrpChIP [L123b_2_min_stat]

description:
processed data file:
123b_min_stat_LrpKOsub.bedgraph
WT_min_stat_peaks.bedgraph


title: WTb_2_min_stat_RNAPChIP [R123b_2_min_stat]

description:
processed data file:
123b_min_stat_rnap_LrpKOsub.bedgraph
WT_min_stat_deseq.csv


title: WTb_2_min_stat_Input [I123b_2_min_stat]

description:
processed data file:
123b_min_stat_LrpKOsub.bedgraph
123b_min_stat_rnap_LrpKOsub.bedgraph


title: D114Ea_1_min_log_Input [I142a_1_min_log]


title: WTb_1_min_stat_Input [I123b_1_min_stat]


title: WTb_1_min_stat_LrpChIP [L123b_1_min_stat]


title: WTa_1_min_stat_RNAPChIP [R123a_1_min_stat]

description:
processed data file:
123a_min_stat_rnap_LrpKOsub.bedgraph
WT_min_stat_deseq.csv


title: WTa_1_min_stat_LrpChIP [L123a_1_min_stat]

description:
processed data file:
123a_min_stat_LrpKOsub.bedgraph
WT_min_stat_peaks.bedgraph


title: WTa_2_min_stat_RNAPChIP [R123a_2_min_stat]


title: WTa_1_min_stat_Input [I123a_1_min_stat]

description:
processed data file:
123a_min_stat_LrpKOsub.bedgraph
123a_min_stat_rnap_LrpKOsub.bedgraph


title: WTa_2_min_stat_LrpChIP [L123a_2_min_stat]


title: WTb_2_liv_log_RNAPChIP [R123b_2_liv_log]

description:
processed data file:
123b_liv_log_rnap_LrpKOsub.bedgraph
WT_liv_log_deseq.csv


title: WTb_2_liv_log_Input [I123b_2_liv_log]

description:
processed data file:
123b_liv_log_LrpKOsub.bedgraph
123b_liv_log_rnap_LrpKOsub.bedgraph


title: WTb_2_liv_log_LrpChIP [L123b_2_liv_log]

description:
processed data file:
123b_liv_log_LrpKOsub.bedgraph
WT_liv_log_peaks.bedgraph


title: WTb_1_min_stat_RNAPChIP [R123b_1_min_stat]


title: WTa_2_min_stat_Input [I123a_2_min_stat]


title: WTa_2_liv_log_RNAPChIP [R123a_2_liv_log]

description:
processed data file:
123a_liv_log_rnap_LrpKOsub.bedgraph
WT_liv_log_deseq.csv


title: WTa_1_liv_log_LrpChIP [L123a_1_liv_log]

description:
processed data file:
123a_liv_log_LrpKOsub.bedgraph
WT_liv_log_peaks.bedgraph


title: WTb_1_min_log_RNAPChIP [R123b_1_min_log]

description:
processed data file:
123b_min_log_rnap_LrpKOsub.bedgraph
WT_min_log_deseq.csv


title: WTb_1_liv_log_Input [I123b_1_liv_log]


title: WTa_2_liv_log_LrpChIP [L123a_2_liv_log]


title: WTb_2_min_log_LrpChIP [L123b_2_min_log]

description:
processed data file:
123b_min_log_LrpKOsub.bedgraph
WT_min_log_peaks.bedgraph


title: WTb_1_liv_log_LrpChIP [L123b_1_liv_log]


title: WTb_2_min_log_Input [I123b_2_min_log]

description:
processed data file:
123b_min_log_LrpKOsub.bedgraph
123b_min_log_rnap_LrpKOsub.bedgraph


title: WTb_1_liv_log_RNAPChIP [R123b_1_liv_log]


title: WTa_2_min_log_Input [I123a_2_min_log]

description:
processed data file:
123a_min_log_LrpKOsub.bedgraph
123a_min_log_rnap_LrpKOsub.bedgraph


title: WTb_2_min_log_RNAPChIP [R123b_2_min_log]


title: WTb_1_min_log_LrpChIP [L123b_1_min_log]


title: WTa_1_min_log_Input [I123a_1_min_log]


title: WTa_1_liv_log_Input [I123a_1_liv_log]

description:
processed data file:
123a_liv_log_LrpKOsub.bedgraph
123a_liv_log_rnap_LrpKOsub.bedgraph


title: WTa_2_min_log_LrpChIP [L123a_2_min_log]

description:
processed data file:
123a_min_log_LrpKOsub.bedgraph
WT_min_log_peaks.bedgraph


title: WTa_1_min_log_RNAPChIP [R123a_1_min_log]

description:
processed data file:
123a_min_log_rnap_LrpKOsub.bedgraph
WT_min_log_deseq.csv


title: WTb_1_min_log_Input [I123b_1_min_log]


title: WTa_1_liv_log_RNAPChIP [R123a_1_liv_log]


title: WTa_2_liv_log_Input [I123a_2_liv_log]


title: WTa_2_min_log_RNAPChIP [R123a_2_min_log]


title: LLC-ADAM2-OVA_3_treated

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Ave, Room 1080

country: Canada

institute: Lunenfeld- Tanenbaum Research Institute

description: Adam 2_3_treated

data_processing:
The fastq files are aligned to mm10 using Hisat2 in paired-end mode
The aligned sam files are converted to soorted bam files, using Samtools sort command
Raw counts are obtained using Subread FeatureCounts using Ensembl mm10 annotation file (Mus_musculus.GRCm38.102.gtf)
Supplementary files format and content: Count tables (not normalized), Tab-limited text files

source_name: Lung cancer

growth_protocol: LLC1 cell lines were grown in DMEM supplemented with 10%FBS and 1% penicillin/streptomycin.

