title: LNCap output2-A7

city: shenzhen

first: Guoli

address: penfei street

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences

description: Library name: LNCap output2-A7

data_processing:
bowtie2 aligns sequencing data to the hg38 genome, samtools filters comparison data, and CRADLE software identifies silencer.
Assembly: hg38
Supplementary files format and content: bed file records silencer location and silencer activity

source_name: LNCap

extract_protocol:
293T, K562 and LNCap were inoculated with 10 % FBS (Gibco; Cat 10437028) and 1% penicillin streptomycin P/S (Sigma; cat P0781) in DMEM (Thermo Fisher; Cat 10566024), cell lines are induced in iCD1 medium(Delicell, Cat 820250). iPSCs and mESCs were cultured in N2B27-2i/LIF medium (Neural Basal, F12,1%Glutamax, 1%NEAA, 1%Sodium pyruvate, 0.1mM β-me, 1%B27, 0.5% N2, 0.5% P/s(optional), mLif(1:8000), 3uM CHIR99021(1:4000), 1 uM PD0325901). The culture conditions of all cells were 37 °C, 5 % carbon dioxide. The construction of the random input DNA library involves three main steps: creating insert fragments, preparing the linearized vector, and seamless assembly cloning. First, the genome is fragmented into 300-400 base pair segments using an ultrasonic disruptor. The library construction kit (Roche; KK8514) is used to add homologous arms and Illumina adapters to these fragments. Next, the Ss-STARR-seq vector is digested with AgeI-HF and SalI-HF enzymes (NEB). The fragmented DNA is then recombined with the linearized vector using Gibson's homologous recombination enzyme (NEB). The quality of the library clones is verified through Sanger sequencing. Forty recombination reactions are set up, and the products are purified using a DNA purification kit (ZYMO; d4013). The purified DNA is transformed into competent cells (Thermo Fisher Scientific; c6400) and cultured in 15 liters of LB medium. When the bacterial culture reaches an optical density (OD) between 1.0 and 1.2, PCR amplification is performed using 100 ng of plasmid as a template. The PCR conditions include initial denaturation at 98°C for 45 seconds, followed by 20 cycles of denaturation at 98°C for 15 seconds, annealing at 60°C for 30 seconds, and extension at 72°C for 30 seconds. The amplified products are recovered through 2% agarose gel electrophoresis and prepared for high-throughput sequencing. Cells transfected with the input library were harvested for RNA extraction using TURBOTM DNase (Thermo Fisher Scientific) and Dynabeads Oligo (dT)25 (Thermo Fisher Scientific). The enriched mRNA was reverse transcribed into cDNA using SuperScript TM IV Reverse Transcriptase (Thermo Fisher Scientific) and specific primers. AmbionTM RNase H was then used to degrade any remaining RNA in the cDNA product. The cDNA was purified and amplified via PCR using the HiFi high fidelity enzyme Ready Mix (Roche). The PCR protocol involved initial denaturation at 98°C for 45 seconds, followed by 20 cycles of 98°C for 15 seconds, 60°C for 30 seconds, and 72°C for 30 seconds. The PCR products were separated by 2% agarose gel electrophoresis to create the output library for high-throughput sequencing.
The construction of the random input DNA library involves three main steps: creating insert fragments, preparing the linearized vector, and seamless assembly cloning. First, the genome is fragmented into 300-400 base pair segments using an ultrasonic disruptor. The library construction kit (Roche; KK8514) is used to add homologous arms and Illumina adapters to these fragments. Next, the Ss-STARR-seq vector is digested with AgeI-HF and SalI-HF enzymes (NEB). The fragmented DNA is then recombined with the linearized vector using Gibson's homologous recombination enzyme (NEB). The quality of the library clones is verified through Sanger sequencing. Forty recombination reactions are set up, and the products are purified using a DNA purification kit (ZYMO; d4013). The purified DNA is transformed into competent cells (Thermo Fisher Scientific; c6400) and cultured in 15 liters of LB medium. When the bacterial culture reaches an optical density (OD) between 1.0 and 1.2, PCR amplification is performed using 100 ng of plasmid as a template. The PCR conditions include initial denaturation at 98°C for 45 seconds, followed by 20 cycles of denaturation at 98°C for 15 seconds, annealing at 60°C for 30 seconds, and extension at 72°C for 30 seconds. The amplified products are recovered through 2% agarose gel electrophoresis and prepared for high-throughput sequencing. Cells transfected with the input library were harvested for RNA extraction using TURBOTM DNase (Thermo Fisher Scientific) and Dynabeads Oligo (dT)25 (Thermo Fisher Scientific). The enriched mRNA was reverse transcribed into cDNA using SuperScript TM IV Reverse Transcriptase (Thermo Fisher Scientific) and specific primers. AmbionTM RNase H was then used to degrade any remaining RNA in the cDNA product. The cDNA was purified and amplified via PCR using the HiFi high fidelity enzyme Ready Mix (Roche). The PCR protocol involved initial denaturation at 98°C for 45 seconds, followed by 20 cycles of 98°C for 15 seconds, 60°C for 30 seconds, and 72°C for 30 seconds. The PCR products were separated by 2% agarose gel electrophoresis to create the output library for high-throughput sequencing.

value: LNCap


title: tgrB1-_04hr : replicate 3

status: Public on Dec 06 2024

type: SRA

city: Houston

first: Gad

last: Shaulsky

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

library_source: transcriptomic

data_processing:
After demultiplexing, we used Genialis Web tool  (https://www.genialis.com/ ) to perform data processing. The data was preprocessed by running BBDuk (ver 3. 1.2) on paired-end reads to trim illumina adaptor sequence (Minimum length = 30, Kmer length = 23, Maximum Hamming distance for kmers =1, k_trim “r”, quality_trim “r”, trim_quality = 28) and mapped to the D. discoideum genome with bowtie version 0.12.7. Read qualities were used. Other parameters: seed length = 28, allowed mismatches = 2, allowed up to 1 alignment per read, with bowtie options -a, -m 1, --best, --strata. Unmapped reads were trimmed from 3' by 2 nucleotides, which was repeated 1 more time.
Raw expression values were computed as the number of reads that were uniquely mapped to gene exons.
Normalized expression were scaled with mappable exon lengths. This normalization is similar to the RPKM normalization (Reads Per Kilobase of exon per Megabase of library size), but instead of dividing by exon lengths we used the uniquely mappable parts of the exon. To obtain uniquely mappable parts, all possible subsequences of the reference genome (of the same length as reads in raw data) are mapped back to the reference genome, obtaining the number of uniquely mapped sequences to the exons (Exon_mappable). As a library size we used the total number of all uniquely mapped reads from the experiment, excluding the non-polyadenylated genes (N_unique). Normalized expressions were computed as follows: Exp = 10^9*raw/(N_unique * Exon_mappable)
Assembly: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked.
Supplementary files format and content: Processed data files are tab-separated files with two columns: the first containing gene names and the second its expression. Files ending with “_preprocessed_mapped_expression_rc.tab.gz" contain raw expression values while files ending with "_ preprocessed_mapped_expression_rpkum_polya.tab.gz" contain normalized expression values.

molecule: polyA RNA

organism: Dictyostelium discoideum

growth_protocol: All strains were cultured axenically in HL5.

extract_protocol:
At each time point, we harvested the cells, resuspended with 1 mL of Trizol® (life technologies, CA, USA) and extracted total RNA according to the manufacturer’s recommended protocol. We performed two rounds of poly-A selection and fragmented 100 ng of the resulting mRNA into approximately 200 bases fragments. We prepared cDNA and the second strand.
We prepared Illumina multiplexed libraries. We prepared 108 individual libraries separately (one from each sample), three categories and added a unique barcode to each library in each category at the final step of PCR amplification. We pooled equal amounts of DNA from each library in each category and sequenced one pool per lane of a flow cell on Illumina NovaSeq6000 using the manufacturer's recommended pipeline (PE, read length = 151 bases). Since the illumina sequence reads for rapgapB- and rapgapB- tgrB1- strains were low, they were sequenced twice. Therefore, we obtained 4 fastq file for each of these samples. We combined those fastq file to analyze them.

treatment_protocol: The cells were washed with phospate buffer, resuspended with PDF and plated at 1.7x10e6 cells/sq.cm on one cellulose filter on top of a paper pad soaked with PDF .

tag: strain

tag: genotype

value: tgrB1 crisprKO

tag: replicate

tag: developmental time

value: 4 hr

tag: treatment

value: on Black filter


title: LNCap output2-A2

last: Li

country: China

description: Library name: LNCap output2-A2

molecule: total RNA

organism: Mus musculus

tag: cell line


title: LNCap output2-A6

description: Library name: LNCap output2-A6


title: LNCap output2-A5

description: Library name: LNCap output2-A5


title: LNCap output1-A20

description: Library name: LNCap output1-A20


title: tgrB1-_04hr : replicate 2


title: tgrB1-_00hr : replicate 1

value: 0 hr


title: tgrB1-_00hr : replicate 3


title: tgrB1-_00hr : replicate 2


title: LNCap output2-A1

description: Library name: LNCap output2-A1


title: tgrB1-_12hr : replicate 2

value: 12 hr


title: AX4_20hr : replicate 3

value: WT

value: 20 hr


title: 4T07-TGL cells, sgControl, rep2

first: Junfeng

last: Zhang

address: 2130 W. Holcombe Blvd

department: Department of Cancer Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
STAR 2.4.2a was used to align the RNA-seq reads to the reference mouse genome (mm10) and to count the number of reads mapping to each gene in the Ensembl GRCm38.80 gene model. Differential expression analysis was performed using the DESeq2 package(v.1.10.0)in R (v.4.3.1;http://www.R-project.org/).
Assembly: mm10
Supplementary files format and content: txt files includes raw counts for each sample

source_name: 4T07-TGL cells

growth_protocol: 4T07-TGL cells were cultured in Dulbecco's Modified Eagle Medium (Gibco) with 10% fetal bovine serum (FBS, Gibco) at 37 °C in 5% CO2. All cell lines used in this study were confirmed Mycoplasma-negative using the Universal Mycoplasma Detection Kit (ATCC 30-1012K).

extract_protocol:
Total RNA was extracted from cells using the RNeasy Mini Kit (Qiagen)
RNA-seq on 4TO7-TGL cells with or without Brd7 KO was performed in the MD Anderson Advanced Technology Genomics Core (ATGC).

value: 4T07-TGL cells

tag: cell type

value: breast cancer cells

value: Control


title: LNCap output1-A19

description: Library name: LNCap output1-A19


title: AX4_20hr : replicate 2


title: LNCap output2-A4

description: Library name: LNCap output2-A4


title: tgrB1-_04hr : replicate 1


title: AX4_16hr : replicate 2

value: 16 hr


title: LNCap output1-A14

description: Library name: LNCap output1-A14


title: LNCap output1-A11

description: Library name: LNCap output1-A11


title: LNCap output1-A17

description: Library name: LNCap output1-A17


title: LNCap output1-A12

description: Library name: LNCap output1-A12


title: LNCap output1-A15

description: Library name: LNCap output1-A15


title: AX4_12hr : replicate 3


title: LNCap output1-A10

description: Library name: LNCap output1-A10


title: AX4_16hr : replicate 1


title: AX4_20hr : replicate 1


title: AX4_12hr : replicate 2


title: LNCap output1-A16

description: Library name: LNCap output1-A16


title: LNCap output1-A6

description: Library name: LNCap output1-A6


title: AX4_08hr : replicate 3

value: 8 hr


title: AX4_08hr : replicate 2


title: LNCap output1-A18

description: Library name: LNCap output1-A18


title: AX4_12hr : replicate 1


title: AX4_16hr : replicate 3


title: AX4_08hr : replicate 1


title: LNCap output1-A8

description: Library name: LNCap output1-A8


title: LNCap output2-A10

description: Library name: LNCap output2-A10


title: LNCap output2-A13

description: Library name: LNCap output2-A13


title: AX4_04hr : replicate 3


title: LNCap output1-A13

description: Library name: LNCap output1-A13


title: LNCap output1-A7

description: Library name: LNCap output1-A7


title: AX4_04hr : replicate 1


title: LNCap output1-A9

description: Library name: LNCap output1-A9


title: AX4_00hr : replicate 3


title: AX4_00hr : replicate 2


title: LNCap output2-A11

description: Library name: LNCap output2-A11


title: LNCap output2-A14

description: Library name: LNCap output2-A14


title: LNCap output2-A8

description: Library name: LNCap output2-A8


title: S38_Fx1A_LNAME

city: Groton

first: Thomas

middle: A

last: Lanz

state: CT

address: Eastern Point Rd

department: Multi-Omics & Biomarkers

institute: Pfizer

description:
Library name: itox015276
Column name in Renal_model_expression.xlsx: itox015276

