title: CS39_PilR-PA4547_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS39_PilR-PA4547_PAO1_rep1

status: Public on Jul 27 2021

type: SRA

city: Zurich

first: Julian

last: Trouillon

address: Otto-Stern-Weg 3

department: Institute of Molecular Systems Biology

country: Switzerland

institute: ETH Zurich

description: adaptor-ligated sheared genomic DNA

library_source: genomic

data_processing:
Library strategy: DAP-seq
Read trimming using Trimmomatic
Alignment using Bowtie2
Peak calling using MACS2
closest features called with BEDtools
Genome_build: PAO1, PA14, IHMA87
Supplementary_files_format_and_content: excel table, list of RRs binding to the promoter region of each gene

molecule: genomic DNA

organism: Pseudomonas aeruginosa

source_name: purified genomic DNA from liquid cultures

extract_protocol:
After cell-fre protein expression, soluble His-tagged proteins were bound to cobalt magnetic beads and incubated with adaptor-ligated sheared genomic DNA. After washes and isolation of bead-protein-DNA complexes, the bound DNA regions were eluted by heating and then used for library preparation.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain


title: CS39_PilR-PA14_60260_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS39_PilR-IHMA87_05008_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS38_RoxR-PA4493_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS39_PilR-IHMA87_05008_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS38_RoxR-PA4493_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS38_RoxR-PA14_58300_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS38_RoxR-IHMA87_04815_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS38_RoxR-PA14_58300_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS38_RoxR-IHMA87_04815_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS41_PmrA-PA14_63150_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS37_ColR-PA4381_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS37_ColR-PA4381_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS37_ColR-PA14_56950_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS37_ColR-IHMA87_04696_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS36_PprB-PA4296_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS37_ColR-PA14_56950_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS37_ColR-IHMA87_04696_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS40_CbrB-IHMA87_05201_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS36_PprB-PA4296_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS36_PprB-PA14_55810_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS36_PprB-PA14_55810_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS36_PprB-IHMA87_04597_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS39_PilR-PA14_60260_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS35_BfiR-PA4196_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS36_PprB-IHMA87_04597_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS35_BfiR-PA14_09690_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS35_BfiR-PA4196_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS35_BfiR-PA14_09690_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS35_BfiR-IHMA87_00739_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS35_BfiR-IHMA87_00739_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS34_BfmR-_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS34_BfmR-_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS34_BfmR-PA4101_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS34_BfmR-IHMA87_00822_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS34_BfmR-PA4101_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS34_BfmR-IHMA87_00822_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS33_PA4080_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS33_PA4080_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS33_PA4080-PA14_11120_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS32_PA4032_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS32_PA4032-PA14_11680_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS33_PA4080-PA14_11120_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS32_PA4032_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS31_RocA1-PA3948_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS32_PA4032-IHMA87_00896_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS32_PA4032-IHMA87_00896_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS31_RocA1-PA14_12780_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS31_RocA1-IHMA87_00998_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS31_RocA1-IHMA87_00998_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS31_RocA1-PA14_12780_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS30_NarL-PA3879_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS30_NarL-PA3879_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS30_NarL-PA14_13730_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS30_NarL-PA14_13730_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS30_NarL-IHMA87_01064_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS30_NarL-IHMA87_01064_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS33_PA4080-IHMA87_00845_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS33_PA4080-IHMA87_00845_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS2_CreB-PA14_06060_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS2_CreB-PA0463_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS2_CreB-PA0463_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS32_PA4032-PA14_11680_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS2_CreB-IHMA87_00444_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS2_CreB-PA14_06060_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS31_RocA1-PA3948_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS29_TtsR-PA3714_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS29_TtsR-PA14_16350_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS29_TtsR-PA14_16350_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS29_TtsR-IHMA87_01254_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS29_TtsR-IHMA87_01254_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS28_ErdR-PA14_17670_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS28_ErdR-PA3604_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS28_ErdR-PA14_17670_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS28_ErdR-PA3604_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS28_ErdR-IHMA87_01366_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS27_CpxR-PA14_22760_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS27_CpxR-PA14_22760_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS27_CpxR-PA3204_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS26_GltR-PA3192_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS26_GltR-PA3192_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS26_GltR-PA14_22940_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS27_CpxR-IHMA87_01740_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS2_CreB-IHMA87_00444_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS26_GltR-IHMA87_01753_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS29_TtsR-PA3714_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS26_GltR-IHMA87_01753_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS25_CprR-PA3077_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS25_CprR-IHMA87_01871_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS24_RocA2-PA3045_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS24_RocA2-PA14_24710_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS24_RocA2-PA3045_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS27_CpxR-PA3204_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS24_RocA2-IHMA87_01902_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS25_CprR-PA14_24350_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS23_AtvR-PA2899_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS26_GltR-PA14_22940_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS28_ErdR-IHMA87_01366_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS24_RocA2-PA14_24710_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS23_AtvR-PA14_26570_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS24_RocA2-IHMA87_01902_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS25_CprR-PA14_24350_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS23_AtvR-PA14_26570_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS22_CopR-PA2809_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS23_AtvR-IHMA87_02066_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS23_AtvR-IHMA87_02066_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS22_CopR-PA2809_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS25_CprR-PA3077_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS22_CopR-PA14_27810_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS25_CprR-IHMA87_01871_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS22_CopR-PA14_27810_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS22_CopR-IHMA87_02262_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS21_PfeR-_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS21_PfeR-_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS21_PfeR-PA2686_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS21_PfeR-IHMA87_03812_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS23_AtvR-PA2899_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS20_BqsR-PA2657_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS21_PfeR-IHMA87_03812_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS20_BqsR-PA14_29730_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS20_BqsR-PA2657_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS20_BqsR-IHMA87_02453_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS20_BqsR-IHMA87_02453_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS1_PA0034_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS20_BqsR-PA14_29730_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS1_PA0034_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS1_PA0034-IHMA87_00036_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS1_PA0034-IHMA87_00036_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS22_CopR-IHMA87_02262_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS1_PA0034-PA14_00430_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS19_GacA-PA14_30650_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS19_GacA-PA2586_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS19_GacA-IHMA87_02519_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS19_GacA-PA2586_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS19_GacA-IHMA87_02519_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS18_CzcR-PA2523_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS18_CzcR-PA14_31960_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS18_CzcR-PA14_31960_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS18_CzcR-IHMA87_02628_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS18_CzcR-PA2523_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS17_DsbR-PA2479_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS21_PfeR-PA2686_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS18_CzcR-IHMA87_02628_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS17_DsbR-PA14_32580_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS17_DsbR-PA14_32580_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS1_PA0034-PA14_00430_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS16_PA2376_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS17_DsbR-IHMA87_02671_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS17_DsbR-PA2479_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS17_DsbR-IHMA87_02671_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS16_PA2376_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS16_PA2376-IHMA87_02778_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS16_PA2376-PA14_33920_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS16_PA2376-PA14_33920_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS15_EraR-PA1980_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS19_GacA-PA14_30650_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS15_EraR-PA1980_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS15_EraR-PA14_38900_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS16_PA2376-IHMA87_02778_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS15_EraR-IHMA87_03140_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS14_ErbR-PA1978_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS14_ErbR-PA14_38930_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS14_ErbR-PA1978_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS15_EraR-IHMA87_03140_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS14_ErbR-IHMA87_03142_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS14_ErbR-IHMA87_03142_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS14_ErbR-PA14_38930_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS13_ParR-PA1799_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS13_ParR-PA1799_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS13_ParR-PA14_41260_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS13_ParR-IHMA87_03330_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS13_ParR-IHMA87_03330_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS12_KdpE-PA1637_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS12_KdpE-PA1637_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS12_KdpE-PA14_43340_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS12_KdpE-PA14_43340_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS12_KdpE-IHMA87_03532_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS15_EraR-PA14_38900_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS12_KdpE-IHMA87_03532_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS11_PA1437-PA14_45880_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS11_PA1437_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS11_PA1437-IHMA87_03730_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS10_PA1397_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS10_PA1397-PA14_46360_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS10_PA1397-PA14_46360_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS11_PA1437-IHMA87_03730_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS13_ParR-PA14_41260_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS10_PA1397-IHMA87_03790_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS10_PA1397_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS10_PA1397-IHMA87_03790_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS11_PA1437-PA14_45880_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: H-CN-B

city: Weihai

first: Yang

last: Liu

state: Shandong

address: No.3 Mishan East Rd,Wendeng District

department: Department of Critical Care Medicine

country: China

institute: Weihai Central Hospital，Shangdong,China

library_source: transcriptomic

data_processing:
Quality control was performed using Fastp
We used Kallisto software to quantify the reads obtained by sequencing
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

molecule: total RNA

organism: Homo sapiens

source_name: huvec transfect with empty plasmid

growth_protocol: HUVECs were obtained from the American Type Culture Collection, cultured in DMEM (HyClone; Cytiva) containing 10% (v/v) FBS (Gibco; Thermo Fisher Scientific, Inc.) and 1% penicillin and incubated at 37˚C in an atmosphere with 10% CO2.

extract_protocol:
RNA was extracted. Briefly, cells were lysed on ice with RNeasy lysis buffer (Qiagen GmbH) after washing with ice-cold PBS. RNA was then extracted using a spin column (Qiagen GmbH) and purified with a high-purity RNA isolation kit (Roche Diagnostics GmbH).
RNA-seq library was constructed using Hieff NGSR MaxUP II DNA Library Prep Kit for Illumina (Yeasen, Shanghai, China) following manufacturer’s instruction. Sequencing was performed by Novogene Biotech (Beijing, China) using HiSeq X Ten system (Illumina, San Diego, CA).PE150

treatment_protocol: The pcDNA3.1-miR-124 plasmid was constructed by inserting the miR-124 sequence into the commercially available pcDNA3.1 vector (Sangon Biotech Co., Ltd.). To overexpress miR-124, HUVECs were transfected with the pcDNA3.1-miR-124 plasmid using Lipofectamine® 2000 (Invitrogen; Thermo Fisher Scientific, Inc.) according to the manufacturer’s instructions.

tag: cell type

value: HUVEC


title: H-124-C

source_name: huvec transfect with micro 124 expression plasmid


title: H-CN-A


title: H-124-B


title: H-CN-C


title: OE_LncR2_24h_1

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description:
expressed_gene_FPKM.txt
expressed_gene_reads.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2  --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments --no-discordant. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2 and Qvalue <= 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: cell line

growth_protocol: HK-2 cells were cultured in a culture flask with Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 μg/mL streptomycin, and 100 U/mL penicillin at 37 °C in a humidified atmosphere of 5% CO2 and 95% air. Cells (1× 104) were seeded in 24-well culture plates.

extract_protocol:
For the RNA-seq library, the total RNA was extracted from HK-2 cell samples by using TRIzol Reagent (Ambion) following the manufacturer’s  instructions. The total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the  absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). The RNA integrity was further verified by 1.5% agarose gel electrophoresis. For each sample, 5 μg of the total RNA was used to prepare the RNA-seq library. The Ribosomal RNAs were depleted with rRNA (Human/Mouse/Rat) Removal Kit  (Ribo-Zero™, RZH1046, Epicentre, and MGIEasy, 1000005953 for the tissue and HK-2 cell samples, respectively) before they were used for directional RNA-seq library preparation.
Purified mRNAs were iron-fragmented at 95 °C, followed by end repair and 5′ adaptor ligation. Then, reverse transcription was performed with RT primer harboring the 3′ adaptor sequence and randomized hexamer. The cDNAs were purified and PCR amplified. PCR products corresponding to 200–500 bps was purified, quantified, and stored at −80 °C until they were used for sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer’s instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

treatment_protocol: After the cells reached 70% confluence, we transfected the vector into the HK-2 cells using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. The cells were then incubated at 37 °C for 48 h.