extract_protocol:
Tumors were flash frozen on dry ice, and RNA was extraceted using Trizol reagent. Total RNA was treated with DNAase easy (cat#E1009_A) from Zymo Researech.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries prepared using standard Ilumina protocols
Paired-End RNA sequenencing

treatment_protocol: Cell were transduced with a construct containing ADAM2-OVA-Puromycin or a mock construct containing OVA-puromycin. Cell were maintened in media supplemented with 10ug/ml of puromycin. LLC1 cells were split 1 in 4 every second day or 1/8 every 4th day. For s.c. injections of cells, mice were anesthesized with 2.5% isoflorane with oxygen. LLC-CTLR-OVA or LLC-ADAM2-OVA cell lines were gently injected subcutaneously in the upper right backside of mice. 1x10^5 cells were injected per mouse for all the experiments. Intravenous injection of 15-20x10^6 OT-I  was performed on D14 after tumor reached the volume between 100-600 mm^3, followed by immunization with OVA/CFA on day 1 and OVA/IFA on day 7.

value: Lung cancer

value: Lewis Lung Carcinoma Cell Line (LLC1)

value: G12C Kras mutant

value: Treated=Adoptive Cell Transfer of CD8 OT-I T cells


title: LLC-ADAM2-OVA_2_treated

description: Adam 2_2_treated


title: WTa_1_min_log_LrpChIP [L123a_1_min_log]


title: LLC-ADAM2-OVA_2_untreated

description: Adam 2_2_untreated


title: hiPSC with biallelic KI of WT MYH7, rep 2

city: Seattle

first: Kai-Chun

state: Washington

address: 850 Republican Street

department: University of Washington, School of Medicine

institute: Institute for Stem Cell and Regenerative Medicine

description:
Table_S2.xlsx
DKI clone 56 iPSCs - rep 2

data_processing:
First step: bcl2fastq to demultiplex reads
Second step: pear -q30 to generation >q30 paired reads of the 57-bp sequence containing all five mutagenized codons
Third step: count reads for plasmid libraries (Table_S1.xlsx), iPSC libraries (Table_S2.xlsx), iPS-CM libraries (Table_S3.xlsx)
Supplementary files format and content: Table_S1.xlsx, Table_S2.xlsx, Table_S3.xlsx all show counted reads from plasmid libraries, iPSC libraries, and iPS-CM libraries
Library strategy: CRaTER

extract_protocol:
DNA extracted from iPS/cardiomyocytes with Qiagen DNeasy kit
First PCR appends custom adapter sequences (see Matreyek et al., Nat Methods 2019) and second PCR appends indices and P5/P7 sequences

value: cell line

value: iPSC

value: pluripotent stem cell


title: LLC-CTLR-OVA_3_treated


title: LLC-CTLR-OVA_3_untreated


title: LLC-CTRL-OVA_1_treated


title: LLC-CTRL-OVA_1_untreated


title: LLC-ADAM2-OVA_1_treated

description: Adam 2_1_treated


title: hiPSC with heterozygous KI of MYH7 Variant Library, rep 1

description:
Table_S2.xlsx
Test 81 2 million Q2 sort - rep 1


title: hiPSC-derived cardiomyocytes with heterozygous KI of MYH7 Variant Library, rep 2

description:
Table_S3.xlsx
T25_Test_81_2_million_Cardios_Replicate_2_harvest_5_31

value: IPS-CM

value: pluripotent stem cell-derived cardiomyocyte

value: harvested 25 days after activation of differentiation


title: Chlamydia Infected 48hpi Exp_Replicate_1

type: RNA

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, 0.75µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted single-color raw data txt files were further analyzed using R and the associated BioConductor package limma. Background was removed using method normexp with offset 15, followed by quantile normalization.

label_protocol: RNA was labeled with the single-color Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: Primary mesenchymal cells from the human fallopian tube were grown in corresponding media as described in the accompanying publication (materials and methods).

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.

treatment_protocol: Cells were cultured and infected with C.trachomatis as described in the accompanying publication.

tag: condition

tag: replicate


title: LLC-CTLR-OVA_2_treated

tag: tissue


title: LLC-ADAM2-OVA_1_untreated

description: Adam 2_1_untreated

tag: cell line


title: Chlamydia Infected 48hpi Exp_Replicate_2


title: Chlamydia Infected 24hpi Exp_Replicate_3


title: Non-infected Exp_Replicate_3

source_name: Non-infected Exp_Replicate_3

value: NI


title: Chlamydia Infected 48hpi Exp_Replicate_3


title: Non-infected Exp_Replicate_2

source_name: Non-infected Exp_Replicate_2


title: Chlamydia Infected 24hpi Exp_Replicate_2


title: hiPSC with biallelic KI of WT MYH7, rep 1

description:
Table_S2.xlsx
DKI clone 56 iPSCs - rep 1

tag: cell type


title: Non-infected Exp_Replicate_1

source_name: Non-infected Exp_Replicate_1


title: Chlamydia Infected 24hpi Exp_Replicate_1


title: Plasmid DNA (pJet-MYH7-mTagBFP2-EF1α-BSD) mutagenized at p.866

description:
Table_S1.xlsx
1-199 lib

library_source: other

molecule: other

organism: synthetic construct

value: Plasmid DNA


title: hiPSC with heterozygous KI of MYH7 Variant Library, rep 2

description:
Table_S2.xlsx
Test 81 2 million Q2 sort - rep 2


title: Plasmid DNA (pJet-MYH7-mTagBFP2-EF1α-BSD) mutagenized at p.865

description:
Table_S1.xlsx
1-196 lib


title: Plasmid DNA (pJet-MYH7-mTagBFP2-EF1α-BSD) mutagenized at p.852

description:
Table_S1.xlsx
1-198 lib


title: hiPSC-derived cardiomyocytes with heterozygous KI of MYH7 Variant Library, rep 1