data_processing:
the reads were aligned to the Rattus norvegicus reference genome version 6.0 via Salmon version 1.4.0
normalization factors were determined via the edgeR package (version 3.40.2)
DESeq2 was used for differential expression
Benjamini-Hochberg p-value adjustment
Assembly: Rn6.0
Supplementary files format and content: xlsx file with VSD-normalized values

organism: Rattus norvegicus

source_name: kidney

extract_protocol:
RNA was extracted via Neasy Lipid Tissue (Qiagen).
Library preparation was performed with the Quantseq 3’ mRNA-Seq Library Preparation Kit FWD for Illumina (Lexogen #015.96) from 500 ng of total RNA input according to the manufacturer’s recommendations

tag: tissue

value: kidney


title: S37_Fx1A_LNAME

description:
Library name: itox015275
Column name in Renal_model_expression.xlsx: itox015275


title: LNCap output1-A5

description: Library name: LNCap output1-A5


title: S36_Fx1A_LNAME

description:
Library name: itox015274
Column name in Renal_model_expression.xlsx: itox015274


title: LNCap output2-A12

description: Library name: LNCap output2-A12


title: S35_Fx1A_LNAME

description:
Library name: itox015273
Column name in Renal_model_expression.xlsx: itox015273


title: LNCap output2-A9

description: Library name: LNCap output2-A9


title: LNCap output6-A2

description: Library name: LNCap output6-A2


title: LNCap output5-A19

description: Library name: LNCap output5-A19


title: S32_Fx1A_LNAME

description:
Library name: itox015270
Column name in Renal_model_expression.xlsx: itox015270


title: LNCap output5-A17

description: Library name: LNCap output5-A17


title: S30_Fx1A_LNAME

description:
Library name: itox015268
Column name in Renal_model_expression.xlsx: itox015268


title: S28_LNAME

description:
Library name: itox015266
Column name in Renal_model_expression.xlsx: itox015266


title: S29_Fx1A_LNAME

description:
Library name: itox015267
Column name in Renal_model_expression.xlsx: itox015267


title: LNCap output5-A20

description: Library name: LNCap output5-A20


title: LNCap output5-A15

description: Library name: LNCap output5-A15


title: LNCap output5-A18

description: Library name: LNCap output5-A18


title: S27_LNAME

description:
Library name: itox015265
Column name in Renal_model_expression.xlsx: itox015265


title: AX4_00hr : replicate 1


title: LNCap output2-A15

description: Library name: LNCap output2-A15


title: S26_LNAME

description:
Library name: itox015264
Column name in Renal_model_expression.xlsx: itox015264


title: LNCap output6-A3

description: Library name: LNCap output6-A3


title: LNCap output6-A1

description: Library name: LNCap output6-A1


title: S25_LNAME

description:
Library name: itox015263
Column name in Renal_model_expression.xlsx: itox015263


title: LNCap output5-A16

description: Library name: LNCap output5-A16


title: S24_LNAME

description:
Library name: itox015262
Column name in Renal_model_expression.xlsx: itox015262


title: S33_Fx1A_LNAME

description:
Library name: itox015271
Column name in Renal_model_expression.xlsx: itox015271


title: LNCap output5-A14

description: Library name: LNCap output5-A14


title: S34_Fx1A_LNAME

description:
Library name: itox015272
Column name in Renal_model_expression.xlsx: itox015272


title: LNCap output6-A4

description: Library name: LNCap output6-A4


title: S23_LNAME

description:
Library name: itox015261
Column name in Renal_model_expression.xlsx: itox015261


title: S31_Fx1A_LNAME

description:
Library name: itox015269
Column name in Renal_model_expression.xlsx: itox015269


title: AX4_04hr : replicate 2


title: S21_LNAME

description:
Library name: itox015259
Column name in Renal_model_expression.xlsx: itox015259


title: LNCap output6-A5

description: Library name: LNCap output6-A5


title: LNCap output6-A8

description: Library name: LNCap output6-A8


title: S20_LNAME

description:
Library name: itox015258
Column name in Renal_model_expression.xlsx: itox015258


title: S22_LNAME

description:
Library name: itox015260
Column name in Renal_model_expression.xlsx: itox015260


title: LNCap output6-A14

description: Library name: LNCap output6-A14


title: S16_Fx1A

description:
Library name: itox015254
Column name in Renal_model_expression.xlsx: itox015254


title: S15_Fx1A

description:
Library name: itox015253
Column name in Renal_model_expression.xlsx: itox015253


title: S19_LNAME

description:
Library name: itox015257
Column name in Renal_model_expression.xlsx: itox015257


title: S17_Fx1A

description:
Library name: itox015255
Column name in Renal_model_expression.xlsx: itox015255


title: LNCap output6-A10

description: Library name: LNCap output6-A10


title: LNCap output6-A13

description: Library name: LNCap output6-A13


title: S10_Fx1A

description:
Library name: itox015248
Column name in Renal_model_expression.xlsx: itox015248


title: S18_Fx1A

description:
Library name: itox015256
Column name in Renal_model_expression.xlsx: itox015256


title: LNCap output6-A16

description: Library name: LNCap output6-A16


title: LNCap output6-A6

description: Library name: LNCap output6-A6


title: S12_Fx1A

description:
Library name: itox015250
Column name in Renal_model_expression.xlsx: itox015250


title: S14_Fx1A

description:
Library name: itox015252
Column name in Renal_model_expression.xlsx: itox015252


title: S9_Fx1A

description:
Library name: itox015247
Column name in Renal_model_expression.xlsx: itox015247


title: LNCap output6-A9

description: Library name: LNCap output6-A9


title: LNCap output6-A12

description: Library name: LNCap output6-A12


title: LNCap output2-A3

description: Library name: LNCap output2-A3


title: LNCap output6-A15

description: Library name: LNCap output6-A15


title: LNCap output6-A7

description: Library name: LNCap output6-A7


title: S13_Fx1A

description:
Library name: itox015251
Column name in Renal_model_expression.xlsx: itox015251


title: S7_vehicle

description:
Library name: itox015245
Column name in Renal_model_expression.xlsx: itox015245

value: vehicle


title: LNCap output6-A17

description: Library name: LNCap output6-A17


title: LNCap output6-A18

description: Library name: LNCap output6-A18


title: S6_vehicle

description:
Library name: itox015244
Column name in Renal_model_expression.xlsx: itox015244


title: LNCap output6-A19

description: Library name: LNCap output6-A19


title: S11_Fx1A

description:
Library name: itox015249
Column name in Renal_model_expression.xlsx: itox015249


title: LNCap output7-A2

description: Library name: LNCap output7-A2


title: LNCap output6-A11

description: Library name: LNCap output6-A11


title: S5_vehicle

description:
Library name: itox015243
Column name in Renal_model_expression.xlsx: itox015243


title: LNCap input1-A6

description: Library name: LNCap input1-A6

library_source: genomic

molecule: genomic DNA


title: S8_vehicle

description:
Library name: itox015246
Column name in Renal_model_expression.xlsx: itox015246


title: S4_vehicle

description:
Library name: itox015242
Column name in Renal_model_expression.xlsx: itox015242


title: LNCap input1-A5

description: Library name: LNCap input1-A5


title: LNCap input1-A1

description: Library name: LNCap input1-A1


title: S3_vehicle

description:
Library name: itox015241
Column name in Renal_model_expression.xlsx: itox015241


title: S2_vehicle

description:
Library name: itox015240
Column name in Renal_model_expression.xlsx: itox015240


title: LNCap input1-A7

description: Library name: LNCap input1-A7


title: S1_vehicle

description:
Library name: itox015239
Column name in Renal_model_expression.xlsx: itox015239


title: LNCap input1-A9

description: Library name: LNCap input1-A9


title: LNCap input1-A4

description: Library name: LNCap input1-A4


title: LNCap input1-A2

description: Library name: LNCap input1-A2


title: LNCap input1-A10

description: Library name: LNCap input1-A10


title: LNCap input1-A16

description: Library name: LNCap input1-A16


title: LNCap output4-A13

description: Library name: LNCap output4-A13


title: LNCap input1-A3

description: Library name: LNCap input1-A3


title: LNCap input1-A15

description: Library name: LNCap input1-A15


title: LNCap input1-A13

description: Library name: LNCap input1-A13


title: LNCap input1-A12

description: Library name: LNCap input1-A12


title: Small RNA_cwf10-1_Rep1

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

description: Small RNA_cwf10-1_Rep1

data_processing:
Single ended short reads were quality trimmed with fastp (Chen et al., 2018) and aligned to the reference using Novoalign ( http:// www.novocraft.com/products/novoalign). SGR files were generated from BAM files using custom scripts (available on request).
Assembly: S. pombeV2 reference (Wood et al. 2002) with the sequence of the full 40 kbmatregion provided on a separate contig (MAT).
Supplementary files format and content: SGR format of either unique (filtered) or unique+multimapping (unfiltered) Counts per 10 Million Mapped Reads (CP10M).

organism: Schizosaccharomyces pombe

source_name: Yeast Whole Cells

growth_protocol: Cell were grown at 30°C then shifted to 36°C for 5hrs

extract_protocol:
MasterPure Yeast RNA Purification Kit
NEBNext Small RNA Library Prep Set for Illumina for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).

value: mat1Msmt0 leu1-32 ade6-210 ura4D18 cwf10-1 Otr1R (Sph1)::ura4+

value: Yeast Whole Cells

tag: growth

value: Growth in YEA 30 C, shifted to 36 C for 5hrs


title: Small RNA_swi6∆_Rep1

description: Small RNA_swi6∆_Rep1

value: mat1Msmt0 ade6-216 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+ swi6delta::NatMX6

value: Growth in YEA 30 C


title: Small RNA_swi6∆ cenH CCAATATGAC_Rep1

description: Small RNA_swi6∆CCAATATGAC_Rep1

value: mat1Msmt0 ade6-210 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+ cenH CCAATATGAC swi6delta::NatMX6


title: Small RNA_swi6∆php3∆_Rep1

description: Small RNA_swi6∆php3∆_Rep1

value: mat1Msmt0 ade6-216 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+ php3delta::KanMX6 swi6delta::NatMX6


title: Small RNA_swi6∆cwf10-1_Rep1

description: Small RNA_swi6∆cwf10-1_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E swi6delta::NatMX6 cwf10-1, Otr1R (Sph1)::ura4+


title: Small RNA_swi6∆_Rep2

description: Small RNA_swi6∆_Rep2


title: LNCap output4-A14

description: Library name: LNCap output4-A14

value: LNCap


title: Small RNA_swi6∆moc3∆_Rep1

description: Small RNA_swi6∆moc3∆_Rep1

value: mat1Msmt0 ade6-216 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+ moc3delta::KanMX6 swi6delta::NatMX6


title: Small RNA_php3∆_Rep1

description: Small RNA_php3∆_Rep1

value: mat1Msmt0 ade6-210 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+ php3delta::KanMX6


title: Small RNA_WT_Rep1

description: Small RNA_WT_Rep1

value: mat1Msmt0 ade6-216 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+


title: Small RNA_moc3∆_Rep1

description: Small RNA_moc3∆_Rep1

value: mat1Msmt0 ade6-216 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+ moc3delta::KanMX6


title: LNCap input1-A17

description: Library name: LNCap input1-A17


title: RNA_clr4∆_Rep1

data_processing:
Single ended short reads were quality trimmed with fastp  (Chen et al. 2018) and aligned to the reference genome using the STAR aligner (Dobin et al., 2013).
Assembly: S. pombeV2 reference (Wood et al. 2002) with the sequence of the full 40 kbmatregion provided on a separate contig (MAT).
Supplementary files format and content: Bedgraph format of read counts normalized to reads per million mapped reads (RPM).

growth_protocol: Cells were grown in YEA at 30°C and shifted to 18°C for 2hrs.

extract_protocol:
Hot-phenol method
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).