tag: cell line

tag: tissue

value: renal tubular epithelial cells

tag: treatment

value: exposed to cisplatin for 24h


title: OE_LncR2_24h_2


title: OE_LncR2_0h_3

value: exposed to cisplatin for 0h


title: OE_LncR2_24h_3


title: H-124-A


title: OE_LncR2_0h_1


title: OE_LncR2_0h_2


title: CS11_PA1437_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: PB012-S21-U45_S21

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

country: USA

institute: Columbia University

data_processing:
For pooled RNA-seq, reads were aligned to the mouse reference genome GRCm38 and transcriptome annotation (Gencode vM10) using the STAR aligner with parameters –sjdbOverhang 65 –twopassMode Basic after trimming poly(A)-tails from the 3’-ends. The aligned reads were demultiplexed using the well-identifying barcodes, correcting all single-nucleotide errors. All reads with the same well-identifying barcode, UMI, and gene mapping were collapsed to represent an individual transcript. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance one of another UMI with the same well-identifying barcode and gene. For each 96-well plate, after generating a final list of individual transcripts with unique combinations of well-identifying barcodes, UMIs, and gene mapping, we produced a molecular count matrix for downstream analysis.
For full-length RNA-seq, the first 15 bp of Read 2 (UMI and TSO sequences) were removed using fastx-trimmer (http://hannonlab.cshl.edu/fastx_toolkit/index.html), and paired-end reads then were depleted of rRNA by alignment to mouse 5S, 5.8S, 18S, and 28S rRNA using bowtie2 (Langmead and Salzberg, 2012). rRNA-depleted paired-end reads were then aligned to the mouse genome (GENCODE M25, GRCm38.p6) using STAR 2.6.7a (Dobin et al., 2013). Uniquely mapped reads were then quantified at the exon level using featureCounts version 1.6 (Liao et al., 2014).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file that contains the gene expression counts of each sample.

organism: Mus musculus

extract_protocol:
Frozen tissues were thawed on ice in a glass-glass dounce homogenizer with 1-1.5 mL of ice-cold lysis buffer (20 mM HEPES pH 7.4, 150 mM KCl, 10 mM MgCl2, 0.5 mM DTT, 100 µg/mL cycloheximide (CHX), 1x EDTA-free protease inhibitors (Roche), and 100 U/ml SUPERaseIN). Tissues were lysed on ice using 30 strokes each with A and B pestles. Lysates were transferred to pre-chilled Eppendorf tubes and centrifuged at 1,000 xg 4°C for 10 minutes, after which the supernatant was transferred to a new tube. 1/9th the volume of 10% Igepal CA-630 was added to the lysates (final concentration 1%) and they were rotated at 4°C for 15 minutes. Lysates were clarified by centrifuging at 20,000 xg 4°C for 10 minutes and transferred to a new tube. 5% of the lysate was reserved as Input and frozen at -80°C. 1.5 µg (for striatal samples) or 6 µg (for midbrain samples) of biotinylated rabbit anti-HA was then added and the lysates were rotated overnight at 4°C. Streptavidin T1 Dynabeads (ThermoFisher, catalog #65601) were then added to the lysates (5 µL per µg of biotinylated antibody) and rotated for 30 minutes at 4°C. Beads were captured on a magnetic rack and the lysate was discarded. Beads were resuspended in 500 µL of ice-cold high salt buffer (20 mM HEPES pH 7.4, 350 mM KCl, 10 mM MgCl2, 1% Igepal CA-630, 0.5 mM DTT, 100 µg/mL cycloheximide (CHX), 1x EDTA-free protease inhibitors (Roche), and 100 U/mL SUPERaseIN) and transferred to a new tube. Beads were rotated for 30 minutes at 4°C, then captured on a magnetic rack and washed again 3 more times with ice-cold high salt buffer (four washes total over two hours). After the last wash, beads were resuspended in 100 µL of ribosome release buffer (20 mM HEPES pH 7.4, 50 mM EDTA, 100 U/mL SUPERaseIN) and incubated for 10 minutes at room temperature. Beads were captured on a magnetic rack and the eluate containing released mRNA was transferred to a new tube. Beads (with eL22-HA still bound) were flash frozen on liquid nitrogen and stored at -80°C. The aqueous mRNA eluate was purified using the RNEasy MinElute kit (Qiagen, catalog #74204) according to the manufacturer’s instructions. RNA was eluted in 14 µL of nuclease free water supplemented with 20 U/mL SUPERaseIN and stored at -80°C.  For synaptosome preparation, ventral midbrain or striatal dissections were homogenized in 1 mL of ice-cold 0.32 M sucrose with 5 mM HEPES pH 7.4, 10 mM MgCl2, 100 µg/mL cycloheximide (CHX), 1x EDTA-free protease inhibitors (Roche), and 100 U/ml SUPERaseIN. Nuclei and large debris were cleared at 2,000 xg for 10 minutes at 4°C. The supernatant (S1) was further centrifuged at 7,000 xg for 15 minutes at 4°C to yield the P2 pellet. The supernatant (S2) (cytoplasm and light membranes) was removed from the P2 pellet, which was washed by resuspension in 1 mL of ice-cold 0.32 M sucrose buffer (HEPES, MgCl2, CHX, and inhibitors as above) and re-centrifuged at 10,000xg at 4°C prior to lysis. P2 pellets were lysed in 1 ml of lysis buffer (5 mM HEPES pH 7.4, 150 mM KCl, 10 mM MgCl2, 1% Igepal CA-620, 100 µg/ml cycloheximide, 1x EDTA-free protease inhibitors (Roche), and 100 U/ml SUPERaseIN). After resuspension, samples were incubated at 4°C on a rotor for 15 minutes. The resulting synaptosome lysate was subjected to RiboTag IP as described below. Synaptosomes were prepared from the striatum or cortex of VGLUT1venus or DAT-Cre eGFP-expressing mice by homogenization in 1ml of ice-cold isosmolar buffer (0.32M sucrose, 4mM HEPES pH7.4, protease inhibitor cocktail Set 3 EDTA-free (EMD Millipore Corp.)), using a 2ml-glass-Teflon homogenizer with 12 strokes at 900 rpm. The homogenizer was rinsed with 250μL of isosmolar buffer and 3 manual strokes and then, the pestle was rinsed with additional 250μl of isosmolar buffer. The final 1.5ml of homogenate (H) was centrifuged at 1000xg for 5min at 4°C in a benchtop microcentrifuge. The supernatant (S1) was separated from the pellet (P1) and centrifuged at 12,600xg for 8min at 4°C. The supernatant (S2) was discarded and the synaptosomes-enriched pellet (P2) was resuspended in 0.5 ml of isosmolar buffer and layered on a two-step Ficoll density gradient (900µl of 7.5% and 900µl of 13% Ficoll, 4mM HEPES). The gradient was centrifuged at 50,000xg for 21min at 4°C (Beckman Coulter Optima MAX XP ultracentrifuge with a TL-55 rotor). Sucrose synaptosomes were recovered at the 7.5/13% Ficoll interface using a 0.5ml syringe.  Ficoll gradient-purified synaptosomes were diluted in PBS containing 1µg /ml FM4-64 and stored on ice throughout FASS procedures. The FACSAria-II (BD Biosciences) was operated with the following settings: 70μm Nozzle, sample shaking 300rpm at 4°C, FSC neutral density (ND) filter 1.0, 488nm laser on, area scaling 1.18, window extension 0.5, sort precision 0-16-0, FSC (340 V), SSC (488/10nm, 365V), FITC (EGFP) (530/30nm, 700V), PerCP (FM4-64) (675/20 nm, 700 V). Thresholding on FM4-64 was set with a detection threshold at 800. Samples were analyzed and sorted at rates of 15,000-20,000 events/s and flow rate of 3. Data was acquired using BD FACS DIVA 6. Cytometry plots were generated using FCS Express 7 (De Novo Software).
Pooled RNA-seq was performed using the low-input RNA-seq protocol reported in Snyder et al, Science Immunology, 2019.  The protocol for plate based, 3’ end unique molecular indicator (UMI)-based RNA sequencing of single cells has been described previously (Snyder et al., 2019) and was further modified to accommodate ultra-low input RiboTag IP samples. See Supplementary File 1 for sequences of all custom primers and oligonucleotides used in this protocol. Briefly, an estimated 20 – 500 pg of total RNA (based on qPCR, see above) for each sample was loaded into the wells of a 96 well plate in a volume of 6 µL of nuclease-free water containing 1 U/µL SUPERaseIN (ThermoFisher). After adding 1.5 µL of 10 µM barcoded RT primer (Integrated DNA Technologies), primer annealing was performed at 72°C for 3 minutes. Reverse transcription was performed by adding 7.5 µL RT mix to each well (2.81 µL of 40% polyethylene glycol 8000, 0.15 µL of 100 mM dNTPs, 3 µL of 5X Maxima H RT Buffer, 0.2 µL of 200 U/µL Maxima H Reverse Transcriptase (ThermoFisher), 0.2 µL of 20 U/µL SUPERaseIN, and 0.15 µL of 100 µM Template Switching Oligo (Integrated DNA Technologies), and 1 µL of nuclease free water). Reverse transcription was performed at 42°C for 90 minutes, followed by 10 cycles of 50°C for 2 minutes, 42°C for 2 minutes, 75°C for 10 minutes, followed by a 4°C hold. Excess primers were removed by adding 2 µL of Exonuclease I mix (1.875U ExoI in water) to each well and incubating at 37°C for 30 minutes, 85°C for 15 minutes, 75°C for 30 seconds, 4°C hold. All wells were pooled into a single 15-ml falcon tubes and cDNA was purified and concentrated using Dynabeads™ MyOne™ Silane beads (ThermoFisher) according to the manufacturer’s instructions. The cDNA was split into duplicate reactions containing 25µl cDNA, 25µl 2x HIFI HotStart Ready Mix (Kapa Biosystems), and 0.2M SMART PCR Primer. PCR was run as follows: 37°C for 30 minutes, 85°C for 15 minutes, 75°C for 30 seconds, 4°C hold. Duplicate reactions were combined and purified using 0.7 volumes AMPure XP beads (Beckman Coulter). The amplified cDNA was visualized on an Agilent 2100 Bioanalyzer and quantified using a Qubit II fluorometer (ThermoFisher). Sequencing libraries were constructed using Nextera XT (Illumina) with modifications. A custom i5 primer was used (NexteraPCR) with 0.6ng input cDNA and 10 cycles of amplification was performed. Unique i7 indexes were used for each plate. After amplification, the library was purified with two rounds of AMPure XP beads, visualized on the Agilent 2100 Bioanalyzer and quantified using the Qubit II fluorometer. Libraries were sequenced on an Illumina NextSeq 500 using the 75 cycle High Output kit (read lengths 26(R1) x 8(i) x 58(R2)). Custom sequencin