description:
Table_S3.xlsx
T25_Test_81_2_million_Cardios_Replicate_1_harvest_5_31


title: LLC-ADAM2-OVA_3_untreated

description: Adam 2_3_untreated

tag: genotype


title: Plasmid DNA (pJet-MYH7-mTagBFP2-EF1α-BSD) mutagenized at p.848

description:
Table_S1.xlsx
1-163 lib


title: Mock_IP_control_replicate_2 [Mock_R2]

city: Guildford

first: Waleed

last: Albihlal

state: Surrey

address: Stag Hill Campus

department: Microbial Sciences

country: United Kingdom

institute: University of Surrey

description:
fRIP-seq
lib_0010_S10_L002

data_processing:
Low quality reads were trimmed using FastX_tool kit with a minimum phred33 score of 20 and with a minimum read length thresold of 20 bp
Reads were mapped to Saccharomyces cerivisae genome version R64-2-1 using GMAP/GSNAP (Wu and Watanabe, 2005) allowing a maximum of 3 mismatches output in BAM format.
Unmapped reads were filtered out using samtools (Li et al., 2009)
Reads mapped to multiple genomic regions were filtered out using samtools (Li et al., 2009)
Data were scaled, normalized to total RNA and enrichment of fRIP-seq targets over mock IP control were calculated using custom R scripts.
Genome_build: R64-2-1
Supplementary_files_format_and_content: raw_genomic_read_count

growth_protocol: Cells were grown in rich YPD media at 30C to mid-log phase (OD600 = 0.6)

extract_protocol:
Cells were pelleted at room temperature then washed three times with 1X PBS. Cell pellets were flash-frozen in liquid nitrogen then ground under cryogenic conditions to fine powder. Cell powders were then resuspended in fRIP lysis buffer.
RNA was converted to cDNA Bioline Sensifast cDNA synthesis kit. cDNA was the converted to double-stranded cDNA using NEBNext® Ultra II Non-Directional RNA Second Strand Synthesis Module (New England Biolabs) followed by shearing DNA to an average fragment size of 150 bp using Covaris S220 focused sonicator. Sequencing libraries were constructed using JetSeq DNA library preparation kit (Bioline, Cat# BIO-68025). Total RNA samples were ribo-depleted using ribo-zero gold rRNA removal kit (Illumina, cat# MRZY1306) then processed the same way as the fRIP-seq samples.

treatment_protocol: Cells were crosslinked with formaldehyde to a final concentration of 0.3%

tag: strain background

tag: genotype/variation

value: Wild type

tag: medium

value: YDP

tag: growth stage

value: Mid-log phase (OD600 = 0.6)


title: Pfk1_fRIP-seq_replicate_2 [Pfk1_R2]

description:
fRIP-seq
lib_0005_S5_L002


title: Pollen_rep1_CSPh1b

city: Saskatoon

first: Sateesh

last: Kagale

state: SK

address: 110 Gymnasium Place

department: Aquatic and Crop Resource Development

institute: National Research Council Canada

data_processing:
Basecalls performed using CASAVA
Short Illumina reads were filtered using Trimmomatic by trimming adapter and low quality sequences and removing reads shorter than 75 bp
Filtered reads were aligned to the wheat reference genome (IWGSC v1.0) using STAR
Transcript abundance was estimated using the RSEM (v1.3.3) and the IWGSC v1.1 annotation, and the expected read counts and transcripts per million (TPM) values were generated
Genome_build: IWGSCv1.0
Supplementary_files_format_and_content: Matrix table with TPM values for each sample
Supplementary_files_format_and_content: Matrix table with readcounts values for each sample

organism: Triticum aestivum

source_name: Pollen

growth_protocol: Plants were grown in a growth chamber at aconstant temperature of 21±1°C, a photoperiod of 16 h day and 8 h night and the minimum photosynthetic photon flux density of 400 μmol m−2 s−1 during the day

extract_protocol:
Meiocytes were isolated using MioCapture protocol (Shunmugam et al. 2018 BMC Plant Biology 18: 293)
TruSeq RNA sequencing libraries were constructed following the manufacturer’s instructions (Illumina, http://www.illumina.com/)

treatment_protocol: Plants were treated every two weeks using water soluble 20-20-20 fertilizer  at a rate of 3.0 g L-1 and chelated micronutrient mix at a rate of 0.3 g L-1

tag: tissue/stage

value: Pollen

value: Chinese Spring CSPh1b

tag: process

value: Ph1b mutant


title: total_RNA-seq_replicate_2 [RNA_R2]

description:
total RNA-seq
lib_0002_S2_L002


title: Mock_IP_control_replicate_1 [Mock_R1]

description:
fRIP-seq
lib_0009_S9_L002


title: Pfk1_fRIP-seq_replicate_1 [Pfk1_R1]

description:
fRIP-seq
lib_0003_S3_L002


title: total_RNA-seq_replicate_1 [RNA_R1]

description:
total RNA-seq
lib_0001_S1_L002


title: Pfk2_fRIP_ses_replicate_1 [Pfk2_R1]