value: mat1Msmt0 leu1-32 ade6-216 ura4 clr4delta::KanMX6 otr1R(Spn1)::ura4

value: Growth in YEA 30 C and 18 C/2hrs


title: RNA_clr4∆php2∆_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E php2delta::NatMX6 clr4delta::KanMX6


title: Small RNA_WT_Rep2

description: Small RNA_WT_Rep2


title: LNCap input1-A11

description: Library name: LNCap input1-A11


title: RNA_php2∆_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E php2delta::NatMX6 otr1R(Spn1)::ura4


title: LNCap output4-A12

description: Library name: LNCap output4-A12


title: LNCap input1-A8

description: Library name: LNCap input1-A8


title: LNCap output4-A15

description: Library name: LNCap output4-A15


title: RNA_WT_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4DS/E


title: Small RNA_cenH CCAATATGAC_Rep1

description: Small RNA_cenH CCAATATGAC_Rep1

value: mat1Msmt0 ade6-210 his2 ura4D18 mat2Pdelta(Bg-Bs)-XbaI:ura4+ cenH CCAATATGAC

value: Yeast Whole Cells


title: LNCap output5-A3

description: Library name: LNCap output5-A3


title: LNCap output4-A10

description: Library name: LNCap output4-A10


title: Replicate 1 (E36), che-2(e1033) AMsh

city: New York

first: Katherine

middle: Celina

last: Varandas

state: New York

address: 1230 York Ave

institute: The Rockefeller University

description:
Library name: E36 C+
E36 C+

data_processing:
Fastq files were generated with CASAVA v1.8.2, and examined using FASTQC for sequence quality. Reads were aligned to C. elegans WS262 genome release (https://downloads.wormbase.org/releases/WS262/species/c_elegans/PRJNA13758/) using the STAR v2.3 aligner with parameters (--out-FilterMultimapNmax 10 --outFilterMultimapScoreRange 1). The alignment results were evaluated using RNA-SeQC v1.17 to make sure all samples had a consistent alignment rate and no obvious 5′ or 3′ bias. Aligned reads were summarized through featureCounts with gene models from Ensemble (Caenorhabditis_elegans. WBcel235.77.gtf) at gene level unstranded. Specifically, the uniquely mapped reads (NH “tag” in bam file) that overlapped with an exon (feature) by at least 1 bp on either strand were counted and then the counts of all exons annotated to an Ensemble gene (meta features) were summed into a single number. rRNA genes, mitochondrial genes and genes with length <40 bp were excluded from downstream analysis.
Assembly: C. elegans WS262 genome release (https://downloads.wormbase.org/releases/WS262/species/c_elegans/PRJNA13758/)
Supplementary files format and content: csv file contains raw counts for each replicate and sample

organism: Caenorhabditis elegans

source_name: AMsh glia

growth_protocol: ~2 million synchronized larvae expressing F16F9.3pro::dsRed in wild type or che-2(e1033) background (OS4079 and OS11549) were grown from L1 arrest in S-basal liquid culture containing E. coli HB101 at 20°C, shaking.

extract_protocol:
RNA was extracted from Trizol LS-treated cells by phase separation, following the manufacturers guidelines. RNA was purified using PicoPure RNA isolation kit. 0.4-5ng purified total RNA was obtained per sample. All subsequent steps were performed by the Rockefeller University Genomics Resource Center. RNA quality was verified using an Agilent Bioanalyzer to ensure sample degradation had not occurred.
mRNA amplification and cDNA preparation were performed using the SMARTer mRNA amplification kit.
Labelled samples were sequenced using an Illumina HiSeq 2000 sequencer and standard Illumina sequencing primers.

treatment_protocol: After 36-42 hours, late-stage larvae (L3 and L4) were pelleted by centrifugation (2 min, 1,300 rpm) and subsequently washed ten times with M9 to remove excess bacteria. Each wash consisted of a brief (10 second, 1300 rpm) centrifugation, such that most animals were pelleted, but bacteria remained in suspension. Animals were then dissociated using SDS-DTT (0.25% SDS; 200 mM DTT; 20 mM HEPES, pH 8.0; 3% sucrose) and Pronase E (15 mg/ml), as previously described.66 SDS-DTT was added at a 2:1 ratio the volume of packed animal pellet, followed by 4 min incubation on ice. After washing, 4:1 ratio of Pronase E was added to the packed animals’ pellet and animals were incubated rotating at 20°C for 5 min, followed by 12 min of gentle homogenization (2mL dounce homogenizer, pestle clearance 0.0005-0.0025 inches). After washes with ice-cold egg buffer (1.18 M NaCl; 480 mM KCl; 20 mM CaCl2; 20 mM MgCl2; 250 mM HEPES, pH 7.3) to remove Pronase E, cells were filtered through a 5μM filter to remove undigested animal fragments, and immediately sorted by FACS. AMsh glia cell sorting was performed using a BD FACS Aria sorter (Rockefeller University Flow Cytometry Resource Center), with egg buffer as the sheath buffer to preserve cell viability. Dead cell exclusion was carried out using DAPI, while DRAQ5 was used to distinguish nucleated cells from non-nucleated cell fragments. Gates for size and granularity were adjusted to exclude cell aggregates and debris. Gates for fluorescence were established using wild type non-fluorescent animals. 168,356-240,125 dsRed-positive events were sorted per replicate, which represented 0.1−0.4% of total events (after scatter exclusion), which is roughly the expected labeled-cell frequency in the animal (~0.21%). dsRed-negative events from the same gates of size and granularity, representing all other cell types, were also sorted for comparison. Cells were sorted directly into TRIzol LS at a ratio 3:1 (TRIzol to cell volume).

value: AMsh glia

value: Cell Isolation and FACS


title: Replicate 1 (E36), che-2(e1033) non-AMsh

description:
Library name: E36 C-
E36 C-

source_name: non-AMsh glia

value: non-AMsh glia


title: Replicate 3 (E36), wild type non-AMsh

description:
Library name: E36 W-
E36 W-

value: wild type


title: LNCap output4-A6

description: Library name: LNCap output4-A6


title: LNCap output4-A8

description: Library name: LNCap output4-A8


title: Replicate 2 (E35), che-2(e1033) non-AMsh

description:
Library name: E35 C-
E35 C-


title: LNCap input1-A14

description: Library name: LNCap input1-A14


title: Replicate 2 (E35), wild type AMsh

description:
Library name: E35 W+
E35 W+


title: LNCap output4-A11

description: Library name: LNCap output4-A11


title: LNCap output7-A3

description: Library name: LNCap output7-A3


title: LNCap output4-A9

description: Library name: LNCap output4-A9


title: Replicate 1 (E36), wild type AMsh

description:
Library name: E36 W+
E36 W+


title: Replicate 2 (E35), che-2(e1033) AMsh

description:
Library name: E35 C+
E35 C+


title: LNCap output4-A7

description: Library name: LNCap output4-A7


title: LNCap output5-A2

description: Library name: LNCap output5-A2


title: Replicate 2 (E35), wild type non-AMsh

description:
Library name: E35 W-
E35 W-


title: Replicate 1 (E30), che-2(e1033) AMsh

description:
Library name: E30 C+
E30 C+


title: LNCap output4-A16

description: Library name: LNCap output4-A16


title: Replicate 1 (E30), che-2(e1033) non-AMsh

description:
Library name: E30 C-
E30 C-


title: Replicate 1 (E30), wild type AMsh

description:
Library name: E30 W+
E30 W+


title: LNCap output5-A6

description: Library name: LNCap output5-A6


title: LNCap output4-A20

description: Library name: LNCap output4-A20


title: LNCap output5-A4

description: Library name: LNCap output5-A4


title: Replicate 1 (E30), wild type non-AMsh

description:
Library name: E30 W-
E30 W-


title: P0_PAE_Norm_8 (P0_Norm8.20230418)

city: Rockville

first: Qiaoping

last: Yuan

address: 5625 Fishers Lane, Suite 3S32

institute: NIAAA

description: AmpliSeq

data_processing:
Alignment and gene expression count were performed using Ion Torrent AmpliSeqRNA Plugin v0.5.4.0 (Thermo Fisher) using mm10 genome.
AmpliSeq count data was analyzed using DESeq2 1.34.0
Assembly: mm10
Supplementary files format and content: rpm files: first column contains Gene Symbols; second column contains RPM of the the gene expresion value

source_name: Brain

extract_protocol:
Offspring were harvested at E14 or postnatal day 0 (P0). After taking body and brain weights, the prefrontal cortex was isolated for RNA isolation.
Libraries were generated using Ion AmpliSeq™ Library Kit Plus (Thermo Fisher Scientific, 4488990) per the manufacturer’s instructions.

treatment_protocol: Pregnant C57BL6/J mice were treated with 2.9 g/kg of EtOH from embryonic day 7 (E7) to E13.

value: Brain

value: Wildtype

value: EtOH


title: P0_PAE_Norm_9 (P0_Norm9.20230418)

description: AmpliSeq


title: LNCap output4-A18

description: Library name: LNCap output4-A18

value: LNCap


title: LNCap output4-A19

description: Library name: LNCap output4-A19


title: P0_PAE_Norm_7 (P0_Norm7.20230222)

description: AmpliSeq


title: P0_PAE_Norm_6 (P0_Norm6.20230222)

description: AmpliSeq


title: P0_PAE_Norm_3 (P0_Norm3.20230110)

description: AmpliSeq


title: LNCap output5-A5

description: Library name: LNCap output5-A5


title: LNCap output5-A1

description: Library name: LNCap output5-A1


title: LNCap output5-A10

description: Library name: LNCap output5-A10


title: P0_PAE_Norm_5 (P0_Norm5.20230404)

description: AmpliSeq


title: LNCap output5-A9

description: Library name: LNCap output5-A9


title: LNCap output5-A7

description: Library name: LNCap output5-A7


title: P0_PAE_Norm_5 (P0_Norm5.20230329)

description: AmpliSeq


title: P0_PAE_Norm_4 (P0_Norm4.20230329)

description: AmpliSeq


title: LNCap output5-A8

description: Library name: LNCap output5-A8


title: P0_PAE_Norm_2 (P0_Norm2.20221021)

description: AmpliSeq


title: P0_PAE_Norm_12 (P0_Norm12.20230511)

description: AmpliSeq


title: P0_PAE_Norm_4 (P0_Norm4.20230404)

description: AmpliSeq


title: P0_PAE_Norm_11 (P0_Norm11.20230509)

description: AmpliSeq


title: LNCap output5-A11

description: Library name: LNCap output5-A11


title: LNCap output7-A4

description: Library name: LNCap output7-A4


title: LNCap output5-A13

description: Library name: LNCap output5-A13


title: LNCap output7-A11

description: Library name: LNCap output7-A11


title: LNCap output7-A5

description: Library name: LNCap output7-A5


title: LNCap output4-A17

description: Library name: LNCap output4-A17


title: LNCap output5-A12

description: Library name: LNCap output5-A12


title: P0_PAE_Norm_10 (P0_Norm10.20230511)

description: AmpliSeq


title: P0_PAE_Mid_9 (P0_Mid9.20230511)

description: AmpliSeq


title: LNCap output7-A7

description: Library name: LNCap output7-A7


title: LNCap output7-A6

description: Library name: LNCap output7-A6


title: P0_PAE_Mid_8 (P0_Mid8.20230511)

description: AmpliSeq


title: P0_PAE_Mid_7 (P0_Mid7.20230511)

description: AmpliSeq


title: P0_PAE_Norm_12 (P0_Norm12.20230509)

description: AmpliSeq


title: LNCap output7-A9

description: Library name: LNCap output7-A9


title: LNCap output7-A14

description: Library name: LNCap output7-A14


title: P0_PAE_Mid_6 (P0_Mid6.20230511)

description: AmpliSeq


title: P0_PAE_Mid_5 (P0_Mid5.20230511)

description: AmpliSeq


title: P0_PAE_Mid_4 (P0_Mid4.20230511)

description: AmpliSeq


title: LNCap output7-A10

description: Library name: LNCap output7-A10


title: LNCap output7-A15

description: Library name: LNCap output7-A15


title: LNCap output7-A8

description: Library name: LNCap output7-A8


title: P0_PAE_Mid_11 (P0_Mid11.20230509)

description: AmpliSeq


title: P0_PAE_Mid_2 (P0_Mid2.20230511)

description: AmpliSeq


title: LNCap output7-A12

description: Library name: LNCap output7-A12


title: P0_PAE_Mid_10 (P0_Mid10.20230511)

description: AmpliSeq


title: P0_PAE_Mid_12 (P0_Mid12.20230509)

description: AmpliSeq


title: LNCap output7-A18

description: Library name: LNCap output7-A18


title: LNCap output8-A3

description: Library name: LNCap output8-A3


title: P0_PAE_Mid_11 (P0_Mid11.20230511)