tag: brain region

value: substantia nigra reticulata

tag: age

tag: genotype

tag: batch

tag: preparation

value: RiboTag immunoprecipitation

tag: molecule subtype

value: rRNA-depleted total RNA


title: PB012-S16-U40_S16

value: ventral tagmental area


title: PB012-S18-U42_S18


title: PB012-S19-U43_S19


title: PB012-S17-U41_S17


title: PB012-S20-U44_S20


title: PB012-S07-U31_S7

value: RiboTag input


title: PB012-S06-U30_S6


title: PB012-S05-U29_S5


title: PB012-S14-U38_S14

value: substantia nigra pars compacta


title: PB012-S04-U28_S4


title: PB012-S08-U32_S8


title: PB012-S09-U33_S9


title: PB012-S02-U26_S2


title: PB012-S03-U27_S3


title: PB012-S13-U37_S13


title: PB012-S01-U25_S1


title: BH_SCRNA_376

molecule: polyA RNA

value: ventral midbrain synaptosome

value: polyA RNA


title: BH_SCRNA_375


title: BH_SCRNA_374


title: BH_SCRNA_372


title: PB012-S15-U39_S15


title: BH_SCRNA_367


title: BH_SCRNA_371


title: BH_SCRNA_370


title: BH_SCRNA_365


title: BH_SCRNA_364


title: BH_SCRNA_363


title: BH_SCRNA_359


title: BH_SCRNA_373


title: BH_SCRNA_360


title: BH_SCRNA_368


title: BH_SCRNA_361


title: BH_SCRNA_357


title: BH_SCRNA_356


title: BH_SCRNA_369


title: BH_SCRNA_366


title: BH_SCRNA_362


title: BH_SCRNA_351


title: BH_SCRNA_355


title: BH_SCRNA_350


title: BH_SCRNA_348


title: BH_SCRNA_349


title: BH_SCRNA_353


title: BH_SCRNA_347


title: BH_SCRNA_345


title: BH_SCRNA_346


title: BH_SCRNA_344


title: BH_SCRNA_343


title: BH_SCRNA_341


title: BH_SCRNA_358


title: BH_SCRNA_339


title: BH_SCRNA_338


title: BH_SCRNA_337


title: BH_SCRNA_354


title: BH_SCRNA_340


title: BH_SCRNA_333

value: striatum


title: BH_SCRNA_334


title: BH_SCRNA_335


title: BH_SCRNA_336


title: BH_SCRNA_332


title: BH_SCRNA_342


title: BH_SCRNA_331


title: BH_SCRNA_328


title: BH_SCRNA_326


title: BH_SCRNA_325


title: BH_SCRNA_327


title: BH_SCRNA_324


title: BH_SCRNA_329


title: BH_SCRNA_321


title: BH_SCRNA_320


title: BH_SCRNA_319


title: BH_SCRNA_322


title: BH_SCRNA_323


title: BH_SCRNA_316


title: BH_SCRNA_317


title: BH_SCRNA_315


title: BH_SCRNA_314


title: BH_SCRNA_330


title: BH_SCRNA_313


title: BH_SCRNA_311


title: BH_SCRNA_310


title: BH_SCRNA_309


title: BH_SCRNA_312


title: BH_SCRNA_308


title: BH_SCRNA_306


title: BH_SCRNA_304


title: BH_SCRNA_303


title: BH_SCRNA_318


title: BH_SCRNA_305


title: BH_SCRNA_302


title: BH_SCRNA_299


title: BH_SCRNA_301


title: BH_SCRNA_300


title: BH_SCRNA_297


title: BH_SCRNA_298


title: BH_SCRNA_296


title: BH_SCRNA_294


title: BH_SCRNA_292


title: BH_SCRNA_291


title: BH_SCRNA_293


title: BH_SCRNA_352


title: BH_SCRNA_307


title: BH_SCRNA_287


title: BH_SCRNA_288


title: BH_SCRNA_290


title: BH_SCRNA_289


title: BH_SCRNA_286


title: BH_SCRNA_285


title: BH_SCRNA_284


title: BH_SCRNA_283


title: BH_SCRNA_282


title: BH_SCRNA_295


title: BH_SCRNA_276


title: BH_SCRNA_277


title: BH_SCRNA_279


title: BH_SCRNA_280


title: BH_SCRNA_278


title: BH_SCRNA_275


title: BH_SCRNA_273


title: BH_SCRNA_274


title: BH_SCRNA_270


title: BH_SCRNA_268


title: BH_SCRNA_269


title: BH_SCRNA_272


title: BH_SCRNA_267


title: BH_SCRNA_264


title: BH_SCRNA_266


title: BH_SCRNA_281


title: BH_SCRNA_263


title: BH_SCRNA_262


title: BH_SCRNA_261


title: BH_SCRNA_257


title: BH_SCRNA_259


title: BH_SCRNA_256


title: BH_SCRNA_255


title: BH_SCRNA_254

value: striatum synaptosome


title: BH_SCRNA_271


title: BH_SCRNA_252


title: BH_SCRNA_260


title: BH_SCRNA_251


title: BH_SCRNA_258


title: BH_SCRNA_249


title: BH_SCRNA_265


title: BH_SCRNA_247


title: BH_SCRNA_248


title: BH_SCRNA_246


title: BH_SCRNA_253


title: BH_SCRNA_245


title: BH_SCRNA_244


title: BH_SCRNA_243


title: BH_SCRNA_242


title: BH_SCRNA_241


title: BH_SCRNA_240


title: BH_SCRNA_250


title: BH_SCRNA_238


title: BH_SCRNA_234


title: BH_SCRNA_235


title: BH_SCRNA_239


title: BH_SCRNA_237


title: BH_SCRNA_236


title: BH_SCRNA_233


title: BH_SCRNA_232


title: BH_SCRNA_231


title: BH_SCRNA_230


title: BH_SCRNA_228


title: BH_SCRNA_227


title: BH_SCRNA_223


title: BH_SCRNA_222

value: cortex synaptosome

value: fluorescence activated synaptosome sorting


title: BH_SCRNA_226


title: BH_SCRNA_225


title: BH_SCRNA_221


title: BH_SCRNA_224


title: BH_SCRNA_218


title: BH_SCRNA_213


title: BH_SCRNA_214


title: BH_SCRNA_212


title: BH_SCRNA_216


title: BH_SCRNA_217


title: BH_SCRNA_215


title: BH_SCRNA_201

value: small particle synaptosome


title: BH_SCRNA_210


title: BH_SCRNA_209


title: BH_SCRNA_211


title: BH_SCRNA_208


title: BH_SCRNA_202


title: BH_SCRNA_203


title: BH_SCRNA_207


title: BH_SCRNA_204


title: BH_SCRNA_200


title: BH_SCRNA_229


title: BH_SCRNA_220


title: BH_SCRNA_198


title: 60_Wapl.KO_Rec8.TEV

city: Vienna

first: Bart

middle: Johan H

last: Dequeker

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechology

data_processing:
Base calling was performed by VBCF NGS facility and NGS facility in the Department of Totipotency, MPIB
Mapping: iterative mapping (see Imakaev et al, 2012) using bwa
Read filtering was performed as in Flyamer et al., 2017:
Summary of filtering: If two reads map to the same strand, and each side of the read is within 500 bp of any side of the other read, we retain only one copy of the read. We separate the genome into 500 bp bins. If any two bins are interacting more than once, only one interaction is counted. Since each region is only present in the single cell up to 4 times (in oocytes), we eliminated all 500 bp bins that form more than 8 unique interactions with other bins.
Filtered reads were then binned at different resolutions (we provide 4 resolutions) using read start as a read position and stored in the Cool file format. No normalization was applied to the data.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix of whole-genome locus interaction frequencies binned at 1kb, 10kb, 40kb, and 100kb resolutions stored in the Cool file format.

source_name: oocyte

extract_protocol:
snHi-C protocol according to Flyamer et al., 2017
The library preparation was performed following the standard DNA sample preparation protocol by the VBCF NGS unit or the NGS facility in the Department of Totipotency, MPIB

value: Rec8TEV/TEVWaplfl/fl (Tg)Zp3-Cre

value: +TEV

tag: developmental stage

value: GV oocyte - SN


title: 59_Wapl.KO_Rec8.TEV


title: BH_SCRNA_196


title: BH_SCRNA_195


title: BH_SCRNA_199


title: BH_SCRNA_197


title: BH_SCRNA_219


title: BH_SCRNA_194


title: BH_SCRNA_205


title: BH_SCRNA_206


title: 58_Wapl.KO_Rec8.TEV


title: 54_Wapl.KO_Rec8.TEV


title: 53_Wapl.KO_Rec8.TEV

value: -TEV


title: 56_Wapl.KO_Rec8.TEV


title: 55_Wapl.KO_Rec8.TEV


title: 50_Wapl.KO_Rec8.TEV


title: 51_Wapl.KO_Rec8.TEV


title: 48_Wapl.KO_Rec8.TEV


title: 49_Wapl.KO_Rec8.TEV


title: BH_SCRNA_193


title: 46_Wapl.KO_Rec8.TEV


title: 52_Wapl.KO_Rec8.TEV


title: 47_Wapl.KO_Rec8.TEV


title: BH_SCRNA_192


title: 45_Wapl.KO_Rec8.TEV


title: 44_Wapl.KO_Rec8.TEV


title: 57_Wapl.KO_Rec8.TEV


title: BH_SCRNA_186


title: BH_SCRNA_180


title: BH_SCRNA_183


title: BH_SCRNA_184


title: BH_SCRNA_189


title: BH_SCRNA_185


title: BH_SCRNA_188


title: BH_SCRNA_187


title: 43_Wapl.KO_Rec8.TEV


title: BH_SCRNA_190


title: 40_Wapl.KO_Rec8.TEV


title: BH_SCRNA_178


title: 39_Wapl.KO_Rec8.TEV


title: 42_Wapl.KO_Rec8.TEV


title: 41_Wapl.KO_Rec8.TEV


title: BH_SCRNA_174


title: BH_SCRNA_177


title: 37_Wapl.KO_Rec8.TEV


title: BH_SCRNA_172


title: BH_SCRNA_175


title: BH_SCRNA_176


title: BH_SCRNA_173


title: BH_SCRNA_191


title: BH_SCRNA_181


title: BH_SCRNA_171


title: 36_Wapl.KO_Rec8.TEV


title: 35_Wapl.KO_Rec8.TEV


title: 38_Wapl.KO_Rec8.TEV


title: BH_SCRNA_170


title: 31_Wapl.KO_Rec8.TEV


title: 32_Wapl.KO_Rec8.TEV


title: 28_Wapl.KO_Rec8.TEV


title: BH_SCRNA_179


title: 27_Wapl.KO_Rec8.TEV


title: 33_Wapl.KO_Rec8.TEV


title: 30_Wapl.KO_Rec8.TEV


title: BH_SCRNA_166


title: BH_SCRNA_163


title: BH_SCRNA_169


title: 34_Wapl.KO_Rec8.TEV


title: BH_SCRNA_168


title: BH_SCRNA_164


title: BH_SCRNA_167


title: 23_Wapl.KO_Rec8.TEV


title: 25_Wapl.KO_Rec8.TEV


title: 24_Wapl.KO_Rec8.TEV


title: 26_Wapl.KO_Rec8.TEV


title: 22_Wapl.KO_Rec8.TEV


title: BH_SCRNA_159


title: BH_SCRNA_160


title: BH_SCRNA_158


title: BH_SCRNA_182


title: 21_Wapl.KO_Rec8.TEV


title: BH_SCRNA_157


title: BH_SCRNA_165


title: BH_SCRNA_161


title: BH_SCRNA_162


title: 20_Wapl.KO_Rec8.TEV


title: 19_Wapl.KO_Rec8.TEV


title: BH_SCRNA_156


title: BH_SCRNA_155


title: 18_Wapl.KO_Rec8.TEV


title: 29_Wapl.KO_Rec8.TEV


title: BH_SCRNA_153


title: BH_SCRNA_154


title: 15_Wapl.KO_Rec8.TEV


title: 14_Wapl.KO_Rec8.TEV


title: BH_SCRNA_152


title: 17_Wapl.KO_Rec8.TEV


title: 12_Wapl.KO_Rec8.TEV


title: 13_Wapl.KO_Rec8.TEV


title: BH_SCRNA_143


title: BH_SCRNA_145


title: BH_SCRNA_148


title: BH_SCRNA_144


title: BH_SCRNA_149


title: BH_SCRNA_151


title: BH_SCRNA_146


title: BH_SCRNA_147


title: BH_SCRNA_150


title: 16_Wapl.KO_Rec8.TEV


title: BH_SCRNA_142


title: BH_SCRNA_140


title: BH_SCRNA_139


title: BH_SCRNA_141


title: BH_SCRNA_138


title: BH_SCRNA_135


title: BH_SCRNA_136


title: BH_SCRNA_137


title: BH_SCRNA_134


title: BH_SCRNA_133


title: BT294

type: RNA

city: Candiolo

first: Francesca

last: De Bacco

country: Italy

institute: Candiolo Cancer Institute

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using Cubic Spline normalization using GenomeStudio software

label: biotin

source_name: glioblastoma

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: DMEM-F12, B27, EGF 20ng/ml, FGF 20ng/ml