description:
fRIP-seq
lib_0007_S7_L002


title: Anther_rep2_CSPh1b

source_name: Anthers

value: Anthers


title: Plasmid DNA (pJet-MYH7-mTagBFP2-EF1α-BSD) mutagenized at p.850

description:
Table_S1.xlsx
1-197 lib


title: Pfk2_fRIP_ses_replicate_2 [Pfk2_R2]

description:
fRIP-seq
lib_0008_S8_L002


title: Pollen_rep2_CSPh1b


title: Anther_rep3_CSPh1b


title: Anther_rep1_CSPh1b


title: Leaf_rep1_CSPh1b

source_name: Leaf

value: Leaf


title: Leaf_rep2_CSPh1b


title: Flag leaf_rep3_CSPh1b

source_name: Flag leaf

value: Flag leaf


title: Pollen_rep3_CS

value: Chinese Spring

value: Reproductive control


title: Flag leaf_rep2_CSPh1b


title: LLC-CTLR-OVA_2_untreated

tag: strain

value: Lung cancer

value: Lewis Lung Carcinoma Cell Line (LLC1)

value: G12C Kras mutant


title: Leaf_rep3_CSPh1b


title: Pollen_rep1_CS


title: Flag leaf_rep1_CSPh1b


title: Anther_rep3_CS


title: Pollen_rep3_CSPh1b


title: Anther_rep2_CS


title: Leaf_rep2_CS

value: Vegetative control


title: Pollen_rep2_CS


title: Leaf_rep1_CS


title: Metaphase-II_rep2_CS

source_name: Meiocytes

value: Meiocytes

value: Meiosis


title: Metaphase-I_rep3_CS


title: Flagleaf_rep2_CS


title: Metaphase-I_rep1_CS


title: Metaphase-II_rep1_CS


title: Pachytene_rep1_CS


title: Flagleaf_rep1_CS


title: Metaphase-I_rep2_CS


title: Diplotene/Diakinesis_rep2_CS


title: Anther_rep1_CS


title: Zygotene_rep3_CS


title: Leaf_rep3_CS


title: Pachytene_rep3_CS


title: Pre-meiotic G2_rep1_CS


title: Flagleaf_rep3_CS


title: Metaphase-II_rep3_CS


title: Diplotene/Diakinesis_rep1_CS


title: Pachytene_rep2_CS


title: Zygotene_rep2_CS


title: Leptotene_rep2_CS


title: U2OSr-2

city: Shenyang

first: Ming

last: He

state: Liaoning

address: No. 36 Sanhao Street

institute: Shengjing Hospital of China Medical University

description:
test
miRCURY LNA miRNA Custom PCR Panels (catalog: 339330, QIAGEN)

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/au/analyze/
For the normalization it uses the average of five housekeeping genes: SNORD61, SNORD68, SNORD72, SNORD95, SNORD96A.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

source_name: MTX-resistant U2OS cells

label_protocol: miRNA and mRNA were collected by RNeasy Micro Kit (catalog: 74004, QIAGEN). A total of 300ng RNA was then reverse transcribed to cDNA by ProtoScript® II Reverse Transcriptase (catalog: M0368, New England Biolabs, Ipswich, MA, USA).  Quantitative real-time PCR (qRT-PCR) was performed with Luna® Universal One-Step RT-qPCR Kit (catalog: E3005, New England Biolabs). Reactions were conducted with the Applied Bio-systems MiniAmp Thermal Cyclers (Thermo Fisher Scientific, Waltham, MA, USA) using the following steps: 40 cycles of 95 °C for 15 seconds, 60 °C for 10 seconds, and 72 °C for 20 seconds. Following the previously discussed method2-ΔΔCq method, gene expression was normalized to the GAPDH to examine the relative expression. pGPU6/Neo vector, miRNA mimics, small interfering RNA (siRNA), short-hairpin RNA (shRNA), miR-197-3p mutation, and the primers for detection were generated by GenePharma (Shanghai, China). The primers for gene detection list in Supplementary Table S2.

growth_protocol: human osteosarcoma cell lines U2OS (catalog: HTB-96) and MG63 (catalog: CRL-1427) were sourced from the American Type Culture Collection (Manassas, VA, USA). U2OS and MG63 were cultured in Dulbecco's modified Eagle medium (catalog: BE12-604F, Lonza, Basel, Switzerland) supplemented with 10% fetal bovine serum (catalog: F7524, Sigma-Aldrich, St. Louis, MO, USA). All cells were kept at 37 °C in a 5% CO2 environment.

extract_protocol: Total RNA was collected from fresh cells with the miRNeasy Micro Kit (catalog: 217084, QIAGEN, Hilden, Germany) according to the manufacturer’s protocol (Qiagen, Hilden, Germany).

treatment_protocol: Parental U2OS cells were initially exposed to 3ng/ml (0.01 µM) MTX. Subjecting the parental cell lines to stepwise raised MTX concentrations, MTX-resistant subclones were produced.

value: MTX-resistant U2OS cells

value: human osteosarcoma U2OS cells


title: U2OSp-3

description:
Control
miRCURY LNA miRNA Custom PCR Panels (catalog: 339330, QIAGEN)

source_name: parental U2OS cells

treatment_protocol: U2OS cells were taken from a moderately differentiated tibia sarcoma, possessing epithelial adherent morphology. U2OS cells are positive for cartilage markers but negative for nearly all osteoblastic markers.