description: AmpliSeq


title: LNCap output7-A13

description: Library name: LNCap output7-A13


title: LNCap output8-A4

description: Library name: LNCap output8-A4


title: P0_PAE_Mid_3 (P0_Mid3.20230511)

description: AmpliSeq


title: P0_PAE_Norm_1 (P0_Norm1.20221021)

description: AmpliSeq


title: P0_PAE_Low_7 (P0_Low7.20230404)

description: AmpliSeq


title: P0_PAE_Low_6 (P0_Low6.20230329)

description: AmpliSeq


title: LNCap output8-A5

description: Library name: LNCap output8-A5


title: LNCap output8-A2

description: Library name: LNCap output8-A2


title: LNCap output7-A20

description: Library name: LNCap output7-A20


title: LNCap output8-A8

description: Library name: LNCap output8-A8


title: P0_PAE_Low_9 (P0_Low9.20230418)

description: AmpliSeq


title: P0_PAE_Low_5 (P0_Low5.20230329)

description: AmpliSeq


title: LNCap output7-A17

description: Library name: LNCap output7-A17


title: P0_PAE_Mid_1 (P0_Mid1.20230511)

description: AmpliSeq


title: P0_PAE_Low_6 (P0_Low6.20230404)

description: AmpliSeq


title: P0_PAE_Low_8 (P0_Low8.20230222)

description: AmpliSeq


title: P0_PAE_Low_3 (P0_Low3.20230110)

description: AmpliSeq


title: LNCap output8-A10

description: Library name: LNCap output8-A10


title: LNCap output7-A16

description: Library name: LNCap output7-A16


title: LNCap output7-A19

description: Library name: LNCap output7-A19


title: P0_PAE_Low_7 (P0_Low7.20230329)

description: AmpliSeq


title: LNCap output8-A9

description: Library name: LNCap output8-A9


title: P0_PAE_Low_13 (P0_Low13.20230511)

description: AmpliSeq


title: LNCap output8-A6

description: Library name: LNCap output8-A6


title: LNCap output8-A1

description: Library name: LNCap output8-A1


title: P0_PAE_Low_11 (P0_Low11.20230511)

description: AmpliSeq


title: P0_PAE_Low_5 (P0_Low5.20230404)

description: AmpliSeq


title: P0_PAE_Low_10 (P0_Low10.20230418)

description: AmpliSeq


title: P0_PAE_Low_4 (P0_Low4.20230110)

description: AmpliSeq


title: LNCap output3-A6

description: Library name: LNCap output3-A6


title: LNCap output3-A1

description: Library name: LNCap output3-A1


title: LNCap output3-A7

description: Library name: LNCap output3-A7


title: LNCap output2-A20

description: Library name: LNCap output2-A20


title: P0_Con_7 (P0_Con7.20230329)

description: AmpliSeq

value: Saline


title: LNCap output8-A11

description: Library name: LNCap output8-A11


title: LNCap output3-A2

description: Library name: LNCap output3-A2


title: LNCap output8-A7

description: Library name: LNCap output8-A7


title: P0_PAE_Low_13 (P0_Low13.20230509)

description: AmpliSeq


title: P0_Con_6 (P0_Con6.20230110)

description: AmpliSeq


title: LNCap output2-A18

description: Library name: LNCap output2-A18


title: P0_Con_5 (P0_Con5.20230110)

description: AmpliSeq


title: LNCap output6-A20

description: Library name: LNCap output6-A20


title: P0_PAE_Low_2 (P0_Low2.20230110)

description: AmpliSeq


title: LNCap output7-A1

description: Library name: LNCap output7-A1


title: P0_PAE_Low_12 (P0_Low12.20230509)

description: AmpliSeq


title: P0_PAE_Low_12 (P0_Low12.20230511)

description: AmpliSeq


title: LNCap output2-A19

description: Library name: LNCap output2-A19


title: LNCap output3-A5

description: Library name: LNCap output3-A5


title: LNCap output3-A3

description: Library name: LNCap output3-A3


title: LNCap output3-A4

description: Library name: LNCap output3-A4


title: P0_Con_2 (P0_Con2.20221021)

description: AmpliSeq


title: LNCap output2-A16

description: Library name: LNCap output2-A16


title: P0_PAE_Low_1 (P0_Low1.20221021)

description: AmpliSeq


title: P0_Con_9 (P0_Con9.20230222)

description: AmpliSeq


title: P0_Con_8 (P0_Con8.20230418)

description: AmpliSeq


title: LNCap output3-A12

description: Library name: LNCap output3-A12


title: P0_Con_15 (P0_Con15.20230418)

description: AmpliSeq


title: LNCap output9-A20

description: Library name: LNCap output9-A20


title: P0_Con_7 (P0_Con7.20230222)

description: AmpliSeq


title: LNCap output3-A11

description: Library name: LNCap output3-A11


title: LNCap output2-A17

description: Library name: LNCap output2-A17


title: P0_Con_13 (P0_Con13.20230418)

description: AmpliSeq


title: LNCap output3-A17

description: Library name: LNCap output3-A17


title: P0_Con_3 (P0_Con3.20221021)

description: AmpliSeq


title: LNCap output3-A10

description: Library name: LNCap output3-A10


title: P0_Con_13 (P0_Con13.20230404)

description: AmpliSeq


title: LNCap output3-A8

description: Library name: LNCap output3-A8


title: P0_Con_3 (P0_Con3.20230222)

description: AmpliSeq


title: P0_Con_8 (P0_Con8.20230222)

description: AmpliSeq


title: P0_Con_2 (P0_Con2.20230418)

description: AmpliSeq


title: LNCap output8-A16

description: Library name: LNCap output8-A16


title: P0_Con_11 (P0_Con11.20230418)

description: AmpliSeq


title: LNCap output3-A9

description: Library name: LNCap output3-A9


title: P0_Con_16 (P0_Con16.20230418)

description: AmpliSeq


title: LNCap output4-A4

description: Library name: LNCap output4-A4


title: P0_Con_4 (P0_Con4.20230329)

description: AmpliSeq


title: P0_Con_14 (P0_Con14.20230418)

description: AmpliSeq


title: LNCap output8-A12

description: Library name: LNCap output8-A12


title: LNCap output9-A1

description: Library name: LNCap output9-A1


title: LNCap output9-A4

description: Library name: LNCap output9-A4


title: P0_Con_1 (P0_Con1.20230329)

description: AmpliSeq


title: LNCap output4-A5

description: Library name: LNCap output4-A5


title: P0_Con_12 (P0_Con12.20230404)

description: AmpliSeq


title: LNCap output8-A20

description: Library name: LNCap output8-A20


title: LNCap output3-A13

description: Library name: LNCap output3-A13


title: LNCap output8-A15

description: Library name: LNCap output8-A15


title: P0_Con_10 (P0_Con10.20230222)

description: AmpliSeq


title: E14_PAE_Norm_8 (E14_Norm8.20230418)

description: AmpliSeq


title: E14_PAE_Norm_7 (E14_Norm7.20230222)

description: AmpliSeq


title: LNCap output9-A6

description: Library name: LNCap output9-A6


title: P0_Con_10 (P0_Con10.20230418)

description: AmpliSeq


title: LNCap output9-A9

description: Library name: LNCap output9-A9


title: E14_PAE_Norm_9 (E14_Norm9.20230125)

description: AmpliSeq


title: E14_PAE_Norm_8 (E14_Norm8.20230316)

description: AmpliSeq


title: E14_PAE_Norm_9 (E14_Norm9.20230110)

description: AmpliSeq


title: LNCap output8-A19

description: Library name: LNCap output8-A19


title: LNCap output9-A7

description: Library name: LNCap output9-A7


title: E14_PAE_Norm_6 (E14_Norm6.20230125)

description: AmpliSeq


title: LNCap output9-A5

description: Library name: LNCap output9-A5


title: LNCap output9-A8

description: Library name: LNCap output9-A8


title: P0_Con_11 (P0_Con11.20230404)

description: AmpliSeq


title: LNCap output9-A11

description: Library name: LNCap output9-A11


title: E14_PAE_Norm_5 (E14_Norm5.20221021)

description: AmpliSeq


title: E14_PAE_Norm_6 (E14_Norm6.20221021)

description: AmpliSeq


title: P0_Con_1 (P0_Con1.20230418)

description: AmpliSeq


title: E14_PAE_Norm_3 (E14_Norm3.20221004)

description: AmpliSeq


title: LNCap output9-A12

description: Library name: LNCap output9-A12


title: LNCap output9-A10

description: Library name: LNCap output9-A10


title: LNCap output9-A2

description: Library name: LNCap output9-A2


title: LNCap output8-A18

description: Library name: LNCap output8-A18


title: E14_PAE_Norm_2 (E14_Norm2.20230125)

description: AmpliSeq


title: LNCap output8-A17

description: Library name: LNCap output8-A17


title: LNCap output4-A1

description: Library name: LNCap output4-A1


title: E14_PAE_Norm_2 (E14_Norm2.20221004)

description: AmpliSeq


title: E14_PAE_Norm_10 (E14_Norm10.20230127)

description: AmpliSeq


title: E14_PAE_Norm_12 (E14_Norm12.20230418)

description: AmpliSeq


title: LNCap output9-A13

description: Library name: LNCap output9-A13


title: LNCap output9-A15

description: Library name: LNCap output9-A15


title: LNCap output3-A14

description: Library name: LNCap output3-A14


title: E14_PAE_Norm_1 (E14_Norm1.20230125)

description: AmpliSeq


title: LNCap output3-A15

description: Library name: LNCap output3-A15


title: E14_PAE_Norm_4 (E14_Norm4.20221004)

description: AmpliSeq


title: E14_PAE_Mid_9 (E14_Mid9.20230316)

description: AmpliSeq


title: E14_PAE_Norm_1 (E14_Norm1.20221004)

description: AmpliSeq


title: E14_PAE_Mid_8 (E14_Mid8.20230316)

description: AmpliSeq


title: LNCap output3-A16

description: Library name: LNCap output3-A16


title: LNCap output9-A14

description: Library name: LNCap output9-A14


title: E14_PAE_Mid_8 (E14_Mid8.20230404)

description: AmpliSeq


title: LNCap output4-A2

description: Library name: LNCap output4-A2


title: E14_PAE_Norm_11 (E14_Norm11.20230222)

description: AmpliSeq


title: E14_PAE_Mid_7 (E14_Mid7.20221021)

description: AmpliSeq


title: E14_PAE_Mid_6 (E14_Mid6.20230316)

description: AmpliSeq


title: E14_PAE_Mid_7 (E14_Mid7.20230127)

description: AmpliSeq


title: LNCap output9-A18

description: Library name: LNCap output9-A18


title: E14_PAE_Mid_4 (E14_Mid4.20230316)

description: AmpliSeq


title: LNCap output8-A13

description: Library name: LNCap output8-A13


title: LNCap output3-A18

description: Library name: LNCap output3-A18


title: LNCap output4-A3

description: Library name: LNCap output4-A3


title: LNCap output9-A17

description: Library name: LNCap output9-A17


title: E14_PAE_Mid_3 (E14_Mid3.20230316)

description: AmpliSeq


title: LNCap output8-A14

description: Library name: LNCap output8-A14


title: E14_PAE_Mid_5 (E14_Mid5.20230316)

description: AmpliSeq


title: E14_PAE_Norm_10 (E14_Norm10.20230110)

description: AmpliSeq


title: E14_PAE_Mid_2 (E14_Mid2.20221004)

description: AmpliSeq


title: E14_PAE_Mid_2 (E14_Mid2.20230125)

description: AmpliSeq


title: LNCap output9-A3

description: Library name: LNCap output9-A3


title: LNCap output9-A16

description: Library name: LNCap output9-A16


title: E14_PAE_Mid_14 (E14_Mid15.20230404)

description: AmpliSeq


title: LNCap output3-A19

description: Library name: LNCap output3-A19


title: E14_PAE_Mid_13 (E14_Mid14.20230316)

description: AmpliSeq


title: LNCap input1-A18

description: Library name: LNCap input1-A18


title: E14_PAE_Mid_12 (E14_Mid12.20230509)

description: AmpliSeq


title: LNCap input2-A1

description: Library name: LNCap input2-A1


title: LNCap input1-A20

description: Library name: LNCap input1-A20


title: LNCap input2-A11

description: Library name: LNCap input2-A11


title: LNCap input2-A3

description: Library name: LNCap input2-A3


title: E14_PAE_Mid_10 (E14_Mid10.20230509)