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: neurosphere

tag: gender

value: male

tag: neurosphere derivation time

value: First surgery

tag: previous treatments

value: Treatment naive

tag: idh status

value: wt

tag: tert promoter status


title: BH_SCRNA_130

value: RiboTag input


title: BH_SCRNA_132


title: BT274

description: replicate 1


title: BT266

description: replicate 1

source_name: DIPG


title: BT322

description: replicate 1


title: BT261

description: replicate 1


title: BH_SCRNA_127


title: BH_SCRNA_129


title: BT235

description: replicate 1


title: BT246

description: replicate 1


title: BT279

description: replicate 1

value: female


title: BT284

description: replicate 1


title: BT517

description: replicate 1


title: BT287

description: replicate 1


title: BT206

description: replicate 1


title: BT219

description: replicate 1


title: BH_SCRNA_126

value: polyA RNA


title: BT245

description: replicate 1


title: BT398

description: replicate 1


title: BH_SCRNA_125

value: striatum


title: BT249

description: replicate 1


title: BT138

description: replicate 1


title: BT283

description: replicate 1


title: BH_SCRNA_131


title: BH_SCRNA_128


title: BH_SCRNA_124


title: BH_SCRNA_123


title: BT371

description: replicate 1


title: BH_SCRNA_122


title: BH_SCRNA_118

value: RiboTag immunoprecipitation


title: BH_SCRNA_121


title: BT333

description: replicate 1


title: BH_SCRNA_120


title: BH_SCRNA_117


title: BT500

description: replicate 1


title: BT490

description: replicate 1

value: mut


title: BT513

description: replicate 1


title: BH_SCRNA_114


title: BT493

description: replicate 1


title: BH_SCRNA_115


title: BT487

description: replicate 1


title: BT330

description: replicate 1


title: BH_SCRNA_116


title: BH_SCRNA_112


title: BH_SCRNA_111


title: BH_SCRNA_119


title: BT480

description: replicate 1


title: BH_SCRNA_113


title: BT155

description: replicate 1


title: BH_SCRNA_110


title: BT449

description: replicate 1


title: BT442

description: replicate 1


title: BH_SCRNA_109


title: BT423

description: replicate 1


title: BT202

description: replicate 1


title: BT157

description: replicate 1


title: BT201

description: replicate 1


title: BT468

description: replicate 1


title: BH_SCRNA_108


title: BH_SCRNA_105


title: BH_SCRNA_106


title: BT150

description: replicate 1


title: BH_SCRNA_107


title: BT470

description: replicate 1


title: BH_SCRNA_104


title: BH_SCRNA_101


title: BH_SCRNA_102


title: BH_SCRNA_100


title: BH_SCRNA_99


title: BH_SCRNA_97


title: BT332.3

description: replicate 3


title: BT454

description: replicate 1


title: BH_SCRNA_98


title: BT379.3

description: replicate 3


title: BT463

description: replicate 1


title: BH_SCRNA_96


title: BT451

description: replicate 1


title: BT434

description: replicate 1


title: BT445

description: replicate 1


title: BT209

description: replicate 1


title: BH_SCRNA_94


title: BT430

description: replicate 1


title: BH_SCRNA_93


title: BT446

description: replicate 1


title: BH_SCRNA_90


title: BH_SCRNA_88


title: BH_SCRNA_91


title: BH_SCRNA_89


title: BH_SCRNA_95


title: BH_SCRNA_87


title: BH_SCRNA_92


title: BT452

description: replicate 1


title: BT437

description: replicate 1


title: BT205.3

description: replicate 3


title: BT428

description: replicate 1


title: BT422

description: replicate 1


title: BT299.3

description: replicate 3


title: BT418

description: replicate 1


title: BH_SCRNA_86


title: BT415

description: replicate 1


title: BT419

description: replicate 1


title: BT414

description: replicate 1


title: BT453

description: replicate 1


title: BT413

description: replicate 1


title: BH_SCRNA_84


title: BH_SCRNA_85


title: BH_SCRNA_83


title: BH_SCRNA_81


title: BH_SCRNA_82


title: BH_SCRNA_80


title: BH_SCRNA_79


title: BH_SCRNA_77


title: BT308.3

description: replicate 3


title: BT302.4

description: replicate 4


title: BT408

description: replicate 1


title: BH_SCRNA_78


title: BH_SCRNA_76


title: BH_SCRNA_74


title: BH_SCRNA_75


title: BH_SCRNA_73


title: BT462

description: replicate 1


title: BH_SCRNA_72


title: BH_SCRNA_71


title: BT334.3

description: replicate 3


title: BT483

description: replicate 1


title: BT456

description: replicate 1


title: BT417

description: replicate 1


title: BT302.3

description: replicate 3


title: BT421

description: replicate 1


title: BH_SCRNA_70


title: BT479

description: replicate 1


title: BT443

description: replicate 1


title: BT326.3

description: replicate 3


title: BT467

description: replicate 1


title: BT407

description: replicate 1


title: BT404

description: replicate 1


title: BH_SCRNA_69


title: BH_SCRNA_68


title: BH_SCRNA_65


title: BH_SCRNA_66


title: BH_SCRNA_103


title: BH_SCRNA_67


title: BT358.4

description: replicate 4


title: BH_SCRNA_64


title: BT273.3

description: replicate 3


title: BH_SCRNA_63


title: BH_SCRNA_62


title: BT332.2

description: replicate 2


title: BT358.3

description: replicate 3


title: BH_SCRNA_61


title: BT299.2

description: replicate 2


title: BT159.2

description: replicate 2


title: BT332

description: replicate 1


title: BT299

description: replicate 1


title: BT326

description: replicate 1


title: BH_SCRNA_60


title: BT326.2

description: replicate 2


title: BH_SCRNA_57


title: BH_SCRNA_53


title: BH_SCRNA_56


title: BH_SCRNA_58


title: BH_SCRNA_55


title: BH_SCRNA_59


title: BT159

description: replicate 1


title: BH_SCRNA_54


title: BT337

description: replicate 1


title: BT337.2

description: replicate 2


title: BH_SCRNA_49


title: BH_SCRNA_50


title: BT358.2

description: replicate 2


title: BH_SCRNA_48


title: BT328.2

description: replicate 2


title: BT297

description: replicate 1


title: BT358

description: replicate 1


title: BH_SCRNA_51


title: BT297.2

description: replicate 2


title: BT373

description: replicate 1


title: BH_SCRNA_52


title: BH_SCRNA_47


title: BT232.2

description: replicate 2


title: BT328

description: replicate 1


title: BT379.2

description: replicate 2


title: BT232

description: replicate 1


title: BT314.2

description: replicate 2


title: BH_SCRNA_44


title: BH_SCRNA_43


title: BH_SCRNA_42


title: BT379

description: replicate 1


title: BH_SCRNA_46


title: BT334.2

description: replicate 2


title: BH_SCRNA_40


title: BT334

description: replicate 1


title: BT205.2

description: replicate 2


title: BH_SCRNA_41


title: BT314

description: replicate 1


title: BH_SCRNA_36


title: BH_SCRNA_38


title: BH_SCRNA_39


title: BH_SCRNA_45


title: BH_SCRNA_37


title: BT308

description: replicate 1


title: BH_SCRNA_34


title: BT205

description: replicate 1


title: BH_SCRNA_35


title: BT308.2

description: replicate 2


title: BH_SCRNA_33


title: BH_SCRNA_32


title: BT302

description: replicate 1


title: BT302.2

description: replicate 2


title: BT275.2

description: replicate 2


title: BH_SCRNA_30


title: BT275

description: replicate 1


title: BT273.2

description: replicate 2


title: BH_SCRNA_28


title: BH_SCRNA_27


title: BH_SCRNA_25


title: BH_SCRNA_29


title: LB

city: Porto

first: Ana

middle: Rita Rego

last: Lopes

state: Porto

address: Rua Dr. Roberto Frias s/n

country: Portugal

institute: Faculdade de Engenharia Universidade do Porto

data_processing:
Raw sequences were first quality-filtered (Q<5) using prinseq. The reads that were longer than 20 bp were kept and aligned to the G. molinativorax ON4T genome.
The number of reads by gene or by cds was evaluated using eXpress
Genome_build: CP028426.gb; CP028427.gb
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest

organism: Gulosibacter molinativorax

source_name: ON4T biomass growing in LB

growth_protocol: An ON4T inoculum, was prepared. To obtain the mRNA libraries from strain ON4T under different growth conditions, 30 mL of respectively, MMM and Luria-Bertani Broth (LB) were inoculated.

extract_protocol:
Total RNA was extracted using the RNeasy extraction kit (QIAGEN GmbH) and for mRNA enrichment, the subtractive hybridization protocol as described by Stewart et al. (2010) was used.
The library preparation followed the protocol for whole transcription libraries in the kit Ion total RNA-Seq kit v2 (Life Technologies)

treatment_protocol: About 15-20 mL culture of exponetially growing cells were sampled and centrifuged at 9000 rpm, for 10 min, at 8 ºC to remove the supernatant. The resulting cell pellet was stabilized with RNAprotect® Cell Reagent (Qiagen, with a proportion of 1:1). Further, aliquots of 1.5 mL of this mixture (cells + RNA protect solution) were frozen with liquid N2, and preserved at -80 ºC until RNA extraction.

tag: strain


title: B cells from spleen of non-pregnant mouse 88

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

hyb_protocol: Quality assessment of hybridizations was monitored by inspection of scan images and by carefully reviewing exo- and endogenous controls using the Expression Console software (Affymetrix Inc.).

scan_protocol: Standard Affymetrix protocol

data_processing: We carried out QC and normalization procedures in R/Bioconductor using the “oligo” package. The Robust Multichip Average algorithm (RMA) was employed for background adjustment, quantile normalization and probe set values summarization.

source_name: splenic B cells from non-pregnant mouse

label_protocol: Total RNA prepared from mouse B cells (200 ng, RIN≥7.4) was provided to the Department of Functional Genomics of the University Medicine Greifswald for processing and final hybridization.

growth_protocol: Old virgin C57BL/6 females were allogenically mated (1:1) with BALB/c males until detection of vaginal plug. This day was considered as day 0 of pregnancy. Non-pregnant virgin age-matched C57BL/6 females were used as controls.