value: parental U2OS cells


title: Leptotene_rep3_CS


title: MSS12, WT, Untreated, WT2

city: London

first: Ana Luisa

last: Gil Martinez

address: 33 Queen Square

department: Clinical and Movement Neurosciences

institute: University College London

data_processing:
Run data were demultiplexed and converted to fastq files using Illumina’s BCL Convert Software v3.75.  At the same time, the unique molecular index was moved into the read header for downstream analysis.
FASTQ files were then quality and adapter trimmed by fastp v0.23.2 before being aligned to the mouse genome UCSC mm10 using RNA-STAR v2.5.2b.
Quality of alignment was assessed using PicardCommandLine CollectRNASeqMetrics v2.8.1 to ensure absence of ribosomal RNA contamination and majority presence of mRNA.
Aligned reads were then UMI deduplicated using Je-suite v1.2.1 to and reads per transcript were counted by FeatureCounts in order to produce a digital output of gene expression.
Assembly: mm10
Supplementary files format and content: The data table contains one row per annotated feature and one column per sequenced sample.

source_name: Liver

extract_protocol:
RNA was extracted from liver samples using Qiagen RNeasy kits (74004) following kit instructions.
cDNA libraries were prepared with the Kapa mRNA Hyper Prep kit (KapaBiosystem, Pleasanton, CA, USA) according to manufacturer’s instructions. Libraries were evaluated by MultiQC v1.12. The samples were then sequenced on an Illumina NextSeq 1000/2000 P2 with around 16 million pair-end 50-bp reads per sample at UCL Genomics.

treatment_protocol: AslNeo/Neo animals were given systemic administration of hASL mRNA or Luc mRNA at dose of 1mg/kg or 2mg/kg for IV and IP injections, respectively. Untreated WT littermates were used as controls.

value: Liver

value: WT

tag: treatment


title: MSS7, WT, Untreated, WT1


title: MSS15, AslNeo/Neo mutants, Treated, MutTrt4

value: AslNeo/Neo mutants

value: hASL enconding mRNA encapsulated in Lipid Nanoparticles


title: Pre-meiotic G2_rep3_CS


title: Pre-meiotic G2_rep2_CS


title: MSS14, AslNeo/Neo mutants, Treated, MutTrt3


title: MSS3, AslNeo/Neo mutants, Untreated, MutUnt3

value: Luciferase (Luc) encoding mRNA encapsulated in Lipid Nanoparticles (LNPs)


title: Leptotene_rep1_CS


title: U2OSp-2


title: MSS1, AslNeo/Neo mutants, Untreated, MutUnt1


title: MSS16, WT, Untreated, WT4


title: Zygotene_rep1_CS


title: Diplotene/Diakinesis_rep3_CS


title: U2OSr-1


title: MIC21_VDJ

city: Pamplona

first: Cristina

last: Perez

address: Av. Pio XII 55

country: Spain

institute: Cima Universidad de Navarra

description: 10x Genomics

data_processing:
Sample demultiplexing, alignment to the reference genome and single-cell gene count was performed using the Cell Ranger Single-Cell Software Suite v.2.0.1 (https://www.10xgenomics.com/). Expression matrixes were analyzed with the R package seurat 4.0 (https://satijalab.org/seurat/) and cells were filtered according to < 10% mitochondrial expression and at least 200 (but less than 2500) mRNA counts per cell. Once scaled and normalized, a genelist including the most variable genes was obtained by the FindVariableFeatures function. After removing genes belonging to the immunoglobulin families (which could work as a confounding factor during clustering), the genelist was used to derive the principal component analysis (PCA) vectors for each sample. The first 100 PCA were used to align samples (batch removal) using the R package harmony. The new harmonized coordinates were used to develop UMAPs (dimensionality reduction). The shared nearest neighbor (SNN) algorithm based on 50 batch-corrected dimensions was used for clustering the cells into homogeneous groups that were manually identified according to the expression of canonical genes (see Supplemental Information) obtained from curated gene-sets. A sequential subclustering strategy (which consists basically in repeating the same steps as before on a specific subpopulation) to focus on clonotypic T cells was performed. Reconstruction of T cell trajectories was performed by ordering single cells in “pseudotime” according to their RNA expression through Monocle 2 R package. This package accurately resolves biological processes (ordering cells) by learning an explicit principal graph from the single cell genomics data through Reverse Graph Embedding algorithm.
Assembly: mm10
Supplementary files format and content: BM_T_mice.rds

source_name: bone marrow

extract_protocol:
scRNA-seq + scTCR-seq were performed in 13 bone marrow aspirates from 2 healthy (Ycɣ1), 3 MGUS (BIcɣ1), 3 MM (BIcɣ1), 3 MGUS (MIC) and 2 MM (MIC) bearing mice. Cells were FACS sorted (a mix of 0.8x10^5 T cells + 0.8x10^5 NK cells + 0.25x10^5 monocytes + 0.15x10^5 B cells) in 100 µL of PBS+0.05% BSA. Samples with at least 90% viability were processed using the 10X Genomics (CA, USA) scRNA/TCRseq kit, following the manufacturer’s instructions (Chromium Next GEM Single Cell V(D)J v1.1 protocol rev F for human samples and Chromium Next GEM Single Cell 5’ v2 Dual Index protocol rev B for mice samples). Quality control was performed with Qubit Fluorometric Quantification (ThermoFisher Scientific, MA, USA) using the double-stranded DNA high-sensitivity assay kit, and with TapeStation (Agilent, Santa Clara, CA) using high-sensitivity screentapes. Libraries were sequenced on a NextSeq 550 (Illumina, San Diego, CA).
WES was performed in 71 BM samples isolated from GFP+ CD138+B220− PCs (purity, >99%), including 62 samples from the MM stage, 3 samples of pooled PCs from nine mice at the MGUS stage (3 mice with similar genotype were included on each pooled sample), and 6 samples from MM-derived cell lines. As MM reference controls, 5TGM1 and 12598Vk*Myc cell lines were also characterized.
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 5’ v2 Dual Index protocol rev B, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Of note, according to TCR-seq protocol from manufacturer, we further sequenced (after specific amplification) CDR3 sequences from each CD3+ T cells.
scRNA-seq, scTCR-seq, WES