description: AmpliSeq


title: LNCap input2-A2

description: Library name: LNCap input2-A2


title: LNCap input2-A10

description: Library name: LNCap input2-A10


title: E14_PAE_Low_9 (E14_Low9.20230222)

description: AmpliSeq


title: LNCap input1-A19

description: Library name: LNCap input1-A19


title: E14_PAE_Mid_1 (E14_Mid1.20230404)

description: AmpliSeq


title: E14_PAE_Low_8 (E14_Low8.20230110)

description: AmpliSeq


title: E14_PAE_Low_8 (E14_Low8.20230127)

description: AmpliSeq


title: LNCap input2-A4

description: Library name: LNCap input2-A4


title: E14_PAE_Mid_11 (E14_Mid11.20230404)

description: AmpliSeq


title: LNCap input2-A7

description: Library name: LNCap input2-A7


title: E14_PAE_Mid_11 (E14_Mid11.20230316)

description: AmpliSeq


title: E14_PAE_Low_6 (E14_Low6.20221021)

description: AmpliSeq


title: E14_PAE_Mid_13 (E14_Mid14.20230404)

description: AmpliSeq


title: E14_PAE_Low_7 (E14_Low7.20230316)

description: AmpliSeq


title: LNCap output9-A19

description: Library name: LNCap output9-A19


title: LNCap input2-A6

description: Library name: LNCap input2-A6


title: E14_PAE_Low_6 (E14_Low6.20230127)

description: AmpliSeq


title: LNCap input2-A14

description: Library name: LNCap input2-A14


title: E14_PAE_Mid_14 (E14_Mid15.20230316)

description: AmpliSeq


title: LNCap input2-A12

description: Library name: LNCap input2-A12


title: LNCap input2-A9

description: Library name: LNCap input2-A9


title: LNCap input2-A8

description: Library name: LNCap input2-A8


title: E14_PAE_Low_5 (E14_Low5.20221021)

description: AmpliSeq


title: LNCap input2-A5

description: Library name: LNCap input2-A5


title: LNCap output1-A3

description: Library name: LNCap output1-A3


title: E14_PAE_Mid_1 (E14_Mid1.20230316)

description: AmpliSeq


title: E14_PAE_Low_4 (E14_Low4.20230509)

description: AmpliSeq


title: LNCap input2-A13

description: Library name: LNCap input2-A13


title: E14_PAE_Low_3 (E14_Low2.20221004)

description: AmpliSeq


title: E14_PAE_Low_4 (E14_Low4.20221021)

description: AmpliSeq


title: E14_PAE_Low_3 (E14_Low2.20230125)

description: AmpliSeq


title: LNCap input2-A19

description: Library name: LNCap input2-A19


title: E14_PAE_Low_2 (E14_Low13.20230511)

description: AmpliSeq


title: E14_PAE_Low_11 (E14_Low11.20230329)

description: AmpliSeq


title: LNCap input2-A20

description: Library name: LNCap input2-A20


title: LNCap output1-A4

description: Library name: LNCap output1-A4


title: E14_PAE_Low_10 (E14_Low10.20230222)

description: AmpliSeq


title: LNCap input2-A16

description: Library name: LNCap input2-A16


title: LNCap output1-A1

description: Library name: LNCap output1-A1


title: E14_PAE_Low_5 (E14_Low5.20230127)

description: AmpliSeq


title: E14_PAE_Low_1 (E14_Low1.20221004)

description: AmpliSeq


title: E14_PAE_Low_1 (E14_Low1.20230125)

description: AmpliSeq


title: LNCap output1-A2

description: Library name: LNCap output1-A2


title: E14_PAE_Low_12 (E14_Low12.20230418)

description: AmpliSeq


title: LNCap input2-A15

description: Library name: LNCap input2-A15


title: E14_Con_9 (E14_Con9.20221021)

description: AmpliSeq


title: K562 output11-A17

description: Library name: K562 output11-A17


title: K562 output11-A16

description: Library name: K562 output11-A16


title: E14_PAE_Low_12 (E14_Low12.20230316)

description: AmpliSeq


title: LNCap input2-A18

description: Library name: LNCap input2-A18


title: K562 output11-A12

description: Library name: K562 output11-A12


title: E14_Con_8 (E14_Con8.20230127)

description: AmpliSeq


title: E14_Con_7 (E14_Con7.20221021)

description: AmpliSeq


title: K562 output11-A15

description: Library name: K562 output11-A15


title: E14_Con_8 (E14_Con8.20221021)

description: AmpliSeq


title: E14_Con_6 (E14_Con6.20230125)

description: AmpliSeq


title: K562 output11-A18

description: Library name: K562 output11-A18


title: LNCap input2-A17

description: Library name: LNCap input2-A17


title: K562 output11-A19

description: Library name: K562 output11-A19


title: K562 output11-A14

description: Library name: K562 output11-A14


title: E14_Con_5 (E14_Con5.20230125)

description: AmpliSeq


title: K562 output11-A13

description: Library name: K562 output11-A13


title: E14_Con_7 (E14_Con7.20230127)

description: AmpliSeq


title: E14_Con_6 (E14_Con6.20221004)

description: AmpliSeq


title: K562 output1-A3

description: Library name: K562 output1-A3


title: K562 output1-A4

description: Library name: K562 output1-A4


title: K562 output11-A20

description: Library name: K562 output11-A20


title: K562 output1-A2

description: Library name: K562 output1-A2


title: E14_Con_3 (E14_Con3.20230125)

description: AmpliSeq


title: K562 output1-A6

description: Library name: K562 output1-A6


title: K562 output1-A1

description: Library name: K562 output1-A1


title: E14_Con_4 (E14_Con4.20221004)

description: AmpliSeq


title: E14_Con_4 (E14_Con4.20230404)

description: AmpliSeq


title: E14_Con_3 (E14_Con3.20221004)

description: AmpliSeq


title: K562 output1-A8

description: Library name: K562 output1-A8


title: E14_Con_2 (E14_Con2.20221004)

description: AmpliSeq


title: K562 output1-A5

description: Library name: K562 output1-A5


title: K562 output1-A11

description: Library name: K562 output1-A11


title: E14_Con_14 (E14_Con14.20230222)

description: AmpliSeq


title: E14_Con_11 (E14_Con11.20230127)

description: AmpliSeq


title: K562 output1-A10

description: Library name: K562 output1-A10


title: K562 output1-A7

description: Library name: K562 output1-A7


title: E14_Con_11 (E14_Con11.20221021)

description: AmpliSeq


title: K562 output9-A8

description: Library name: K562 output9-A8


title: E14_Con_15 (E14_Con15.20230404)

description: AmpliSeq


title: E14_Con_10 (E14_Con10.20230222)

description: AmpliSeq


title: K562 output1-A9

description: Library name: K562 output1-A9


title: E14_Con_1 (E14_Con1.20221004)

description: AmpliSeq


title: K562 output9-A3

description: Library name: K562 output9-A3


title: E14_Con_5 (E14_Con5.20221004)

description: AmpliSeq


title: E14_Con_13 (E14_Con13.20230222)

description: AmpliSeq


title: K562 output1-A15

description: Library name: K562 output1-A15


title: K562 output1-A13

description: Library name: K562 output1-A13


title: PCNVRFS2_37C, E

city: Würzburg

first: Redmond

last: Smyth

state: Bayern

address: Josef-Schneider-Straße 2, D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description:
Library name: PCNVRFS2_37C, E
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
PCNVRFS2_37C.xml

library_source: other

data_processing:
Trimming with cutadapt
Aligned with bowtie
Mutations counted with rf-count
Data normalisation with rf-norm
Assembly: Aligned against specific sequence; CGNVRFS1 GATGCTGAGGAGCCATTTGCCGCCCACATTTTCATTCTTAAAATCGTACTGGGTTTTCAGTTCGTGTTTTTGCACTAGGGTCAAAAACACGCACTATGAAAACCCTAGTAATTGCCGTCATCCTGTTGAATTGTTTTGGAGGAAGTATGGCTCAGTATTACGACCATT; CGNVRFS2 AAGAAGACTTTAATTCAGAGTTTAGAAGATCATAACCTGAAGCGTAAAGTTTTAAAGCGTGAAGGAATGTCACCATATTCTTTGGCAGATATACAAACTATTCTGTTAAGTGGTGATAAAACAAAATTCTATCAAATACACTCTAAAATTGTAGGAGGTGTAGAACAA; HCNVRFS1 ATAATGATACGAATTTATAAGGCCCTAGGAGCGGAAGTCATATCGCCGCATTTAAACTCCAAAGCTTCGAAGCAACCGACCGGCTCGAAGCTCTCGACACAGGTCGGTCTTCACATGATTATGACTATATTGATGTTGGTGGTTTGCATGACATTACTGATGATATTGtaataa; HCNVRFS2 AAACAGGCCGAGGCGACGCCGTTCATGAGGAATTTCCCTGAATTGTTTCAGGGAAATGCCTAGAGTCTTCCGGTATGCCCAATACTGGAAGACAGAACGACATTGGGACAAAACAACCAAGACCTGCCCCGAAACCGCCTGATGAGGATATAAGATTAGATCAAATAC; PCNVRFS1 TAATGGCGCGCTTTCGTCTTGACGAAGAAAAGGCAGTTGAAAATCAGGCTTTAAACGTGCATCCGCTGGAGCTGGCTCGACCCAGTGTGAACAATCAGAGCCGAACGCAGCAGTTATTGGCACCAGTGAGACAAGTTCCTGTGCAACAAGCGCTGACGCGCCCGAGC; PCNVRFS2 GATTATTTTCGATCTTCGCACGATGCTGCGTCGCCGCTTTTGAGTTTCCTTTAAACTAGTCTTGTCTAGCGGTAGACGTAAAACCCCGCGCAGTCTCATCGATTTCAAACTTGCCCAGTGTAAGTATGAATTGGATTGGTATTTTC; WPNVRFS1 TTATTCGTATACTTAAGTTTCTTGGAGCTAGTGACATTGGTATTAGTAATTTAAACTTCAAAGCTTCAGCGGTGACGTCCGCAACTCTGGAGCTTCCTCCTGCGGACATCGCGATGCTAATTCTCTTGGGAGTTTTAACCAGCTGCGCAGTACTATTTCTGATGTGC; WPNVRFS2 AAATGATAATAAAGAAAGTGAATCTCTTATTAAAGATTCATATTCTTCGGGAAACGATGTGAATCTTCGTTGGAGTCCTCCGAGCCACGAAGATCTACGGAATCGGGGGATCCGCGTGAATCGCTAGTGCCTTCATTGGGACGTTCACATTGGATTAAACAGCG
Supplementary files format and content: Xml files containing DMS reactivities

molecule: other

organism: Nidovirales

source_name: whole virus

extract_protocol:
Trizol
Reverse transcribed with MarathonRT, amplified with gene specific primers containing illumina tails. Barcoding with illumina barcoded primers.