extract_protocol: Total RNA was purified using TriFast reagent and QC was performed using Bioanalyzer 2100 (Agilent Technologies)

treatment_protocol: Total B cells were magnetically isolated by negative selection from the spleen of non-pregnant (NP; n=4) and pregnant (P; n=4) mice (day 14 of pregnancy) by using a commercially available kit (Pan B cell isolation kit, Miltenyi Biotec, Germany) following supplier recommendations. Only samples with purity above 98%, analyzed by flow cytometry, were used for RNA isolation

tag: condition

value: non-pregnant


title: B cells from spleen of pregnant mouse 86

source_name: splenic B cells from pregnant mouse

value: pregnant


title: BH_SCRNA_31


title: BT273

description: replicate 1

tag: cell type


title: B cells from spleen of pregnant mouse 70


title: B cells from spleen of pregnant mouse 76


title: B cells from spleen of non-pregnant mouse 82


title: B cells from spleen of non-pregnant mouse 81


title: MM

source_name: ON4T biomass growing in mineral medium supplemented with molinate (MMM)


title: BH_SCRNA_26


title: BH_SCRNA_24


title: BH_SCRNA_23


title: BH_SCRNA_22


title: BH_SCRNA_18


title: BH_SCRNA_21


title: BH_SCRNA_20


title: BH_SCRNA_19


title: BH_SCRNA_16


title: BH_SCRNA_15


title: BH_SCRNA_17


title: BH_SCRNA_11


title: ncd6_WT_S17

city: Memphis

first: Yong

last: Cheng

state: Tennessee

address: 262 Danny Thomas Place

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

description: amplicon sequencing

data_processing:
Library strategy: Amplicon sequencing
Data was processed by CrisprEsso2
CRISPResso -r1 $COL1 -a $COL3 -g $COL2 -o ${label}_5_29 --discard_indel_reads
Genome_build: hg19
Supplementary_files_format_and_content: excel table

growth_protocol: HEK293T cells were seeded in a 48-well plate at density of ~5 × 104  per well, transfected 24 h post-seeding with PE plasmid, pegRNA plasmid, and nicking gRNA plasmid (750:250:83) and 0.78 μl TransIT (Mirus) (per well).

extract_protocol:
Cells were collected 72h after transfection and lysed in 150 μl prepared DNA lysis buffer (10 mM Tris-HCl, pH 7.5; 0.05% SDS; 25μg/ml proteinase K). DNA lysates were incubated at 37 °C for 1h, followed by an 80 °C enzyme inactivation step for 30 min.
For each sample, the target regions were amplified by first round of PCR (PCR1) using gene-specific primers flanking the target sequence. The PCR1 was performed in a 25 μl volume including 100ng genomic DNA, 1.25 μl of 10 μM each primer, 12.5 μl 2 × Phusion High-Fidelity PCR mix (Thermo) and 0.75 μl DMSO. PCR1 reactions were carried out as follows: 98 °C for 2 min, then 34 cycles of (98 °C for 10 s, 65°C for 30 s, 72 °C for 30 s), and a final 72 °C extension for 5 min. PCR1 products were purified by electrophoresis in a 1.5% agarose gel or using AMPure beads. In a secondary ‘barcoding’ PCR (PCR2), the amplicons were indexed with primer pairs containing appropriate Illumina forward and reverse adaptor sequences. The 25 μl PCR2 was performed with 10ng purified PCR1 products, 2.5 μl of 10 μM forward and reverse barcoding primers, 12.5 μl 2 × Phusion High-Fidelity PCR mix (Thermo) and 0.75 μl DMSO. The PCR2 reactions were carried out as follows: 98 °C for 2 min, then 10 cycles of (98 °C for 10 s, 65 °C for 20 s, and 72 °C for 30 s), followed by a final 72 °C extension for 2 min. PCR2 products were purified by electrophoresis with a 1.5% agarose gel and DNA concentration was measured by fluorometric quantification (Qubit, Thermo). Amplicon libraries were sequenced on the Illumina MiSeq instrument according to the manufacturer’s protocols. After demultiplexing, FASTQ files were analyzed using CRISPResso2 with --discard_indel_reads.

tag: cell line

tag: control

value: Yes


title: BH_SCRNA_12

tag: brain region


title: BH_SCRNA_9

tag: age


title: BH_SCRNA_14

tag: genotype


title: BH_SCRNA_13

tag: batch


title: ncd6_PD_S33

description: amplicon sequencing

value: No

value: PrimeDesign


title: ncd4_WT_S15

description: amplicon sequencing


title: ncd4_EP_S27

description: amplicon sequencing

value: Easy-Prime


title: ncd4_PD_S31

description: amplicon sequencing


title: ncd3_PD_S26

description: amplicon sequencing


title: ncd3_WT_S14

description: amplicon sequencing


title: BH_SCRNA_10

tag: preparation


title: BH_SCRNA_6

tag: molecule subtype


title: B cells from spleen of pregnant mouse 75


title: ncd1_WT_S12

description: amplicon sequencing


title: 293R3_ncd6_S39_EP

description: amplicon sequencing


title: B cells from spleen of non-pregnant mouse 90


title: ncd1_PD_S30

description: amplicon sequencing


title: 293R1_ncd6_S23_EP

description: amplicon sequencing


title: BH_SCRNA_8


title: BH_SCRNA_7


title: BH_SCRNA_4


title: 293R4_ncd6_S47_EP

description: amplicon sequencing


title: BH_SCRNA_5


title: 293R2_ncd6_S31_EP

description: amplicon sequencing


title: 293R4_ncd5_S46_EP

description: amplicon sequencing


title: 293R3_ncd5_S38_EP

description: amplicon sequencing


title: 293R2_ncd5_S30_EP

description: amplicon sequencing


title: BH_SCRNA_2


title: BH_SCRNA_3


title: BH_SCRNA_1


title: 126_C57BL/6J_aged

value: aged

tag: developmental stage

value: GV oocyte - SN


title: 293R1_ncd5_S22_EP

description: amplicon sequencing


title: 125_C57BL/6J_aged


title: Wildtype scRNAseq - P70

city: Houston

first: Odemaris

middle: Narvaez

last: del Pilar

state: Texas

address: 6565 MD Anderson Blvd

department: Pulmonary

institute: MD Anderson Cancer Center

data_processing:
Chromium single-cell RNA-seq output was processed with Cell Ranger using “cellranger count” and “cellranger aggr”.
Further analysis was carried out using Loupe Cell Browser (10x Genomics) or an R package Seurat
Genome_build: mm10
Supplementary_files_format_and_content: tsv and mtx files can be opened with Seurat (R package) and analyzed. Cloupe file can be opened with Loupe cell browser to visualize the data.

source_name: Whole lung

extract_protocol:
FACS-purified lung cells were processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics) using the Chromium Single Cell 3' Library and Gel Bead Kit in accordance with the manufacturer’s user guide (v2, rev D).
The libraries were sequenced on an Illumina NextSeq500 using a 26X124 sequencing run format with 8 bp index (Read1).

value: mesenchymal cells

value: wildtype


title: 124_C57BL/6J_aged


title: Wildtype scRNAseq - P13


title: 122_C57BL/6J_aged


title: 293Ctrl_ncd2_S3

description: amplicon sequencing


title: 121_C57BL/6J_aged


title: Wildtype scRNAseq - P7


title: Wildtype scRNAseq - E19


title: 120_C57BL/6J_aged


title: 293R2_ncd2_S27_EP

description: amplicon sequencing


title: 293R1_ncd2_S19_EP

description: amplicon sequencing


title: 293R3_ncd3_S36_EP

description: amplicon sequencing


title: Wildtype scRNAseq - P20


title: 293R3_ncd1_S34_EP

description: amplicon sequencing


title: 119_C57BL/6J_aged


title: 293R4_ncd1_S42_EP

description: amplicon sequencing


title: 293R2_ncd3_S28_EP

description: amplicon sequencing


title: 293R4_ncd3_S44_EP

description: amplicon sequencing


title: 293R2_ncd1_S26_EP

description: amplicon sequencing


title: Wildtype scRNAseq - E17


title: 118_C57BL/6J_aged


title: Product, biological replicate 5, technical replicate 2

city: Gwanak

last: Baek

state: Seoul

address: Gwank 1

country: South Korea

institute: Seoul National University

description:
in vitro transcribed RNA
In vitro processing with the purified Microprocessor complex
Products_MP_only.csv
Products_set5_2

data_processing:
We utilized FASTX Toolkit (version 0.0.13.2; http://hannonlab.cshl.edu/fastx_toolkit/), cutadapt (version 2.3; Martin, 2011), and seqtk (version 1.2; https://github.com/lh3/seqtk) for sequence processing.
We trimmed bases after the first 70 bases using fastx_trimmer (-l 70), then applied quality filtering with fastq_quality_filter (-q 25 -p 80).
For input libraries, only intact reads were collected by checking 5′ and 3′ common sequences from forward and reverse reads, respectively (cutadapt -g GCCTATTCAGTTACAGCG/ GTTGCTAGCTTCAGTACG --trimmed-only --no-trim). We then trimmed the first 3 bases that were added to desynchronize sequencing cycles (cutadapt -u 3).
For cleavage product libraries, we trimmed Illumina 3′ or 5′ adapter sequence from the 3′ end of the forward or reverse reads, respectively, and filtered out the trimmed reads shorter than 40 nt (cutadapt -a TGGAATTCTCGGGTGCCAAGG/ GATCGTCGGACTGTAGAACTCTGAAC -m 40). Moreover, PCR duplicates were disposed using fastx_collapser.
We aligned the assembled reads to the pri-miRNA construct backbones using Bowtie2 (version 2.2.4; Langmead and Salzberg, 2012), allowing up to 2 mismatches (--local --score-min L,-16,2 --no-mixed --no-discordant --norc).
Genome_build: Pri-miRNA construct sequences
Supplementary_files_format_and_content: csv files were built by counting read counts for each fragment with the unique start and end position for each pri-miRNA.

source_name: In vitro processing

growth_protocol: DNA templates harboring 125 pri-miRNA sequences were commercially synthesized on a massive parallel synthesis platform (Celemics). Common sequences were added at the ends for PCR amplification. T7 promoter was also added at the 5′ end during the PCR amplification step. Using these templates, the minimal pri-miRNAs were in vitro transcribed by using the MEGAscript T7 Transcription Kit (Thermo Fisher Scientific).

extract_protocol:
RNAs were obtained by phenol extraction and ethanol precipitation.
The eluate was incubated with 0.5 μl of 10 μM 3′ adapter (Illumina, TruSeq Small RNA Library Prep Kit), which is modified with additional six degenerated bases at the 5′ end, at 70°C for 2 min. The 3′ adapter-ligated fragments were dissolved in 3 μl of TDW and incubated with 0.5 μl of 10 μM 5′ adapter (Illumina, TruSeq Small RNA Library Prep Kit), which is modified with additional six degenerated bases at the 3′ end, at 70°C for 2 min. The adapter-ligated fragments were reverse-transcribed using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific) and RT primer (Illumina, TruSeq Small RNA Library Prep Kit). For Illumina sequencing, cDNA was amplified by PCR that utilized Phusion High-Fidelity DNA polymerase (Thermo Fisher Scientific) and PCR primers from TruSeq Small RNA Library Prep Kit (Illumina). Meanwhile, input substrates were also reverse-transcribed using custom RT primers and PCR-amplified using PCR primers from TruSeq Small RNA Library Prep Kit (Illumina).

treatment_protocol: 40 fmol of pri-miRNA substrate was incubated with 200 fmol of recombinant Microprocessor at 37°C for 1 h in the 10 μl buffer containing 500 mM NaCl, 50 mM Tris-HCl pH 7.5, 2 mM MgCl2, 1 mM DTT, 1 U/μl SUPERase·In RNase inhibitor (Thermo Fisher Scientific) and 200 ng/μl UltraPure BSA (Thermo Fisher Scientific).

tag: protocol

value: In vitro processing


title: 293R1_ncd1_S18_EP

description: amplicon sequencing


title: Product, biological replicate 5, technical replicate 1

description:
in vitro transcribed RNA
In vitro processing with the purified Microprocessor complex
Products_MP_only.csv
Products_set5_1


title: 293R4_ncd2_S43_EP

description: amplicon sequencing


title: UCSF LGNET FGFR2-fused #8

type: genomic

city: Stanford

first: David

middle: A.

last: Solomon

state: CA

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

description: FGFR2-fused low-grade neuroepithelial tumor

hyb_protocol: bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan instrument following standard recommended Illumina scanner setting

data_processing: Methylation data were preprocessed using the minfi package (v.1.30.0) in R. The detection p-value for each sample was computed. Functional normalization with NOOB background correction and dye-bias normalization was performed.