value: bone marrow

value: bone marrow immune cells

value: T cells

value: MIC


title: MIC7_VDJ

description: 10x Genomics


title: MIC21_SC

description: 10x Genomics

library_source: transcriptomic single cell


title: MSS11, AslNeo/Neo mutants, Treated, MutTrt2


title: MIC7_SC

description: 10x Genomics


title: U2OSp-1


title: MSS13, WT, Untreated, WT3


title: MIC4_SC

description: 10x Genomics


title: MSS6, AslNeo/Neo mutants, Untreated, MutUnt4


title: MIC3_SC

description: 10x Genomics


title: MIC2_VDJ

description: 10x Genomics


title: MIC3_VDJ

description: 10x Genomics


title: seg1Δnce102Δpil1Δ, biol rep 2

city: Prague

first: Jakub

last: Zahumensky

address: Videnska 1083

department: Functional Organization of Biomembranes

country: Czech Republic

institute: Institute of Experimental Medicine, CAS

data_processing:
rRNA and tRNA removed using SortMeRNA
Filtered reads aligned to S288C genome reference using GSNAP
Differential gene expression analyzed using DESeq2 (including LFC shrinkage and count normalization using the median of ratios method(DESeq() command)
For PCA and hierarchical clustering, rlog2 transformed counts were used
Assembly: S288C_reference_genome_R64-3-1_20210421 (obtained from the SGD)
Supplementary files format and content: DESeqDataSet.tsv - gene expression counts normalized by median of ratios method (command: DESeq(dds, parallel = TRUE)); tab-delimited matrix
Supplementary files format and content: DESeqTransform.tsv - regularized log2 transformation of DESeqDataSet (command: rlog(dds, blind = FALSE)); tab-delimited matrix

molecule: polyA RNA

source_name: budding yeast cells

growth_protocol: Strains were grown in standard synthetic complete (SC) media at 28°C for 24 hours

extract_protocol:
Cells were washed with 10 mM NaF/NaN3 and lysed using beating with glass beads. RNA was isolated using RNeasy® Plus Mini Kit (includes gDNA removal columns) followed by DNA digestion with DNase Max® Kit. mRNA was enriched by polyA selection.
polyA

treatment_protocol: no treatment

value: budding yeast cells

value: MAT{alpha} his3{delta}1 leu2{delta}0 LYS2 MET15 ura3{delta}0 seg1{delta} nce102{delta} pil1{delta}


title: seg1Δnce102Δpil1Δ, biol rep 1


title: pil1Δ, biol rep 3

value: BY4742 pil1{delta}

value: MAT{alpha}; his3{delta}1; leu2{delta}0; lys2{delta}0; ura3{delta}0; pil1::kanMX4


title: 2751_VDJ

description: 10x Genomics


title: 2752_SC

description: 10x Genomics


title: MSS10, AslNeo/Neo mutants, Treated, MutTrt1


title: U2OSr-3


title: 2752_VDJ

description: 10x Genomics


title: MSS2, AslNeo/Neo mutants, Untreated, MutUnt2


title: MIC2_SC

description: 10x Genomics


title: wildtype, biol rep 1

value: MAT{alpha} his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0


title: MIC4_VDJ

description: 10x Genomics


title: YC101_SC

description: 10x Genomics


title: 6917_SC

description: 10x Genomics


title: YC101_VDJ

description: 10x Genomics


title: 2751_SC

description: 10x Genomics


title: seg1Δnce102Δpil1Δ, biol rep 3


title: pil1Δ, biol rep 2


title: YC102_SC

description: 10x Genomics


title: 2264_SC

description: 10x Genomics


title: wildtype, biol rep 3


title: DG_young meRIP_rep3

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

institute: German Center for Neurodegenerative Diseases (DZNE)

description: m6A immunoprecipitated fraction

data_processing:
Base calling was performed automatically by the sequencing machine (HiSeq 2000)
Demultiplexing and fastq generation were performed with bcl2fastq 2.20.2
Reads with quality <20 were removed with Cutadapt 1.11.0
Mapping was performed with STAR 2.5.2b
m6A peaks were obtained with MeTPeak 1.0.0, using only mapped reads
Differential methylation regions were determined with Exomepeak 2.16.0
Assembly: mm10
Supplementary files format and content: Bed files contain detected m6A sites or differentially methylated regions

source_name: Hippocampal dentate gyrus young

extract_protocol:
Brain regions were dissected on ice and flash frozen. RNA was extracted from tissue using TRI Reagent (Sigma) and cleaned with the clean and concentrator kit (Zymo research). RNA was processed as described previously (Berulava 2020): rRNA was depleted  (NEBNext ribosomal RNA removal kit, NEB) and fragmented to ~80 nt with fragmentation reagents (Invitrogen). 10 ug of rRNA depleted RNA were pooled from 3-4 mice for each replicate and used for immunoprecipitation with an m6A-speciic anitbody. Inputs correspond to 500 ng of RNA that were not immunoprecipitated, .
Mouse samples were prepared with the TruSeq Stranded Total RNA Library Prep Kit (Illumina).