value: whole virus

tag: sample type

value: in vitro transcribed RNA

tag: temperature

tag: virus

value: Pomacea canaliculata nidovirus (PCNV)

tag: frameshift site


title: K562 output1-A16

description: Library name: K562 output1-A16


title: WPNVRFS1_22C, E

description:
Library name: WPNVRFS1_22C, E
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
WPNVRFS1_22C.xml


title: E14_Con_1 (E14_Con1.20230125)

description: AmpliSeq


title: K562 output9-A7

description: Library name: K562 output9-A7


title: WPNVRFS2_22C, E

description:
Library name: WPNVRFS2_22C, E
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
WPNVRFS2_22C.xml


title: WPNVRFS1_37C, E

description:
Library name: WPNVRFS1_37C, E
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
WPNVRFS1_37C.xml


title: K562 output2-A2

description: Library name: K562 output2-A2


title: K562 output1-A12

description: Library name: K562 output1-A12


title: K562 output2-A7

description: Library name: K562 output2-A7


title: PCNVRFS1_22C, E

description:
Library name: PCNVRFS1_22C, E
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
PCNVRFS1_22C.xml


title: K562 output2-A1

description: Library name: K562 output2-A1


title: WPNVRFS2_37C, E

description:
Library name: WPNVRFS2_37C, E
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
WPNVRFS2_37C.xml


title: HCNVRFS2_22C, E

description:
Library name: HCNVRFS2_22C, E
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
HCNVRFS2_22C.xml

value: Haemadipsa cavatuses nidovirus (HCNV)


title: HCNVRFS2_37C, E

description:
Library name: HCNVRFS2_37C, E
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
HCNVRFS2_37C.xml


title: HCNVRFS1_22C, E

description:
Library name: HCNVRFS1_22C, E
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
HCNVRFS1_22C.xml


title: K562 output1-A14

description: Library name: K562 output1-A14


title: PCNVRFS2_22C, E

description:
Library name: PCNVRFS2_22C, E
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
PCNVRFS2_22C.xml


title: K562 output1-A17

description: Library name: K562 output1-A17


title: K562 output2-A4

description: Library name: K562 output2-A4


title: HCNVRFS1_37C, E

description:
Library name: HCNVRFS1_37C, E
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
HCNVRFS1_37C.xml


title: K562 output1-A19

description: Library name: K562 output1-A19


title: PCNVRFS1_37C, E

description:
Library name: PCNVRFS1_37C, E
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
PCNVRFS1_37C.xml


title: K562 output1-A18

description: Library name: K562 output1-A18


title: K562 output9-A4

description: Library name: K562 output9-A4


title: K562 output9-A5

description: Library name: K562 output9-A5


title: CGNVRFS2_37C, E

description:
Library name: CGNVRFS2_37C, E
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
CGNVRFS2_37C.xml

value: Crassostrea gigas nidovirus (CGNV)


title: CGNVRFS2_22C, E

description:
Library name: CGNVRFS2_22C, E
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
CGNVRFS2_22C.xml


title: K562 output2-A3

description: Library name: K562 output2-A3


title: CGNVRFS1_37C, E

description:
Library name: CGNVRFS1_37C, E
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
CGNVRFS1_37C.xml


title: K562 output9-A6

description: Library name: K562 output9-A6


title: CGNVRFS1_22C, E

description:
Library name: CGNVRFS1_22C, E
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
CGNVRFS1_22C.xml


title: K562 output9-A11

description: Library name: K562 output9-A11


title: WPNVRFS2_37C, D

description:
Library name: WPNVRFS2_37C, D
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
WPNVRFS2_37C.xml


title: K562 output9-A10

description: Library name: K562 output9-A10


title: WPNVRFS2_22C, D

description:
Library name: WPNVRFS2_22C, D
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
WPNVRFS2_22C.xml


title: WPNVRFS1_37C, D

description:
Library name: WPNVRFS1_37C, D
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
WPNVRFS1_37C.xml


title: K562 output9-A14

description: Library name: K562 output9-A14


title: PCNVRFS2_37C, D

description:
Library name: PCNVRFS2_37C, D
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
PCNVRFS2_37C.xml


title: K562 output9-A13

description: Library name: K562 output9-A13


title: PCNVRFS2_22C, D

description:
Library name: PCNVRFS2_22C, D
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
PCNVRFS2_22C.xml


title: K562 output9-A18

description: Library name: K562 output9-A18


title: PCNVRFS1_37C, D

description:
Library name: PCNVRFS1_37C, D
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
PCNVRFS1_37C.xml


title: K562 output9-A9

description: Library name: K562 output9-A9


title: K562 output9-A12

description: Library name: K562 output9-A12


title: PCNVRFS1_22C, D

description:
Library name: PCNVRFS1_22C, D
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
PCNVRFS1_22C.xml


title: HCNVRFS2_37C, D

description:
Library name: HCNVRFS2_37C, D
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
HCNVRFS2_37C.xml


title: HCNVRFS2_22C, D

description:
Library name: HCNVRFS2_22C, D
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
HCNVRFS2_22C.xml


title: K562 output9-A19

description: Library name: K562 output9-A19


title: K562 output1-A20

description: Library name: K562 output1-A20


title: HCNVRFS1_37C, D

description:
Library name: HCNVRFS1_37C, D
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
HCNVRFS1_37C.xml


title: K562 output9-A17

description: Library name: K562 output9-A17


title: HCNVRFS1_22C, D

description:
Library name: HCNVRFS1_22C, D
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
HCNVRFS1_22C.xml


title: K562 output11-A2

description: Library name: K562 output11-A2


title: K562 output11-A10

description: Library name: K562 output11-A10


title: K562 output9-A16

description: Library name: K562 output9-A16


title: CGNVRFS2_37C, D

description:
Library name: CGNVRFS2_37C, D
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
CGNVRFS2_37C.xml


title: CGNVRFS2_22C, D

description:
Library name: CGNVRFS2_22C, D
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
CGNVRFS2_22C.xml


title: WPNVRFS1_22C, D

description:
Library name: WPNVRFS1_22C, D
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
WPNVRFS1_22C.xml


title: K562 output11-A1

description: Library name: K562 output11-A1


title: CGNVRFS1_37C, D

description:
Library name: CGNVRFS1_37C, D
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
CGNVRFS1_37C.xml


title: CGNVRFS1_22C, D

description:
Library name: CGNVRFS1_22C, D
File description: E_ is untreated, D_ is DMS treated, RFS1 Is reading frameshift 1, RFS2 is reading frameshift 2
CGNVRFS1_22C.xml


title: K562 output11-A5

description: Library name: K562 output11-A5


title: K562 output11-A11

description: Library name: K562 output11-A11


title: K562 output9-A15

description: Library name: K562 output9-A15


title: K562 output9-A20

description: Library name: K562 output9-A20


title: E14_Con_2 (E14_Con2.20230127)

description: AmpliSeq


title: Dvir_1

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab

department: QCB

institute: Princeton

data_processing:
Micro-C data for D. melanogaster were aligned to the Berkeley Drosophila Genome Project (BDGP) Release 6 reference assembly with BWA-MEM 82 using parameters -S -P -5 -M.
The resultant BAM files were parsed, sorted, de-duplicated, filtered, and split with pairtools (https://github.com/mirnylab/pairtools).  We removed pairs where only half of the pair could be mapped, or where the MAPQ score was less than three.
The resultant files were indexed with pairix (https://github.com/4dn-dcic/pairix).
The pairs files for individual replicates were merged with pairtools, and then used to generate contact matrices at 100bp resolution with Cooler.
Finally, balancing and mcool file generation was performed using Cooler’s zoomify tool.
Assembly: dm6
Supplementary files format and content: mcool
Library strategy: Micro-C

organism: Drosophila virilis

source_name: embryo

extract_protocol:
Embryos were collected on yeasted apple juice plates in population cages. For nc1-8 embryos, plates were changed every 30 mins, and subjected to immediate fixation. For nc14 embryos, plates were laid for 1 hour, then collected, incubated for 2 hours at 25℃, and subjected to fixation. For stage 10-12 embryos, plates were laid for 2 hours, incubated for 6 hours at 25C, and subjected to fixation.
Micro-C libraries were prepared as previously described in Batut…Levine 2022.

value: embryo

value: wt

tag: Stage

value: Dvir


title: WT L rep 3

city: Saint-Anne-de-Bellevue

first: Jaswinder

last: Singh

state: QC

address: 21111 Rue Lakeshore, Plant Science Department, Raymond Building, R2037

country: Canada

institute: McGill University

data_processing:
Raw reads were quality checked through Fastqc (version 0.11.5)
High quality reads were aligned to OT3098 using Kallisto (version 0.43.1)
Estimated counts and TPM were generated using Kallisto (version 0.43.1)
Assembly: Avena sativa OT3098
Supplementary files format and content: tsv files include estimated counts and TPM for each sample

organism: Avena sativa

source_name: Leaf

extract_protocol:
Total RNA was extracted using the Spectrum Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO, USA) following manufacturer’s protocol with minor modifications.
RNA libraries for RNA-seq were prepared using Nextera DNA Library Preparation Kit (Illumina) following manufacturer's protocol.

value: Leaf

value: WT


title: K562 output11-A7

description: Library name: K562 output11-A7


title: K562 output11-A4

description: Library name: K562 output11-A4


title: K562 output11-A9

description: Library name: K562 output11-A9


title: WT L rep 1


title: K562 output11-A6

description: Library name: K562 output11-A6


title: D35A L rep 1

value: transgenic


title: WT L rep 2


title: WT S rep 3

source_name: Seed

value: Seed


title: D35A L rep 3


title: WT S rep 2


title: WT S rep 1


title: K562 output11-A8

description: Library name: K562 output11-A8


title: K562 output2-A6

description: Library name: K562 output2-A6


title: K562 output2-A8

description: Library name: K562 output2-A8


title: K562 output2-A5

description: Library name: K562 output2-A5


title: D23 S rep 3


title: D23 S rep 1


title: K562 output2-A13

description: Library name: K562 output2-A13


title: K562 output2-A18

description: Library name: K562 output2-A18


title: Control iMG Rep2, expressing a non-targeting sgRNA related to CRISPRa

first: Falak

last: Sher

address: 630 W 168th street

institute: Columbia University

data_processing:
Standard Kallisto workflow was applied for accurate quantification of transcript abundances from RNA-Seq data. DESeq2 was used for differential gene expression analysis
Assembly: hg19

organism: Homo sapiens

source_name: iPSCs expressing CRISPRa with non-targeting sgRNA (control) were generated and differentiated into microglia (iMG) using the protocol from PMID: 38600587

growth_protocol: iPSCs with CRISPRa targeting LINE1 overexpression were generated and differentiated into microglia (iMG) following the protocol in PMID: 38600587.

extract_protocol:
RNAeasy kits. (QIAGEN, Cat. No. 74104)
TruSeq Stranded mRNA Library Prep Kit (Illumina, Cat No. 20020595) using the KAPA HiFi HotStart Ready Mix (Roche, KK2601) for the final PCR step

treatment_protocol: No treatment

value: iPSC-derived microglia

value: Control


title: Control iMG Rep3, expressing a non-targeting sgRNA related to CRISPRa


title: K562 output2-A10

description: Library name: K562 output2-A10


title: K562 output2-A11

description: Library name: K562 output2-A11


title: K562 output3-A1

description: Library name: K562 output3-A1


title: D35A L rep 2


title: K562 output11-A3

description: Library name: K562 output11-A3


title: K562 output2-A9

description: Library name: K562 output2-A9


title: CRISPRa-mediated LINE-1 overexpressing iMG Rep2

source_name: iPSCs with CRISPRa targeting LINE1 overexpression were generated and differentiated into microglia (iMG) following the protocol in PMID: 38600587.

value: LINE1 Over-expression


title: CRISPRa-mediated LINE-1 overexpressing iMG Rep3


title: K562 output2-A12

description: Library name: K562 output2-A12


title: CRISPRa-mediated LINE-1 overexpressing iMG Rep1


title: K562 output3-A2

description: Library name: K562 output3-A2


title: K562 output2-A20

description: Library name: K562 output2-A20


title: K562 output3-A7

description: Library name: K562 output3-A7


title: K562 output3-A12

description: Library name: K562 output3-A12


title: K562 output2-A16

description: Library name: K562 output2-A16


title: NBM4_CD14

city: St. Louis

first: Tim

last: Kong

state: MO

address: CSRB 8838

institute: Washington University School of Medicine

description: Library name: 153_NBM4_CD14

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
TMM normalization size factors in EdgeR were calculated to adjust for samples for differences in library size.
Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.
Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Assembly: GrCh38
Supplementary files format and content: Comma-separated values of raw counts.

source_name: Sorted CD14+ cells

extract_protocol:
The CD34- cell fraction was then enriched for CD14+ cells with bead purification.Total RNA from cell lines was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) with DNAse treatment following the manufacturer's protocol.
Samples were then indexed, pooled, and sequenced by Illumina NovaSeq 6000 following standard Illumina protocol.