label: Cy5 and Cy3

source_name: low-grade neuroepithelial tumor tissue

label_protocol: standard Illumina protocol

growth_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients.  No ex vivo culture or xenografting was performed.

extract_protocol: Tumor tissue was selectively punched from formalin-fixed, paraffin-embedded tissue blocks using using 2.0 mm disposable biopsy punches (Integra Miltex Instruments, cat# 33-31-P/25) or selectively scraped from unstained sections cut from formalin-fixed, paraffin-embedded tissue blocks.  Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients at time of initial diagnosis before any radiation or chemotherapy had been administered.  No ex vivo culture or xenografting was performed.

tag: patient sex

value: Female

tag: patient age at dx (yrs)

tag: fusion type


title: 117_C57BL/6J_aged


title: 293Ctrl_ncd5_S6

description: amplicon sequencing


title: Hippocampus, Gulf War toxicants, 6

city: East Orange

first: Bruce

last: Citron

state: NJ

address: 385 Tremont Ave.

department: Pharmacology, Physiology, & Neuroscience, Rutgers- NJMS

institute: VA New Jersey Health Care System

data_processing:
Sequence reads were mapped to the Mus musculus reference genome with CLC Genomics Workbench version 20.0.3.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were determined with CLC Genomics Workbench.
Gene expression comparisons were determined with CLC Genomics Workbench Differential Analysis for RNA-Seq.
Supplementary_files_format_and_content: GWI Hi RPKMs.txt

source_name: Hippocampus

extract_protocol:
Hippocampi were immediately dissected, flash frozen, stored at -70°, RNA was extracted with TRIzol followed by Rneasy cleanup. Poly(A) selection was performed with oligo d(T) magnetic beads.
NEBNext Ultra RNA Library Prepr Kit for Illumina followed by purification with AMPure XP beads.
Equimolar amounts of barcoded libraries were pooled and sequenced with an Illumina NextSeq 500 Sequencing System with a 1x75 configuration.

tag: Sex

value: male

value: 12 weeks

tag: tissue

value: Hippocampus

tag: exposure

value: Gulf War toxicants


title: Product, biological replicate 4, technical replicate 2

description:
in vitro transcribed RNA
In vitro processing with the purified Microprocessor complex
Products_MP_only.csv
Products_set4_2


title: Product, biological replicate 4, technical replicate 1

description:
in vitro transcribed RNA
In vitro processing with the purified Microprocessor complex
Products_MP_only.csv
Products_set4_1


title: Hippocampus, Gulf War toxicants, 5

tag: strain


title: 116_C57BL/6J_aged


title: Product, biological replicate 3, technical replicate 2

description:
in vitro transcribed RNA
In vitro processing with the purified Microprocessor complex
Products_MP_only.csv
Products_set3_2


title: 293R1_ncd3_S20_EP

description: amplicon sequencing

tag: cell line


title: UCSF LGNET FGFR2-fused #7

value: Male


title: Hippocampus, Gulf War toxicants, 4


title: 123_C57BL/6J_aged


title: Hippocampus, Gulf War toxicants, 2


title: Product, biological replicate 3, technical replicate 1

description:
in vitro transcribed RNA
In vitro processing with the purified Microprocessor complex
Products_MP_only.csv
Products_set3_1


title: Product, biological replicate 2, technical replicate 2

description:
in vitro transcribed RNA
In vitro processing with the purified Microprocessor complex
Products_MP_only.csv
Products_set2_2


title: Input, biological replicate 5, technical replicate 2

description:
in vitro transcribed RNA
Input_MP_only.csv
Input_set5_2

source_name: In vitro transcription

value: In vitro transcription


title: Product, biological replicate 2, technical replicate 1

description:
in vitro transcribed RNA
In vitro processing with the purified Microprocessor complex
Products_MP_only.csv
Products_set2_1


title: Input, biological replicate 5, technical replicate 1

description:
in vitro transcribed RNA
Input_MP_only.csv
Input_set5_1


title: Hippocampus, Control, 6

value: Vehicle


title: 115_C57BL/6J_aged


title: 114_C57BL/6J_aged


title: UCSF LGNET FGFR2-fused #3

value: FGFR2-INA fusion


title: 113_C57BL/6J_aged


title: Input, biological replicate 4

description:
in vitro transcribed RNA
Input_MP_only.csv
Input_set4


title: Input, biological replicate 3, technical replicate 1

description:
in vitro transcribed RNA
Input_MP_only.csv
Input_set3_1


title: Input, biological replicate 3, technical replicate 2

description:
in vitro transcribed RNA
Input_MP_only.csv
Input_set3_2


title: UCSF LGNET FGFR2-fused #2

value: FGFR2-ACTR1A fusion


title: Hippocampus, Control, 5


title: UCSF LGNET FGFR2-fused #5

value: FGFR2-KIAA1598 fusion


title: Input, biological replicate 1, technical replicate 2

description:
in vitro transcribed RNA
Input_MP_only.csv
Input_set1_2


title: Input, biological replicate 2 [set2]

description:
in vitro transcribed RNA
Input_MP_only.csv
Input_set2


title: 112_C57BL/6J_aged


title: UCSF LGNET FGFR2-fused #4


title: 111_C57BL/6J_aged


title: Hippocampus, Control, 4


title: Hippocampus, Gulf War toxicants, 1


title: 110_C57BL/6J_aged


title: Enhancer - barcode assignmennt CHEQ-seq SOX10-KD

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

description:
processed data file:
CHEQ-seq_SOX10-KD_enh-BC_list.tsv

data_processing:
Library strategy: CHEQ-seq
Enhancer - barcode assignment files are processed with a custom script. Enhancers and barcodes are separated with cutadapt. Enhancers are mapped to the human hg19 genome using minimap.
Raw cDNA and plasmid reads are first processed with a custom script to extract and count each barcode before associating them to the corresponding enhancer based on the enhancer - bc assignment list.
Enhancer activity from MPRA assay is estimated via a custom R script. Enhancers are first filtered based on the number of BCs identified in the sequencing reads. Thresholds of 5 (for the H3K37ac library and enhancer tiling library), 10 (for ATAC-seq library) or 20 (for the SOX-MITF combinations library) BCs per enhancer are selected based on the complexity of the library and the sequencing saturation of the enhancer - BC assignment samples. For the remaining enhancers, BC counts are aggregated per enhancer and then a count per million (CPM) normalisation is applied. Plasmid (input) and cDNA (output) samples are merged by keeping only enhancers remaining in both samples after filtering. Input normalisation is done by dividing CPM normalised cDNA counts by CPM normalised plasmid counts resulting in a FC value. For libraries with shuffled sequences, a basal expression normalisation is further applied by dividing the FC value of the enhancer by the median FC value of the shuffled sequences. For CHEQ-seq SOX10-KD library, enhancer activity from cDNA and plasmid barcode counts is performed with DEseq2.
Genome_build: hg19
Supplementary_files_format_and_content: Enhancer to barcode assignment lists are tables containing two columns: Enhancer name; barcode associated to that enhancer. Enhancer activity matrices are table containing: Enhancer name; Enhancer class; Enhancer activity Fold Change (one column per cell line). DEseq2 result table contains the following columns: Enhancer name; baseMean; log2FoldChange; lfcSE; stat; pvalue; padj; enhancer class.
CHEQ-seq_5p_H3K27ac_enh-BC_list.tsv: Enhancer to barcode assignment list
CHEQ-seq_Intron_H3K27ac_enh-BC_list.tsv: Enhancer to barcode assignment list
CHEQ-seq_ATAC_enh-BC_list.tsv.gz: Enhancer to barcode assignment list
CHEQ-seq_Enhancer-tiling-A_enh-BC_list.tsv.gz: Enhancer to barcode assignment list
CHEQ-seq_Enhancer-tiling-B_enh-BC_list.tsv.gz: Enhancer to barcode assignment list
CHEQ-seq_SOX10-KD_enh-BC_list.tsv: Enhancer to barcode assignment list
CHEQ-seq_SOX-MITF_combinations_enh-BC_list.tsv.gz: Enhancer to barcode assignment list
CHEQ-seq_5p_H3K27ac_processed.tsv: Enhancer activity matrix for CHEQ-seq 5' H3K27ac
CHEQ-seq_Intron_H3K27ac_processed.tsv: Enhancer activity matrix for CHEQ-seq Intron H3K27ac
CHEQ-seq_ATAC_processed.tsv: Enhancer activity matrix for CHEQ-seq ATAC
STARR-seq_ATAC_processed.tsv: Enhancer activity matrix for STARR-seq ATAC
CHEQ-seq_Enhancer_tiling_A_processed.tsv: Enhancer activity matrix for CHEQ-seq Enhancer tiling A
CHEQ-seq_Enhancer_tiling_B_processed.tsv: Enhancer activity matrix for CHEQ-seq Enhancer tiling B
CHEQ-seq_SOX10-KD_processed.tsv: DEseq2 result table for CHEQ-seq SOX10-KD
CHEQ-seq_SOX-MITF_combinations_processed.tsv: Enhancer activity matrix for CHEQ-seq SOX - MITF combinations

organism: synthetic construct

source_name: Plasmid

growth_protocol: Melanoma cell lines were cultured with Ham's F-10 nutrient mix + 10% FBS + 0.5% penicillin/streptomycin in an incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from the cell with the innuPREP RNA Mini Kit 2.0 (Analytik Jena) , followed by mRNA isolation using the Dynabeads mRNA purification kit (Ambion). cDNA synthesis was performed with the GoScript RT kit and oligo dT primer (Promega). DNA was extracted with a plasmid extraction protocol from Qiagen.
Plasmid libraries, extracted plasmids and cDNA were prepared for sequencing with two rounds of PCR. The first PCR targets the random barcode present within the transcript. The second PCR adds sequencing indexes to the PCR product.

value: Plasmid


title: Hippocampus, Control, 3


title: 108_C57BL/6J_aged

value: aged


title: Hippocampus, Control, 1


title: Hippocampus, Control, 2


title: CHI4, rep4a

city: East Lansing

first: koichi

last: Sugimoto

state: MI

address: 612 Wilson Rd

institute: Michigan State University

description: Lane 1

data_processing:
Sequence reads were trimmed using the Trimmomatic software (Bolger et al., 2014) to eliminate adaptor sequences and low quality reads.
The remaining reads were mapped to the Solanum lycopersicum L. reference genome sequence (ITAG 2.5 genome) using Tophat2 software (Kim et al., 2003).
The mapped reads were then aligned using SAMtools (Li et al., 2009) and counted by HTSeq (Anders et al., 2015).
Genome_build: ITAG2.4_gene_models.gff3 (ITAG 2.4 is gene structure information, ITAG 2.5 is genome assembly)
Supplementary_files_format_and_content: *_20_sorted_n_count2.count.txt: HTSeq count data; tab-delimited text files include cpm values for each sample.

organism: Solanum lycopersicum

source_name: glandular cells of type VI trichome

growth_protocol: Plants grew on the potted soil in the growth chamber under 250 μE and 28 ºC for 5 weeks.

extract_protocol:
Total RNA was extracted with RNeasy kit (Qiagen) according to the manufacturer's instructions.
Sequencing libraries were prepared from total RNA with the TruSeq RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Glandular cells of type VI trichome was collected as described in Schilmiller et al. (2010) Plant Physiology 153: 1212-1223.