tag: age

value: 3 months

value: Hippocampal dentate gyrus

tag: rip antibody

value: m6A (Synaptic systems 202 003)


title: 1728_VDJ

description: 10x Genomics


title: 2264_VDJ

description: 10x Genomics


title: DG_young input_rep3

description: 5% input before IP


title: 1728_SC

description: 10x Genomics


title: pil1Δ, biol rep 1


title: 2573_VDJ

description: 10x Genomics


title: 2573_SC

description: 10x Genomics


title: CA3_young meRIP_rep3

description: m6A immunoprecipitated fraction

source_name: Hippocampal CA3 young

value: Hippocampal CA3


title: DG_young meRIP_rep2

description: m6A immunoprecipitated fraction


title: 6917_VDJ

description: 10x Genomics


title: DG_young input_rep1

description: 5% input before IP


title: AMO1 cells, EV1 [M_EV1]

city: Boston

first: TENGTENG

last: YU

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

data_processing:
The multiplexed RNA-Seq libraries were subject to deep sequencing using the Illumina Hi-Seq 2000/2500 platform.
For data analysis, RNA-seq reads were mapped using MapSplice14 and quantified using RSEM15.
Read counts were upper quantile normalized and log2 transformed.
Raw read counts were used for differential gene expression analysis by DESeq16.
Assembly: hg38
Supplementary files format and content: excel files include RPKM values for each Sample

growth_protocol: AMO1 cells were grown in RPMI-1640 (Invitrogen, Carlsbad, CA) with 10% fetal bovine serum (Hyclone, Logan, UT), 2 mM/L L-glutamine, 100U/ml penicillin and 100 μg/ml streptomycin (Invitrogen).

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

value: Multiple myeloma cells

value: Empty vector

value: lentivirus transduction with PCDH vector


title: AMO1 cells, PHF19 OE2 [M_OE2]

value: PHF19 overexpression


title: DG_young input_rep2

description: 5% input before IP


title: AMO1 cells, PHF19 OE1 [M_OE1]


title: wildtype, biol rep 2


title: YC102_VDJ

description: 10x Genomics

value: bone marrow


title: DG_young meRIP_rep1

description: m6A immunoprecipitated fraction


title: AMO1 cells, EV2 [M_EV2]