value: Sorted CD14+ cells

tag: disease state

value: Healthy bone marrow donor


title: NBM7_CD14

description: Library name: 156_NBM7_CD14


title: NBM8_CD14

description: Library name: 157_NBM8_CD14


title: K562 output2-A17

description: Library name: K562 output2-A17


title: NBM5_CD14

description: Library name: 154_NBM5_CD14


title: NBM6_CD14

description: Library name: 155_NBM6_CD14


title: NBM3_CD14

description: Library name: 152_NBM3_CD14


title: NBM2_CD14

description: Library name: 151_NBM2_CD14


title: K562 output2-A14

description: Library name: K562 output2-A14


title: K562 output3-A6

description: Library name: K562 output3-A6


title: NBM14_CD14

description: Library name: 150_NBM14_CD14


title: K562 output2-A15

description: Library name: K562 output2-A15


title: K562 output3-A5

description: Library name: K562 output3-A5


title: NBM12_CD14

description: Library name: 148_NBM12_CD14


title: NBM9_CD14

description: Library name: 158_NBM9_CD14


title: NBM13_CD14

description: Library name: 149_NBM13_CD14


title: K562 output2-A19

description: Library name: K562 output2-A19


title: K562 output3-A13

description: Library name: K562 output3-A13


title: K562 output3-A4

description: Library name: K562 output3-A4


title: NBM10_CD14

description: Library name: 146_NBM10_CD14


title: NBM1_CD14

description: Library name: 145_NBM1_CD14


title: NBM11_CD14

description: Library name: 147_NBM11_CD14


title: ET9_CD14

description: Library name: 144_ET9_CD14

value: Essential thrombocythemia


title: K562 output3-A3

description: Library name: K562 output3-A3


title: K562 output6-A15

description: Library name: K562 output6-A15


title: MF30_CD14

description: Library name: 142_MF30_CD14

value: Myelofibrosis


title: ET8_CD14

description: Library name: 141_ET8_CD14


title: K562 output6-A14

description: Library name: K562 output6-A14


title: K562 output3-A15

description: Library name: K562 output3-A15


title: MF29_CD14

description: Library name: 140_MF29_CD14


title: D23 S rep 2


title: K562 output3-A10

description: Library name: K562 output3-A10


title: K562 output3-A16

description: Library name: K562 output3-A16


title: ET14_CD14

description: Library name: 139_ET14_CD14


title: Control iMG Rep1, expressing a non-targeting sgRNA related to CRISPRa


title: ET13_CD14

description: Library name: 138_ET13_CD14


title: ET15_CD14

description: Library name: 143_ET15_CD14


title: ET11_CD14

description: Library name: 134_ET11_CD14


title: K562 output3-A14

description: Library name: K562 output3-A14


title: K562 output6-A20

description: Library name: K562 output6-A20


title: K562 output3-A11

description: Library name: K562 output3-A11


title: K562 output3-A9

description: Library name: K562 output3-A9


title: K562 output6-A17

description: Library name: K562 output6-A17


title: PV8_CD14

description: Library name: 136_PV8_CD14

value: Polycythemia vera


title: K562 output6-A16

description: Library name: K562 output6-A16


title: K562 output6-A19

description: Library name: K562 output6-A19


title: ET7_CD14

description: Library name: 133_ET7_CD14


title: MF27_CD14

description: Library name: 132_MF27_CD14


title: K562 output8-A1

description: Library name: K562 output8-A1


title: ET6_CD14

description: Library name: 128_ET6_CD14


title: K562 output8-A9

description: Library name: K562 output8-A9


title: ET12_CD14

description: Library name: 135_ET12_CD14


title: K562 output3-A8

description: Library name: K562 output3-A8


title: MF25_CD14

description: Library name: 130_MF25_CD14


title: K562 output8-A6

description: Library name: K562 output8-A6


title: PV5_CD14

description: Library name: 126_PV5_CD14


title: K562 output8-A4

description: Library name: K562 output8-A4


title: K562 output8-A11

description: Library name: K562 output8-A11


title: ET5_CD14

description: Library name: 125_ET5_CD14


title: MF26_CD14

description: Library name: 131_MF26_CD14


title: ET3_CD14

description: Library name: 123_ET3_CD14


title: K562 output8-A5

description: Library name: K562 output8-A5


title: ET4_CD14

description: Library name: 124_ET4_CD14


title: K562 output8-A10

description: Library name: K562 output8-A10


title: K562 output8-A7

description: Library name: K562 output8-A7


title: PV6_CD14

description: Library name: 129_PV6_CD14


title: K562 output6-A18

description: Library name: K562 output6-A18


title: ET2_CD14

description: Library name: 120_ET2_CD14


title: MF23_CD14

description: Library name: 121_MF23_CD14


title: MF24_CD14

description: Library name: 127_MF24_CD14


title: MF32_CD14

description: Library name: 118_MF32_CD14


title: K562 output8-A13

description: Library name: K562 output8-A13


title: K562 output8-A19

description: Library name: K562 output8-A19


title: MF28_CD14

description: Library name: 137_MF28_CD14


title: ET10_CD14

description: Library name: 122_ET10_CD14


title: K562 output8-A3

description: Library name: K562 output8-A3


title: K562 output8-A2

description: Library name: K562 output8-A2


title: K562 output8-A12

description: Library name: K562 output8-A12


title: MF20_CD14

description: Library name: 116_MF20_CD14


title: K562 output8-A20

description: Library name: K562 output8-A20


title: MF21_CD14

description: Library name: 117_MF21_CD14


title: PV7_CD14

description: Library name: 115_PV7_CD14


title: K562 output9-A2

description: Library name: K562 output9-A2


title: K562 output9-A1

description: Library name: K562 output9-A1


title: MF18_CD14

description: Library name: 113_MF18_CD14


title: K562 output8-A8

description: Library name: K562 output8-A8


title: MF19_CD14

description: Library name: 114_MF19_CD14


title: K562 output8-A15

description: Library name: K562 output8-A15


title: K562 output8-A16

description: Library name: K562 output8-A16


title: K562 output8-A18

description: Library name: K562 output8-A18


title: MF15_CD14

description: Library name: 111_MF15_CD14


title: MF22_CD14

description: Library name: 119_MF22_CD14


title: MF14_CD14

description: Library name: 110_MF14_CD14


title: K562 output3-A17

description: Library name: K562 output3-A17


title: K562 output3-A19

description: Library name: K562 output3-A19


title: MF13_CD14

description: Library name: 109_MF13_CD14


title: MF12_CD14

description: Library name: 106_MF12_CD14


title: ET1_CD14

description: Library name: 108_ET1_CD14


title: K562 output4-A1

description: Library name: K562 output4-A1


title: K562 output3-A18

description: Library name: K562 output3-A18


title: K562 output4-A2

description: Library name: K562 output4-A2


title: MF31_CD14

description: Library name: 107_MF31_CD14


title: MF10_CD14

description: Library name: 104_MF10_CD14


title: K562 output4-A5

description: Library name: K562 output4-A5


title: K562 output3-A20

description: Library name: K562 output3-A20


title: K562 output8-A14

description: Library name: K562 output8-A14


title: MF11_CD14

description: Library name: 105_MF11_CD14


title: MF7_CD14

description: Library name: 101_MF7_CD14


title: MF9_CD14

description: Library name: 103_MF9_CD14


title: K562 output4-A4

description: Library name: K562 output4-A4


title: MF17_CD14

description: Library name: 112_MF17_CD14


title: K562 output4-A6

description: Library name: K562 output4-A6


title: PV4_CD14

description: Library name: 100_PV4_CD14


title: MF6_CD14

description: Library name: 99_MF6_CD14


title: K562 output4-A3

description: Library name: K562 output4-A3


title: MF5_CD14

description: Library name: 98_MF5_CD14


title: K562 output4-A10

description: Library name: K562 output4-A10


title: MF4_CD14

description: Library name: 97_MF4_CD14


title: K562 output4-A16

description: Library name: K562 output4-A16


title: K562 output4-A13

description: Library name: K562 output4-A13


title: MF3_CD14

description: Library name: 96_MF3_CD14


title: MF2_CD14

description: Library name: 95_MF2_CD14


title: K562 output4-A9

description: Library name: K562 output4-A9


title: K562 output4-A12

description: Library name: K562 output4-A12


title: K562 output4-A15

description: Library name: K562 output4-A15


title: PV3_CD14

description: Library name: 94_PV3_CD14


title: PV2_CD14

description: Library name: 93_PV2_CD14


title: K562 output4-A8

description: Library name: K562 output4-A8


title: K562 output8-A17

description: Library name: K562 output8-A17


title: MF8_CD14

description: Library name: 102_MF8_CD14


title: K562 output4-A11

description: Library name: K562 output4-A11


title: K562 output4-A7

description: Library name: K562 output4-A7


title: K562 output5-A8

description: Library name: K562 output5-A8


title: K562 output6-A4

description: Library name: K562 output6-A4


title: K562 output4-A18

description: Library name: K562 output4-A18


title: K562 output4-A14

description: Library name: K562 output4-A14


title: NBM7_CD34

description: Library name: 88_NBM7_CD34

source_name: Sorted CD34+ cells

extract_protocol:
CD34+ cells were enriched with bead purification.Total RNA from cell lines was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) with DNAse treatment following the manufacturer's protocol.
Samples were then indexed, pooled, and sequenced by Illumina NovaSeq 6000 following standard Illumina protocol.