value: leaf type VI glandular trichomes

tag: sampling time

tag: genotype/variation

value: complemented line #4


title: CHI9, rep4b

description: Lane 2

value: complemented line #9


title: 106_C57BL/6J_young

tag: age

value: young

value: GV oocyte - SN


title: af, rep4b

description: Lane 2

value: af mutant


title: CHI4, rep4b

description: Lane 2


title: CHI9, rep4a

description: Lane 1


title: CHI9, rep3b

description: Lane 2


title: af, rep4a

description: Lane 1


title: 107_C57BL/6J_aged


title: 105_C57BL/6J_young


title: CHI4, rep3b

description: Lane 2


title: CHI4, rep3a

description: Lane 1


title: 426_Downhill Run delEx44 DMD

city: Dallas

first: Jiwoong

last: Kim

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for quality and adapter trimming. The mouse reference genome sequence and gene annotation data, mm10, were downloaded from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). The qualities of RNA-sequencing libraries were estimated by mapping the reads onto mouse transcript and ribosomal RNA sequences (Ensembl release 89) using Bowtie (v2.3.4.3) (Langmead and Salzberg, 2012). STAR (v2.7.2b) (Dobin et al., 2013) was employed to align the reads onto the mouse genome, SAMtools (v1.9) (Li et al., 2009) was employed to sort the alignments, and HTSeq Python package (Anders et al., 2015) was employed to count reads per gene. edgeR R Bioconductor package (Gentleman et al., 2004; Robinson et al., 2010; McCarthy et al., 2012) was used to normalize read counts and identify differentially expressed (DE) genes. KEGG (Kanehisa et al., 2017) pathway data was downloaded using KEGG API (https://www.kegg.jp/kegg/rest/keggapi.html) and gene ontology (GO) data was downloaded from NCBI FTP (ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz). The enrichment of DE genes to pathways and GOs were calculated by Fisher's exact test in R statistical package.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Quadriceps Muscle

extract_protocol:
Quadriceps muscle was harvested and flash frozen in liquid nitrogen. RNA was extracted using miRNAeasy mini kit (Cat#217004).
Libraries were constructed using the Illumina TruSeq RNA Sample Prep Kit.

treatment_protocol: DelEx44 DMD mice injected intraperitoneally with 8 x 10^13 vg/kg each of scAAV9-sgRNA and ssAAV9-SpCas9 on day P4. At one month of age, tissue was either harvested or mice were run downhill. Mice were run at a 15 degree decline at a speed of 12 m/min every other day for 1 month.

value: Quadriceps Muscle

value: 8 Weeks

tag: genotype


title: Input, biological replicate 1, technical replicate 1

description:
in vitro transcribed RNA
Input_MP_only.csv
Input_set1_1


title: 16_Sedentary corrected-delEx44 DMD

value: 4 Weeks

value: CRISPR-Cas9 treated delEx44


title: af, rep3b

description: Lane 2


title: UCSF LGNET FGFR2-fused #6

value: Male


title: 109_C57BL/6J_aged


title: 427_Downhill Run delEx44 DMD


title: 104_C57BL/6J_young


title: CHI9, rep3a

description: Lane 1


title: UCSF LGNET FGFR2-fused #9

value: Female

value: FGFR2 rearrangement


title: af, rep3a

description: Lane 1


title: 15_Sedentary corrected-delEx44 DMD


title: Hippocampus, Gulf War toxicants, 3

value: male

value: 12 weeks

value: Hippocampus

value: Gulf War toxicants


title: CHI9, rep2a

description: Lane 1

value: leaf type VI glandular trichomes


title: CHI4, rep2b

description: Lane 2

value: complemented line #4


title: CHI9, rep2b

description: Lane 2

value: complemented line #9


title: 102_C57BL/6J_young

value: young


title: CHI9, rep1b

description: Lane 2


title: 38_Sedentary delEx44 DMD


title: CHI4, rep2a

description: Lane 1


title: CHI9, rep1a

description: Lane 1


title: 100_C57BL/6J_young

value: GV oocyte - SN


title: af, rep2b

description: Lane 2

value: af mutant


title: 101_C57BL/6J_young


title: CHI4, rep1b

description: Lane 2


title: 99_C57BL/6J_young


title: af, rep1b

description: Lane 2


title: 73_Sedentary WT

value: Quadriceps Muscle

value: WT


title: af, rep1a

description: Lane 1


title: 293R3_ncd2_S35_EP

description: amplicon sequencing

tag: control

value: No

value: Easy-Prime


title: Enhancer - barcode assignmennt CHEQ-seq Intron H3K27ac

description:
processed data file:
CHEQ-seq_Intron_H3K27ac_enh-BC_list.tsv

value: Plasmid


title: 14_Sedentary corrected-delEx44 DMD

value: 4 Weeks

value: CRISPR-Cas9 treated delEx44


title: 97_C57BL/6J_young


title: 37_Sedentary delEx44 DMD


title: 103_C57BL/6J_young


title: 98_C57BL/6J_young


title: Enhancer - barcode assignmennt CHEQ-seq 5' H3K27ac

description:
processed data file:
CHEQ-seq_5p_H3K27ac_enh-BC_list.tsv


title: 39_Sedentary delEx44 DMD


title: 72_Sedentary WT


title: DN4_WT46

city: Cologne

first: Mauro

last: Corrado

address: Joseph-Stelzmann-Str. 26

country: Germany

institute: University of Cologne

data_processing:
Sequenced libraries were processed with deepTools, using STAR, for trimming and mapping, and feature Counts to quantify mapped reads.
Raw mapped reads were processed in R (Lucent Technologies) with DESeq2 to generate normalized read counts to visualize as heatmaps using Morpheus (Broad Institute) and determine differentially expressed genes with greater than 2 fold change and lower than 0.05 adjusted P value.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is a matrix with raw counts for features in samples, obtained with featureCounts.

source_name: WT_DN4 thymocytes

growth_protocol: Freshly sorted thymocytes

extract_protocol:
RNA isolation was performed using the RNeasy kit (Qiagen) as per manufacturer’s instructions and RNA was quantified using Qubit 2.0 (Thermo Fisher Scientific).
Libraries were prepared using the TruSeq stranded mRNA kit (Illumina) and sequenced in a HISeq 3000 (Illumina)

treatment_protocol: no treatment

tag: cell type

value: DN4 thymocytes


title: DN4_WT48


title: DN4_WT40


title: CCI_f_PAG_6

city: Sydney

first: Gila

last: Moalem-Taylor

state: NSW

address: Wallace Wurth Building, Level 3, Room 355B

department: School of Medical Sciences

country: Australia

institute: University of New South Wales

description: processed data file: Injury_PAG_TPM_counts.xlsx

data_processing:
Illumina NextSeq500 using a High Output v2 kit to generate 2 x 38 bp reads
Transcripts were quantified using Salmon v1.4
Raw read counts were processed and normalized in R using DESeq2’s median of ratio method and low abundance genes were filtered below a mean count of 5 reads/sample
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft excel workbook of gene counts

source_name: Periaqueductal gray and rostroventral medulla

extract_protocol:
Each block of tissue was homogenised using a dounce glass tissue homogeniser. Mononuclear cells were separated through Percoll (GE Healthcare Life Sciences) 37%/70% gradient centrifugation. Mononuclear cells were isolated from the interface and stained on ice for 30 min with combinations of BV650 rat anti-mouse CD11b (marking myeloid cells; 1:300), FITC rat anti-mouse Ly6C (marking monocytes/macrophages; 1:300) and APC rat anti-mouse 4D4 (marking resident microglia; 1:1000) in blocking buffer containing 0.2% bovine serum albumin (BSA, Sigma-Aldrich) in HBSS. Cell sorting was performed using FACSAriaIII cell sorter (Becton Dickson). Microglial cells were identified as CD11b+ Ly6C- 4D4+
cDNA libraries were generated from sorted cells using the Smart-seq2 protocol

tag: treatment

value: CCI

value: Microglia


title: 95_C57BL/6J_young

source_name: oocyte

tag: developmental stage


title: DN4_WT05


title: DN4_KO51

source_name: OPA1 KO_DN4 thymocytes

value: OPA1 KO


title: CHI4, rep1a

description: Lane 1

value: leaf type VI glandular trichomes


title: CCI_f_PAG_5

value: Periaqueductal gray and rostroventral medulla


title: 94_C57BL/6J_young


title: 93_C57BL/6J_young


title: DN3_WT48

source_name: WT_DN3 thymocytes

value: DN3 thymocytes


title: CCI_f_PAG_4


title: DN3_WT46


title: DN4_KO45


title: DN3_WT05


title: DN3_KO49

source_name: OPA1 KO_DN3 thymocytes


title: 91_C57BL/6J_young

value: young


title: CCI_f_PAG_3


title: 96_C57BL/6J_young

value: GV oocyte - SN


title: 92_C57BL/6J_young


title: CCI_f_PAG_2


title: Sham_f_PAG_6

value: Sham


title: DN3_KO45


title: CCI_f_PAG_1


title: CHEQ-seq SOX-MITF combinations MM087 cDNA

description:
processed data file:
CHEQ-seq_SOX-MITF_combinations_processed.tsv

source_name: Melanoma cell line

tag: molecule subtype

value: mRNA


title: 90_C57BL/6J_young


title: DN4_KO49


title: CHEQ-seq SOX-MITF combinations MM087 plasmid


title: 89_C57BL/6J_young


title: 88_C57BL/6J_young


title: CHEQ-seq Enhancer tiling B MM099 plasmid

description:
processed data file:
CHEQ-seq_Enhancer_tiling_B_processed.tsv


title: DN3_KO51


title: 87_C57BL/6J_young


title: CHEQ-seq SOX-MITF combinations MM074 plasmid


title: CHEQ-seq SOX-MITF combinations MM001 plasmid


title: CHEQ-seq Enhancer tiling B MM099 cDNA rep 2


title: Sham_f_PAG_3


title: CHEQ-seq SOX-MITF combinations MM074 cDNA


title: 85_ICRF_aged.virgin


title: CHEQ-seq Enhancer tiling B MM029 cDNA rep 2


title: Sham_f_PAG_2


title: CHEQ-seq Enhancer tiling B MM087 plasmid


title: Sham_f_PAG_4


title: Sham_f_PAG_1


title: 86_ICRF_aged.virgin


title: CHEQ-seq Enhancer tiling B MM029 plasmid


title: CHEQ-seq Enhancer tiling B MM087 cDNA rep 3


title: 84_ICRF_aged.virgin


title: CCI_f_S1_6

description: processed data file: Injury_S1_TPM counts.xlsx

source_name: Contralateral posterior thalamus and S1 (hindlimb)


title: CHEQ-seq Enhancer tiling B MM057 cDNA rep 2


title: CHEQ-seq Enhancer tiling B MM087 cDNA rep 2


title: CHEQ-seq Enhancer tiling A MM099 plasmid

description:
processed data file:
CHEQ-seq_Enhancer_tiling_A_processed.tsv


title: CCI_f_S1_5

value: Contralateral posterior thalamus and S1 (hindlimb)