title: CA3_young input_rep3

description: 5% input before IP


title: CA3_young meRIP_rep2

description: m6A immunoprecipitated fraction


title: CA3_young input_rep1

description: 5% input before IP


title: CA1_young meRIP_rep3

description: m6A immunoprecipitated fraction

source_name: Hippocampal CA1 young

value: Hippocampal CA1


title: CA3_young meRIP_rep1

description: m6A immunoprecipitated fraction


title: CA1_young meRIP_rep2

description: m6A immunoprecipitated fraction


title: CA1_young meRIP_rep1

description: m6A immunoprecipitated fraction


title: CA1_young input_rep3

description: 5% input before IP


title: CA1_young input_rep2

description: 5% input before IP


title: CA1_young input_rep1

description: 5% input before IP


title: ACC_young meRIP_rep3

description: m6A immunoprecipitated fraction

source_name: Anterior cingulate cortex young

value: Anterior cingulate cortex


title: CA3_young input_rep2

description: 5% input before IP


title: ACC_young input_rep3

description: 5% input before IP


title: ACC_young meRIP_rep2

description: m6A immunoprecipitated fraction


title: ACC_young meRIP_rep1

description: m6A immunoprecipitated fraction


title: ACC_young input_rep1

description: 5% input before IP


title: ACC_young input_rep2

description: 5% input before IP


title: DG_old input_rep3

description: 5% input before IP

source_name: Hippocampal dentate gyrus aged

value: 16 months


title: DG_old meRIP_rep2

description: m6A immunoprecipitated fraction


title: CA3_old input_rep2

description: 5% input before IP

source_name: Hippocampal CA3 aged


title: DG_old input_rep2

description: 5% input before IP


title: DG_old meRIP_rep1

description: m6A immunoprecipitated fraction


title: CA3_old meRIP_rep3

description: m6A immunoprecipitated fraction


title: CA3_old meRIP_rep1

description: m6A immunoprecipitated fraction


title: DG_old input_rep1

description: 5% input before IP


title: CA3_old input_rep1

description: 5% input before IP


title: CA3_old meRIP_rep2

description: m6A immunoprecipitated fraction


title: CA1_old meRIP_rep2

description: m6A immunoprecipitated fraction

source_name: Hippocampal CA1 aged


title: CA1_old meRIP_rep3

description: m6A immunoprecipitated fraction


title: CA1_old input_rep3

description: 5% input before IP


title: CA1_old input_rep2

description: 5% input before IP


title: ACC_old meRIP_rep2

description: m6A immunoprecipitated fraction

source_name: Anterior cingulate cortex aged


title: ACC_old input_rep2

description: 5% input before IP


title: ACC_old input_rep3

description: 5% input before IP


title: ACC_old meRIP_rep1

description: m6A immunoprecipitated fraction


title: DG_old meRIP_rep3

description: m6A immunoprecipitated fraction


title: ACC_old meRIP_rep3

description: m6A immunoprecipitated fraction


title: CA1_old input_rep1

description: 5% input before IP


title: CA1_old meRIP_rep1

description: m6A immunoprecipitated fraction


title: CA3_old input_rep3

description: 5% input before IP


title: KNT2

city: Sydney

first: Jinbiao

last: Chen

state: NSW

address: Building 93, RPA Hospital, Missenden Rd

institute: Centenary Institute

data_processing:
The original raw data from Illumina HiSeqTM are transformed to Sequenced Reads by base calling. Raw data are recorded in a FASTQ file, which contains sequence information (reads) and corresponding sequencing quality information.
Raw reads are filtered to remove reads containing adapters or reads of low quality, so that downstream analyses are based on clean reads. The filtering process is as follows: (1) Discard reads with adaptor contamination. (2) Discard reads when uncertain nucleotides constitute more than 10 percents of either read (N > 10%). (3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50 percents of the read.
After quality control procedures, short reads were mapped to mouse genome assembly (mm10) by STAR version 2.7.3a. Mapped reads were quantified by featureCounts version 2.0.0 from Subread package.
Transcripts Per Million (TPM) was used to reduce non-biologically derived variability inherent in RNA sequencing technologies [Wagner GP, et al. Theory Biosci. 2012; 131(4):281-5. Abrams ZB, et al. BMC bioinformatics. 2019; 20(Suppl 24):679]
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each gene and each sample

source_name: knockout non-tumour liver repl2

extract_protocol:
Tissues were flash frozen on dry ice, and total RNA was harvested using Trizol reagent. All samples need to pass through the following four steps before library construction: (1) Nanodrop: tests RNA purity (OD260/OD280)  (2) Agarose Gel Electrophoresis: tests RNA degradation and potential contamination (3) Agilent 2100: checks RNA integrity
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: 36 weeks

value: miR-181ab1 knockout

value: diethylnitrosamine (DEN):25mg/kg body weight, i.p. once, at postnatal day 12


title: KT2

source_name: knockout liver tumour rep2

value: liver tumour


title: ACC_old input_rep1

description: 5% input before IP


title: KT1

source_name: knockout liver tumour rep1


title: HPr1-AR cells, treat2 smRNA

city: WEST HOLLYWOOD

first: Moray

last: Campbell

state: CA

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQC and Trimmomatic
Trimmed sequence reads were mapped to hg38 using Rsubread (with small RNA alignment options)
FASTQ files were aligned to the genome (hg38) using Rsubread (with small RNA alignment options). Expression counts were called against the miRbase consensus miRnome using featureCounts and a standard edgeR pipeline determined differentially expressed miRNA.
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: All cells were maintained at 37oC and 5.0% CO2 (Sanyo); HPr1AR, RC43N, RC43T,  cells were maintained in keratinocyte serum free media (supplemented with 25mg of Bovine pituitary extract, 10ug EGF and 10% FBS); LNCaP cells were maintained in RPMI 1640 containing 10% FBS. All media contained 100 U/mL Penicillin-Streptomycin. 1α,25(OH)2D3 was kept as 10mM EtOH stocks. Cell lines were authenticated by STR profiling and confirmed mycoplasma free.

extract_protocol:
Total RNA was isolated via TRIzol® reagent
Cell lines were treated as RNA-Seq and library preparation included ligation of 5’ and 3’ RNA adapters to the mature miRNAs 5ʹ‐phosphate and 3ʹ‐hydroxyl groups and 11-13 PCR cycles using a universal primer and a primer containing one of 48 index sequences, which allowed pooling of libraries and multiplex sequencing.  Prior to pooling, each individual sample’s amplified cDNA construct was visualized on a DNA-HS Bioanalyzer DNA chip (Agilent Technologies) for mature miRNA and other small RNA products (140-150bp).  Successful constructs were purified using a Pippen prep (Sage Inc.), using 125 – 160 bp product size settings with separation on a 3% agarose gel. The purified samples were validated for size, purity and concentration using a DNA-HS Bioanalyzer chip.

treatment_protocol: Cells were grown to 70% confluence and treated with 1α,25(OH)2D3 (100nM, 8hr) or EtOH in biological triplicate samples and analyzed by RNA-Seq.

value: WT

value: European American prostate cancer


title: HPr1-AR cells, treat3 smRNA


title: KN3

source_name: knockout normal liver rep3

value: untreated


title: HPr1-AR cells, veh control1 smRNA

value: Vehicle


title: HPr1-AR cells, veh control3 smRNA


title: KN1

source_name: knockout normal liver rep1


title: HPr1-AR cells, veh control2 smRNA


title: WT3

source_name: wild type liver tumour rep3

value: wild type


title: HPr1-AR cells, treat1 smRNA


title: WT2

source_name: wild type liver tumour rep2


title: LNCaP cells, treat2 smRNA

source_name: LNCaP

value: LNCaP

value: European American non-malignant prostate


title: WT1

source_name: wild type liver tumour rep1


title: KNT3

source_name: knockout non-tumour liver repl3


title: LNCaP cells, treat1 smRNA


title: LNCaP cells, veh control3 smRNA


title: LNCaP cells, veh control1 smRNA


title: LNCaP cells, veh control2 smRNA


title: KNT1

source_name: knockout non-tumour liver repl1


title: WN3

source_name: wild type normal liver rep3


title: WNT2

source_name: wild type non-tumour liver rep2


title: RC43N cells, treat3 smRNA

value: African American prostate cancer


title: WNT1

source_name: wild type non-tumour liver rep1


title: KN2

source_name: knockout normal liver rep2


title: KT3

source_name: knockout liver tumour rep3


title: RC43N cells, treat2 smRNA


title: WN1

source_name: wild type normal liver rep1


title: RC43N cells, treat1 smRNA