value: Sorted CD34+ cells


title: NBM6_CD34

description: Library name: 87_NBM6_CD34


title: NBM9_CD34

description: Library name: 90_NBM9_CD34


title: K562 output5-A4

description: Library name: K562 output5-A4


title: PV1_CD14

description: Library name: 91_PV1_CD14


title: NBM4_CD34

description: Library name: 85_NBM4_CD34


title: NBM14_CD34

description: Library name: 84_NBM14_CD34


title: NBM5_CD34

description: Library name: 86_NBM5_CD34


title: K562 output5-A7

description: Library name: K562 output5-A7


title: NBM8_CD34

description: Library name: 89_NBM8_CD34


title: NBM13_CD34

description: Library name: 83_NBM13_CD34


title: K562 output5-A6

description: Library name: K562 output5-A6


title: K562 output5-A9

description: Library name: K562 output5-A9


title: K562 output5-A3

description: Library name: K562 output5-A3


title: NBM11_CD34

description: Library name: 81_NBM11_CD34


title: K562 output4-A17

description: Library name: K562 output4-A17


title: MF1_CD14

description: Library name: 92_MF1_CD14


title: NBM12_CD34

description: Library name: 82_NBM12_CD34


title: NBM10_CD34

description: Library name: 80_NBM10_CD34


title: K562 output4-A19

description: Library name: K562 output4-A19


title: sAML34_CD34

description: Library name: 79_sAML34_CD34

value: Post-MPN secondary acute myeloid leukemia


title: K562 output5-A5

description: Library name: K562 output5-A5


title: K562 output5-A19

description: Library name: K562 output5-A19


title: ET9_CD34

description: Library name: 77_ET9_CD34


title: sAML33_CD34

description: Library name: 78_sAML33_CD34


title: K562 output5-A11

description: Library name: K562 output5-A11


title: sAML32_CD34

description: Library name: 76_sAML32_CD34


title: sAML31_CD34

description: Library name: 75_sAML31_CD34


title: K562 output5-A17

description: Library name: K562 output5-A17


title: sAML29_CD34

description: Library name: 73_sAML29_CD34


title: MF30_CD34

description: Library name: 71_MF30_CD34


title: sAML28_CD34

description: Library name: 72_sAML28_CD34


title: K562 output5-A15

description: Library name: K562 output5-A15


title: K562 output5-A12

description: Library name: K562 output5-A12


title: MF29_CD34

description: Library name: 69_MF29_CD34


title: K562 output5-A18

description: Library name: K562 output5-A18


title: K562 output5-A10

description: Library name: K562 output5-A10


title: ET8_CD34

description: Library name: 70_ET8_CD34


title: K562 output5-A13

description: Library name: K562 output5-A13


title: sAML27_CD34

description: Library name: 68_sAML27_CD34


title: sAML26_CD34

description: Library name: 67_sAML26_CD34


title: sAML30_CD34

description: Library name: 74_sAML30_CD34


title: MF28_CD34

description: Library name: 66_MF28_CD34


title: K562 output5-A16

description: Library name: K562 output5-A16


title: K562 output6-A1

description: Library name: K562 output6-A1


title: K562 output6-A7

description: Library name: K562 output6-A7


title: sAML25_CD34

description: Library name: 65_sAML25_CD34


title: K562 output6-A9

description: Library name: K562 output6-A9


title: K562 output5-A1

description: Library name: K562 output5-A1


title: K562 output5-A20

description: Library name: K562 output5-A20


title: K562 output6-A8

description: Library name: K562 output6-A8


title: K562 output5-A14

description: Library name: K562 output5-A14


title: ET7_CD34

description: Library name: 62_ET7_CD34


title: sAML24_CD34

description: Library name: 64_sAML24_CD34


title: sAML22_CD34

description: Library name: 61_sAML22_CD34


title: K562 output6-A10

description: Library name: K562 output6-A10


title: MF25_CD34

description: Library name: 58_MF25_CD34


title: MF26_CD34

description: Library name: 59_MF26_CD34


title: K562 output6-A3

description: Library name: K562 output6-A3


title: K562 output6-A5

description: Library name: K562 output6-A5


title: MF27_CD34

description: Library name: 60_MF27_CD34


title: K562 output6-A12

description: Library name: K562 output6-A12


title: K562 output6-A6

description: Library name: K562 output6-A6


title: K562 output6-A2

description: Library name: K562 output6-A2


title: MF24_CD34

description: Library name: 55_MF24_CD34


title: ET6_CD34

description: Library name: 56_ET6_CD34


title: PV6_CD34

description: Library name: 57_PV6_CD34


title: ET5_CD34

description: Library name: 53_ET5_CD34


title: 293T output4-12

description: Library name: 293T output4-12


title: 293T output5-A1

description: Library name: 293T output5-A1


title: sAML21_CD34

description: Library name: 52_sAML21_CD34


title: K562 output6-A11

description: Library name: K562 output6-A11


title: ET4_CD34

description: Library name: 51_ET4_CD34


title: sAML20_CD34

description: Library name: 50_sAML20_CD34


title: PV5_CD34

description: Library name: 54_PV5_CD34


title: ET3_CD34

description: Library name: 49_ET3_CD34


title: 293T output5-A9

description: Library name: 293T output5-A9


title: 293T output4-11

description: Library name: 293T output4-11


title: MF23_CD34

description: Library name: 48_MF23_CD34


title: sAML23_CD34

description: Library name: 63_sAML23_CD34


title: K562 output4-A20

description: Library name: K562 output4-A20


title: K562 output5-A2

description: Library name: K562 output5-A2


title: ET2_CD34

description: Library name: 47_ET2_CD34


title: 293T output8-A11

description: Library name: 293T output8-A11


title: 293T output9-A3

description: Library name: 293T output9-A3


title: 293T output1-A9

description: Library name: 293T output1-A9


title: sAML19_CD34

description: Library name: 46_sAML19_CD34


title: sAML18_CD34

description: Library name: 45_sAML18_CD34


title: MF22_CD34

description: Library name: 44_MF22_CD34


title: 293T output9-A1

description: Library name: 293T output9-A1


title: 293T output9-A4

description: Library name: 293T output9-A4


title: 293T output9-A6

description: Library name: 293T output9-A6


title: MF21_CD34

description: Library name: 43_MF21_CD34


title: MF20_CD34

description: Library name: 42_MF20_CD34


title: MF18_CD34

description: Library name: 40_MF18_CD34


title: 293T output5-A8

description: Library name: 293T output5-A8


title: 293T output9-A2

description: Library name: 293T output9-A2


title: sAML17_CD34

description: Library name: 39_sAML17_CD34


title: MF19_CD34

description: Library name: 41_MF19_CD34


title: 293T output5-A10

description: Library name: 293T output5-A10


title: MF17_CD34

description: Library name: 38_MF17_CD34


title: 293T output8-A3

description: Library name: 293T output8-A3


title: MF16_CD34

description: Library name: 36_MF16_CD34


title: 293T output9-A5

description: Library name: 293T output9-A5


title: 293T output9-A7

description: Library name: 293T output9-A7


title: sAML16_CD34

description: Library name: 37_sAML16_CD34


title: sAML15_CD34

description: Library name: 35_sAML15_CD34


title: sAML14_CD34

description: Library name: 34_sAML14_CD34


title: 293T output8-A8

description: Library name: 293T output8-A8


title: 293T output1-A8

description: Library name: 293T output1-A8


title: 293T output8-A9

description: Library name: 293T output8-A9


title: MF15_CD34

description: Library name: 33_MF15_CD34


title: 293T output8-A4

description: Library name: 293T output8-A4


title: MF14_CD34

description: Library name: 32_MF14_CD34


title: sAML13_CD34

description: Library name: 31_sAML13_CD34


title: 293T output8-A10

description: Library name: 293T output8-A10


title: sAML11_CD34

description: Library name: 29_sAML11_CD34


title: 293T output9-A9

description: Library name: 293T output9-A9


title: 293T output9-A14

description: Library name: 293T output9-A14


title: 293T output9-A11

description: Library name: 293T output9-A11


title: MF13_CD34

description: Library name: 28_MF13_CD34


title: 293T output9-A12

description: Library name: 293T output9-A12


title: 293T output9-A15

description: Library name: 293T output9-A15


title: sAML12_CD34

description: Library name: 30_sAML12_CD34


title: MF12_CD34

description: Library name: 25_MF12_CD34


title: ET1_CD34

description: Library name: 27_ET1_CD34


title: 293T output9-A8

description: Library name: 293T output9-A8


title: MF11_CD34

description: Library name: 24_MF11_CD34


title: MF10_CD34

description: Library name: 23_MF10_CD34


title: 293T output9-A13

description: Library name: 293T output9-A13


title: 293T output8-A7

description: Library name: 293T output8-A7


title: K562 output6-A13

description: Library name: K562 output6-A13


title: MF9_CD34

description: Library name: 22_MF9_CD34


title: 293T output4-6

description: Library name: 293T output4-6


title: 293T output1-A3

description: Library name: 293T output1-A3


title: sAML10_CD34

description: Library name: 26_sAML10_CD34


title: 293T output4-7

description: Library name: 293T output4-7


title: MF7_CD34

description: Library name: 20_MF7_CD34


title: 293T output4-8

description: Library name: 293T output4-8


title: sAML9_CD34

description: Library name: 19_sAML9_CD34


title: sAML8_CD34

description: Library name: 18_sAML8_CD34


title: 293T output5-A5

description: Library name: 293T output5-A5


title: MF8_CD34

description: Library name: 21_MF8_CD34


title: 293T output1-A4

description: Library name: 293T output1-A4


title: PV4_CD34

description: Library name: 17_PV4_CD34


title: sAML7_CD34

description: Library name: 16_sAML7_CD34


title: 293T output5-A6

description: Library name: 293T output5-A6


title: 293T output9-A10

description: Library name: 293T output9-A10


title: 293T output5-A7

description: Library name: 293T output5-A7


title: MF5_CD34

description: Library name: 14_MF5_CD34


title: 293T output5-A12

description: Library name: 293T output5-A12


title: sAML6_CD34

description: Library name: 12_sAML6_CD34


title: MF3_CD34

description: Library name: 11_MF3_CD34


title: 293T output9-A16

description: Library name: 293T output9-A16


title: 293T output5-A13

description: Library name: 293T output5-A13


title: 293T output1-A1

description: Library name: 293T output1-A1


title: sAML5_CD34

description: Library name: 9_sAML5_CD34


title: PV3_CD34

description: Library name: 6_PV3_CD34


title: 293T input

description: Library name: 293T input


title: 293T output9-A18

description: Library name: 293T output9-A18


title: MF4_CD34

description: Library name: 13_MF4_CD34


title: sAML2_CD34

description: Library name: 5_sAML2_CD34


title: MF6_CD34

description: Library name: 15_MF6_CD34


title: 293T output8-A5

description: Library name: 293T output8-A5


title: 293T output1-A11

description: Library name: 293T output1-A11


title: sAML1_CD34

description: Library name: 4_sAML1_CD34


title: 293T output5-A11

description: Library name: 293T output5-A11


title: 293T output9-A17

description: Library name: 293T output9-A17


title: 293T output8-A6

description: Library name: 293T output8-A6


title: PV2_CD34

description: Library name: 3_PV2_CD34


title: 293T output4-3

description: Library name: 293T output4-3


title: 293T output4-4

description: Library name: 293T output4-4


title: sAML4_CD34

description: Library name: 8_sAML4_CD34


title: MF1_CD34

description: Library name: 2_MF1_CD34


title: PV1_CD34

description: Library name: 1_PV1_CD34


title: 293T output1-A12

description: Library name: 293T output1-A12


title: 293T output4-5

description: Library name: 293T output4-5


title: 293T output1-A10

description: Library name: 293T output1-A10


title: GBM27, mRNA

first: Briana

middle: Amicarella

last: Burns

address: 1 Baylor Plaza

description: Library name: GBM27_mRNA

data_processing:
Data quality control was performed using fastp to remove adapter sequences and low-quality reads (Q20, Q30).
Clean reads were aligned to the GRCh38 reference genome using HISAT2 v2.0.5.
Gene expression quantification was performed using featureCounts v1.5.0-p3 to generate raw counts and FPKM values.
Assembly: Hg38
Supplementary files format and content: comma separated values include gene-level read counts for each sample for each batch
Supplementary files format and content: comma separated values include normalized gene expression matrix using FPKM values for each batch

source_name: Human monocyte-derived dendritic cells

growth_protocol: Human monocyte-derived dendritic cells, doubly-loaded with both tumor mRNA and lysate were prepared as described in Decker et al, Vaccine; 2006.

extract_protocol:
Total RNA was extracted from dendritic cell using the Trizol method according to the protocol using the ThermoFisher Trizol protocol
mRNA libraries were prepared using poly-T oligo-attached magnetic beads and sequenced on an Illumina NovaSeq 6000 platform with paired-end 150 bp reads.

value: Human monocyte-derived dendritic cells

tag: batch number

value: mRNA


title: GBM27, double loaded

description: Library name: GBM27_2x

value: Double-Loaded


title: GBM24, double loaded

description: Library name: GBM24_2x


title: 293T output6-A2

description: Library name: 293T output6-A2


title: sAML3_CD34

description: Library name: 7_sAML3_CD34


title: GBM24, mRNA

description: Library name: GBM24_mRNA


title: 293T output6-A5

description: Library name: 293T output6-A5


title: GBM17, double loaded

description: Library name: GBM17_2x


title: 293T output6-A1

description: Library name: 293T output6-A1


title: 293T output6-A10

description: Library name: 293T output6-A10


title: GBM17, mRNA

description: Library name: GBM17_mRNA


title: cDNA from Patient-derived CTCs from BC patient 001 (timepoint 6, exp 2)

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

data_processing:
Trim Galore! (v0.6.6; parameters: –q 20 –length 20)
Mapping using STAR (v 2.5.9a) to human (GRCh38)  with splice junctions from the human GENCODE annotation (release 40)
The gene-level expression counts were computed with featureCounts from the subread package (v.2.0.3; parameters: -t exon -g gene_id --minOverlap 10 -Q 10) using the human gene annotations from GENCODE (release 40)
Samples were retained for further analyses if they had at least 500’000 reads, at least 5’000 genes with non-zero expression and less than 50% of reads mapping to mitochondrial genes
Assembly: GRCh38 and GENCODE release 40
Supplementary files format and content: counts.txt.gz are tab-delimited files containing raw counts for each library
Supplementary files format and content: processed_counts_matrix.txt.gz is a tab-delimited matrix containing raw counts for all libraries

source_name: CTC

extract_protocol:
Using CellCelector, an automated single-cell picking system (ALS), pools of single CTCs, CTC clusters and CTC–WBC clusters (range of 5–40 cells) were collected and immediately transferred into tubes (Axygen, 321-032-501, Thermofisher AB-0620) containing 10 µl RLT Plus lysis buffer and 1 U SUPERase IN RNase inhibitor (Invitrogen, AM2694). Samples were immediately frozen and kept at −80 °C until further processing. Following a previously published protocol for parallel DNA and RNA sequencing from individual cells (Macaulay, I. C. et al., 2016), genomes and transcriptomes of lysed cells were separated
Amplified cDNA was prepared on-bead according to the Smart-seq2 protocol. Libraries were prepared using Nextera XT (Illumina)

value: CTC

tag: donor

tag: number of ctcs

tag: number of wbcs attached

tag: timepoint


title: cDNA from Patient-derived CTCs from BC patient 001 (timepoint 3, exp 2)


title: cDNA from Patient-derived CTCs from BC patient 001 (timepoint 1, exp 2)


title: GBM16, mRNA

description: Library name: GBM16_mRNA


title: 293T output6-A4

description: Library name: 293T output6-A4


title: cDNA from Patient-derived CTCs from BC patient 001 (timepoint 6, exp 1)


title: GBM8, double loaded

description: Library name: GBM8_2x


title: cDNA from Patient-derived CTCs from BC patient 001 (timepoint 3, exp 1)


title: cDNA from Patient-derived CTCs from BC patient 001 (timepoint 2, exp 1)


title: 293T output6-A11

description: Library name: 293T output6-A11


title: GBM8, mRNA

description: Library name: GBM8_mRNA


title: 293T output6-A3

description: Library name: 293T output6-A3


title: GBM28, double loaded

description: Library name: GBM28_2x


title: 293T output6-A13

description: Library name: 293T output6-A13