title: 83_ICRF_aged.virgin


title: af, rep2a

description: Lane 1

value: af mutant


title: CHEQ-seq Enhancer tiling A MM029 plasmid rep 2


title: CHEQ-seq SOX-MITF combinations MM001 cDNA


title: 81_ICRF_aged.virgin


title: CCI_f_S1_4


title: CHEQ-seq Enhancer tiling A MM029 cDNA rep 2


title: CHEQ-seq Enhancer tiling A MM099 cDNA rep 2


title: 82_ICRF_aged.virgin


title: CCI_f_S1_3


title: 80_ICRF_aged.virgin


title: CHEQ-seq Enhancer tiling A MM087 cDNA rep 2


title: CHEQ-seq Enhancer tiling A MM087 cDNA rep 3


title: CHEQ-seq Enhancer tiling A MM087 cDNA rep 1


title: 79_ICRF_aged.virgin


title: CCI_f_S1_2


title: Sham_f_PAG_5


title: CCI_f_S1_1


title: CHEQ-seq Enhancer tiling A MM057 plasmid


title: CHEQ-seq Enhancer tiling A MM057 cDNA rep 2


title: CHEQ-seq Enhancer tiling A MM074 cDNA rep 2


title: 78_ICRF_aged.virgin


title: 77_ICRF_aged.virgin


title: Sham_f_S1_5


title: STARR-seq ATAC MM099 cDNA

description:
processed data file:
STARR-seq_ATAC_processed.tsv


title: STARR-seq ATAC MM047 plasmid


title: 75_ICRF_aged.virgin


title: 76_ICRF_aged.virgin


title: CHEQ-seq Enhancer tiling A MM074 plasmid


title: Sham_f_S1_4


title: STARR-seq ATAC MM047 cDNA


title: CHEQ-seq Enhancer tiling A MM087 plasmid


title: STARR-seq ATAC MM029 cDNA


title: 74_ICRF_aged.mated


title: Sham_f_S1_3


title: STARR-seq ATAC MM099 plasmid


title: STARR-seq ATAC MM029 plasmid


title: Sham_f_S1_2


title: STARR-seq ATAC MM087 plasmid


title: Sham_f_S1_1


title: 72_ICRF_aged.mated


title: CCI_f_PFC_6

description: processed data file: Injury_PFC_TPM counts.xlsx

source_name: Prefrontal cortex, amygdala, hippocampus


title: STARR-seq ATAC MM087 cDNA


title: STARR-seq ATAC MM057 plasmid


title: CCI_f_PFC_5

value: Prefrontal cortex, amygdala, hippocampus


title: STARR-seq ATAC MM074 cDNA


title: 70_ICRF_aged.mated


title: CHEQ-seq ATAC MM099 plasmid

description:
processed data file:
CHEQ-seq_ATAC_processed.tsv

value: Plasmid


title: STARR-seq ATAC MM001 cDNA


title: STARR-seq ATAC MM001 plasmid


title: STARR-seq ATAC MM057 cDNA


title: 73_ICRF_aged.mated


title: CCI_f_PFC_4


title: STARR-seq ATAC MM074 plasmid


title: CHEQ-seq ATAC MM047 plasmid


title: 68_ICRF_aged.mated


title: CCI_f_PFC_3


title: CCI_f_PFC_2


title: CHEQ-seq ATAC MM099 cDNA


title: CHEQ-seq ATAC MM047 cDNA


title: CHEQ-seq ATAC MM029 cDNA


title: CCI_f_PFC_1


title: 67_ICRF_aged.mated


title: Sham_f_S1_6


title: 71_ICRF_aged.mated


title: CHEQ-seq ATAC MM087 plasmid


title: CHEQ-seq ATAC MM087 cDNA rep 3


title: 65_ICRF_aged.mated


title: CHEQ-seq ATAC MM074 plasmid


title: 69_ICRF_aged.mated


title: CHEQ-seq ATAC MM087 cDNA rep 2


title: Sham_f_PFC_6


title: CHEQ-seq ATAC MM029 plasmid


title: CHEQ-seq ATAC MM087 cDNA rep 1


title: 66_ICRF_aged.mated


title: Sham_f_PFC_5


title: Sham_f_PFC_4


title: CHEQ-seq ATAC MM074 cDNA


title: CHEQ-seq ATAC MM057 plasmid


title: 63_ICRF_aged.mated


title: CHEQ-seq ATAC MM057 cDNA


title: 64_ICRF_aged.mated


title: Sham_f_PFC_3


title: CHEQ-seq ATAC MM001 plasmid


title: 62_ICRF_aged.mated


title: Sham_f_PFC_2


title: CHEQ-seq Intron H3K27ac MM087 cDNA rep 3

description:
processed data file:
CHEQ-seq_Intron_H3K27ac_processed.tsv


title: CHEQ-seq ATAC MM001 cDNA


title: CHEQ-seq Intron H3K27ac MM087 cDNA rep 2


title: 74_Sedentary WT

value: Quadriceps Muscle

value: 4 Weeks

value: WT


title: 61_ICRF_aged.mated


title: CHEQ-seq 5' H3K27ac MM087 cDNA rep 3

description:
processed data file:
CHEQ-seq_5p_H3K27ac_processed.tsv


title: CHEQ-seq 5' H3K27ac MM087 cDNA rep 2


title: Sham_f_PFC_1


title: CCI_f_SC_6

description: processed data file: Injury_SC_TPM counts.xlsx

source_name: Ipsilateral lumbar spinal cord (L3-5)

value: CCI

value: Ipsilateral lumbar spinal cord (L3-5)


title: AM8_WT

city: Cleveland

first: Srinivasan

last: Dasarathy

state: OH

address: 9500 Euclid Ave

department: Inflammation and Immunity

institute: Cleveland Clinic Lerner Research Institute

data_processing:
Downstream analysis of RNAseq datasets was performed using a combination of programs including STAR, HTseq, Cufflink and Novogene’s wrapped scripts.
Alignments were parsed using TopHat and differential expressions were determined through DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with FPKM for each sample and differential expression of genes

extract_protocol:
Total RNA was extracted using the RNeasy Plus minikit (Qiagen, Germantown, MD)
RNAseq libraries were generated using the RNeasy Plus minikit (Qiagen, Germantown, MD) and sequenced on an Illumina HiSEQ400 instrument (using protocols provided by manufacturer) by Novogene (Sacramento, CA).

treatment_protocol: In vivo studies in ammonia-treated or vehicle-treated mice were performed in 8–10-week-old wild type animals bred on a C57BL/6J background (Jackson Laboratory, Bar Harbor, ME). In brief, an Alzet miniosmotic pump (Model 2004, Alzet, Cupertino, CA, USA) pre-filled either with ammonium acetate (Am) (released at a rate of 2.5 mmol/kg/day) or sterile phosphate buffered saline (PBS) was implanted in the mice as described previously. Mice were sacrificed 4 weeks after pump implantation and gastrocnemius muscle was rapidly collected and flash frozen.

value: Ammonium acetate

value: skeletal muscle


title: Am7_WT


title: Am6_WT


title: CCI_f_SC_5

value: Microglia


title: CCI_f_SC_4


title: Single cell thymic CD19+CD21-CD35- [HE006]

first: Hector

last: Cordero

address: 650W 168th Street

description: Single cell thymic CD19+CD21-CD35-

data_processing:
The sequencing was done using Chromium Single Cell 3′ Reagent Kits v2 (10X Genomics) according to the manufacturer’s instructions via NovaSeq 6000
The raw data from each sample were demultiplexed, aligned to the GRCh38-1.2.0. human reference genome.
UMI counts were quantified using the 10X Genomics Cell Ranger pipeline (v2.1.1, 10X Genomics).
Data analysis with the filtered barcode matrix files was done by using the Seurat package version 3.0 (Butler et al., 2018)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Thymus

growth_protocol: B cells were obtained from neonatal thymuses

extract_protocol:
Chromium Single Cell 3′ Reagent Kits v2 (10X Genomics) according to the manufacturer’s instructions
The libraries were quantified using KAPA hgDNA Quantification and QC Kit (Kapa Biosystems)

treatment_protocol: B cells were isolated by magnetic cell sorting with EasySep Human B Cell Enrichment Kit (Stem Cell Technologies) following the manufacturer’s instructions and stained in PBS with 2% FCS for 45min with the fluorochrome conjugated antibodies

value: 4 days


title: Single cell thymic CD19+CD21-CD35- [HE005]

description: Single cell thymic CD19+CD21-CD35-


title: Single cell thymic CD19+CD21-CD35- [HE007]

description: Single cell thymic CD19+CD21-CD35-

value: 4 months


title: Am5_WT


title: RERF-LC-AI_Maspin_2nd

city: Yonago

first: Takahiro

last: Matsushige

state: Tottori

address: 86 Nishi-cho

department: Faculty of Medicine

country: Japan

institute: Tottori University

data_processing:
Adapter trimming and quality trimming were performed using trimmomatic (ver. 0.39).
Cleaned RNA-seq reads were aligned to the GRCh38.p13 genome assembly using BWA (ver. 0.7.17).
Calculating mapping statistics from BAM file were performed using SAMtools (ver. 1.10).
The analysis data of mapping statistics of transcript IDs was compiled for each gene using gene IDs.
Nromalization using the Trimmed Mean of M-values (TMM) method for comparing the expression levels of each genes was performed using edgeR (ver. 3.16.5). Normalization; ( Read of the gene/total reads of  sample)x(total reads of the sample with the least total reads)
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: ReadCount_gene.txt

source_name: RERF-LC-AI cells stably expression maspin and ZsGreen (Maspin-P2A-ZsGreen)

growth_protocol: RERF-LC-AI-control and -maspin cells were seeded at a density of 3.6 × 105 in 6 well plates, and maintained in Eagle’s minimum essential medium.

extract_protocol:
Total RNA from RERF-LC-AI-maspin and REERF-LC-AI-control cells was recovered using RNeasy Mini Kit according to the manufacturer’s instructions.
To purify the strand-specific mRNA library, the mRNA was reverse transcribed into cDNA using random primers, and then the synthesized double-strand cDNA was fragmented, and the cDNA was subsequently ligated adapters. Transcriptome sequencing in strand-specific mRNA-seq library was performed using illumine NovaSeq 6000 Sequencing System.

value: RERF-LC-AI

value: lung squamous cell carcinoma cell line

value: stable expression of maspin and ZsGreen (Maspin-P2A-ZsGreen)


title: CCI_f_SC_3


title: Am4_WT


title: PBS8_WT

value: Phosphate buffered saline


title: RERF-LC-AI_Maspin_1st


title: RERF-LC-AI_control_1st

source_name: RERF-LC-AI cells stably expression ZsGreen

value: stably expression ZsGreen


title: RERF-LC-AI_Maspin_3rd


title: RERF-LC-AI_control_3rd


title: RERF-LC-AI_control_2nd


title: Single cell thymic CD19+CD21-CD35- [HE008]

city: New York

institute: Columbia University

description: Single cell thymic CD19+CD21-CD35-


title: CCI_f_SC_1


title: PBS7_WT


title: PBS5_WT


title: Sham_f_SC_6

value: Sham


title: Sham_f_SC_5


title: PBMCs, Mo_25

city: Harbin

first: Jinwen

last: Zhang

address: NanGang

institute: College of Bioinformatics

data_processing:
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Bowtie2 v2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with gene reads count for every gene and every sample

source_name: symptomatic

extract_protocol:
Total RNA was isolated and purified using TRIzol(Life, cat.265709, CA, USA) following the manufacturer's procedure.
After the quality inspection of Agilent 2100 Bioanalyzer (Agilent, cat.G2939AA, CA, USA) and NanoPhotometer® (Implen, cat.N60, Munich, Germany), poly (A) RNA is purified from 1μg total RNA using VAHTS® mRNA Capture Beads with Oligo (dT) (Vazyme, cat.N401-01, Nanjing, China) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using VAHTS® Universal V6 RNA-seq Library Prep Kit (Vazyme, cat.NR604, Nanjing, China) under 94℃   8min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by reverse transcription reagent, which were next used to synthesise U-labeled second-stranded DNAs. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, size selection was performed with VAHTS® DNA Clean Beads (Vazyme, cat. N411, Nanjing, China). Then the ligated products are amplified with PCR. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (Guangzhou Huayin Health Technology Co., Ltd. Guangzhou, China) following the vendor's recommended protocol.

tag: disease state

value: COVID-19 patient

value: male

tag: immune response

value: symptomatic

value: PBMCs


title: PBMCs, Mo_13

value: female


title: PBMCs, Mo_26


title: PBMCs, Mo_24


title: PBMCs, Mo_14


title: PBMCs, Mo_18


title: PBMCs, Mo_5


title: PBMCs, Mo_11


title: Sham_f_SC_4

value: Ipsilateral lumbar spinal cord (L3-5)


title: PBMCs, Mo_2


title: Sham_f_SC_3


title: CCI_f_SC_2

value: CCI